MOLECULAR MODELLING & DRUG DESIGN

What is Molecular modeling ?

Molecular modelling encompasses all theoretical methods and computational techniques used to model or mimic the behaviour of molecules. A science that elucidates and validates experimental evidence through imagination, visualization, and rationalization Applied in many areas of research (Academic/Industrial)

Capabilities of Molecular Modeling

Capabilities of Molecular Modeling at Ranbaxy
Structure-based
Crystal Structure analysis Homology Modeling

Ligand-based
SAR, 2D- & 3D-QSAR Lead Identification

Pharmacophore Development

Computational Analysis of Protein-Ligand Interactions In-Sillico BBB,Solubility,Caco-2 &Toxicity Predictions

Hits from Database Searches

Modification of ligands within the active-site for better binding

Prioritization of Hits

Lead Optimization

Lead Hopping

Application of Molecular Modeling

Molecular modelling methods are now routinely used to

investigate the structure, dynamics, surface properties and thermodynamics of inorganic, biological and polymeric systems.
The types of biological activity that have been

investigated using molecular modelling include protein folding, enzyme catalysis, protein stability, conformational changes associated with biomolecular function, and molecular recognition of proteins, DNA, and membrane complexes.

Popular software for molecular modelling

AMBER classical AutoDock CHARMM classical

Drug Design / drug discovery

Whats a drug? A substance that treats/cure a disease. A small molecule that interacts with a target, (often protein involved in the disease process; activator/inhibitor) Drug discovery: The process of finding such a small molecule combination of approaches Drug discovery or drug design? In principle: Design is more rational and targeted, and discovery is more serendipitous. But design and discovery share a lot and are ~ synonymous in a pharmaceutical context.

Drug Design
Structure based Ligand based

Target (structure) based drug design

Receptor structure

Ligand (analog) based drug design

Receptor

is known Mechanism is known Ligands and their biological activities are known/ unknown

structure is not known Mechanism is known/ unknown Ligands and their biological activities are known

High Resolution Structural Biology

Determine atomic structure Analyze why molecules interact

The Reward: UnderstandingControl

Anti-tumor activity Duocarmycin SA

Atomic interactions

Shape

CAUTION. Don't be a naive user!?! When computers are applied to biology, it is vital to understand the difference between mathematical & biological significance computers dont do biology, they do sums quickly methods macromolecular structure

protocols

Structure determination methods

Receptor Structure
REQUIREMENT A Model Receptor

Known

Unknown Analog Based Drug Design

Homology Modeling Receptor Mapping

REQUIREMENT Lead Compound and derivatives with biological data

Structure Based Drug Design

Docking
Molecular Dynamics Simulations Rigid Docking FlexiDock Quantum Mechanical (BRABO) Simulated Annealing Monte Carlo Simulations PCA ANN

QSAR
Quantum Mechanics for Alignment CoMFA CoMSIA Quantum Mechanical Descriptors

GA

SINGLE MOLECULE

SYBYL, INSIGHT II, CERIUS2, MOE, AMBER (CDAC), DOCK, AUTODOCK

Structure Based Drug Design

Compound databases, Microbial broths, Plants extracts, Combinatorial Libraries Random screening synthesis 3D structure by Crystallography, NMR, electron microscopy (or) Homology Modeling Target Enzyme (or) Receptor

Lead molecule

Receptor-Ligand Complex Testing 3D QSAR

Docking Linking or Binding

3D ligand Databases

Redesign to improve affinity, specificity etc.

Drug and Target : Lock and Key ?

Most of the drugs FIT well to their targets

Some Locks are known but not all !!

Study of protein crystals give the details of the lock. Knowing the lock structure, we can DESIGN some keys.
This is achieved by COMPUTER Algorithms

This is called STRUCTURE BASED DRUG DESIGN

Algorithms

Lock structure (from experiment)

Keyconstructed by computer

Variations on the Lock and Key Model

1- Which structure of the lock should be targeted? 2- Is the binding pocket a good target? 3- Is structure-based design relevant for my receptor? -Is the 3D structure reliable?

-Is the binding pocket static enough?

4- Which key fits best? 5- What are the prerequisite physicochemical properties for the key for better binding?

The ligand has been identified

Ligand Active site Non-Ligands

Docking of Ligand to the Active site of Protein

3D Structure of the Complex

Experimental Information: The active site can be identified based on the position of the ligand in the crystal structures of the proteinligand complexes
If Active Site is not KNOWN?????

Building Molecules at the Binding Site

Identify the binding regions

Evaluate their disposition in space

Search for molecules in the library of ligands for similarity

Structure Based Ligand Design

H N O

Docking Building
O
O H O HN

Linking

? ? ?

