STRUCTURE BASED DRUG DESIGN

DOCKING AND DE NOVO DRUG DESIGN

PRESENTED BY
ADAM SHAHUL HAMEED
REG NO:2014419001
M.TECH- COMPUTATIONAL BIOLOGY
INTRODUCTION TO DRUG AND DRUG DESIGN
 The drug is most commonly an organic small
molecule that activates or inhibits the function of
a bio molecule such as a protein, which in turn
results in a therapeutic benefit to the patient.

 Drug design, or rational drug design or simply

rational design, is the inventive process of
finding new medications based on the
knowledge of a biological target.

 Drug design involves the design of small

molecules that are complementary in shape and
charge to the bio molecular target with which 2
they interact and therefore will bind to it.
 INTRODUCTION TO DRUG AND DRUG DESIGN
 Drug design frequently but not necessarily relies
on computer modeling techniques.
 This type of modeling is often referred to as
computer aided drug design.
 Finally, drug design that relies on the knowledge
of the three-dimensional structure of the bio
molecular target is known as structure-based
drug design.
 The phrase “drug design” is to some extent a
misnomer.
 A more accurate term is ligand design (i.e.,
design of a small molecule that will bind tightly to 3
its target).
 BACKGROUND
 Biomolecular target (proteins or nucleic acids) is a key molecule
involved in a particular metabolic or signaling pathway that is leading
to a specific disease condition or pathology or to the infectivity or
survival of a microbial pathogen.
 In Some cases, small molecules will be designed to inhibit the target
function in the specific pathway (diseased state).
 Small molecules (inhibitors or modulators) will be designed that are
complementary to the active site/allosteric site of target.
 In some other cases, small molecules will be designed or developed
to enhance the normal pathway by promoting specific biomolecular
molecules in the normal pathways that may have been affected in the
diseased state. 4
 BACKGROUND
 Small molecules (drugs) can be designed so as not to affect any other
important “off-target” molecules or anti targets, since drug interactions
with off-target molecules may lead to undesirable side effects.

 Sequence homology is often used to identify such risks.

 Most commonly, drugs are organic small molecules produced through

chemical synthesis, but biopolymer-based drugs (also known as
biologics) produced through biological processes are becoming

increasingly more common.

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 INTRODUCTION TO 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.

 If an experimental structure of a target is not available, it may be

possible to create a homology model of the target based on the
experimental structure of a related protein.

 Using the structure of the biological target, candidate drugs that are
predicted to bind with high affinity and selectivity to the target may be
designed using interactive graphics and the intuition of a medicinal
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chemist.
 NMR Spectroscopy
X-ray Crystallography

Homology Modelling
 INTRODUCTION TO SBDD
 Structure-based design is one of the first techniques to be used in
drug design.
 Structure based drug design that has helped in the discovery process
of new drugs.
 In parallel, information about the structural dynamics and electronic
properties about ligands are obtained from calculations.
 This has encouraged the rapid development of the structure based
drug design.
 structure-based drug design can be divided roughly into two
categories.
1. Ligand based Drug Design Or Database Searching
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2. Receptor based Drug Design
 LIGAND BASED DRUG DESIGN
 The first category is about “finding” ligands for a given receptor, which
is usually referred as database searching.

 In this case, a large number of potential ligand molecules are

screened to find those fitting the binding pocket of the receptor.

 This method is usually referred as ligand-based drug design.

 The key advantage of database searching is that it saves synthetic

effort to obtain new lead compounds.

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 RECEPTOR BASED DRUG DESIGN

 Another category of structure-based drug design methods is

about “building” ligands, which is usually referred as receptor-
based drug design.

 In this case, ligand molecules are built up within the constraints

of the binding pocket by assembling small pieces in a stepwise
manner.

 These pieces can be either individual atoms or molecular

fragments.

