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Chiral discrimination in a mutated IDH enzymatic reaction in cancer: a computational perspective

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Abstract

Chiral discrimination in biological systems, such as l-amino acids in proteins and d-sugars in nucleic acids, has been proposed to depend on various mechanisms, and chiral discrimination by mutated enzymes mediating cancer cell signaling is important in current research. We have explored how mutated isocitrate dehydrogenase (IDH) catalyzes the oxidative decarboxylation of isocitrate to α-ketoglutarate which in turn is converted to d-2-hydroxyglutatrate (d-2HG) as a preferred product instead of l-2-hydroxyglutatrate (l-2HG) according to quantum chemical calculations. Using transition state structure modeling, we delineate the preferred product formation of d-2HG over l-2HG in an IDH active site model. The mechanisms for the formation of d-2HG over l-2HG are assessed by identifying transition state structures and activation energy barriers in gas and solution phases. The calculated reaction energy profile for the formation of d-2HG and l-2HG metabolites shows a 29 times higher value for l-2HG as compared to d-2HG. Results for second-order Møller–Plesset perturbation theory (MP2) do not alter the observed trend based on Density Functional Theory (DFT). The observed trends in reaction energy profile explain why the formation of D-2HG is preferred over l-2HG and reveal why mutation leads to the formation of d-2HG instead of l-2HG. For a better understanding of the observed difference in the activation barrier for the formation of the two alternative products, we performed natural bond orbital analysis, non-covalent interactions analysis and energy decomposition analysis. Our findings based on computational calculations clearly indicate a role for chiral discrimination in mutated enzymatic pathways in cancer biology.

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Acknowledgements

This work was financially supported by Department of Science and Technology (DST), Science and Engineering Research Board (SERB), India (Ref: YSS/2014/001019). We thank Dr. Venkatesan S. Thimmakondu, San Diego State University, San Diego for helping us to plot the NCI signatures. We also thank anonymous referees for critical comments and suggestions.

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  1. Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India

    Masthan Thamim & Krishnan Thirumoorthy

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  1. Masthan Thamim
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Correspondence to Krishnan Thirumoorthy.

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Thamim, M., Thirumoorthy, K. Chiral discrimination in a mutated IDH enzymatic reaction in cancer: a computational perspective. Eur Biophys J 49, 549–559 (2020). https://doi.org/10.1007/s00249-020-01460-x

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