Molecular Docking and Simulation Studies Predict Lactyl-CoA as the Substrate for P300 Directed Lactylation

According to Warburg effects, cancer cells are known to produce lactate as an end product instead of pyruvate and accumulation of lactate is linked to metabolic reprogramming. Hiowever, substantial exist in terms of the non-metabolic role of lactate including modification of histones during epigenetic regulation, in particular.

Methods

This study employs in silico molecular docking and molecular dynamics study to determine the potential mechanisms of lactylation on histone proteins that achieve epigenetic changes in cancer and non-cancer cells. Here, we tested three potential substrate sources for lactylation, namely lactate (CHEBI ID:24996), lactyl-CoA (CHEBI ID:15529) and (R)-Slactoylglutathione (PubChem ID-440018). A histone acetyltransferase p300 (HAT p300) enzyme (PDB ID: 6GYR) was considered as a potential candidate for the lactylation process.

Results

Among the studied substrates for the lactylation process, molecular docking reveals a highly efficient binding affinity (docking energy -8.6 Kcal/Mol) of lacyl-CoA with p300 enzyme. On the other hand, lactate and (R)-S-Lactoylglutathione did not shown any significant and specific binding to HAT p300 enzyme. Furthermore, molecular dynamics simulation study suggestsa stable binding of lactyl-CoA at the substrate-binding site of p300 with amino acid residues ASP-1399, HIS1402, ARG-1410, THR1411, TYR1414, TRP1436, ASP1454 and LYS1456.

Conclusion

In conclusion, our data support that lactyl-CoA is a potential substrate for lactylation carried out by the HAT p300 enzyme. However, lactyl-CoA is not detected at the physiological level in cancer and non-cancer supporting cells such as macrophage. Based on our data and existing views on lactylation, the authors propose an involvement of pro-tumor bacteria in this that converts lactate to lactyl-CoA and lactyl-CoA is shuttled to the macrophage within the tumor microenvironment. Due to lactyl-CoA entry into macrophages (anti-tumorigenic)s, lactylation process allow the transcriptional changes and achieve the M1 to M2 macrophage polarization (pro-tumor) and in turn, promotes the tumor growth and survival.