Principles of drug discovery


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Principles of drug discovery

  1. 1. SUBMITTED TO<br /> JAWAHARLAL NEHRU TECHNOLOGICAL UNIVERSITY HYDERABAD,<br />In the partial fulfillment of M.Pharm.I year, I semester.<br />CMR GROUP OF INSTITOTIONS ·<br />(Approved by AICTE and affiliated to JNTU Hyderabad.)<br /> Kandlakoya(V), Medchal(M), Hyderabad-501401<br />Under the guidance of, Prepared By,<br />Dr T.Vedhavathi, V.kavya lakshmi, Mpharm; PhD, Mpharm IST yr pharmacology, <br />CMR collage of pharmacy. Reg. No. 10T21S0105. <br /> <br /> C.M.R COLLEGE OF PHARMACY<br /> (Approved by AICTE & PCI)<br /> (Affiliated to JNTU)<br /> . Kandlakoya, Medchal<br /> <br /> CERTIFICATE<br />This is to verify that this is a bonafied record of the seminar entitled “Principles of drug discovery” presented by V.kavya lakshmi (10T21S0105), during the academic year 2010-2011 for partial fulfillment in degree of Masters of Pharmacy of Jawaharlal Nehru Technological University, Hyderabad.<br />PRINCIPAL: INTERNAL GUIDE:<br />Rajeswar dutt Dr T.Vedavathi<br /> <br /> DECLARATION<br /> I here by declare that the seminar work entitled “Principles of drug discovery”submitted to the {JNTUH} is a record work of seminar, under the guidance of Dr.Vedhavathi professor of C.M.R college of pharmacy.<br /> V.kavya lakshmi,<br /> Regno:10T21S0105 <br /> <br />IntroductionTime course involved in drug discoveryHistorical back groundApproachesRational approaches in drug discoveryPreclinical studiesClinical studiesNovel approaches<br /> INDEX<br /> <br /> Principles of drug discovery<br /> Drug discovery is the process by which drugs are discovered and/or designed.<br />In the past most drugs have been discovered either by identifying the active ingredient from traditional remedies or by serendipitous discovery. A new approach has been to understand how diseases and infections are controlled at the molecular and physiological level and to target specific entities based on this knowledge.<br />The process of drug discovery involves the identification of substances, synthesis, characterization, screening and assays for therapeutic efficacy. Once a compound has shown its value in these tests, it will begin the process of drug development prior to clinical trails<br />Despite advances in technology and understanding of biological systems, drug discovery is still a lengthy, "expensive, difficult, and inefficient process" with low rate of new therapeutic discovery. Currently, the research and development cost of each new molecular entity (NME) is approximately US$1.8 billion.<br />Information on the human genome, its sequence and what it encodes has been hailed as a potential windfall for drug discovery, promising to virtually eliminate the bottleneck in therapeutic targets that has been one limiting factor on the rate of therapeutic discovery. However, data indicates that "new targets" as opposed to "established targets" are more prone to drug discovery project failure in general. This data collaborates some thinking underlying a pharmaceutical industry trend beginning at the turn of the twenty-first century and continuing today which finds more risk aversion in target selection among multi-national pharmaceutical companies.<br />Time course involved in drug discovery<br /><ul><li>The time course in a drug discovery involves at least ten years and more than ten years.
  2. 2. The processes of new drug discovery and development are long, complicated and dependent upon the expertise of a wide variety of scientific, technical and managerial groups.
  3. 3. Here are the different stages of drug discovery and development.
  4. 4. There are four stages in the drug discovery. They are
  5. 5. Synthesis or isolation of the compound which involves different techniques like extraction methods, chromatographic techniques for isolation and different methods of synthesis. This section in drug discovery takes 1-2 yrs
  6. 6. Preclinical studies: These are done before testing on humans </li></ul>So these are called as animal studies. They includes different topics of study like <br />Screening <br />Evaluation <br />Pharmacokinetics <br />Toxicity testing <br />All these process takes place 2-4yrs. <br />Then apply for grant of permission for clinical trail from concerned associations.<br />This takes 0.5-1yr. <br />After the approval Pharmaceutical formulation, standardization of chemicals/biological/immunological assays of new drug applications are estimated. <br /><ul><li>Clinical studies
  7. 7. Phase IV or post market surveillance is the time involving step, which cannot be predicted.
  8. 8. As the drug may be success with out any adverse effects or it is rejected or send back for further optimization.
  9. 9. Success rate in getting from an initial compound to an approved and commercially available product is very low.
