UNIT-I

Points to be covered in this topic

......._. □ INTRODUCTION
......._. □ STAGES OF DRUG DISCOVERY
....._._. □ STAGES OF DRUG DEVELOPMENT
............ □ LEAD DISCOVERY
............ □ ANALOG BASED DRUG DESIGN
( CADD ]

r- Structure based
drug design
______
..... I
r _,._: Ligand based
drug design -.

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□ INTRODUCTION
• Drug discovery involves identification of the compound which have the
potential to be converted into a therapeutic product.
• Drug discovery is the initial phase characterized by a search for
appropriate targets or effects and identification of small molecules or
biologics that selectively modulate those targets.
• Drug discovery and development is complex, time consuming, costly
process which carries commercial risk.
• Discovering and developing new treatments for diseases and other
medical conditions is a lengthy and expensive process. Millions of
dollars and years of work is involved in getting a therapeutic product
manufactured, tested, approved and marketed for use of patients.
• Drug discovery and development are broadly divided into two category.
a) Preclinical evaluation:- This step validates the safety and biological
activity of a therapeutic compound through in vitro and animal studies.
b) Clinical trials:- It follow preclinical studies and are designed to
determine the safe and most effective dosages, route of a dministra tion,
efficacy (how well the therapeutic compound works) a nd patient
outcomes.

□ STAGES OF DRUG DISCOVERY

In vivo
Disease
selection Studies
l.ead
01:acovety

Th•Dn,g
0.v•lopm•nt
,,oc..,

Hl9h•Thro119hpu1 I Longhudlnal I Non•lnvaslv•

In Vivo Imaging Solutlon1 to Support Drug Development

from FWIFILM Vlsuallonla
•!• Disease selection:- It is important to concentrate on disease where
there is a need for new drugs.
•!• Drug target identification
• Once a therapeutic area has been identified, the next stage is to identi fy a
suitable drug target (e.g.. receptor, enzyme or nucleic acid).
• To understanding of which, bio macromolecules are involved 1n a
particular disease state is also important.
► Discovery of drug targets
• If a drug or a poison produces a biological effect, there must be a
molecular target for that agent in the body.
• Many early drugs such as the analgesic morphine are a natural product
derived from plants, and interact with a molecular target in the human
body.
► Specificity and selectivity of target between species
• The more selective a drug is for its target, the less chance that it will
interact with different targets and have undesirable side effects.
► Specificity and selectivity of target within the body
• Selectivity is also important for drugs acting on targets within the body.
These inhibitors should ideally interact with a specific kind of receptor
rather than a variety of different receptors. For example, receptor
agonists and antagonists.
; Targeting drugs to specific organ and tissues
• Targeting drugs against specific receptor subtypes often allow drugs to be
targeted against specific organs or against specific area of the brain.
•!• Lead discovery:- lead
Discovery

• Once the therapeutic target has been identified, 111\

scientists must then find one or more leads ( e.g., ~
• chemical compounds or molecules) that interact with the therapeutic
target so as to induce the desired therapeutic effects, e .g., through
a ntiviral or antibacterial aclivity.
•!• Medicinal chemistry:-
• It prepare -or select appropriate compounds for biological evaluation that,
if found to be active, could serve as lead compounds.
• They then evaluate the structure-activity relationships (SAR) of analogous
compounds with regard to their in vitro and in vivo efficacy and safety.
•!• In vitro studies:-
• In vitro tests do not involve live animals. Inst ead, specific tissues, cells,
or enzymes are used.
• Enzyme inhibitors can be treated on the pure enzyme in solution .
• For example, HIV protease has been cloned and expressed in the
bacterium E.coli.
• A variety of experiments can be carried out on this enzyme to determine
whether the enzyme inhibitor is competitive or non-competitive, and
to determine ICSO values.
•!• In vitro studies:-
• In vivo test on animals often involve inducing a clinical condition in the
animal to produce observable symptoms.
• The animal is then treated to see whether the drug alleviates the problem
by eliminating the observable symptoms.
• For example, the developments of non-steroidal anti-inflammatory drugs
were carried out by inducing inflammation on test animals, then testing
drugs to see whether they relived the inflammation.

