1) Bradykinin receptor antagonists and thrombin inhibitors were presented. Bradykinin is a 9-amino acid peptide that promotes inflammation by binding to B1 and B2 G protein-coupled receptors.
2) Conformationally constrained bradykinin antagonist peptides were designed to probe the receptor binding site. NMR studies showed the peptides adopt a beta-turn structure when binding.
3) Receptor binding experiments on cloned human receptors showed similar binding affinities, providing insights into antagonist interactions with bradykinin receptors.
In this slide I covered the detailed about hansch analysis, Free-Wilson analysis, and Mixed approach. I also gave a detailed application for each points.
Relationship between hansch analysis and free wilson analysisKomalJAIN122
This document provides an overview of quantitative structure-activity relationship (QSAR) modeling techniques including Hansch analysis, Free-Wilson analysis, and Topliss schemes. It discusses how QSAR relates the biological activity of drugs to their physicochemical properties through equations. Specifically, it explains that Hansch equations relate activity to hydrophobicity, electronic effects, and steric factors. Examples of Hansch equations are provided. The Free-Wilson approach derives equations based on the presence or absence of substituents. Topliss schemes provide a methodical approach to substituent selection for optimization.
This document summarizes the main types of biological drug targets: receptors. It discusses four main classes of receptors: 1) G-protein coupled receptors, which bind ligands and activate G-proteins to interact with ion channels or enzymes, 2) ligand gated ion channel receptors, which open channels to allow ion passage upon ligand binding, 3) enzyme linked receptors with intracellular enzyme domains that are activated by ligand binding to induce intracellular signaling cascades, and 4) nuclear receptors within cells that directly bind DNA to regulate gene expression in response to ligands such as steroid hormones.
Active constituent of drugs used in diabetic therapyAkshay Kank
In this slide the active constituents which is isolated from herbal sources used for to treat the type 1 and type 2 diabetes is covered. 'Gymnema' and 'swerita chirata' herbal plant is also covered in the slide.This work help in to focus the herbal emphasis on diabetes.
This document summarizes the Pinner pyrimidine synthesis reaction. The reaction involves the condensation of a non-N-substituted amidine and β-keto ester (β-diketone) in the presence of an acid catalyst to form a pyrimidine heterocyclic ring. The mechanism proceeds through protonation, nucleophilic attack, dehydration, and deprotonation steps. Pyrimidine derivatives synthesized via this reaction are used in drugs to treat conditions like malaria, viruses, and cancer.
Sythesis of heterocyclic drugs ketoconazole and metronidazoleandhra university
A Heterocyclic compounds are those which has atoms of at least two different elements as members of its ring.
Heterocyclic chemistry is a branch of organic chemistry dealing with the synthesis, properties, and applications of these heterocycles.
This document provides an overview of prodrug design. It defines a prodrug as an inactive derivative of a drug molecule that undergoes biotransformation to release the active drug. Prodrugs are classified based on their structure and include carrier-linked, bipartite, tripartite, mutual, and bioprecursor prodrugs. The document discusses various rationales for prodrug design such as improving solubility, absorption, patient acceptability, and site-specific drug delivery. Common functional groups used in prodrugs include esters, amides, phosphates, and carbamates. The document also covers practical considerations and approaches for overcoming limitations like pre-systemic metabolism and blood-brain barrier penetration.
This document summarizes several organic reactions used in heterocyclic chemistry. It describes the Debus–Radziszewski reaction for imidazole synthesis, the Knorr reaction for pyrrole synthesis, the Pinner reaction for pyrimidine synthesis, the Combes reaction for quinoline synthesis, the Bernthsen reaction for acridine synthesis, the Smiles rearrangement, and the Traube reaction for purine synthesis. For each reaction, it provides the starting materials, product, mechanism, and some applications. The document is intended to present an overview of important heterocyclic reactions for students of pharmaceutical chemistry.
In this slide I covered the detailed about hansch analysis, Free-Wilson analysis, and Mixed approach. I also gave a detailed application for each points.
Relationship between hansch analysis and free wilson analysisKomalJAIN122
This document provides an overview of quantitative structure-activity relationship (QSAR) modeling techniques including Hansch analysis, Free-Wilson analysis, and Topliss schemes. It discusses how QSAR relates the biological activity of drugs to their physicochemical properties through equations. Specifically, it explains that Hansch equations relate activity to hydrophobicity, electronic effects, and steric factors. Examples of Hansch equations are provided. The Free-Wilson approach derives equations based on the presence or absence of substituents. Topliss schemes provide a methodical approach to substituent selection for optimization.
This document summarizes the main types of biological drug targets: receptors. It discusses four main classes of receptors: 1) G-protein coupled receptors, which bind ligands and activate G-proteins to interact with ion channels or enzymes, 2) ligand gated ion channel receptors, which open channels to allow ion passage upon ligand binding, 3) enzyme linked receptors with intracellular enzyme domains that are activated by ligand binding to induce intracellular signaling cascades, and 4) nuclear receptors within cells that directly bind DNA to regulate gene expression in response to ligands such as steroid hormones.
Active constituent of drugs used in diabetic therapyAkshay Kank
In this slide the active constituents which is isolated from herbal sources used for to treat the type 1 and type 2 diabetes is covered. 'Gymnema' and 'swerita chirata' herbal plant is also covered in the slide.This work help in to focus the herbal emphasis on diabetes.
This document summarizes the Pinner pyrimidine synthesis reaction. The reaction involves the condensation of a non-N-substituted amidine and β-keto ester (β-diketone) in the presence of an acid catalyst to form a pyrimidine heterocyclic ring. The mechanism proceeds through protonation, nucleophilic attack, dehydration, and deprotonation steps. Pyrimidine derivatives synthesized via this reaction are used in drugs to treat conditions like malaria, viruses, and cancer.
Sythesis of heterocyclic drugs ketoconazole and metronidazoleandhra university
A Heterocyclic compounds are those which has atoms of at least two different elements as members of its ring.
Heterocyclic chemistry is a branch of organic chemistry dealing with the synthesis, properties, and applications of these heterocycles.
This document provides an overview of prodrug design. It defines a prodrug as an inactive derivative of a drug molecule that undergoes biotransformation to release the active drug. Prodrugs are classified based on their structure and include carrier-linked, bipartite, tripartite, mutual, and bioprecursor prodrugs. The document discusses various rationales for prodrug design such as improving solubility, absorption, patient acceptability, and site-specific drug delivery. Common functional groups used in prodrugs include esters, amides, phosphates, and carbamates. The document also covers practical considerations and approaches for overcoming limitations like pre-systemic metabolism and blood-brain barrier penetration.
This document summarizes several organic reactions used in heterocyclic chemistry. It describes the Debus–Radziszewski reaction for imidazole synthesis, the Knorr reaction for pyrrole synthesis, the Pinner reaction for pyrimidine synthesis, the Combes reaction for quinoline synthesis, the Bernthsen reaction for acridine synthesis, the Smiles rearrangement, and the Traube reaction for purine synthesis. For each reaction, it provides the starting materials, product, mechanism, and some applications. The document is intended to present an overview of important heterocyclic reactions for students of pharmaceutical chemistry.
Stereochemistry is the ‘chemistry of space’ , that is stereochemistry deals with the spatial arrangements of atoms and groups in a molecule.
Stereochemistry can trace its roots to the year 1842 when the French chemist Louis Pasteur made an observation that the salts of tartaric acid collected from a wine production vessel have the ability to rotate plane-polarized light, whereas the same salts from different sources did not have this ability.
Isomers are compounds that contain exactly the same number of atoms, i.e., they have exactly the same empirical formula, but differ from each other by the way in which the atoms are arranged.
Constitutional isomers, also known as structural isomers, are specific types of isomers that share the same molecular formula but have different bonding atomic organization and bonding patterns.
Stereoisomers are molecules having the same molecular formula and the atomic arrangement, but differ in their spatial arrangement.
Geometric isomers are two or more coordination compounds which contain the same number and types of atoms, and bonds (i.e., the connectivity between atoms is the same), but which have different spatial arrangements of the atoms.
There are 2 types of geometric isomers, ‘cis’ and ‘trans’.-cis isomers: when similar groups are present on the same side of the double bonds, then they are termed as cis.- trans isomers: when similar groups are present on the opposite sides of the double bonds then they are called trans isomers.
cis-diethylstilbestrol has only 7% of the estrogenic activity of trans-diethylstilbesterol.
Cisplatin have anticancer activity where ae trans platin is an inactive compound.
In chemistry, a molecule or ion is called chiral if it cannot be superposed on its mirror image by any combination of rotations, translations, and some conformational changes.
Chirality is the property of being non identical to ones mirror image.
Chiral center is defined as the atom bearing 4 different atoms or group of atoms.
Molecules that form nonsuperimposable mirror images, and thus exist as enantiomers, are said to be chiral molecules.
For a molecule to be chiral, it cannot contain a plane of symmetry.
The term enantioselectivity refers to the efficiency with which the reaction produces one enantiomer.
Enantiomers are stereoisomers that are non-superimposable mirror images.
Have identical properties.
Similar shapes
Diastereomers are stereoisomers that are non superimposable and are not mirror images.
Have distinct physical properties.
Have different molecular shapes.
Enantiomers consist of a pair of molecules that are mirror images of each other and are not superimposable.
When a molecule contains only one chiral centre , the two stereoisomers are known as enantiomers.
These may be referred to or labelled using the configurational descriptors as either:
R(rectus meaning right handed) or S(sinister meaning left handed),
D(dextrorotatory)or L (laevorotatory)
E-Entgegen or Z- Zusamen
This document summarizes information about several antifungal drugs, including their molecular formulas, properties, synthesis methods, and uses. It discusses Ketoconazole, Terconazole, Metronidazole, and Miconazole. For each drug, it provides the molecular formula, describes the synthesis starting from various reactants and reaction steps, and lists clinical uses such as treating fungal infections, jock itch, and vaginal thrush. The document aims to provide information on the preparation and applications of important antifungal heterocyclic compounds.
This document discusses peptidomimetics, which are small protein-like chains designed to mimic peptides while having no peptide bonds and a molecular weight under 700 Daltons. Peptidomimetics are derived from bioactive peptides and aim to improve stability, transport properties, and activity while reducing degradation. They are classified based on their modifications from the original peptide. Common modification methods include cyclization, retro-inverso design, and restricting conformations through disulfide bonds or metal chelation. Peptidomimetics have therapeutic value as they can overcome issues like poor oral bioavailability that limit peptide drugs, as demonstrated for somatostatin analogs. Recent advances include using peptidomimetics to enhance peptide vaccines
This document discusses Traube purine synthesis and several purine derivatives including mercaptopurine, theophylline, and thioguanine. It provides information on:
- Traube first introduced purine synthesis in 1900 involving introduction of a one carbon fragment to bridge nitrogen atoms in pyrimidine rings.
- Mercaptopurine is used to treat cancers and autoimmune diseases but has side effects like bone marrow suppression and increased cancer risk.
- Theophylline is found in tea and used for respiratory issues like asthma as it relaxes bronchial muscles and stimulates the respiratory center.
- Thioguanine is used for certain cancers and inflammatory bowel disease.
Bioisosterism is a strategy used in drug design that involves replacing one chemical group with another that has similar physical or chemical properties. This is done to improve properties like potency, selectivity, toxicity, and pharmacokinetics without significantly changing the chemical structure. Common bioisosteric replacements include replacing hydrogen with fluorine, replacing carboxylic acids with amides or esters, or replacing phenyl rings with heteroaromatic or saturated rings. The application of bioisosterism has been an important concept in medicinal chemistry for nearly 80 years and will continue to play a role in drug discovery and optimization.