  10. 10. < 2% of new compounds investigated may show suitable biological activity
  11. 11. Modification of an existing drug can yield as little as 1% suitable compounds
  12. 12. < 10% of these compounds result in successful human clinical trials and reaches the market place
  13. 13. Schematic representation of drug discovery process </li></ul>Generally the "target" is the naturally existing cellular or molecular structure involved in the pathology of interest that the drug-in-development is meant to act on. However, the distinction between a "new" and "established" target can be made without a full understanding of just what a "target" is. This distinction is typically made by pharmaceutical companies engaged in discovery and development of therapeutics.<br />"Established targets" are those for which there is a good scientific understanding, supported by a lengthy publication history, of both how the target functions in normal physiology and how it is involved in human pathology. This does not imply that the mechanism of action of drugs that are thought to act through particular established targets is fully understood. Rather, "established" relates directly to the amount of background information available on a target, in particular functional information. The more such information is available, the less investment is (generally) required to develop a therapeutic directed against the target. The process of gathering such functional information is called "target validation’ in pharmaceutical industry parlance. Established targets also include those that the pharmaceutical industry had experience mounting drug discovery campaigns against in the past; such a history provides information on the chemical feasibility for developing a small molecular therapeutics, against the target and can provide licensing opportunities and freedom-to-operate indicators with respect to small-molecule therapeutic candidates.<br />In general, "new targets" are all those targets that are not "established targets" but which have been the subjects of drug discovery campaigns. These typically include newly discovered proteins, or proteins whose function has now become clear as a result of basic scientific research.<br />The majority of targets currently selected for drug discovery efforts are proteins. Two classes predominate: G-protein-coupled receptors (or GPCRs) and protein kinases.<br />HISTORICAL BACKGROUND<br />The idea that effect of drug in human body are mediated by specific interactions of the drug molecule with biological macromolecules, (proteins or nucleic acids in most cases) led scientists to the conclusion that individual chemicals are required for the biological activity of the drug. This made for the beginning of the modern era in pharmacology, as pure chemicals, instead of crude extracts, became the standard drugs. Examples of drug compounds isolated from crude preparations are morphine as the active agent in opium, and digoxin (a heart stimulant) originating from Digitalis lanata. Organic chemistry also led to the synthesis of many of the co- chemicals isolated from biological sources.<br />SCREENING & DESIGNING<br />The process of finding a new drug against a chosen target for a particular disease usually involves high-throughput screening (HTS), wherein large libraries of chemicals are tested for their ability to modify the target. For example, if the target is a novel GPCR (G protein coupled receptors) compounds will be screened for their ability to inhibit or stimulate that receptor. If the target is a protein kinase, the chemicals will be tested for their ability to inhibit that kinase.<br />Another important function of HTS is to show how selective the compounds are for the chosen target. The ideal is to find a molecule which will interfere with only the chosen target, but not other, related targets. To this end, other screening runs will be made to see whether the "hits" against the chosen target will interfere with other related targets - this is the process of cross-screening. Cross-screening is important, because the more unrelated targets are compound hits. This leads to off-target toxicity with that compound once it reaches the market.<br />There are two types of screening <br />Random screening <br />Non random screening<br />Random Screening<br />In the absence of known drugs and other compounds with desired activity, a random screening is a valuable approach. Random screening involves no intellectualization; all compounds are tested in the bioassay without regard to their structures. Prior to 1935 (the discovery of sulfa drugs) this was essentially the only approach; today this method is still an important approach to discover drugs or leads, particularly because it is now possible to screen such huge numbers of compounds rapidly with HTSs. This is the lead discovery method of choice when nothing is known about the receptor target. <br />The two major classes of materials screened are synthetic chemicals and natural (Microbial, plant and marine) products. An example of a random screen of synthetic and natural compounds was the “war on cancer” declared by Congress and the National Cancer Institute in the early 1970s. Any new compound submitted was screened in a mouse tumor bioassay. Few new anticancer drugs resulted from that screen, but many known anticancer drugs also did not show activity in the screen used, so a new set of screens was devised that gave more consistent results. In the 1940s and 1950s, a random screen of soil samples by various pharmaceutical companies in search of new antibiotics was undertaken. However, in this case, not only were numerous leads uncovered, but two important antibiotics, streptomycin and the tetracyclines were found. Screening of microbial broths, particular strains of Streptomyces was a common random screen methodology prior to 1980.<br /> Nonrandom (or Targeted or Focused) Screening<br />Nonrandom screening also called targeted or focused screening and is a more narrow approach than the random screening. In this case, compounds having a vague resemblance to weakly active compounds uncovered in a random screen, or compounds containing different functional groups than leads, may be tested selectively. By the late 1970s, the National Cancer Institute’s random screen was modified to a nonrandom screen because of budgetary and manpower restrictions. Also, the single tumor screen was changed to a variety of tumor screens because it was realized that cancer is not just a single disease.<br />It is very unlikely that a perfect drug candidate will emerge from these early screening runs. It is more often observed that several compounds are found to have some degree of activity, and if these compounds share common chemical features, one or more pharmacophores can then be developed<br />While HTS is a commonly used method for novel drug discovery, it is not the only method. It is often possible to start from a molecule which already has some of the desired properties. Such a molecule might be extracted from a natural product or even be a drug on the market which could be improved upon (so-called "me too" drugs). Other methods, such as virtual high throughput screening, where screening is done using computer-generated models and attempting to "dock" virtual libraries to a target are also often used.<br />Another important method for drug discovery is drug design, whereby the biological and physical properties of the target are studied and a prediction is made of the sorts of chemicals that might fit into an active site. One example is fragment-based lead discoveries (FBLD). Novel pharmacophores can emerge very rapidly from these exercises.<br />Once a lead compound series has been established with sufficient target potency and selectivity and favorable drug-like properties, one or two compounds will then be proposed for drug development. The best of these is generally called the lead compound, while the other will be designated as the "backup".<br />Approaches <br />Nature of source for drug discovery<br />Despite the rise of combinatorial chemistry as an integral part of lead discovery process, natural products still play a major role as starting material for drug discovery.  A report was published in 2007,[7] covering years 1981-2006 details the contribution of biologically occurring chemicals in drug development. According to this report, of the 974 small molecule new chemical entities, 63% were natural derived or semi synthetic derivatives of natural products. For certain therapy areas, such as antimicrobials, anti neoplastics, antihypertensive and anti-inflammatory drugs and the numbers were higher. Natural products may be useful as a source of novel chemical structures for modern techniques of development of antibacterial therapies. Despite the implied potential, only a fraction of Earth’s living species has been tested for bioactivity.