□ STAGES OF DRUG DEVELOPMENT

• Drug discovery normally refers to the process of taking a compound that
has been identified through the steps necessary to bring it to market.
•!• Preclinical trials:-
• Preclinical development is the stage of research b~tween drug discovery
a nd clinical development, which typically includes:
 • Develop1nent of synthetic process that will enable the compound to be
manufactured in reproducible purity on large (multi kilogram) scale.
• Develop1nent of a for1nulation, in most cases a solution or suspension of
the drug that can be administered to animals in toxicity tests and a
solution or suspension or pill that can be administered to human s 1n
clinical trials.
• Toxicity testing in animals under conditions prescribed by the regulatory
authorities in the region where the clinical trials will occur (the FDA in the
US; the European Medicines Agency in Europe; the Japanese Ministry of
Health and Welfare in Japan).
• Following toxicity studies, gaining permission from the regulatory
authorities to administer the drug to human. In the US, such permission
is obtained through the submission of the FDA of an Investigational New
Drug (IND) application which summarizes the discovery and preclinical
development research done to date.

•!• Clinical trials:-

• Clinical trials are used to determine whether new biomedical or
behavioural interventions are safe, efficacious, and effective.
• Clinical development is normally conducted in three phases (Phase 1-111)
prior to applying for regulatory approval to market the drug:

Preclinical Phase 1 FDA Review

To Confirm
Safety and
Effectiveness

Drug Approved for Drug Submitted

Drug Approved
Testing in Humans for FDA Approval
, Phase I: Clinical trials test a new biomedical intervention in a small
group of people (e.g., 20- 80) for the first time to evaluate safety (e.g.,
to determine a safe dosage range, and to identify side effects).
, Phase II: Clinical trials study the biomedical or behavioral intervention
in a larger group of people (several hundred) to determine efficacy
and to further evaluate its safety.
', Phase III: Studies investigate the efficacy of the biomedical or behavioral
intervention in large groups of human subjects (from several hundred
to several thousand) by comparing the intervention to other standard or
experimental interventions as well as to monitor adverse effects, and to
collect information that will allow the intervention to be used safely.
► Phase IV: Studies are conducted after the intervention has been
marketed. These studies are designed to monitor effectiveness of the
approved intervention in the general population and to collect
information about any adverse effects.

□ LEAD DISCOVERY
• Once a target & a testing system has been chosen, the next is to find a
"Lead Compound" which shows the desired pharmaceutical activity.
• A lead compound is generally defined as a new chemical entity that could
potentially be developed into a new drug by optimizing its beneficial
effects and minimizing its side effects.
• Lead compounds are typically used as starting points in the drug design
to give new drug entities.
• Drug Design strategies can be used to . improve the compound's
pharmacodynamics and pharmacokinetic properties.
• It is the process of chemical modification of lead molecules and their
subsequent characterization in order to obtain drug-like compounds.
• The developed leads are characterized by in vitro and in vivo biological
activities, physicochemical properties, pharmacokinetic and
toxicological properties.
• Lead optintization includes selection of ligand libraries, and then
ntaking chemical modifications to molecules and characterize them
with suitable properties to become a drug.
• Lead opti1nization includes identifica tion of pharmacophores,
opti111ization of functional groups, structura l activity re lations hip
stud ies, and ho1nologation
•!• Serendipitous drug discovery:-
• It is also called lead discovery without a lead (Finding something new
while looking for something else), accidental or unexpected drug
discovery is called serendipitous drug discovery.
• Penicillin discovery- Staphylococcus culture contaminated with mold
• Warfarin discovery- Catties fed with clover hay
• Nitrous oxide discovery as anaesthetics (nitrogen fillings released NOi)
• Cisplatin discovery- Effects of electric field on E. coli growth (Platinum
conducting fields)
• Saccharin discovery
• Lithium discovery

~
~
?i
,,,,c.. .
H
= 0
OH
CH 2 NH ~ S CH3 II
HC, ,,,,c ...
0
~N
"__/c13 ,
CH 2 ' CH3

C 0
Penlclllln I/ ' OH
0
Warfarln

0
Cl i.&o
I s~
11 2 N- Pt - Cl \
NH
I Li
Nll 2
0 Lithiun1
Ctsplattn Saccharin
•!• Rational approaches to lead discovery based on
traditional medicine:-
• Rational approaches have become the major route of Jea d discovery.
• The first step is to identify the cause of disease state .
, Many diseases arise from:
• Imbalance of particular chemicals in the body.
• Invasion of foreign organism.
• Abnormal cell growth .
, The effect of imbalance can be corrected by:-
• Antagonism or agonism of a receptor.
• Inhibition of particular enzyme
• Inhibition of enzymes of foreign organism .
• Interference with biosynthesis of DNA.
• Inhibition of abnormal cell growth .
• Lead compound were obtained from the following sources.
i. Plant:-
• Morphine is a pain 1nedication of the opiate family that is found naturally
in a number of plants and animals.
• In 1805, morphine was first isolated from opium by Sertumer
(German pharmacist)
• Schaumann first identified and recognized the presence of a
quaternary carbon aton1 in the morphine molecule, in the field of drug
design of narcotic analgesics.
• Intensive research further led to the evolution of Pethidine
(meperidine) which incidentally combines both the properties of
morphine and atropine.
HO

