Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development

Kwangho Nam, Yihan Shao, Dan T. Major, Magnus Wolf-Watz

Research output: Contribution to journalReview articlepeer-review

2 Scopus citations

Abstract

Understanding enzyme mechanisms is essential for unraveling the complex molecular machinery of life. In this review, we survey the field of computational enzymology, highlighting key principles governing enzyme mechanisms and discussing ongoing challenges and promising advances. Over the years, computer simulations have become indispensable in the study of enzyme mechanisms, with the integration of experimental and computational exploration now established as a holistic approach to gain deep insights into enzymatic catalysis. Numerous studies have demonstrated the power of computer simulations in characterizing reaction pathways, transition states, substrate selectivity, product distribution, and dynamic conformational changes for various enzymes. Nevertheless, significant challenges remain in investigating the mechanisms of complex multistep reactions, large-scale conformational changes, and allosteric regulation. Beyond mechanistic studies, computational enzyme modeling has emerged as an essential tool for computer-aided enzyme design and the rational discovery of covalent drugs for targeted therapies. Overall, enzyme design/engineering and covalent drug development can greatly benefit from our understanding of the detailed mechanisms of enzymes, such as protein dynamics, entropy contributions, and allostery, as revealed by computational studies. Such a convergence of different research approaches is expected to continue, creating synergies in enzyme research. This review, by outlining the ever-expanding field of enzyme research, aims to provide guidance for future research directions and facilitate new developments in this important and evolving field.

Original languageEnglish
JournalACS Omega
DOIs
StatePublished - 20 Feb 2024

Bibliographical note

Publisher Copyright:
© 2024 The Authors. Published by American Chemical Society

Funding

The authors acknowledge the financial support from the National Institute of General Medical Sciences of the National Institute of Health: R01GM132481 (K.N. and M.W.W.), R44GM133270 (K.N. and Y.S.), R21GM148895 (K.N. and D.T.M.), and R01GM135392 (Y.S.); and the Swedish Research Council: VR 2021-04513 (M.W.W).

FundersFunder number
National Institutes of HealthR01GM132481, R01GM135392, R44GM133270, R21GM148895
National Institute of General Medical Sciences
VetenskapsrådetVR 2021-04513

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