<br />Plant-derived<br />Prior to Paracelsus, the vast majority of traditionally used crude drugs in Western medicine were plant-derived extracts. This has resulted in a pool of information about the potential of plant species as an important source of starting material for drug discovery. A different set of metabolites is sometimes produced in the different anatomical parts of the plant (e.g. root, leaves and flower), and botanical knowledge is crucial also for the correct identification of bioactive plant materials.<br />Microbial metabolites<br />Microbes compete for living space and nutrients. To survive in these conditions, many microbes have developed abilities to prevent competing species from proliferating. Microbes are the main source of antimicrobial drugs. Streptomyces species have been a source of antibiotics. The classical example of an antibiotic discovered as a defense mechanism against another microbe is the discovery of penicillin in bacterial cultures contaminated by Penicillium fungi in 1928.<br />Marine invertebrates<br />Marine invertebrates are the potential sources for new agents.[9]. Arabinose nucleosides discovered from marine invertebrates in 1950s, demonstrating for the first time that sugar moieties other than ribose and deoxyribose can yield bioactive nucleoside structures. However, it was 2004 when the first marine-derived drug was approved. The cone snail toxinziconotide, also known as Prialt, was approved by the Food and Drug Administration to treat severe neuropathic pain. Several other marine-derived agents are now in clinical trials for indications such as cancer, anti-inflammatory use and pain. One class of these agents is bryostatin-like compounds, under investigation as anti-cancer therapy.<br />Chemical diversity of drug sources<br />As above mentioned, combinatorial chemistry was a key technology enabling the efficient generation of large screening libraries for the needs of high-throughput screening. However, now, after two decades of combinatorial chemistry, it has been pointed out that despite the increased efficiency in chemical synthesis, no increase in lead or drug candidates have been reached. This has led to analysis of chemical characteristics of combinatorial chemistry products, compared to existing drugs and/or natural products. The synthetic, combinatorial library compounds seem to cover only a limited and quite uniform chemical space, whereas existing drugs and particularly natural products, exhibit much greater chemical diversity, distributing more evenly to the chemical space.The most prominent differences between natural products and compounds in combinatorial chemistry libraries is the number of chiral centers (much higher in natural compounds), structure rigidity (higher in natural compounds) and number of aromatic moieties (higher in combinatorial chemistry libraries). Other chemical differences between these two groups include the nature of heteroatoms (O and N enriched in natural products, and S and halogen atoms more often present in synthetic compounds), as well as level of non-aromatic unsaturation (higher in natural products). As both structure rigidity and chirality are both well-established factors in medicinal chemistry known to enhance compounds specificity and efficacy as a drug, it has been suggested that natural products compare favorable to today's combinatorial chemistry libraries as potential lead molecules.<br />Rational approach<br />Drug discovery hit to lead<br />Early drug discovery involves several phases from target identification to preclinical development. The identification of small molecule modulators of protein function and the process of transforming these into high-content lead series are key activities in modern drug discovery. The Hit-to-Lead phase is usually the follow-up of high-throughput screening (HTS). It includes the following steps:<br />Hit confirmation<br />The Hit confirmation phase will be performed during several weeks as follows:<br />Re-testing: compounds that were found active against the selected target are re-tested using the same assay conditions used during the HTS.<br />Dose response curve generation: several compound concentrations are tested using the same assay, an IC50 or EC50 value is then generated. Methods are being developed that may allow the reuse of the compound that generated the hit in the initial HTS step. These molecules are removed from beads and transferred to a microarray for quantitative assessment of binding affinities in a "seamless" approach that could allow for the investigation of more hits and larger libraries<br />Orthogonal testing: Confirmed hits are assayed using a different assay which is usually closer to the target physiological condition or using a different technology.<br />Secondary screening: Confirmed hits are tested in a functional assay or in a cellular environment. Membrane permeability is usually a critical parameter.<br />Chemical amenability: Medicinal chemists will evaluate compounds according to their synthesis feasibility and other parameters such as up-scaling or costs<br />Intellectual property evaluation: Hit compound structures are quickly checked in specialized databases to define patentability<br />Biophysical testing: Nuclear magnetic resonance (NMR), Isothermal Titration Calorimetry, dynamic light scattering, surface Plasmon resonance  dual polarization interferometry, micro scale thermophoresis(MST) are commonly used to assess whether the compound binds effectively to the target, the stoichiometry of binding, any associated conformational change  and to identify promiscuous inhibitors.<br />Hit ranking and clustering: Confirmed hit compounds are then ranked according to the various hit confirmation experiments.<br />Hit expansion<br />Following hit confirmation, several compound clusters will be chosen according to their characteristics in the previously defined tests. An Ideal compound cluster will:<br />have compound members that exhibit a high affinity towards the target (less than 1 µM)<br />Moderate molecular weight and lipophilicity (usually measured as cLogP). Affinity, molecular weight and lipophilicity can be linked in single parameter such as ligand efficiency  and lipophilic efficiency to assess drug likeness<br />Show chemical tractability<br />Be free of Intellectual property<br />Interfere neither with the P450  enzymes nor with the P-glycoprotein’s<br />Not bind to human serum albumin<br />Be soluble in water (above 100 µM)<br />Be stable<br />Have a good drug likeness<br />Exhibit cell membrane permeability<br />Show significant biological activity in a cellular assay<br />Not exhibit cytotoxicity<br />Not be metabolized rapidly<br />Show selectivity versus other related targets<br />The project team will usually select between three and six compound series to be further explored. The next step will allow testing analogous compounds to define Quantitative structural activity relationship (QSAR). Analogs can be quickly selected from an internal library or purchased from commercially available sources. Medicinal chemists will also start synthesizing related compounds using different methods such as combinatorial chemistry, high-throughput chemistry or more classical organic chemistry synthesis.<br />Lead optimizations<br />The objective of this drug discovery phase is to synthesize lead compounds, new analogs with improved potency, reduced off-target activities, and physiochemical/metabolic properties suggestive of reasonable in vivo pharmacokinetics. This optimization is accomplished through chemical modification of the hit structure, with modifications chosen by employing structure-activity analysis (SAR) as well as structure-based design if structural information about the target is available.<br /> <br />Drug designing based on receptor and ligand structure<br />Structural elucidation<br />The elucidation of the chemical structure is critical to avoid the re-discovery of a chemical agent that is already known for its structure and chemical activity. Mass spectrometry, often used to determine structure is a method in which individual compounds are identified based on their mass/charge ratio, after ionization. Chemical compounds exist in nature as mixtures, so the combination of liquid chromatography and mass spectrometry (LC-MS) is often used to separate the individual chemicals. Databases of mass spectra’s for known compounds are available. Nuclear magnetic resonance spectroscopy is another important technique for determining chemical structures of natural products. NMR yields information about individual hydrogen and carbon atoms in the structure, allowing detailed reconstruction of the molecule’s architecture.<br />Molecular modeling<br />Structural Modifications to Increase Potency and the Therapeutic Index <br />1. Homologation <br />2. Chain Branching <br />3. Ring-Chain Transformations <br />4. Bioisosterism<br />5. Combinatorial Chemistry<br />a Combnitorial synthesis<br />b Split Synthesis: Peptide Libraries<br />c. Encoding Combinatorial Libraries <br />d. Nonpeptide Libraries <br />6. SAR by NMR/SAR by MS<br />7. Peptidomimetic<br />8. CADD<br />Homologation<br /><ul><li>A homologous series is a group of compounds that differ by a constant unit, generally a CH2 group.
