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  • Poster presentation
  • Open Access

Development of target focused library against drug target of P. falciparumusing SVM and Molecular docking

Journal of Cheminformatics20124 (Suppl 1) :P48

  • Published:


  • Support Vector Machine
  • Radial Basis Function
  • Dock
  • Molecular Docking
  • Antimalarial Drug

PfHslV, a homolog of β subunit of 20S proteasome forms the proteolytic core of the PfHslUV machinery in P. falciparum [1, 2]. PfHslV has no homolog in the human host and it is a promising drug target essential to the plasmodial metabolism. The use of single proteasome inhibitor targeting these threonine proteases has a potential to be antimalarial drug candidate. One of our recent studies identified several promising inhibitors against 20S β5 subunit of P. falciparum [3]. The present study adopts a similar knowledge based virtual screening strategy using Support Vector Machines (SVM) and molecular docking to build a focused library of potential PfHslV inhibitors. SVM model has been trained using 170 molecular descriptors of 64 inhibitors and 208 putative non-inhibitors. The non-linear classifier based on Radial Basis Function (RBF) kernel yielded classification accuracy of 97%. The SVM model rapidly predicted inhibitors from NCI library and were subsequently docked in to the active site of an optimised three-dimensional model of PfHslV. The novel drug-like PfHslV inhibitors with very good binding affinity and novel scaffold can be a good starting point to develop new antimalarial drugs.

Authors’ Affiliations

Structural and Computational Biology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110070, India
Department of Computer Science, Jamia Millia Islamia, New Delhi, 110025, India


  1. Ramasamy G, Gupta D, Mohmmed A, Chauhan VS: Characterization and localization of Plasmodium falciparum homolog of prokaryotic ClpQ/HslV protease. Mol Biochem Parasitol. 2007, 152: 139-148. 10.1016/j.molbiopara.2007.01.002.View ArticleGoogle Scholar
  2. Subramaniam S, Mohmmed A, Gupta D: Molecular modeling studies of the interaction between Plasmodium falciparum HslU and HslV Subunits. J Biomol Struct Dyn. 2009, 26: 403-524.View ArticleGoogle Scholar
  3. Subramaniam S, Mehrotra M, Gupta D: Support Vector Machine based prediction of P. falciparum proteasome inhibitors and development of focused library by molecular docking. Comb Chem High Throughput Screen. 2011, 14 (10): 898-907. 10.2174/138620711797537058.View ArticleGoogle Scholar


© Subramaniam et al; licensee BioMed Central Ltd. 2012

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.