Quantum chemical, spectroscopic, and in silico molecular docking and molecular dynamics studies on thymotrinan, which has immunomodulatory and neuroprotective properties

Er A., Çelik S., Özel A., Akyüz S.

SCIENTIFIC REPORTS, cilt.16, ss.1-21, 2026 (SCI-Expanded, Scopus)

  • Yayın Türü: Makale / Tam Makale
  • Cilt numarası: 16
  • Basım Tarihi: 2026
  • Doi Numarası: 10.1038/s41598-026-66302-w
  • Dergi Adı: SCIENTIFIC REPORTS
  • Derginin Tarandığı İndeksler: Academic Search Ultimate (EBSCO), Natural Science Collection (ProQuest), Biological Science Database (ProQuest), Biomedical Reference Collection: Corporate Edition (EBSCO), Health Research Premium Collection (ProQuest), Scopus, Science Citation Index Expanded (SCI-EXPANDED), BIOSIS, Chemical Abstracts Core, EMBASE, MEDLINE, Directory of Open Access Journals, Zoological Record
  • Sayfa Sayıları: ss.1-21
  • İstanbul Kültür Üniversitesi Adresli: Evet

Özet

Thymotrinan is an immunomodulating tripeptide containing the Arg-Lys-Asp sequence.In this study, the structural, vibrational, and electronic properties, as well as the bioactivity of

thymotrinan, have been thoroughly examined.The conformational preferences of thymotrinan

were evaluated through conformational analysis, and the lowest-energy conformer was then

optimized using DFT/WB97XD/6-31++G(d,p) theory level.The vibrational wavenumbers of the

optimized structure were calculated, and the molecular electrostatic potential (MEP) and frontier

molecular orbital (HOMO, LUMO) analyses were performed. To analyze how thymotrinan

interacts with the α7 nicotinic acetylcholine receptor chimera and to evaluate its potential to inhibit

α-Bungarotoxin, a snake venom protein, molecular docking studies were performed between

thymotrinan and target proteins, including the α7nAchR chimera in complex with α-BTx(PDB ID

4HQP), the α7nAchR chimera without the α-BTx protein(α-BTx-removed 4HQP), and α-

BTx(PDB code: 1IK8).Afterwards, the thymotrinan-1IK8 complex was subjected to 200 ns of all-

atom molecular dynamics (MD) simulations to demonstrate its stability.Based on the MD

trajectory, the binding free energy of the complex was estimated to be -18.545 kcal/mol using the

MM-PBSA method.In addition, in silico pharmacological predictions suggest that thymotrinan

may exhibit anticancer activity against multiple cancer cell lines and antibacterial activity against

a range of bacterial species. However, experimental validation of these findings remains required.