Morphine Pethidine
• Ehrhardt suggested a general formul a relevant to the analgesic activity
in 1919 as below:
0
I
X-C- CO R

•
'
Ar
Where, Ar is aromatic ring and X is basic side chain and carbonyl
function in the form of ester, ketone or an amide. Later on general
fornntla is modified as follows:

COR Cf I
I / 3
C-(CH 2 )n-N,
CH 3

~ I
~

• Successfully led to the development of the following three narcotics:-

0
/ \N-CH2
\.._J ci2
C

rf 't)
Methadone Dextromoramid

ii. Microbes:- Most of antibiotics as lead are obtained from microbes as

follows:-
0 0
II II
R-C-HN R-C-HN s

.Ai--N .Ai--N
X
o=c
I C00H
COOH
Penicillin Cephalosporin
iii. Anhnals:- Epibatidine is obtained from frog skin
N Cl
"=:
Epibatidine
HN

iv. Marine:-
• Laminine is obtained from Laminaria angustata, it is having hypotensive
activity.
• Ara-C is obtained from Caribben sponge, which is having anticancer
activity.

HO

Ara-C

OH OH

• 2-cyno, 4,5-dibromoprole is obtained from Agelaoriods, it is having

antimicrobial activity.
Br

Br
NH Br
2-cyno,4,5- dibromoprole
• Aeroplysinine 1s obtained from asparagops1s taxiformis, having
antimicrobial
OCH3
Br Br

OH

Aeroplysinine
•!• Random screening
• Screening refers to the exercise to conducting a biological assay on a
la rge collection of contpounds to identify those compound s that have
the desired activity.
• Initially, these compounds may bind weakly to the target and are known
as the hits. Hit can be considered as predecessor to leads.
• It includes screening of all new chemical entities obtained from natural
source or synthetic chemical libraries for multiple targets.
• This method requires huge cost and time, but new structures with
unexpected and unknown activity can be explored.
• This type of screening is applicable when the receptor is unknown, and the
availability of High Throughput Screening (HTS), large ligand libraries
could be screened.
• Examples for drugs discovered through random screening - streptomycin,
tetracycline.
► Fragment based screening:-
• To identify simple molecules (fragments) possessing typically modest
affinity for a target, with the intent of connecting two or more of these
fragments to create a useful lead compound. EXAMPLE (X-ray
crystallography or NMR spectrometry)
► Computational approaches:-
• The structure of several lmown ligands, computational approaches may be
used to design potential lead compounds.
• The screening of organisms became very popular after the discovery of
penicillin.

krffnlng ~ Fragment Hits c:::> Design

Fragment based screening

Computational approaches
•!• Non- Random screening
• This ruethod of screening is also called targeted or focused screening, is
also called narrow approach or more focussed screening. This type of
screening is applicable to compounds which are uncovered in random
scr eening.
• The 1nolecules with structural similarity are screened for the selected I
target, which increases the chance or development of successful drug•
like molecules.
•!• Discovery of drug through drug metabolism:-
• During drug metabolism studies, metabolites (drug degradation products
generated in vivo) that are isolated are screened to determine if the
activity observed is derived from the drug candidate or from a metabolite.
► Examples:-
• SUlindac sulfide is the active metabolite of Sulindac, which exhibits
anti-inflammatory activity, Terfenadine was found to be cardiotoxic,
when its metabolism is inhibited by certain antifungal drugs.
• Fexofenadine is the metabolite of terfenadine, which is a safer drug,
does not exhibit drug interactions
F

Q
OC
,.-()
~I
CH 2
I '/ '/
OH
tt! CH1 N :-.._
~
o=c
0
CH2 CH2
I H3 C
OH
H
' c\
c.,,, Terfenadlne
Sullndac 3
C:11 3

