CHAPTER PROPOSAL SUBMISSION FORM

1. Provisional title of the proposed manuscript: Applications of Molecular Docking in Virtual Screening of
bioactive small molecules.

2. Author details

Scientific Title: Assistant Professor

Full Name: Sri Lavvanya Priya Sathyan
Affiliation: MetaProcambial Labs, Erode, India
Position: Research Technologist

3. Co-authors (include all your co-authors if possible at this stage)

3.1.

Scientific Title: Professor & Director

Full Name: Eganathan Palanisami
Affiliation: MetaProcambial Labs, Erode, India
Position: Director & Senior Scientist

3.2.

Scientific Title:
Full Name:
Affiliation:
Position:

4. Keywords (enter min.3): Molecular Docking, bioactive small molecules, virtual screening.
5. Define your subject area: My eight years of research work focused on Molecular modeling, Molecular
Docking and computational drug design. Cyanobacterial compounds and plant small molecules are my
central areas of research.

6. Write a short description of the chapter, clearly explaining the aims topics research methods and key
results of the chapter.

Introduction (max 150 words) :

Kitchen et al (2004) stated that the modern drug discovery includes docking, a computational technique
that places a small molecule (ligand) in the binding site of its macromolecular target (receptor) and
estimates its binding affinity. Protein-ligand docking aims to predict and rank binding orientation of
ligands in a target protein of known 3D structure (Sousa et al 2006).

Molecular Docking continues to hold great promise in the field of computer based drug design which
screens, small molecules by orienting and scoring them in the binding site of a protein. This method
gives insight into the molecular basis of the biological activities for better understanding of the action
mechanism and increased knowledge about drug interaction mechanisms. Hence docking plays an
important role in the rational drug design (Jorgensen 1991). Given the biological and pharmaceutical
significance of molecular docking, considerable efforts have been directed towards improving the
methods used to predict docking.

Body - research methods (max 150 words):

Two approaches are particularly used for molecular docking. In the first approach, a matching technique
that describes the protein and the ligand as complementary surfaces are used (Meng et al 2004). The
second step simulates the actual docking process in which the ligand-protein pairwise interaction
energies are calculated (Joseph-McCarthy et al 2007). Molecular docking ultimately seeks to predict the
best mode by which a given compound will fit into a binding site of a macromolecular target. As a result,
this usually involves two independent steps:
(i) Docking: Determines the orientation of a ligand relative to the receptor.
(ii) Scoring: Evaluates the ligand orientation. Scoring is used to evaluate the interaction between a ligand
and its target protein by ranking how the ligand fits into the binding pocket or by
predicting the absolute binding affinity between the ligand and its target protein.

Conclusion- key results (max 150 words):

Molecular Docking provides an array of valuable tools for drug design and analysis. Commercial software
programs continue to expand upon the core user interface. New algorithms from industry and academia
are quickly incorporated into the high end packages. Public domain packages are becoming more stable
and offering functionality that rivals some of the commercial offerings computers continue to double in
speed every year and a half while graphic displays became more sophisticated and intuitive. All of these
elements make molecular docking an integral part of drug design. It continues to extend its role in
exciting new techniques such as computational enzymology, genomics, and proteomic search engines.

References:

1) Kitchen, DB, Decornez, H, Furr, JR & Bajorath, J 2004, Docking and scoring in virtual screening for
drug discovery: methods and applications‟, Nature reviews Drug discovery, vol. 3, no.11, pp.
935–949.

2) Sousa, SF, Fernandes, PA & Ramos, MJ 2006, Protein-ligand docking: current status and future
challenges‟, Proteins, vol.65, no.1, pp.15-26.

3) Jorgensen, WL 1991, „Rusting of the lock and key model for protein ligand binding‟, Science, vol.
254, no. 5034, pp.954–955.

4) Meng, EC, Polacco, BJ & Babbitt, PC 2004, „Superfamily active site templates‟, Proteins, vol.55,
no.4, pp.962–976.

5) Joseph-McCarthy, D, Baber, JC, Feyfant, E, Thompson, DC & Humblet, C 2007, Lead optimization
via high-throughput molecular docking‟, Current opinion in drug discovery & development,
vol.10, no.3, pp.264–274.

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