ISSN 2410-7751 (Print)
ISSN 2410-776X (Online)
Biotechnologia Acta Т. 19, No. 1, 2026
P. , Bibliography , Engl.
UDC: 616.23/.25,616.986.988:616.24-002-07-084.001.5
doi:
Full text: (PDF, in English)
IN SILICO STUDY OF THE ANTICORONAVIRAL ACTIVITY OF ALIPHATIC AMINOCARBOXYLIC COMPOUNDS
Smetiukh M.P.1,2 , Soloviov S.O. 1,2
1 Igor Sikorsky Kyiv Polytechnic Institute, Ukraine
2 Shupyk National University of Health Care of Ukraine, Kyiv
Aim. To evaluate the potential interactions of short-chain aliphatic aminocarboxylic compounds with key coronavirus proteases—the main protease (Mpro) and papain-like protease (PLpro) of SARS-CoV-2 and IBV—using molecular docking.
Methods. Hort-chain aminocarboxylic compounds were used as ligands. Initial structures were obtained from PubChem or built in Avogadro/MarvinSketch, followed by 3D optimization, verification of protonation at pH 7.4, correction of charge states, and conversion to .mol2 format (OpenBabel) for compatibility with SwissDock. Docking was performed using experimental 3D structures of Mpro and PLpro of SARS-CoV-2 and IBV from the PDB. Structure preparation and analysis were carried out in Avogadro, MarvinSketch, OpenBabel, the PubChem 3D Conformer Generator, SwissDock (EADock DSS/AutoDock Vina), and PyMOL.
Results. Aliphatic aminocarboxylic compounds exhibited moderate binding affinity toward Mpro (ΔG from −3.0 to −4.3 kcal/mol), with docking poses predominantly localized in peripheral hydrophobic pockets rather than stably in the catalytic region. Longer-chain ligands, including 7-aminoheptanoic and 8-aminocaprylic acids, showed more stable binding. Extension of the carbon chain enhanced hydrophobic packing and stabilized binding within an Mpro pocket. The non-ionized form of 6-aminocaproic acid bound more favorably than its hydrochloride, consistent with reduced affinity under strong ionization.
Conclusions. Docking indicated moderate binding and predominantly peripheral localization of complexes. Longer chains improve docking scores, whereas strong ionization impairs binding. Conserved Mpro architecture between SARS-CoV-2 and IBV supports the use of IBV as a safer screening model. The most reliable in vitro candidates were identified as 4-aminobutyric acid and 6-aminocaproic acid.
Keywords: SARS-CoV-2, infectious bronchitis virus, coronavirus, molecular docking, aminocarboxylic compounds, Mpro, antiviral agents, in silico.
© Palladin Institute of Biochemistry of the National Academy of Sciences of Ukraine, 2026