This document summarizes Array Bridge's services for analyzing biosimilars and biologics. It discusses how Array Bridge uses antibody arrays to analyze the 3D conformational comparability of biosimilars at the molecular level. This helps assess biosimilarity during development. It also describes how they provide ELISA kits and services to quantify host cell proteins and residual DNA/proteins as impurities in biologics. Array Bridge helps customers with analysis, method development and validation to support biosimilar and biologics development and meet regulatory requirements.
The document discusses a new technology for analyzing the three-dimensional conformational structure of monoclonal antibodies (mAbs). It describes how the technology was developed using an antibody array to measure epitope exposure on mAbs. Case studies show the technology can detect minor conformational differences between biosimilar and reference mAbs, and distinguish between mAbs that were clinical successes versus failures. The technology provides a unique conformational signature for each mAb.
The document discusses parallelizing the conformational search problem for small molecules. It presents the sequential nature of the problem and proposes a parallel computing solution using MPI. It describes a master-worker topology and shows results demonstrating speedup from using 4, 6, 8, and 10 processes on test cases of molecules with 5, 10, and 15 rotatable bonds. Speedup increases with more processes and rotatable bonds, with efficiencies generally between 50-80%.
Domainex has contributed to three clinical candidates through its drug discovery programs for clients. It uses a variety of technologies like combinatorial domain hunting, LeadBuilder for virtual screening, and integrated medicinal and computational chemistry. Domainex has a highly experienced team of drug discovery scientists and has successfully delivered ion-channel blockers, kinase inhibitors, and anti-thrombotics into clinical trials for clients. It provides concise drug discovery services from hit identification to candidate selection through its expertise in computational chemistry, library synthesis, and medicinal chemistry.
This document discusses structure-based drug design. It begins by explaining that structure-based drug design relies on knowledge of the three-dimensional structure of biological targets, usually determined through methods like X-ray crystallography. The structure of the target is then used to design ligands that will bind to the target. The process involves identifying drug targets, determining the target's structure, performing computer-aided drug design to identify potential binding ligands, and building or modifying ligands to optimize binding to the target.
Computer Aided Drug Design and Discovery : An Overview (2006)Girinath Pillai
The document discusses computer aided drug design and virtual screening. It describes how virtual screening can be used to discover new inhibitors for drug development by simulating the binding of compounds to protein targets. The document outlines the drug discovery process and different types of virtual screening techniques, such as ligand-based and structure-based approaches. It also discusses molecular docking methods and tools that are commonly used to simulate compound binding as part of virtual screening.
This document discusses methods for conformational analysis of molecules, which is needed to identify a molecule's lowest energy conformation. It describes systematic search methods that systematically explore all torsion angles combinations but are limited by computational time. It also describes model-building methods that construct conformations by joining molecular fragments. Available technologies for conformational analysis include software tools from Accelrys, Molecular Networks, OpenEye, Schrodinger, and Tripos.
Molecular modelling can help reduce the time and risks of drug development. It is applied to target structural characterization, developing focused libraries for hit discovery, and lead development and optimization. Fragment-based drug design is an important advance, where drug candidates are built inside the target's binding site using small molecule fragments to improve affinity from micromolar to millimolar to nanomolar levels. Molecular modelling supports medicinal chemistry decisions by providing structural insights into how drug candidates interact with their targets.
Structure based computer aided drug designThanh Truong
The document discusses structure-based computer-aided drug design. It describes the drug discovery process and challenges involved in predicting how small molecules bind to protein targets. Key steps in molecular docking include describing the receptor and ligand, sampling possible binding configurations, and scoring the interactions to estimate binding affinity. Genetic and simulated annealing algorithms are commonly used to sample configurations. The accuracy of docking depends on factors like receptor and ligand flexibility.
The document discusses a new technology for analyzing the three-dimensional conformational structure of monoclonal antibodies (mAbs). It describes how the technology was developed using an antibody array to measure epitope exposure on mAbs. Case studies show the technology can detect minor conformational differences between biosimilar and reference mAbs, and distinguish between mAbs that were clinical successes versus failures. The technology provides a unique conformational signature for each mAb.
The document discusses parallelizing the conformational search problem for small molecules. It presents the sequential nature of the problem and proposes a parallel computing solution using MPI. It describes a master-worker topology and shows results demonstrating speedup from using 4, 6, 8, and 10 processes on test cases of molecules with 5, 10, and 15 rotatable bonds. Speedup increases with more processes and rotatable bonds, with efficiencies generally between 50-80%.
