1. Rationale : Endogenous lead compounds often simple and flexible (e.g. adrenaline)Endogenous lead compounds often simple and flexible (e.g. adrenaline) Fit several targets due to different active conformations (e.g. adrenergic receptor types and subtypes)Fit several targets due to different active conformations (e.g. adrenergic receptor types and subtypes) 10. Rigidification Rigidify molecule to limit conformations - conformational restraintRigidify molecule to limit conformations - conformational restraint Increases activity (more chance of desired active conformation)Increases activity (more chance of desired active conformation) Increases selectivity (less chance of undesired active conformations )Increases selectivity (less chance of undesired active conformations )Disadvantage: Molecule more complex and may be more difficultMolecule more complex and may be more difficult to synthesise

2. Methods - Introduce rings Bonds within ring systems are locked and cannot rotate freely 10. Rigidification Test rigid structures to see which ones have retained active conformation

3. Examples - Combretastatin (anticancer agent) 10. Rigidification More active Less activeRotatablebond

4. Methods - Steric Blockers 10. Rigidification Flexible side chain Coplanarity allowed Orthogonal rings preferred Introduce steric block Introduce steric block

5. Rationale (isosteres) : Replace a functional group with a group of same valency (isostere)e.g. OH replaced by SH, NH 2, CH 3 O replaced by S, NH, CH 2Replace a functional group with a group of same valency (isostere)e.g. OH replaced by SH, NH 2, CH 3 O replaced by S, NH, CH 2 Leads to more controlled changes in steric/electronic propertiesLeads to more controlled changes in steric/electronic properties May affect binding and / or stabilityMay affect binding and / or stability 11. Isosteres and Bio-isosteres

6. a-Classical Isosteres, they are divided into five classes as illustrated in the following table: Class 1 (monovalent) 2 (divalent) 3 (trivalent) 4 (tetravalent) 5 (rings) F,Cl,Br,I OH,SH NH 2, PH 2 CH 3 -O- -S- -Se- -Te- -N= -P= -As= -Sb= -CH= =C= =Si= =N + = =P= =As= =Sb + = -CH=CH -S- -O- -NH-

7. Grimm's Hydride Displacement Law CNOFNeNa CHNHOHFH- CH 2 NH 2 OH 2 FH 2 + CH 3 NH 3 OH 3 + CH 4 NH 4 + It is an early hypothesis to describe bioisosterism, the ability of certain chemical groups to function as or mimic other chemical groups. According to Grimm, each vertical column (of Table below) would represent a group of isosteres. Table 1: Grimm's Hydride Displacement Law

8. 1) Classical Isosteres: - Replacement of univalent atoms and groups Replacement of CH 3 group of the oral hypoglycemic tolbutamide, by its monovalent isostere Cl in chloropropamide increases the duration of action. Examples

9. Interchange of divalent atoms or groups The replacement of -O- of procaine by -NH- in procainamide leads to prolong antiarrhythmic action due to the considerable stability of the amide function over the ester function.

10. Introduction of trivalent atoms or groups Aminopyrine and its isostere are about equally active as antipyretics.

11. Ring equivalents

12. Nonclassical Isosteres b- Nonclassical Isosteres, they are also known and include paired examples such as H and F, - CO 2 H and –SO 3 H, and –CO- and –SO 2 -. Some of the examples of isosteric replacement that have provided useful drugs are include:

13. Isosterism and Bioisosterism is a lead modification approach that has been shown to be useful to : Attenuate Toxicity Modify the activity of a lead May have a significant role in the alteration of metabolism of the lead

14. Useful for SAR Replacing OCH 2 with CH=CH, SCH 2, CH 2 CH 2Replacing OCH 2 with CH=CH, SCH 2, CH 2 CH 2 eliminates activity Replacing OCH 2 with NHCH 2 retains activityReplacing OCH 2 with NHCH 2 retains activity Implies O involved in binding (HBA)Implies O involved in binding (HBA) 11. Isosteres and Bio-isosteres Propranolol (  -blocker)