Chemistry of Prostaglandins, leukotrienes and thromboxanes(Advance medicinal ...Rohit kaushiK.
This document provides an overview of a presentation on eicosanoids, prostaglandins, leukotrienes, and thromboxanes. It discusses how these compounds are synthesized from arachidonic acid and their roles in regulating cellular functions and mediating processes like inflammation, smooth muscle contraction, platelet aggregation, and uterine contraction. The presentation covers the biosynthesis, receptors, inhibitors, degradation and biochemical actions of each class of compounds.
This document summarizes strategies for analog design of lead compounds in drug discovery. It discusses various types of modifications that can be made including bioisosteric replacements, rigid analogs, alterations of chain branching, changes in ring size or position, use of fragments of lead molecules, and variations in interatomic distances. Examples are provided to illustrate how each type of modification can impact pharmacological activity. The overall goal of analog design is to develop new compounds with similar or improved biological and chemical properties as the lead molecule.
This document provides an introduction to Quantitative Structure Activity Relationships (QSAR) analysis using Hansch analysis. It discusses how QSAR attempts to correlate biological activity to measurable physicochemical properties of drugs using mathematical equations. It covers key topics like hydrophobicity, electronic effects, and steric effects of drug molecules and substituents. The document also explains the Hansch equation that relates biological activity to parameters like hydrophobicity (π), electronic effects (σ), and steric effects (Es). Examples of QSAR analyses and a table of common substituent parameters are also included.
This document discusses several reagents used in organic synthesis:
1) Wittig reagent is used to synthesize alkenes from ketones and aldehydes via the Wittig reaction. It is prepared from triphenylphosphine and alkyl halides.
2) Diazopropane is used for cyclopropanation of alkenes and is prepared by oxidation of acetohydrazone.
3) BOP reagent is commonly used for peptide coupling and esterification due to its ability to form reactive hydroxybenzotriazolyl intermediates. It involves generation of a carboxylate anion which attacks the phosphorus center.
Synthetic Reagent and Its Applications (M. Pharm)MohdShafeeque4
The document summarizes various synthetic reagents and their applications. It describes 12 reagents including aluminium isopropoxide, N-bromosuccinimide, diazomethane, dicyclohexylcarbodiimide, Wilkinson reagent, Wittig reagent, osmium tetroxide, titanium chloride, diazopropane, diethyl azodicarboxylate, triphenylphosphine, and BOP reagent. For each reagent, it provides information on chemical formula, structure, preparation method, and typical applications. The document serves as a useful reference for organic chemistry students and researchers.
The Knorr pyrazole synthesis converts a hydrazine or its derivatives and a 1,3-dicarbonyl compound to a pyrazole using an acid catalyst. The mechanism involves an acid-catalyzed imine formation where the hydrazine attacks either carbonyl carbon, followed by attack of the other nitrogen on the other carbonyl group. This diimine compound then deprotonates to form the pyrazole product. The reaction is used to synthesize compounds such as metal chelates, photographic dyes, herbicides, and biologically active molecules.
This presentation discusses drug target identification and validation. It introduces drug targets as specific sites where drugs bind to exert their therapeutic effects. Target identification methods include genomics, proteomics, and bioinformatics. Targets are then validated using techniques like siRNAs and antisense oligonucleotides to demonstrate the functional role of targets in disease and ensure drug interactions produce the desired therapeutic response.
Chemistry of prostaglandins, leukotrienes and thromboxanesAbhimanyu Awasthi
The document summarizes a presentation on the chemistry of prostaglandins, leukotrienes, and thromboxanes. Prostaglandins, leukotrienes, and thromboxanes are oxygen metabolites of arachidonic acid that form a family of lipid substances with intrinsic biological activities. They are involved in processes like inflammation, platelet aggregation, and vascular homeostasis. The presentation covers their biosynthesis from arachidonic acid, sub-families, properties, and biologically important examples like prostacyclin, thromboxane A2, and leukotriene B4. It also discusses the enzymes and pathways involved in their synthesis.
Chemistry of Prostaglandins,Leukotrienes and Thromboxanes.pptxPurushothamKN1
This document provides an overview of prostaglandins, leukotrienes, and thromboxanes. It discusses their introduction, classification, chemical structures, biosynthesis, regulation, mechanisms of action, functions, and applications. Specifically, it notes that prostaglandins are derived from arachidonic acid and have diverse hormone-like effects. Leukotrienes are inflammatory mediators produced from arachidonic acid oxidation. They are involved in inflammation and hypersensitivity reactions. Thromboxanes are involved in blood clotting and are derived from arachidonic acid through a biosynthetic pathway involving thromboxane-A-synthase.
1) The document discusses the synthon approach, which involves breaking down a target molecule into simpler starting materials through imaginary bond breaking (disconnection) or functional group interconversion.
2) Key terms are defined, including disconnection, synthon, and functional group interconversion. Basic rules of disconnection are outlined.
3) An example of using the synthon approach to synthesize the drug benzocaine from toluene is provided, outlining the multi-step reaction pathway and identifying specific synthons.
Global and local restrictions Peptidomimetics ASHOK GAUTAM
Peptidomimetics are small protein-like chains designed to mimic peptides but with greater stability and specificity. They are created either by modifying existing peptides or designing new structures that mimic peptides. Peptidomimetics incorporate conformational constraints locally or globally to restrict flexibility and exclude potential conformations, allowing for more targeted interaction with biological targets. Conformational constraints are needed to improve properties like stability, activity, and selectivity for applications like drug development and targeted cancer therapies. Common constraints include cyclization, disulfide bonds, and restricted amino acids.
solid phase synthesis Presentation by komalKomal Rajgire
The document summarizes solid phase synthesis. It begins with an introduction describing how solid phase synthesis involves coupling reagents to a solid support to perform multi-step reactions leading to a target molecule. It then discusses various aspects of planning solid phase synthesis such as suitable resin supports, linkers, protective groups, and monitoring reactions. Examples of resin types, linkers, and protective groups are provided. The document concludes by outlining advantages such as simplified purification and green chemistry principles, as well as disadvantages such as potential low reaction rates. Applications mentioned include combinatorial synthesis, peptide synthesis, and DNA synthesis.
Drug resistance occurs through several mechanisms: mutation, selective pressure, and gene transfer allow microbes to develop resistance. Strategies to combat resistance include international collaboration on surveillance and incentives for new drugs, national treatment guidelines and education programs, and community efforts like rational antibiotic use and hygiene. Genetic changes allow microbes to develop resistance through various mechanisms like mutation, selective pressure, and horizontal gene transfer between microbes.
The Free-Wilson approach correlates the biological activity of parent structures and analogues bearing different substituents. In 1964, Free and Wilson derived a mathematical model representing structural features as 1s and 0s correlated to biological activity. The method assumes substituents make additive contributions to biological activity. Free-Wilson analysis directly relates structural features to biological properties using only presence/absence of substituents as descriptors. It represents activity as the sum of group contributions and a reference compound activity. Drawbacks include needing substitution at two positions and only predicting combinations previously analyzed.
This document reviews 3,4-dihydropyrimidines thione, their chemistry and pharmacological potentials. It begins with background on pyrimidine structures and properties. It then discusses the chemical properties of pyrimidines and derivatives, including electrophilic and nucleophilic reactions. Biological importance is explained by pyrimidine's presence in nucleic acids, vitamins, and other biologically active compounds. Dihydropyrimidines are introduced as compounds obtained from cyclocondensation reactions. Several studies evaluating dihydropyrimidines as calcium channel blockers, antihypertensives, antibacterials, antifungals, and antioxidants are summarized.
This document describes research on triplex formation by oligodeoxynucleotides (ODNs) containing 5-methyldeoxycytidine conjugated to spermine (5-Me-dC-N4-(spermine)). The key findings are:
1) ODNs containing 5-Me-dC-N4-(spermine) form stable triplexes at physiological pH (pH 7.3), unlike unmodified ODNs which only form triplexes under acidic conditions.
2) The triplex stability for 5-Me-dC-N4-(spermine) ODNs decreases with decreasing pH, in contrast to unmodified ODNs whose stability increases under acidic conditions
Stereochemistry is the ‘chemistry of space’ , that is stereochemistry deals with the spatial arrangements of atoms and groups in a molecule.
Stereochemistry can trace its roots to the year 1842 when the French chemist Louis Pasteur made an observation that the salts of tartaric acid collected from a wine production vessel have the ability to rotate plane-polarized light, whereas the same salts from different sources did not have this ability.
Isomers are compounds that contain exactly the same number of atoms, i.e., they have exactly the same empirical formula, but differ from each other by the way in which the atoms are arranged.
Constitutional isomers, also known as structural isomers, are specific types of isomers that share the same molecular formula but have different bonding atomic organization and bonding patterns.
Stereoisomers are molecules having the same molecular formula and the atomic arrangement, but differ in their spatial arrangement.
Geometric isomers are two or more coordination compounds which contain the same number and types of atoms, and bonds (i.e., the connectivity between atoms is the same), but which have different spatial arrangements of the atoms.
There are 2 types of geometric isomers, ‘cis’ and ‘trans’.-cis isomers: when similar groups are present on the same side of the double bonds, then they are termed as cis.- trans isomers: when similar groups are present on the opposite sides of the double bonds then they are called trans isomers.
cis-diethylstilbestrol has only 7% of the estrogenic activity of trans-diethylstilbesterol.
Cisplatin have anticancer activity where ae trans platin is an inactive compound.
In chemistry, a molecule or ion is called chiral if it cannot be superposed on its mirror image by any combination of rotations, translations, and some conformational changes.
Chirality is the property of being non identical to ones mirror image.
Chiral center is defined as the atom bearing 4 different atoms or group of atoms.
Molecules that form nonsuperimposable mirror images, and thus exist as enantiomers, are said to be chiral molecules.
For a molecule to be chiral, it cannot contain a plane of symmetry.
The term enantioselectivity refers to the efficiency with which the reaction produces one enantiomer.
Enantiomers are stereoisomers that are non-superimposable mirror images.
Have identical properties.
Similar shapes
Diastereomers are stereoisomers that are non superimposable and are not mirror images.
Have distinct physical properties.
Have different molecular shapes.
Enantiomers consist of a pair of molecules that are mirror images of each other and are not superimposable.
When a molecule contains only one chiral centre , the two stereoisomers are known as enantiomers.
These may be referred to or labelled using the configurational descriptors as either:
R(rectus meaning right handed) or S(sinister meaning left handed),
D(dextrorotatory)or L (laevorotatory)
E-Entgegen or Z- Zusamen
This document summarizes information about several antifungal drugs, including their molecular formulas, properties, synthesis methods, and uses. It discusses Ketoconazole, Terconazole, Metronidazole, and Miconazole. For each drug, it provides the molecular formula, describes the synthesis starting from various reactants and reaction steps, and lists clinical uses such as treating fungal infections, jock itch, and vaginal thrush. The document aims to provide information on the preparation and applications of important antifungal heterocyclic compounds.
This document discusses peptidomimetics, which are small protein-like chains designed to mimic peptides while having no peptide bonds and a molecular weight under 700 Daltons. Peptidomimetics are derived from bioactive peptides and aim to improve stability, transport properties, and activity while reducing degradation. They are classified based on their modifications from the original peptide. Common modification methods include cyclization, retro-inverso design, and restricting conformations through disulfide bonds or metal chelation. Peptidomimetics have therapeutic value as they can overcome issues like poor oral bioavailability that limit peptide drugs, as demonstrated for somatostatin analogs. Recent advances include using peptidomimetics to enhance peptide vaccines
This document discusses Traube purine synthesis and several purine derivatives including mercaptopurine, theophylline, and thioguanine. It provides information on:
- Traube first introduced purine synthesis in 1900 involving introduction of a one carbon fragment to bridge nitrogen atoms in pyrimidine rings.
