1
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Chudyk EI, Beer M, Limb MAL, Jones CA, Spencer J, van der Kamp MW, Mulholland AJ. QM/MM Simulations Reveal the Determinants of Carbapenemase Activity in Class A β-Lactamases. ACS Infect Dis 2022; 8:1521-1532. [PMID: 35877936 PMCID: PMC9379904 DOI: 10.1021/acsinfecdis.2c00152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Indexed: 11/28/2022]
Abstract
β-lactam antibiotic resistance in Gram-negative bacteria, primarily caused by β-lactamase enzymes that hydrolyze the β-lactam ring, has become a serious clinical problem. Carbapenems were formerly considered "last resort" antibiotics because they escaped breakdown by most β-lactamases, due to slow deacylation of the acyl-enzyme intermediate. However, an increasing number of Gram-negative bacteria now produce β-lactamases with carbapenemase activity: these efficiently hydrolyze the carbapenem β-lactam ring, severely limiting the treatment of some bacterial infections. Here, we use quantum mechanics/molecular mechanics (QM/MM) simulations of the deacylation reactions of acyl-enzyme complexes of eight β-lactamases of class A (the most widely distributed β-lactamase group) with the carbapenem meropenem to investigate differences between those inhibited by carbapenems (TEM-1, SHV-1, BlaC, and CTX-M-16) and those that hydrolyze them (SFC-1, KPC-2, NMC-A, and SME-1). QM/MM molecular dynamics simulations confirm the two enzyme groups to differ in the preferred acyl-enzyme orientation: carbapenem-inhibited enzymes favor hydrogen bonding of the carbapenem hydroxyethyl group to deacylating water (DW). QM/MM simulations of deacylation give activation free energies in good agreement with experimental hydrolysis rates, correctly distinguishing carbapenemases. For the carbapenem-inhibited enzymes, free energies for deacylation are significantly higher than for the carbapenemases, even when the hydroxyethyl group was restrained to prevent interaction with the DW. Analysis of these simulations, and additional simulations of mutant enzymes, shows how factors including the hydroxyethyl orientation, the active site volume, and architecture (conformations of Asn170 and Asn132; organization of the oxyanion hole; and the Cys69-Cys238 disulfide bond) collectively determine catalytic efficiency toward carbapenems.
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Affiliation(s)
- Ewa I. Chudyk
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Michael Beer
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
- School
of Cellular and Molecular Medicine, University
of Bristol Medical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Michael A. L. Limb
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Charlotte A. Jones
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - James Spencer
- School
of Cellular and Molecular Medicine, University
of Bristol Medical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Marc W. van der Kamp
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
- School
of Biochemistry, University of Bristol Medical
Sciences Building, University Walk, Bristol BS8 1TD, United
Kingdom
| | - Adrian J. Mulholland
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
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2
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Ramos-Guzmán CA, Velázquez-Libera JL, Ruiz-Pernía JJ, Tuñón I. Testing Affordable Strategies for the Computational Study of Reactivity in Cysteine Proteases: The Case of SARS-CoV-2 3CL Protease Inhibition. J Chem Theory Comput 2022; 18:4005-4013. [PMID: 35549334 PMCID: PMC9115880 DOI: 10.1021/acs.jctc.2c00294] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
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Cysteine proteases are an important target for the development of inhibitors that could
be used as drugs to regulate the activity of these kinds of enzymes involved in many
diseases, including COVID-19. For this reason, it is important to have methodological
tools that allow a detailed study of their activity and inhibition, combining
computational efficiency and accuracy. We here explore the performance of different
quantum mechanics/molecular mechanics methods to explore the inhibition reaction
mechanism of the SARS-CoV-2 3CL protease with a hydroxymethyl ketone derivative. We
selected two density functional theory (DFT) functionals (B3LYP and M06-2X), two
semiempirical Hamiltonians (AM1d and PM6), and two tight-binding DFT methods (DFTB3 and
GFN2-xTB) to explore the free energy landscape associated with this reaction. We show
that it is possible to obtain an accurate description combining molecular dynamics
simulations performed using tight-binding DFT methods and single-point energy
corrections at a higher QM description. The use of a computational strategy that
provides reliable results at a reasonable computational cost could assist the in silico
screening of possible candidates during the design of new drugs directed against
cysteine proteases.
