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.
References:
[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.
Acknowledgements:
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.