- Mercaptopurine is used to treat cancers and autoimmune diseases but has side effects like bone marrow suppression and increased cancer risk.
- Theophylline is found in tea and used for respiratory issues like asthma as it relaxes bronchial muscles and stimulates the respiratory center.
- Thioguanine is used for certain cancers and inflammatory bowel disease.
Bioisosterism is a strategy used in drug design that involves replacing one chemical group with another that has similar physical or chemical properties. This is done to improve properties like potency, selectivity, toxicity, and pharmacokinetics without significantly changing the chemical structure. Common bioisosteric replacements include replacing hydrogen with fluorine, replacing carboxylic acids with amides or esters, or replacing phenyl rings with heteroaromatic or saturated rings. The application of bioisosterism has been an important concept in medicinal chemistry for nearly 80 years and will continue to play a role in drug discovery and optimization.
Chemistry of Prostaglandins, leukotrienes and thromboxanes(Advance medicinal ...Rohit kaushiK.
This document provides an overview of a presentation on eicosanoids, prostaglandins, leukotrienes, and thromboxanes. It discusses how these compounds are synthesized from arachidonic acid and their roles in regulating cellular functions and mediating processes like inflammation, smooth muscle contraction, platelet aggregation, and uterine contraction. The presentation covers the biosynthesis, receptors, inhibitors, degradation and biochemical actions of each class of compounds.
This document summarizes strategies for analog design of lead compounds in drug discovery. It discusses various types of modifications that can be made including bioisosteric replacements, rigid analogs, alterations of chain branching, changes in ring size or position, use of fragments of lead molecules, and variations in interatomic distances. Examples are provided to illustrate how each type of modification can impact pharmacological activity. The overall goal of analog design is to develop new compounds with similar or improved biological and chemical properties as the lead molecule.
This document provides an introduction to Quantitative Structure Activity Relationships (QSAR) analysis using Hansch analysis. It discusses how QSAR attempts to correlate biological activity to measurable physicochemical properties of drugs using mathematical equations. It covers key topics like hydrophobicity, electronic effects, and steric effects of drug molecules and substituents. The document also explains the Hansch equation that relates biological activity to parameters like hydrophobicity (π), electronic effects (σ), and steric effects (Es). Examples of QSAR analyses and a table of common substituent parameters are also included.
This document discusses several reagents used in organic synthesis:
1) Wittig reagent is used to synthesize alkenes from ketones and aldehydes via the Wittig reaction. It is prepared from triphenylphosphine and alkyl halides.
2) Diazopropane is used for cyclopropanation of alkenes and is prepared by oxidation of acetohydrazone.
3) BOP reagent is commonly used for peptide coupling and esterification due to its ability to form reactive hydroxybenzotriazolyl intermediates. It involves generation of a carboxylate anion which attacks the phosphorus center.
Synthetic Reagent and Its Applications (M. Pharm)MohdShafeeque4
The document summarizes various synthetic reagents and their applications. It describes 12 reagents including aluminium isopropoxide, N-bromosuccinimide, diazomethane, dicyclohexylcarbodiimide, Wilkinson reagent, Wittig reagent, osmium tetroxide, titanium chloride, diazopropane, diethyl azodicarboxylate, triphenylphosphine, and BOP reagent. For each reagent, it provides information on chemical formula, structure, preparation method, and typical applications. The document serves as a useful reference for organic chemistry students and researchers.
The Knorr pyrazole synthesis converts a hydrazine or its derivatives and a 1,3-dicarbonyl compound to a pyrazole using an acid catalyst. The mechanism involves an acid-catalyzed imine formation where the hydrazine attacks either carbonyl carbon, followed by attack of the other nitrogen on the other carbonyl group. This diimine compound then deprotonates to form the pyrazole product. The reaction is used to synthesize compounds such as metal chelates, photographic dyes, herbicides, and biologically active molecules.
This presentation discusses drug target identification and validation. It introduces drug targets as specific sites where drugs bind to exert their therapeutic effects. Target identification methods include genomics, proteomics, and bioinformatics. Targets are then validated using techniques like siRNAs and antisense oligonucleotides to demonstrate the functional role of targets in disease and ensure drug interactions produce the desired therapeutic response.
Chemistry of prostaglandins, leukotrienes and thromboxanesAbhimanyu Awasthi
The document summarizes a presentation on the chemistry of prostaglandins, leukotrienes, and thromboxanes. Prostaglandins, leukotrienes, and thromboxanes are oxygen metabolites of arachidonic acid that form a family of lipid substances with intrinsic biological activities. They are involved in processes like inflammation, platelet aggregation, and vascular homeostasis. The presentation covers their biosynthesis from arachidonic acid, sub-families, properties, and biologically important examples like prostacyclin, thromboxane A2, and leukotriene B4. It also discusses the enzymes and pathways involved in their synthesis.
Chemistry of Prostaglandins,Leukotrienes and Thromboxanes.pptxPurushothamKN1
This document provides an overview of prostaglandins, leukotrienes, and thromboxanes. It discusses their introduction, classification, chemical structures, biosynthesis, regulation, mechanisms of action, functions, and applications. Specifically, it notes that prostaglandins are derived from arachidonic acid and have diverse hormone-like effects. Leukotrienes are inflammatory mediators produced from arachidonic acid oxidation. They are involved in inflammation and hypersensitivity reactions. Thromboxanes are involved in blood clotting and are derived from arachidonic acid through a biosynthetic pathway involving thromboxane-A-synthase.
1) The document discusses the synthon approach, which involves breaking down a target molecule into simpler starting materials through imaginary bond breaking (disconnection) or functional group interconversion.
2) Key terms are defined, including disconnection, synthon, and functional group interconversion. Basic rules of disconnection are outlined.
3) An example of using the synthon approach to synthesize the drug benzocaine from toluene is provided, outlining the multi-step reaction pathway and identifying specific synthons.
Global and local restrictions Peptidomimetics ASHOK GAUTAM
Peptidomimetics are small protein-like chains designed to mimic peptides but with greater stability and specificity. They are created either by modifying existing peptides or designing new structures that mimic peptides. Peptidomimetics incorporate conformational constraints locally or globally to restrict flexibility and exclude potential conformations, allowing for more targeted interaction with biological targets. Conformational constraints are needed to improve properties like stability, activity, and selectivity for applications like drug development and targeted cancer therapies. Common constraints include cyclization, disulfide bonds, and restricted amino acids.
solid phase synthesis Presentation by komalKomal Rajgire
The document summarizes solid phase synthesis. It begins with an introduction describing how solid phase synthesis involves coupling reagents to a solid support to perform multi-step reactions leading to a target molecule. It then discusses various aspects of planning solid phase synthesis such as suitable resin supports, linkers, protective groups, and monitoring reactions. Examples of resin types, linkers, and protective groups are provided. The document concludes by outlining advantages such as simplified purification and green chemistry principles, as well as disadvantages such as potential low reaction rates. Applications mentioned include combinatorial synthesis, peptide synthesis, and DNA synthesis.
Drug resistance occurs through several mechanisms: mutation, selective pressure, and gene transfer allow microbes to develop resistance. Strategies to combat resistance include international collaboration on surveillance and incentives for new drugs, national treatment guidelines and education programs, and community efforts like rational antibiotic use and hygiene. Genetic changes allow microbes to develop resistance through various mechanisms like mutation, selective pressure, and horizontal gene transfer between microbes.
The Free-Wilson approach correlates the biological activity of parent structures and analogues bearing different substituents. In 1964, Free and Wilson derived a mathematical model representing structural features as 1s and 0s correlated to biological activity. The method assumes substituents make additive contributions to biological activity. Free-Wilson analysis directly relates structural features to biological properties using only presence/absence of substituents as descriptors. It represents activity as the sum of group contributions and a reference compound activity. Drawbacks include needing substitution at two positions and only predicting combinations previously analyzed.
This document reviews 3,4-dihydropyrimidines thione, their chemistry and pharmacological potentials. It begins with background on pyrimidine structures and properties. It then discusses the chemical properties of pyrimidines and derivatives, including electrophilic and nucleophilic reactions. Biological importance is explained by pyrimidine's presence in nucleic acids, vitamins, and other biologically active compounds. Dihydropyrimidines are introduced as compounds obtained from cyclocondensation reactions. Several studies evaluating dihydropyrimidines as calcium channel blockers, antihypertensives, antibacterials, antifungals, and antioxidants are summarized.
This document describes research on triplex formation by oligodeoxynucleotides (ODNs) containing 5-methyldeoxycytidine conjugated to spermine (5-Me-dC-N4-(spermine)). The key findings are:
1) ODNs containing 5-Me-dC-N4-(spermine) form stable triplexes at physiological pH (pH 7.3), unlike unmodified ODNs which only form triplexes under acidic conditions.
2) The triplex stability for 5-Me-dC-N4-(spermine) ODNs decreases with decreasing pH, in contrast to unmodified ODNs whose stability increases under acidic conditions
This document summarizes the design and testing of a bisubstrate inhibitor for the insulin receptor tyrosine kinase (IRK). Researchers designed a compound that links ATPγS to a peptide substrate analog via a two-carbon spacer, setting the distance between the nucleophilic atom and phosphoryl group to mimic a dissociative transition state as suggested by previous studies of IRK's mechanism. Testing found this compound to be a potent and selective competitive inhibitor of IRK, with a Ki of 370 nM, making it the most potent inhibitor reported for this important signaling enzyme. A crystal structure confirmed the inhibitor bound as designed and validated the mechanism-inspired approach.
Structural and biochemical studies of cold shock domain containing proteins.
This thesis examines cold shock domain containing proteins through three chapters:
[1] A novel DNA microarray approach is developed to determine the sequence specificity of single-stranded nucleic acid binding proteins. Using this method, the major cold shock protein CspB from Bacillus subtilis is shown to bind preferentially to pyrimidine-rich sequences, with a high affinity for the consensus sequence 5'-GTCTTTG/T-3'.
[2] Six cold shock proteins from Salmonella typhimurium (CspA, B, C, D, E, and H) are cloned, expressed, and purified.
(1) The study used computational methods like molecular docking and molecular dynamics simulations to model interactions between acridine drugs and putative G-quadruplexes found in ribosomal DNA and RNA.
(2) The simulations found that shorter loop G-quadruplexes were more stable than longer loop structures, and certain acridines with amino groups stabilized parallel G-quadruplex topologies better than antiparallel forms.
(3) The specificities and relative stabilities of interactions between acridines and G-quadruplex loop structures were analyzed to quantify binding and guide rational drug design targeting G-quadruplexes involved in cancer processes.
This study used computational methods to identify peptide inhibitors of the interaction between the death receptor DR6 and the N-terminal fragment of amyloid precursor protein (NAPP), which is implicated in Alzheimer's disease (AD). A focused peptide library was virtually screened and peptides were docked and scored against the NAPP binding site. Several tetrapeptides were predicted to bind strongly to NAPP, particularly Pro-Lys-Trp-Trp, which was predicted to inhibit the DR6-NAPP interaction through hydrogen bonding with key NAPP residues. Future work will include synthesizing and testing the top peptides to validate the computational predictions.
1. The document discusses molecular simulations comparing the human pancreatic ribonuclease (HP-RNase) to ribonuclease A (RNase A) to understand their differences in substrate binding and catalysis.
