Pharmaceutical Pharmaceutical (medicinal) (medicinal) chemistrychemistry

IntroductionIntroduction

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PharmDr. Pavol Ježko, PhD.Department of Pharmaceutical ChemistryFaculty of Pharmacy, Comenius UniversityOdbojarov 10, 832 32 Bratislava, Slovakia

Tel: + 421 250 117 395e-mail: jezko@fpharm.uniba.sk; p.jezko@gmail.com

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DefinitionDefinition ofof pharmaceuticalpharmaceutical chemistrychemistry

• pharmaceutical chemistry– discovery

– development

– identification and interpretation of the mode of action of biologically active compounds at the molecular levelbiologically active compounds at the molecular level

• pharmaceutical chemistry is an interdisciplinary science• pharmacology, biochemistry, molecular biology, imunology

(life sciences)

• organic, physical, theoretical chemistry, molecular spectroscopy, crystallography, (chemical sciences)

• information technology

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Drugs

• Organic (inorganic) compounds and biomolecules(proteins, antibodies, …) that activates or inhibits the functionof a target with benefit to the patient

� activity (target binding place stereoelectronic compatibility)

� low toxicity (selectivity, antitargets: CYP, hERG, P-glycoprotein...)

� bioavailablity (physico-chemical and pharmacological properties

ensuring drug-likeness)

Three mainThree main phases ofphases of drug actiondrug action

• pharmaceutical phase (biopharmaceutical)

�release of drug from the drug form

• pharmacokinetic phase (what makes the body with the drug)• pharmacokinetic phase (what makes the body with the drug)

�ADME

• pharmacodynamic phase (what makes the drug with the organism)

�character and quality of drug interactionswith interaction site of the biological system

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Basic terms in pharmaceutical chemistry

• TARGET (biomacromolecule to interfere with)

• BINDING POCKET – ACTIVE SITE(part of the target appropriate to bind a small ligand)

• PHARMACOPHORE (a part of a molecule that is recognized at a receptor site and is

responsible for that molecule's biological activity)

• LIGAND organic molecule possessing target affinity, that has to be stereo-

electronically compatible with binding pocketelectronically compatible with binding pocket

� ACTIVE is a compound detected by usually HTS

� HIT is a active compound identified in a screen with confirmed structure and activity, that need to be developed into lead compound

� LEAD is a active compound with convenient properties: drug-likeness,

solubility, synthetic feasibility, patentability

� DRUG CANDIDATE high activity, good selectivity, in vivo efficiency

� DRUG after success in clinical trials approved by FDA, EMEA

• DRUG-LIKENESS complex properties

– (ADME/Tox: Absorption/Distribution/Metabolism/Excretion/Toxicity)

� selection of disease (cardiovascular, autoimmune, infectious, hereditary, mental, cancer …)

� molecular mechanism of the pathology (medicine, molecular biology)

� selection of a key biomolecule to influence

� new active structure/compound identification: in Silico design, HTS,

Drug development basic chronology

� new active structure/compound identification: in Silico design, HTS,of organic molecules possessing appropriate drug-like properties(biologists, computer chemists)

� organic synthesis (chemists)

� biological or biophysical assays (biologists)

� optimization of activity and other molecular properties

� IP protection + clinical trials + up-scale synthesis + approval

PharmaceuticalPharmaceutical chemistrychemistry includesincludes::

•• TheThe processprocess ofof discoverydiscovery = identification and production of new active compounds� natural resources� synthesis� biotechnology� design - computer aided drug design (CADD)

• The optimization process� synthetic modification of the lead sceleton (structures) to

improve the effect , selectivity and suppress toxicity (S.A.R.)

• The development process� optimization of synthetic processes for mass production of the

drug� modification of pharmacokinetic properties of the

drug (suitable for clinical use)7

A) The Natural World

Micro-organisms (bacteria, fungi)

Marine chemistry (corals, bacteria, fish etc)

Plant life (flowers, trees, bushes)

Animal life (frogs, snakes, scorpions)

Biochemicals (neurotransmitters, hormones)

Pure natural products, bioextracts (e.g. plant, or

microbial) Ethnopharmacology (Chinese

From were to get active compounds?

