Molecular Dynamics Simulation-Driven Focused Virtual Screening and Experimental Validation of Inhibitors for MTDH-SND1 Protein–Protein Interaction

Abstract

Protein–protein interactions (PPIs), in general, are attractive yet challenging drug targets. As a typical PPI, MTDH-SND1 interaction has recently been reported to be a promising drug target to malignant breast cancer and other cancer types. However, the lack of well-defined deep pockets on the MTDH-SND1 interface makes it a tough target for rational drug discovery attempts. To address this issue, in this study, a long time-scale molecular dynamics (MD) simulation-driven focused screening strategy was proposed and reported. A total of 12 virtual hits were purchased and tested in SPR assay, yielding 10 SND1 binders with micromolar or less affinities. As an example, compound L5, the second best hit with a K D of 2.64 μM, was further assayed in MDA-MB-231 breast cancer cells, showing an antiproliferation IC50 value of 57 μM in a CCK8 assay with a dampened interruption between MTDH and SND1 proteins detected by immunofluorescence colocalization imaging. As the most potent small molecule inhibitor in the class so far, our preliminary study combining molecular dynamics simulation and in vitro cellular functional evidence indicates L5 could serve as a lead compound for future optimization or pharmacologic studies, and the MD-driven focused screening strategy could be useful for other PPI drug discovery attempts.

Peptide Drug Design Using Alchemical Free Energy Calculation: An Application and Validation on Agonists of Ghrelin Receptor

“…The entropy contribution was not considered in this study as adding the entropy contribution may lead to additional errors. This setup has been used successfully to characterize the potential binding mode of the ligand on different protein–ligand systems in our previous studies. − …”

Overcoming MTDH and MTDH-SND1 complex: driver and potential therapeutic target of cancer

“…Changing the linkage position of the amine and substituting the N atom of the triazolopyridine in the B fragment simultaneously results in a significant decrease in inhibition activity, suggesting that the linkage mode between the A and B fragments and the alpha N of the triazolopyridine may be important structural affecting the binding of small molecule inhibitors to SND1. Although no direct hydrogen bond between the sulfonamide group and the SND1 pocket was observed from the co-crystal structure, Xu et al suggested that the sulfonamide group, rather than the methyltriazolopyridinamine part, might form a hydrogen bond with SND1 R255 based on molecular dynamics simulation study of C26-A6 132 . The reports of compound C26 series as well as two SND1 co-crystals validate the hydrophobic pocket in the MTDH-SND1 complex with potential binding ability to small molecule inhibitors.…”

“…Based on the discovery of C26 series molecules and the evaluation of anti-tumor activity, Xu et al discovered 7 small molecules that could bind to SND1 protein with KD value less than 15μM from 1.2 million molecules by molecular docking and various molecular dynamics simulations 132 . Among them, compound L5 had an IC50 value of 57 μM for MDA-MB-231 cell proliferation and immunofluorescence (IF) assay verified that L5 inhibited the PPI of MTDH-SND1 in cells.…”

“…The protein-protein inhibition activity of compound L5 must be further verified by splitluciferase or FRET experiments, and the in vivo activity of small-molecule inhibitor needs further confirmation. Meanwhile, researchers reported that the hydrogen bond interactions between C26s and SND1 R255 contributed significantly to the binding of the ligands to SND1, based on their molecular dynamics simulation 132,133 . These studies supplemented the research on the binding mode of MTDH-SND1 small molecule inhibitors with SND1 and guided further small molecule development.…”