2. Experimental results show that HP-RNase preferentially cleaves substrates in an endonucleolytic manner, while RNase A shows more exo activity. Molecular dynamics simulations and free energy calculations of the two enzymes were performed.
3. Analysis of distances and free energy calculations revealed that the mutant RNase A had a higher free energy barrier for endonucleolytic cleavage compared to wild type HP-RNase, providing a potential explanation for their different activities.
This document describes the synthesis of novel N-(3-arylprop-2-ynyl)substituted olanzapine derivatives as potential inhibitors of PDE4B (phosphodiesterase 4B). The target compounds were prepared using a Pd/C-mediated coupling reaction between a terminal alkyne derived from olanzapine and various iodoarenes. Some of the synthesized compounds showed promising inhibition of PDE4B in vitro, with one compound exhibiting over 63% inhibition. Docking studies supported the experimental findings. The results indicate that modifying olanzapine by introducing an appropriate 3-arylprop-2-ynyl moiety can convert it into a PDE inhibitor, offering a potential new
This document describes a study that used molecular docking to evaluate 9-substituted adenine derivatives as inhibitors of phosphodiesterase type-4 (PDE4) in order to assess their potential anti-inflammatory effects. The study used docking software to predict how well the adenine derivatives could bind to and inhibit the PDE4 enzyme. A total of 22 adenine derivative compounds were analyzed in the docking studies. The results aimed to identify promising lead compounds for further investigation as potential new anti-inflammatory drug candidates.
This document describes a study that characterized the major and minor groove environments of DNA using fluorescent probes. Specifically:
- Fluorescent oligonucleotides were created by incorporating a dansyl fluorophore into the major groove at specific sites.
- The fluorescence properties of these probes were used to estimate that the dielectric constant of the major groove is around 55D, compared to 20D for the minor groove.
- Binding of the minor groove ligand netropsin could be quantitatively monitored by changes in fluorescence of the dansyl group in the major groove, suggesting an information network between the two grooves.
The document discusses the effect of substrate concentration on the enzyme catalase. It was hypothesized that increasing the concentration of hydrogen peroxide substrate would increase the rate of catalase activity, measured by decreased time for an enzyme-coated paper circle to rise in a solution. Potato samples containing catalase were placed in hydrogen peroxide solutions of varying concentrations and temperatures to produce oxygen. Results showed less gas was produced at higher inhibitor concentrations, as more enzymes were inhibited, reducing active sites for reaction.
Human aldo-keto reductases (AKR) of the 1A, 1B, 1C and 1D subfamilies are involved in the pre-receptor regulation of nuclear (steroid hormone and orphan) receptors by regulating the local concentrations of their lipophilic ligands. AKR1C3 is one of the most interesting isoforms. It was cloned from human prostate and the recombinant protein was found to function as a 3-, 17- and 20-ketosteroid reductase with a preference for the conversion of Δ4-androstene-3,17- dione to testosterone implicating this enzyme in the local production of active androgens within the prostate. Using a validated isoform specific real-time RT-PCR procedure the AKR1C3 transcript was shown to be more abundant in primary cultures of epithelial cells than stromal cells, and its expression in stromal cells increased with benign and malignant disease. Using a validated isoform specific monoclonal Ab, AKR1C3 protein expression was also detected in prostate epithelial cells by immunoblot analysis.
Immunohistochemical staining of prostate tissue showed that AKR1C3 was expressed in adenocarcinoma and surprisingly high expression was observed in the endothelial cells. These cells are a rich source of prostaglandin G/H synthase 2 (COX-2) and
vasoactive prostaglandins (PG) and thus the ability of recombinant AKR1C enzymes to act as PGF synthases was compared. AKR1C3 had the highest catalytic efficiency (kcat/Km) for the 11-ketoreduction of PGD2 to yield 9α,11β-PGF2 raising the prospect that AKR1C3 may govern ligand access to peroxisome proliferator activated receptor (PPARγ). Activation of PPARγ is often a pro-apoptotic signal and/or leads to terminal differentiation, while 9α,11β- PGF2 is a pro-proliferative signal. AKR1C3 is potently inhibited by non-steroidal anti- inflammatory drugs suggesting that the cancer chemopreventive properties of these agents may be mediated either by inhibition of AKR1C3 or COX. To discriminate between these effects we developed potent AKR1C inhibitors based on N-phenylanthranilic acids that do not inhibit COX-1 or COX-2. These compounds can now be used to determine the role of AKR1C3 in producing two proliferative signals in the prostate namely testosterone and 9α,11β-PGF2.
This document reports on a study that measured protein folding thermodynamics and kinetics inside living E. coli cells and under physiologically relevant conditions using fluorine NMR spectroscopy. The results show that:
1) The model protein SH3 is not stabilized inside cells as predicted by crowding theory, and charge-charge interactions between SH3 and cellular components slow folding kinetics.
2) Cosolutes commonly used to mimic the cellular interior do not capture these effects and do not provide physiologically relevant information.
3) The findings establish that protein surfaces play an essential role in cellular environments through charge-charge interactions, contradicting predictions of crowding theory based only on volume exclusion effects.
Advanced Medicinal Chemistry of GPCR Receptorsaurabh gupta
Contents:-
Introduction
Structure of G-protein
Signal Molecules / Ligands of GPCRs
G- Protein Mediated Pathways
Receptor Site Theories
Forces involved in drug receptor interactions
Proton euilibria in minor groove of dnamganguly123
1) The document describes an experiment testing the prediction that regions of increased hydrogen ion density exist in the grooves of DNA. Probes with variable linker lengths and a proton-sensitive carboxyl group were attached to DNA in the minor groove.
2) The apparent pKa values of the carboxyl groups were higher than in free solution, increasing with shorter linker lengths. This agrees with calculations showing higher hydrogen ion density in the grooves.
3) The experiment provides experimental evidence supporting the theoretical prediction of acidic domains with elevated hydrogen ion density in the DNA minor groove.
In-Silico Identification of inhibitors for Controlling Rice BlastNisha Juyal
The document describes a study that used in-silico methods to identify potential anti-fungal agents that could inhibit rice blast fungus. The study used virtual screening to dock compounds from the ZINC database against two enzymes (THNR and SDH) involved in melanin biosynthesis in the fungus. The top scoring compounds from docking were validated using PyRx software. Four compounds were identified as potential inhibitors that bound strongly to both enzyme targets. These compounds could be further optimized and tested experimentally as potential anti-fungal drugs to control rice blast disease.
A mechanism of ryanodine receptor modulation ... [cardiovasc resdrucsamal
This study explores the functional relationship between protein kinase A (PKA) phosphorylation and binding of FK506 binding proteins (FKBP12/12.6) to the ryanodine receptor (RyR). The results show that the affinity of RyR1/2 binding to FKBP12/12.6 is greater when the channel is closed versus open. Phosphorylation and the drug K201 reduced this affinity by increasing the dissociation rate, shifting RyR to an open state. The findings support a model where phosphorylation and K201 similarly alter RyR conformation and regulate FKBP12/12.6 binding.
This document describes a study that used computational modeling to design novel inhibitors of BACE1, the enzyme involved in Alzheimer's disease pathogenesis. Researchers designed biaryl and fused-ring compounds targeting the S2 pocket of BACE1. They synthesized compounds based on these scaffolds and tested them for inhibitory activity against BACE1 and the related enzyme BACE2. One compound reduced amyloid beta 40 production in cells by 65%, indicating inhibitory activity against BACE1 with potential for treating Alzheimer's disease. The document discusses the rationale for targeting the flexible S2 pocket and for using less polar compounds that form fewer hydrogen bonds to gain selectivity against BACE2.
This document describes the design, synthesis, and evaluation of novel thrombin inhibitors incorporating P3-P4 lactam sulfonamide moieties. The inhibitors were designed to exploit interactions with thrombin's S2 and S3 sites to improve selectivity over related serine proteases. A series of 5-7 membered lactam rings were synthesized and incorporated a P1 argininal group. X-ray crystallography of one inhibitor bound to thrombin confirmed the predicted binding mode. In vitro testing showed several inhibitors had low nanomolar IC50 values against thrombin and good selectivity over trypsin and factor Xa. Overall, the lactam sulfonamides represent a new class of orally bioavailable
PARP-1 inhibitors have shown promise in oncology by potentiating the effects of DNA damaging chemotherapy agents. Cephalon identified a pyrrolocarbazole hit that inhibited PARP-1 but had poor properties. Through structure-based design and SAR studies, they developed CEP-8983, a potent PARP inhibitor. A prodrug, CEP-9722, was synthesized to improve solubility and pharmacokinetics. In preclinical studies, CEP-8983 and its active metabolite CEP-9397 potentiated the effects of temozolomide in tumor cell lines. CEP-9722 advanced to Phase 1 and 2 clinical trials for evaluation as monotherapy and
Similar to bradykinin receptor antagonist and thrombin inhibitors (20)
The ability to recreate computational results with minimal effort and actionable metrics provides a solid foundation for scientific research and software development. When people can replicate an analysis at the touch of a button using open-source software, open data, and methods to assess and compare proposals, it significantly eases verification of results, engagement with a diverse range of contributors, and progress. However, we have yet to fully achieve this; there are still many sociotechnical frictions.
Inspired by David Donoho's vision, this talk aims to revisit the three crucial pillars of frictionless reproducibility (data sharing, code sharing, and competitive challenges) with the perspective of deep software variability.
Our observation is that multiple layers — hardware, operating systems, third-party libraries, software versions, input data, compile-time options, and parameters — are subject to variability that exacerbates frictions but is also essential for achieving robust, generalizable results and fostering innovation. I will first review the literature, providing evidence of how the complex variability interactions across these layers affect qualitative and quantitative software properties, thereby complicating the reproduction and replication of scientific studies in various fields.
I will then present some software engineering and AI techniques that can support the strategic exploration of variability spaces. These include the use of abstractions and models (e.g., feature models), sampling strategies (e.g., uniform, random), cost-effective measurements (e.g., incremental build of software configurations), and dimensionality reduction methods (e.g., transfer learning, feature selection, software debloating).
I will finally argue that deep variability is both the problem and solution of frictionless reproducibility, calling the software science community to develop new methods and tools to manage variability and foster reproducibility in software systems.
Exposé invité Journées Nationales du GDR GPL 2024
Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...AbdullaAlAsif1
The pygmy halfbeak Dermogenys colletei, is known for its viviparous nature, this presents an intriguing case of relatively low fecundity, raising questions about potential compensatory reproductive strategies employed by this species. Our study delves into the examination of fecundity and the Gonadosomatic Index (GSI) in the Pygmy Halfbeak, D. colletei (Meisner, 2001), an intriguing viviparous fish indigenous to Sarawak, Borneo. We hypothesize that the Pygmy halfbeak, D. colletei, may exhibit unique reproductive adaptations to offset its low fecundity, thus enhancing its survival and fitness. To address this, we conducted a comprehensive study utilizing 28 mature female specimens of D. colletei, carefully measuring fecundity and GSI to shed light on the reproductive adaptations of this species. Our findings reveal that D. colletei indeed exhibits low fecundity, with a mean of 16.76 ± 2.01, and a mean GSI of 12.83 ± 1.27, providing crucial insights into the reproductive mechanisms at play in this species. These results underscore the existence of unique reproductive strategies in D. colletei, enabling its adaptation and persistence in Borneo's diverse aquatic ecosystems, and call for further ecological research to elucidate these mechanisms. This study lends to a better understanding of viviparous fish in Borneo and contributes to the broader field of aquatic ecology, enhancing our knowledge of species adaptations to unique ecological challenges.
