Protein Ligand Complex Guided Approach for Virtual Screening

ISSN: 1875-5402 (Online)
ISSN: 1386-2073 (Print)


Volume 20, 10 Issues, 2017


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Combinatorial Chemistry & High Throughput Screening

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Editor-in-Chief:
Gerald H. Lushington
LiS Consulting, Lawrence
KS
USA


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Protein Ligand Complex Guided Approach for Virtual Screening



Combinatorial Chemistry & High Throughput Screening, 18(6): 577-590.

Author(s): Muthukumarasamy Karthikeyan, Deepak Pandit and Renu Vyas.

Affiliation: Digital Information Resource Centre, CSIR- National Chemical Laboratory, Pune- 411008, India.

Abstract

The target ligand association data is a rich source of information which is not exploited enough for drug design efforts in virtual screening. A java based open-source toolkit for Protein Ligand Network Extraction (J-ProLiNE) focused on protein-ligand complex analysis with several features integrated in a distributed computing network has been developed. Sequence alignment and similarity search components have been automated to yield local, global alignment scores along with similarity and distance scores. 10000 proteins with co-crystallized ligands from pdb and MOAD databases were extracted and analyzed for revealing relationships between targets, ligands and scaffolds. Through this analysis, we could generate a protein ligand network to identify the promiscuous and selective scaffolds for multiple classes of proteins targets. Using J-ProLiNE we created a 507 x 507 matrix of protein targets and native ligands belonging to six enzyme classes and analyzed the results to elucidate the protein-protein, protein-ligand and ligand-ligand interactions. In yet another application of the J-ProLiNE software, we were able to process kinase related information stored in US patents to construct disease-gene-ligand-scaffold networks. It is hoped that the studies presented here will enable target ligand knowledge based virtual screening for inhibitor design.

Keywords:

Complexes, protein, ligand, scaffolds, sequences, similarity score, virtual screening.



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Article Details

Volume: 18
Issue Number: 6
First Page: 577
Last Page: 590
Page Count: 14
DOI: 10.2174/1386207318666150703112620
Price: $58
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