Chapter 2 Drug Discovery,Design,and Development 21 Drug Discovery…… 4,8 A.Drug Discovery without a Lead 1.Penicillins 9 2.Librium.......1 B.Lead Disc0very… 11 1.Random Screening.......... 13 2.Nonrandom (or Targeted or Focused)Screening...............14 3.Drug Metabolism Studies............... …14 4.Clinical Observations................. .15 5.Rational Approaches to Lead Discovery、...… 16 2.2 Lead Modification:Drug Design and Development............... 17 A.Identification of the Active Part:The Pharmacophore...........17 B.Functional Group Modification............................................... 21 C.Structure-Activity Relationships.............................................. 21 D.Privileged Structures and Drug-Like Molecules............... 24 E.Structure Modifications to Increase Potency and the Therapeutic Index 25 1.Homologation..................................... 26 2.Chain Branching.................................................. 26 3.Ring-Chain Transformations....................................... 28 4. Bi0iS0 sterism,,…… 29 5.Combinatorial Chemistry........................................ a.General Aspects................ 34 b.Split Synthesis:Peptide Libraries............................ 36 c.Encoding Combinatorial Libraries.................... 3 d.Nonpeptide Libraries........................... 41 6.SAR by NMR/SAR by MS...................... 7.Peptidomimetics........... 47 F.Structure Modifications to Increase Oral Bioavailability........................... 51 1.Electronic Effects:The Hammett Equation.................................. 51 2.Lipophilicity Effects............................................ 53
8 Chapter 2 Drug Discovery,Design,and Development a.Importance of Lipophilicity................................... 53 b.Measurement of Lipophilicities. 55 c.Computerization of Log P Values........................................61 d.Membrane Lipophilicity.……4. 62 3.Effects of lonization on Lipophilicity and Oral Bioavailability 62 4.Other Properties that Influence Oral Bioavailability and Ability to Cross the Blood-Brain Barrier..........................65 G.Quantitative Structure-Activity Relationships.......................... 66 1.Historical......... 66 2.Steric Effects:The Taft Equation and Other Equations..................67 3.Methods Used to Correlate Physicochemical Parameters with Biological Activity......................... …,68 a.Hansch Analysis:A Linear Multiple Regression Analysis 68 b.Free and Wilson or de novo Method..........................70 c.Enhancement Factor............................. .71 d.Manual Stepwise Methods:Topliss Operational Schemes and Others.....71 e.Batch Selection Methods:Batchwise Topliss Operational Scheme, Cluster Analysis,and Others..73 4.Computer-Based Methods of QSAR Related to Receptor Binding: 3D-QSAR................... 75 H.Molecular Graphics-Based Drug Design.......................................... 78 l.Epilogue…444… 86 2.3 General References 87 2.4 Problems.................. 100 2.5 References............... 105 2.1 Drug Discovery Drug discovery is a very time-consuming and expensive process.Estimates of the average time required to bring a drug to the market range from 12-15 years at an average cost of about $800million.For approximately every 10.000 compounds that are evaluated in animal studies, 10 will make it to human clinical trials in order to get I compound on the market.The clinical trials consist of three phases prior to drug approval:phase I(generally a few months to a year and a half)evaluates the safety,tolerability (dosage levels and side effects),pharmacokinetic properties,and pharmacological effects in 20-100 healthy volunteers:phase II(about 1-3 years)assesses the effectiveness of the drug,determines side effects and other safety aspects, and clarifies the dosing regimen in a few hundred diseased patients;and phase III(about 2-6 years)is a larger trial with several thousand patients in clinics and hospitals that establishes the efficacy of the drug and monitors adverse reactions from long-term use.Once the new drug application(NDA)is submitted to the Food and Drug Administration(FDA).it can be several months to several years before it is approved for commercial use.Phase IV studies are considered to be the results found with a drug that has already been allowed onto the drug market and is in general use.Drug candidates(or new chemical entiries.NCE.as they are
Section 2.1 Drug Discovery 9 often called)that fail late in this process result in huge,unrecovered financial losses for the company.This is why the cost to purchase a drug is so high.It is not that it costs that much to manufacture that one drug.but that the profits are needed to pay for all of the drugs that fail to make it to market after large sums of research funds have already been expended. In general,drugs are not discovered.What is more likely discovered is known as a lead compound.The lead is a prototype compound that has a number of attractive characteristics, such as the desired biological or pharmacological activity,but may have other undesirable characteristics.for example,high toxicity,other biological activities,absorption difficulties. insolubility,or metabolism problems.The structure of the lead compound is modified by syn- thesis to amplify the desired activity and to minimize or eliminate the unwanted properties to a point where adrug candidate,a compound worthy of extensive biological,pharmacological. and animal studies,is identified:then a clinical drug,a compound ready for clinical trials,is developed.Prior to an elaboration of approaches to lead discovery and lead modification,two common drugs discovered without a lead are discussed. 