Andrew S. Murkin

PhD

Andrew Murkin.

Andrew S. Murkin

PhD

Andrew S. Murkin

PhD

Research Interests

Bioorganic chemistry: Determination of enzyme mechanisms and transition states; synthesis of inhibitors, alternative substrates, and isotopically labeled compounds; enzyme kinetics

Education

  • Postdoctoral Fellow, Albert Einstein College of Medicine, 2004-2009
  • PhD, University of British Columbia, 2004
  • Postdoctoral Fellow, Albert Einstein College of Medicine, 2004-2009

Awards and Honors

  • National Science Foundation CAREER Award, 2013
  • DuPont Young Professor Award, 2012
  • Natural Science and Engineering Research Council (NSERC) Scholarship, 1999

Specializations

  • Enzyme mechanisms
  • Determination of transition-state structures of enzyme-catalyzed reactions
  • Synthesis of enzyme inhibitors

Research Summary

The primary goal of research in the Murkin Laboratory is to understand the mechanisms of enzymatic processes related to disease and to develop inhibitors that may prove beneficial in drug development. The group employs two main approaches for such “rational design” of inhibitors: transition state mimicry and covalent inhibition.

Stable compounds that resemble the reaction’s transition state are often potent inhibitors. To design such compounds, the enzymatic transition-state structure is elucidated by a combination of experiment and computation. First, multiple kinetic isotope effects (KIEs) are measured, which give a quantitative description of the bonding changes the substrate undergoes as it traverses through the transition state. Then, a transition-state model is generated by matching experimental KIEs to those calculated using quantum mechanical computation. This model serves as a blueprint for the design of transition-state analogues.

An alternative rational strategy is the design of mechanism-based or targeted covalent inhibitors. In the former, the enzyme processes the inhibitor partially through its mechanism as if it were a substrate, but an important feature stops the reaction at an intermediate stage, trapping the enzyme as a covalent adduct. In the latter, a scaffold that is known to bind reversibly to the target enzyme is affixed with a carefully chosen electrophilic group that reacts with a neighboring amino acid residue only after binding tightly to the enzyme, leading to highly selective inhibition.

In the Murkin Laboratory, students gain expertise in many of the chemical, biochemical, and biophysical tools essential for pursuing careers in academia or industry. Among these methods are protein expression, enzyme kinetics, and synthesis of inhibitors and isotopically labeled compounds. Projects are directed at drug targets in infectious diseases including malaria, tuberculosis, and bacterial infections.

Selected Recent Publications

* = authors contributed equally

  • Ray, S.; Murkin, A.S.* New Electrophiles and Strategies for Mechanism-Based and Targeted Covalent Inhibitor Design. Special Issue Invitation, Biochemistry 2019, 58, 5234-5244.
  • Ray, S.; Kreitler, D.F.; Gulick, A.M.; Murkin, A.S.* The Nitro Group as a Masked Electrophile in Covalent Enzyme Inhibition. ACS Chem Biol 2018, 13, 1470-1473.
  • Pham, T.V.; Murkin, A.S.; Moynihan, M.M.; Harris, L.; Tyler, P.C.; Shetty, N.; Sacchettini, J.C.; Huang, H.-L. A; Meek, T.D.  Mechanism-based Inactivator of Isocitrate Lyases 1 and 2 from Mycobacterium Tuberculosis. Proc Nat Acad Sci 2017, 114, 7617-7622.
  • Kholodar, S.A.; Allen, C.L.; Gulick, A.M.; Murkin, A.S. The Role of Phosphate in a Multistep Enzymatic Reaction: Comparison of Reactions of the Substrate and Intermediate in Pieces. J Am Chem Soc 2015, 137, 2748-2756. doi:10.1021/ja512911f.
  • Murkin, A.S.; Manning, K.A.; Kholodar, S.A. Mechanism and Inhibition of 1-Deoxy-D-xylulose-5-phosphate Reductoisomerase. Bioorg Chem 2014, 57, 171-185.
  • Kholodar, S.A.*; Tombline, G.*; Liu, J.; Tan, Z.; Allen, C.L.; Gulick, A.M.; Murkin, A.S. Alteration of the Flexible Loop in 1-Deoxy-D-xylulose-5-phosphate Reductoisomerase Boosts Enthalpy-Driven Inhibition by Fosmidomycin. Biochemistry 2014, 53, 3423-3431.
  • Moynihan, M.M.; Murkin, A.S. Cysteine Is the General Base That Serves in Catalysis by Isocitrate Lyase and in Mechanism-Based Inhibition by 3-Nitropropionate. Biochemistry 2014, 53, 178-187.