15. Structure based drug design (SBDD) Structure based drug design (SBDD) Procedure Crystallise target protein with bound ligand (e.g. enzyme + inhibitor or ligand)Crystallise target protein with bound ligand (e.g. enzyme + inhibitor or ligand) Acquire structure by X-ray crystallographyAcquire structure by X-ray crystallography Identify binding site (region where ligand is bound)Identify binding site (region where ligand is bound) Identify binding interactions between ligand and target (modelling)Identify binding interactions between ligand and target (modelling) Identify vacant regions for extra binding interactions (modelling)Identify vacant regions for extra binding interactions (modelling) ‘Fit’ analogues into binding site to test binding capability (modelling)‘Fit’ analogues into binding site to test binding capability (modelling) Strategy Carry out drug design based on the interactions between the lead compound and the target binding site

16. Design of Antihypertensives - ACE inhibitors ACE = Angiotensin converting enzymeACE = Angiotensin converting enzyme Angiotensin II - hormone which stimulates constriction of blood vessels - causes rise in blood pressureAngiotensin II - hormone which stimulates constriction of blood vessels - causes rise in blood pressure ACE inhibitors - useful antihypertensive agentsACE inhibitors - useful antihypertensive agents ACE - membrane bound zinc metalloproteinase not easily crystallisedACE - membrane bound zinc metalloproteinase not easily crystallised Study analogous enzyme which can be crystallisedStudy analogous enzyme which can be crystallised Structure based drug design Structure based drug design

17. Carboxypeptidase

18. Carboxypeptidase mechanism Structure based drug design Structure based drug design Hydrolysis

19. Inhibition of carboxypeptidase Structure based drug design Structure based drug design No hydrolysis

20. Lead compounds for ACE inhibitor Structure based drug design Structure based drug design

21. Proposed binding mode Structure based drug design Structure based drug design

22. Extension and bio-isostere strategies Structure based drug design Structure based drug design

23. Extension strategies Structure based drug design Structure based drug design

24. Computer-Assisted Drug Design (CADD) 1. Direct design of active substances which can be envisaged when the 3D structure of the target molecule is known. In this case the macromolecule can be built with the aid of computer then the fit of the host molecule with its receptor can be optimized. The structure of the ligand, its substituents and confirmation can be modified and the most favorable conditions for interaction (docking) can be simulated on the screen. In practice molecular modeling uses two approaches:

25. gDock: Web Docking Tool Sketch StructureDocked Structure

26. 2. Indirect design of active substances, on the other hand, constitutes the only possible approach when the 3D structure of the target molecule is unknown. In this situation comparison of a set of ligands selective for a given receptor is undertaken in order to reveal the molecular information that the compounds have in common despite apparently different chemical formula.

27. 8. Pharmacokinetics – drug design Aims To improve pharmacokinetic properties of lead compoundTo improve pharmacokinetic properties of lead compound To optimise chemical and metabolic stability (stomach acids / digestive enzymes / metabolic enzymes)To optimise chemical and metabolic stability (stomach acids / digestive enzymes / metabolic enzymes) To optimise hydrophilic / hydrophobic balance (solubility in blood / solubility in GIT / solubility through cell membranes / access to CNS / excretion rate)To optimise hydrophilic / hydrophobic balance (solubility in blood / solubility in GIT / solubility through cell membranes / access to CNS / excretion rate)

28. Drugs must be polar - to be soluble in aqueous conditions - to interact with molecular targetsDrugs must be polar - to be soluble in aqueous conditions - to interact with molecular targets Drugs must be ‘lipophilic’ - to cross cell membranes - to avoid rapid excretionDrugs must be ‘lipophilic’ - to cross cell membranes - to avoid rapid excretion Drugs must have both hydrophilic and lipophilic characteristicsDrugs must have both hydrophilic and lipophilic characteristics Many drugs are weak bases with pK a ’s 6-8Many drugs are weak bases with pK a ’s 6-8 8. Pharmacokinetics – drug design

29. Rationale: Metabolism of drugs usually occurs at specific sites. Introduce groups at a susceptible site to block the reactionMetabolism of drugs usually occurs at specific sites. Introduce groups at a susceptible site to block the reaction Increases metabolic stability and drug lifetimeIncreases metabolic stability and drug lifetime Oral contraceptive - limited lifetime 8.1.1 Metabolic blockers 8.1 Drug stability

30. Rationale: Metabolism of drugs usually occurs at specific groups.Metabolism of drugs usually occurs at specific groups. Remove susceptible group or replace it with metabolically stable group [ e.g. modification of tolbutamide (oral hypoglycemic)]Remove susceptible group or replace it with metabolically stable group [ e.g. modification of tolbutamide (oral hypoglycemic)] Susceptible group Unsusceptible group 8.1.2 Remove / replace susceptible metabolic groups TOLBUTAMIDE Rapidly excreted - short lifetime

