Brian Shoichet, PhD

What I do

Our lab develops new methods for drug discovery, adopting two strategies to do so. On the one hand, we reduce biology to its molecular components, and seek to change how these fit together using synthetic molecules we design. On the other hand, we investigate how the biological molecules operate together, both in health and disease. Both processes involve intensive modeling and close collaboration between theory and experiment.

My research expertise

Molecular recognition, Structure-based inhibitor discovery, Computational chemical biology, Protein structure/function, Pharmacological networks, Chemical information in biology, Molecular docking, Promiscuous inhibition, βlactamase Gprotein coupled receptors

Degrees

PhD, Molecular Docking, University of California, San Francisco, 1991
BSc, Chemistry, Massachusetts Institute of Technology (MIT), 1985
BSci, History, Massachusetts Institute of Technology (MIT), 1985

Biography

The Shoichet lab seeks to discover chemical reagents that can illuminate biological problems. A longstanding effort to do so is by exploiting protein structures to predict new reagents and therapeutic leads (structure-based ligand discovery). Two ongoing projects are 1. Developing new computational methods for ligand discovery and 2. Applying these to G-Protein Coupled Receptors (GPCRs), which are the single largest family of signaling receptors in human cells.

Allied with this effort is an experimental research program that 3. Tests the new methods in well-controlled systems, determining x-ray crystal structures and measuring binding thermodynamics. The experimental program has led to unexpected discoveries, including the observation that many drugs and reagents can form colloidal aggregates in solution. This has led us to investigate 4. How the physical organic chemistry of drugs affects their behavior in vitro and in vivo, influencing drug delivery and formulation.

A new effort turns the entire structural view on its head, 5. Developing computational methods to relate receptors by the similarity of their ligands, rather than by protein sequence or structure. This changes pharmacological relationships dramatically—targets that would normally be considered sequence neighbors are pushed far apart (because their ligands are dissimilar), whereas other targets that supposedly have nothing to do with one another become neighbors (because their ligands are very similar). Since the new relationships are articulated by ligands, they may be directly tested both on isolated receptors and, increasingly, against model whole organisms, such as zebra fish, C. elegans and mice. This project seeks to discover the integrated chemical circuits through which drugs and reagents affect whole organisms. "