Mechanism and Kinetics of Aztreonam Hydrolysis Catalyzed by Class-C β-Lactamase: A Temperature-Accelerated Sliced Sampling Study

Abstract

Enhanced sampling of large number of collective variables (CVs) is inevitable in molecular dynamics (MD) simulations of complex chemical processes such as enzymatic reactions. Because of the computational overhead of hybrid quantum mechanical/molecular mechanical (QM/MM)-based MD simulations, especially together with density functional theory, predictions of reaction mechanism, and estimation of free-energy barriers have to be carried out within few tens of picoseconds. We show here that the recently developed temperature-accelerated sliced sampling method allows one to sample large number of CVs, thereby enabling us to obtain rapid convergence in free-energy estimates in QM/MM MD simulation of enzymatic reactions. Moreover, the method is shown to be efficient in exploring flat and broad free-energy basins that commonly occur in enzymatic reactions. We demonstrate this by studying deacylation and reverse acylation reactions of aztreonam drug catalyzed by a class-C β lactamase (CBL) bacterial enzyme. Mechanistic details and nature of kinetics of aztreonam hydrolysis by CBL are elaborated here. The results of this study point to characteristics of the aztreonam drug that are responsible for its slow hydrolysis.

Exploring high‐dimensional free energy landscapes of chemical reactions

“…Temperature of the auxiliary variables was set to 1,000 K, while the system temperature was kept at 300 K. In total, 16 umbrella windows were placed at equal distance from 1.3 to 2.9 Å along CV1. It was observed that the free energy barrier converges within 9 ps (per umbrella window) . The converged free energy surface was computed using the reweighting procedure explained in Reference 146 and then projected to CV1 and CV2 as shown in Figure .…”

“…Protein backbone is shown as transparent ribbons. (Reprinted with permission from Reference . Copyright 2018 American Chemical Society)…”

“…Free energy surface of alanine tripeptide was also mapped using four CVs, and free energies were showing good convergence within 10 ns per umbrella window (and 31 umbrella windows were used) . Awasthi et al used TASS to study deacylation and reverse acylation reactions of aztreonam drug catalyzed by class‐C β lactamase enzyme. These simulations were using DFT‐based QM/MM MD methods.…”

Elucidating the Molecular Basis of Avibactam‐Mediated Inhibition of Class A β‐Lactamases

“…15,16 In fact, this is also seen in the computational study on aztreonam (which is a β-lactam inhibitor) with class C β-lactamase. 17 Many other works further proposed mechanistic details of reverse acylation, considering it to be kinetically preferable over hydrolysis. [18][19][20][21] Based on point mutational studies 18,19 and high-resolution crystal structure captured by Lahiri et al, 20 a general base catalyzed mechanism is suggested for the recyclization of avibactam.…”

Statistical Mechanics in Theoretical Chemistry in India : Past, present and a bit of future

“…See, for example, Refs. (Das and Paul, 2017;Chand et al, 2018;Dasari and Mallik, 2018;Kaur and Kashyap, 2018;Awasthi et al, 2016;Awasthi and Nair, 2017;Awasthi et al, 2018;Chugh and Ranganathan, 2016;Ghosh and Ranganathan, 2017;Chugh and Ranganathan, 2017;Sarkar et al, 2019;Maity and Reddy, 2018;Nandi et al, 2017;Hridya and Mukherjee, 2018;Sharma and Ghorai, 2018;Ahalawat and Murarka, 2017;Rout and Srinivasan, 2018;Shekar and Swathi, 2018;Kumawat and Chakrabarty, 2017;Palchowdhury and Bhargava, 2018;Mandal et al, 2018;Ahalawat and Mondal, 2018;Hasnain and Bandyopadhyay, 2015;Dutta and Nandi, 2015) for representative work from these groups in recent years. Also, many institutes now have multiple research groups working in statistical mechanics and computer simulations.…”