Computational Modeling of Water and Proteins in Drug Discovery

Author

Anthony Cruz Balberdy, The Graduate Center, City University of New YorkFollow

Date of Degree

6-2021

Document Type

Dissertation

Degree Name

Ph.D.

Program

Chemistry

Advisor

Thomas P. Kurtzman

Committee Members

Gustavo E. López

Emilio Gallicchio

Nicolas Giovambattista

Subject Categories

Biophysics | Chemistry | Other Chemistry | Physical Chemistry

Keywords

Solvation Thermodynamic Mapping, Drug Design, Drug Discovery, Molecular Modeling, Homology Modeling, Docking, GIST, SSTMap

Abstract

This thesis aims to improve how structural and thermodynamic properties of water on protein surfaces can be exploited to aid early stage drug discovery and lead optimization. We first discuss our development of SSTMap, a public domain software suite that maps out the properties of water on biomolecular surfaces. We then show the utility of these maps in describing differences in binding affinities between congeneric pairs of ligands. We then discuss our use of solvation maps in the prospective discovery of novel binders to cytochrome C peroxidase. Finally, we present our creation and validation of a homology model of Interleukin-24 (IL-24).

Recommended Citation

Cruz Balberdy, Anthony, "Computational Modeling of Water and Proteins in Drug Discovery" (2021). CUNY Academic Works.
https://academicworks.cuny.edu/gc_etds/4340