2.1.A Drug Discovery without a Lead A.1 Penicillins In 1928 Alexander Fleming noticed a green mold growing in a culture of Staphylococcus aureus,and where the two had converged,the bacteria were lysed.This led to the discovery of penicillin,which was produced by the mold.Actually,Fleming was not the first to make this observation;John Burdon-Sanderson had done so in 1870,ironically also at St.Mary's Hospital in London,the same institution where Fleming made the rediscovery!2 Joseph Lister had treated a wounded patient with Penicillium,the organism later found to be the producer of penicillin(although the strains discovered earlier than Fleming's strain did not produce penicillin,but,rather,another antibiotic,mycophenolic acid).After Fleming observed this phenomenon,he tried many times to repeat it without success;it was his colleague. Dr.Ronald Hare,3.41 who was able to reproduce the observation.It only occurred the first time because a combination of unlikely events all took place simultaneously.Hare found that very special conditions were required to produce the phenomenon initially observed by Fleming.The culture dish inoculated by Fleming must have become accidentally and simultaneously contaminated with the mold spore.Instead of placing the dish in the refrigerator or incubator when he went on vacation as is normally done,Fleming inadvertently left it on his lab bench.When he returned the following month,he noticed the lysed bacteria.Ordinarily. penicillin does not lyse these bacteria;it prevents them from developing,but it has no effect if added after the bacteria have developed.However,while Fleming was on vacation(July to August)the weather was unseasonably cold,and this provided the particular temperature required for the mold and the staphylococci to grow slowly and produce the lysis.Another extraordinary circumstance was that the particular strain of the mold on Fleming's culture was a relatively good penicillin producer,although most strains of that mold(Penicillium)produce no penicillin at all.The mold presumably came from the laboratory just below Fleming's where research on molds was going on at that time. Although Fleming suggested that penicillin could be useful as a topical antiseptic,he was not successful in producing penicillin in a form suitable to treat infections.Nothing more was done until Sir Howard Florey at Oxford University reinvestigated the possibility of producing penicillin in a useful form.In 1940 he succeeded in producing penicillin that could be administered topically and systemically sI but the full extent of the value of penicillin
10 Chapter 2 Drug Discovery,Design,and Development was not revealed until the late 1940s.161 Two reasons for the delay in the universal utilization of penicillin were the emergence of the sulfonamide antibacterials (sulfa drugs,2.1:see Chapter 5.Section 5.4.B.2,p.254)in 1935 and the outbreak of World War II. H:N SO-NHR sulfa drugs 2.1 No studies related to the pharmacology,production,and clinical application of penicillin were permitted until after the war to prevent the Germans from having access to this wonder drug.Allied scientists who were interrogating German scientists involved in chemotherapeutic research were told that the Germans thought the initial report of penicillin was made just for commercial reasons to compete with the sulfa drugs.They did not take the report seriously. The original mold was Penicillium notatum,a strain that gave a relatively low yield of penicillin.It was replaced by Penicillium chysogenum,which had been cultured from a mold growing on a grapefruit in a market in Peoria,Illinois! For many years debate raged regarding the actual structure of penicillin(2.2),8 but the correct structure was elucidated in 1944 with an X-ray crystal structure by Dorothy Crowfoot Hodgkin(Oxford):the crystal structure was not actually published until 1949Several differ- ent penicillin analogs(R group varied)were isolated early on;only two of these early analogs (2.2.R =PhOCH2,penicillin V:and 2.2.R=CH2Ph,penicillin G)are still in use today. H日 CH CH; COOH H penicillin V(R=PhOCH2) penicillin G(R CH2Ph) 2.2 A.2 Librium The first benzodiazepine tranquilizer drug,chlordiazepoxide HCI [7-chloro-2-(methylamino)- 5-phenyl-3H-1.4-benzodiazepine 4-oxide:2.3:Librium],was discovered serendipitously.1 Dr.Leo Sternbach at Roche was involved in a program to synthesize a new class of tranquilizer drugs.He originally set out to prepare a series of benzheptoxdiazines(2.4),but when R was CHaNR2 and R2 was CHs,it was found that the actual structure was that of a quinazoline 3-oxide(2.5). NHCH HCI chlordiazepoxide HCI 2.3 2.5
Section 2.1 Drug Discovery 11 CH2CI H N NHCH3 CHNH2 2.6 CH NH2 CH2NHCH3 NHCH3 人 CH2-CI 0 2.3 OH Scheme 2.1 Mechanism for formation of Librium. However,none of these compounds gave any interesting pharmacological results.The program was abandoned in 1955 in order for Stembach to work on a different project.In 1957 during a general laboratory cleanup a vial containing what was thought to be 2.5(X=7-CL, R=CH2NHCH3,R2=C6Hs)was found and,as a last effort,was submitted for pharma- cological testing.Unlike all of the other compounds submitted,this one gave very promising results in six different tests used for preliminary screening of tranquilizers.Further inves- tigation revealed that this compound was not a quinazoline 3-oxide,but was instead the benzodiazepine 4-oxide,2.3,presumably produced in an unexpected reaction of the corre- sponding chloromethyl quinazoline 3-oxide(2.6)with methylamine (Scheme 2.1).If this compound had not been found in the laboratory cleanup,all of the negative pharmacolog- ical results would have been reported for the quinazoline 3-oxide class of compounds,and benzodiazepine 4-oxides may not have been discovered for many years to come. The examples of drug discovery without a lead are relatively few in number.The typical occurrence is that a lead compound is identified,and its structure is modified to give,eventually, the compound that goes to the clinic. 2.1.B Lead Discovery Penicillin V and Librium are,indeed,two important drugs that were discovered without a lead. However,once they were identified,they then became lead compounds for second-generation analogs.A myriad of penicillin-derived antibacterials have been synthesized as a result of the structure elucidation of the earliest penicillins.Diazepam(2.7,Valium)was synthesized at Roche even before Librium was introduced on to the market:this drug was derived from the lead compound Librium and is almost 10 times more potent than the lead