EWOCS-I: The catalog of X-ray sources in Westerlund 1 from the Extended Weste...Sérgio Sacani
Context. With a mass exceeding several 104 M⊙ and a rich and dense population of massive stars, supermassive young star clusters
represent the most massive star-forming environment that is dominated by the feedback from massive stars and gravitational interactions
among stars.
Aims. In this paper we present the Extended Westerlund 1 and 2 Open Clusters Survey (EWOCS) project, which aims to investigate
the influence of the starburst environment on the formation of stars and planets, and on the evolution of both low and high mass stars.
The primary targets of this project are Westerlund 1 and 2, the closest supermassive star clusters to the Sun.
Methods. The project is based primarily on recent observations conducted with the Chandra and JWST observatories. Specifically,
the Chandra survey of Westerlund 1 consists of 36 new ACIS-I observations, nearly co-pointed, for a total exposure time of 1 Msec.
Additionally, we included 8 archival Chandra/ACIS-S observations. This paper presents the resulting catalog of X-ray sources within
and around Westerlund 1. Sources were detected by combining various existing methods, and photon extraction and source validation
were carried out using the ACIS-Extract software.
Results. The EWOCS X-ray catalog comprises 5963 validated sources out of the 9420 initially provided to ACIS-Extract, reaching a
photon flux threshold of approximately 2 × 10−8 photons cm−2
s
−1
. The X-ray sources exhibit a highly concentrated spatial distribution,
with 1075 sources located within the central 1 arcmin. We have successfully detected X-ray emissions from 126 out of the 166 known
massive stars of the cluster, and we have collected over 71 000 photons from the magnetar CXO J164710.20-455217.
ANAMOLOUS SECONDARY GROWTH IN DICOT ROOTS.pptxRASHMI M G
Abnormal or anomalous secondary growth in plants. It defines secondary growth as an increase in plant girth due to vascular cambium or cork cambium. Anomalous secondary growth does not follow the normal pattern of a single vascular cambium producing xylem internally and phloem externally.
ESR spectroscopy in liquid food and beverages.pptxPRIYANKA PATEL
With increasing population, people need to rely on packaged food stuffs. Packaging of food materials requires the preservation of food. There are various methods for the treatment of food to preserve them and irradiation treatment of food is one of them. It is the most common and the most harmless method for the food preservation as it does not alter the necessary micronutrients of food materials. Although irradiated food doesn’t cause any harm to the human health but still the quality assessment of food is required to provide consumers with necessary information about the food. ESR spectroscopy is the most sophisticated way to investigate the quality of the food and the free radicals induced during the processing of the food. ESR spin trapping technique is useful for the detection of highly unstable radicals in the food. The antioxidant capability of liquid food and beverages in mainly performed by spin trapping technique.
The debris of the ‘last major merger’ is dynamically youngSérgio Sacani
The Milky Way’s (MW) inner stellar halo contains an [Fe/H]-rich component with highly eccentric orbits, often referred to as the
‘last major merger.’ Hypotheses for the origin of this component include Gaia-Sausage/Enceladus (GSE), where the progenitor
collided with the MW proto-disc 8–11 Gyr ago, and the Virgo Radial Merger (VRM), where the progenitor collided with the
MW disc within the last 3 Gyr. These two scenarios make different predictions about observable structure in local phase space,
because the morphology of debris depends on how long it has had to phase mix. The recently identified phase-space folds in Gaia
DR3 have positive caustic velocities, making them fundamentally different than the phase-mixed chevrons found in simulations
at late times. Roughly 20 per cent of the stars in the prograde local stellar halo are associated with the observed caustics. Based
on a simple phase-mixing model, the observed number of caustics are consistent with a merger that occurred 1–2 Gyr ago.
We also compare the observed phase-space distribution to FIRE-2 Latte simulations of GSE-like mergers, using a quantitative
measurement of phase mixing (2D causticality). The observed local phase-space distribution best matches the simulated data
1–2 Gyr after collision, and certainly not later than 3 Gyr. This is further evidence that the progenitor of the ‘last major merger’
did not collide with the MW proto-disc at early times, as is thought for the GSE, but instead collided with the MW disc within
the last few Gyr, consistent with the body of work surrounding the VRM.
Phenomics assisted breeding in crop improvementIshaGoswami9
As the population is increasing and will reach about 9 billion upto 2050. Also due to climate change, it is difficult to meet the food requirement of such a large population. Facing the challenges presented by resource shortages, climate
change, and increasing global population, crop yield and quality need to be improved in a sustainable way over the coming decades. Genetic improvement by breeding is the best way to increase crop productivity. With the rapid progression of functional
genomics, an increasing number of crop genomes have been sequenced and dozens of genes influencing key agronomic traits have been identified. However, current genome sequence information has not been adequately exploited for understanding
the complex characteristics of multiple gene, owing to a lack of crop phenotypic data. Efficient, automatic, and accurate technologies and platforms that can capture phenotypic data that can
be linked to genomics information for crop improvement at all growth stages have become as important as genotyping. Thus,
high-throughput phenotyping has become the major bottleneck restricting crop breeding. Plant phenomics has been defined as the high-throughput, accurate acquisition and analysis of multi-dimensional phenotypes
during crop growing stages at the organism level, including the cell, tissue, organ, individual plant, plot, and field levels. With the rapid development of novel sensors, imaging technology,
and analysis methods, numerous infrastructure platforms have been developed for phenotyping.
BREEDING METHODS FOR DISEASE RESISTANCE.pptxRASHMI M G
Plant breeding for disease resistance is a strategy to reduce crop losses caused by disease. Plants have an innate immune system that allows them to recognize pathogens and provide resistance. However, breeding for long-lasting resistance often involves combining multiple resistance genes
What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
What are greenhouse gasses how they affect the earth and its environment what is the future of the environment and earth how the weather and the climate effects.
ESPP presentation to EU Waste Water Network, 4th June 2024 “EU policies driving nutrient removal and recycling
and the revised UWWTD (Urban Waste Water Treatment Directive)”
Nucleophilic Addition of carbonyl compounds.pptxSSR02
Nucleophilic addition is the most important reaction of carbonyls. Not just aldehydes and ketones, but also carboxylic acid derivatives in general.
Carbonyls undergo addition reactions with a large range of nucleophiles.
Comparing the relative basicity of the nucleophile and the product is extremely helpful in determining how reversible the addition reaction is. Reactions with Grignards and hydrides are irreversible. Reactions with weak bases like halides and carboxylates generally don’t happen.
Electronic effects (inductive effects, electron donation) have a large impact on reactivity.
Large groups adjacent to the carbonyl will slow the rate of reaction.
Neutral nucleophiles can also add to carbonyls, although their additions are generally slower and more reversible. Acid catalysis is sometimes employed to increase the rate of addition.
hematic appreciation test is a psychological assessment tool used to measure an individual's appreciation and understanding of specific themes or topics. This test helps to evaluate an individual's ability to connect different ideas and concepts within a given theme, as well as their overall comprehension and interpretation skills. The results of the test can provide valuable insights into an individual's cognitive abilities, creativity, and critical thinking skills
Sharlene Leurig - Enabling Onsite Water Use with Net Zero Water
bradykinin receptor antagonist and thrombin inhibitors
1. BRADYKININ RECEPTOR ANTAGONISTS AND
THROMBIN INHIBITORS
ADVANCED MEDICINAL CHEMISTRY-I
Presented by
T.Bhanusri
21031S0215
M.PHARM 1ST YEAR 1ST SEM
Pharmaceutical chemistry
IST(Centre of pharmaceutical
science),JNTUH
Under the guidance of
DR.S.Shoba rani
M.PHARM(Ph.D)
Associate professor
HOD of CPS, JNTUH
Former Additional controller of
examination, JNTUH
3. Bradykinin (in Greek brady- = slow; -kinin =
to move) is a peptide that promotes
inflammation.
Bradykinin is a 9-amino acid peptide chain.
Bradykinin is a linear nonapeptide messenger
belonging to the kinin group of proteins, with
amino acid sequence RPPGFSPFR.
The amino acid sequence of bradykinin is :
Arg-pro-pro-Gly-phe-ser-pro-phe-Arg.
The empirical formula is C50H73N15O11.
Introduction
Structure of
bradykinin
4. A class of drugs called angiotension
converting enzyme inhibitors (ACE
inhibitors) increase bradykinin levels
by inhibiting its degradation , thereby
increasing its blood pressure lowering
effect.
Enzymatically produced from kallidin
in the blood, it is a powerful
vasodilator that causes smooth muscle
contraction, and may mediate
inflammation .
It has a role as a human blood serum
metabolite and a vasodilator agent.
It is a tautomer of a bradykinin(2+).
Structure of
bradykinin
5. history
1920’s and
1930’s
Characterized a hypotensive substance in urine and
found a similar material in saliva,plasma and a variety
of tissues.
Established that kallikreins generate a
pharmacologically active substance from an inactive
precursor present in plasma
1948
Named the active substance kallidin and showed it to
be a polypeptide cleaved from a plasma globulin that
they termed as kallinogen
Frey
,kraut,
werle
Werle,
gotze,
keppler
Werle,
berek
-
Rocha e
silva and
associate
d
Reported that trpsin and certain snake venoms acted on plasma
globulin to produce a substance that lowered bp and caused
developing contraction of the gut.
1937
6. -
1960
1960
-
Elliot and
coworkers The nonpeptide bradykinin was isolated
Synthesized the nonpeptide bradykinin.
because of this slow response, they named
the substance bradykinin.
Boissonnas
and
associated
9. Kinin receptors:
Existence of two types bradykinin receptor: B1 and B2.
Both are GPCR and mediate similar effects.
B1
Normally expresses at very low levels but
are strongly induced in inflamed ar
damaged tissues by cytokines such as IL-1
Respond to des-Arg9-bradykinin and des-
Arg9-kallidin but not to bradykinin itself.
Likely that B1 receptors play asignificant
role in inflammation and hyperalgesia
Constitutively expressed in most normal
tissues.
Selectively binds bradykinin and kallidin
and mediates the majority of their effects.
The B2 receptors activates PLA2 and
PLC via interaction with distinct G
proteins.
B2
11. Solution conformation of bradykinin
2-D NMR with empirical energy calculation:
on basis of spectral data , biological results from conformationally restricted analogs, as well as the
relationship between ordering in bradykinin and the dielectric environment of the solvent.
In aqueous solution bradykinin is conformationally random, the biologically active form of the peptide is
likely ordered and stabilized within the lipid bilayer of the cell membrane prior to binding with its
receptor. Hence the nature of receptor might be hydrophobic.
The appropriate solvent environment should be able to stimulate, at least in terms of hydrophobicity and
dielectric constant, the nature of a cell membrane, and a 90:10 d8-dioxane-H2O mixture was selected for
NMR experiments.
It was anticipated that under these nonsolvating conditions the conformational diversity of bradykinin
might be severely restricted.
The ultimate analysis of the two-dimensional NMR data collected at 500 MHz supported a single major
conformational species. There were five HN-CαH connectivities, one for each amide. This was confirmed
in the 13C NMR spectrum where only nine carbonyl resonances, one for each amino acid, were present.
3-D strctures: Not known the receptors and sructure of bradykinin
12. NOESY:
Based on multiple observed long range amide-to-amide nucear overhauser effects
(NOEs), that it was indeed a single major conformational species.
Although bradykinin contains three proline residues, the absence of any strong CαHi
-CαHj +, cross peaks in the nuclear overhauser enhancement spectroscopy (NOESY)
spectrum was taken as proof that all peptide bonds were trans.
