Discovery of a novel lactate dehydrogenase tetramerization domain using epitope mapping and peptides

Léopold Thabault,Maxime Liberelle,Katarina Koruza,Esra Yildiz,Nicolas Joudiou,Joris Messens,Lucie Brisson,Johan Wouters,Pierre Sonveaux,Raphaël Frédérick

doi:10.1016/j.jbc.2021.100422

Abstract

Despite being initially regarded as a metabolic waste product, lactate is now considered to serve as a primary fuel for the tricarboxylic acid cycle in cancer cells. At the core of lactate metabolism, lactate dehydrogenases (LDHs) catalyze the interconversion of lactate to pyruvate and as such represent promising targets in cancer therapy. However, direct inhibition of the LDH active site is challenging from physicochemical and selectivity standpoints. However, LDHs are obligate tetramers. Thus, targeting the LDH tetrameric interface has emerged as an appealing strategy. In this work, we examine a dimeric construct of truncated human LDH to search for new druggable sites. We report the identification and characterization of a new cluster of interactions in the LDH tetrameric interface. Using nanoscale differential scanning fluorimetry, chemical denaturation, and mass photometry, we identified several residues (E62, D65, L71, and F72) essential for LDH tetrameric stability. Moreover, we report a family of peptide ligands based on this cluster of interactions. We next demonstrated these ligands to destabilize tetrameric LDHs through binding to this new tetrameric interface using nanoscale differential scanning fluorimetry, NMR water–ligand observed via gradient spectroscopy, and microscale thermophoresis. Altogether, this work provides new insights on the LDH tetrameric interface as well as valuable pharmacological tools for the development of LDH tetramer disruptors.

Highlights

While lactate has long been considered as a mere byproduct of glycolysis, it is regarded as a potential purpose of accelerated glycolysis in cancer, in the light of the numerous benefits it provides to tumor growth [3]
Targeting lactate dehydrogenases (LDHs) tetrameric interface can yield to molecules disrupting both lactate dehydrogenase heart isozyme homotetramer (LDH-1) and lactate dehydrogenase muscle isozyme homotetramer (LDH-5), which is in line with the current pan-LDH inhibition strategy [16]
We first mapped the interactions made by one subunit with an LDH dimer (A–C or B–D) using the Molecular Operating Environment (MOE; Chemical Computing Group [ChemComp]) software [42]

Summary

Introduction

While lactate has long been considered as a mere byproduct of glycolysis, it is regarded as a potential purpose of accelerated glycolysis in cancer, in the light of the numerous benefits it provides to tumor growth [3]. It has been shown that one LDH isoenzyme can compensate for the Discovery of a lactate dehydrogenase tetramerization domain genetic disruption of the other in order to sustain the Warburg phenotype [23] These studies support the idea that dual LDH inhibitors could bring an additional therapeutic value over selective isoenzyme inhibition. An inherent difficulty in achieving therapeutic LDH inhibition stems from its high intracellular concentration; LDHs are highly concentrated in cancer cells, with protein concentrations reported in the micromolar range [29] This high cellular concentration often hampers the observation of cell-based inhibition below that micromolar threshold, even for the more potent nanomolar inhibitors reaching micromolar concentrations in tumors [29, 32]. Targeting the LDH oligomeric state could reduce its intracellular concentration, leading to substoichiometric inhibition, higher efficacy

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Conclusion