title: Library design using BCUT chemistry-space descriptors and multiple four-point pharmacophore fingerprints: simultaneous optimization and structure-based diversity.
abstract: New applications of fingerprints of multiple potential 4-point three-dimensional (3D) pharmacophores in combinatorial library design and virtual screening are presented. Preliminary results demonstrating the feasibility of a simulated annealing process for combinatorial reagent selection that concurrently optimizes product diversity in BCUT chemistry space and in terms of unique 4-point pharmacophores are discussed, and the advantage of using a customized chemistry-space derived for the library design is demonstrated. In addition, an extension to the multiple pharmacophore method for structure-based design that uses the shape of the target site as an additional constraint is presented. This development enables the docking process to be quantified in terms of the number and identities of the pharmacophoric hypotheses that can be matched by a compound or a library of compounds. The design of an example combinatorial library based on the Ugi condensation reaction and a serine protease active site is described.
authors.affiliation: Department of Macromolecular Structure and Biopharmaceuticals, Bristol-Myers Squibb Pharmaceutical Research Institute, P.O. Box 4000, Princeton, NJ 08543, USA. jonathan.mason@bms.com
authors.forename: J S
authors.initials: JS
authors.lastname: Mason
authors.forename: B R
authors.initials: BR
authors.lastname: Beno
mesh_terms: D001665:Binding Sites; D020650:Combinatorial Chemistry Techniques; D003196:Computer Graphics; D003198:Computer Simulation; D015195:Drug Design; D065427:Factor Xa Inhibitors; D007202:Indicators and Reagents; D008956:Models, Chemical; D008958:Models, Molecular; D011485:Protein Binding
chemical_list: D065427:Factor Xa Inhibitors; D007202:Indicators and Reagents