Molecular Dynamics Simulation-Driven Focused Virtual Screening and Experimental Validation of Inhibitors for MTDH-SND1 Protein–Protein Interaction
Molecular Docking Simulation
Drug Discovery
Humans
Proteins
Membrane Proteins
RNA-Binding Proteins
Female
Breast Neoplasms
Molecular Dynamics Simulation
Endonucleases
3. Good health
DOI:
10.1021/acs.jcim.3c00310
Publication Date:
2023-05-25T08:37:20Z
AUTHORS (7)
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 KD 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.
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