.

1. Various approaches used in rug
Design and Drug Discovery
Mr. Prashant Joshi

2. The “Drug”
• A Drug candidate is a ligand or macromolecular entity
that binds to the biological target and in this way either
initiates a process of mimicking or inhibiting biological
process in human body.
• The process of identifying new drugs is ……….drug
discovery.
Science 2004, 303, 1813-8

3. • Drug Discovery, 1900- 1970: Chemical and natural product libraries were used to identify lead
compounds. ~ Penicillin’s, Aspirin.
• Drug Discovery, 1970-80: Lead compounds were modified by traditional medicinal chemistry
methods largely relying on chemical modification of the lead compound. ~ Sulphonamides
• Drug Discovery, 1980-90: QSAR, Combinatorial Chemistry ~ ACE Inhibitors
• Drug discovery 2000 to 2010: Bioinformatics, In-silico drug design, Rational Drug design, 3 D
QSAR
In-vivo > In-vitro > In-silico.
• Drug discovery 2010 to current : Genome mining.
Drug design & Discovery Aspects
Yesterday, Today and Tomorrow

4. •Competitive Pharma environment: To remain competitive, bring 3-4
Drugs / year is compulsive task for pharma companies.
•Process patent will not help much for India.
• GATT & TRIPS Agreements in global market from 2005:
•Increase in Target Protein Structures: Need of new technologies
which can help to analyze the targets easily design efficient drugs
rationally at low cost.
Why computer aided drug design be next wave?

5. • Drug Discovery cost ~ $ 850 - $1,000 Million
• 15 years’ minimum time period to Bring a discovered Drug
into Market. Except life saving drugs in terminal ill patients.
• 2/3 rd Cost in Failures
• 40 % poor ADME, 35% Toxicity, 10 % lack of efficacy
• No idea of activity before synthesis.
• Previously Most drug discovered by Serendipity discovery.
Challenges in drug discovery.

6. Drug Design: Old School Practices and Current Scenario
Traditionally, Lead Ientification and Optimization in Drug discovery is achieved by:
Therefore, structure based drug design was came into picture….
Science 2004, 303, 1813-8
 Serendipity : Discovery by chance or luck : Penicillins, Benzodiazepins
 HTS : Screening of chemical libraries : Paclitaxel, Mupirocin, Bedaquillin
 Traditional Knowledge: Ethnopharmacological usage : Salicylates, Atropine
 Rationale drug design : Substrate/inhibitor mimicry : Opioids, Nerve gases
These processes leads to higher rate of lead attrition and failure in clinical trials.
 Lack of mode of action.
 Lack of target requirement information.
 Lack of Pharmacokinetics knowledge.

7. Drug Discovery Process
Science 2004, 303, 1813-8
Target
selection
Proof of
efficacy
Clinical trials &
Therapeutics
 Genomics
 Proteomics
 Bioinformatics
 Target validation
 Assay developments.
 Lead identification
 HTS and vHTS
 In-silico studies
Lead
Discovery
Medicinal
Chemistry
 Lead optimization
 SAR generation
 X-ray Crystallography
 Formulation development
 In-vitro studies
 In-vivo studies
 PK/PD refinement
 Biomarker identification
 Safety studies
 Pharmacokinetics
 Clinical efficacy
 Marketing

8. Drug design and types of drug design
Drug design is the inventive process of finding new medications based on the
knowledge of a biological target/existing ligand. In the most basic sense, drug
design involves the design of molecules that acts as drug.
Existing Ligand guided drug design: Ligand-based drug design (or indirect drug
design) relies on knowledge of other molecules that bind to the biological target of
interest. These other molecules may be used to derive a pharmacophore model that
defines the minimum necessary structural characteristics a molecule must possess in
order to bind to the target.
Target protein guided drug design also called SBDD. Structure-based drug design
(or direct drug design) relies on knowledge of the three dimensional structure of the
biological target obtained through methods such as x-ray crystallography or NMR
spectroscopy.

9. Recent Success stories of Structure Based Drug Design
Captopril
(Bristol Mayor squibb)
Dorzolamide
(Merck & Comp.)
Rofecoxib
(Merck & Comp.)
Zanamivir
(Merck & Comp.)
Amprenavir
(Glaxosmithkine)
Nelfinavir
(Agoroun)
Imatinib
(Novartis)
Annu. Rev. Pharmacol. Toxicol. 1987, 27, 193-213 Expert Opin. Drug Discov. 2010, 5, 633-654
and many more….

10. drug design involved two steps:
 Lead identification: Identification of initial chemical core structure,
which have desired biological effect in moderate potency can be
optimized to superior drug candidate.
 Lead optimization: Chemical modification in lead structure by
medicinal chemist in order to improve the biological activity or the
physiochemical properties.
 e.g. taxol and optimized drug is paclitaxel.
 Similarly, nalidaxic acid is lead candidate and optimized drug is
ciprofloxacin.
 Similarly, Morphine is lead candidate and sufentanyl is the superior
anti-nociceptive drug.

