The Effect of a Tightly Bound Water Molecule on Scaffold Diversity in the Computer-aided De Novo Ligand Design of CDK2 Inhibitors

Overview

Journal J Mol Model

Publisher Springer

Specialty Molecular Biology

Date 2005 Dec 24

PMID 16374623

Citations 6

Authors

Alfonso T Garcia-Sosa

Ricardo L Mancera

Affiliations

Soon will be listed here.

Abstract

We have determined the effects that tightly bound water molecules have on the de novo design of cyclin-dependent kinase-2 (CDK2) ligands. In particular, we have analyzed the impact of a specific structural water molecule on the chemical diversity and binding mode of ligands generated through a de novo structure-based ligand generation method in the binding site of CDK2. The tightly bound water molecule modifies the size and shape of the binding site and we have found that it also imposed constraints on the observed binding modes of the generated ligands. This in turn had the indirect effect of reducing the chemical diversity of the underlying molecular scaffolds that were able to bind to the enzyme satisfactorily. [Figure: see text].

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