1
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Sharma H, Raju B, Narendra G, Motiwale M, Sharma B, Verma H, Silakari O. QM/MM Studies on Enzyme Catalysis and Insight into Designing of New Inhibitors by ONIOM Approach: Recent Update. ChemistrySelect 2023. [DOI: 10.1002/slct.202203319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Himani Sharma
- Molecular Modeling Lab (MML) Department of Pharmaceutical Sciences and Drug Research Punjabi University Patiala Punjab 147002 India
| | - Baddipadige Raju
- Molecular Modeling Lab (MML) Department of Pharmaceutical Sciences and Drug Research Punjabi University Patiala Punjab 147002 India
| | - Gera Narendra
- Molecular Modeling Lab (MML) Department of Pharmaceutical Sciences and Drug Research Punjabi University Patiala Punjab 147002 India
| | - Mohit Motiwale
- Molecular Modeling Lab (MML) Department of Pharmaceutical Sciences and Drug Research Punjabi University Patiala Punjab 147002 India
| | - Bhavna Sharma
- Molecular Modeling Lab (MML) Department of Pharmaceutical Sciences and Drug Research Punjabi University Patiala Punjab 147002 India
| | - Himanshu Verma
- Molecular Modeling Lab (MML) Department of Pharmaceutical Sciences and Drug Research Punjabi University Patiala Punjab 147002 India
| | - Om Silakari
- Molecular Modeling Lab (MML) Department of Pharmaceutical Sciences and Drug Research Punjabi University Patiala Punjab 147002 India
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2
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Dalal V, Golemi-Kotra D, Kumar P. Quantum Mechanics/Molecular Mechanics Studies on the Catalytic Mechanism of a Novel Esterase (FmtA) of Staphylococcus aureus. J Chem Inf Model 2022; 62:2409-2420. [PMID: 35475370 DOI: 10.1021/acs.jcim.2c00057] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
FmtA is a novel esterase that shares the penicillin-binding protein (PBP) core structural folding but found to hydrolyze the removal of d-Ala from teichoic acids. Molecular docking, dynamics, and MM-GBSA of FmtA and its variants S127A, K130A, Y211A, D213A, and K130AY211A, in the presence or absence of wall teichoic acid (WTA), suggest that active site residues S127, K130, Y211, D213, N343, and G344 play a role in substrate binding. Quantum mechanics (QM)/molecular mechanics (MM) calculations reveal that during WTA catalysis, K130 deprotonates S127, and the nucleophilic S127 attacks the carbonyl carbon of d-Ala bound to WTA. The tetrahedral intermediate (TI) complex is stabilized by hydrogen bonding to the oxyanion holes. The TI complex displays a high energy gap and collapses to an energetically favorable acyl-enzyme complex.
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Affiliation(s)
- Vikram Dalal
- Department of Biosciences and Bioengineering, IIT Roorkee, Roorkee, Uttrakhand 247667, India
| | - Dasantila Golemi-Kotra
- Department of Biology, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, IIT Roorkee, Roorkee, Uttrakhand 247667, India
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3
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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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4
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Gimenez-Dejoz J, Tsuchiya K, Tateishi A, Motoda Y, Kigawa T, Asano Y, Numata K. Computational study on the polymerization reaction of d-aminopeptidase for the synthesis of d-peptides. RSC Adv 2020; 10:17582-17592. [PMID: 35515590 PMCID: PMC9053604 DOI: 10.1039/d0ra01138j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/28/2020] [Indexed: 02/02/2023] Open
Abstract
Almost all natural proteins are composed exclusively of l-amino acids, and this chirality influences their properties, functions, and selectivity. Proteases can recognize proteins composed of l-amino acids but display lower selectivity for their stereoisomers, d-amino acids. Taking this as an advantage, d-amino acids can be used to develop polypeptides or biobased materials with higher biostability. Chemoenzymatic peptide synthesis is a technique that uses proteases as biocatalysts to synthesize polypeptides, and d-stereospecific proteases can be used to synthesize polypeptides incorporating d-amino acids. However, engineered proteases with modified catalytic activities are required to allow the incorporation of d-amino acids with increased efficiency. To understand the stereospecificity presented by proteases and their involvement in polymerization reactions, we studied d-aminopeptidase. This enzyme displays the ability to efficiently synthesize poly d-alanine-based peptides under mild conditions. To elucidate the mechanisms involved in the unique specificity of d-aminopeptidase, we performed quantum mechanics/molecular mechanics simulations of its polymerization reaction and determined the energy barriers presented by the chiral substrates. The enzyme faces higher activation barriers for the acylation and aminolysis reactions with the l-stereoisomer than with the d-substrate (10.7 and 17.7 kcal mol-1 higher, respectively). The simulation results suggest that changes in the interaction of the substrate with Asn155 influence the stereospecificity of the polymerization reaction.