Domainex has contributed to three clinical candidates through its drug discovery programs for clients. It uses a variety of technologies like combinatorial domain hunting, LeadBuilder for virtual screening, and integrated medicinal and computational chemistry. Domainex has a highly experienced team of drug discovery scientists and has successfully delivered ion-channel blockers, kinase inhibitors, and anti-thrombotics into clinical trials for clients. It provides concise drug discovery services from hit identification to candidate selection through its expertise in computational chemistry, library synthesis, and medicinal chemistry.
This document discusses structure-based drug design. It begins by explaining that structure-based drug design relies on knowledge of the three-dimensional structure of biological targets, usually determined through methods like X-ray crystallography. The structure of the target is then used to design ligands that will bind to the target. The process involves identifying drug targets, determining the target's structure, performing computer-aided drug design to identify potential binding ligands, and building or modifying ligands to optimize binding to the target.
Computer Aided Drug Design and Discovery : An Overview (2006)Girinath Pillai
The document discusses computer aided drug design and virtual screening. It describes how virtual screening can be used to discover new inhibitors for drug development by simulating the binding of compounds to protein targets. The document outlines the drug discovery process and different types of virtual screening techniques, such as ligand-based and structure-based approaches. It also discusses molecular docking methods and tools that are commonly used to simulate compound binding as part of virtual screening.
This document discusses methods for conformational analysis of molecules, which is needed to identify a molecule's lowest energy conformation. It describes systematic search methods that systematically explore all torsion angles combinations but are limited by computational time. It also describes model-building methods that construct conformations by joining molecular fragments. Available technologies for conformational analysis include software tools from Accelrys, Molecular Networks, OpenEye, Schrodinger, and Tripos.
Molecular modelling can help reduce the time and risks of drug development. It is applied to target structural characterization, developing focused libraries for hit discovery, and lead development and optimization. Fragment-based drug design is an important advance, where drug candidates are built inside the target's binding site using small molecule fragments to improve affinity from micromolar to millimolar to nanomolar levels. Molecular modelling supports medicinal chemistry decisions by providing structural insights into how drug candidates interact with their targets.
Structure based computer aided drug designThanh Truong
The document discusses structure-based computer-aided drug design. It describes the drug discovery process and challenges involved in predicting how small molecules bind to protein targets. Key steps in molecular docking include describing the receptor and ligand, sampling possible binding configurations, and scoring the interactions to estimate binding affinity. Genetic and simulated annealing algorithms are commonly used to sample configurations. The accuracy of docking depends on factors like receptor and ligand flexibility.
If you want to know more, please visit https://www.creative-proteomics.com/s...
Stable isotope labeling using amino acids in cell culture (SILAC) is a powerful method based on mass spectrometry that identifies and quantifies relative differential changes in protein abundance. First used in quantitative proteomics in 2002, it provides accurate relative quantification without any chemical derivatization or manipulation.
Classical RIPA buffer is comprised of low concentration of sodium dodecyl sulfate (SDS, a denaturing detergent), deoxycholate for disruption of protein-protein interactions and other components. To get More information, come to Invent Biotechnologies
A miniaturized sandwich immunoassay platformQing Chen
This document describes a new miniaturized sandwich immunoassay platform (MSIP) for detecting protein-protein interactions (PPIs) in a high-throughput manner. The MSIP combines antibody microarray technology with co-immunoprecipitation methods to allow simple, rapid, and large-scale PPI detection using small amounts of cell lysate. Evaluation of the MSIP showed it could accurately identify both known interacting and non-interacting protein pairs. Compared to traditional resin-based co-immunoprecipitation, the MSIP has higher sensitivity and throughput while being simpler and more cost-effective. The MSIP is presented as an effective method for validating PPIs identified by other techniques like yeast two-hybrid screening
The document discusses using proteomics to develop vaccines. It describes how proteomics can help understand protein interactions for vaccine development. The document then focuses on developing a vaccine for Lassa fever. It outlines computational methods used to analyze the Lassa virus glycoprotein, including determining its structure, domains, and interactions within cells. The goal is to use this analysis to develop a stabilized vaccine candidate against Lassa virus that can protect humans.
This document discusses downstream processing and chromatography techniques used in downstream processing. It begins by stating that downstream processing, which can account for up to 60% of production costs, is needed to separate and purify desired products after fermentation or enzyme reactions. Chromatography is commonly used for purification and separation in downstream processing. The document then describes the main types of chromatography used - gel filtration chromatography, ion exchange chromatography, and affinity chromatography - and explains the principles behind each technique. It provides examples of their industrial applications and summarizes the key objectives of learning about chromatography in downstream processing.
