E3 - MOLECULAR DOCKING AND MODELING

Addition Polymer

Made from monomers directly combining together; polymer has all the atoms in the monomer

Condensation Polymer

Results when monomers combine such that small molecules are split away

Molecular recognition

Ability of biomolecules to recognize other biomolecules and selectively interact with them in order to promote fundamental biological events

Molecular docking

Involves placing molecules in appropriate configurations to interact with a receptors

In molecular modeling, what is molecular docking

Study of how two or more molecules structures fit together

Importance of molecular recognition

• Understand molecular function and biological process

• Design novel therapeutic agents

Molecular docking classification of molecules

Small molecules (ligands), proteins, nucleic acid

Types of docking systems

Protein-ligand, protein-protein, nucleic acid-protein

This is the most understood type of docking system

ligand-protein

Typical applications of molecular docking

• Virtual screening

• Lead hopping

  • Increasing HTS hit rates

Lock and Key theory

A susbtrate fits into the active site of a macromolecule

Induced-Fit Theory

Ligand and target mutually adapt to each other through small conformational changes for optimal fit

Conformation Ensemble model

Pre-existing ensemble of conformational states that a protein has, switching from one state to another

Computational docking

predicts the optimal binding orientation and conformation of interacting molecules in space and to extimate the stability of their complex

What does molecular docking predict

Whether two molecules interact or not, the binding affinity, and 3D structure of the complex

Shape complementarty

Primary criterion for evaluating the fit in the computational docking of two candidate structures

Other criteria for molecular docking

Chemical and physicochemical complementarity

How does energy dictate molecular associations

The complex that has a lower potential energy is the preferred configuration

Category of Docking software

Molecular representation, Scoring method, Seraching algorithm

Molecular representation

Way to represent structures and properties

Scoring method

Assess the quality of docked complexes

Search algorithm

Decides which poses to generate

How is ligand prepared

Removing any counter ion, slats, or water molecules, all reactive and undesirable compounds

What should be generated for a ligand

All optical isomers, cis/trans isomers, tautomers, and protonation states of the structure

Factors leading to the formation of ligand-receptor complex

1. The interaction energies between two molecules

2. The desolvation and solvation energies associated with the interacting molecules

3. The entropic factors that occur upon binding

Force-Field Calculation

The energies obtained by force field methods can be used directly to approximate free energies of binding

Feature based matching

Matches local complementarity features among molecuels involved in the recognition

Stepwise search

Explores the “search space” guided by a scoring fucntion

Autodock Vina

Docking program based on a simple scoring funnction and rapid conformational search

Autodock

Docking program based on free-energy force field and rapid genetic algorithm search methodR

accoon

Interactive tool for virtual screening and analysis

AutoDockTools

Interactive GUI for coordinate prep, docking and analysis

AutoLigand

Program that predicts optimal sites of ligand binding on receptors

Assumptions in the Experiment

• Conformational space is reduced due to a rigid receptor and fixed bond angels and lengths in the ligand. NO INDUCED FIT BINDING

• A simplified scoring function based on empirical free energies of binding is used to score poses for each conformation search

• Ordered water molecules mediate interactions between ligands and receptors

Methods for Handling Ligand Flexibility

1. Ligand-ensemble docking method

2. Fragmentation Method

   1. Stochastic conformational search method

Ligand-Ensemble Docking Method

• Low energy conformers are generated by conformational analysis

• Rigid docking is applied for each conformer to find the most favorable small molecule protein complex

Two approached to Fragmentation Docking Method

Place-and-hoin and Incremental

Place-and-join

Splitting into subparts then assess the reconnection based on their relative locatin

Incremental

Initial core is docking and new fragments are progressively added until the structure is complete

Stochastic Search Method

Modifying the conformation in the receptor site and optimizing it directly

Types of Protein Flexibility

1. Smal atom flucturations

2. Side-chain flexibility

3. Backbone flexibility

   1. Domain movements

Soft docking method

Allows slight penetrations between the receptor and the ligan molecules, allowing for overlap

Soft scoring effect

Increase the chances of not overlooking good solutions

Energetics of soft scoring

When calculated with force fields, steroic clashes correspond to high energies

Side Chain Flexibility enables

Maximazation of favorable interactions with the protein

What is the most complex and time consuming types of flexibility

Backbone and side chain flexibility

Multiple Protein Search approach

Use of multiple structures of the target protein as obtained from experiimental methods or theoretical simulations

Three mechanisms of domain movements

Intrinsic flexibility, hinged domain, ball and socket

Intrinsic flexibility

Large motion of domain

Hinged domain

Small rotation, involved small number of residues

Ball-and-socket

Combination of hinge and shear motions

GUI

streamlines docking workflows with automated server connections and ligand library management. It supports multiple receptor targets with flexible residues and provides an intuitive setup for docking parameters. Results are automatically retrieved, processed, and filtered based on key properties and interactions. Users can efficiently analyze and export refined virtual screening results, making the process seamless and user-friendly.

AutoDock is designed to solve this

Docking os small, drug-like molecuels to biological macromolecules of known structure

Approach for docking very large ligands with too many degrees of freedom

Fragmentation method

Best way to determine the simulation and search the avialbele conformation space

Clustering analysis

Virtual Screening with Raccoon Use

Docking and ranking of hundred of compounds to a macromolecular target

Limitations of X-ray crystallography

• Needs crystals, hard for protein

• Resolution problems, loops, side chains, tautomeric state

  • Ambiguous in bound ligands

NMR limitations

• Mass restricting (only 64KDa)

• Poor resolution power

• Sensitivity loss and increased spectral complexity

Threading approach

Aligns the target protein sequence to known protein folds in the structural database assuming similar sequences will adopt to similar 3D conformationsT

Use of Threading Approach

When homologous structures are unavailable

Ab-Initio Method

Involved force fields, molecular dynamics simulations, and energy minimization techniques to explore possible conformation

Ab-Initio Method use

No protein template is available

Homology Modeling

Builds 3D structure based on similarity to known protein structure (template)

What type of modelling approach does MODELLER has

Homology

How does MODELLER work

• Template acts as guide to build new model ]

• Optimization function runs to minimize restraints then constructs model

Software for Molecular Dynamics analysis

NAMD/VMD, GROMACS, AMBER

Molecualr Dynamics use

5ns run for removing molecular clashses and 20 ns for loop refinement

Swiss Strcture Assessment

Analysis via Ramachandran plot

SAVES programs

ProVE, Verify3D, Whatcheck, Procheck, ERRAT

ProVE

Calcilates componetns on solvent-exculeded volume of protein (van der Walls and void volume)

Verify3D

Checks the model structure on 3D profile

Whatcheck

Checks sterochemical quality (Z score and RMS-Z)

Procheck

Normality of geometry of the residues in a given protein structure

ERRAT

Verifies protein structure based on pattern of nonboneded or randomized atomic interactions