Drug discovery and development is and always has been the most exciting part of clinical pharmacology. It is my attempt to compile the basic concepts from various books, articles and online journals. Feel free to comment.

1. Drug Discovery &
Development
Dr. Prashant Shukla
Junior Resident
Dept of Pharmacology
1/29/2015 1

2. Definitions:
 Drug: A chemical substance of known
structure, other than a nutrient or an
essential dietary ingredient, which, when
administered to a living organism,
produces a biological effect.
 Discovery phase: Identification of a new
chemical entity as a potential therapeutic
agent.
 Development phase: Compound is tested
for safety and efficacy for one or more
clinical indications, and in suitable
formulations and dosage form.1/29/2015 2

3. An important change:
The term “ drug discovery” is classical and
conventional. It should be replaced with
the term “ drug invention”.
In the past, drugs were discovered as
natural products and used as such.
Now, drugs are sculpted and brought into
being by pharmacologists in air
conditioned labs.
The term invention emphasizes this
process. 1/29/2015 3

4. New Drug definition (CDSCO)
According to Rule 122 E:
1/29/2015 4
(a) A new substance of chemical, biological or
biotechnological origin; in bulk or prepared
dosage form; used for prevention, diagnosis,
or
treatment of disease in man or animal; which,
except during local clinical trials, has not been
used in the country to any significant extent;
and which, except during local clinical trials,
has not been recognized in the country as
effective and safe for the proposed claim.

5. New Drug definition (CDSCO)
1/29/2015 5
 (b) A drug already approved by the
licensing authority, which is now proposed
to be marketed with modified or new
indications, dosage forms (including SR
dosage form) and route of administration.

6. New Drug definition (CDSCO)
1/29/2015 6
 (c) A fixed dose combination of two or more
drugs, individually approved earlier, and
now proposed to be combined for the first
time in a fixed ratio, or if the ratio of
ingredients in an already marketed
combination is proposed to be changed,
with certain claims, viz. indications, dosage
form (including SR dosage form) and route
of administration.

7. Stages of the New drug
synthesis:
 Drug discovery: Candidate molecules are
chosen on the basis of their
pharmacological properties.
 Preclinical development: Non-human
studies (e.g. toxicity testing,
pharmacokinetic analysis and formulation)
are performed.
 Clinical development: The selected
compound is tested for efficacy, side
effects and potential dangers in1/29/2015 7

8. *
1/29/2015 8

9. 1/29/2015 9

10. Drug discovery
 Usual time duration: 2-5 years
 Usual no. of projects: 100
 It consists of following components:
1. Target selection and validation
2. Lead-finding or Lead generation
3. Lead optimisation
4. Pharmacological profiling
1/29/2015 10

11. Reverse Pharmacology
 AKA target based drug discovery (TDD)
 A hypothesis is first made that modulation
of the activity of a specific protein
target will have beneficial therapeutic
effects.
 The reverse pharmacology approach
takes about 2 years to obtain a new drug
candidate.
 It is much faster and more efficient than1/29/2015 11

12. Comparison:
1/29/2015 12

13. Properties of ideal drug target:
1/29/2015 13

14. Various targets of drug action
1/29/2015 14
 The majority of drug targets are
a) G-protein coupled receptors (est total
5000)
b) Nuclear receptors (est total
>150)
c) Ion channels (est total 1000)
d) Enzymes (est total
uncertain)
 Currently we are exploiting only 120 distinct drug
targets.

15. Target identification strategies
 Gene Expression profiling: Genomics
 Focussed Proteomics
 Metabolic pathways analysis: Molecular
Biology
 Phenotype analysis
 Genetic association1/29/2015 15

16. Target identification
strategies...
 Inverse Docking: It is a computational
docking program in which a specific
small molecule of interest is tested
against a library of receptor structures.
 Bio informatics: It derives knowledge
from computational analysis of
biological data. It includes information
stored in genetic code, patients
statistics and scientific literature.
1/29/2015 16

17.  In the earlier times, the complex
biological responses of chemicals were
first seen. And then the drug targets
were explored for those chemicals.
 Now target identification has become the
first step of drug discovery.
 Limitation: Drugs which do not act
through receptors- Antacids, Osmotic
diuretics, Alkylating agents, Psoralens
and Activated charcoal can not be
1/29/2015 17

