Structural, Vibrational, Electronic Properties, Molecular Docking, and Molecular Dynamics Studies of a Rice Bran-Derived Lipopentapeptide
RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A, cilt.100, sa.8, ss.1675-1698, 2026 (SCI-Expanded, Scopus)
- Yayın Türü: Makale / Tam Makale
- Cilt numarası: 100 Sayı: 8
- Basım Tarihi: 2026
- Doi Numarası: 10.1134/s0036024426701190
- Dergi Adı: RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A
- Derginin Tarandığı İndeksler: Science Citation Index Expanded (SCI-EXPANDED), Scopus, Aerospace Database, Chemical Abstracts Core, Compendex, Materials Science & Engineering Collection (ProQuest), Technology Collection (ProQuest)
- Sayfa Sayıları: ss.1675-1698
- İstanbul Kültür Üniversitesi Adresli: Evet
Özet
Lipopeptides are natural molecules with amphiphilic properties that exhibit various biological activities due to their lipid and peptide components. In this study, the structural, electronic, and vibrational properties of C16-Glu-Gln-Arg-Pro-Arg (C16-EQRPR), a newly synthesized lipopentapeptide formed by attaching palmitic acid to the N-terminus of the pentapeptide, were analyzed. Additionally, its antiviral and anticancer properties were evaluated through molecular docking studies. First, conformational analysis of C16-EQRPR was performed using the MMFF molecular mechanics method, and the lowest-energy conformer obtained was then optimized using DFT/wb97xd/6-31G(d,p) level of theory. The geometric parameters of the optimized structure were reported. Vibrational frequencies were calculated using the same level of theory and compared with experimental results. Complete vibrational assignments were made based on the potential energy distribution (PED) of the vibrational modes. Molecular electrostatic potential (MEP) analysis was performed for the optimized structure. The anticancer and antiviral effects of the lipopeptide were computationally assessed through molecular docking simulations of C16-EQRPR binding to the active sites of various targets, including B-DNA, ACE2, integrins (alpha 5 beta 3, alpha IIB beta 3, and alpha 5 beta 1), human serum albumin, EGFR, FYN, and apo, as well as the holo forms of SARS-CoV-2 MPro and SARS-CoV-2 spike glycoprotein. Following molecular docking calculations, the interaction of lipopentapeptide with integrin alpha 5 beta 1(PDB ID: 4WK0) was analyzed in detail using molecular dynamics simulations. This study aims to characterize the molecular and biological features of the C16-EQRPR lipopeptide, highlighting its potential as both an anticancer and antiviral agent. However, experimental validation of these findings remains required.