  14. 14. For many series of compounds, lengthening of a saturated carbon side chain from one (methyl) to five to nine atoms (pentyl to nonyl) produces an increase in pharmacological effects. Lengthening results in a sudden decrease in potency
  15. 15. This phenomenon corresponds to increased lipophilicity of the molecule to permit penetration into cell membranes until its lowered water solubility becomes problematic in its transport through aqueous media.
  16. 16. In the case of aliphatic amines, another problem is micelle formation, which begins at about C12.</li></ul> Chain branching<br /><ul><li> This effectively removes the compound from potential interaction with the appropriate receptors.
  17. 17. Then chain branching flowers the potency of a compound because a branched alkyl chain is less lipophilic than the corresponding straight alkyl chain as a result of larger molar volumes and shapes of branched compounds.
  18. 18. This phenomenon is exemplified by the lower potency of the compounds having isoalkyl chains
  19. 19. For example, phenethylamine (PhCH2CH2NH2) is an excellent substrate for monoamine oxidase.</li></ul> Ring-Chain Transformations<br /><ul><li>Another modification that can be made is the transformation of alkyl substituent’s into cyclic analogs, which often does not affect potency greatly.
  20. 20. However, a ring-chain transformation could have an important pharmacokinetic effect, such as to increase lipophilicity or decrease metabolism, which could make the drug more effective in vivo. Also by connecting substituents into a ring, pharmacodynamic properties could be enhanced by constraining the groups into a particularly favorable conformation. Of course, it also could constrain the molecule into an unfavorable conformation, and potency could drop different activities can result from a ring-chain transformation as well. For example, if the dimethylamino group of the tranquilizer chlorpromazine is substituted by a methyl piperazine ring (X = Cl, R = CH2CH2CH2N NCH3; prochlorperazine), antiemetic (prevents nausea)</li></ul>Bioisosterism<br /><ul><li>Bioisosteres are substituents or groups that have chemical or physical similarities, and which produce broadly similar biological properties.
  21. 21. Bioisosterism is an important lead modification approach that has been shown to be useful to attenuate toxicity or to modify the activity of a lead, and may have a significant role in the alteration of pharmacokinetics of a lead.
  22. 22. There are classical isosteres and nonclassical isosteress
  23. 23. Nonclassical bioisosteres do not have the same number of atoms and do not fit the steric and electronic rules of the classical isosteres, but do produce similar biological activity change: size, shape, electronic distribution, lipid solubility, water solubility, pKa, chemical reactivites and hydrogen bonding. Because a drug must get to the site of action, then interact with it bioisosteric modifications made to a molecule may have one or more of the effects.</li></ul>Combinatorial Chemistry<br /> General Aspects<br /><ul><li>Combinatorial chemistry involves the synthesis or biosynthesis of chemical libraries (a family of compounds having a certain base chemical structure) of molecules with in a short period of time for the purpose of biological screening, particularly for lead discovery or lead modification.
  24. 24. Typically, these chemical libraries are prepared in a systematic and repetitive way by covalent assembly of building blocks (various reactant molecules that build up parts of the overall structure)
  25. 25. To give a diverse array of molecules with a common scaffold (the parent structure in the family of compounds).
  26. 26. Combinatorial synthesis
  27. 27. Split synthesis
  28. 28. Encoding combinatorial library
  29. 29. Nonpeptidal synthesis</li></ul>Combinatorial synthesis<br /><ul><li>The advantage of this methodology is that it is carried out on a solid (polymeric) support, so that isolation and purification of the product of each reaction can be performed by simple filtration and washing with a variety of solvents of the polymeric support to which the building blocks have been attached.
  30. 30. Because of the insolubility of the polymer, everything not attached to the polymer is removed, which allows the use of excess reagents to drive the synthetic reactions.
  31. 31. The disadvantages of this methodology are the difficulty in scaling up the reactions and the sluggishness of reactions.
  32. 32. An alternative strategy (covalent scavenger technology) is to carry out the reactions in solution with excess reagent, which is then scavenged with a polymeric-supported scavenger after the reaction is completed
  33. 33. In this approach, filtration removes the excess reagent attached to the scavenger polymer, leaving the product in solution.
  34. 34. Another approach is to use polymer-supported reagents with solution reactions.
  35. 35. To avoid problems of heterogeneous polymer reactions, soluble polyethylene glycol polymers can be used </li></ul>Split synthesis (Peptide Libraries)<br /><ul><li>The initial approach, known as a split synthesis (also called mix and split, split and pool, or the divide, couple, recombine method), is the most common general lead discovery approach for making large libraries (104–106 compounds) that are assayed as library mixtures.
  36. 36. The result of a split synthesis is a collection of polymer beads, each containing one library member, i.e., one bead, one compound.
  37. 37. The library contains every possible combination of every building block.
  38. 38. The serious limitations are that it is applicable only to the synthesis of sequenceable
  39. 39. oligomers and each bead carries only about 100–500 pmol of product, which makes structure determination difficult or impossible.
  40. 40. For simple compounds mass spectrometric methods may be used but this is not applicable if the library contains many thousands or millions of members that may not be pure or are isomeric with other library members. In that case, encoding methods need to be utilized.
  41. 41. For example: how the split synthesis approach would be applied to a small (27-member) library of all possible tripeptides of three amino acids.
  42. 42. This method can be extrapolated to any size library.
  43. 43. A homogeneous mixture of all of the tripeptides of His, Val, and Ser could be synthesized on a Merrifield resin
  44. 44. Note that a Merrifield synthesis starts at the ‘C’ terminus and builds to the ‘N’ terminus.
  45. 45. The homogenization step is very important to ensure that each tube contains the same mixture of resin-bound compounds.
  46. 46. The process shown in Scheme was carried out, but starting with 20 separate tubes containing methyl benzhydryl amine (MBHA) polystyrene as the resin. (This resin produces peptide amides when peptides are cleaved from it.)
  47. 47. A combinatorial library of penta=peptides containing the 20 standard amino acids was constructed on the MBHA resin, homogenized, then separated into 20 tubes.
