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Ligand Binding and Linkage

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Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked. In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...

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TANGO: A high through-put conformation generation and semiempirical method-based optimization tool for ligand

Vivek Gavane¹, Shruti Koulgi¹, Vinod Jani¹

¹HPC - Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing, Pune, India.

Journal of Computational Chemistry

|October 27, 2018

Summary

TANGO generates and optimizes lead molecule conformations using semiempirical calculations and MPI for efficient load balancing. This tool aids in high-throughput screening for drug discovery by providing stable molecular conformations.

Keywords:

conformation generation mopac optimization torsion library

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Area of Science:

Computational chemistry
Drug discovery and development

Background:

Lead optimization is critical in drug discovery.
Determining accurate 3D conformations of lead molecules is challenging.

Purpose of the Study:

To introduce TANGO, a novel tool for conformation generation and optimization.
To leverage semiempirical energy calculations and MPI for efficient conformational analysis.

Main Methods:

Conformation generation via torsion angle rotation of exocyclic bonds.
Energy calculations using MOPAC.
Implementation of Message Passing Interface (MPI) for parallel processing.
Master-slave architecture for load balancing.

Main Results:

TANGO demonstrates significant scalability across multiple nodes and cores.
The tool efficiently generates semiempirically optimized small molecule conformations.
Stable and alternate stable conformers are identified through conformational ensemble generation.

Conclusions:

TANGO is a valuable tool for high-throughput conformation generation in drug discovery.
The use of MPI enhances the efficiency and scalability of conformational analysis.
The generated conformational ensembles aid in understanding ligand molecule stability.