18. Target Validation
 To identify the most useful target among
the various identified targets, Target
Validation is done.
 Identified targets are analysed and
compared for
1. Ability to regulate biological and
chemical process/ molecules in the
body.
2. Association with a specific disease.
 It is done using genetic knockout,1/29/2015 18

19. Lead finding/ Lead generation
Approaches to new drug molecule
1. NEWER TECHNIQUES
 Molecular modeling
 Combinatorial chemistry
 Biotechnology
 Genetic medicine
 Immunopharmacology
1/29/2015 19
BIOLOGICS or
BIOLOGICAL
COMPOUNDS

20. Molecular modelling
 AKA Rational drug designing.
 Aided by three dimensional computer
graphics.
 Allows design of structure based on new &
known molecules.
 Highly selective targeted compounds are
created by enhancing desired properties of
known molecules. 1/29/2015 20

21. Combinatorial
chemistry
 It is systematic and repetitive covalent
connection of set of different building
blocks of varying structures to each
other to yield a large array of diverse
molecular entities.
 This process is
1. Faster, more efficient and cheaper.
2. Millions of compounds can be
synthesized : Chemical Compound1/29/2015 21

22. Limitations of Combinatorial
chemistry:
1. Building and maintaining huge
compound libraries is a costly
business.
2. Even the largest compound collection
represents only a fraction of the
number of “drug like” molecules that
exists in theory- estimated to be about
1060 .
1/29/2015 22

23. Biotechnology
 Therapeutic agents produced by
biotechnology rather than conventional
synthetic chemistry are called
Biopharmaceuticals.
 Involve the use of recombinant DNA
technology /genetic engineering
1. to clone & express human genes.
2. to produce large amount of hormones
like insulin.
1/29/2015 23

24. Genetic medicine
 Transfer of Genetic material
1. A single gene which is typical for gene
therapy.
2. Fragments of coding sequences (as in
RNA modification therapy- MC being anti
sense oligonucleotide strategy).
3. Entire genome (as in the case of SSC
and ESC therapy).
 Vectors are Viruses and Liposome-
plasmid complex.
 Diseases addressed: Hereditary
diseases like SCID, Haemophillia, etc.1/29/2015 24

25. Immunopharmacology
 Deals with finding the Biological
immune modifiers or Immuno-
modulating agents that cause selective
up-regulation or down-regulation of
specific immune responses.
 Examples include:
1. Rituximab- Anti CD 20 monoclonal
antibody for RA.
2. Adalimumab- Anti TNF-α inhibitor
antibody for RA. 1/29/2015 25

26. Lead finding/ Lead generation
Approaches to new drug molecule:
2. OLDER TECHNIQUES
 Animal models as human disease.
 Natural Products like plants , animals &
micro- Organisms:
1. Random screening approach
2. Ethnobiological approach
 Traditional Medicines.
 Modification of structure of known drugs to
develop “Me-too/ derivative medications/
follow-up drugs” drugs.
1/29/2015 26

27. Source of leads: Plants
1/29/2015 27
 Papaver somniferum: Morphine
 Atropa belladona: Atropine
 Rauwolfia serpentina: Reserpine
 Digitalis lanata: Digoxin
 Strychnos toxifera: d- TC
 Pilocarpus microphyllus: Pilocarpine
 Salix alba (Willow bark): Aspirin
 Bark of Yew tree: Paclitaxel
 Cinchona tree: Quinine

28. Source of leads: Animals
 Kraits: α- Bungarotoxin
 Marine invertebrates: Arabinose
nucleosides
 Cone snail toxin: Ziconotide (Prialt)
 Marine invertebrates: Bryostatin-like
compounds
 Dinoflagellates: Saxitoxin1/29/2015 28

29. Source of leads: Micro-
organisms Streptomyces notatum: Penicillin
 Streptomyces venezuelae:
Chloramphenicol
 Penicilium griseofulvum: Griseofulvin
 Streptomyces griseus: Streptomycin
 Streptomyces gradiae: Neomycin
1/29/2015 29

30. SCREENING
 The usual approach is to clone the
target protein- the human form. This is
because the sequence variation among
species is associated with
pharmacological differences and it is
essential to optimise for activity in
humans.
 An assay system is then developed to
measure the functional activity of the
target protein. 1/29/2015 30

31. Desired characteristics of the
assay:
1. Should run automatically (if possible,
with an optical read out e.g.
Fluorescence or optical absorbance).
2. Should be in a miniaturised multiwell
plate format- for reasons of speed and
economy.
 Robotically controlled assay has
become the standard starting point for
most drug discovery projects.
e.g. High through put screening1/29/2015 31

