DRUG DISCOVERY, NEW DRUG, STEPS, DRUG DEVELOPMENT, VIRTUAL SCREENING, HIGH THROUGHPUT SCREENING, preclinical, lipinski rule, lead, hit, QSAR, DOCKING

1. Principles of
Drug Discovery
& Development
Presented by…
Name – Dhara Mehta
Subject – PDTT
UNIT - 1

2. CONTENTS
2
01 Introduction
02 Phases
03 Target Id & validation
04 HIT Id & validation
05 Candidate Selection & Profiling

3. 01
Introduction
3
Drug – A substance intended for use in diagnosis, cure, mitigation, treatment, or prevention of
disease.
Drug discovery is initiated when there is some clinical condition or we want to find more efficacious
therapeutic derivative of already existing condition.
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.
So, whole process is basically developing a new drug from an initial idea to launch of therapeutic
product and it’s a complex process which can take 13-15 years and costs around 2 Billion USD.

4. 4
A new drug means ; a drug, including active pharmaceutical ingredient or
phytopharmaceutical drug. which has not been used in the country to any significant
extent has not been approved as safe and efficacious by Central Licencing Authority
(CLA) ie. DCG(1) with respect to its claims;
Or a drug approved by the CLA for certain claims and proposed to be marketed with
modified or new claims including indication, route of administration, dosage and dosage
form;
Or a fixed dose combination of two or more drugs, approved by CLA separately for
certain claims and proposed to be combined for the first time in a fixed ratio, or where
the ratio of ingredients in an approved combination is proposed to be changed with
certain claims including indication, route of administration, dosage and dosage form;
What is a "new drug"?....(CDSCO)

5. 5
Or . a modified or sustained release form of a drug or novel drug delivery
system of any drug approved by the Central Licencing Authority;
Or a vaccine, r-DNA derived product, living modified organism, monoclonal
anti- body, stem cell derived product, gene therapeutic product or xenografts,
intended to be used as drug.

6. Phases
6
Drug Discovery
Pre-clinical Development
Clinical Development
Regulatory Approval
Post Marketing Surveillance

7. 1) Target Identification
7
Target identification often involves genetics and utilizes molecular
biology techniques to perform a variety of studies in cell-based
models.
Common biological targets include proteins such as receptors,
enzymes, ion-channels, and transporters.
Data mining of available biomedical data has led to a significant
increase in target identification.
Afterward, scientists and researchers record the target’s
therapeutic characteristics.

8. Target
Identification
Tools
• Animal models
• Biomarkers
• Expression Profile
• Cell-line
• Data banks
8

9. 9
Target is disease-modifying and/or has a proven function in the pathophysiology of a disease.
Drug targets must be efficacious, safe, usable, and capable of meeting clinical and commercial requirements.
Modulation of the target is less important under physiological conditions or in other diseases.
If the druggability is not obvious (e.g. as for kinases) a 3D-structure for the target protein or a close homolog
homolog should be available for a druggability assessment.
Target has a favorable 'assayability' enabling high throughput screening.
Target expression is not uniformly distributed throughout the body.
A target/disease-specific biomarker exists to monitor therapeutic efficacy.
Properties of IdealTarget

10. Target Identification
Strategies
• Gene Expression profiling: Genomics
• Focussed Proteomics
• Metabolic pathways analysis: MolecularBiology
• Phenotype analysis
• Genetic association
10

11. Target
identification
strategies
11
• 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.

12. 12
Another powerful approach is to look for genetic
associations, for example, is there a link between a genetic
genetic polymorphism and the risk of disease or disease
disease progression or is the polymorphism functional.
Example – Alzheimer's Disease (AD) patients commonly
commonly have mutations in the amyloid precursor protein
protein or presenilin genes which lead to the production and
production and deposition in the brain of increased amounts
amounts of theAbeta peptide, characteristic of AD.
There are also examples of phenotypes in humans where
where mutations can nullify or overactivate the receptor, for
receptor, for example, the voltage-gated sodium channel
channel NaV, both mutations incur a pain phenotype,
insensitivity or oversensitivity respectively.

13. Limitation
13
• Drugs which do not act through
receptors- Antacids, Osmotic diuretics,
Alkylating agents, Psoralens and
Activated charcoal can not be
recognised

14. Target
Validation
Once identified, the target then needs to be fully prosecuted.
Validation techniques range from in vitro tools through the
use of whole animal models, to modulation of a desired
target in disease patients.
To validate targets, researchers use modern tools and
techniques such as disease association, bioactive
molecules, cell-based models, protein interactions, signaling
pathways analysis, functional analysis of genes, in vitro
genetic manipulation, antibodies, and chemical genomics.
Evaluation of its potential as targets.(Bioassay)
Finding pathway- Mechanism of Action.

15. Hit
Identification
15
Once a target is validated, the search for a hit
compound begins.
A hit compound is a molecule that has been
demonstrated to modulate the target of interest in an in
vitro biological assay.
Hits can be identified through a variety of methods with
high-throughput screening (HTS), virtual screening,
and fragment-based screening representing popular
approaches.
Hit is converted to Lead.