B) The Synthetic World

C) The Virtual World

microbial) Ethnopharmacology (Chinese

traditional medicine...)

LMW synthetic compounds(traditional, combinatorial synthesis, historical

corporate chemical collections, commercial

sources)

Computer aided drug design (CADD)

to call them „active compounds“ evaluation through biological screening is essential

Pharmaceutical research and Pharmaceutical research and development (R & D)development (R & D)

• discovery of a new lead sceleton is a key step in any research program

• nowdays it is also the most problematic stage of development of a new drug

Discovery of new lead structures in 70s 20th centuryDiscovery of new lead structures in 70s 20th century

- random selection (random observation, a happy discovery, screening a large number of compounds)

Nowdays: racional procedures

• based on the knowledge structure of endogenous metabolites, enzymes, receptors and the nature of the biochemical defect that caused the disease

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Structure – activity relationship• primary task of the medical chemist is to identify leading sceleton and its

subsequent modification in order to obtain a suitable candidate to drug that

may be introduced into clinical practice

• leading structure may have some deficiencies, chemical and biological

characteristics: a lack of specificity, low activity, metabolic, chemical

instability, high toxicity, low bioavailability, poor solubilityinstability, high toxicity, low bioavailability, poor solubility

• irrational approach: make all the easy and available variations of the leading

sceleton

• rational process: methods and approaches that describe the relationship

between drug structure and its activity

- knowledge of the spatial (3D) structure of the receptors at atomic level

resolution)

- knowledge of the conformation of ligands and their interaction with target

macromolecules10

StrategiesStrategies ofof modificationmodification existingexisting structuresructures

• by chemical modification will be prepared new

compounds, which will have higher

activity, lower toxicity, or better dosage formactivity, lower toxicity, or better dosage form

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BioisostericBioisosteric substitutionsubstitution

• is based on the knowledge that certain

physical properties of chemically different

compounds are strikingly similar

• bioisosters are considered a group of

compounds which have the chemical and

physical properties that produce similar

biological effect

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Classical bioisostersClassical bioisosters• Are of similar size, shape and valence electron configuration

Classical isosters that can serve as bioisosters:

monovalent atoms and groups

A: –CH3 –NH2 –OH –F –Cl

B: –Cl –PH2 –SH

bivalent atoms and groups

A: –CH2– –NH– –O– –S– –Se–

B: –COCH2– –CONH– –COO– –COS–

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B: –Cl –PH2 –SH

C: –Br –i-Pr

D: –I –t-Bu

B: –COCH2– –CONH– –COO– –COS–

ring equivalents

A: –CH=CH– –S– (benzene; tiophene)

B: –CH= –N= (benzene; pyridine)

C: –O– –S– –CH2– –NH–

(tetrahydrofurane; tetrahydrotiophene;

cyclopentane; pyrrolidine)

trivalent tetravalent

A: –CH= –N= A: >C< >Si<

B: –P= –As= B: =C= =N+= =P+=

NonclassicalNonclassical bioisostersbioisosters

• Are of different number

of atoms, do not meet

the steric and electron

rules of classical

bioisosters, but evoke

similar biological activity

O

R

R

R

R CN

CN

S O

R

R

S

O

OR

R

R SO2 N

R

R

R CH

R

CN

COOH

CONHCN

PO(OH)OEt

SO2NHR

CONHOH

PO(OH)NH2

SO3H

O N

OH

O

O

OH

N

N

N

N

CH3

H

R COO R

NR R S

R R

NOMe

R

Nonclassical bioisosters of Carbonyl group

Nonclassical bioisosters of Carboxyl group

Nonclassical bioisosters of Ester group

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R COO R

N O NNOMe

R

R CONH RR CONMe R R CSNH RR CH2NH R C C

R

R R

R

R CH2S R

R OH R NHCOR R NHSO2R R CH2OH R NHCONH2 R NHCN R CH(CN)2

OH

OH

N

NH

X

O

OHX = O, NR

N

O

OH

Nonclassical bioisosters of Amide group

Nonclassical bioisosters of Hydroxyl group

Nonclassical bioisosters of Catechol group

Nonclassical bioisosters of Halogen

Halogen CF3 CN NCN2 C(CN)3

Nonclassical bioisosters of Urea-likeNHC(=S)NH2 NHC(=NCN)NH2 NHC(=CHNO2)NH2

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SystematicSystematic screeningscreening