Microorganisms such as bacteria, actinomycetes, and fungi are ubiquitous on our planet. They are widely distributed in soil, water, the human body and other environments. Microorganisms and their activities are of great importance to biogeochemical cycles and to all biological systems. Creative Proteomics provides a one-stop proteomics service from sample collection, protein separation, to protein quantification and bioinformatics analysis. We offer both relative quantification (including iTRAQ, TMT and SILAC) and absolute quantification (such as SRM/MRM and PRM) approaches to help you discover, detect and quantify proteins in a broad array of samples. https://www.creative-proteomics.com/services/proteomics-service.htm
Microorganisms such as bacteria, actinomycetes, and fungi are ubiquitous on our planet. They are widely distributed in soil, water, the human body and other environments. Microorganisms and their activities are of great importance to biogeochemical cycles and to all biological systems. Creative Proteomics provides a one-stop proteomics service from sample collection, protein separation, to protein quantification and bioinformatics analysis. We offer both relative quantification (including iTRAQ, TMT and SILAC) and absolute quantification (such as SRM/MRM and PRM) approaches to help you discover, detect and quantify proteins in a broad array of samples. https://www.creative-proteomics.com/services/proteomics-service.htm
Structural genomics is a field that aims to determine the 3D structures of all proteins encoded by a genome. It involves determining structures on a large scale using techniques like X-ray crystallography and NMR. This allows identification of novel protein folds and potential drug targets. Comparative genomics compares genomic features between organisms and provides insights into evolution and conserved sequences and functions. It is a key tool in fields like medicine and agriculture.
This document describes the development and validation of a novel whole-cell bioluminescence method for rapid and real-time microbiological testing using Escherichia coli ATCC 8739. Five E. coli promoters were fused to a lux operon and validated against traditional culture methods. The bioluminescence method demonstrated accuracy, precision, limit of detection, linearity, range, and equivalence to standard methods. Promoter strength was highest for the outer membrane lipoprotein promoter, followed by the ribosomal protein, twin arginine translocase, lysine decarboxylase, and lysyl-tRNA synthetase promoters. The bioluminescence emission profile resembled bacterial growth kinetics,
Inhibitors for Attachment Protein BabA of Helicobacter pyloriPremier Publishers
Helicobacter pylori causes gastric pathologies to human after attachment to gastric epithelial layer via BabA protein, which is considered as one of the most important virulence factors. The study aimed to find inhibitors to this protein using structure-based drug design (SBDD) approach on the protein 3D structure (pdb ID 4zh0) . Large number of molecules / ligands were obtained as the protein gets many binding pockets. Checking and filtering the compounds depending on different parameters such as types of toxicity , ADME (absorption, distribution, metabolism, and excretion ) characters and others , only 6 molecules were obtained , these were redocked with the protein , they gave reasonable binding affinity at root-mean-square deviation (RMSD) of zero which represented by mode 1 of results performed by AutoDock vina.
This document describes a study that used bioinformatics tools to analyze the interaction between a 14-amino acid peptide derived from buffalo prolactin (buPRL) and the bradykinin B1 receptor. Molecular docking was performed between structures of the receptor and the peptide, as well as somatostatin and a scrambled version of the peptide. The docking results indicated that the buPRL peptide binds to the receptor's active site, similarly to somatostatin. The binding energies of the buPRL peptide-receptor complex and somatostatin-receptor complex were comparable, suggesting the buPRL peptide may act as an antagonist of the kallikrein-kinin system by binding to
58.Comparative modelling of cellulase from Aspergillus terreusAnnadurai B
The document discusses homology modeling of the cellulase enzyme in Aspergillus terreus. It begins with an abstract that describes cellulase as a widely used hydrolytic enzyme involved in converting biomass to simpler sugars. It then provides details on homology modeling and the steps involved, which include template recognition, alignment, backbone and loop modeling, and model validation. The document discusses modeling of the cellulase protein from Aspergillus terreus using templates from the PDB and visualization software. It evaluates the modeled cellulase structure using validation servers to check accuracy.
Crimson Publishers-Stable Labeled Isotopes as Internal Standards: A Critical ...CrimsonPublishersMAPP
SIL internal standards are commonly used in LC-MS/MS analyses to improve accuracy and precision. There are two main types: structurally similar analogs or isotopically labeled compounds containing stable isotopes like deuterium, carbon-13, or nitrogen-15. SIL standards provide structural information to understand analyte fragmentation patterns and metabolism. Their use has been shown to reduce ionization variations compared to analog standards. However, SIL standards can still cause ion suppression or enhancement and may not fully correct for matrix effects. While very useful, SIL standards also have limitations like expense and potential for different retention times versus analytes. Overall they remain a preferred choice but alternative standards may still be needed in some cases.