16. Source of
Lead
16
PLANT
Papaver somniferum: Morphine
Atropa belladona: Atropine
Rauwolfia serpentina: Reserpine
Digitalis lanata: Digoxin
Strychnos toxifera: d- TC
Pilocarpus microphyllus: Pilocarpine
Bark of Yew tree: Paclitaxel
Cinchona tree: Quinine

17. Source of
leads: Animal
17
Kraits: a- Bungarotoxin
Marine invertebrates:
Arabinosenucleosides
Cone snail toxin:
Ziconotide
Marine invertebrates:
Bryostatin- compounds

18. Source of leads:
Microrganisms
18
Streptomyces notatum: Penicillin
Streptomyces venezuelae:
Chloramphenicol
Penicilium griseofulvum:
Griseofulvin
Streptomyces griseus:
Streptomycin
Streptomyces gradiae: Neomycin

19. Lead
Generation
Techniques
Molecular modelling
Combinatorial chemistry
Biotechnology
Genetic medicine
Immunopharmacology

20. Molecular Modeling
20
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.

21. Biotechnology
21
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.

22. Genetic medicine
22
Transfer of Genetic material.
A single gene which is typical for gene therapy.
Fragments of coding sequences (as in RNA modification therapy- being anti
sense oligonucleotide strategy
Entire genome (as in the case of SSC therapy). Vectors are Viruses and
Liposome- plasmid complex. Diseases addressed: Hereditary diseases like
SCID, Haemophillia, etc

23. Immunopharmacology
23
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 Rheumatoid Arthritis.
2. Adalimumab- Anti TNF-α inhibitor antibody for RA.

24. SCREENING
24
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.

25. 25
Assay DevelopmentAndScreening
Assay development in drug discovery is a crucial component of drug discovery workflow.Assays are test
Assays are test systems that evaluate the effects of the new drug candidate at the cellular, molecular,
molecular, and biochemical levels.
HighThroughputScreening
HighThroughput Screening (HTS) uses robotics, data processing/control software, liquid handling
handling devices, and sensitive detectors to rapidly conduct millions of pharmacological, chemical, and
chemical, and genetic tests, eliminating hours of painstaking testing by scientists. HTS identifies active
identifies active compounds, genes, or antibodies that affect human molecules.

26. Desired
Characteristics
of the Assay
26
Should run automatically (if possible, with
an optical read out e.g. Fluorescence or
optical absorbance
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
screening.

27. Virtual screening (VS)
27
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.

28. 28

29. 29
VS can be used to reduce the initial number of compounds before using
before using expensive HTS methods.
The number of possible virtual molecules available forVS is much higher
much higher than those available for HTS.
Disadvantage is that it can not substitute the real screening.
Two types of approaches used in virtual screening
Target based virtual screening (TBVS), or Receptor based virtual
screening1
Ligand based virtual screening (LBVS), or Similarity based virtual
screening

30. Target based virtual screening (TBVS
30
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.

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(TBVS)TBVS relies on 3D structures of protein targets and on
and on 3D databases of chemicals.
TBVS allows the identification of structurally novel ligands that
ligands that may present interaction modes similar to the
already known ligands.
Even new interaction pattern identification with different parts
parts of the target's active sites.
This methodology uses virtual filtering of all Aunilahla linanda
linanda ina mahla datahana

32. Ligand based virtual screening (LBVS).
32
There is no structural
information about the
target.
The screening focuses
on physical and
chemical based
searches among the
ligands.
Through
pharmacophore patter
matching.On similarity
searching using
descriptors that may be
1D, 2D or 3D.

33. Lipinski Rule of Five
• Poor absorption or permeation are more likely when
there are:
1) More than 5 H-bond donors
2) The molecular weight is over 500
3) The CLog P is over 5 (or MLOGP is over 4.15)
4) The sum of N's and O's is over 10
• Substrates for transporters and natural products are
exceptions.
33

34. Ligand based virtual screening (LBVS)
34
The complete structure
of the ligands can be
considered in the
quantitative structure-
activity relationships
(QSAR) methods.
1
QSAR methods can
make accurate
prediction of the
relative conformation
and alignment of the
ligands.
2
LBVS are more limited
than TBVS since it is
biased by the
properties of the
already known ligands
for a given target.
3

35. 35
Aspect Ligand-based virtual screening Structure-based virtual
screening
Three- dimensional protein
structure
Unknown Known
Drug design information and
starting point
Drug design can be based on processes
using the known ligands of a target protein
as the starting point
Reliable information on the three-dimensional
structure and active sites of the target
protein can be obtained from x-ray
crystallography, nuclear magnetic resonance,
or three-dimensional structure databases,
and incorporated into a computer model;
compounds binding to the target can be
designed
Frequently used techniques Molecular similarity approaches,
quantitative structure-activity
relationships, pharmacophore models
Docking, molecular dynamics simulation
Screening Databases can be screened to find
molecules with similar fingerprints by
using the molecular fingerprints of known
ligands
Molecule database screening can be done by
various types of docking software
Process involved Selection of the data set and extraction of
structural/empirical descriptors, variable
selection, model construction, validation/
evaluation
An assortment of successive computational
stages is involved, including target and
database preparation, docking and
postdocking examination, and prioritization
of compounds for biological testing
Software programs used to
perform virtual screening
uNITY, MACCS-3D, Catalyst, Phase, ROCS Glide, FlexX, Gold, AutoDock Vina, AutoDock
4.0

