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HOMOLOGY MODELING AND MOLECULAR DOCKING: TOOLS FOR

DRUG DISCOVERY

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What is Bioinformatics

• Science that uses the instruments of informatics to analyze biological data in order to formulate hypothesis about life

• 1990s term started appearing in scientific journals

• 1960s onwards laboratories were able to use computers with good graphical performance

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Storage, retrieval and analysis of biological data with informatics tools

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Central Dogma of Life

StructuralFunctional: Catalyst & TransportSignalingImmunityToxins

Disease and Therapy

Functions of Proteins

FLOW OF INFORMATION

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Role in current research????To know how cellular activities are

altered in different disease states

Combining biological data to form a comprehensive picture of these

activities

POSTGENOMIC ERA- learned how to interpret and manipulate a genome.

A wonderful but also worrisome achievement

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Drug Discovery & DevelopmentIdentify disease

Isolate proteininvolved in disease (2-5 years)

Find a drug effectiveagainst disease protein(2-5 years)

Preclinical testing(1-3 years)

Formulation &Scale-up

Human clinical trials(2-10 years)

FDA approval(2-3 years)

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Impact of new technology on drug discovery

• The last few years have seen a number of “revolutionary” new technologies:– Gene chips, genomics and HGP– Bioinformatics & Molecular biology– More protein structures– High-throughput screening & assays– Virtual screening and library design– Docking– Combinatorial chemistry– In-vitro ADME testing– Other computational methods

Identify disease

Isolate protein

Find drug

Preclinical testing

GENOMICS, PROTEOMICS & BIOPHARM.

HIGH THROUGHPUT SCREENING

MOLECULAR MODELING

VIRTUAL SCREENING

COMBINATORIAL CHEMISTRY

IN VITRO & IN SILICO ADME MODELS

Potentially producing many more targetsand “personalized” targets

Screening up to 100,000 compounds aday for activity against a target protein

Using a computer topredict activity

Rapidly producing vast numbersof compounds

Computer graphics & models help improve activity

Tissue and computer models begin to replace animal testing9

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R&D spending up, new drugs down

Source: http://bio-associate.blogspot.in/2013/02/forget-in-house-r-enter-fully.html

To overcome these limitations R&D industry/Academia usingHomology Modeling and Docking tools

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HOMOLOGY

existence of shared ancestry between a pair of structures or genes, in different species

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Determining Structure

• NMR

• X-ray diffraction

• Electron Microscopy

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Why we need a Model???• If the structure of target protein has not been

experimentally determined!!!• One can try to build a model of the protein of interest• Evolutionarily related proteins have similar sequences

and naturally occurring homologous proteins have similar protein structure.

• 3D protein structure is more conserved than would be expected on the basis of sequence conservation alone.

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How to Model

MO

DEL

ING HOMOLOGY

THREADING

ab initio

Based on similar sequence

Based on known folds

From scrap: prop of aa

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Homology ModelingFASTA

sequence

Template search

&selection

Sequence alignment

Model building

Evaluation and

Validation

Modeler, SWISS-Modeler(Dills HP /Cubic lattice model)

QueryTemplate

PROCHECK, VERIFY-3D(Ramachandran plot)RMSD values

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Flow Chart

Structure is the ability to function

“Anifensen theory”

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Sequences vs Structure

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DOCKING

Docking attempts to find the “best” matching between two molecules

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Molecular Docking• Aim of docking:

Whether the two molecules “interact”If so, what is the orientation that maximizes the

“interaction” while minimizing the total “energy” of the complex• ImportanceSignal transductiondrug design: The results of docking can be used to find inhibitors for specific target proteins and thus to design new drugs.

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Types of Docking• Protein-Protein Docking-rigid • Protein-Ligand Docking-flexibleTechniques• Surface representation, that efficiently represents the

docking surface and identifies the regions of interest (cavities and protrusions)

• Connolly surface – atomic sphere• Lenhoff technique- complementary surface• Kuntz et al.,- clusteredSpheres• Alpha shapes- shape

• Surface matching that matches surfaces to optimize a binding score:

• Geometric Hashing

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Docking tools

• GlideDOCK• FlexX• GOLD• AutoDOCK• RosettaDock• Hammerhead • FLOG

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My Recent work @ NIPGR: INSA fellowship

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Model

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Screen shot showing the protein preparation wizard

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Ramachandran plot showing the distribution of residues

Superimposition of iNOS (grey) with final prepared protein (Spectrum)

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Grid generation and Active site identification

Information generated at different points in the Drug Design process

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Gene chip experiments

Project selection decisionsAssay protocols

HTS resultsSeries selection decisionsSAR studies

Protein structures

Combinatorial Expts.PharmacophoresADME studies

Toxicology studiesScaleup reactions

Lead cmpd decisions

Clinical Trials dataDoctor/patient studies

Marketing, surveys, etc27

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Venkatraman Ramakrishnan

Wide scope for research

structure and function of the ribosome-2009

Roger D. Kornberg

molecular basis of eukaryotic transcription2006

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Important Data Banks and References

http://www.ncbi.nlm.nih.gov/

http://www.rcsb.org/pdb/home/home.do

http://www.uniprot.org/

Pymol

OERS