This document discusses materials and methods used in a study involving the chemical fipronil and zinc. Twenty male albino rats were divided into four groups of five rats each: a control group, a zinc group that received zinc supplementation, a fipronil group exposed to the insecticide fipronil, and a combination group exposed to both zinc and fipronil. Biochemical assays were conducted to assess oxidative stress markers like superoxide dismutase, catalase, glutathione peroxidase, glutathione-S-transferase, glutathione, lipid peroxidation, and total protein in the rats. Chemicals used including fipronil and zinc sulfate were obtained from reputable suppliers. Kits for the biochemical assays were purchased from a diagnostic
The document discusses the SILAC technique, which uses stable isotope labeling of amino acids in cell culture for quantitative proteomics. It works by metabolically incorporating stable isotope labelled amino acids into the entire proteome of cells, allowing detection of differences in protein abundance between samples. The technique provides accurate relative quantification without chemical manipulation. It can be used to characterize protein differences between samples, investigate post-translational modifications, and distinguish protein-protein interactions. While powerful and reproducible, it requires long cell cultures so is only appropriate for cell samples.
Identifying candidate antimalarial compounds by searching for molecular mimet...Reis Fitzsimmons
The objective is to use a KNIME workflow to determine promising antimalarial drug target candidates from a list of 284 compounds by comparing them to endogenous malaria parasite metabolites. The author collected metabolite data from databases and analyzed chemical similarity between the compounds and metabolites using the ECFP4 fingerprint and Tanimoto coefficient in KNIME. Initial results analyzing over 4,998 general metabolites and 250,642 malaria metabolites found no compounds with high chemical similarity. Statistical analysis revealed the malaria metabolite molecular weights were similarly distributed to the antimalarial compounds, despite low chemical similarity. Further analysis of millions more parasite-specific metabolites may be needed to find optimal drug targets interacting with malaria metabolic pathways.
Here are the key points about sequence and structure of proteins:
- Protein sequences can be compared to determine similarity and relate unknown sequences to known protein families/categories. Sequence databases are searched for matches.
- Sequence alignment involves sliding two sequences past each other to find the position with the most matched residues. However, it misses some alignments.
- Gaps can be introduced in alignments to account for insertions/deletions between similar sequences from different genes. This increases matching possibilities.
- Beyond simple amino acid identity comparisons, there are two types of substitutions that better reflect evolutionary changes:
1) Conservative substitutions substitute amino acids within the same chemical property groups.
2) Semi-conservative substitutions substitute amino
Genome-scale in silico atpE gene knockout in Escherichia coli could drive nov...Khadem2016
One of the applications of E. coli genome-scale model is in the biological discovery of underground metabolic functions of partially characterized genes and/or enzymes. Here we report for the first time, a failed prediction of atpE gene knockout of no growth in the most recent E. coli reconstruction iJ01366 model, and a positive experimental growth on glucose, enabling a model-driven biological discovery of the underground metabolic function of this gene in E. coli metabolism. These findings unfolded what could be described as either scope gaps in the reconstruction or true biological gaps (knowledge gaps) on the missing atpE gene function in E. coli metabolism. This study informs other studies that the gaps could be pursued into the E. coli metabolism, leading to a model-driven discovery in the future.
One of the applications of E. coli genome-scale model is in the biological discovery of underground metabolic functions of partially characterized genes and/or enzymes. Here we report for the first time, a failed prediction of atpE gene knockout of no growth in the most recent E. coli reconstruction iJ01366 model, and a positive experimental growth on glucose, enabling a model-driven biological discovery of the underground metabolic function of this gene in E. coli metabolism. These findings unfolded what could be described as either scope gaps in the reconstruction or true biological gaps (knowledge gaps) on the missing atpE gene function in E. coli metabolism. This study informs other studies that the gaps could be pursued into the E. coli metabolism, leading to a model-driven discovery in the future. This can be achieved by using gap filling algorithms (such as GrowMatch, SMILEY
If you want to know more, please visit https://www.creative-proteomics.com/s...
Stable isotope labeling using amino acids in cell culture (SILAC) is a powerful method based on mass spectrometry that identifies and quantifies relative differential changes in protein abundance. First used in quantitative proteomics in 2002, it provides accurate relative quantification without any chemical derivatization or manipulation.