11. Lead identification is complex process

12. Drug Design techniques
Target Structure guided drug design
1. Docking of ligands to target protein
2. Induced fit screening protocols
3. MD simulation
4. FBDD
5. AL/ML techniques
Ligand Structure guided drug design
1. Pharmacophore screening
2. 2D/3D Similarity search
3. QSAR
4. AL/ML techniques
Virtual
screening
Used in combination or parallel form
Science 2004, 303, 1813-8 Curr. Opin. Struct. Biol. 2000, 10, 401-404. Annu. Rev. Pharmacol. Toxicol. 1987, 27, 19
Lead identification

13. Ligand Structure optimization for biological activity based on :
1. SAR
2. QSAR
3. Drug receptor or Ligand-protein interaction analysis & optimization,
and modern techniques to perform these studies we required NCE’s by
Potent
preclinical
candidate
Science 2004, 303, 1813-8 Curr. Opin. Struct. Biol. 2000, 10, 401-404. Annu. Rev. Pharmacol. Toxicol. 1987, 27, 193-213
Lead optimization
1. Lab Synthesis
2. Combinatorial synthesis
3. Parallel synthesis
4. Solid phase synthesis
5. Click synthesis

14. What is structure based Drug Design ?
Science 2004, 303, 1813-8

15. What is Docking?
Docking attempts to find the “best” matching between two
molecules. i.e. host and guest molecule. Where host is protein and
guest is both ligand and protein.
Challenge: Identification of the
ligand’s correct binding geometry in
the binding site (Binding Mode)
Observation: Similar ligands can bind
at quite different orientations in the
active site.

16. The interaction of a drug with its
receptor is a complex process.
Many factors are involved in the
intermolecular association such
as hydrophobic; Van der Waal’s,
hydrogen bonding and
electrostatic forces.
Ligand docking to receptor
Ligand database Target Protein
Molecular docking
Ligand docked into protein
•The process of “DOCKING” can be defined as a fitting of a ligand to binding sites
which tries to mimic the natural course of interaction of the ligand and its receptor via
a lowest energy pathway. Usually the receptor is kept rigid while the conformation of
the drug molecule is allowed to change. The molecules are physically moved closer to
none another and the preferred docked conformation is minimized

17. Protein-ligand docking
• What docking does?
• It Predicts...
• The pose of the molecule in the binding
site
• The binding affinity or a score
representing the strength of binding

18. Pose vs. binding site
• Binding site (or “active site”)
• The part of the protein where the ligand binds is
generally a cavity on the protein surface and can be
identified by looking at the crystal structure of the
protein bound with a known inhibitor
• Pose (or “binding mode”)
• The geometry of the ligand in the binding site
• Geometry = location, orientation and
conformation

19. Docking approaches
• Shape complementarity: Geometric matching/ shape complementarity methods
describe the protein and ligand as a set of features that make them dockable.
These features may include molecular surface / complementary
surface descriptors.
• The complementarity between the two surfaces amounts to the shape matching
description that may help finding the complementary pose of docking the target
and the ligand molecules.
• Another approach is to describe the hydrophobic features of the protein using
turns in the main-chain atoms.
• shape complementarity based approaches are typically fast and robust, they
cannot usually model the movements or dynamic changes in the ligand/ protein
conformations accurately

20. Docking approaches
• Simulation: Simulating the docking process is much more complicated. In this
approach, the protein and the ligand are separated by some physical distance, and
the ligand finds its position into the protein's active site after a certain number of
“moves” in its conformational space.
• The moves incorporate rigid body transformations such as translations and
rotations, as well as internal changes to the ligand's structure including torsion
angle rotations.
• Each of these moves in the conformation space of the ligand induces a total
energetic cost of the system. Hence, the system's total energy is calculated after
every move.
• The obvious advantage of docking simulation is that ligand flexibility is easily
incorporated,

21. Steps in ligand-protein docking
• Protein preparation:
• Ligand Preparation:
• Definition of binding site and docking methodology:
• Evaluation of binding poses:
• Scoring of poses:

22. 1. Preparation of protein structure
• PDB structures often contain water molecules: In general, all water
molecules are removed except where it is known that they play an important
role in coordinating to the ligand
• PDB structures are missing all hydrogen atoms: So incorporates
H atom.
• An incorrect assignment of protonation states
in the active site will give poor results
• Glutamate, Aspartate have COO- or COOH
where OH is hydrogen bond donor, O- is not
• Histidine is a base and its neutral form has
two tautomers
H
N
H N
R
+
N
H N
R
R
NH
N