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Affiliation(s)
- Carlos A Ramos-Guzmán
- Departamento de Química Física, Universitat de Valencia, Burjassot, Valencia 46100, Spain
| | - José Luis Velázquez-Libera
- Departamento de Química Física, Universitat de Valencia, Burjassot, Valencia 46100, Spain.,Departamento de Bioinformática, Facultad de Ingeniería, Centro de Bioinformática, Simulación y Modelado (CBSM), Universidad de Talca, Talca 3460000, Chile
| | - J Javier Ruiz-Pernía
- Departamento de Química Física, Universitat de Valencia, Burjassot, Valencia 46100, Spain
| | - Iñaki Tuñón
- Departamento de Química Física, Universitat de Valencia, Burjassot, Valencia 46100, Spain
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3
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Hirvonen VA, Weizmann TM, Mulholland AJ, Spencer J, van der Kamp MW. Multiscale Simulations Identify Origins of Differential Carbapenem Hydrolysis by the OXA-48 β-Lactamase. ACS Catal 2022; 12:4534-4544. [PMID: 35571461 PMCID: PMC9097296 DOI: 10.1021/acscatal.1c05694] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/22/2022] [Indexed: 12/27/2022]
Abstract
OXA-48 β-lactamases are frequently encountered in bacterial infections caused by carbapenem-resistant Gram-negative bacteria. Due to the importance of carbapenems in the treatment of healthcare-associated infections and the increasingly wide dissemination of OXA-48-like enzymes on plasmids, these β-lactamases are of high clinical significance. Notably, OXA-48 hydrolyzes imipenem more efficiently than other commonly used carbapenems, such as meropenem. Here, we use extensive multiscale simulations of imipenem and meropenem hydrolysis by OXA-48 to dissect the dynamics and to explore differences in the reactivity of the possible conformational substates of the respective acylenzymes. Quantum mechanics/molecular mechanics (QM/MM) simulations of the deacylation reaction for both substrates demonstrate that deacylation is favored when the 6α-hydroxyethyl group is able to hydrogen bond to the water molecule responsible for deacylation but disfavored by the increasing hydration of either oxygen of the carboxylated Lys73 general base. Differences in free energy barriers calculated from the QM/MM simulations correlate well with the experimentally observed differences in hydrolytic efficiency between meropenem and imipenem. We conclude that the impaired breakdown of meropenem, compared to imipenem, which arises from a subtle change in the hydrogen bonding pattern between the deacylating water molecule and the antibiotic, is most likely induced by the meropenem 1β-methyl group. In addition to increased insights into carbapenem breakdown by OXA β-lactamases, which may aid in future efforts to design antibiotics or inhibitors, our approach exemplifies the combined use of atomistic simulations in determining the possible different enzyme-substrate substates and their influence on enzyme reaction kinetics.
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Affiliation(s)
- Viivi
H. A. Hirvonen
- School
of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K.
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
| | - Tal Moshe Weizmann
- School
of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K.
| | - Adrian J. Mulholland
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
| | - James Spencer
- School
of Cellular and Molecular Medicine, University
of Bristol, University
Walk, Bristol BS8 1TD, U.K.
| | - Marc W. van der Kamp
- School
of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K.
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
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4
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Charzewski Ł, Krzyśko KA, Lesyng B. Exploring Covalent Docking Mechanisms of Boron-Based Inhibitors to Class A, C and D β-Lactamases Using Time-dependent Hybrid QM/MM Simulations. Front Mol Biosci 2021; 8:633181. [PMID: 34434961 PMCID: PMC8380965 DOI: 10.3389/fmolb.2021.633181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 07/19/2021] [Indexed: 11/13/2022] Open
Abstract
Recently, molecular covalent docking has been extensively developed to design new classes of inhibitors that form chemical bonds with their biological targets. This strategy for the design of such inhibitors, in particular boron-based inhibitors, holds great promise for the vast family of β-lactamases produced, inter alia, by Gram-negative antibiotic-resistant bacteria. However, the description of covalent docking processes requires a quantum-mechanical approach, and so far, only a few studies of this type have been presented. This study accurately describes the covalent docking process between two model inhibitors - representing two large families of inhibitors based on boronic-acid and bicyclic boronate scaffolds, and three β-lactamases which belong to the A, C, and D classes. Molecular fragments containing boron can be converted from a neutral, trigonal, planar state with sp2 hybridization to the anionic, tetrahedral sp3 state in a process sometimes referred to as morphing. This study applies multi-scale modeling methods, in particular, the hybrid QM/MM approach which has predictive power reaching well beyond conventional molecular modeling. Time-dependent QM/MM simulations indicated several structural changes and geometric preferences, ultimately leading to covalent docking processes. With current computing technologies, this approach is not computationally expensive, can be used in standard molecular modeling and molecular design works, and can effectively support experimental research which should allow for a detailed understanding of complex processes important to molecular medicine. In particular, it can support the rational design of covalent boron-based inhibitors for β-lactamases as well as for many other enzyme systems of clinical relevance, including SARS-CoV-2 proteins.