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Affiliation(s)
- Joan Gimenez-Dejoz
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science 2-1 Hirosawa Wako-shi Saitama 351-0198 Japan
| | - Kousuke Tsuchiya
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science 2-1 Hirosawa Wako-shi Saitama 351-0198 Japan
| | - Ayaka Tateishi
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science 2-1 Hirosawa Wako-shi Saitama 351-0198 Japan
| | - Yoko Motoda
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science 2-1 Hirosawa Wako-shi Saitama 351-0198 Japan
| | - Takanori Kigawa
- Laboratory for Cellular Structural Biology, RIKEN Center for Biosystems Dynamics Research 1-7-22 Suehiro-cho, Tsurumi Yokohama 230-0045 Japan
| | - Yasuhisa Asano
- Biotechnology Research Center, Department of Biotechnology, Toyama Prefectural University 5180 Kurokawa Imizu Toyama 939-0398 Japan
| | - Keiji Numata
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science 2-1 Hirosawa Wako-shi Saitama 351-0198 Japan
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5
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Kim DH, Kim KR, Hah SS. Syntheses of Two Cephem‐Containing Chemical Inducers of Dimerization to Develop a General Method of the Covalent Approach to Fused Proteins Using a Yeast Hybrid System. B KOREAN CHEM SOC 2020. [DOI: 10.1002/bkcs.11931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Do Hyun Kim
- Department of Chemistry and Research Institute for Basic SciencesKyung Hee University Seoul 02447 South Korea
| | - Kyeong Rae Kim
- Department of Chemistry and Research Institute for Basic SciencesKyung Hee University Seoul 02447 South Korea
| | - Sang Soo Hah
- Department of Chemistry and Research Institute for Basic SciencesKyung Hee University Seoul 02447 South Korea
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6
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Dynamical Behavior of β-Lactamases and Penicillin- Binding Proteins in Different Functional States and Its Potential Role in Evolution. ENTROPY 2019. [PMCID: PMC7514474 DOI: 10.3390/e21111130] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
β-Lactamases are enzymes produced by bacteria to hydrolyze β-lactam-based antibiotics, and pose serious threat to public health through related antibiotic resistance. Class A β-lactamases are structurally and functionally related to penicillin-binding proteins (PBPs). Despite the extensive studies of the structures, catalytic mechanisms and dynamics of both β-lactamases and PBPs, the potentially different dynamical behaviors of these proteins in different functional states still remain elusive in general. In this study, four evolutionarily related proteins, including TEM-1 and TOHO-1 as class A β-lactamases, PBP-A and DD-transpeptidase as two PBPs, are subjected to molecular dynamics simulations and various analyses to characterize their dynamical behaviors in different functional states. Penicillin G and its ring opening product serve as common ligands for these four proteins of interest. The dynamic analyses of overall structures, the active sites with penicillin G, and three catalytically important residues commonly shared by all four proteins reveal unexpected cross similarities between Class A β-lactamases and PBPs. These findings shed light on both the hidden relations among dynamical behaviors of these proteins and the functional and evolutionary relations among class A β-lactamases and PBPs.
