18.09.

2022

Introduction to Medicinal Chemistry

and Drug Development
Prof. Dr. Malte Brasholz Department of Chemistry University of Rostock

Can Tho University MOMA Vietnam project

September 2022

History of Medicine

Paintings by Robert Thom (1915-1979)

An Egyptian physician (1500 B.C.) treats a patient for lockjaw in accordance with directions on a papyrus scroll, while priests perform prescribed rites.
Egyptian medicine occupied a dominant position in the ancient world for 2500 years.

NIH National library of medicine digital collections 2

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History of Medicine

melanin

Vitiligo syndrome

psoralen

Amni majus

Wikimedia commons 3

History of Medicine

Museum of Traditional Vietnamese Medicine, Ho Chi Minh City

http://fitomuseum.com.vn 4

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History of Medicine

Paintings by Robert Thom (1915-1979)

Persian-born physician Rhazes (865-925 A.D.) was first to describe measles and smallpox; to observe pupilary reaction to light; to publish a text on
children's diseases. He represented Arabic medicine at its best.

NIH National library of medicine digital collections 5

History of Medicine

“Peasants at the quack“ (Lambert Doomer, 1624-1700)

“Therapy is the administration of an agent that is unknown about to a patient

who is even less known about” (Voltaire, 1694-1778)
kunst-fuer-alle.de 6

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History of Medicine

Paintings by Robert Thom (1915-1979)

In 1855, Dr. Rudolf Virchow (1821-1902) while professor at Wurzburg University, Germany, propounded his theory of cellular pathology. Lecturing and
demonstrating at this specially made desk in the Wurzburg Krankenhaus, the slight, short, fiery professor used microscopes to convince students that
cells were reproduced from other cells, and that diseease results from disturbance of cells by injury or irritants.

NIH National library of medicine digital collections 7

History of Medicine – the beginning of „chemotherapy“

Arsphenamin (Salvarsan), 1907

Paul Ehrlich and Sahachiro Hata

Frankfurt, 1910

Wikimedia commons 8

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History of Medicine – the beginning of „chemotherapy“

Sulfamidochrysoidin
(Prontosil) Penicillin
(Markteinführung 1942)

Gerhard Domagk Alexander Fleming, 1928

Bayer, 1932

Wikimedia commons 9

Important areas in Medicinal Chemistry today

 Pharmacology:
 Pharmacodynamics
- Mode of action of a drug, drug target interaction, dose-response behavior
 Parmacokinetics
- Absorption, Distribution, Metabolism, Excretion of a drug (ADME)

 Drug development:
 Identification of new drug targets
 Development of new drugs for specific targets
 Screening of substance libraries
- Natural products & synthetic compounds
 Chemical synthesis of substance libraries (combinatorial chemistry)
 Lead optimization, quantitative structure-activity relationships (QSAR)
 In silico methods for drug design

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I. Pharmocodynamics:
drug-target interactions

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Drug targets in human Medicine

N. Dunlap, D. M. Huryn, Medicinal Chemistry, CRC Press, 1st edition 2018

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1. Enzymes as drug targets

Main functions of enzymes in the organism

 Synthesis of amino acids and proteins, nucleic acids, fatty acids, vitamins,

coenzymes

 Break-down of proteins, nucleic acids, lipids, carbohydrates, xenobiotics

 Activation / deactivation of specific proteins and other enzymes

 Modification of proteins and nucleic acids

…

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Enzyme classes
(International Union of Biochemistry and Molecular Biology, IUBMB)

 Oxidoreductases
Oxidations and reductions

 Transferases
Group transfer reactions

 Hydrolases
Hydrolysis reactions

 Lyases
Addition or removal of groups to form double bonds

 Isomerases
Isomerizations and intramolecular group transfers

 Ligases
Joining two substrates at the expense of ATP hydrolysis

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Enzymes as drug targets: pro‘s and con‘s