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Affiliation(s)
| | | | - Bogdan Lesyng
- Department of Biophysics, Faculty of Physics, University of Warsaw, Warsaw, Poland
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5
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Thu ZM, Sun J, Ji J, He L, Ji J, Iqbal Z, Myo KK, Gao Y, Zhai L, Mu Y, Tang D, Vidari G, Yang H, Yang Z. Synthesis and antibacterial evaluation of new monobactams. Bioorg Med Chem Lett 2021; 39:127878. [PMID: 33636305 DOI: 10.1016/j.bmcl.2021.127878] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 02/08/2021] [Accepted: 02/10/2021] [Indexed: 10/22/2022]
Abstract
Monobactams play an important role in antibiotic drug discovery. Based on the structural characteristics of aztreonam and its biological targets, six new monobactam derivatives (2a-c and 3a-c) were synthesized and their in vitro antibacterial activities were investigated. Compounds 2a-c showed higher activities against tested gram-negative bacteria than that of parent aztreonam. Monobactam 2c exhibited the most potent activities, with MIC ranging from 0.25 to 2 μg/mL against most bacteria.
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Affiliation(s)
- Zaw Min Thu
- Ningxia Centre of Organic Synthesis and Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, No. 590, Huanghe East Road, Jinfeng District, Yinchuan, Ningxia 750002, PR China; Department of Chemistry, Kalay University, Kalay 03044, Sagaing Region, Myanmar
| | - Jian Sun
- Ningxia Centre of Organic Synthesis and Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, No. 590, Huanghe East Road, Jinfeng District, Yinchuan, Ningxia 750002, PR China
| | - Jingwen Ji
- Ningxia Centre of Organic Synthesis and Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, No. 590, Huanghe East Road, Jinfeng District, Yinchuan, Ningxia 750002, PR China
| | - Lili He
- Ningxia Centre of Organic Synthesis and Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, No. 590, Huanghe East Road, Jinfeng District, Yinchuan, Ningxia 750002, PR China
| | - Jinbo Ji
- Ningxia Centre of Organic Synthesis and Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, No. 590, Huanghe East Road, Jinfeng District, Yinchuan, Ningxia 750002, PR China
| | - Zafar Iqbal
- Ningxia Centre of Organic Synthesis and Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, No. 590, Huanghe East Road, Jinfeng District, Yinchuan, Ningxia 750002, PR China
| | - Ko Ko Myo
- Ningxia Centre of Organic Synthesis and Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, No. 590, Huanghe East Road, Jinfeng District, Yinchuan, Ningxia 750002, PR China; Department of Chemistry, Kalay University, Kalay 03044, Sagaing Region, Myanmar
| | - Yuanyu Gao
- Ningxia Centre of Organic Synthesis and Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, No. 590, Huanghe East Road, Jinfeng District, Yinchuan, Ningxia 750002, PR China
| | - Lijuan Zhai
- Ningxia Centre of Organic Synthesis and Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, No. 590, Huanghe East Road, Jinfeng District, Yinchuan, Ningxia 750002, PR China
| | - Yangxiu Mu
- Ningxia Centre of Organic Synthesis and Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, No. 590, Huanghe East Road, Jinfeng District, Yinchuan, Ningxia 750002, PR China
| | - Dong Tang
- Ningxia Centre of Organic Synthesis and Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, No. 590, Huanghe East Road, Jinfeng District, Yinchuan, Ningxia 750002, PR China
| | - Giovanni Vidari
- Medical Analysis Department, Faculty of Science, Tishk International University, Erbil 44001, Kurdistan Region, Iraq
| | - Haikang Yang
- Ningxia Centre of Organic Synthesis and Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, No. 590, Huanghe East Road, Jinfeng District, Yinchuan, Ningxia 750002, PR China.
| | - Zhixiang Yang
- Ningxia Centre of Organic Synthesis and Engineering Technology, Ningxia Academy of Agriculture and Forestry Sciences, No. 590, Huanghe East Road, Jinfeng District, Yinchuan, Ningxia 750002, PR China.