32. Virtual screening (VS)
 It is based on the computationally
inferred or simulated real screening.
 Advantages compared to laboratory
experiments are:
1.low costs.
2.Investigate compounds that have not
been synthesized yet.
1/29/2015 32

33. Virtual screening (VS)...
3. VS can be used to reduce the initial
number of compounds before using
expensive HTS methods.
4.The number of possible virtual
molecules available for VS is much
higher than those available for HTS.
 Disadvantage is that it can not substitute
the real screening.
1/29/2015 33

34. Two types of approaches used in
virtual screening
I. Target based virtual screening
(TBVS), or Receptor based virtual
screening
II. Ligand based virtual screening
(LBVS), or Similarity based virtual
screening.
1/29/2015 34

35. Target based virtual screening
(TBVS)
 Exploits the molecular recognition between
the ligand and a target protein information
about the target.
 Selection of chemical that has high affinity
for the target’s active site.
 Structural information can be determined
by Nuclear Magnetic Resonance(NMR) or
X-ray diffraction.
1/29/2015 35

36. Target based virtual screening
(TBVS)
 TBVS relies on 3D structures of protein
targets and on 3D databases of chemicals.
 TBVS allows the identification of structurally
novel ligands that may present interaction
modes similar to the already known ligands.
 Even new interaction pattern identification
with different parts of the target’s active
sites.
 This methodology uses virtual filtering of all1/29/2015 36

37. Ligand based virtual screening
(LBVS)
 There is no structural information about
the target.
 The screening focuses on physical and
chemical based searches among the
ligands.
 Through pharmacophore pattern
matching.
 On similarity searching using descriptors
that may be 1D, 2D or 3D.1/29/2015 37

38. Chris Lipinski’s rule of five
 Linear descriptors (1D) are used to
identify chemicals which do not violate
any rules for solubility and permeability:
1. H-bond donors <5.
2. Molecular weight <500.
3. Partitioning coefficient (Log P) <5.
4. H-bond acceptors <10 (=5×2).
 The “rule of five”name came from the
cutoffs all being multiples of five. But
there are only four rules.
1/29/2015 38

39. Ligand based virtual screening
(LBVS)
 The complete structure of the ligands can
be considered in the quantitative structure-
activity relationships (QSAR) methods.
 QSAR methods can make accurate
prediction of the relative conformation and
alignment of the ligands.
 LBVS are more limited than TBVS since it
is biased by the properties of the already
known ligands for a given target.
1/29/2015 39

40. High through put screening
(HTS) The “Real Screening”.
 It is the process of testing a large number
of diverse chemical structures against
disease targets to identify “hits”.
 Compared to traditional screening
methods, HTS is characterised by:
1. Simplicity
2. Rapidness
3. High information harvest
4. Based on ligand-target interaction
principle 1/29/2015 40

41. High through put screening...
 Various technologies used for HTS are:
1. Fluorescence
2. Nuclear Magnetic Resonance (NMR)
3. Affinity chromatography
4. Surface plasmon resonance
5. DNA microarray
 HTS can analyse around 10,000-
100,000 samples/day.
1/29/2015 41

42. End results of screens:
 Hit: A molecule with confirmed
concentration-dependent activity in a
screen, and known chemical structure.
 Progressible hit: A representative of a
compound series with activity via
acceptable mechanism of action and
some limited structure-activity relationship
1/29/2015 42

43. Lead Optimisation
The aim of this stage is:
1. Increase the potency of the
compound on its target.
2. Increase its selectivity.
3. Increase its metabolic stability.
Usually one project out of five passes this
stage.
1/29/2015 43

44. Lead Optimisation...
 Various steps:
1. Identification of the Pharmacophore
(relevant groups on a molecule that
interact with a receptor and are
responsible for the biological activity).
2. Functional group modification:
Modification of the group may enable
or disable certain biological effects.
1/29/2015 44

45. 1/29/2015 45
3. Structure-Activity relationship:
Some of these features are important for
the activity and the others are not.
(1) NH2 and sulfonyl (R) should be para.
(2) NH2 should be unsubstituted.
(3) Benzene ring should not be replaced
by other ring systems.