 Enzymes often isolable, available in large amount, well-characterized

 Easier development of inhibition assays

 Enzyme kinetics make analysis of inhibition relatively easy

 Substrate mimetics are good starting point for inhibitor structure optimization

 Substrate-enzyme oder inhibitor-enzyme complexes can often be crystallized

 Specifity for a single enzyme is often hard to realize

 Some substrates have high concentration in the body, high concentration of inhibitor necessary

 Physical properties of best inhibitor sometimes come with unfavorable pharmacokinetics

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1.1 Enzyme catalysis

Protein structure

D. V. Vranken, G. Weiss, Introduction to Bioorganic Chemistry and Chemical Biology 16

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Enzyme catalysis

Catalytic mechanisms
 Acid-base catalysis
 Stabilzation of transition states
 Reactions via covalently bound intermediates

G. L. Patrick, An introduction to medicinal chemistry, 6th edition

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Enzyme catalysis

N. Dunlap, D. M. Huryn, Medicinal Chemistry, CRC Press, 1st edition 2018

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Aminoacids

Wikimedia commons 19

Ligand-enzyme interactions on the molecular level

G. L. Patrick, An introduction to medicinal chemistry, 6th edition

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1) H-bonding interactions

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2) Van-der-Waals interactions

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3) Electrostatic interactions

G. L. Patrick, An introduction to medicinal chemistry, 6th edition

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4) Hydrophobic interactions

G. L. Patrick, An introduction to medicinal chemistry, 6th edition

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Principle of multivalence

C. Meier
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Key-and-lock principle vs. Induced fit

 Example: lactate dehydrogenase (LDH)

G. L. Patrick, An introduction to medicinal chemistry, 6th edition

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Key-and-lock principle vs. Induced fit

 Example: lactate dehydrogenase (LDH)

G. L. Patrick, An introduction to medicinal chemistry, 6th edition

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Cofaktors / Coenzymes

Cofactors
 Assist the protein by accelerating the catalytic reaction
 Can act as redox reagents
 Non-peptidic small molecules
- bound covalently
- bound by non-covalent (ionic) interactions
 Metal ions (Mg2+, Zn2+, Fe2+, Fe3+, Cu2+, Co2+, Mn2+)
- function as Lewis acid
- function as redox-active center

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Cofaktors / Coenzymes

Lactate dehydrogenase M tetramer (LDH5) + 4 NADH (green) + 4 oxamic acid, Human

https://www.rcsb.org/structure/1i10
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Cofaktors / Coenzymes

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LDH catalytic cycle

Schematic illustration of the full LDH catalytic process.

DOI: (10.1021/acsomega.8b02813) 31

Nucleophilic catalysis: the catalytic triade

Hydrolase enzymes!
 e. g. Chymotrypsin
- a serine protease

G. L. Patrick, An introduction to medicinal chemistry, 6th edition

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Stabilization of the transition state (TS)

 e. g. Chymotrypsin

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Metalloenzymes

 e. g. Histone deacylase
- a metallo hydrolase enzyme

G. L. Patrick, An introduction to medicinal chemistry, 6th edition

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1.2 Enzyme regulation

a) „Internal control“

 e.g. Glycogen phosphorylase

G. L. Patrick, An introduction to medicinal chemistry, 6th edition

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Allosteric regulation

 e.g. Glycogen phosphorylase

G. L. Patrick, An introduction to medicinal chemistry, 6th edition

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Glycogen phosphorylase

G. L. Patrick, An introduction to medicinal chemistry, 6th edition

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Glycogen phosphorylase - mechanism

G. L. Patrick, An introduction to medicinal chemistry, 6th edition

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Enzyme regulation

b) „External control“

G. L. Patrick, An introduction to medicinal chemistry, 6th edition

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Importance of chirality

Bindung of sulfonamide inhibitors to carboanhydrase

G. Klebe, Wirkstoffdesign, Spektrum Verlag, 2nd Edition 2009.

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Importance of chirality

Shares of the shares of 1983–2002 worldwide approved achiral, enantiomerically pure and racemic or
diastereomeric drugs. For the new launches in recent years, this relationship has clearly shifted in the direction of
enantiomerically pure compounds.