• systematic testing of new compounds without the known mechanism of action and pharmacological potential

• extensive screening - a comprehensive • extensive screening - a comprehensive pharmacological assessment is subjected to a limited number of “advanced“ structures

• random screening - from large number of compounds (hundreds-thousands) is looking for one which is active in the indication

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The use of biological information

• monitor the effects of random compounds for

new discoveries about biological processes

taking place in biology and medicine

– observation of people - folk medicine (Digitalis,

opiates, quinine, atropine, cocaine)

– observations in animals - in vivo pharmacological

tests on animals (Vinca rosea - vincristine,

vinblastine)17

Rational drug development

• rational design consist of the knowledge of

the molecular level of the disease

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GeneticsGenetics, , genomicsgenomicsand and drugdrug developmentdevelopment

• Over the last 15 to 25 years there has been progress in several scientific fields, particularly combinatorial chemistry, genomics, proteomics and bioinformatics, which are promise for the future in a streamlining of procedures discovering new drugs.procedures discovering new drugs.

• The main idea of new methods of research and drug development is to identify the biological action, gene or protein that is disrupted in the disease process.

• Then, on the basis of this knowledge could be design a drug that specifically interact with the site of action

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Computationalpharmaceutical chemistry

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Computationalpharmaceutical chemistry

• Computational chemistry– is a discipline using mathematical methods for the

calculation (computer-assisted) of molecular properties or for the simulation of molecular behaviourfor the simulation of molecular behaviour

– most used methods• quantum mechanics

• classical mechanics

• Computational pharmaceutical chemistry– Main object of study

• drugs

• biological systems associated with drugs (proteins, enzymes, receptors...) 21

Drug design and development

Drug-like molecule

• Necessary condition– biological activity = f (3D structure + physicochemical

properties)properties)

• Sufficient condition– high-affinity ligand must exhibit also good pharmacokinetic

and toxicological properties• pharmacokinetic ADMET (Absorption, Distribution, Metabolism,

Excretion and toxicity ) parameters

• (poor biopharmaceutical properties and toxicity are one of themajor reason for drug development failure)

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Molecular modeling

and

medicinal chemistry

• Molecular modeling methods

– Quantum chemistry

– Molecular Mechanics

– Molecular Dynamics and Monte Carlo

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Electronic structure methods• semi-empirical methods (MNDO, AM1, PM3, ...)

– programs: MOPAC, HyperChem, Gaussian, ...

• ab initio methods

– Hartree-Fock methods

– electronic correlation methods

• Moller-Plesset Pertubation Theory (MP2, MP3, MP4, MP5)

• Density functional methods• Density functional methods

– B3LYP, B3P86, BLYP, ...

• Hybrid methods

– ONIOM, QM/MM approaches

– Programs: Gaussian, Jaguar,...

• Use of these methods:

– Geometry and energy calculations

• in gas phase

• solvent effect 24

ComputerComputer--AssistedAssisted DrugDrug DesignDesign

•• CADD (CADD (ComputerComputer--AssistedAssisted DrugDrug DesignDesign))

was developed by applying methods and

theories of computational chemistry to study theories of computational chemistry to study

the properties of drugs

• can be applied to any active molecules, which

interact with the receptor is known

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Computer-assisted drug design (CADD)

• Computer-assisted drug design– involves all computer-assisted techniques used to discover, design and optimize

biologically active compounds with a putative use as drugs

• CADD is the science and art of finding molecules of potential therapeutic value thatsatisfy a whole range of quantitative criteria such as high potency, high specificity, minimal toxic effect and good bioavailabity

• CADD relies on computers, information science, statistics, mathematics, physics, biology and medicine

• CADD implies the use of computer graphics to visualize and manipulate chemicalstructures, to synthesize “ in silico “ new molecules, to determine theirconformation, and to assess the similarities aind dissimilarities between series ofmolecules

• CADD also involves the calculation of the interaction energy between drugmolecules and hypothetical or experimentally determined macromoleculasstructures

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Computer assisted drug design

AIM:

• to discover, enhance, study biologically active molecules that will bind

to a selected target and if so how strongly before a compound

is synthesized

• to estimate drug-like properties and use them for elimination of

undesirable structures

• it still takes several iterations of design, synthesis, and testing before

an optimal molecule is discovered

Do we

know 3D

structure

?