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6
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Galdadas I, Qu S, Oliveira ASF, Olehnovics E, Mack AR, Mojica MF, Agarwal PK, Tooke CL, Gervasio FL, Spencer J, Bonomo RA, Mulholland AJ, Haider S. Allosteric communication in class A β-lactamases occurs via cooperative coupling of loop dynamics. eLife 2021; 10:e66567. [PMID: 33755013 PMCID: PMC8060031 DOI: 10.7554/elife.66567] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 03/19/2021] [Indexed: 12/16/2022] Open
Abstract
Understanding allostery in enzymes and tools to identify it offer promising alternative strategies to inhibitor development. Through a combination of equilibrium and nonequilibrium molecular dynamics simulations, we identify allosteric effects and communication pathways in two prototypical class A β-lactamases, TEM-1 and KPC-2, which are important determinants of antibiotic resistance. The nonequilibrium simulations reveal pathways of communication operating over distances of 30 Å or more. Propagation of the signal occurs through cooperative coupling of loop dynamics. Notably, 50% or more of clinically relevant amino acid substitutions map onto the identified signal transduction pathways. This suggests that clinically important variation may affect, or be driven by, differences in allosteric behavior, providing a mechanism by which amino acid substitutions may affect the relationship between spectrum of activity, catalytic turnover, and potential allosteric behavior in this clinically important enzyme family. Simulations of the type presented here will help in identifying and analyzing such differences.
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Affiliation(s)
- Ioannis Galdadas
- University College London, Department of ChemistryLondonUnited Kingdom
| | - Shen Qu
- University College London School of Pharmacy, Pharmaceutical and Biological ChemistryLondonUnited Kingdom
| | - Ana Sofia F Oliveira
- University of Bristol, Centre for Computational Chemistry, School of ChemistryBristolUnited Kingdom
| | - Edgar Olehnovics
- University College London School of Pharmacy, Pharmaceutical and Biological ChemistryLondonUnited Kingdom
| | - Andrew R Mack
- Veterans Affairs Northeast Ohio Healthcare System, Research ServiceClevelandUnited States
- Case Western Reserve University, Department of Molecular Biology and MicrobiologyClevelandUnited States
| | - Maria F Mojica
- Veterans Affairs Northeast Ohio Healthcare System, Research ServiceClevelandUnited States
- Case Western Reserve University, Department of Infectious Diseases, School of MedicineClevelandUnited States
| | - Pratul K Agarwal
- Department of Physiological Sciences and High-Performance Computing Center, Oklahoma State UniversityStillwaterUnited States
| | - Catherine L Tooke
- University of Bristol, School of Cellular and Molecular MedicineBristolUnited Kingdom
| | - Francesco Luigi Gervasio
- University College London, Department of ChemistryLondonUnited Kingdom
- University College London, Institute of Structural and Molecular BiologyLondonUnited Kingdom
- University of Geneva, Pharmaceutical SciencesGenevaSwitzerland
| | - James Spencer
- University of Bristol, School of Cellular and Molecular MedicineBristolUnited Kingdom
| | - Robert A Bonomo
- Veterans Affairs Northeast Ohio Healthcare System, Research ServiceClevelandUnited States
- Case Western Reserve University, Department of Molecular Biology and MicrobiologyClevelandUnited States
- Case Western Reserve University, Department of Infectious Diseases, School of MedicineClevelandUnited States
- Case Western Reserve University, Department of BiochemistryClevelandUnited States
- Case Western Reserve University, Department of PharmacologyClevelandUnited States
- Case Western Reserve University, Department of Proteomics and BioinformaticsClevelandUnited States
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES)ClevelandUnited States
| | - Adrian J Mulholland
- University of Bristol, Centre for Computational Chemistry, School of ChemistryBristolUnited Kingdom