G. Klebe, Wirkstoffdesign, Spektrum Verlag, 2nd Edition 2009.

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1.3 Enzyme kinetics

k1 k3
(1) E+S E·S E+P k2 >> k3
k2

(2) Boundary conditions (a) [S] >> [E]

(b) d [ES]
=0
dt

(3) Michaelis-Menten equation

vmax · [S] v = reaction rate

k 2 + k3 k2
v =
Km = Michaelis constant = but when k2 >> k3, Km =
Km + [S] k1 k1

v
×
× Km large: weak binding
× Km small: strong binding
×
×

[S]
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(4) Lineweaver-Burk plot

Inverse Michaelis-Menten equation

1 Km 1 1
= · +
v vmax [S] vmax

1
v
× Km
vmax
×
×
1
vmax
×

̶ 1 1
Km [S]

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1.4 Enzyme inhibition

Classification of enzyme inhibitors (1) by target

N. Dunlap, D. M. Huryn, Medicinal Chemistry, CRC Press, 1st edition 2018

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Classification of enzyme inhibitors (2) by type of interaction

N. Dunlap, D. M. Huryn, Medicinal Chemistry, CRC Press, 1st edition 2018

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Example: Transpeptidase

Google images 46

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Example: Transpeptidase

Google images 47

Classification of enzyme inhibitors (2) by site of binding

N. Dunlap, D. M. Huryn, Medicinal Chemistry, CRC Press, 1st edition 2018

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Classification of enzyme inhibitors (3) by mode of inhibition

N. Dunlap, D. M. Huryn, Medicinal Chemistry, CRC Press, 1st edition 2018

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Lineweaver-Burk plots Noncompetitive inhibitor

1
v

Competitive inhibitor
1
1 vmax
v
1
[S]
̶ 1
Km

1 Uncompetitive inhibitor
vmax
1
1 v
[S]
̶ 1 ̶ 1
Km Km

Red lines: substrate alone 1

Blue lines: inhibitor + substrate vmax
1
[S]
̶ 1 50
Km

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IC50 Determination

 Inhinitor concentration, at which a biological process is inhibited by 50%

- cell growth (cell count)
- enzyme activity (reaction rate)
- receptor regulation +/-

% inhibition
IC50
100 ×
× ×
××
×
×

×
50 ×
×
×
× ×
× ×
× × ×
log [ I ]

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Concentration dependence of enzyme affinity / Cheng-Prusoff equation

 In the presence of a competitive inhibitor, the affinity of  Cheng-Prusoff equation

the enzyme for its substrate decreases → Km becomes - definition via IC50
larger - better comparison of
Ki values

Km [E]·[I] IC50
Kmobs = · [ I ] + Km with Ki = Ki =
Ki [ E·I ] [S]
1 +
Km

Kmobs

Km
Ki

Km

[I]

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1.6 Inhibitor development (1) treatment of hypertension

Renin-angiotensin-aldosterone system

Wikimedia commons
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Proteases

 Catalyze the hydrolysis of peptide bonds

 Contribute to physiological processes of

- Digestion
- Blood clotting
- Catabolism
- Apoptose

 → Overactivity and misactivity induce many diseases

 Peptide hydrolysis
- unspecific
- highly specific by recognition of certain AS sequences or motifs

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Protease mechanism

N. Dunlap, D. M. Huryn, Medicinal Chemistry, CRC Press, 1st edition 2018

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Protease classes

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Angiotensin converting enzyme (ACE)

Angiotensin I

Crystal Structure of Human Angiotensin Converting Enzyme in complex with Lisinopril

Protein Data Bank in Europe, https://www.ebi.ac.uk/pdbe/entry/pdb/1o86

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ACE catalytic reaction

Angiotensinogen (452 AS)

Renin (kidneys)

Angiotensin I (10 AS)