NH -f_O

j-oH
Cl ....-!! N

Oxazepam
• Cetirizine is the 1netabolite of Hydroxyzine, discovered from metabolic
studies
• Oxazepa111 is the 1netabolite of Diazepam, discovered from metabolic
studies.
•!• Discovery of drug through clinical observation:-
• S0111eti1nes a drug candidate during clinical trials will exhibit more th a n
one pharntacological activity, that is, it may produce a sid e effect. This
contpound, then, can be used as a lead for the secondary activity.
► Exan1ples:-
• Sulpha drug sulphathiazole used specifically for treating typhoid,
lowered blood glucose drastically. This led to the development of
sulfonylureas as oral hypoglycaemic agents
• Sildenafil designed as antianginal drug possess adverse effect as
penile erection, which led to relaunch the drug in treatment of erectile
dysfunction, which was a blockbuster drug.

H 3 C- N
t \N - fl S
\__/ II
0

Sulfa drug
Sildenafil

• Clonidine was discovered as a nasal decongestant, the adverse effect of

it is sedation and lowering of blood pressure. Further studies on it led
to development this drug as a antihypertensive drug.

Cl N
NH-<]
NH
r.I

Clonldlne
 --- ---

□ ANALOG BASED DRUG DESIGN

• Analog design is defined as the modification of a drug molecule or of I
'
any bioactive con1pound in order to prepare a new molecule showi ng
1
chemical or biological similarity with the original model compou nd.
•!• Ob jective of analog based drug design:-
• Analogue based drug design modifies the chemical structure of the lead
compound having desirable pharmacological property w ith
1
minimizing the adverse effects, and enhance the drug-likene ~s
features such as physicochemical properties that could result in a better
therapeutic agent.
• Analogues in pharmacological study design aims to understand the
biological or pathophysiological phenomenon of disease.
•!• Bioisosterism:-
• Isosteres are defined as those compounds or functional groups of
atoms that have same number and arrangement of electrons is called
as Isosteres.
• Bioisosteres are the compounds or groups that possess nearly equal
molecular shape, mass, volume, having approximately same
electronic distribution, exhibit similar physical properties such as
hydrophobicity, and having similar physical and chemical properties
eliciting a similar pharmacological effect.
• This term coined by Harries L. Friedman and extended by Alfred
Burger.
•!• Classification of bioisosteres:- There are two types of isosteres:
• Classical isosteres
• Non-classical isosteres
1. Classical Bioisosteres:- They have similarities of shape and
electronic configuration of atoms, groups and molecules which they I
replace. Various exa111ples are as follows:-
a) Univalent or monovalent atoms:-
F,H OH., NH F, OH, NH or CH 3 for H SH, OH Cl, Br, CF3
b) Bivalent or Divalent atoms and groups
- CH= S- - CH = O- - CH = NH <= CH-

- CH 2 - - NH- - O- - 5-

c) Trivalent atoms and groups

- CH = - N= - P= - As =

d) Tetravalent atoms and group

= ~= = C=
__
-
....
r -
+
= As =

e) Ring equivalents

0 0 0
2. Non-classical Bioisosteres:- They do not obey the stearic and
electronic definition of classical isosteres.
• Non-classical bioisosteres are functional groups with dissimilar valence
electronic configuration.
a) carboxyl (COOH) bioisosteres

- S0 2 NH 2 - CO NHOH - CONHCN

b) Hydroxyl (OH) bioisosteres

- NHCONH 2 - NHS0 2CH 3 - NHCN

c) Amide {CONH 2) bioisosteres

0 CF3 ~
\ ck.NH
\C
'NH II \

d) Halogen isosterism
CJ CN CF3
e) Retroisosterism
0 0
II II
C C
R/ 'o ---•► 0 / ' R
I I J
R1 R

•!• Bioisoste r ic replacement strategies

• lsosteric modification involves the replacement of a n atom , or group of
atoms, in a molecule by another group with similar electronic and steric
configuration.
• Two molecules or molecular fragments containing an identical n umber
and arrangement of electrons should have similar properties are termed
as isosteres, e.g. CO, N2 , CO 2 , N2 O, CH 2 N2 , CH 2 =CO and CH4.
► CASE STUDY 1:- The design of captopril
• The design of ACE inhibitors demonstrates how it is possible to design
drugs for a protein target in a rational manner, even if the structure of
the target has not been determined.
• First of all, it was assumed that the active site contained the zinc ion and
arginine group. Succinyl praline was chosen, since praline is present on
the terminus of teprotide (a known inhibitor of ACE).