46. 4. Structure modification to increase potency
and therapeutic index:
A. Homologation: a homologous series is a
group of compounds that differ by a
constant unit, usually CH2.
B. Chain branching
C. Ring-chain transformation
Affects (1) lipophilicity,
(2) interaction with the enzyme or
receptor. It could increase or decrease
drug potency and therapeutic index.
D. Bioisosterism.
1/29/2015 46

47. 5. Quantitative structure-activity
relationships (QSAR-rational drug
design)
Based on the fact “the biological properties
of compounds are a function of its
physico-chemical parameters”.
Fundamental physicochemical parameters
a) Electronic effects: Hammett equation
b) Lipophilicity effects: Hansch equation
c) Steric effects: Taft equation1/29/2015 47

48. 6. Molecular graphics-based drug design: To
find a structure match, a computer
technology called DOCKING is used. It is
the computer-assisted movement of a
terminal-displayed molecule into its receptor.
 Docking algorithms deal with ligand
conformation prediction and orientation
within the target active site. It predicts the
various forces acting between target and
ligand.
 Scoring function is a mathematical function
to rank protein-ligand complexes according
to their predicted binding affinity.1/29/2015 48

49.  The main problem is that lead
optimisation often seems impossible
despite much ingenious and back-
breaking chemistry. It is because lead
compounds, like anti social teenagers,
refuse to give up their bad habits.
 In other cases, the compounds
although they produce the desired
effects on the target molecule and have
no other obvious defects, fail to produce
the desired effects in animal models of
disease. This implies that the target is1/29/2015 49

50.  Out of the above steps, Target
identification and Lead Finding is often
carried out in academic research
laboratories.
 Screening for biologic activity and
chemical modification of a known active
molecule are usually carried out in
industries due to their high costs.
 Translational research/ medicine or
Experimental medicine: The process of
moving from the basic science laboratory
to the clinic. It involves the pre clinical1/29/2015 50

51. 1/29/2015 51

52. Pre clinical development
 Usual time duration: 1.5 years
 Usual no. of Compounds: 20
 The aims of pre clinical testing are:
1. Pharmacokinetics
2. Short term toxicology
3. Formulation
4. Synthesis scale up
1/29/2015 52

53. Work falls in four categories:
1. Safety Pharmacology:
Pharmacological testing to check that
the drug does not produce any
hazardous side effects.*
2. Preliminary toxicological testing to
eliminate genotoxicity and to determine
the maximum non-toxic dose of the
drug (usually when given daily for 28
days, and tested in two species).
1/29/2015 53

54. Work falls in four categories:
3. Animal studies: Pharmacokinetic testing i.e.
studies on absorption, metabolism,
distribution and elimination in laboratory
animals like Mice, chicken, monkeys, and
guinea pigs.
4. Chemical and pharmaceutical
development:
a) Feasibility of large- scale synthesis and
purification
b) Stability of the compound under various
conditions
c) To develop a formulation suitable for1/29/2015 54

55. Animal studies: components
 Toxicology studies: Extended
programme in animals studies. These
could be acute, sub acute or chronic
toxicity studies.
1. Acute: 24-48 hours
2. Sub Acute: Few weeks
3. Chronic: For months
1/29/2015 55

56. Animal studies: components...
 Mutagenicity studies: comprises of in
vitro tests where either unicellular
organisms or tissue cultures are
exposed to the drug.
Following battery of tests is used:
1. Ames test in S. Typhimurium.
2. Cytogenetic assay in mammalian
cells.
3. Micronucleus assay in rodent
hematopoietic cells.
 First two tests should be completed
before Phase I study commences.
1/29/2015 56

57. Animal studies: components...
 Carcinogenicity studies:
Two animal species with low incidence
of spontaneous tumours are used. 3
doses- high, low and intermediate are
employed.
The study usually lasts for most of the
animal’s life.
Detailed autopsy and histological
examination are performed at the end of
the study.
1/29/2015 57

58. Animal studies: components...
 Reproductive studies: Extensive studies of
a potential drug in the pregnant animals is
mandatory.
PK variations and plasma conc. of the
drug in mother and foetus are recorded.
Aims: Teratogenic potential
Effect on gametes, uterine
growth, parturition, post natal
development and lactation.
1/29/2015 58

59. Animal studies: End
parameters1. Therapeutic dose =
Lethal dose(LD 50)/ Effective dose (ED
50)
2.Maximum Tolerated dose (MTD)
3.Minimal lethal dose (LD10)
4.No adverse effect level (NOAEL) dose: It
is the largest amount of drug which
causes no detectable adverse effect
with regards to morphology,
physiology, growth, reproduction and
life span of the organism exposed to1/29/2015 59

