MOLECULAR DOCKING

V. Subramanian
Chemical Laboratory
Central Leather Research Institute
Adyar, Chennai
subbu@clri.info
 Introduction
• Drug discovery  take years to decade for
discovering a new drug and very costly
• Effort  to cut down the research timeline and
cost by reducing wet-lab experiment  use
computer modeling
 Drug discovery

Chemical + biological system  desired response?

 TRADITIONAL DRUG DESIGN

Lead generation:
Natural ligand / Screening

Biological Testing

Drug Design Cycle

If promising
Synthesis of New Compounds

Pre-Clinical Studies
 Finding lead compound
• A lead compound is a small molecule that serves as the starting
point for an optimization involving many small molecules that
are closely related in structure to the lead compound
• Many organizations maintain databases of chemical compounds
• Some of these are publically accessible others are proprietary
• Databases contain an extremely large number of compounds
(ACS data bases contains 10 million compounds)
• 3D databases have information about chemical and geometrical
features
» Hydrogen bond donors
» Hydrogen bond acceptors
» Positive Charge Centers
» Aromatic ring centers
» Hydrophobic centers
 Finding lead compound
• There are two approaches to this problem
– A computer program AutoDock (or similar
version Affinity (accelrys)) can be used to
search a database by generating “fit”
between molecule and the receptor
– Alternatively one can search 3D
pharmacophore
 Structure based drug design
• Drug design and development
• Structure based drug design exploits the 3D
structure of the target or a pharmacophore
– Find a molecule which would be expected to
interact with the receptor. (Searching a data base)
– Design entirely a new molecule from
“SCRATCH” (de novo drug/ligand design)
• In this context bioinformatics and
chemoinformatics play a crucial role
 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
Studies
 Structure based drug design
• SBDD:
• drug targets (usually proteins)
• binding of ligands to the target (docking)

↓
“rational” drug design

(benefits = saved time and $$)

Schematics for structure based drug design
Select and Purify the
target protein
Obtain known
inhibitor

X-Ray structural
determination of native
protein

X-Ray structural
determination of
inhibitor complex

Model inhibitor Synthesis, Evaluate

with preclinical, clinical,
computational invitro, invivo, cells,
tools animals, & humans
Determine IC50

Drug
Structure Based Drug Design have the potential to shave off years and millions of
dollars
 Working at the intersection
• Structural Biology
• Biochemistry
• Medicinal Chemistry
• Toxicology
• Pharmacology
• Biophysical Chemistry
• Natural Products Chemistry
• Chemical Ecology
• Information Technology
 Molecular docking-definition
• It is a process by which two molecules
are put together in 3 Dimension

• Best ways to put two molecules together

• Using molecular modeling and

computational chemistry tools
 Molecular docking
• Docking used for finding binding modes of
protein with ligands/inhibitors
• In molecular docking, we attempt to predict
the structure of the intermolecular complex
formed between two or more molecules
• Docking algorithms are able to generate a
large number of possible structures
• We use force field based strategy to carry out
docking
Oxygen transport molecule (101M)
with surface and myoglobin ligand
Influenza virus b/beijing/1/87 neuraminidase
complexed with zanamivir
Influenza virus b/beijing/1/87 neuraminidase
complexed with zanamivir
 Plasma alpha antithrombin-iii and
pentasaccharide protein with heparin ligand
 Steps of molecular docking
• Three steps
(1) Definition of the structure of the target
molecule