HN O H

HN

O H O

? ?

HN

S
O H O

O
O H O

HN

O N

HN

S
O H O

Structure based drug design

Define Pharmacophore
H O H O O H O O H O O

Ligand Design

O H O

O O

DB Search
O H
O H
O H

Molecular Docking
The process of docking a ligand to a binding site mimics the natural course of interaction of the ligand and its receptor via a lowest energy pathway. Put a compound in the approximate area where binding occurs and evaluate the following:
Do the molecules bind to each other? If yes, how strong is the binding? How does the molecule (or) the protein-ligand complex

look like. (understand the intermolecular interactions) Quantify the extent of binding.

Molecular Docking (contd)

Computationally predict the structures of proteinligand complexes from their conformations and orientations.
The orientation that maximizes the interaction reveals the most accurate structure of the complex. The first approximation is to allow the substrate to do a random walk in the space around the protein to find the lowest energy.

Algorithms used while docking

Fast shape matching (e.g., DOCK and Eudock), Incremental construction (e.g., FlexX, Hammerhead, and SLIDE), Tabu search (e.g., PRO_LEADS and SFDock), Genetic algorithms (e.g., GOLD, AutoDock, and Gambler), Monte Carlo simulations (e.g., MCDock and QXP),

Some Available Programs to Perform Docking

Affinity AutoDock BioMedCAChe CAChe for Medicinal Chemists DOCK DockVision

FlexX Glide GOLD Hammerhead PRO_LEADS SLIDE VRDD

 Thus to design a structure based drug we should know the molecules properties and its behavior by studing the molecular mechanics and molecular dynamics. By knowing the molecular interactions and its properties we can be able to design a ligand or drug or key to the target.

Molecular mechanics
Molecular mechanics is one aspect of

molecular modelling, as it refers to the use of classical mechanics/Newtonian mechanics to describe the physical basis behind the models.

 Molecular mechanics methods are based on the following principles:

Nuclei and electrons are lumped into atom-like

particles. Atom-like particles are spherical (radii obtained from measurements or theory) and have a net charge (obtained from theory). Interactions are based on springs and classical potentials. Interactions must be preassigned to specific sets of atoms. Interactions determine the spatial distribution of atom-like particles and their energies.

Objective of Molecular mechanics

The object of molecular mechanics is to

predict the energy associated with a given conformation of a molecule. However, molecular mechanics energies have no meaning as absolute quantities. Only differences in energy between two or more conformations have meaning.

Emprical Force-Field Molecular Mechanism

The mechanical molecular model considers atoms as spheres and bonds as springs. The mathematics of spring deformation can be used to describe the ability of bonds to stretch, bend, and twist: Non-bonded atoms (greater than two bonds apart) interact through van der Waals attraction, steric repulsion, and electrostatic attraction/repulsion. These properties are easiest to describe mathematically when atoms are considered as spheres of characteristic radii.

A simple molecular mechanics

A simple molecular mechanics energy equation is

given by: Energy = Stretching Energy + Bending Energy + Torsion Energy + Non-Bonded Interaction Energy
These equations together with the data (parameters)

required to describe the behavior of different kinds of atoms and bonds, is called a force-field.
In the context of molecular modeling, a force field refers to

the form and parameters of mathematical functions used to describe the potential energy of a system of particles (typically molecules and atoms).

 The mathematical form of the energy terms

varies from force-field to force-field. The more common forms are :

Stretching Energy Bending Energy

Torsion Energy
Non-Bonded Energy

STRETCHING ENERGY
The stretching energy equation is based on Hooke's law. The "kb" parameter controls the stiffness of the bond spring, while "ro" defines its equilibrium length. Unique "kb" and "ro" parameters are assigned to each pair of bonded atoms based on their types (e.g. C-C, C-H, O-C, etc.). This equation estimates the energy associated with vibration about the equilibrium bond length. This is the equation of a parabola, as can be seen in the following plot

Components

bond length Bonds behave like spring with equilibrium bond length depending on bond type. Increase or decrease from equilibrium length requires higher energy.

BENDING ENERGY
The bending energy equation is also based on Hooke's law. The k parameter controls the stiffness of the angle spring, while o" defines its equilibrium angle. This equation estimates the energy associated with vibration about the equilibrium bond angle

bond angle Bond angles have equilibrium value eg 108 for H-C-H Behave as if sprung.

Increase or decrease in angle

requires higher energy.

