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Understanding the covalent inhibition of Clavulanate against β-lactamases (TEM-1 and KPC-2) with QM/MM screening methods.
1 , * 2 , 3 , 4 , * 3
1  Doctorado en Ciencias Aplicadas, Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Casilla 721, Talca, Chile.
2  Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Casilla 721, Talca, Chile.
3  Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK.
4  Molecular Bioscience, School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK.


β-lactamases are a primary cause of bacterial resistance to β-lactam antibiotics for many important human pathogens (particularly Gram-negative bacteria) [1]. Inhibitors of β-lactamase have been implemented as a dual therapy with antibiotics, but there are only four inhibitors clinically approved and resistance to these compounds is also rising [2]. For β-lactam inhibitors, after acylation, the opening of five-membered ring leads to the formation of a transient imine intermediate then it rearranges several times to form a trans or cis final enamine inhibition-products. Slow hydrolysis of this product by the enzyme leads to an inhibited β-lactamase [2]. A computational study of reaction mechanism for the first step on the deacylation of the inhibitor clavulanate with TEM-1 (inhibited) and KPC-2 (hydrolyzed) enzymes using QM/MM Umbrella Sampling with DFTB method is presented [3]. 2D free energies surfaces for the reactions were calculated using the weighted histogram analysis method (WHAM) and the minimum energy path (MEP) was identified; where the highest point along the MEP is taken as the transition state giving the activation free energy “ΔGcalc”.Our results show that TEM-1 and KPC-2 have an approximate 5 kcal/mol difference in ΔGcalc. Such results are in good agreement with inhibition experimental data for two enzymes in which KPC-2 is less inhibited by clavulanate than TEM-1. We hope our methodology can assist the design and development of covalent inhibitors through a computational screening of inhibitory activity of other molecules.


[1] Hermann, J. C., Pradon, J., Harvey, J. N., & Mulholland, A. J. J. Phys. Chem. A (2009), 113(43), 11984–11994.

[2] Drawz, S. M., Papp-Wallace, K. M., & Bonomo, R. a. Antimicrob. Agents Chemother (2014), 58(4), 1835–1846.

[3] Chudyk, E. I., Limb, M. a L., Jones, C., Spencer, J., van der Kamp, M. W., & Mulholland, A. J. Chem Commun, (2014), 50, 14736–14739.


R.F thanks the Royal Society of Chemistry (RSC) for financial support through Researcher Mobility Grant (R. Fritz 16 Round 1). JAM and RF thank financial support through project FONDECYT No. 1140618.

Keywords: QM/MM; antibiotic resistance; beta-lactamases