36. HIGH THROUGH PUT
SCREENING (HTS)
The Real Screening
36
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

37. HIGH
THROUGH
PUT
SCREENING...
37
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.

38. End results of screens:
38
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

39. 39
Leads can also be obtained by molecular modeling aided by 3D computer graphics that allow the
allow the design of structures based on new and known molecules to enhance their desired and
and eliminate their undesired properties to produce highly selective targeted compounds.
A combinatorial chemistry wherein random mixing and matching of large numbers of chemical building
chemical building blocks to produce libraries of all possible combinations can also be attempted to get
attempted to get leads.
This technique generates billions of compounds, screened by high-throughput screening (HTS),
(HTS), meaning thousands a day.
If any of these compounds show a positive response, traditional laboratory methods are used to
used to manufacture them at a large scale.
Using biotechnology proteins as drugs, the use of recombinant DNA technology/genetic engineering to
engineering to clone and express human genes is another method used to obtain leads.

40. Lead
Optimization
40
Lead optimization is a process that begins with a
compound that displays a potential biological action and
confirms with the identification of the best compound.
Molecules are chemically modified and characterized to
obtain compounds with desired properties to become a
drug.
Leads are optimized for efficacy and potency in vitro and
in vivo, physiochemical properties, pharmacokinetic
properties, and toxicological aspects.
As this process requires simultaneous optimization of
multiple parameters it is time-consuming and costly.
Although this stage is a major hurdle in drug discovery it
contributes to turning a biologically active chemical into
an effective and safe drug in the drug discovery process.

41. Lead
Optimisation
41
The aim of this stage is:
Increase the potency of the
compound on its target
Increase its selectivity
Increase its metabolic stability.
Usually one project out of five
passes this stage.

42. 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.
• 3. S.A.R
42

43. 43
4. Structure modification to increase potency and
therapeutic index:
• A. Homologation: a homologous series is a group of
of compounds that differ by a constant unit, usually
usually CH2.
• B. Chain branching
• C. Ring-chain transformationAffects (1) lipophilicity,(2)
lipophilicity,(2) interaction with the enzyme or receptor.
receptor. It could increase or decrease drug potency and
potency and therapeutic index.
• D. Bioisosterism.

44. 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 equation
QSAR (Quantitative structure
activity relationship) is a
mathematical relationship
between a biological activity of a
molecular system and its
geometric and chemical
characteristics.

45. 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.

46. Candidate Selection
46
This candidate selection process will often include version and form screening
to identify potential salts and crystal forms with favorable properties.
Animal efficacy studies in additional models will continue and preliminary rodent
toxicology and genotoxicology will be assessed at this stage as well.
If pharmacokinetics in higher species was not conducted during lead
optimization, it will occur at this stage prior to selection of the clinical candidate
molecule.
Formulation development also often begins at this stage in support of animal
efficacy and toxicology studies.

47. Candidate Profiling
47
Once the clinical candidate molecule is identified, it moves into a host of profiling studies to
prepare for human clinical trials.
The optimized final version and form will be chosen and formulation studies to optimize the
drug product for clinical studies will commence, as will GMP synthesis of the active
pharmaceutical ingredient (API).
Rodent and higher species dose-range finding and repeat-dose, multi-day toxicology
studies are completed during this time.
Likewise, definitive genotoxicology is assessed under GLP conditions. Studies done during
candidate profiling will make up critical components of the Investigational New Drug (IND)
application, which must be evaluated and approved by the FDA prior to clinical trials.

48. Pre clinical
48
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

49. 49
Work falls in four categories:
1. Safety Pharmacology:Pharmacological testing to check that the
that the drug does not produce any hazardous side effects.*
2. Preliminary toxicological testing to eliminate genotoxicity and to
and to determine the maximum non-toxic dose of the drug (usually
(usually when given daily for 28 days, and tested in two species).
species).

50. 50
3.Animal studies: Pharmacokinetic
Pharmacokinetic testing i.e.studies
i.e.studies on absorption,
metabolism, distribution and
elimination in laboratory animals
animals like Mice, chicken,
monkeys, and guinea pigs.
4. Chemical and pharmaceutical
pharmaceutical development:a)
Feasibility of large-scale synthesis
synthesis and purificationb)
Stability of the compound under
various conditionsc)To develop a
a formulation suitable for

51. Animal Studies
Components
51
Toxicology studies
Mutagenicity studies
Carcinogenicity studies
Reproductive studies

52. 52
• https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3058157/
• https://www.fda.gov/patients/learn-about-drug-and-device-approvals/drug-
development-process
• https://www.unthsc.edu/college-of-pharmacy/research-and-innovation/drug-
discovery-and-development/
Reference

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