H2N-Asp-Arg-Val-Tyr-Ile-His-Pro-Phe-His-Leu-CO2H

ACE (lung, blood vessels, kidneys)

Angiotensin II (8 AS)
Vasoconstrictor
H2N-Asp-Arg-Val-Tyr-Ile-His-Pro-Phe-CO2H Blood pressure

ACE 2 (lung, blood vessels, heart, colon, kidneys)

Angiotensin 1-7 (7 AS)

Vasodilator
H2N-Asp-Arg-Val-Tyr-Ile-His-Pro-CO2H Blood pressure

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ACE inhibitors

Teprotide

Bothrops jararaca

Wikimedia commons
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ACE inhibitors

N. Dunlap, D. M. Huryn, Medicinal Chemistry, CRC Press, 1st edition 2018

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N. Dunlap, D. M. Huryn, Medicinal Chemistry, CRC Press, 1st edition 2018

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1.7 Inhibitor development (2) treatment of hypercholesterolemia

Role of cholesterol

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Wikimedia commons

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Cholesterol biosynthesis

Front. Biosci. 2014, 19, 416. 63

Cholesterol biosynthesis – Mevalonate pathway

HMG-CoA

HMG-CoA Reductase

Breitmaier
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HMG-CoA Reductase mechanism

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HMG-CoA Reductase: inhibition by statins

Synthetic statins

Natural statins

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2022

2009 2022

2009

https://njardarson.lab.arizona.edu
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2. Receptors as drug targets

 Receptors: transmembrane proteins with external binding site

 → external stimulus → cellular response
 Regulation of cellular activity in entire organs
 Activated through
- neurotransmitters: neuronal receptors
- hormones: hormone receptors
 Activating ligand, the ‘agonist‘ binds and is released again; no catalytic reaction
involved
 Deactivating ligands are ‘antagonists‘
 Three types of membrane receptors
- Ion channel receptors
- Kinase receptors
- G-Protein coupled receptors

 Study of ligand-receptor interaction is more difficult as receptors cannot be isolated like

enzymes

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Nervous system

VectorMine / Shutterstock.com
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Neuronal vs. hormone receptors

G. L. Patrick, An introduction to medicinal chemistry, 6th edition

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Induced fit model

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Neurotransmitters and hormones

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2.1 Ion channel receptors

 Channel shaped proteins with hydrophilic AS on the inside

 Enable ions to traverse the cell membrane through their pores

 Specificity for respective ion: Na+, K+, Ca2+, Cl-

 Cellular elektrolyte concentration ↔ membrane potential

 Essential for neurotransmission and muscle function

 Ligand-gated ion channels (LGICs) vs. Voltage-gated ion channels (VGICs)

 Receptor malfunction is associated with disease

- heart diseases
- neurological disorders
- chronical pain
- etc.

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Ligand-gated ion channel receptors (LGICs)

G. L. Patrick, An introduction to medicinal chemistry, 6th edition

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Nicotinic acetylcholin receptor (nAChR)

Nicotinic acetylcholin receptor (nAChR)

(Wikipedia)
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Ligand-gated ion channel receptors: examples

N. Dunlap, D. M. Huryn, Medicinal Chemistry, CRC Press, 1st edition 2018

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Voltage-gated ion channel receptors (VGICs)

N. Dunlap, D. M. Huryn, Medicinal Chemistry, CRC Press, 1st edition 2018

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Action potential

Threshold voltage
Na+-channels close
Repolarization
K+-channels open

Depolarization
Na+-channels open

Resting potential Stimulus

Spektrum.de
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Voltage-gated ion channel receptors: examples

N. Dunlap, D. M. Huryn, Medicinal Chemistry, CRC Press, 1st edition 2018

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2.2 G-Protein coupled receptors (GPCRs)

 Transmembrane proteins that steer signal transduction into the cell

 Ligand neurotransmitter or hormone

 Large family of receptors, > 550 in humans

 Binding of extracellular ligand → G-protein is bound at the interior part of receptor and
fragments → intracellular effector is activated → secondary messengers are
released