Classical RIPA buffer is comprised of low concentration of sodium dodecyl sulfate (SDS, a denaturing detergent), deoxycholate for disruption of protein-protein interactions and other components. To get More information, come to Invent Biotechnologies
A miniaturized sandwich immunoassay platformQing Chen
This document describes a new miniaturized sandwich immunoassay platform (MSIP) for detecting protein-protein interactions (PPIs) in a high-throughput manner. The MSIP combines antibody microarray technology with co-immunoprecipitation methods to allow simple, rapid, and large-scale PPI detection using small amounts of cell lysate. Evaluation of the MSIP showed it could accurately identify both known interacting and non-interacting protein pairs. Compared to traditional resin-based co-immunoprecipitation, the MSIP has higher sensitivity and throughput while being simpler and more cost-effective. The MSIP is presented as an effective method for validating PPIs identified by other techniques like yeast two-hybrid screening
The document discusses using proteomics to develop vaccines. It describes how proteomics can help understand protein interactions for vaccine development. The document then focuses on developing a vaccine for Lassa fever. It outlines computational methods used to analyze the Lassa virus glycoprotein, including determining its structure, domains, and interactions within cells. The goal is to use this analysis to develop a stabilized vaccine candidate against Lassa virus that can protect humans.
This document discusses downstream processing and chromatography techniques used in downstream processing. It begins by stating that downstream processing, which can account for up to 60% of production costs, is needed to separate and purify desired products after fermentation or enzyme reactions. Chromatography is commonly used for purification and separation in downstream processing. The document then describes the main types of chromatography used - gel filtration chromatography, ion exchange chromatography, and affinity chromatography - and explains the principles behind each technique. It provides examples of their industrial applications and summarizes the key objectives of learning about chromatography in downstream processing.
Microorganisms such as bacteria, actinomycetes, and fungi are ubiquitous on our planet. They are widely distributed in soil, water, the human body and other environments. Microorganisms and their activities are of great importance to biogeochemical cycles and to all biological systems. Creative Proteomics provides a one-stop proteomics service from sample collection, protein separation, to protein quantification and bioinformatics analysis. We offer both relative quantification (including iTRAQ, TMT and SILAC) and absolute quantification (such as SRM/MRM and PRM) approaches to help you discover, detect and quantify proteins in a broad array of samples. https://www.creative-proteomics.com/services/proteomics-service.htm
Microorganisms such as bacteria, actinomycetes, and fungi are ubiquitous on our planet. They are widely distributed in soil, water, the human body and other environments. Microorganisms and their activities are of great importance to biogeochemical cycles and to all biological systems. Creative Proteomics provides a one-stop proteomics service from sample collection, protein separation, to protein quantification and bioinformatics analysis. We offer both relative quantification (including iTRAQ, TMT and SILAC) and absolute quantification (such as SRM/MRM and PRM) approaches to help you discover, detect and quantify proteins in a broad array of samples. https://www.creative-proteomics.com/services/proteomics-service.htm
Structural genomics is a field that aims to determine the 3D structures of all proteins encoded by a genome. It involves determining structures on a large scale using techniques like X-ray crystallography and NMR. This allows identification of novel protein folds and potential drug targets. Comparative genomics compares genomic features between organisms and provides insights into evolution and conserved sequences and functions. It is a key tool in fields like medicine and agriculture.
This document describes the development and validation of a novel whole-cell bioluminescence method for rapid and real-time microbiological testing using Escherichia coli ATCC 8739. Five E. coli promoters were fused to a lux operon and validated against traditional culture methods. The bioluminescence method demonstrated accuracy, precision, limit of detection, linearity, range, and equivalence to standard methods. Promoter strength was highest for the outer membrane lipoprotein promoter, followed by the ribosomal protein, twin arginine translocase, lysine decarboxylase, and lysyl-tRNA synthetase promoters. The bioluminescence emission profile resembled bacterial growth kinetics,
Inhibitors for Attachment Protein BabA of Helicobacter pyloriPremier Publishers
Helicobacter pylori causes gastric pathologies to human after attachment to gastric epithelial layer via BabA protein, which is considered as one of the most important virulence factors. The study aimed to find inhibitors to this protein using structure-based drug design (SBDD) approach on the protein 3D structure (pdb ID 4zh0) . Large number of molecules / ligands were obtained as the protein gets many binding pockets. Checking and filtering the compounds depending on different parameters such as types of toxicity , ADME (absorption, distribution, metabolism, and excretion ) characters and others , only 6 molecules were obtained , these were redocked with the protein , they gave reasonable binding affinity at root-mean-square deviation (RMSD) of zero which represented by mode 1 of results performed by AutoDock vina.