In total, 35 interproton distances were extracted from the NOESY spectrum and,
whenever possible, stereospecific assignments for pro-R and pro-S hydrogens were
made explicitly
Temperature dependant:
A temperature-dependent study of the chemical shifts of the amide protons resulted in
a near-linear dependence suggesting no major conformational changes were
coinciding with the temperature change and thereby allowing a comparison of slopes
(∆δ/∆t).
The lowest values obtained for these slopes corresponded to Phe8 and Arg9
suggesting solvent sequestering for these amides.
13. CHARMm – version 21:
Utilizing custom routines written using the program CHARMm, version 21 [21], the
interproton distances were incorporated into the potential-energy expression in the form
of an additional potential-energy term.
Computational stratergy:
Given the high Chou and Fasman probability of β-turns in the sequences Pro2-Pro3-Gly4-Phe5
and Ser6- Pro7-Phe8-Arg9 (3.79 × 10-4 and 1.99 × 10-4, respectively), the computational
strategy employed was to begin from two initial structures: (a) an extended β strand, and (b) a
structure containing these two predicted β turns.
NOE restrains:
Analysis of the two average structures obtainedfrom the two unique starting points demonstrated
convergence to a similar conformational species.
In each , the sum of the NOE restraints energy was less thab 4.7 kcal/mol and the RMS deviation
from the target distances was below Å.
Similar results were obtained for each simulation when they were repeated without the
electrostatic term being included in the total potential-energy function.
This important data lends credence to the hypothesis that the final structures are derived from
the NOE restraints and not by poorly represented electrostatic interactions.
14. A similar C-terminal turn structure was observed in an
analogous NMR study of a first-generation kinin antagonist,
NPC 567 (DArg0-Arg1-Pro2-Hyp3-Gly4-Phe5-Ser6-DPhe7-
Phe8-Arg9), although the type of turn was not the same.
Our initial speculation was that this slight structural
difference might partially account for the functional
differences of bradykinin and NPC 567.
These solution conformations, one of an agonist and the
other of an antagonist, were subsequently used to focus the
design and synthesis of conformationally constrained peptide
analogues of NPC 567.
15. Conformationally constrained bradykinin antagonist peptides
The ligand based approach of conformationally constrained peptides has been widely
used.
The process involves the incorporation of conformational constrains into the known
peptides, either agonist or antagonist , which enforce a predictable geometry.
A series of peptides containing these types of constraints can be useful for
extrapolating the steric and electronic environment of a given binding site.
The structural information can be derived regardless of whether or not the constrained
peptide binds to the target receptor.
Since peptides can be prepared rapidly , it is typical to establish a structure activity
relationship using them and then at some time later transpose that information onto a
nonpeptide lead molecule in an attempt to improve its potency.
As part of an expansion upon the hypothesis that a C- terminal β turn was a structural
prequisit to high affinity antagonist binding, novel series of constrained decapeptides
was prepared.
These peptides are of the sequence:
17. Lowest 5 kcal mol-1 of the calculated overall potential
energy surface for a model peptide of Ser-DHype(trans
propyl)-Oic-Arg. The contour interval is 0.5 Kcalmol-1
and the highest (outermost) and lowest contour energy
values are labeled. Superimposed on the contour plots are
values for ψi+1 and ψi+2 from each of the thirty structures
generated from the NMR data corresponding to the
tetrapeptide Ser-DHype(trans propyl)-Oic-Arg
The C-terminal portion of a
representative member of
this class of peptides was
shown—first by empirical
calculation , then by NMR
at 600 MHz—to adopt a β
turn nearly unambiguously
(figure ).
Moreover, it was shown by
calculation that the turn
was adopted regardless of
the nature of the ether
group (alkyl, aryl, etc.) or
its geometry (cis or trans).
18. Hence, a diverse series of these peptides was initially
used as a tool to probe the steric and electrostatic
topology of an antagonist binding site on the
bradykinin B2 receptor in the guinea pig ileum.
The cis ethers, in all cases, bound to the receptor
with significantly lower affinity than did the trans.
A more complete listing of the peptides used in the
study is shown in Table 1.
These results support the hypothesis that the domain
of the receptor that binds these antagonist ligands is
partly made up of a hydrophobic cavity about one
side of the C-terminal.
However, adjacent to the other side of the turn, there
appears to be same type of steric interference ( or
lack of a pocket) that might otherwise accommodate
the ethers of the cis configuration
19. Receptor binding curves for the binding of NPC
17410 and NPC 17643 to B2 receptors from the
guinea pig ileum and cloned rat and human B2
receptors. Legends are noted on the figure.
More recently, bradykinin B2 receptors
have been cloned from both rat and
human sources.
In receptor-binding experiments using
these new receptors, selected members
of the DHype-containing decapeptides
were used to probe these receptors, a
representative sample of the data is
shown in Figure.
NPC 17643( a trans propyl ether at
position 7) and NPC 17410( a cis
propyl ether of D-4-hydroxyproline at
position 7) were used.
20. NPC17643
NPC17410
Behave similarly in binding assays directed toward the bradykinin B2
receptors in guinea pig,rat and human.
Bound with similar affinity to both the guinea pig and rat bradykinin B2
receptors, but had an appreciably higher affinity for the human B2
receptor
The des-Arg9 forms of these peptides have also been shown to have high affinity for
the recently cloned human B1 receptor.
An extension of the work described herein would be to use a more complete series of
des-Arg9 DHype-containing nonapeptides to probe the binding site of this new receptor
where other interesting pharmacological differences are likely to exist since the B1
receptor is only 33% homologous to the human B2.
21. DHype
1st 2nd 3rd
Incorporated a novel β-turn
mimetic that was
alternatively functionalized
and used to probe the
unknown topology of the
guinea pig, rat, and human
bradykinin B2 receptors.
subsequent molecular
biological and
computational procedures
in the elucidation of an
antagonist binding site
certain members of
this series of
decapeptides contain
alkyl ethers of D-4-
hydroxyproline at
position seven.
Experimentalexperimen
tal evidence that high-
affinity decapeptide
bradykinin receptor
antagonists adopt a C-
terminal β turn in the
receptor-bound
conformation
22. Finally, several members of the series (i.e., NPC 17731, NPC 17761, NPC 17974) are among the
most potent antagonists for this receptor yet reported.
Hence, there may be applications for these compounds as human therapeutics.
Several “second generation” decapeptide antagonists have been reported, but the prototype from
the class, which was first to be reported, is HOE 140 (DArg0-Arg1-Pro2-Hyp3-Gly4-Thi5-Ser6-
DTic7-Oic8- Arg9).
This decapeptide has also been shown to preferentially adopt a C-terminal β turn.
There are two factors that must be considered when applying structure-activity-relationship (SAR)
information from a series of peptides toward the design of nonpeptide mimetics and putative
library scaffolds.
One is in regard to the backbone conformation that primarily serves as a structural scaffold upon
which the various functionalities (side chains) are attached.
The other factor is the side chains themselves whose spatial positions are primarily dictated by the
backbone structure.
With the exception of the Cα-methyl-Phe5-containing peptide (NPC 18540), each conformational
constraint caused a significant, at least 1000-fold, loss in binding affinity with respect to the
unconstrained parent peptide, NPC 18545.
23. A systematic study of the relative importances of amides and side chains in a prototypical
second generation antagonist, NPC 18545 (DArg0-Arg1-Pro2-Hyp3-Gly4-Phe5-Ser6-DTic7-
Oic8-Arg9) .
The elimination of all chirality and sidechain moieties in the segment Arg1-Pro2-Hyp3-Gly4-
Phe5 via replacement by Gly1-Gly2-Gly3- Gly4-Gly5 (NPC 18152), led to a peptide that no
longer binds the receptor.
NPC 18149 (DArg0-Arg1-Gly2-Gly3-Gly4-Phe5-Ser6-DTic7-Oic8-Arg9; Ki = 13.7 nM;
Guinea pig ileum) was taken as the lead peptide, the relative contributions to binding affinity
from each amide bond in the segment Arg1-Gly2-Gly3-Gly4-Phe5 were examined.
The conclusions drawn from the data are that in terms of structural or electrostatic interactions
with this antagonist site on the receptor, the amide bond linking residues two and three may not
be as critical as those linking residues three to four and four to five.
Each of these investigations was aimed toward an understanding of either the backbone
conformation of this prototypical decapeptide or the relative importance of the functional
groups in the side chains that make significant contributions to receptor affinity.
From the former, nonpeptide frameworks and scaffolds can be imagined. From the latter,
insights into which functionality is required for high-affinity binding is derived. The remaining
challenge is to reassemble these fragments onto synthetically feasible nonpeptide frameworks as
potential new lead compounds.
24. Elucidation of an agonist binding site on the B2 receptor
Receptor binding site on the basis of receptor binding data from conformationally
constrained ligands.
G-Protein-coupled receptors do not lend themselves to analysis by either NMR or x-ray
crystallography due to their structural dependence on an intact cell membrane.
In our laboratories we pursued this valuable structural information by utilizing a
combination of structural homology modeling, molecular dynamics, systematic
conformational searching methods, and mutagenesis experiments.
The combination of these techniques led to a proposed model of bradykinin bound to the
agonist site on its receptor.
A hydrophobicity (Kyte-Doolittle) calculation [42] on the amino acid sequence of the rat
bradykinin receptor yielded seven segments, each of which were 21 to 25 contiguous
residues with predominantly hydrophobic side chains.
These were presumed to be the seven transmembrane portions of the receptor.
Cartesian coordinates of the backbone atoms within each of these seven segments were built
by structural homology from the cryomicroscopic structure of the analogous segments of
bacteriohodopsin.
25. Subsequently, side chains were added to these seven segments as appropriate for the rat
bradykinin receptor, and the resulting geometry was optimized via constrained energy
minimization to alleviate bad contacts.
Extracellular and intracellular loops were extracted from the Protein Data Bank library,
following a geometric search based upon a vector defined by terminal alpha carbons in
adjacent helices.
The model was subsequently subjected to a series of constrained and unconstrained energy
minimizations as well as molecular dynamics simulations. The resulting structure of the
receptor was used in a novel two-step docking procedure.
bradykinin adopts a C-terminal β turn upon complexation with the receptor, the φ, ψ
backbone dihedral angles in the tetrapeptide corresponding to the C-terminus of
bradykinin (Ser-Pro-Phe-Agr) were constrained in a harmonic fashion (force constant = 15
Kcal Å-1 mol1) to values that define a type II' β-turn.
This tetrapeptide probe was then systematically translated about the interior of a
theoretical box inscribing the rat receptor model.
The translations were such that the tetrapeptide probe molecule was incrementally
repositioned within the receptor by following a 3 Å × 3 Å × 3 Å grid pattern.
26. Complete group of contour plots showing energy of
interaction between probe and receptor. Each contour plot
corresponds to a different horizontal slice as part of the
first stage in the conformational search. Darker gray
indicates most favorable interaction and the light shades
represent least favorable interactions
At each new position, both the probe
and receptor were reset to their initial
conformations, then the geometry of
the complex was optimized using
200 steps of steepest descent
followed by 500 steps of Adopted-
Basis Newton-Raphson energy
minimization.
Subsequently, the sum of the steric
and electrostatic contributions to the
overall potential energy (interaction
energy)—as measured only between
the tetrapeptide probe molecule and
the atoms of the receptor—were
calculated.
27. Several mutant receptors were made such that each contained either a point mutation or a small
cluster of point mutations, wherein native residues, having negatively charged side chains (Asp,
Glu), were replaced by alanine(s). Table 2 lists the initial cluster mutations (rat) that were
prepared as well as the follow-up single point mutations (rat).Therefore a receptor containing a
double mutation (Asp268,286 rarrow.gif Ala268,286) would be expected to show a much more
dramatic loss in affinity for bradykinin than would receptors containing the individual point
mutations. The appropriate double mutation experiment confirmed this by causing a 500-fold loss
in affinity for bradykinin, as predicted (Table 2)
28. Proposed model of bradykinin bound to the rat B2
receptor at the agonist binding site. Only the upper
portion of the receptor is shown as gray helical ribbons.