Target selection

Do we

know 3D

structure

of homolog

protein?

SBDD LBDD

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What

compound

?

New lead

compound

Optimized

structure

Database

searching

Molecular

docking

Design

de novo

Fragment

docking

What

compound

?

New lead

compoundOptimized

structure

Database

searching

Active

analog

model

Design

de novo

QSAR

model

Pharmacophore

model

Rational methods in drug design

• Structure-based drug design SBDD

• Ligand-based drug design LBDD

• Fragment-based drug design FBDD

Structure Based Drug Design - SBDD

• relies on knowledge of the 3D structure of the biological target obtained through X-ray crystallography or NMR spectroscopy

• SBDD be divided roughly into two categories

“finding” ligands for a given receptor (database searching). A large • “finding” ligands for a given receptor (database searching). A large

number of potential ligand molecules are screened to find those fitting

the binding pocket of the receptor. It saves synthetic effort to obtain

new active compounds.

• “building” ligands (receptor-based drug design). In this case, ligand molecules are built up within the constraints of the binding pocket by assembling small pieces (atoms, fragments) in a stepwise manner. The

key advantage is that novel structures, not contained in any database, can be suggested.

Ligand Based Drug Design

LBDD (indirect DD)

• relies on knowledge of known molecules that bind to thebiological target (known: structure and bioactivity IC50)

• These molecules (ligands) may be used to derive a pharmacophore modelwhich defines the minimum necessary structural characteristics a moleculewhich defines the minimum necessary structural characteristics a molecule

must possess in order to bind to the target.

• Virtual screening (based on pharmacophore models; high-throughput

docking) including drug property filtering (Zinc database)

• Alternatively, a quantitative structure-activity relationship (QSAR) in which

a correlation between calculated properties of molecules and their

experimentally determined biological activity may be derived. These may

be used to predict the activity of new analogues.

PharmacophorePharmacophore

• spatial (3D) arrangement of functional groups

of ligand molecules that react with the active

site of the receptor

• actually defines "natural" dimensions of the

ligand molecule

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EGFR (ErbB, HER1) tyrosine kinase receptor: abnormal or over-expressed in the breast, lung,

brain, prostate, gastrointestinal tract, ovaries cancer. EGFR is a receptor for EGF proteins (1986

Nobel Prize). Upon activation by its growth factor, EGFR forms active homodimer possessing

intracellular TK activity that initiate several signal transduction cascades leading to DNA

synthesis and cell proliferation. Gefitinib inhibits EGFR by binding to the ATP-binding site.

Thus receptor and therefore alsomalignant cells are inhibited.

EGFR inhibitor gefinitib (IRRESA)(approved for refractory lung cancer, AstraZeneca)

4-anilinoquinazoline SAR optimized

Lead I, good in vitro activity, in vivo

hampered by rapid metabolism

caused by cytochrome P450

enzymes

main metabolic products I, II both met. routes

blocked

Cl- similar in size and lipophilicity as Me- group

F- almost the same size as H- (no steric effect)

both groups are resistant to oxidation, better in vivo

activity, pharmacokinetic properties improved by

morpholino group, because of basic nitrogen that

enhanced water solubility

What should compound fulfill to become a drug?

• Biol. active, chemically stable compound possessing appropriate:

� pharmacodynamic properties (activity, selectivity)

� pharmacokinetic properties (bioavailability: ADME/TOX)

� others (novelty, scale up synthesis...)