This document describes a study that used bioinformatics tools to analyze the interaction between a 14-amino acid peptide derived from buffalo prolactin (buPRL) and the bradykinin B1 receptor. Molecular docking was performed between structures of the receptor and the peptide, as well as somatostatin and a scrambled version of the peptide. The docking results indicated that the buPRL peptide binds to the receptor's active site, similarly to somatostatin. The binding energies of the buPRL peptide-receptor complex and somatostatin-receptor complex were comparable, suggesting the buPRL peptide may act as an antagonist of the kallikrein-kinin system by binding to
58.Comparative modelling of cellulase from Aspergillus terreusAnnadurai B
The document discusses homology modeling of the cellulase enzyme in Aspergillus terreus. It begins with an abstract that describes cellulase as a widely used hydrolytic enzyme involved in converting biomass to simpler sugars. It then provides details on homology modeling and the steps involved, which include template recognition, alignment, backbone and loop modeling, and model validation. The document discusses modeling of the cellulase protein from Aspergillus terreus using templates from the PDB and visualization software. It evaluates the modeled cellulase structure using validation servers to check accuracy.
Crimson Publishers-Stable Labeled Isotopes as Internal Standards: A Critical ...CrimsonPublishersMAPP
SIL internal standards are commonly used in LC-MS/MS analyses to improve accuracy and precision. There are two main types: structurally similar analogs or isotopically labeled compounds containing stable isotopes like deuterium, carbon-13, or nitrogen-15. SIL standards provide structural information to understand analyte fragmentation patterns and metabolism. Their use has been shown to reduce ionization variations compared to analog standards. However, SIL standards can still cause ion suppression or enhancement and may not fully correct for matrix effects. While very useful, SIL standards also have limitations like expense and potential for different retention times versus analytes. Overall they remain a preferred choice but alternative standards may still be needed in some cases.
This document discusses materials and methods used in a study involving the chemical fipronil and zinc. Twenty male albino rats were divided into four groups of five rats each: a control group, a zinc group that received zinc supplementation, a fipronil group exposed to the insecticide fipronil, and a combination group exposed to both zinc and fipronil. Biochemical assays were conducted to assess oxidative stress markers like superoxide dismutase, catalase, glutathione peroxidase, glutathione-S-transferase, glutathione, lipid peroxidation, and total protein in the rats. Chemicals used including fipronil and zinc sulfate were obtained from reputable suppliers. Kits for the biochemical assays were purchased from a diagnostic
The document discusses the SILAC technique, which uses stable isotope labeling of amino acids in cell culture for quantitative proteomics. It works by metabolically incorporating stable isotope labelled amino acids into the entire proteome of cells, allowing detection of differences in protein abundance between samples. The technique provides accurate relative quantification without chemical manipulation. It can be used to characterize protein differences between samples, investigate post-translational modifications, and distinguish protein-protein interactions. While powerful and reproducible, it requires long cell cultures so is only appropriate for cell samples.
Identifying candidate antimalarial compounds by searching for molecular mimet...Reis Fitzsimmons
The objective is to use a KNIME workflow to determine promising antimalarial drug target candidates from a list of 284 compounds by comparing them to endogenous malaria parasite metabolites. The author collected metabolite data from databases and analyzed chemical similarity between the compounds and metabolites using the ECFP4 fingerprint and Tanimoto coefficient in KNIME. Initial results analyzing over 4,998 general metabolites and 250,642 malaria metabolites found no compounds with high chemical similarity. Statistical analysis revealed the malaria metabolite molecular weights were similarly distributed to the antimalarial compounds, despite low chemical similarity. Further analysis of millions more parasite-specific metabolites may be needed to find optimal drug targets interacting with malaria metabolic pathways.
Here are the key points about sequence and structure of proteins:
- Protein sequences can be compared to determine similarity and relate unknown sequences to known protein families/categories. Sequence databases are searched for matches.
- Sequence alignment involves sliding two sequences past each other to find the position with the most matched residues. However, it misses some alignments.
- Gaps can be introduced in alignments to account for insertions/deletions between similar sequences from different genes. This increases matching possibilities.
- Beyond simple amino acid identity comparisons, there are two types of substitutions that better reflect evolutionary changes:
1) Conservative substitutions substitute amino acids within the same chemical property groups.
2) Semi-conservative substitutions substitute amino
Genome-scale in silico atpE gene knockout in Escherichia coli could drive nov...Khadem2016
One of the applications of E. coli genome-scale model is in the biological discovery of underground metabolic functions of partially characterized genes and/or enzymes. Here we report for the first time, a failed prediction of atpE gene knockout of no growth in the most recent E. coli reconstruction iJ01366 model, and a positive experimental growth on glucose, enabling a model-driven biological discovery of the underground metabolic function of this gene in E. coli metabolism. These findings unfolded what could be described as either scope gaps in the reconstruction or true biological gaps (knowledge gaps) on the missing atpE gene function in E. coli metabolism. This study informs other studies that the gaps could be pursued into the E. coli metabolism, leading to a model-driven discovery in the future.
