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II-B. MEDICINAL CHEMISTRY

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Drug Discovery CheckpointsTarget Identification1 gggcgtggag gagcccaccg accggagacc atttggggcc tggagatgcc atcggagggc61 aggagctcat cctggagagg ccaccgtaag gcctgacctg ggcctgggga gcttggcttg121 aggaagctnt gggccgacca aggccgccag gagatgggt

Target Characterization

Lead Definition

Lead Optimization

Candidate EvaluationDrug Formulation

Clinical Testing

1-2 y2-6 y

7 y

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Stages in the Drug Discovery Process

Lombardino, J. G.; Lowe, J. A., "A guide to drug discovery: The role of the medicinal chemist in drugdiscovery - then and now." Nature Rev. Drug Disc. 2004, 3, 853-862.

10 Year Trends in Biomedical Research

50% Decline in newproduct submissions

250% increase in R & Dexpenditures

NME = New molecular entitiesBLA = Biologics

FDA Report March 2004: Innovation or Stagnation, Challenge and Opportunity on theCritical Path to New Medical ProductsWoosley & Cossman. Clin Pharm Therap. 81:129, 2007

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Drug Potencies & Rate of Target Innovation

High Target Innovation

Re-Use of Established Mechanisms

• Ca. 130 “privileged druggable domains” cover all current drug targets (vs. total number ofprotein families (16,000) and folds (10,000).• Of ca. 1,620 distinct human protein sequences are linked to a genetic disease, only 105 areactual drug targets.• Target innovation is slow - The average rate over the past 20 years has been quite constantat 5 new “drugged” targets per year.• The first approved indications for drugs acting on new targets are usually orphan diseases.

Median affinity = 20 nM

The State-of-the-Art in Drug Discovery:

Small, incremental advances in fundamental biology,chemistry, and clinical sciences

“The Most Fruitful Basis for the Discovery of a NewDrug is to Start with an Old Drug”

James Black - 1988 Nobel Prize in Physiology andMedicine

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Current Drug Discovery Challenges

In Search of New Leads…..

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Medicinal Chemistry

The science that deals with the discovery or designof new therapeutic agents and their developmentinto useful medicines.

It involves:

• Organic Synthesis

• Biological Target Identification & AssayDevelopment

• Structure-Activity Relationships (SAR)

• Absorption, distribution, metabolism, andexcretion (ADME)

Why Is Structural Diversity An Issue?

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‘Drug-like’ & ‘Lead-like’ Properties

‘Drug-like’ & ‘Lead-like’ Properties

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‘Drug-like’ & ‘Lead-like’ Properties• Reactive functionalities should be filtered:

Where Did (Do) Our Drugs Come From?

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Screening of natural product extracts

High-Pressure AcceleratedSolvent Extractor System

DCM & MeOHExtracts

Parallel HPLC

HT Solvent Concentrator

Multiwell PlatesFor HTS

Examples of Natural Products as Leads &Drugs

Cardiac glycosides, morphine, quinine, salicylic acid, taxol,camptothecin, penicillin, cyclosporin A, warfarin, artemisine….

O

HO

RO

N

R = H: MorphineR = Me: Codeine

(pain killer)

HO

H H

OH

H

HO

H H

OH

HH

17-ethynylestradiol norethindrone

(the "Pill"; contraceptive)

Clarithromycin(antibacterial)

O

O

O

OH

OMeHO

O

O

O

OMe

OH

OHO

N

HOO N

S

O

NH2

CO2H

HH

Ampicillin(antibiotic)

N

O

O

OH

CO2H

Clavulanic acid(!-lactamase inhibitor)

Augmentin(antibiotic)

NN

O

O

O

N

HN

NNH

HN

N

O

O

O

OO

O

N

O

OH

N

O

NH

Cyclosporine A

1 2

3

4

567

89

1011

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Drug DiscoveryOne way to “discover” drugs

Serendipitous Drug Discovery

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Serendipitous Discovery of Librium without a Lead

In 1955 Roche set out to prepare a series ofbenzheptoxadiazines as potential new tranquilizerdrugs, but the actual structure was found to be that of aquinazoline 3-oxide.

In 1957, during a lab cleanup, a vial containing what wasthought to be the latter compound (X = 7-Cl, R1 = CH2NHCH3,R2 = C6H5) was sent for testing, and it was highly active.

Further analysis showed that the actual structure of the compoundwas the benzodiazepine 4-oxide, Librium, presumably producedin an unexpected reaction of the corresponding chloromethylquinazoline 3-oxide with methylamine.

Librium

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“Me Too” CompoundsCopying existing drugs with only minor chemical variations is usually referred to as“me too” research. Interestingly, sometimes these close analogs demonstrate major(usually unexpected) advantages, like the bioavailable, broad-spectrum lactamase-resistant penicillins, polar H1 antihistamines without sedative side effects, statins,or PDE5 inhibitors.