23. Preparation of protein structure
• Crystallography gives electron density, not molecular structure
• In poorly resolved crystal structures of proteins, isoelectronic groups can
give make it difficult to deduce the correct structure
• Affects asparagine, glutamine, histidine and affects hydrogen
bonding pattern.
R
O
NH2
R
NH
2
O
R
N
N
N
N
R

24. 2. Ligand Preparation
• A reasonable 3D structure is required as starting point
• During docking, the bond lengths and angles in ligands are held fixed;
only the torsion angles are changed
• The protonation state and tautomeric form of a particular ligand
could influence its hydrogen bonding ability: Either protonate as
expected for physiological pH and use a single tautomer Or generate and dock
all possible protonation states and tautomers, and retain the one with the
highest score OH O
H+
Enol Ketone

25. Docking algorithms: Rigid Docking
• We can classify the various search algorithms for docking based on the type of
bonding such as (covalent docking and non-covalent docking). Further non-covalent
docking could be broadly categorized based on the degrees of freedom of chemical
bonds that they consider in ligand structures and protein.
• Rigid docking: The ligand as well as protein is treated as a rigid structure during the
docking. Only the translational and rotational degrees of freedom are considered.
• To deal with the problem of ligand conformations, a large number of conformations
of each ligand are generated in advance and each is docked separately e.g. FRED
(Fast Rigid Exhaustive Docking), and DOCK
3. Definition of binding site and docking methodology:

26. The DOCK algorithm – Rigid ligand docking
AR Leach, VJ Gillet, An Introduction to Cheminformatics

27. Flexible ligand docking:
• Flexible docking: Conformations of each molecule are generated on-the-fly by the search
algorithm during the docking process and The algorithm can avoid considering
conformations that do not fit. Sometimes they also uses Stochastic search methods:
Stochastic means that they incorporate a incremental degree of randomness to whole
molecule. E.g. Genetic algorithms (GOLD), and Simulated annealing (AutoDock).
• Incremental construction methods:
• These construct conformations of the ligand within the binding site in a series of stages
• First one or more “base fragments” are identified which are docked into the binding site
• The orientations of the base fragment then act as anchors for a systematic
conformational analysis of the remainder of the ligand e.g. : FlexX and GLIDE.

28. Incremental construction methods

29. Incremental construction methods
Base fragment Chain lengthening Building molecule

30. Handling protein conformations and flexibility
• Most docking software treats the protein as rigid: Rigid Receptor Approximation.
This approximation may be invalid for a particular protein-ligand complex as...
• the protein may deform slightly to accommodate different ligands (ligand-induced fit)
• protein side chains in the active site may adopt different conformations.
• Some docking programs allow protein side-
chain flexibility: For example, selected side
chains are allowed to undergo torsional rotation
around acyclic bonds.
• Larger protein movements can only be handled
by separate dockings to different protein
conformations e.g. Ensemble docking (e.g.
GOLD 5.0)

31. 4. Evaluation of binding poses
• Typically, protein-ligand docking software consist of two main
components which work together:
1. Search algorithm: Generates a large number of poses of a molecule in the
binding site
2. Scoring function: Calculates a score or binding affinity
for a particular pose
To give:
• The pose of the molecule in the
binding site
• The binding affinity or a score of pose
representing the strength of binding

32. Search Algorithms
for optimal ligand
protein pose
• Monte carlo simulation
• Genetic algorithems
• Simulated Annealing
• Fragment Based Methods
Evaluation of ligand
protein pose:
Scoring functions
• Shape & Chemical
Complementary Scores
• Empirical Scoring
• Force Field Scoring
• Knowledge-based Scoring
• Consensus Scoring

33. An Effective Binding Free Energy Function in GLIDE
vdW desol elec const
vdW
desol
elec
const
ΔG=ΔE +ΔG +ΔE +ΔG
ΔE :
ΔG :
ΔE :
ΔG :
Van der Waals energy; i.e. Shape complementarity
Desolvation energy; i.e. Hydrophobicity
Electrostatic interaction energy and
Translational, rotational and vibrational free energy changes
desol
ΔG = N ΔG
N :
ΔG :
i i
i
i
i

Number of atoms of type i
Desolvation energy for an atom of type i
5. scoring of binding poses

34. The perfect scoring function will…
• Accurately calculate the binding affinity
– Will allow actives to be identified in a virtual screen
– Be able to rank actives in terms of affinity
• Score the poses of an active higher than poses of an inactive
– Will rank actives higher than inactive in a virtual screen
• Score the correct pose of the active higher than an incorrect pose of
the active
– Will allow the correct pose of the active to be identified
Where “actives” = molecules with biological activity

35. Various docking programs are:
• Glide
• Gold
• Autodock
• Dock
• Surflex

37. Thank you