One of the applications of E. coli genome-scale model is in the biological discovery of underground metabolic functions of partially characterized genes and/or enzymes. Here we report for the first time, a failed prediction of atpE gene knockout of no growth in the most recent E. coli reconstruction iJ01366 model, and a positive experimental growth on glucose, enabling a model-driven biological discovery of the underground metabolic function of this gene in E. coli metabolism. These findings unfolded what could be described as either scope gaps in the reconstruction or true biological gaps (knowledge gaps) on the missing atpE gene function in E. coli metabolism. This study informs other studies that the gaps could be pursued into the E. coli metabolism, leading to a model-driven discovery in the future. This can be achieved by using gap filling algorithms (such as GrowMatch, SMILEY
Genome-scale in silico atpE gene knockout in Escherichia coli could drive nov...
Comparability at Molecular level
1.
2. YOUR PATH TO SUCCESS
Antibody Arrays for Biosimilar Conformational
Comparability Analysis
3. 3-D Conformational comparability Analysis
Process-related Impurity Analysis
Array Bridge provides ELISA based analysis for Host Cell a homologous counterpart in the human body, these
Proteins from CHO (Chinese Hamster Ovary ) and E. coli antibodies could interfere with the physiological function
host. The development and production of the ELISA kits of the protein through cross-reactivity. Thirdly, HCPs
are under cGMP to ensure uninterrupted product supply themselves could act as agonist or antagonist to interfere
and consistent quality. Host Cell Proteins are proteins and with the human normal metabolism. Because of these
their derivatives from the hosts used for biologics reasons, in biologics development, significant resource is
development and production. Higher levels of HCP will allocated during process development to reduce HCP
pose risks in several areas. levels in the biologics product.
First, HCPs from CHO and E. coli could be recognized by
the human immune system as no self molecules, eliciting
an immune reaction. Depending on the level and composi-
tion of the HCPs, the reaction could range from none and
mild reaction to severe reactions. Secondly, some HCPs
could induce the production of antibodies. If the HCP has
4. Protein Conformational Arrays, a new
approach for biologics three–dimensional
structure comparability analysis
Protein Conformational Array ELISA provides a The FDA guidance
systematic, sensitive and robust comparability testing further stated that
for biologics (therapeutic proteins) at molecular level. “The three dimensional
An array of polyclonal antibodies was designed systemati- conformation of a
cally covering the whole biologics sequence and the assay protein is an important
is in an easy-to-use ELISA format, these Protein Confor- factor in its biological
mational Array ELISAs (PCA ELISA) can provide valuable function. Protein
information on the 3-D structure and heterogeneity of generally exhibit
biologics, and can be used at many stages and aspects complex three-dimen-
of biologics development including cell line selection, sional conformations
process development, formulation development and (tertiary structure
product release testing. and, in some cases,
quaternary structure) due to their large size and the
It is known that the clinical and biological properties of a rotational characteristics of protein alpha carbons.
biologics are the results of their basic properties such as The resulting flexibility enables dynamic, but subtle,
amino acid sequence and three-dimensional structure, as changes in protein conformation over time, some of which
well as the production, purification, formulation and storage may be absolutely required for functional activity.”
conditions. One of the major challenges in biologics develop- “... at the same time, a protein’s three-dimensional
ment is protein immunogenicity, unwanted immunogenicity conformation can often be difficult to define precisely
could lead to reduced or loss of drug efficacy, altered using current physiochemical analytical technology.”
pharmacokinetics (PK), general immune and hypersensitivity
reaction, and neutralization of the natural counterpart in Because of the close relation between protein conforma-
the human body. Multiple studies have demonstrated that tion and its immunogenicity, several analytical techniques
protein conformation stability is closely related to its and bioassays have been used to probe conformational
immunogenicity. One recent study indicated that a protein comparability in biologics. For example, protein intrinsic
has a threshold of conformational stability to prevent the fluorescence, analytical ultracentrifugation, gel filtration,
immunogenicity of foreign proteins. Another strong indica- light scattering and bioassays have all been employed for
tion that protein conformation is closely related to its protein conformational analysis. However these approach-
immunogenicity is through the study of protein aggregation. es have their respective limitations, generally they lack
Multiple studies showed that protein aggregation is a major the desired sensitivity, coverage and throughput to
source of immunogenicity. provide the information about protein 3-D structure.
In the case of monoclonal antibody biologics, Bioassays
In the recently published document for biosimilar developed based on target-antibody recognition will
development by the Food and Drug Administration detect some changes in the CDR (complementarity
(Guidance for Industry, Quality Considerations in determining region) regions, but can’t measure changes
Demonstrating Biosimilarity to a Reference Protein in the rest of the biologics molecule.