 The key advantage of such a method is that novel structures,

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not contained in any database, can be suggested.
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 Structure-based Drug Design (SBDD)

Natural ligand / Screening

Molecular Biology & Protein Chemistry

3D Structure Determination of Target

and Target-Ligand Complex
Modelling

Drug Design Cycle

Structure Analysis
Biological Testing
and Compound Design
If promising

Synthesis of New Compounds

Pre-Clinical 12
Studies
Structure-based Drug Design (SBDD)

Ligand database Target Protein

Molecular docking

Ligand docked into protein’s active site

Pharmacokinetic and Pharmacodynamic optimization 13

 DOCKING

• Docking refers to the ability to position a ligand in the active or

a designated site of a protein and calculate the specific
binding affinities.
• Docking algorithms can be used to find ligands and binding
conformations at a receptor site close to experimentally
determined structures.
• Docking algorithms are also used to identify multiple proteins
to which a small molecule can bind.
• Some of the docking programs are GOLD (Genetic
Optimization for Ligand Docking), AUTODOCK, LUDI, HEX
etc. 14
 What is Docking?
•Docking attempts to find the “best” matching between two molecules

•It includes finding the Right Key for the Lock

•Given two biological molecules determine:

- Whether the two molecules “interact”

- If so, what is the orientation that maximizes the “interaction” while

minimizing
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the total “energy” of the complex

 Goal: To be able to search a database of molecular structures and

retrieve all molecules that can interact with the query structure
Docking Protocol

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 How DOCK works…….
Generate molecular surface of protein

Cavities in the receptor are used to

define spheres (blue); the centres
are potential locations for ligand atoms.

Sphere centres are matched to ligand

atoms, to determine possible orientations

for the ligand. 104 orientations generated

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 Virtual screening, to identify
potential lead compounds from a
large dataset
 Known structures of organic compounds
 Libraries of Virtual Compounds

 Programs calculate affinity for protein

 Narrow down to small number of
possiblities
 Surface representation that efficiently
represents the docking surface and
identifies the regions of interest (cavities
and protrusions)
 Surface matching that matches surfaces
to optimize a binding score
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 Pose prediction
• If we know exactly where and how
a known ligand binds...

– We can see which parts are

important for binding

– We can suggest changes to

improve affinity

– Avoid changes that will ‘clash’

with the protein

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 Introducing flexibility:
Whole molecule docking programs
• Monte Carlo methods (MC)
• Molecular Dynamics (MD)
• Simulated Annealing (SA)
• Genetic Algorithms (GA)

Available in packages:
 Auto Dock (MC,GA,SA)
 GOLD (GA)
 Sybyl (MD)

 Glide (Schrodinger)

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 MOLECULAR DOCKING

 Aim:
To achieve an optimized conformation for both receptor and ligand & the
relative orientation between protein and ligand such that the free energy of the overall
system is minimized

 Successful docking methods search high-dimensional spaces effectively and use a

scoring function that correctly ranks candidate dockings.

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 IMPORTANCE

Molecular Docking
Identification of the
ligand’s Prediction of the
correct binding binding affinity
geometry (Scoring Function)
(pose) in the binding
site
(Binding Mode)

Rational Design Of 22

Drugs
 TYPES OF DOCKING

Rigid Docking (Lock and Key)

In rigid docking, the internal
geometry of both the receptor and ligand are
treated as rigid.

Flexible Docking (Induced fit)

An enumeration on the rotations of
one of the molecules (usually smaller one) is
performed. Every rotation the energy is calculated;
later the most optimum pose is selected.

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DOCKING CAN BE BETWEEN….
 Protein - Ligand

 Protein – Protein

 Protein – Nucleotide

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LIGAND – PROTEIN DOCKING

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LIGAND-PROTEIN DOCKING

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 TYPES OF INTERACTIONS

 Electrostatic forces - Forces with electrostatic origin are due to the charges residing in
the matter.

 Electrodynamics forces - The most widely known is probably the van der Waals
interaction.

 Steric forces - These are caused by entropy. For example, in cases where entropy is
limited, there may be forces to minimize the free energy of the system.

 Solvent-related forces – These are due to the structural changes of the solvent. These
structural changes are generated, when ions, colloids, proteins etc, are added into the
structure of solvent. The most commonly are Hydrogen bond and hydrophobic
interactions
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A TYPICAL DOCKING WORKFLOW

TARGET LIGAND
SELECTION SELECTION

TARGET LIGAND
PREPARATION PREPARATION

DOCKING

EVALUATING 28
DOCKING RESULT
 KEY STAGES IN DOCKING
Receptor selection and Ligand selection and
preparation preparation
Building the Receptor Ligands can be obtained from
The 3D structure of the receptor should various databases like ZINC,
be considered which can be downloaded PubChem or can be sketched
from PDB. using tools like Chemsketch.
The available structure should be
processed. Docking
The receptor should be biologically The ligand is docked onto the
active and stable. receptor and the interactions are
checked.
Identification of the Active Site
The active site within the receptor
should be identified. The scoring function generates
The receptor may have many active score, depending on which the
sites but the one of the interest should be best fit ligand is selected.
selected.
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 Why is docking important?
• It is the key to rational drug design: The results of docking can be used
to find inhibitors for specific target proteins and thus to design new drugs.