31. Rationale: Used if the metabolically susceptible group is important for bindingUsed if the metabolically susceptible group is important for binding Shift its position to make it unrecognisable to metabolic enzymeShift its position to make it unrecognisable to metabolic enzyme Must still be recognisable to targetMust still be recognisable to targetExample:Salbutamol Susceptible group Unsusceptible group 8.1.3 Shifting susceptible metabolic groups

32. Rationale: Drug ‘smuggled’ into cell by carrier proteins for natural building block (e.g. amino acids or nucleic acid bases)Drug ‘smuggled’ into cell by carrier proteins for natural building block (e.g. amino acids or nucleic acid bases) Increases selectivity of drugs to target cells and reduces toxicity to other cellsIncreases selectivity of drugs to target cells and reduces toxicity to other cellsExample: Anticancer drugs Anticancer drugs Alkylating group is attached to a nucleic acid baseAlkylating group is attached to a nucleic acid base Cancer cells grow faster than normal cells and have a greater demand for nucleic acid basesCancer cells grow faster than normal cells and have a greater demand for nucleic acid bases Drug is concentrated in cancer cells - Trojan horse tacticDrug is concentrated in cancer cells - Trojan horse tactic 8.3.1 Linking a biosynthetic building block 8.3 Drug targeting Non selective alkylating agent Toxic Uracil Mustard

33. Rationale: Toxicity is often due to specific functional groupsToxicity is often due to specific functional groups Remove or replace functional groups known to be toxic e.g.Remove or replace functional groups known to be toxic e.g.  aromatic nitro groups  aromatic amines  bromoarenes  hydrazines  polyhalogenated groups  hydroxylamines Vary substituentsVary substituents Vary position of substituentsVary position of substituents 9. Reducing drug toxicity

34. Definition: Inactive compounds which are converted to active compounds in the body. Uses: Improving membrane permeabilityImproving membrane permeability Prolonging activityProlonging activity Masking toxicity and side effectsMasking toxicity and side effects Varying water solubilityVarying water solubility Drug targetingDrug targeting Improving chemical stabilityImproving chemical stability 9.1 Prodrugs

35. Example: Aspirin for salicylic acid 9.1.2 Prodrugs to mask toxicity and side effects Mask groups responsible for toxicity/side effectsMask groups responsible for toxicity/side effects Used when groups are important for activityUsed when groups are important for activity Salicylic acid Analgesic, but causes stomach ulcers due to phenol group Aspirin Phenol masked by ester Hydrolysed in body

36. Example: Cyclophosphoramide for phosphoramide mustard Cyclophosphoramide for phosphoramide mustard (anticancer agent) 9.1.2 Prodrugs to mask toxicity and side effects Cyclophosphoramide Non toxicNon toxic Orally activeOrally active Phosphoramide mustard Alkylating agentAlkylating agent Phosphoramidase (liver)

37. 9.1.3 Prodrugs to enhance patient acceptability Used to reduce solubility of foul tasting orally active drugsUsed to reduce solubility of foul tasting orally active drugs Less soluble on tongueLess soluble on tongue Less revolting tasteLess revolting taste Example: Palmitate ester of chloramphenicol (antibiotic) Palmitate ester Esterase Chloramphenicol

38. 9.1.4 Prodrugs to increase water solubility Often used for i.v. drugsOften used for i.v. drugs Allows higher concentration and smaller dose volumeAllows higher concentration and smaller dose volume May decrease pain at site of injectionMay decrease pain at site of injection Example: Succinate ester of chloramphenicol (antibiotic) Succinate ester Esterase Chloramphenicol

39. Drug Metabolism Identification of drug metabolites in test animals Properties of drug metabolites Toxicology In vivo and in vitro tests for acute and chronic toxicity Pharmacology Selectivity of action at drug target Formulation Stability tests Methods of delivery Preclinical trials

40. Phase I trials first introduction of IND (investigational new drug) in humans first introduction of IND (investigational new drug) in humans usually only healthy adult volunteers (no patients) usually only healthy adult volunteers (no patients) purpose is to investigate metabolic and pharmacological actions of the compound in humans purpose is to investigate metabolic and pharmacological actions of the compound in humans use dose-ranging (increasing dosages) to determine what side effects may occur use dose-ranging (increasing dosages) to determine what side effects may occur usually 20 – 80 subjects in the trial usually 20 – 80 subjects in the trial

