Novel Peptide Inhibitors for Lactate Dehydrogenase A (LDHA): A Survey to Inhibit LDHA Activity via Disruption of Protein-Protein Interaction

Abstract

Lactate dehydrogenase A (LDHA) is a critical metabolic enzyme belonging to a family of 2-hydroxy acid oxidoreductases that plays a key role in anaerobic metabolism in the cells. In hypoxia condition, the overexpression of LDHA shifts the metabolic pathway of ATP synthesis from oxidative phosphorylation to aerobic glycolysis and the hypoxia condition is a common phenomenon occurred in the microenvironment of tumor cells; therefore, the inhibition of LDHA is considered to be an excellent strategy for cancer therapy. In this study, we employed in silico methods to design inhibitory peptides for lactate dehydrogenase through the disturbance in tetramerization of the enzyme. Using peptide as an anti-cancer agent is a novel approach for cancer therapy possessing some advantages with respect to the chemotherapeutic drugs such as low toxicity, ease of synthesis, and high target specificity. So peptides can act as appropriate enzyme inhibitor in parallel to chemical compounds. In this study, several computational techniques such as molecular dynamics (MD) simulation, docking and MM-PBSA calculation have been employed to investigate the structural characteristics of the monomer, dimer, and tetramer forms of the enzyme. Analysis of MD simulation and protein-protein interaction showed that the N-terminal arms of each subunit have an important role in enzyme tetramerization to establish active form of the enzyme. Hence, N-terminal arm can be used as a template for peptide design. Then, peptides were designed and evaluated to obtain best binders based on the affinity and physicochemical properties. Finally, the inhibitory effect of the peptides on subunit association was measured by dynamic light scattering (DLS) technique. Our results showed that the designed peptides which mimic the N-terminal arm of the enzyme can successfully target the C-terminal domain and interrupt the bona fide form of the enzyme subunits. The result of this study makes a new avenue to disrupt the assembly process and thereby oppress the function of the LDHA.

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

“…We have indeed previously found that LDH N-terminal domain truncation leads to dimers (LDH-Htr) (Figure 1a). 16 In agreement with previous studies, 35 only the association of dimers A-C and B-D in a tetramer can explain the role of this N-terminal domain in the stabilization of the tetrameric state (Figure 1a). Based on this hypothesis, we first mapped the interactions made by one subunit with a LDH dimer (A-C or B-D) using the Molecular Operating Environment (MOE) software.…”

“…29,34 Recently, new advances in the development of ligands targeting LDH oligomeric interface have offered new avenues towards LDH inhibition. 16,35,36 Targeting protein self-association is an emerging concept in drug design that can bring several advantages over classical orthosteric inhibition. First, targeting the LDH oligomeric interface could unravel new allosteric sites, potentially leading to compounds displaying improved drug-like features compare to LDH active site inhibitors.…”

“…To this end, tool compounds able to target the LDH oligomeric interface instead of its active site have been recently developed. 16,[35][36][37] Targeting a protein oligomeric state is still an underexplored strategy that can provide several benefits over active-site targeting, and could thus overcome the existing difficulties encountered with LDH orthosteric inhibitors. Targeting LDH selfassembly could indeed lead to the identification of new and potentially more druggable allosteric sites.…”

Lactate in the Regulation of Tumor Microenvironment and Therapeutic Approaches

“…These peptides were developed based on its active conformation and the interaction interface of LDHA subunits where the N-terminal arm (residues 5–17) acts as an anchor to maintain the position and distance between the two LDHA subunits. Thus, these new peptides mimic the anchoring of the LDHA subunits avoiding its tetramerization (176). These novel anti-cancer agents designed for therapy have promising advantages like low toxicity, ease of synthesis and high target specificity whereas the classical pharmalogical therapeutics.…”

Investigation of Critical Binding Pattern in SARS-CoV-2 Spike Glycoprotein with Angiotensin-Converting Enzyme 2: An in Silico Analysis 

“…It seems that the inhibition of Spike-ACE2 interaction is the most straightforward and e cient method for the prevention of SARS-CoV-2 infection using peptides or small molecules. Previously, we have performed computational methods to understand the protein-protein interaction pattern at atomic levels to seek potentially speci c peptide inhibitors for cancer treatment 10,11 . In this study, several computational methods were utilized, including molecular dynamics simulation, MM-PBSA and interaction pattern analyses.…”