May & Baker Ltd. (1972)

Turko, I. V.; Ballard, S. A.; Francis,S. H.; Corbin, J. D., "Inhibition ofcyclic GMP-binding cyclic GMP-specific phosphodiesterase (type 5)by sildenafil and relatedcompounds." Mol. Pharmacol. 1999,56, 124-130.

Pfizer (1999) Pfizer (1992)

Rational Drug Discovery

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Structure-Activity Relationships (SARs)

Structurally specific drugs (most drugs):Act at specific sites (receptor or enzyme)Activity/potency susceptible to smallchanges in structure

Structurally nonspecific drugs:No specific site of actionSimilar activities with varied structures(various gaseous anesthetics, sedatives,antiseptics)

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Example of SAR

Lead: sulfanilamide (R = H)Thousands of analogs synthesized

From clinical trials, various analogs werefound to possess several different activities:

• Antimicrobial• Antidiabetic• Diuretic• Antihypertensive

sulfa drugs

H2N SO2NHR

Sulfadrug SAR

J. Drews Science 287, 1960 -1964 (2000)

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Rational Drug Discovery - Piroxicam• It took Pfizer ~18 years to develop the anti-inflammatory drugpiroxicam, which was launched in 1980 during the “golden age ofrational drug discovery”.• The starting point for the development was chemistry-driven, i.e. toidentify acidic, but not carboxylic acid-containing (salicylic acid)structurally novel compounds.• Measurement of a physical property (pKa) as well as serum half-life indogs was the guide for the synthesis program.• Several generations of leads were refined and ultimately led to asuccessful structure with an acceptable safety and activity profile:

Bioisosterism

Bioisosteres - substituents or groups withchemical or physical similarities thatproduce similar biological properties.Can attenuate toxicity, modify activity oflead, and/or alter pharmacokinetics oflead.

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Classical Isosteres1. Univalent atoms and groups

a. CH3 NH2 OH F Clb. Cl PH2 SHc. Br i-Prd. I t-Bu

2. Bivalent atoms and groups

a.

b.

CH2 NH O S Se

CONHR CO2RCOCH2R COSR

3. Trivalent atoms and groups

a.

b.

CH N

P As

4. Tetravalent atoms

C Sia.

b. C N P

5. Ring equivalents

a.

b.

c.

CH CH S (e.g., benzene, thiophene)

CH N (e.g., benzene, pyridine)

O S CH2 NH(e.g., tetrahydrofuran,tetrahydrothiophene,cyclopentane, pyrrolidine)

Do not have thesame number ofatoms and do notfit steric andelectronic rules ofclassical isosteres,but have similarbiological activity.

Non-ClassicalIsosteres

1. Carbonyl group

O

CC

CNNC O

S SO O

SN

O

OR

CN

O CN

CH

NOH

C

NOCH3

C

2. Carboxylic acid group

S

O

O

N

R

HC

OH

OO

S

O

OH P

NH2

OH

O

P

OEt

OH

O O

C NH

CN

ArS

NH

NH

O O

ONH

SAr

O O

O

SNH

SAr

O O

OO

NO

OH

NS

OH

ON

OH

NN

OH

CH3

NH

XO

O O

O

OHN

NN

NH

N

NOH

N N

NOH

N

N OHN

N

OH

OH

F

F

3. Amide group

CNH2

O O

CHN

CNH2

S

CCH2

O OH

CH2 HNC

NH2

O

HNC

O

O

COR

O

HNS

O

ON

CH3

NH2

N

NH2

H2C

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4. Ester group

COR

O O

SNRR'

O-

O

CN

F

R N

SN

R'

N

ON

R'

N

S

N

R'

NN

O

OR

NN

S

OR

NN

N

OR

R'

N

NN

N

R'N

OOR

5. Hydroxyl group

OH NHCR

O

NHCNH2

O

NHSO2R CH2OH

NHCR CH(CN)2

6. Catechol

HO

HO

HN

NX

HO

O

X = O, NR

N

O

HO

SHN

O

HO

7. Halogen

X CF3 CN N(CN)2 C(CN)3

8. Thioether

S ONC CN

N

CN

9. Thiourea

S

HN NH2

N

HN NH2

CN

HN NH2

NO2N

NH2

SO2NH2

10. Azomethine

NCN

C

11. Pyridine

N

NO2

N+

R NR3

12. Benzene

N N

N S ON

O

N

S

N

O

N

HN

13. Ring equivalents

NO R'

R

RN

O

RR

R'

O

HN

H3C

R

O

O

N

NH

NH2

H

R

14. Spacer group

(CH2)3

15. Hydrogen

H F

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Examples of Bioisosteric Analogues

Antihistamines

R X (CH2)n Y X = NH, O, CH2

Y = N(CH3)2 (n = 2)

N

NH

(n = 1)

(n = 1, 2)NH

N

Diphenhydramine

(Benadryl)

Fexofenadine(Allegra)

Ph

O

Ph

NNHO

Ph

Ph OH

CO2H

Otaka, A.; Mitsuyama, E.; Watanabe, J.; Watanabe, H.; Fujii, N., "Synthesis of fluorine-containing bioisosterescorresponding to phosphoamino acids and dipeptide units." Biopolymers 2004, 76, 140-149.