  48. 48. To each of the 20 different tubes was added a different N-acetylamino acid, so that in each tube there was a combinatorial library of all possible resin-linked N-acetyl hexa peptides having the same N terminus.
  49. 49. Each tube contained all of the N-acetyl hexa peptides starting with a different N-terminal amino acid.
  50. 50. An aliquot from each of the 20 tubes is removed and assayed.
  51. 51. The most potent aliquot indicates which amino acid is best.
  52. 52. Then this process is repeated, except in the next interaction a combinatorial library of MBHA-bound tetrapeptides is made, is split into 20 tubes, a different amino acid is coupled in each tube at the next-to-N-terminal position, then each tube is N-terminal capped with N-acetyl Arg, because that was shown in the previous assay</li></ul> Encoding Combinatorial Libraries<br /><ul><li>A more rapid approach would be to test the entire library at once and identify the active component of the library directly.
  53. 53. As mentioned above, with large libraries of complex molecules it is not readily possible to determine the structure of the active component.
  54. 54. In that case, encoding methods are needed. This is similar to the way in which proteins are often sequenced in biology.
  55. 55. the protein is not sequenced, but the gene that encodes the protein is Although the structure of the actual compound may not be directly elucidated, certain tag molecules that encode the structure may be determined.
  56. 56. One important approach that involves the attachment of unique arrays of readily analyzable, chemically inert, small molecule tags to each bead in a split synthesis
  57. 57. Ideal encoding tags must survive organic synthesis conditions, not interfere with screening assays, be readily decoded without ambiguity, encode large numbers of compounds the test compound and the encoding tag must be able to be packed into a very small volume.
  58. 58. In the Still method, groups of tags are attached to a bead at each combinatorial step in a split synthesis.
  59. 59. The tags create a record of the building blocks used in that step. At the end of the synthesis the tags are removed and analyzed, which decodes the structure of the compound attached to that bead.
  60. 60. one or more readily cleavable tag molecules (TagsX) are attached to about 1% of the
  61. 61. Polymer bead sites (about 1 pmol/bead), and these encode building block 1 (BB1).</li></ul>Non peptidal synthesis<br /><ul><li>Peptides do not make very useful drugs, especially if an orally active drug is sought. The same techniques described above for the synthesis of peptide libraries could be utilized to prepare nonpeptide libraries;
  62. 62. However, there is an important difference between the chemistry with peptides versus nonpeptides, namely, reactivity.
  63. 63. In a typical peptide coupling reaction the carbodimide-activated N-protected amino acids</li></ul>are all about the same in reactivity with the different amino acids in the growing peptide<br />chain. Because of that, the split synthesis method works well.<br /><ul><li>However, with nonamino acid reagents, such as different acid chlorides, the structure of the acid chloride will affect the rates of reaction with different nucleophiles.</li></ul>That could lead to mixtures in which some of the components have reacted and others have not.<br /><ul><li>For each reaction the conditions have to be worked out to be sure complete reaction has occurred.
  64. 64. Over the years it has been recognized that when large numbers of nonpeptide analogs are screened simultaneously, many false negatives (an active compound that does not produce a hit, i.e., a compound that shows a predetermined level of activity in the assay) and false Positives (an inactive compound that gives a hit) are observed.
  65. 65. A false positive may arise from an impurity in the sample tested or as a result of a complex between more than one compound.
  66. 66. False positives are a waste of time, but false negatives mean that potential drugs (or at least lead compounds) are being overlooked.
  67. 67. It is typical for pharmaceutical companies to carry out single entity screens to avoid these problems. Because of this, individual compounds, rather than mixtures, are synthesized.
  68. 68. Nonetheless, synthesis on a solid support allows the synthesis of large numbers of individual compounds rapidly and robotically.
  69. 69. The reactions are carried out individually in separate micro tubes containing the polymeric support.
  70. 70. Because the library of compounds (in the range of 50–104 compounds in amounts of 1–50 mg) is synthesized in parallel without combining any of the tubes.S
  71. 71. One strategy that can be used for potentially more effective libraries is to select privileged structures as the scaffold.
  72. 72. Another strategy is to design a scaffold based on an important molecular recognition motif in the target receptor.
  73. 73. The libraries should incorporate different sets of (commercially available) building blocks to provide a large number of diverse structures, and they should contain as much functionality as possible as recognition elements.
  74. 74. Molecular diversity, however, is difficult to determine;
  75. 75. Dixon and Villar have found that a protein can bind a set of structurally diverse molecules with similar potent binding affinities, but analogs closely related to these compounds can exhibit very weak binding.
  76. 76. Parallel synthesis can generate many more compounds than can be synthesized traditionally, and the cost per compound is much lower.</li></ul>The main differences among the various combinatorial approaches are the solid support used, the methods for assembling the building blocks, the state (immobilized or in solution) and numbers (a fraction of the total library or individual entities) <br />there different types of combinatorial synthesis.<br />SAR by NMR/SAR by MS<br />Fesik and coworkers at Abbott Laboratories developed a NMR-based approach to screen libraries of small organic molecules and to identify and optimize high-affinity ligands (compounds that bind to receptors) for proteins. <br /><ul><li>This approach, termed SAR by NMR, was initially used to discover compounds with nanomolar affinities (highly potent for the immunosuppressant FK506 binding protein by tethering two molecules with micromolar affinities (low potency).
  77. 77. The first step of the process involves screening a library of small compounds, 10 at a time, by observation of the amide 15N-chemical shift in the heteronuclear single quantum coherence (HSQC) NMR spectrum.
  78. 78. Once a lead is identified, a library of analogs is screened to identify compounds with optimal binding at that site.
  79. 79. Then a second library of compounds is screened to find a compound that binds at a nearby site, and again this compound is optimized by screening a library of related compounds.
  80. 80. Based on the NMR spectrum of the ternary complex of the protein and the two bound ligands, the location and orientation of these ligands are determined, and compounds are synthesized in which the two ligands are covalently attached
  81. 81. Although each individual ligand may be a relatively weak binder, when the two are attached, the binding affinity increases dramatically.
  82. 82. This is because the free energy of binding becomes the sum of three free energies: the two ligands and the linker; the binding affinity is the multiplier of the three binding affinities.
