Pharmaceutical

(medicinal)
chemistry

Introduction
PharmDr. Pavol Ježko, PhD.
Department of Pharmaceutical Chemistry
Faculty of Pharmacy, Comenius University
Odbojarov 10, 832 32 Bratislava, Slovakia
Tel: + 421 250 117 395
e-mail: jezko@fpharm.uniba.sk; p.jezko@gmail.com 1
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Definition of pharmaceutical chemistry
• pharmaceutical chemistry
– discovery
– development
– identification and interpretation of the mode of action of
biologically 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 function
of 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 main phases of drug action
• pharmaceutical phase (biopharmaceutical)

release of drug from the drug form

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

ADME

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

character and quality of drug interactions
with 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 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)
 Drug development basic chronology

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,

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

Pharmaceutical chemistry includes
includes::

• The process of discovery = 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)
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 From were to get active compounds?

Micro-organisms (bacteria, fungi)

A) The Natural World
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
traditional medicine...)

LMW synthetic compounds

B) The Synthetic World (traditional, combinatorial synthesis, historical
corporate chemical collections, commercial
sources)

C) The Virtual World Computer aided drug design (CADD)

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

 Pharmaceutical research and
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 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 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 target10
macromolecules
Strategies of modification existing structures
ructures

• by chemical modification will be prepared new

compounds, which will have higher
activity, lower toxicity, or better dosage form

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 Bioisosteric substitution

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

Classical isosters that can serve as bioisosters:

monovalent atoms and groups bivalent atoms and groups

A: –CH3 –NH2 –OH –F –Cl A: –CH2– –NH– –O– –S– –Se–
B: –Cl –PH2 –SH B: –COCH2– –CONH– –COO– –COS–
C: –Br –i-Pr
D: –I –t-Bu
ring equivalents trivalent tetravalent
A: –CH=CH– –S– (benzene; tiophene) A: –CH= –N= A: >C< >Si<
B: –CH= –N= (benzene; pyridine) B: –P= –As= B: =C= =N+= =P+=
C: –O– –S– –CH2– –NH–
(tetrahydrofurane; tetrahydrotiophene;
cyclopentane; pyrrolidine)
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 Nonclassical bioisosters
Nonclassical bioisosters of Carbonyl group
R R CN R R O R CN
O S R SO2 N R HC
• Are of different number R
S O
R O R
R CN R R
of atoms, do not meet
Nonclassical bioisosters of Carboxyl group
the steric and electron COOH SO 2NHR SO3H
N
rules of classical CONHCN CONHOH OH O HC
3 N
bioisosters, but evoke PO(OH)OEt PO(OH)NH2 O N O N N
OH H
similar biological activity Nonclassical bioisosters of Ester group
N S R
R R R R
R COO R NOMe
N O N R
Nonclassical bioisosters of Amide group R R
R CONH R R CONMe R R CSNH RR CH2NH R C C R CH2S R
R R
Nonclassical bioisosters of Hydroxyl group
R OH R NHCOR R NHSO 2R R CH2OH R NHCONH2 R NHCN R CH(CN)2

Nonclassical bioisosters of Catechol group

HO N O O

N X N
HO HO HO
H X = O, NR
Nonclassical bioisosters of Halogen
Halogen CF3 CN NCN2 C(CN)3
Nonclassical bioisosters of Urea-like 14
NHC(=S)NH2 NHC(=NCN)NH2 NHC(=CHNO2)NH2
15
 Systematic screening
• systematic testing of new compounds without
the known mechanism of action and
pharmacological potential

• 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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 Genetics, genomics
Genetics,
and drug development
• 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.

• 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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 Computational
pharmaceutical chemistry

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 Computational
pharmaceutical chemistry

• Computational chemistry
– is a discipline using mathematical methods for the
calculation (computer-assisted) of molecular properties or
for 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)

• 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 the
major 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

– 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
 Computer--Assisted Drug Design
Computer

• CADD (Computer
(Computer--Assisted Drug Design)
Design)
was developed by applying methods and
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 that
satisfy 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 chemical
structures, to synthesize “ in silico “ new molecules, to determine their
conformation, and to assess the similarities aind dissimilarities between series of
molecules

• CADD also involves the calculation of the interaction energy between drug
molecules and hypothetical or experimentally determined macromoleculas
structures
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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
 Target selection

Do we Do we
know 3D know 3D
structure structure
of homolog
?
protein?

SBDD LBDD

What What
compound compound
? ?

New lead Optimized New lead Optimized

compound structure compound structure

Database Design Database Design

searching de novo searching de novo

Molecular Fragment Active Pharmacophore QSAR

docking docking analog model model
model 28
 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
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 the
biological target (known: structure and bioactivity IC50)

• These molecules (ligands) may be used to derive a pharmacophore model

which 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.
 Pharmacophore
• 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 inhibitor gefinitib (IRRESA)
(approved for refractory lung cancer, AstraZeneca)
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 also malignant cells are inhibited.
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
absorption and diffusion in vivo

Chemical Space

Lead-like Drug-like
Chem Space: 1060 -10200 Drugs
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.
 Bioavailability
• (in vitro) active compound, to perform as drug, has to reach its target
in the human body (in vivo)

• Drug-likeness is qualitative concept to estimate bioavailability from

the molecular structure before the substance is synthesized. The
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, aqueous
blood, penetrate cellular membrane to rich inside the cell) The distribution
coefficient (Log D) is the correct descriptor for ionisable systems. log D is pH
dependent (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:

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 tructure
http://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, mutagenic

or teratogenic properties (RCOX, (RCO)2O, Michael acceptors,
epoxides, -NO2, -NO, -N3, NH-NH, N=N...)

• bad metabolic parameters, e.g. fast metabolism can quickly

destroy the pharmacological activity of the compound (metabolic
half life, metabolic clearance should be determined)

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