Bradykinin backbone and side chain atoms are shown as
thick white licorice. Positions of point mutations having
no significant adverse effects on bradykinin binding are
shown as light gray spheres. Positions of mutations
affecting bradykinin binding are shown as dark gray
spheres
Figure shows a stereoview of
the selected ligand-receptor
complex chosen on the basis
of best agreement with the
results of these mutagenesis
studies.
These residues are remotely
situated with respect to the
proposed site of bradykinin
binding and are colored light
gray in Figure 5.
The mutagenized residues of
this double mutant B2
receptor are colored dark
gray in Figure 5.
29. Furthermore, in contrast to the functional activity of NPC 18325 at the human B2 receptor, the
compound is a functional antagonist as measured against bradykinin-induced contraction of the
isolated guinea pig ileum (pA2 = 5.5). These findings are in agreement with the concept that as a
ligand is made smaller (i.e., fewer contact points possible with the receptor), the subtle structural
differences in the binding sites on species variants of the same receptor become amplified. This
observation further supports a cautionary posture toward developing nonpeptide antagonists for use
in human diseases on the basis of results obtained in some animals including the guinea pig. Taking
this new molecule as a lead structure, together with the receptor model and structure-activity
relationship associated with related peptides including cyclic antagonists, the pursuit of several
related pseudopeptides was undertaken.
30. Elucidation of an antagonist site on the B2 receptor
There have been a variety of single alanine point mutations experimentally
introduced into both rat and human bradykinin B2 receptors.
Several of these have been shown to decrease the affinity of bradykinin to the
receptor and have been implicated structurally near the agonist binding site. In
contrast, at the time of this manuscript, there have been no mutations reported that
adversely affect the ability of any peptide antagonists to bind to the receptor.
Furthermore, antibodies raised against the certain extracellular domains of the
kinin receptor compete with bradykinin for binding to the receptor but have no
inhibitory action on the binding of antagonist peptides.
In addition, it has been shown that bradykinin can be covalently crosslinked to
the B2 receptor while antagonists cannot.
These observations have fostered the belief that the agonist and antagonist
binding sites of the receptor are not the same.
31. specific groups of contiguous residues within
the receptor were identified as possible
contributors to an antagonist binding site. The
NPC 17410 binding to chimeras III, IV, and
VIII showed rat-like pharmacology (low NPC
17410 affinity). The NPC 17410 binding to
chimeras I, II, VI, and VII showed human-like
NPC 17410 pharmacology (high receptor
affinity). Binding to chimeras V and VIII,
however, was similar to rat-like NPC 17410
pharmacology, but the affinity of the compound
was slightly shifted back toward human-like
results.
32. Mutagenesis experiments have been done on this
pair in the rat B2 receptor with interesting results.
Mutations in Thr263 only affect agonist binding,
not antagonist. Mutations in Gln260 affect
binding of bradykinin and first generation
antagonist peptides.
As depicted in the figure, it is possible that the
agonist and antagonist binding sites have
domains on opposite sides of the helix that makes
up TM 6, with Gln260 being situated partly in
both.
Schematic of the primary amino sequence of the human B2 receptor. Shown in black are
residues experimentally identified as contributing to an agonist binding site. The dark gray
residues are suspect positions for contributing to an antagonist site. The residues colored light
gray have been mutagenized only in the rat B2 receptor, but they are conserved in the human.
The Thr263 rarrow.gif Ala mutation interferes with agonist binding only, while Gln260
partially interferes with agonist and first generation antagonist binding.
33. Design and combinatorial synthesis of nonpeptidic antagonists
a significant body of information was generated that provides insights into the key structural
features of bradykinin receptor binding sites and the residues that participate in ligand binding.
In addition, from the ligand-based studies, knowledge about relevant structure-activity
relationships was acquired.
Our modular synthetic strategy was based primarily upon the recognition that high-affinity
ligands appear to be comprised of three domains.
These domains are (1) a positively charged N-terminal segment, (2) a midsection containing a
bend or twist with some hydrophobic substituent attached and, (3) a C-terminal segment of
appropriate hydrophobicity and structurally simulating a type II' β turn.
Models of potent cyclic and linear peptide bradykinin receptor antagonists (described previously)
were used in a comparative fashion to select nonpeptide ring systems from a database of chemical
structures fine chemicals database.
For each, some degree of chemical diversity was achieved by altering one of several parameters
including, o, m, or p substitution of an aromatic ring or nature of alkyl substituent(s) as well as
point(s) of synthetic attachment.
34. Composition of ten original
nonpeptidic libraries of the
sequence DArg-Arg-X-Y-Arg.
X and Y were selected from
the set of scaffolds shown in
Table 1. Also shown are the
subsequent breakdown
libraries from original library
number 1. Two-letter codes
used in the figure correspond
to the different nonpeptide
moieties described in Table 1.
Specifically, PH =
phenanthridinone, CB =
carboline, SP = spirocycle, SC
= Straight chain, CN =
cinnamic acid
35. Lead optimization
We have previously reported that the C-terminal guanidinyl moiety of Arg [9] in
prototypical peptide bradykinin antagonists is likely to behave more as an aromatic
functional group rather than a hydrogenbond donor/acceptor.
This speculation was based on proposed models of the agonist and antagonist binding
sites of this receptor that have been elucidated using molecular biological and
computational procedures.
On this premise, the newly discovered lead compound, I, was altered such that the
Cterminal arginine was replaced by 3',5'-dimethylpyrimidylornithine in an attempt to
increase potency.
This known mimetic of arginine contains an aromatic 3',5'-dimethylpyrimidyl ring in the
side chain rather than the guanidino group on naturally occurring arginine.
The results of the receptor binding assay performed using this compound, IA, are shown
in Table 4 where it is clear that affinity to the human B2 receptor is improved with
respect to compound I.
36. This data is supportive of the notion that the C-terminal residue(s) in this new series of
bradykinin antagonist compounds interact with a hydrophobic environment, perhaps
within the transmembrane domain of the receptor as previously suggested.
The discovery of I and IA is significant in many regards.
First, they are highly nonpeptidic lead compounds that could be further modified to
improve potency and/or reduce molecular weight.
Such improvements might lead to novel therapeutic agents for the treatment of
inflammatory diseases.
Thus far in the kinin antagonist literature there is significant evidence showing that,
for compounds containing a C-terminal arginine residue, removal of that arginine
generally yields compounds that are antagonists of the B1 subtype of the bradykinin
receptor.
Following a similar strategy with compound I could lead to the discovery of a novel
series of nonpeptidic B1 receptor antagonists, although this remains to be
demonstrated
39. I.ROLES OF THROMBIN IN HEMOSTASIS AND THE
THERAPEUTIC UTILITY OF THROMBIN INHIBITORS:
Thrombin is a serine protease.
It plays critical roles in both anticoagulation and blood cloat formation.
In penultimate step of the coagulation cascade;
Soluble fibrinogen
cleavage
Insoluble fibrinogen
thrombin
40. Thrombin activates Coagulation factor (XIII)
stabilize
Fibrin thrombus
Additional clot formation, thrombin participates in anticoagulation functions.
Most drug design efforts focus on thrombin inhibition as a means to prevent
the serious consequences of thrombus formation in myocardial infraction and
stoke.
Thrombin inhibitors clot formation in patients prone to deep vein
thrombosis or repeat hear attack.
Thrombin inhibitors may decreases the incidence of reocclusion , to release
active clot-bound thrombin
Prevents
41. II. STRUCTURE OF THROMBIN
Thrombin consists of two polypeptides, an
A chain of 36 residues and a 259-residue B
chain,linked by a disulfide bond.
The crystallographic structure of thrombin
reveals a globular protein organized about
two ß barrels with overall folding pattern
of the chymotrypsin serine protease
family.
Human thrombin large (red) and
small (green) subunits complex
with prolinamide derivative (PDB
code 1ppb
42. Figure 1 Stereoscopic view of the
crystallographic structure of thrombin
complexed with N-acetyl-(D-Phe)-Pro-
boroArg-OH. Helical regions are
represented in the standard way and
arrows indicate regions of β sheet. Solid
lines show the thrombin bound
conformation of N-acetyl-(D-Phe)-Pro-
boroArg-OH . Active-site residues, His57
and Ser195, are shown with a ball-and-
stick representation.
43. Thrombin’s multionality and regulation of activity are
achieved by specialized subsites on the enzyme’s
surface(fig.2).
Fibrinogen cleavage, for example,involves interactions at the
primary specificity pocket, the extended fibrinogen
recognition exosite, and an additional specificity pocket.
Subsite interactions differ for cleavage of other thrombin
substrates including the thrombin receptor and protein C.
Additional and overlapping subsites exist for thrombin
effector molecules including heparin, antithrombin III, and
heparin cofactor II .
44. Figure 2 Schematic representation of
Subsite Utilization in Thrombin
Complexes.
Fibrinogen interacts with three
thrombin subsites (here thrombin is
represented by a large oval and the
interconnected subsites by an irregular
three-armed shape). Physiological
effectors of thrombin and thrombin
inhibitors form distinct interactions at
these subsites. Additional subsites, such
as the heparin-binding site, exist on the
thrombin surface and are not indicated
here. The catalytic triad is represented
by three circles at the vertices of a
triangle.
45. III.THROMBIN INHIBITORS DIRECTED AT THE
FIBRINOPEPTIDE A BINDING POCKET
The majority of synthetic thrombin
inhibitors interact at the
fibinopeptide A binding
pocket,which include the catalytic
residues Ser 195 and
His57,hydrogen-binding
capabilities with in oxyanion
hole,peptide backbone functional
groups that hydrogen bond with the
peptide backbone of the substrate
and residues involved in amino acid
recognition.
fig 1
Schematic diagram of binding determinants
within the fibrinopeptide A binding pocket of
thrombin and their utilization by N-acetyl-(D-
Phe)-Pro-boroArg-OH
46. Many of the binding determinants are utilized by N-acetyl-(D-Phe)-Pro-
Arg-chloromethylketone (PPACK) and its boronic acid analog (DUP714).
The crystallographic structures of these molecules complexed with
thrombin have both served as starting points for structure-based drug
design and as reference structures for comparison of binding modes of
other inhibitors.
The use of arginine boronate esters as transition-state mimetics results in
potent peptidyl thrombin inhibitors.
These inhibitors, however, exhibit significant affinity for other serine
proteases that have in common a specificity for substrates with basic
residues at P1 (e.g. trypsin, Factor Xa, and plasmin).
Earlier work demonstrated that neutral side chains of P1 boronate esters
impart greater selectivity for thrombin.
47. The boropeptide shown in Figure 2
was investigated as the prototype of
neutral side chain, tripeptide
thrombin inhibitors.
It had a Ki against thrombin of
and shows selectivity relative to
other trypsin-like plasma proteases.
Since these inhibitors have a
neutral residue at the P1 site,
Deadman and coworkers sought to
demonstrate the mode of binding to
thrombin in the absence of a salt
bridge with Asp189.
fig 2
Schematic representation of the active-
site orientation of a “neutral” P1 boronic
acid thrombin inhibitor.
48. Boron-11-NMR, a sensitive probe of the chemical environment
around boronate esters, can distinguish between trigonal and
tetrahedral forms of boron.