60. Animal studies: End
parameters...
NOAEL is calculated in at least three
species with one being a rodent.
NOAEL is extrapolated to humans.
5. Human equivalent dose (HED)= Animal
NOAEL x (Wanimal/ Whuman)1-b
where W is the weight in Kg and b is a
correction factor (equal to 0.67) used to
convert mg/kg to mg/m2
1/29/2015 60

61. Animal studies: End
parameters...
HED (mg/kg) = Animal Dose (mg/kg) x
[Animal Km / Human Km(37)]*
6. The dose to be used for initial human
studies is called “Maximum
recommended starting dose (MSRD)”
calculated as
MRSD = HED/ Safety factor (Sf)
Sf allows the interspecies variability in
drug disposition. Default Sf is 10.1/29/2015 61

62. Good laboratory practices
(GLP)
It is defined by the OECD (Organization
for Economic Co-operation and
Development) principles as
“a quality system concerned with the
organizational process and the
conditions under which non-clinical
health and environment safety studies
are planned, performed, monitored,
recorded, archived and reported.”
1/29/2015 62

63. Good laboratory practices (GLP)...
1/29/2015 63

64. Limitations of pre clinical
testing
1.Toxicity testing is time consuming and
expensive. 2-6 years may be required
to collect and analyse data on toxicity
for testing in humans.
2. Large no. of animals may be needed
to obtain valid pre clinical data. It
raises ethical issues.
1/29/2015 64

65. Limitations of pre clinical
testing...
3.Extrapolations of therapeutic index and
toxicity data from humans are
reasonably predictive for many but not
for all toxicities.
4. For statistical reasons, rare adverse
effects are unlikely to be detected in
preclinical testing.
1/29/2015 65

66. Alternatives to animals:
1/29/2015 66
 Micro-organisms
 Cell components
 Cell cultures
 Tissue cultures
 Tissues slices
 Isolated & perfused organs
 Computer modelling
1. In silico ADMET
2. Physiologically Based PK simulations

67. 5 R’s
1. Reduce the no. of animals used
to a minimum.
2. Refine the way that experiments are
carried out so that the effect on the
animal is minimized and animal
welfare is improved.
3. Replace animal experiments with
alternative (non-animal) techniques
wherever possible.
4. Rehabilitation When death is not the
end point.
5. Reuse Whenever and wherever
1/29/2015 67

68. What after preclinical phase??
Once the preclinical trials are over,
sponsors are required to submit the
“Investigational New Drug” application.
It contains information regarding:
1. Preclinical data: PK, PD &
Toxicological
2. Manufacturing data: Composition,
Manufacturing process, Stability &
Shelf life.
3. Protocol of clinical trials1/29/2015 68

69. In Silico drug design or CADD
1/29/2015 69
Target
Ident.
Target
Validation
Lead
Ident.
Lead Opt
Preclinical
Tox
Clinical
trials
Bioinformatics
Inverse docking
Protein pred.
Target
druggabilty
Tool compound
design
Lib. Design
Docking scoring
De novo design
QSAR
3 D- QSAR
Struc. based
opt.
In silico ADMET
PBPK
simulations
No options

70. Drug Discovery: Past & Present
Criterion Last century Present era
Drug
development
Predominantly
compound centred
Predominantly
target centred
Source of Leads Natural
Compounds
Natural +
Synthetic
compounds
Time taken Many years Few years
First step Finding
appropriate
biological
response
Finding
appropriate drug
target
Safety Lesser safe More safe
Screening Animal disease Virtual Screening/1/29/2015 70

71. Criterion Last century Present era
Animal use Frequent Relatively less
Ethical
Considerations
Less stringent More Stringent
No. of
Compounds
explored
Less More
No. of Targets
explored
Less More
Change in term Drug discovery Drug Invention
1/29/2015 71
Drug Discovery: Past & Present

72. Future Prospects
1/29/2015 72

73. Summary:
1/29/2015 73

74. 1/29/2015 74
Target
identification
Target
validation Lead finding
OLDER TECHNIQUESNEWER TECHNIQUES
Lead
Optimisation
Preclinical
Development
Clinical
Development
VS
HTS
HITS
LEAD COMPOUND

75. Thank you for your patience!
1/29/2015 75