  83. 83. There is a gain of about a factor of 100 in binding affinity by freezing out one bond rotation. Therefore, it is not necessary to optimize the lead much, because ligands with micromolar or even mill molar affinities can attain nanomolar affinities
  84. 84. When linked. An example of this is the identification of the first potent inhibitor of the enzyme stromelysin, a matrix metalloprotease (a family of zinc-containing hydrolytic enzymes responsible for degradation of extracellular matrix components such as collagen and proteoglycans
  85. 85. In normal tissue remodeling and in many disease states such as arthritis, osteoporosis, and cancer) as a potential antitumor agent
  86. 86. The method relies on the development of structure-activity relationships by mass spectrometry (SAR by MS) and utilizes information derived from the binding of known inhibitors to identify novel inhibitors of a target protein with a minimum of synthetic effort. Non covalent complexes of known inhibitors with a target protein are analyzed; these inhibitors are deconstructed into sets of fragments which compete for common or overlapping binding sites on the target protein. The binding of each fragment set can be studied independently. With the use of competition studies, novel members of each fragment set are identified from compound libraries that bind to the same site on the target protein. A novel inhibitor of the target protein was then constructed by chemically linking a combination of members of each fragment set in a manner guided by the proximity and orientation of the fragments derived from the known inhibitors. In the case of stromelysin, a novel inhibitor composed of favorably linked fragments was observed to form a 1:1 complex with stromelysin. Compounds that were not linked appropriately formed higher order complexes with stoichiometries of 2:1 or greater. These linked molecules were subsequently assessed for their ability to block stromelysin function in a chromogenic substrate assay.</li></ul>Peptidomimetics<br /><ul><li>Plants and animals, including human skin, contain a variety of antibiotic peptides. </li></ul> Endogenous peptides also function as analgesics antihypertensive agents, and antitumor<br /> agents <br /><ul><li>However, peptides do not make good drug candidates because they are rapidly</li></ul> Proteolyzed in the GI tract and serum, and they are poorly bioavailable, rapidly excreted,<br /> and can bind to multiple receptors. <br /><ul><li>What is needed is a compound that mimics or blocks the biological effect of a peptide by interacting with its receptor or enzyme, but does not have the undesirable characteristics of peptides; these are peptidomimetics.
  87. 87. A remarkable resemblance was demonstrated between the N-terminal tyrosine structure of these opioid peptides and the morphine phenol ring system, which suggested why they all interacted with these receptors in a similar way.
  88. 88. The design of peptidomimetics can be a lead optimization approach, which uses the desired peptide as the lead compound and modifies it to minimize (or preferably, eliminate) the undesirable pharmokinetic properties.
  89. 89. The generation of peptidomimetics is based on the conformational, topochemical, and electronic properties of the lead peptide when bound toits target receptor or enzyme.The 7 goal is to replace as much of the peptide backbone as possible with nonpeptide fragments while still maintaining the pharmacophoric groups (usually the amino acid side chains) of the peptide. This makes the compound more lipophilic, which increases its bioavailability.
  90. 90. Replacement of the amide bond with alternative groups prevents proteolysis and promotes metabolic stability.
  91. 91. Initially, conformational flexibility has to be retained to allow the pharmacophoric groups a better opportunity to find their binding sites, but further lead refinement should favor the formation of more conformationally restricted analogs that hold appropriate pharmacophoric groups in the bioactive conformation for binding to the target receptor.
  92. 92. Increased lipophilicity and conformational modification of amino acids can be designed into the peptidomimetic. These groups may not be recognized by peptidases. For example conformational restricted analogs of phenylalanine can be incorporated into peptidomimetic receptor ligands.
  93. 93. Likewise, conformational restriction and lipophilicity can be incorporated into peptides
  94. 94. Another approach involves the design of conformationally restricted analogs that mimic characteristics of the receptor-bound conformation of the endogenous peptide, such as turns,α-helices-loops and β-strands This idea can be extended to scaffold peptidomimetics in which importantPharmacophoric residues are held in the appropriate orientation by a rigid template.
  95. 95. Compounds that block the binding of fibrinogen to its receptor (glycoprotein IIb/IIIa) can prevent platelet aggregation and are of potential value in the treatment of strokes and heart attacks. Common and important approach for the conversion of a peptide lead into a peptidomimetic is the use of peptide backbone isosteres .
  96. 96. Peptides in which the amide bonds are replaced with alternative groups are known as pseudo peptides.