| | - Shozeb Haider
- University College London School of Pharmacy, Pharmaceutical and Biological ChemistryLondonUnited Kingdom
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7
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Destiarani W, Mulyani R, Yusuf M, Maksum IP. Molecular Dynamics Simulation of T10609C and C10676G Mutations of Mitochondrial ND4L Gene Associated With Proton Translocation in Type 2 Diabetes Mellitus and Cataract Patients. Bioinform Biol Insights 2020; 14:1177932220978672. [PMID: 33402819 PMCID: PMC7747115 DOI: 10.1177/1177932220978672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 11/14/2020] [Indexed: 11/17/2022] Open
Abstract
The mutation rate of mitochondrial DNA (mtDNA) is 17 times higher than nuclear DNA, and these mutations can cause mitochondrial disease in 1 of 10.000 people. The T10609C mutation was identified in type 2 diabetes mellitus (T2DM) patients and the C10676G mutation in cataract patients, with both mutations occurring in the ND4L gene of mtDNA that encodes ND4L protein. ND4L protein, a subunit of complex I in the respiratory complex, has been shown to play a role in the proton translocation process. The purpose of this study was to investigate the effect of both mutations on the proton translocation mechanism. Mutation mapping showed changes in amino acids M47T (T10609C) and C69W (C10676G). The 100 ns molecular dynamics (MD) simulations performed on native and mutants of ND4L-ND6 subunits. It is revealed that the native model had a similar proton translocation pathway to that of complex I from other organisms. Interestingly, the mutant M47T and C69W showed the interruption of the translocation pathway by a hydrogen bond formation between Glu34 and Tyr157. It is observed that the mutations were restricting the passage of water molecules through the transmembrane region. These results could help to develop the computational assay for the validation of a specific genetic biomarker for T2DM and cataracts.
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Affiliation(s)
- Wanda Destiarani
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang, Indonesia
| | - Rahmaniar Mulyani
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang, Indonesia
| | - Muhammad Yusuf
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang, Indonesia.,Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, Indonesia
| | - Iman Permana Maksum
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang, Indonesia
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8
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Cheng Q, DeYonker NJ. Acylation and deacylation mechanism and kinetics of penicillin G reaction with Streptomyces R61 DD-peptidase. J Comput Chem 2020; 41:1685-1697. [PMID: 32323874 DOI: 10.1002/jcc.26210] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/26/2020] [Accepted: 04/05/2020] [Indexed: 12/20/2022]
Abstract
Two quantum mechanical (QM)-cluster models are built for studying the acylation and deacylation mechanism and kinetics of Streptomyces R61 DD-peptidase with the penicillin G at atomic level detail. DD-peptidases are bacterial enzymes involved in the cross-linking of peptidoglycan to form the cell wall, necessary for bacterial survival. The cross-linking can be inhibited by antibiotic beta-lactam derivatives through acylation, preventing the acyl-enzyme complex from undergoing further deacylation. The deacylation step was predicted to be rate-limiting. Transition state and intermediate structures are found using density functional theory in this study, and thermodynamic and kinetic properties of the proposed mechanism are evaluated. The acyl-enzyme complex is found lying in a deep thermodynamic sink, and deacylation is indeed the severely rate-limiting step, leading to suicide inhibition of the peptidoglycan cross-linking. The usage of QM-cluster models is a promising technique to understand, improve, and design antibiotics to disrupt function of the Streptomyces R61 DD-peptidase.