0
HO)l_cH[
CH 2
y
0
9
N

C0 2H
,,/·y\
Glu- Trp - Pro - Arg - Pro - Gln - Ile - Pro
CO 2H
Succtnyl praline Teprotide

• The next step was to introduce a better group the carboxylate ion to
interact with zinc, and it was discovered that a thiol group led to
increased activity. This resulted in captopril, which was the first non-
peptide ACE inhibitor to become commercially available

Development of captopril
,,. CASE STUDY II:- The design of Oxam niquine
• The first stage in the development of oxamniquine was to find a lead
con1pound, and so a study was made of compounds that were against the
parasite. The tricyclic structure lucanthone was chosen.
• It was decided to simplify the structure to see whether the tricyclic
syste111 was really necessary. This gave a compound called mirasan .

CH 3 I C-- H~
L J

NH CH 2
' NH
A CH 3 NHCH 2CH 2 N
\
C,H'. i

HO - CH 2
oxamnlquine s
/ C2Hs CH 3
NHCH 2CH 2N, Lucanthone
C2Hs

Cl
CH 3
Mirasan
• The optimum structure based on these results was structure (l). It has one
asymmetric center and, as one might expect, the activity was must
greater in one enantiomer than it was in the other.
R
I
Asymmetric centre ....
. (N (:
HN N

0 2N X Cl
CH3 Cll 1
Cll 3
1 2 3

The optimum structure (1) and thetricyclic structure (2) and (3)
• The tricydic structures (2) was also constructed. However, some conflicting
results were obtained compared with the previous results for
structures (1).
• Adding a further methyl group to the aromatic ring to give structure (3)
with increased activity. The resulting increase in activity suggests that a
better fitting conformation is obtained for the binding site..
• Compound (3) was t hree times more active than structure (1). However,
structure (1) was chosen rather than 3 based on preliminary toxicity
results, as well as the fact that it was cheaper to synthesize.
• The methyl group on (1) was replaced by a hydroxyl methylene group to
give oxamniquine. The drug was put on the market in 1975.

► CASE STUDY III: Design of cimetidine

• Cimetidine was developed by utilizing various lead modification
methods to uncover the first Histamine H, receptor antagonist and an
entirely new class drugs.

# N)I:CH 2' s.. .CH 2 ' ..,.. NH NHCH

\ /j CH 2 ~ 3
HN II
Cl I 3 NCN
Cimetidine
• The first lead compound, N-alpha guanylhistamine was very weakly
active as an inhibitor of histamine stimulation. Later it was found to be a
partial agonist, not an antagonist. A more potent isosteres, isothiourea
was synthesized.

QN
X_CHz . . . . ._ ....,....NH Y Nll 2
( /J CH 2
HN NH 2
Cll 3 +

N-alpha guany lhlstamlne Isothiourea isostere

• A purely competitive antagonist was given by homologation of the side

chain. No agonist effects were observed. When methylation and further
h omologation on the tbiourea nitrogen were carried out; the n-methyl
analog called burimamide.
 NY CH2 CH
( _j ' rn( 2'cH[NHY NHCH3
HN S
Burimamide
• Thiaburi1na1nide was developed which is about three times more
potent as a histamine H2 receptor antagonist in vitro than burimamide.

CH2 CH
( NY
_it ' s~ zC H;"NH'l( NHCHi
HN S
Thiaburtmamide
• cyanoguanidine (X-N-CN; cimetidine, Tagamet) and nitroguanidine (X=N-
NO,) were synthesized. They both were potent H, receptor antagonists,
comparable in potency to metiamide, but without granulocytopenia
( cimetidine was slightly more potent than, X=NO).

CH 2
# NX I ' s.,CH 2 ' ....,. NH NHCH
\ /J CH 2 ~ 3
HN II
CH 3 X

✓ Urea (X=O), guanidine (X=NH), cyanoguanidine (X-N-CN; cimetidine)

and nitroguanidine (X=N-NO) analogs
• Cimetidine was first marketed in the United Kingdom in1976; therefore,
it took 12 years from initiation of the H, receptor antagonist program
to commercialization.
• After the introduction of cimetidine to the US drug market, three other H2
receptor antagonists were approved, ranitidine (Zantac, Glaxo
Laboratories), which rapidly became the largest selling drug
worldwide, famotidine and Nizatidine.