  97. 97. These isosteric replacements remove the peptide linkage (thereby stabilizing the peptidomimetics to metabolism) and/or make them less polar and more lipophilic. </li></ul>The hydroxymethylene (also called statine) isostere is one of the early mimetics used in the design of inhibitors of proteases, particularly of HIV protease.Other variants of azapeptides <br />Computer-aided design (CAD), also known as computer-aided design and drafting (CADD) , is the use of computer technology for the process of design and design-documentation. Computer Aided Drafting describes the process of drafting with a computer. CADD software, or environments, provides the user with input-tools for the purpose of streamlining design processes; drafting, documentation, and manufacturing processes. CADD output is often in the form of electronic files for print or machining operations. The development of CADD-based software is in direct correlation with the processes it seeks to economize; industry-based software (construction, manufacturing, etc.) typically uses vector-based (linear) environments whereas graphic-based software utilizes raster-based (pixelated) environments.<br />CADD environments often involve more than just shapes. As in the manual drafting of technical and engineering drawings, the output of CAD must convey information, such as materials, processes, dimensions, and tolerances, according to application-specific conventions.CAD may be used to design curves and figures in two-dimensional (2D) space; or curves, surfaces, and solids in three-dimensional (3D) objects.<br />Pre-clinical development is a stage of research that begins before clinical trials (testing in humans) can begin, and during which important feasibility, iterative testing and safety (also known as Good Laboratory Practice or "GLP") data is collected.<br />The main goals of pre-clinical studies (also named preclinical studies and nonclinical studies) are to determine a product's ultimate safety profile. Products may include new or iterated or like-kind medical devices, drugs, gene therapy solutions, etc. Each class of product may undergo different types of preclinical research. For instance, drugs may undergo pharmacodynamics (PD), pharmacokinetics (PK), ADME, and toxicity testing through animal testing. This data allows researchers to allometrically estimate a safe starting dose of the drug for clinical trials in humans. Medical devices that do not have drug attached will not undergo these additional tests and may go directly to GLP testing for safety of the device and its components. Some medical devices will also undergo biocompatibility testing which helps to show whether a component of the device or all components are sustainable in a living model. Most pre-clinical studies must adhere to Good Laboratory Practices (GLP) in ICH Guidelines to be acceptable for submission to regulatory agencies such as the Food & Drug Administration in the United States.<br />Typically, both in vitro and in vivo tests will be performed. Studies of a drug's toxicity include which organs are targeted by that drug, as well as if there are any long-term carcinogenic effects or toxic effects on mammalian reproduction.<br />The information collected from these studies is vital so that safe human testing can begin. Typically, in drug development studies animal testing involves two species. The most commonly used models are murine and canine, although primate and porcine are also used. The choice of species is based on which will give the best correlation to human trials. Differences in the gut, enzyme activity, circulatory system, or other considerations make certain models more appropriate based on the dosage form, site of activity, or noxious metabolites. For example, canines may not be good models for solid oral dosage forms because the characteristic carnivore intestine is underdeveloped compared to the omnivores, and gastric emptying rates are increased. Also, rodents can not act as models for antibiotic drugs because the resulting alteration to their intestinal flora causes significant adverse effects. Depending on a drugs functional groups, it may be metabolized in similar or different ways between species, which will affect both efficacy and toxicology. Medical device studies also use this basic premise. Most studies are performed in larger species such as dogs, pigs and sheep which allow for testing in a similar sized model as that of a human. In addition, some species are used for similarity in specific organs or organ system physiology (swine for dermatological and coronary stent studies; goats for mammary implant studies; dogs for gastric studies)<br />Based on pre-clinical trials, No Observable Effect Levels (NOEL) on drugs are established, which are used to determine initial phase 1 clinical trial dosage levels on a mass API per mass patient basis. Generally a 1/100 uncertainty factor or "safety margin" is included to account for interspecies (1/10) and inter-individual (1/10) differences.<br />Animal testing in the research-based pharmaceutical industry has been reduced in recent years both for ethical and cost reasons. However, most research will still involve animal based testing for the need of similarity in anatomy and physiology that is required for diverse product development.<br />Preclinical Toxicology Testing and IND Application<br />Preclinical testing analyzes the bioactivity, safety, and efficacy of the formulated drug product. This testing is critical to a drug’s eventual success and, as such, is scrutinized by many regulatory entities. During the preclinical stage of the development process, plans for clinical trials and an Investigative New Drug (IND) application are prepared. Studies taking place during the preclinical stage should be designed to support the clinical studies that will follow.<br />Acute Studies: Acute toxic studies look at the effects of one or more doses administered over a period of up to 24 hours. The goal is to determine toxic dose levels and observe clinical indications of toxicity. Usually, at least two mammalian species are tested. Data from acute toxic studies helps determine doses for repeated dose studies in animals and Phase I studies in humans<br />Repeated Dose Studies: Depending on the duration of the studies, repeated dose studies may be referred to as subacute, subchronic, or chronic. The specific duration should anticipate the length of the clinical trial that will be conducted on the new drug. Again, two species are typically required. <br /> PRECLINICAL STUDIES & CLINICAL STUDIES <br />Genetic Toxicity Studies: These studies assess the likelihood that the drug compound is mutagenic or carcinogenic. Procedures such as the Ames test (conducted in bacteria) detect genetic changes. DNA damage is assessed in tests using mammalian cells such as the Mouse Micronucleus Test. The Chromosomal Aberration Test and similar procedures detect damage at the chromosomal level. <br />Reproductive Toxicity Studies: Segment I reproductive toxic studies look at the effects of the drug on fertility. Segment II and III studies detect effects on embryonic and post-natal development. In general, reproductive toxic studies must be completed before a drug can be administered to women of child-bearing age. <br />Carcinogenicity Studies: Carcinogenicity studies are usually needed only for drugs intended for chronic or recurring conditions. They are time consuming and expensive, and must be planned for early in the preclinical testing process. <br />Toxicokinetic Studies:These are typically similar in design to PK/ADME studies except that they use much higher dose levels. They examine the effects of toxic doses of the drug and help estimate the clinical margin of safety. <br /><ul><li>Grant of permission for clinical trails</li></ul>There are numerous FDA and ICH guidelines that give a wealth of detail on the different types of preclinical toxicology studies and the appropriate timing for them relative to IND and NDA or BLAIn India pharmaceuticals are governed by the Drugs & Cosmetics Act and the Rules framed to implement the provisions in the Act. New chemical entities may not be administered to human subjects in a clinical trial without permission from the <br />Drugs Controller General of India (DCGI). Such permission may be obtained by submitting to the DCGI an application for a clinical trial (CTA). It takes approximately 12 weeks to obtain permission for a clinical trial for most investigational drugs. The duration