• It is gaining importance as the number of proteins whose structure is

known increases

• In addition to new drug discovery, it is of extreme relevance in cellular

biology, where function is accomplished by proteins interacting with
themselves and with other molecular components

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 USES OF DOCKING

 Drug targets
 Protein- ligand interactions that otherwise may be overlooked
 Better understand the Machinery of Life
 Enzyme-inhibitor class
 Antibody-antigen class
 Others
 Protein Therapies
 Engineered Protein Enzymes
 Although the reliability of docking methods is not so high, they can
provide new suggestions
 False positives rates can be reduced using several scoring functions
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in a consensus-scoring strategy
 APPLICATIONS
Virtual screening (hit identification)

 Docking with a scoring function can be used to quickly screen large

databases of potential drugs in silico to identify molecules that are likely
to bind to protein target of interest.

Drug Discovery (lead optimization)

 Docking can be used to predict in where and in which relative

orientation a ligand binds to a protein (binding mode or pose).

 This information may in turn be used to design more potent and

selective analogs.

Bioremediation
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 Protein ligand docking can also be used to predict pollutants that can
be degraded by enzymes.
 FUTURE CHALLENGES FOR DOCKING
• Better Scoring Functions

• High-Throughput Screening

• Tractable Models of Flexibility

• The so-called computational molecular docking problem is far from

being solved. There are two major bottle-necks:

1. The algorithms can handle only a limited extent of

backbone flexibility

2. The availability of selective and efficient scoring functions

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 Different approaches based on structural availibility

Receptor Ligand Approach Comments

known known DOCK receptor Programmes-

based AUTO-DOCK

known unknown De novo based GROW, LEGEND

unknown known Ligand based QSAR

unknown unknown Combinational

based
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 DE NOVO APPROACHES

• De novo design is the approach to build a customized

Ligand for a given receptor.

• This approach involves the ligand optimization.

• Ligand optimization can be done by analyzing protein

active site properties that could be probable area of
contact by the ligand.

• The analyzed active site properties are described to

negative image of protein such as hydrogen bond,
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hydrogen bond acceptor and hydrophobic contact region.
 DE NOVO DRUG DESIGN
 De novo means start afresh, from the beginning, from
the scratch

 It is a process in which the 3D structure of receptor is used

to design newer molecules

 It involves structural determination of the lead target

complexes and lead modifications using molecular
modeling tools.

 Information available about target receptor but no existing

leads that can interact. 36
 PRINCIPLES OF DENOVO DRUG DESIGN

•Assembling possible compounds and evaluating their

quality.
• Searching the sample space for novel structures with
drug like properties.

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Protein Structure Build a model for Protein Structure

 DENOVO DRUG DESIGN
•In de novo design, the structure of the target should be known to
a high resolution, and the binding to site must be well defined.

• This should defines not only a shape constraint but

hypothetical interaction sites, typically consisting of
hydrogen bonds, electrostatic and other non-covalent
interactions.

• These can greatly reducing the sample space, as hydrogen

bonds and other anisotropic interactions can define specific
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orientations.
 DERIVATION OF INTERACTION SITES

A key step to model the binding site as accurately as possible.

• This starts with an atomic resolution structure of the active

site.
• Programs like UCSF , DOCK define the volume available
to a ligand by filling the active site with spheres.

• Further constraints follow, using positions of H-bond

acceptors and donors.

• Other docking algorithms, such as FLOG, GOLD, and

FlexiDock 16 use an all-atom representations to achieve fine
detail.