Product, FDA, February 2012), FDA recommends
“Extensive, robust comparative physicochemical and The Protein Conformational Array developed specifically
functional studies should be performed to evaluate toward monoclonal antibody drugs could provide a
whether the proposed biosimilar product and the sensitive, systematic and efficient way to measure protein
reference product are highly similar. A meaningful conformational comparability. The protein conformational
assessment as to whether the proposed biosimilar array antibodies are developed from the specific sequence
product is highly similar to the reference product of each monoclonal antibody drug; about 30 different
depends on, among other things, the capabilities of antibodies were developed to provide a systematic
available state-of-the-art analytical assays to coverage of the molecule. Studies using marketed
assess, for example, the molecular weight of the monoclonal antibody drugs indicated that these confor-
protein, complexity of the protein (higher order mational arrays can provide detailed information about
structure and post-translational modification), degree the molecule and detect changes that may not be detected
of heterogeneity, functional properties, impurity by the aforementioned techniques including bioassays.
profile, and the degradation profiles denoting stability.”
5. Application — 1
Comparison between marketed monoclonal
antibody drug and biosimilar candidate.
Comparison of Three Lots of Innovator Molecule and a Biosimilar Candidate
2.5
2
OD 450 nm
1.5
1
0.5
0
Ab1
Ab2
Ab3
Ab4
Ab5
Ab6
Ab7
Ab8
Ab9
Ab10
Ab11
Ab12
Ab13
Ab14
Ab15
Ab16
Ab17
Ab18
Ab19
Ab20
Ab21
Ab22
Ab23
Ab24
Ab25
Ab26
Ab27
Ab28
Ab29
Ab30
Reference Lot 1 Reference Lot 2 Reference Lot 3 Biosimilar
Application 2
Formulation development
Application of Conformational Array to Formulation Development
2.5
2
OD 450 nm
1.5
1
0.5
0
Ab1
Ab2
Ab3
Ab4
Ab5
Ab6
Ab7
Ab8
Ab9
Ab10
Ab11
Ab12
Ab13
Ab14
Ab15
Ab16
Ab17
Ab18
Ab19
Ab20
Ab21
Ab22
Ab23
Ab24
Ab25
Ab26
Ab27
Ab28
Ab29
Ab30
Control Pi Buffer, O ion Pi Buffer+400mM NaCL Histidine Buffer
6. About Array Bridge
Array Bridge provides products and services that and documentation. Further, we can help you with ELISA
address two important areas in the development of method qualification or validation. The company also
biologics: biosimilar drug comparability analysis and provides consultation for the development of an effective
impurity analysis. impurity analysis strategy, enabling your program(s) to
meet requirements from regulatory agencies such as FDA
During biosimilar development, biologics comparability and EMA.
is critical to the successful development of the process
and product. From cell line selection to process develop- Array Bridge provides value to our customers through
ment, from formulation development to change control, high quality products and services, and we help you
comparability is closely related to the molecule’s safety develop biologics including biosimilars successfully.
and efficacy. Array Bridge has developed ‘antibody arrays’
to measure biosimilar drug comparability at the molecular
level, providing a sensitive, systematic and robust mea-
surement of biosimilar conformational comparability.
This antibody array-based technology can be used at all
stages of biosimilar development, from cell line selection and
process development to clinical testing and product release.
For impurity analysis, Array Bridge provides ELISA kits and
reagents for Host Cell Protein quantitation and Western
Blot analysis. All the products are manufactured under
cGMP to ensure quality and consistency. In the near future,
Array Bridge will also provide Q-PCR-based residual DNA
quantitation kits for CHO and E. coli-derived biologics and
an ELISA kit for residual Protein A quantitation.
In addition to these products, Array Bridge also provides
services to the biotech industry. If you need to analyze your
samples for impurities (Host Cell Proteins, residual DNA or
Protein A) or for biosimilar conformational comparability,
Array Bridge has scientists with experience working under
cGMP and ICH guidelines to deliver regulatory-ready results
7. Services
Array Bridge provides services in several areas
1. Biosimilar conformational comparability analysis.
2. HO and E. coli Host Cell Protein quantitation, method development, qualification
C
or validation.
3.Western Blot analysis of HCPs in CHO or E. coli-derived biologics using 1-D and 2-D
gel electrophoresis and 1-D and 2-D Western Blot.
4. evelopment of customer-based biosimilar conformational comparability analysis
D
ELISA and HCP ELISA.
5. roviding consultation on the Host Cell Protein strategy for a specific project
P
or platform.
Contact Information
www.arraybridge.com
Phone: 636-284-4212.
Email: support@arraybridge.com
4320 Forest Park Avenue. Ste. 303
St. Louis, MO 63108
ARB-1125