(2) Location of the binding site

(3) Determination of the binding mode

Best ways to put two molecules
together
– Need to quantify or rank solutions

– Scoring function or force field

– Experimental structure may be amongst one

of several predicted solutions

-Need a Search method

 Questions
• Search
– What is it?
– When/why and which search?
• Scoring
– What is it?
• Dimensionality
– Why is this important?
 Spectrum of search
• Local
– Molecular Mechanics
• Short - Medium
– Monte Carlo Simulated Annealing
– Brownian Dynamics
– Molecular Dynamics
• Global
– Docking
 Details of search
Level-of-Detail
• Atom types
• Terms of force field
– Bond stretching
– Bond-angle bending
– Torsional potentials
– Polarizability terms
– Implicit solvation
 Kinds of search
Systematic
• Exhaustive
• Deterministic
• Dependent on granularity of sampling
• Feasible only for low-dimensional
problems
• DOF, 6D search
 Kinds of search
Stochastic
• Random
• Outcome varies
• Repeat to improve chances of success
• Feasible for higher-dimensional problems
• AutoDock, < ~40D search
 Stochastic search methods
• Simulated Annealing (SA)
• Evolutionary Algorithms (EA)
– Genetic Algorithm (GA)
• Others
– Tabu Search (TS)
• Hybrid Global-Local Search
– Lamarckian GA (LGA)
 Simulated annealing
• One copy of the ligand (Population = 1)
• Starts from a random or specific
postion/orientation/conformation (=state)
• Constant temperature annealing cycle
(Accepted & Rejected Moves)
• Temperature reduced before next cycle
• Stops at maximum cycles
 Search parameters
Simulated Annealing
• Initial temperature (K)
• Temperature reduction factor (K-1cycle)
• Termination criteria:
– accepted moves
– rejected moves
– cycles
 Genetic function algorithm
• Start with a random population (50-200)
• Perform Crossover (Sex, two parents ->
2 children) and Mutation (Cosmic rays,
one individual gives 1 mutant child)
• Compute fitness of each individual
• Proportional Selection & Elitism
• New Generation begins if total energy
evals or maximum generations reached
 Search parameters
• Population size
• Crossover rate
• Mutation rate
• Local search
– energy evals
• Termination criteria
– energy evals
– generations
 Dimensionality of molecular
docking
• Degrees of Freedom (DOF)
• Position or Translation
– (x,y,z) = 3
• Orientation or Quaternion
– (qx, qy, qz, qw) = 4
• Rotatable Bonds or Torsions
– (tor1, tor2, … torn) = n
• Total DOF, or Dimensionality,
D=3+4+n
 Docking score
DGbinding = DGvdW + DGelec + DGhbond + DGdesolv +
DGtors
DGvdW
12-6 Lennard-Jones potential
• DGelec
Coulombic with Solmajer-dielectric
• DGhbond
12-10 Potential with Goodford Directionality
• DGdesolv
Stouten Pairwise Atomic Solvation Parameters
• DGtors
Number of rotatable bonds
 Molecular mechanics: theory
• Considering the simple harmonic
approximation, the potential energy
of molecules is given by
V= VBond+ VAngle + VTorsion + Vvdw +
Velec+ Vop
• VBond = 1/2Kr (rij-r0)2
• Where Kr is the stretching force
constant
• VAngle =1/2K (ijk-0)2
• Where K is the bending force
constant
• VTorsion =V/2 (1+ Cos n(+0))
• Where V is the barrier to rotation,
 is torsional angle
 Molecular mechanics: Theory
• Lennard-Jones type of 6-12 potential is used to
describe non-bonded and weak interaction
• Vvdw= (Aij/rij12-Bij/rij6)
• Simple Columbic potential is used to describe
electrostatic interaction
• Velec=(qiqj/rij)
• Out of plane bending/deformation is described
by the following expression
• Vop= 0.5 Kop 2
 The forcefield
• The purpose of a forcefield is to describe the
potential energy surface of entire classes of
molecules with reasonable accuracy
• In a sense, the forcefield extrapolates from the
empirical data of the small set of models used to
parameterize it, a larger set of related models
• Some forcefields aim for high accuracy for a
limited set of elements, thus enabling good
predictions of many molecular properties
• Others aim for the broadest possible coverage of
the periodic table, with necessarily lower accuracy
 Components of a forcefield
• The forcefield contains all the necessary elements for
calculations of energy and force:
– A list of forcefield types
– A list of partial charges
• Forcefield-typing rules
– Functional forms for the components of the energy
expression
• Parameters for the function terms
– For some forcefields, rules for generating parameters that
have not been explicitly defined
– For some forcefields, a way of assigning functional forms
and parameters
The energy expression
 Valence interactions
• The energy of valence interactions is generally accounted for
by diagonal terms:
– bond stretching (bond)
– valence angle bending (angle)
– dihedral angle torsion (torsion)
– inversion, also called out-of-plane interactions (oop)
terms, which are part of nearly all forcefields for covalent
systems
– A Urey-Bradley (UB) term may be used to account for
interactions between atom pairs involved in 1-3
configurations (i.e., atoms bound to a common atom)
• Evalence=Ebond + Eangle + Etorsion + Eoop + EUB
 Non-bond interactions

