Driving Structure-Based Drug Discovery through Cosolvent Molecular Dynamics

• Published in: Journal of medicinal chemistry Vol. 59; no. 23; pp. 10383 - 10399
• Main Authors: Ghanakota, Phani, Carlson, Heather A
• Format: Journal Article
• Language: English
• Published: United States 08.12.2016
• Subjects: Drug Discovery; Molecular Dynamics Simulation
• ISSN: 0022-2623; 1520-4804
• DOI: 10.1021/acs.jmedchem.6b00399

Identifying binding hotspots on protein surfaces is of prime interest in structure-based drug discovery, either to assess the tractability of pursuing a protein target or to drive improved potency of lead compounds. Computational approaches to detect such regions have traditionally relied on energy minimization of probe molecules onto static protein conformations in the absence of the natural aqueous environment. Advances in high performance computing now allow us to assess hotspots using molecular dynamics (MD) simulations. MD simulations integrate protein flexibility and the complicated role of water, thereby providing a more realistic assessment of the complex kinetics and thermodynamics at play. In this review, we describe the evolution of various cosolvent-based MD techniques and highlight a myriad of potential applications for such technologies in computational drug development.