• > 30% of all drug failures can be attributed to poor physiochemical properties: Log P (Log D), pKa, and solubility all have impacts on drug properties: Log P (Log D), pKa, and solubility all have impacts on drug absorption and diffusion in vivo

Chem Space: 1060 - 10200

DB of 11 atoms C,N,O, F: 26 400 000 stable

compounds (110.9 M if stereoisomers included)

J.-L. Reimond J. Chem. Inf. Model. 47, 2007, 342.

Chemical Space

Lead-like Drug-likeDrugs

Bioavailability

• (in vitro) active compound, to perform as drug, has to reach its targetin the human body (in vivo)

• Drug-likeness is qualitative concept to estimate bioavailability fromthe molecular structure before the substance is synthesized. Thedrug-like molecule has to have:drug-like molecule has to have:

� optimal MW and number of HBD, HBA (affecting solubility and absorption)

� optimal water and fat solubility logP (octanol / water) (intestinal lining, aqueousblood, penetrate cellular membrane to rich inside the cell) The distributioncoefficient (Log D) is the correct descriptor for ionisable systems. log D is pHdependent (e.g. at pH = 7.4 is the physiological pH of blood serum)

Lipinski's Rule of Five (Ro5)

Lipinski Ro5(all numbers are multiples of five, empiric rule)

for prediction of bioavailability (not activity!) to quickly

eliminate compounds that have poor physicochemical

properties for oral bioavailabilty

• an orally active drug has no more than one violation of the following criteria:following criteria:

� MW ≤ 500

� Lipophilicity (logP ≤ 5) octanol-water partition coefficient (better log D ≤ 5 respecting the ionic states present at

physiological pH values)

� Sum of hydrogen bond donors ≤ 5 (NH,OH)

� Sum of hydrogen bond acceptors ≤ 10 (N,O)

C. A. Lipinski et al. Adv. Drug Del. Rev. 1997, 23, 3. (Ro5)

Greg M. Pearl et al., Mol. Pharmaceutics, 2007, 4, 556–560. (log D introduced)

Additional drug-like parameters

� MW ≤ 500

� Lipophilicity (logP ≤ 5) octanol-water partition coefficient

� Sum of hydrogen bond donors ≤ 5 (NH,OH)

� Sum of hydrogen bond acceptors ≤ 10 (N,O)

� PSA < 140 Å2(Molecular Polar Surface Area – sum of surfaces of

polar atoms (N,O...with H) that correlates with human intestinal and BBB absorption) for good BBB penetration (PSA < 60 Å2)

� Number of rotatable bonds < 10 (flexibility factor)(high NRB → many conformers)

Ertl, P. in Molecular Drug Properties, R. Mannhold (ed), Wiley-VCH , 2007, 111 – 126.

Ro5 determined from 2D tructurehttp://www.molinspiration.comhttp://www.molinspiration.com

Ertl, P. et al., J. Med. Chem. 2000, 43: 3714-3717. (molecular property prediction toolkit )

Ro5 violations

Absorption as f(PSA, LogP)

• logP(membrane transport connected with fat and water solubility)

• log pKa

(influences binding Ki and also logP)

Intestinal and other absorption• % ABS = 109 – 0.345 PSA (good when %ABS > 30 %)

(lower PSA, higher absorption)Zao YH et al. Pharm Res 2002, 19, 1446-1457.

Brain Blood Barrier penetration• LogBB = -0.0148 PSA + 0.152 CLogP + 0.139

(to estimate CNS penetration and possible side effects)BB = C-brain / C-blood

CNS: logBB > -0.5 (side effects)

non CNS: logBB < -1

Other considerations

• despite good druglikeness some compounds should be avoided as drug candidates:

• If contain substructures with known reactive, toxic, mutagenicor teratogenic properties (RCOX, (RCO)2O, Michael acceptors,or teratogenic properties (RCOX, (RCO)2O, Michael acceptors,

epoxides, -NO2, -NO, -N3, NH-NH, N=N...)

• bad metabolic parameters, e.g. fast metabolism can quicklydestroy the pharmacological activity of the compound (metabolic

half life, metabolic clearance should be determined)

• Inhibit antimetabolites (CYP, hERG, P-glycoprotein)