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Affiliation(s)
- Qianyi Cheng
- Department of Chemistry, University of Memphis, Memphis, Tennessee, USA
| | - Nathan J DeYonker
- Department of Chemistry, University of Memphis, Memphis, Tennessee, USA
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9
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Hirvonen VHA, Mulholland AJ, Spencer J, van der Kamp MW. Small Changes in Hydration Determine Cephalosporinase Activity of OXA-48 β-Lactamases. ACS Catal 2020. [DOI: 10.1021/acscatal.0c00596] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Viivi H. A. Hirvonen
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD United Kingdom
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS United Kingdom
| | - Adrian J. Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS United Kingdom
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol, BS8 1TD United Kingdom
| | - Marc W. van der Kamp
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD United Kingdom
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS United Kingdom
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10
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Lodola A, Callegari D, Scalvini L, Rivara S, Mor M. Design and SAR Analysis of Covalent Inhibitors Driven by Hybrid QM/MM Simulations. Methods Mol Biol 2020; 2114:307-337. [PMID: 32016901 DOI: 10.1007/978-1-0716-0282-9_19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Quantum mechanics/molecular mechanics (QM/MM) hybrid technique is emerging as a reliable computational method to investigate and characterize chemical reactions occurring in enzymes. From a drug discovery perspective, a thorough understanding of enzyme catalysis appears pivotal to assist the design of inhibitors able to covalently bind one of the residues belonging to the enzyme catalytic machinery. Thanks to the current advances in computer power, and the availability of more efficient algorithms for QM-based simulations, the use of QM/MM methodology is becoming a viable option in the field of covalent inhibitor design. In the present review, we summarized our experience in the field of QM/MM simulations applied to drug design problems which involved the optimization of agents working on two well-known drug targets, namely fatty acid amide hydrolase (FAAH) and epidermal growth factor receptor (EGFR). In this context, QM/MM simulations gave valuable information in terms of geometry (i.e., of transition states and metastable intermediates) and reaction energetics that allowed to correctly predict inhibitor binding orientation and substituent effect on enzyme inhibition. What is more, enzyme reaction modelling with QM/MM provided insights that were translated into the synthesis of new covalent inhibitor featured by a unique combination of intrinsic reactivity, on-target activity, and selectivity.
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Affiliation(s)
- Alessio Lodola
- Drug Design and Discovery Group, Department of Food and Drug, University of Parma, Parma, Italy.
| | - Donatella Callegari
- Drug Design and Discovery Group, Department of Food and Drug, University of Parma, Parma, Italy
| | - Laura Scalvini
- Drug Design and Discovery Group, Department of Food and Drug, University of Parma, Parma, Italy
| | - Silvia Rivara
- Drug Design and Discovery Group, Department of Food and Drug, University of Parma, Parma, Italy
| | - Marco Mor
- Drug Design and Discovery Group, Department of Food and Drug, University of Parma, Parma, Italy
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11
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Drulyte I, Obajdin J, Trinh CH, Kalverda AP, van der Kamp MW, Hemsworth GR, Berry A. Crystal structure of the putative cyclase IdmH from the indanomycin nonribosomal peptide synthase/polyketide synthase. IUCRJ 2019; 6:1120-1133. [PMID: 31709067 PMCID: PMC6830212 DOI: 10.1107/s2052252519012399] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 09/05/2019] [Indexed: 05/08/2023]
Abstract
Indanomycin is biosynthesized by a hybrid nonribosomal peptide synthase/polyketide synthase (NRPS/PKS) followed by a number of 'tailoring' steps to form the two ring systems that are present in the mature product. It had previously been hypothesized that the indane ring of indanomycin was formed by the action of IdmH using a Diels-Alder reaction. Here, the crystal structure of a selenomethionine-labelled truncated form of IdmH (IdmH-Δ99-107) was solved using single-wavelength anomalous dispersion (SAD) phasing. This truncated variant allows consistent and easy crystallization, but importantly the structure was used as a search model in molecular replacement, allowing the full-length IdmH structure to be determined to 2.7 Å resolution. IdmH is a homodimer, with the individual protomers consisting of an α+β barrel. Each protomer contains a deep hydrophobic pocket which is proposed to constitute the active site of the enzyme. To investigate the reaction catalysed by IdmH, 88% of the backbone NMR resonances were assigned, and using chemical shift perturbation of [15N]-labelled IdmH it was demonstrated that indanomycin binds in the active-site pocket. Finally, combined quantum mechanical/molecular mechanical (QM/MM) modelling of the IdmH reaction shows that the active site of the enzyme provides an appropriate environment to promote indane-ring formation, supporting the assignment of IdmH as the key Diels-Alderase catalysing the final step in the biosynthesis of indanomycin through a similar mechanism to other recently characterized Diels-Alderases involved in polyketide-tailoring reactions. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at https://proteopedia.org/w/Journal:IUCrJ:S2052252519012399.
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Affiliation(s)
- Ieva Drulyte
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, England
| | - Jana Obajdin
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, England
| | - Chi H. Trinh
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, England
| | - Arnout P. Kalverda
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, England
| | - Marc W. van der Kamp
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, England
- Correspondence e-mail: ,
| | - Glyn R. Hemsworth
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, England
| | - Alan Berry
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, England
- Correspondence e-mail: ,
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