Sequential Molecular Docking Analysis of Amoxicillin–Clavulanic Acid Interaction with TEM-1 β-Lactamase

Abstract

Background: β-lactamase-mediated degradation of β-lactam antibiotics is a major contributor to antimicrobial resistance. Amoxicillin, a widely used β-lactam antibiotic, is particularly susceptible to hydrolysis by Temoniera-1 (TEM-1) β-lactamase. Clavulanic acid, a mechanism-based β-lactamase inhibitor, is co-administered to restore antibiotic efficacy. However, conventional molecular docking approaches typically evaluate ligands independently and do not account for the influence of prior inhibitor binding on subsequent ligand accommodation.

Methods: A sequential molecular docking approach was used to investigate ligandorder effects within the active site of TEM-1 β-lactamase (PDB ID: 1BTL). Clavulanic acid was first docked into the enzyme active site using AutoDock Vina, and the top-ranked pose was retained as a rigid component of the receptor. Amoxicillin was subsequently docked into the inhibitor-occupied complex using identical grid parameters. Protein–ligand interactions were analyzed using Protein-Ligand Interaction Profiler (PLIP)-based distance-dependent interaction profiling.

Results: Clavulanic acid exhibited a binding affinity of −5.878 kcal/mol in the primary docking step. Amoxicillin showed a binding affinity of −7.588 kcal/mol in single-ligand docking, which shifted to −13.033 kcal/mol under sequential docking conditions. Interaction analysis revealed hydrogen bonding and non-covalent contacts with key catalytic residues, including Ser70, Glu166, Ala237, and Gly236. These interactions suggest altered ligand accommodation within a constrained active-site environment following inhibitor placement.

Conclusion: The findings indicate that sequential docking can generate structural hypotheses regarding ligand accommodation under constrained active-site conditions. However, this approach represents a simplified computational model and does not reflect true cooperative binding. Further validation using molecular dynamics simulations and experimental studies is required to substantiate these observations.

Cite this article as: R N, K R. Sequential molecular docking analysis of amoxicillin–clavulanic acid interaction with TEM-1 β-lactamase. Trends in Pharmacy. 2026, 3, 0015, doi: 10.5152/TIP.2026.26002.