• The energy of interactions between non-

bonded atoms is accounted for by
• van der Waals (vdW)
• electrostatic (Coulomb)
• hydrogen bond (hbond) terms in some older
forcefields
• Enon-bond=EvdW + ECoulomb + Ehbond
 Molecular dynamics (MD)
simulations
• A deterministic method
based on the solution of
Newton’s equation of motion
Fi = mi ai
for the ith particle; the
acceleration at each step is
calculated from the negative
gradient of the overall
potential, using
Fi = - grad Vi - = -  Vi

Vi = Sk(energies of
interactions between i and all
other residues k located
within a cutoff distance of Rc
from i)
 Classical molecular dynamics
• Constituent molecules obey
classical laws of motion
• In MD simulation, we have to
solve Newton's equation of motion
• Force calculation is the time
consuming part of the simulation
• MD simulation can be performed
in various ensembles
• NVT, NPT and NVE are the
ensembles widely used in the MD
simulations
• Both quantum and classical
potentials can be used to perform
MD simulation
Calculation of interaction energy
• MM total energy can be used to get interaction
energy of the ligands with biomolecules
• In order to compute the interaction energy,
calculations have to be performed for the
biomolecule, ligands and the biomolecule-
ligand adduct using the same force field
• Eint= Ecomplex - {Ebiomolecule+Eligand}
 Integration of equation of motion
and time step
• A key parameter in the integration algorithm is the
integration time step
• The time step is related to molecular vibration
• The main limitation imposed by the highest-frequency
motion
• The vibrational period must be split into at least 8-10
segments for models to satisfy the Verlet algorithm that
the velocities and accelerations are constant over time step
used
• In most organic models, the highest vibrational frequency
is that of C-H stretching, whose period is of the order of
10-14 s (10fs). Therefore integration step should be 0.5-1 fs
 Stages and duration in MD
simulation
• Dynamics simulations are usually carried out in two
stages, equilibration and data collection
• The purpose of the equilibration is to prepare the system
so that it comes to the most probable configuration
consistent with the target temperature and pressure
• For large system, the equilibration takes long time
because of the vast conformational space it has to search
• The best way to judge whether a model has equilibrated
is to plot various thermodynamic quantities such as
energy, temperature, pressure versus time
• When equilibrated, the system fluctuate around their
average
 Durations of some real
molecular events
Event Approximate duration

Bond stretching   1-20 fs  

Elastic domain modes   100 fs to several ps  

Water reorientation   4 ps  

Inter-domain bending  10 ps-100 ns  

Globular protein tumbling  1-10 ns  

Aromatic ring flipping   100 µs to several seconds  

Allosteric shifts 2 µs to several seconds  

Local denaturation  1 ms to several seconds  

 Free energy simulations
• Ability to predict binding energy
• Free energy perturbation and thermodynamic
integration
• Computational demand and issues related to
sampling prevent this technique in probing
structure based drug design
• Free Energy equation
 De nova design of inhibitor for HIV-I
protease