41. Phase II trials early controlled trials in a patient population, with limited scope, to obtain preliminary data on efficacy early controlled trials in a patient population, with limited scope, to obtain preliminary data on efficacy further indication of side effects, this time in patients further indication of side effects, this time in patients about 200-400 subjects about 200-400 subjects

42. Phase III trials expanded trials in a much larger sample of patients expanded trials in a much larger sample of patients more information about drug efficacy and safety more information about drug efficacy and safety information about benefit : risk ratio information about benefit : risk ratio obtain some information to determine what should be included in the labelling of the marketed drug obtain some information to determine what should be included in the labelling of the marketed drug several hundred to several thousand patient subjects (usually multi-centre studies and very expensive) several hundred to several thousand patient subjects (usually multi-centre studies and very expensive)

43. Phase IV trials not always performed may be required to explore possible side effects in more detail or give a better indication of efficacy may involve a different type of patient (different age range, different male:female ratio) may investigate potential efficacy in a different therapeutic area number of subjects is variable depending upon the reason for the study

44. Drug Discovery Process Time and Money 12 to 24 years 1 drug 50,000 - 5,000,000 compounds are often screened to find a single drug $300 to >$500 million >1,000 “hits” 12 “leads” 6 drug candidates Discovery & Preclinical trials Clinical trials: Phase I, Phase II, Phase III

45. Epidemiology Distribution, frequency and determinants of health problems and diseases in human populations Aim: obtain, interpret and use health information and reduce disease burden Practical interventions and programs Components: 1- Disease Frequency: Rates and Ratios. 2- Disease Distribution:Patterns of the disease distribution. 3- Disease Determinants: To identify underlying causes.

46. Concepts and their application Incidence: the number of new cases, episodes or events occurring over a defined period of time, commonly one year. Prevalence: the total number of existing cases, episodes or events occurring at one point in time, commonly on a particular day. Population at risk: is vital to know about all people at risk of developing a disease or having a health problem, as well as those who are currently suffering from it.

47. Uses of epidemiology Study effects of disease states in populations over time and predict future health needs Diagnose the health of the community Evaluate health services Estimate individual risk from group experience Identify syndromes Complete the clinical picture so that prevention can be accomplished before disease is irreversible Search for cause

48. Pharmacogenetics

49. The term pharmacogenetics comes from the combination of two words: Pharmacogenetics – Study of how genetic differences in a SINGLE gene influence variability in drug response (i.e., efficacy and toxicity) Pharmacogenomics – Study of how genetic (genome) differences in MULTIPLE genes influence variability in drug response (i.e., efficacy and toxicity)

50. AIM OF PHARMACOGENETIC STUDIES  Identify and categorize the genetic factors that underlie the differences and apply this in clinical practice  Rational, individual therapy  Screening for those patients who carry the genes which place them at risk in case of certain therapies  Discovering which drugs are potentially dangerous for carriers of a given polymorphism  Establishing the frequency of pharmacogenetic phenotypes

51. Non-responders and toxic responders Responders treat with convential drugs

52. GENETIC FACTORS: The first observations of genetic variation in drug response date from the 1950’s, involving the muscle relaxant suxamethonium chloride. One in 3500 Caucasians has less efficient variant of the enzyme (butyrylcholinesterase) that metabolizes suxamethonium chloride. As a consequence, the drug’s effect is prolonged, with slower recovery from surgical paralysis.

53. 53 A. Atypical Plasma Cholinesterase a rapid acting, rapid recovery muscle relaxant - 1951 usual paralysis lasted 2 to 6 min in patients occasional patient exhibited paralysis lasting hrs. cause identified as an “atypical” plasma cholinesterase Hydrolysis by pseudocholinesterase choline succinylmonocholine

54. Potential Benefits of Pharmacogenetics  Improve Drug Choices: Each year, many dies of adverse reactions to medicine. Pharmacogenomics will predict who's likely to have a negative or positive reaction to a drug  Safer Dosing Options Testing of Genomic Variation Improve Determination of Correct Dose for Each Individual  Improvement in Drug Development: Permit pharmaceutical companies to determine in which populations new drugs will be effective  Decrease Health Care Costs Reduce number of deaths & hospitalizations due to adverse drug reactions. Reduce purchase of drugs which are ineffective in certain individuals due to genetic variations  Speed Up Clinical Trials for New Drugs