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Gadek, T. R.; Burdick, D. J.; McDowell, R. S.; Stanley, M. S.; Marsters Jr., J. C.;Paris, K. J.; Oare, D. A.; Reynolds, M. E.; Ladner, C.; Zioncheck, K. A.; Lee, W.P.; Gribling, P.; Dennis, M. S.; Skelton, N. J.; Tumas, D. B.; Clark, K. R.; Keating,S. M.; Beresini, M. H.; Tilley, J. W.; Presta, L. G.; Bodary, S. C., "Generation ofan LFA-1 (leukocyte functional antigen–1) antagonist by the transfer of theICAM-1 (intercellular adhesion molecule–1) immunoregulatory epitope to a smallmolecule." Science 2002, 295, 1086-1089.

The interaction of LFA-1 with the ICAM proteins 1, 2, and 3 iscritical to the adhesion, migration, and proliferation oflymphocytes.

A disruption of these protein-protein interactions could lead toagents for the treatment of psoriasis and transplant rejection.

Case Study: Use of a combined rational design - combinatorialchemistry strategy

Rational Drug Discovery - From Hit to Lead

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An epitope comprising residues E34, K39, M64, Y66,N68, and Q73 within ICAM-1’s first domain was identifiedas essential for its interaction with LFA-1. The function ofthis epitope is embedded in the carboxylic acid, amine,sulfide, phenol, and carboxamide chemical functionalitiesof the amino acid side chains of these six residues andtheir display in three dimensions along one face of theprotein.

Molecules which mimic this epitope could capture the LFA-1 binding specificity and safety inherent in ICAM-1’sfunction as a regulator of the immune system.

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More or less serendipitously, compound 1 was found to be an inhibitor of LFA-1.

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Comparison of the inhibition of ICAM-1/LFA-1 binding and theinhibition of mixed lymphocyte reaction (MLR). IC50 values weredetermined from a 4P fit of data from titrations over concentrations of10-3 to 10-10 M. Values reported are the mean±standard deviation forn>2 of experiments run in triplicate. ND, not determined. NA, notapplicable.

Two orthogonal views of the superimposition of compound 4 on the crystalstructure of the first domain of ICAM-1 indicating that compound 4 mimics theICAM-1 epitope. Residues highlighted in blue contribute significantly to LFA-1binding. The E34 side chain of ICAM-1 has been rotated to a low-energyconformation to enhance the overlay with compound 4.

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Conclusions:

Compounds 2 through 4 appear to be mimics of ICAM-1resulting from the transfer of the ICAM epitope to a smallmolecule.Compound 4 is a potent LFA-1 antagonist, which bindsLFA-1, blocks the binding of ICAM-1, and inhibits LFA-1mediated lymphocyte proliferation and adhesion in vitro.

This work represents the first reduction of a nonlinear,discontinuous but contiguous protein epitope(encompassing five residues spanning three different b-strands across the face of a protein surface) from aprotein to a small molecule.

Structure-Based Design of Potent Non-PeptideMDM2 inhibitors

The pharmacologicalhypothesis:

Ding et al. JACS 2005, 127, 10130.

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Structure-Based Design of Potent Non-Peptide MDM2 inhibitors

Structure-BasedDesign:

MDM2

Leu26

Phe19

Trp23

Structure-Based Design of Potent Non-Peptide MDM2 inhibitors

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Structure-Based Design of Potent Non-Peptide MDM2 inhibitors

Structure-Based Design of Potent Non-Peptide MDM2 inhibitors

Structure-Based Strategy:

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Structure-Based Design of Potent Non-Peptide MDM2 inhibitors

Gene-Family Distribution of Current Drugs

Paolini, G. V.; Shapland, R. H. B.; van Hoorn, W. P.;Mason, J. S.; Hopkins, A. L., "Global mapping ofpharmacological space." Nature Biotechnology 2006, 24,805-815.

There currently are >21,000 drug productsavailable. If you remove duplicate activeingredients, salt forms, supplements, vitamins,imaging agents, this number is reduced to 1,357unique drugs of which 1,204 are “small moleculedrugs” and 166 are “biological” drugs.

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Further reading:

Lombardino, J. G.; Lowe, J. A., "A guide to drug discovery: The role ofthe medicinal chemist in drug discovery - then and now." Nat. Rev. DrugDisc. 2004, 3, 853-862.Jorgensen, W. L., "The many roles of computation in drug discovery."Science 2004, 303, 1813-1818.Gustafsson, D.; Bylund, R.; Antonsson, T.; Nilsson, I.; Nystroem, J.-E.;Eriksson, U.; Bredberg, U.; Teger-Nilsson, A.-C., "Case history: A neworal anticoagulant: The 50-year challenge." Nat. Rev. Drug Disc. 2004,3, 649-659.

Dr. P. Wipf Chem 2320 4/5/2007