may be longer for drugs with special significance to the healthcare concerns of the country or those that may be considered controversial since these are liable to be referred to the Indian Council of Medical Research for comments. Ethic Committee approval is not a necessary precondition for regulatory permission to conduct a clinical trial provided the applicant submits an undertaking that the study will not be initiated at individual sites without prior EC approval. If clinical supplies are to be imported, a "Test-Import License" must be applied for. This is done using the format provided in Form 12 of the Drugs & Cosmetics Rules. Import and manufacture of clinical trial supplies is governed by Rules 33 & 34 and provisions contained in Part X-A of the rules<br />Adverse drug reactions occurring during the course of a clinical trial need to be submitted to the DCGI within 14 days if these are unexpected or serious and causally related or result in death. All other serious adverse events need to be submitted along with periodic progress reports. Compliance with GCP guidelines issued by the CDSCO is recommended although this does not have statutory status at the present time. A report on the status of the study with details of enrollment and safety issues needs to be submitted annually and on completion of the study. <br />CLINICAL TRAILS<br />The Clinical studies are grouped according to their objective into three types or phases:<br />Phase I Clinical Development (Human Pharmacology) - Thirty days after a biopharmaceutical company has filed its IND, it may begin a small-scale Phase I clinical trial unless the FDA places a hold on the study. Phase I studies are used to evaluate pharmacokinetic parameters and tolerance, generally in healthy volunteers.  These studies include initial single-dose studies, dose escalation and short-term repeated-dose studies. <br />Phase II Clinical Development (Therapeutic Exploratory) – Phase II clinical studies are small-scale trials to evaluate a drug’s preliminary efficacy and side-effect profile in 100 to 250patients.Additional safety and clinical pharmacology studies are also included. <br />Phase III Clinical Development (Therapeutic Confirmatory) - Phase III studies are large-scale clinical trials for safety and efficacy in large patient populations. While phase III studies are in progress, preparations are made for submitting the Biologics License Application (BLA) or the New Drug Application (NDA).  BLAs are currently reviewed by the FDA’s Center for Biologics Evaluation and Research (CBER).  NDAs are reviewed by the Center for Drug Evaluation and Research (CDER). <br />Randomized double blind comparative trails are done <br />Indications are finalized & guidelines for therapeutic use are formulated <br />Submission of NDA for licensing is done who if satisfied grants permission for marketing <br />Phase 4 (post market surveillance) – On approval of new drug, the importer Should conduct the necessary surveillance and report back to aid the study of ADR’s of the specific drug. the drug approved may be even rejected in this phase in the case of its toxicity beyond the therapeutic effect .so the time period involved cannot be even predicted .<br />Registration of new drugs for marketing in India requires submission of data generated on Indian patients. A 100-patient non-comparative open-label study on patients treated for the primary indication is sufficient. In addition to local data, the NDA must include various other items of information listed in Schedule Y of the Drugs & Cosmetics Rules. <br />Data from prospective post-marketing surveillance is usually required to be submitted to the CDSCO within 2 years of approval of a product. PMS data is considered a prerequisite for renewal of the import license on expiration of validity 3 years from the date of issue. <br />Clinical trials and research conducted on human beings can now be accessed by the general public too. Hitherto, research institutions and companies obtained permission from the regulatory authorities and registration of the trials was voluntary. Now, the Drugs Controller General of India (DCGI) has asked the Indian Council of Medical Research to ensure that while granting permission for clinical trials, the applicants are advised to get the trial registered before initiation of the study. The new rule mandates that trials should be registered before the enrolment of the first patient. Not just fresh human trials but even ongoing trials must be registered.<br />Advanced approaches<br />Bioinformatics :is application of computer technology to the management of biological information it deals with algorithms databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory ,software engineering, data mining, image processing, modeling and simulation, signal processing ,discrete mathematics ,control and system theory ,circuit theory and statistics For generating new knowledge of biology in medicine improving and discovering new model of computation<br />Major research areas<br />Genome annotation, analysis of gene expression, analysis of mutations in cancer, modeling biological systems, structural bioinformatics like prediction of protein structure, molecular interaction, docking algorithms<br />Chemi-informatics:The chemoinformatics concept chemical diversity, depicted as distribution of compounds in the chemical space based on their physicochemical characteristics, is often used to describe the difference between the combinatorial chemistry libraries and natural products<br />micro array techniques: an array is an orderly arrangement of samples were matching of known and unknown DNA samples is done based on base pairing rules .an experiment makes use of common assay systems such as micro plates are standard blotting membranes. the samples spot sizes(probe) are typically less than 200microns in diameter usually contains thousands of spots<br />A typical micro array ex involves hybridization of mRNA molecule to the DNA template from which it is originated .Many DNA samples are used to construct an array. The amount of mRNA bound to each site on the array indicates the expression level of various genes.<br />Conclusion: One should follow the above laid guide lines in order to produce a safe and efficient drug <br />The drug discovery process should follow the ethics with out any compromise in any stages of the process<br />REFERENCES<br />“Textbook of Drug Design and Discovery”. Madsen, Ulf; Krogsgaard-Larsen, Povl; Liljefors, Tommy (2002).  Washington, DC: Taylor & Francis.povl 235-423<br />“Guidebook on Molecular Modeling in Drug Design.” .Boston:Academic Press.  . Pharmacophore Perception, Development, and use in Drug Design. La Jolla, Calif: International University Line. Cohen, N. Claude (1996) Guner, Osman F. (2000) cohen vol II 541-671<br />“Structure-based Drug Discovery” Leach, Andrew R.; Harren Jhoti (2007). . Berlin: Springer. Wang R,Gao Y,Lai L (2000).LigBuilder: A Multi-Purpose Program for Structure-Based Drug Design". Journal of Molecular Modeling 6 (7-8): 498–516.<br />"The many roles of computation in drug discovery". Science 303 (5665) Jorgensen WL (March 2004). s1813–8. <br />“Essentials of medical pharmacology’KD Tripati 6th addition ,process of drug development, p-12-27.<br />“How Drugs Work”, Oxford University Press, Oxford, 2000Hare, R. The Birth of Penicillin, Allen & Unwin, London,1970.Beveridge, W. I. B. , p. 255<br /> "Natural products as sources of new drugs over the last 25 years".Newman DJ, Cragg GM (March 2007 J. Nat. Prod. 70 (3): 461–77. <br />"Structure-based drug design: progress, results and challenges" Verlinde CL, Hol WG..Böhm HJ. "The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure". J(June 1994). Comput. Aided Mol (July 1994).. Structure 2 (7): 577–87<br />“Book of drug discovery “. Fleming, A. Brit. J. Exp. Stone, T.; Darlington, G. Pills, Potions and Poisons. Pathol. 1929, P gen(3)10, 226<br /> “Seeds of Discovery”, W. W. Norton, Abraham, E. P.; Chain, E.; Fletcher, C. M.; sGardner, A. D.; Heatley, N. G.;Jennings, M. A.; Florey, H. W. New York, 1981.Lancet 1941, 2, 177.<br /><br />"Comparison of consensus scoring strategies for evaluating computational models of protein-ligand complexes". J Chem Inf Model 46 (1): Oda A, Tsuchida K, Takakura T, Yamaotsu N, Hirono S (2006). 380–91.<br />“ Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional protein-ligand binding interactions’Deng Z, Chuaqui C, Singh J (January 2004). "". J. Med. Chem. 47(2): 337–44. <br />