 Secondary messengers:
- Inositoltriphosphate, IP3 → induces release of Ca2+ → activates kinases

- cycloAMP → activates kinases

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GPCR activation

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GPCRs overview

N. Dunlap, D. M. Huryn, Medicinal Chemistry, CRC Press, 1st edition 2018

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2.3 Receptor regulation

Diseases caused by receptor malfunction

 Agonist concentration is to high → cell „overheats“ → administration of antagonist
 Agonist concentration is too low → cell / organ does not fulfill function → administration of
agonist

Types of agonists
 Agonist = activating ligand
 Partial agonist = substance that partially fulfills role of an agonist to give a limited biological
response
 Inverse agonist = substance with activity of an antagonist, but with additional reduction of
spontaneous activity of the receptor

Spontaneous activity
 Ligand-independent activity of the receptor
 Chemical equilibrium between active and inactive receptor conformations

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Partial agonists

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Antagonists

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Allosteric antagonists

natural
toxines

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Receptor desensitization

Permanent binding: agonist becomes antagonist

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Cell sensitization

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Dose-response curves

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Affinity, effectivity and potency

Affinity

 Measure of the binding strength ligand ↔ receptor

Effectivity

 Measure of the maximal biological effect of a ligand

- Ligand with a high affinity does not necessarily have high effectivity

Potency

 Relation between concentration of the ligand and defined biological effect

- Ligand can be potent but poorly effective

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Determination of affinity: Scatchard equation

Kb [L] · [R] ?
(1) L+R L·R Kd =
Kd [L·R]

(2) [Rtot] = [R] + [L·R] [R] = [Rtot] ̶ [L·R]

[L] · ( [Rtot] ̶ [L·R] )

(3) Kd =
[L·R]
[L·R]

[L·R] [Rtot] ̶ [L·R] [L]

=
[L] Kd
1
̶
Kd
[L·R]
For = 0 [L·R] = [Rtot] [Rtot]
[L]
[L·R]

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Determination of affinity: radioligand method

(1)  Known ligand of a given receptor is labelled with radionuclide (3H, 14C, 18F, 131I, 35S) to give
radioligand L*

 Addition of L* to cell culture or tissue, equilibration

 Separation of unbound radioligand L*

 Measure of radioactivity in cell culture or tissue, to give [L*·R]

 Repeat for several concentrations of L*, construct Scatchard plot

1
 Scatchard plot gives ̶ = ̶ Kb [L·R]
Kd
L*
[L]
L* + L (competitive)
(2)  Repeat (1) and additionally add the new ligand
L* + L (allosteric)
L for which affinity is to be determined
1
 L displaces L* Slope: ̶
Kd
 Measure decrease of radioactivity in cell [Rtot]
culture or tissue
[L·R]

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Determination of IC50 (mean inhibitory concentration)

 Plot %-fraction of bound radioligand L* versus log [displacing ligand] (which is log [drug])

 The drug is a competitive antagonist here

% L* bound drug 1 drug 2

IC50 IC50
100

50

log [drug ]

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Alternative method: Schild analysis

(1)  Receptor of interest has a known agonist, the natural ligand L

 Record dose-response curve

 Determine EC50 for the natural ligand

= mean effective concentration of agonist
= concentration that induces 50% of the maximum biological effect E (response)

Eobs

Emax
agonist
EC50
1

0.5

log [agonist]
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Alternative method: Schild analysis

(2)  Record dose-response curves for the agonist with increasing concentrations of a
competitive antagonist

Eobs
agonist
Emax
agonist + antagonist
EC50 EC50
1

antagonist
3 concentrations
0.5
agonist only

log [antagonist]

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Alternative method: Schild analysis

(3)  Construct Schild-plot

EC50 (agonist)
Dose ratio r =
EC50 (agonist + antagonist)

Schild equation log (r -1) = log [antagonist] ̶ log Kb

log (r -1)

log [antagonist]
̶ log Kb

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