TORSIONAL ENERGY
The torsion energy is modeled by a simple periodic function

Rotation can occur about single bond in A-B-C-D but energy depends on torsion angle (angle between CD & AB viewed along BC). Staggered conformations (angle +60, -60 or 180 are preferred). Torsional energy varies during rotation about C-C, C-N and C-O single bonds. The maximum values occur at t=0 and represent eclipsing interactions between atoms separated by three sigma bonds.

NON-COVALENT (NON-BONDED) TWO ATOM INTERACIONS

The non-bonded energy represents the pair-wise sum of the energies of all possible interacting non-bonded atoms i and j The non-bonded energy accounts for van der Waals attraction, repulsion and electrostatic interactions.

MOLECULAR DYNAMICS

Molecular Dynamics are used to investigate the structure, dynamics and thermodynamics of biological molecules and their complexes
Protein stability Conformational changes Protein folding Molecular recognition: proteins, DNA, membranes, complexes Ion transport in biological systems

The molecular dynamics method was first introduced by Alder and Wainwright in the late 1950's (Alder and Wainwright, 1957,1959) to study the interactions of hard spheres
The first molecular dynamics simulation of a realistic system was done by Rahman and Stillinger in their simulation of liquid water in 1974 (Stillinger and Rahman, 1974). The first protein simulations appeared in 1977 with the simulation of the bovine pancreatic trypsin inhibitor (BPTI) (McCammon, et al, 1977).

The molecular dynamics simulation method is based on Newtons second law or the equation of motion, F=ma, where F is the force exerted on the particle, m is its mass and a is its acceleration From a knowledge of the force on each atom, it is possible to determine the acceleration of each atom in the system

Integration of the equations of motion then yields a trajectory that describes the positions, velocities and accelerations of the particles as they vary with time. From this trajectory, the average values of properties can be determined The method is deterministic; once the positions and velocities of each atom are known, the state of the system can be predicted at any time in the future or the past

Newtons equation of motion is given by

where Fi is the force exerted on particle i, mi is the mass of particle i and ai is the acceleration of particle i. The force can also be expressed as the gradient of the potential energy,

Integration Algorithms The potential energy is a function of the atomic positions (3N) of all the atoms in the system. Due to the complicated nature of this function, there is no analytical solution to the equations of motion; they must be solved numerically. Numerous numerical algorithms have been developed for integrating the equations of motion. Verlet algorithm Leap-frog algorithm Velocity Verlet Beemans algorithm Important: In choosing which algorithm to use, one should consider the following criteria: The algorithm should conserve energy and momentum. It should be computationally efficient It should permit a long time step for integration.

Integration Algorithms All the integration algorithms assume the positions, velocities and accelerations can be approximated by a Taylor series expansion:

Where r is the position, v is the velocity (the first derivative with respect to time), a is the acceleration (the second derivative with respect to time), etc.

To derive the Verlet algorithm we can write

Summing these two equations, one obtains

The Verlet algorithm uses positions and accelerations at time t and the positions from time t-dt to calculate new positions at time t+dt. The Verlet algorithm uses no explicit velocities.

The Velocity Verlet algorithm This algorithm yields positions, velocities and accelerations at time t. There is no compromise on precision.

The Leap-frog algorithm

In this algorithm, the velocities are first calculated at time t+1/2dt; these are used to calculate the positions, r, at time t+dt. In this way, the velocities leap over the positions, then the positions leap over the velocities. The advantage of this algorithm is that the velocities are explicitly calculated, however, the disadvantage is that they are not calculated at the same time as the positions. The velocities at time t can be approximated by the relationship:

Beemans algorithm
This algorithm is closely related to the Verlet algorithm

The advantage of this algorithm is that it provides a more accurate expression for the velocities and better energy conservation. The disadvantage is that the more complex expressions make the calculation more expensive.

Conclusion
Thus by knowning the interactions between

the atoms or molecules we can study the behavior and its active site and hence it can be used to search a ligand or building a new ligand by denovo processes by using various computer simulations, algorithms, etc.

 The drug is most commonly an organic small molecule that activates

or inhibits the function of a biomolecule such as a protein, which in turn results in a therapeutic benefit to the patient.
In the most basic sense, drug design involves design of small

molecules that are complementary in shape and charge to the biomolecular target to which they interact and therefore will bind to it.
Drug design frequently but not necessarily relies on computer

modeling techniques.This type of modeling is often referred to as computer-aided drug design.

Modeling techniques for prediction of binding affinity are reasonably successful. However there are many other properties such as bioavailability, metabolic half-life, lack of side effects, etc. that first must be optimized before a ligand can become a safe and efficacious drug. These other characteristics are often difficult to optimize using rational drug design techniques.