Screening and Analysis of Potential Inhibitors of SHMT2

Bojin Chen, John Z.H. Zhang

Research output: Contribution to journalArticlepeer-review


Serine hydroxymethyltransferase 2 (SHMT2) has garnered significant attention as a critical catalytic regulator of the serine/glycine pathway in the one-carbon metabolism of cancer cells. Despite its potential as an anti-cancer target, only a limited number of inhibitors have been identified so far. In this study, we employed seven different scoring functions and skeleton clustering to screen the ChemDiv database for 38 compounds, 20 of which originate from the same skeleton structure. The most significant residues from SHMT2 and chemical groups from the inhibitors were identified using ASGBIE (Alanine Scanning with Generalized Born model and Interaction Entropy), and the binding energy of each residue was quantitatively determined, revealing the essential features of the protein–inhibitor interaction. The two most important contributing residues are TYR105 and TYR106 of the B chain followed by LEU166 and ARG425 of the A chain. The findings will be greatly helpful in developing a thorough comprehension of the binding mechanisms involved in drug–SHMT2 interactions and offer valuable direction for designing more potent inhibitors.

Original languageEnglish (US)
Pages (from-to)651-667
Number of pages17
Issue number4
StatePublished - Dec 2023


  • alanine scan
  • binding free energy
  • interaction entropy
  • molecular dynamics simulation
  • virtual screening

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology (miscellaneous)


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