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Open AccessArticle

Binding-Site Match Maker (BSMM): A Computational Method for the Design of Multi-Target Ligands

by Jinming Zhou 1,2,* and Jian Hui Wu 3,4,5,*
1
Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, 688 Yingbin Road, Jinhua 321004, China
2
Drug Discovery and Innovation Center, College of Chemistry and Life Sciences, Zhejiang Normal University, 688 Yingbin Road, Jinhua 321004, China
3
Segal Cancer Center, Montreal, QC H3T 1E2, Canada
4
Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, McGill University, 3755 Cote-Ste-Catherine, Rd., Montreal, QC H3T 1E2, Canada
5
Department of Oncology, McGill University, 3755 Cote-Ste-Catherine, Rd., Montreal, QC H3T 1E2, Canada
*
Authors to whom correspondence should be addressed.
Academic Editor: Maria Novella Romanelli
Molecules 2020, 25(8), 1821; https://doi.org/10.3390/molecules25081821
Received: 29 January 2020 / Revised: 30 March 2020 / Accepted: 1 April 2020 / Published: 16 April 2020
(This article belongs to the Special Issue Multitarget Ligands)
Multi-target ligand strategies provide a valuable method of drug design. However, to develop a multi-target drug with the desired profile remains a challenge. Herein, we developed a computational method binding-site match maker (BSMM) for the design of multi-target ligands based on binding site matching. BSMM was built based on geometric hashing algorithms and the representation of a binding-site with physicochemical (PC) points. The BSMM software was used to detect proteins with similar binding sites or subsites. In particular, BSMM is independent of protein global folds and sequences and is therefore applicable to the matching of any binding sites. The similar sites between protein pairs with low homology and/or different folds are generally not obvious to the visual inspection. The detection of such similar binding sites by BSMM could be of great value for the design of multi-target ligands. View Full-Text
Keywords: multi-target ligand; drug design; geometric hashing; similar binding site multi-target ligand; drug design; geometric hashing; similar binding site
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MDPI and ACS Style

Zhou, J.; Wu, J.H. Binding-Site Match Maker (BSMM): A Computational Method for the Design of Multi-Target Ligands. Molecules 2020, 25, 1821.

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