Discovery of New Candidates Targeting the SH2 Domains of Spleen Tyrosine Kinase (Syk) Through In Silico Studies

Şansaçar M., Sarı C., Yücel M. S., Gencer Akçok E. B., Akçok İ.

ChemistrySelect, cilt.10, sa.22, 2025 (SCI-Expanded) identifier

  • Yayın Türü: Makale / Tam Makale
  • Cilt numarası: 10 Sayı: 22
  • Basım Tarihi: 2025
  • Doi Numarası: 10.1002/slct.202500547
  • Dergi Adı: ChemistrySelect
  • Derginin Tarandığı İndeksler: Science Citation Index Expanded (SCI-EXPANDED), Scopus, Academic Search Premier
  • Anahtar Kelimeler: Drug discovery, Molecular docking, Molecular dynamics, SH2 domains, Spleen tyrosine kinase
  • Abdullah Gül Üniversitesi Adresli: Evet

Özet

Src homology 2 (SH2) domains have become an increasingly popular candidate for researchers to search for novel therapeutics to target different diseases. Spleen tyrosine kinase (Syk) is one of the proteins with two SH2 domains that has a role in the pathogenesis of many diseases. Here, we report the discovery of a promising natural product (NP) inhibitor that targets the N-terminal SH2 (N-SH2) and C-terminal SH2 (C-SH2) domains of Syk simultaneously, through structure-based drug discovery approach. Molecular docking studies, followed by molecular dynamics (MD) simulations and molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) calculations, were utilized to reveal the interactions between NPs from “the COlleCtion of Open NatUral producTs (COCONUT)” database and Syk enzyme. Five natural products that have lowest Scoring and Minimization with AutoDock Vina (SMINA) scores against both SH2 domains of Syk were selected for further studies and compound CNP0265345 has the best binding free energies toward both C-SH2 and N-SH2 of Syk enzyme with −44.54 and −55.98 kcal/mol, respectively. Drug-likeness properties, absorption, distribution, metabolism, and excretion (ADME) and carcinogenicity predictions were also studied. In conclusion, our work highlights a novel drug candidate to target the Syk enzyme of SH2 domains using in silico methods.