• An impressive example of the application

of SBDD is was the design of the HIV-I
protease inhibitor
 De nova design
• It is a member of the aspartyl protease family
with the two active sites
• Structure has tetra coordinated water
molecules tat accepted two hydrogen bond
from the backbone amide hydrogens of
isoleucine in the flaps
• Two hydrogen bonds to the carbonyl oxygens
of the inhibitor
 Application of structure based drug
design: HIV protease inhibitors
• 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 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 enzyme's job
• But HIV protease has only one such
active site in the center of the
molecule where the two halves meet
 Structure based drug design: HIV
protease inhibitors
• The single active site was plugged with a small
molecule so that it is possible shut down the whole
enzyme and theoretically stop the virus' spread in
the body
• Several Inhibitors have been designed based on
– Peptidic inhibitor
– Peptidomemitic compounds
– Non-peptide inhibitors
• Further work has demonstrated the success of this
approach
 Some examples
• Ritonavir (trade name Norvir) is one of a class
of anti-HIV drugs called protease inhibitors
• Saquinavir
• Indinavir is another example of very potent
peptidomimetic compound discovered using
the elements of 3D structure and Structure
Activity Relationship (SAR)
 De nova design…
• The first step was a 3D database search of a
subset of the Cambridge Structural
Database
• The pharmacophore for this search
comprised of two hydrophobic groups and
a hydrogen bond donor or acceptor
• The hydrophobic groups were intented to
bind to the catalytic asp residues
 De nova design…
• The search yielded the hit which contained desired
element of the pharmacophore but it also had oxygen
that could replace the bound water molecules
• The benzene ring in the original compound was
changed to a cyclohexanone, which was able to
position substituents in a more fitting manner
• The DuPont Merck group had explored a series of
peptide based diols that were potent inhibitors but
with poor oral bioavailability
 De nova design
• They have retained the diol functionality and
expanded the six me member ring to a seven
membered diol
• The ketone was changed to cyclic urea to
enhance the hydrogen bonding to the flaps and
to help synthesis
• The compound chosen further studies
including clinical trails was p-
hydroxymethylbenzyl derivative
 P1 8.5-12Å P1’

3.5-6.5Å 3.5-6.5Å

H-bond donor or acceptor

3D hit
3D pharmacophore
Symmetric diol docked into
HIV active site Initial
idea for
inhibitor

Final Molecule selected Stereochemistry required Expand ring to give diol

for clinical Trials for optimal binding and incorporate urea
Host-Guest Interactions with
Collagen: As molecules
Dominated by Geometrical factors
and Solvent Accessible Volumes
Energy minimized structure of 24-
mer collagen triple helix
 Complex Formation of poly phenols
at various collagen sites

Aspargine of T.Helix
and gallic acid

Aspartic acid of
T.Helix and catechin

Lysine of T.Helix and

epigallocatechingallate
 Binding energies different complexes
between polyphenols and triple helix
Binding Energy (Kcal/mol)
Binding Sites in Epigallocatechi
triple helix Gallic acid Pentagalloyl
Catechin (Cat) ngallate
(Gal) glucose (PGG)
(EGCG)
9th residue Ser
of C-chain (α2) 16.5 22.5 35.2 56.6

6th residue Hyp

of A-chain (α1) 14.5 20.8 34.5 48.4

12th residue Lys

of B-chain (α1) 19.2 23.8 37.9 41.1

21st residue Asp

of A-chain (α1) 18.4 20.0 38.2 59.8

17th residue Asn

of C-chain (α2) 14.1 23.7 34.3 52.8
 Interfacial interacting volume Vs Binding
energy of the collagen-poly phenol complex

Interacting Interfacial Volume (Å3)

 Effective solvent inaccessible contact volume
Vs Binding energy of the collagen-poly phenol
complex
Inset: effective solvent inaccessible contact surface area Vs Binding energy of the complex
 Plot of inverse of interacting interfacial volume
(1/Int.Vol.) Vs inverse of binding energy(1/B.E) of the
complexes
 Acknowledgement

• Mr. R. Parthasarathi
• Mr. B. Madhan
• Mr. J. Padmanabhan
• Mr. M. Elango
• Mr. S. Sundar Raman
• Mr. R. Vijayraj
• CSIR & DST, GOI
 Big Thank You

Others have done the work. Some

have used the work. I have
spoken only on behalf of their
behalf.