• Ray-tracing algorithms, such as SMART,represent another

strategy
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 Molecular
dynamics
Lattice based
methods
Based
sampling
Linking

Growing

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 A Single Key Building Block is the starting point or Seed

Fragments are added to provide suitable interactions to both key sites and
space between key sites

These include simple hydrocarbon chains, amines, alcohols, and even

single rings.

In the case of multiple seeds, growth is usually simultaneous and

continues until all pieces have been integrated into a single molecule. 41
GROWING

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Linking

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LINKING
 LINKING

 The fragments, atoms, or building blocks are either

placed at key interaction sites.

 They are joined together using pre-defined rules to

yield a complete molecule.

Linking groups or linkers may be predefined or

generated to satisfy all required conditions . 45
 Lattice based method

The lattice is placed in the binding site, and atoms around key
interaction sites are joined using the shortest path.

Then various iterations, each of which includes translation, rotation or

mutation of atoms, are guided by a potential energy function, eventually
leading to a target molecule.

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 Molecular Dynamics Methods
The building blocks are initially randomly placed and then
by MD simulations allowed to rearrange.

After each rearrangement certain bonds were broken and

the process repeated.

During this procedure high scoring structures were stored for

later evaluation.
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 SCORING

• Each solution should be tested to decide which is the most promising.

This is called as scoring.

• Programs such as LEGEND18, LUDI19, Leap-Frog16, SPROUT20,

HOOK21, and PRO-LIGAND22 attempt this using different scoring
techniques

• These scoring functions vary from simple steric constraints and

H-bond placement to explicit force fields and empirical or knowledge-

based scoring methods.

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 SCORING-(CONT..)
• Programs like GRID and LigBuilder3 set up a grid in
the binding site and then assess interaction energies by
placing probe atoms or fragments at each grid point.

• Scoring functions guide the growth and optimization

of structures by assigning fitness values to the sampled
space

Scoring functions attempt to approximate the binding

•
free energy by substituting the exact physical model with
simplified statistical methods. 50
 SCORING-(CONT..)

Force fields usually involve more computation than the other types of
scoring functions eg:- LEGEND

• Empirical scoring functions are a weighted sum of individual ligand–

receptor interactions.

• Apart from scoring functions, attempts have been made to use NMR,
X-ray analysis and MS to validate the fragments

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 METHOD PROGRAMS AVAILABLE
Site point connection method LUDI

Fragment connection method SPLICE, NEW LEAD,

PRO-LIGAND

Sequential build up methods LEGEND, GROW, SPORUT

Random connection and CONCEPTS, CONCERTS, MCDNLG

disconnection methods
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DE NOVA DESIGN OF INHIBITOR FOR HIV-I PROTEASE
INHIBITOR

 An impressive example of the application of SBDD was the design of

the HIV-I protease Inhibitor.

 The starting point is the series of X-ray structures of the enzyme and
enzyme-inhibitor complex. The enzyme is made up of two equal
halves.

 HIV protease is a symmetrical molecule with 2 equal halves and an

active site near its center like butterfly.

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 DE NOVA DESIGN OF INHIBITOR FOR HIV-I
PROTEASE INHIBITOR

 For most such symmetrical molecules

with two equal halves and an active
site near its center like butterfly

 For most such symmetrical

molecules,both halves have a
“business area”,or active site,that
carries out the enzymes job.

 But HIV protease has only one such

active site in the center of the molecule 54

where the two halves meet.

 HIV 1 PROTEASE INHIBITOR

Structure of enzyme

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Enzyme with inhibitor

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EXAMPLES OF DRUGS DESIGNED BY STRUCTURE-
BASED METHODS
INHIBITOR TARGET DISEASE

ANTI HYPERTENSION
HUMAN RENIN
COLLAGENASE AND ANTICANCER ,ANTIARTHRITIS
STROMELYSIN

PURINE NUCLEOTIDE ANTIDEPRESSANT

PHOSPHORYLASE

THYMIDYLATE SYNTHASE ANTIPROLIFERATION

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 Although a relatively new design method, de novo design
will play an ever-increasing role in modern drug design.

Though yet not able to automatically generate viable drugs

by itself, it is able to give rise to novel and often
unexpected drugs

 when coupled with HTS, is proving to reduce drug

design turn around time.

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 IMPROVE QUALITY OF LIFE

 The emphasis now is not just on finding new ways to treat

human disease, but also on improving the quality of life of
people in general.

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