The 11B-NMR spectrum of this inhibitor complexed with
thrombin showed a single peak at -17 ppm that remained constant
for 7 hours.
The chemical shift suggests boron adopts a tetrahedral geometry
on binding to thrombin and is consistent with the orientation of the
inhibitor in the active site shown in Figure 2.
While the 11B-NMR revealed an interaction within the catalytic
site, it could not distinguish between bonding with Ser195 or
His57
49. Kahn and coworkers recently
investigated the application of
synthesized peptidomimetics as novel
inhibitors of thrombin.
Fibrinogen peptide A mimetic
(FPAM, Figure 3) incorporates a
bicyclic peptidomimetic within the
turn region of fibrinogen peptide A.
The bicyclic peptidomimetic confers
conformational stability to the turn
region as suggested by x-ray crystal
structures of fibrinogen peptide
complexes as well as complexes of
BPTI with thrombin.
fig 3
Schematic representation of the principal
intermolecular interactions of a fibrinogen
peptide A mimetic within the active site of
thrombin
50. Fig 2
Complexed
with arginine
guanidium
Extensive
hydrophobic contacts
within the S2 apolar
binding site
Gly at P3 interact with thrombin via β-sheet-type
hydrogen bond with the carbonyl group gly
216.(Imp in the positioning of the bicyclic ring
corresponding to the β bend
Phenyl rings shows
hydrophobic contact with
11e174
This bicyclic ring,
although not
aromatic , forms
an edge to face
contact with
Trp215
Cyclic template having attachment sites
for three side chains that are
complementary to the S1,S2,S3 sites in
thrombin
51. Obst et al.,departing from thee peptide
template, designed and synthesized novel
nonpeptide inhibitors of thrombin.
Using computational approaches (Insight
II/Discover/CVFF force field), possible
templates were modeled within the active
site of thrombin.
These studies resulted in the synthesis of
thirteen analogs that shared a common
template.
The most active molecule (Ki = 90 nM,
8-fold selective versus trypsin) was
studied further by x-ray crystallography
(Figure 4).
fig 4
Schematic representation of the
principal intermolecular interactions of
a nonpeptide bicyclic inhibitor within
the active site of thrombin
52. +ve charged
benzamidine binds
into the S1 pocket of
thrombin forming a
bidentate hydrogen
bond with Asp189
The proximal
carbonyl of the
rigid template
acts as a
hydrogen-bond
receptor for the
amideNH of
Gly216
The
methylene
dioxybenzyl
group at P3
interact with
thrombin in
two ways
An edge to
face
interaction
was
observed
withTrp215
An oxygen of
methylenedioxy group
acts as an acceptor for a
hydrogen bond with the
OH hydrogen of
Tyr60A
53. Recent communications from Bristol-Myers Squibb [14,15]
describe peptidomimetic inhibitors (Fig5) that were designed
to bind thrombin with N- to C- polypeptide chain sense
opposite that of the substrate and form interactions similar to
those made by the 1st three residues of hirudin
(11e1,Thr2,Tyr3).
In the x-ray crystal structure of BMS-183507 (Ki = 17.2
nM) with thrombin.
54. N-terminal
facing the
catalytic
site
Methyl ester is
exposed to
solvent
A bound water
molecule
hydrogen bonded
to the ser195
hydroxyl
Phe 1-O and the
phe3-NH from
hydrogen bonds
with Gly216
Phe1-NH hydrogen
bonds to the backbone
carbonyl of SER214
The retro –inhibitors
contain a 4-
guanidinobutanoyl
group that extends
into the S1
specificity site
Forming two hydrogen bonds
between the guanidine and
Asp189 in a similar manner to
PPACK.
BMS-183507 forms
only one ,The one
hydrogen bond being
directed to the
carbonyl oxygen of
Gly219
55. cyclotheonamide A (CtA), a
macrocyclic marine natural
product derived from the
Japanese sponge,Theonella sp.,
inhibiys thrombin with an IC50
value of 100 nM and represents a
novel structural class of serine
protease inhibitors.
An x-ray crystal structure of CtA
complexed with thrombin was
used to determine the molecular
basis for this inhibition.(fig 6)
Figure 8 Schematic representation of the
principal intermolecular interactions of
cyclotheonamide A within the active site of
thrombin
56. The Arg-pro unit binds to the S1 and
S2 sites in a similar manner to the
Arg-pro of PPACK.
The Arg guandinium group forms a
bidentate hydrogen bond wth Asp
189 while the pro establishes a
βsheet interaction with the Ser214-
Gly216 backbone.
The α-ketoamide acts as a
transition-state mimetic forming
a tetrahedral hemiketal with the
hydroxyl of Ser195.
57. Starting with the known thrombin inhibitors Argatroban and
Nα(2-naphthyl-sulfonyl-glycyl)-DL-pamidinophenylalanyl-
piperidine (NAPAP), a group at Roche initiated a medicinal
chemistry program to develop thrombin inhibitors with reduced
toxicity and an improved hemodynamic profile.
The discovery program proceeded in four iterative phases which
are shown in Table 1.
Initial screening of low molecular weight organic bases led to the
discovery of 1-amidinopiperidine (1–1) as a new surrogate for
the guanidine and amidine functionality in Argatroban and
NAPAP, respectively.
A distinct advantage of 1-amidinopiperidine is its intrinsic
selectivity for thrombin over trypsin.
58.
59. Application of three-fold iterative strategy of design involving synthesis, x-ray
crystallography, and molecular modeling, this group elaborated the 1-
amidinopiperidine from structures that inhibited in the micromolar range to
some inhibiting in the picomolar range.
In doing so significant improvements in the selectivity of thrombin relative to
trypsin were also achieved.
In the case of the D-amino acid series (1–2), a “second inhibitor binding mode”
that differed from that of Argatroban was identified.
In this new and unexpected binding mode, the S2 pocket is unoccupied and the
napthalenesulfonyl group fills the S3 site and overlaps the front of the S2 site.
The benzyl group of the phenylalanine is oriented toward the protein surface
and is partially exposed to solvent.
The Argatroban or “inhibitor binding” mode was favored by the more potent
L-amino acid series (1–3 and 1–4) where the piperidide (1–3) or Nbenzyl (1–4)
binds to the S2 site and the aryl groups are found in the S3 site.
60. IV.BIVALENT THROMBIN INHIBITORS DIRECTED AT THE
FIBRINOPEPTIDE A BINDING POCKET AND THE
FIBRINOGEN RECOGNITION SITE:
A strategy to prepare highly selective thrombin inhibitors involves linkage
of molecules capable of interacting at distinct subsites.
This approach should result in inhibitors more specific for thrombin: while
serine proteases possess common structural features related to catalysis and
some serine proteases—including the coagulation enzyme Factor Xa—also
exhibit primary substrate specificity for positively charged residues, only
thrombin possesses recognition subsites for fibrinogen and effector
molecules such as thrombomodulin.
Nature has used this strategy in the evolution of hirudin, the anticoagulant
protein produced by the medicinal leech.
61. When this effective anticoagulant binds thrombin, the N-terminal
domain blocks the primary specificity pocket while the C-terminal
residues adopt an extended conformation and make multiple
interactions within the fibrinogen recognition exosite.
Guided by structural and biochemical information, small
molecules capable of simultaneous interactions with both the
primary specificity pocket and the fibrinogen recognition exosite
were designed and synthesized.
These bivalent inhibitors are composed of three regions: a group
to block the primary specificity pocket, a sequence to bind the
fibrinogen recognition site, and a chemical linker.
The bivalent inhibitor approach was first executed with peptides.
62.
63. In 1990, DiMaio et al. (3–3 [22]) used the peptide sequence from hirudin to link (d-Phe)-
Pro-Arg-Pro, known to bind at the primary specificity pocket [23], with hirudin C-
terminal residues, known to bind at the fibrinogen recognition site.
Polyglycine linkers were also used to connect these sequences (Maraganore et al).
Among these hirudin analogs,the tetraglycine linker appeared optimal(3-8,ki=2.3nM).
Most of the peptide-based bivalent inhibitors were slowly cleaved by thrombin.
Incorporation of ketomethylene pseudo peptide bond resulted in a non cleavable bivalent
inhibitor that rretained high thrombin affinity.
Decreased proteolysis in bivalent inhibitors increasingly nonpeptide in character to be
observed.
Chemically simpler linkers were made using multiple methylene-containing glycine
variants.
This was confirmed in the crystal structure of hirutonin-6:thrombin complex (3–26 [26])
where continuous electron density was observed for the entire bivalent inhibitor including
the linker region. The extended nature of the fibrinogen recognition site complicates
attempts to reduce inhibitor molecular weight while maintaining affinity.
64. Only seven residues are present in one of the smallest bivalent inhibitors.
Increasingly nonpeptide substituents have been incorporated into the primary
specificity pocket binding portion of the bivalent inhibitors.
Crystallographic analysis of its complex with thrombin showed the ketone carbonyl
becomes tetrahedrally coordinate by bonding to the side chain of thrombin's active
site residue, Ser195.
Substitutions of cyclohexylalanine for phenylalanine (3–4 compared to 3–5) and the
cyclohexylalanine-containing fibrinogen recognition peptide for the hirudin
sequence (3–17 compared to 3–18) also contribute to the increased affinity of this
bivalent inhibitor
65. Inactivated thrombin as an inhibitor of clot formation:
A means to selectively inhibit thrombin’s role in coagulation
while preserving its anticoagulant functions involves site-directed
mutagenesis of thrombin itself.
By introduction of a single mutation,altered thrombin’s relative
specificity for fibrinogen and protein C.
The engineered thrombin’s increased activation of protein C over
fibrinogen cleavage offers the possibility of inhibiting clot
formation with a modified human protein , a molecule likely to
exhibit few side effects.
66. The role of
structural
information
discovery of thrombin
inhibitors has benefited
from available protein
structural information.
Models of the thrombin overall
structure and its active site
geometry, constructd from
available structures of related
serine proteases,aided in the
design of the mechanism-based
inhibitors such as PPACK and
its boroarginine analog
Unexpected, nonsubstrate
binding mode of early
thrombin inhibitors such as
NAPAP was revealed by x-
ray crystallographic analyses.
Structure-based design methods have
been critical in the optimization of
bivalent inhibitors and inhibitors directed
at the primary specificity
Structures of
inhibitor:thrombin
complexes are essential
for the optimization of
substituents forming
interactions within the
aryl-binding site of the
primary specificity
pocket.
In some cases, minor
alterations of the inhibitor can
result in dramatic changes in
the inhibitor’s overall
interactions with thrombin
67. Roles of
structural
information
Drug discovery efforts have also been
strongly influenced by results of
structural of thrombin complexed with
effectors and structural peptides
For example, recently
the structures of
thrombin complexed
with fibrinopeptide A
and human
prothrombin fragment
F1 have been
determined
In addition to their role
in design of high-
affinity inhibitors,
these structure provide
valuable insights for
design of drugs
specific for the various
subsites and
conformational states
of thrombin
68. VII. CONCLUSION:
Discovery of therapeutically effective thrombin inhibitors
involves issues such as affinity and selectivity,and formulation.
In addition to these relatively common concerns,the complex
invivo mechanisms designed to balanced its pro-and
anticoagulant activites present additional challenges in the
discovery of therapeutically effective thrombin inhibitors.
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Structural based drug design by pandi veerapandion.
Wiliam o foye medicinal chemistry.
Berger’s medicinal chemistry and drug design 6th edition.
The enhanced permeability retention effect: a new paradigm for
drug targeting in infection Ernest A. Azzopardi1,2*, Elaine L.
Ferguson1 and David W. Thomas1 journal.