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7
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Tooke CL, Hinchliffe P, Bragginton EC, Colenso CK, Hirvonen VHA, Takebayashi Y, Spencer J. β-Lactamases and β-Lactamase Inhibitors in the 21st Century. J Mol Biol 2019; 431:3472-3500. [PMID: 30959050 PMCID: PMC6723624 DOI: 10.1016/j.jmb.2019.04.002] [Citation(s) in RCA: 453] [Impact Index Per Article: 90.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 03/27/2019] [Accepted: 04/01/2019] [Indexed: 12/31/2022]
Abstract
The β-lactams retain a central place in the antibacterial armamentarium. In Gram-negative bacteria, β-lactamase enzymes that hydrolyze the amide bond of the four-membered β-lactam ring are the primary resistance mechanism, with multiple enzymes disseminating on mobile genetic elements across opportunistic pathogens such as Enterobacteriaceae (e.g., Escherichia coli) and non-fermenting organisms (e.g., Pseudomonas aeruginosa). β-Lactamases divide into four classes; the active-site serine β-lactamases (classes A, C and D) and the zinc-dependent or metallo-β-lactamases (MBLs; class B). Here we review recent advances in mechanistic understanding of each class, focusing upon how growing numbers of crystal structures, in particular for β-lactam complexes, and methods such as neutron diffraction and molecular simulations, have improved understanding of the biochemistry of β-lactam breakdown. A second focus is β-lactamase interactions with carbapenems, as carbapenem-resistant bacteria are of grave clinical concern and carbapenem-hydrolyzing enzymes such as KPC (class A) NDM (class B) and OXA-48 (class D) are proliferating worldwide. An overview is provided of the changing landscape of β-lactamase inhibitors, exemplified by the introduction to the clinic of combinations of β-lactams with diazabicyclooctanone and cyclic boronate serine β-lactamase inhibitors, and of progress and strategies toward clinically useful MBL inhibitors. Despite the long history of β-lactamase research, we contend that issues including continuing unresolved questions around mechanism; opportunities afforded by new technologies such as serial femtosecond crystallography; the need for new inhibitors, particularly for MBLs; the likely impact of new β-lactam:inhibitor combinations and the continuing clinical importance of β-lactams mean that this remains a rewarding research area.
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Affiliation(s)
- Catherine L Tooke
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Philip Hinchliffe
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Eilis C Bragginton
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Charlotte K Colenso
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Viivi H A Hirvonen
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Yuiko Takebayashi
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom.
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8
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Awasthi S, Gupta S, Tripathi R, Nair NN. Mechanism and Kinetics of Aztreonam Hydrolysis Catalyzed by Class-C β-Lactamase: A Temperature-Accelerated Sliced Sampling Study. J Phys Chem B 2018; 122:4299-4308. [DOI: 10.1021/acs.jpcb.8b01287] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Shalini Awasthi
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Shalini Gupta
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Ravi Tripathi
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Nisanth N. Nair
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
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9
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Bhattacharjee N, Field MJ, Simorre JP, Arthur M, Bougault CM. Hybrid Potential Simulation of the Acylation of Enterococcus faecium l,d-Transpeptidase by Carbapenems. J Phys Chem B 2016; 120:4767-81. [DOI: 10.1021/acs.jpcb.6b02836] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nicholus Bhattacharjee
- DYNAMO/DYNAMOP,
UMR 5075, Université Grenoble 1, CNRS, CEA, Institut de Biologie
Structurale, 71 Avenue des Martyrs,
CS 10090, 38044 Grenoble Cedex 9, France
| | - Martin J. Field
- DYNAMO/DYNAMOP,
UMR 5075, Université Grenoble 1, CNRS, CEA, Institut de Biologie
Structurale, 71 Avenue des Martyrs,
CS 10090, 38044 Grenoble Cedex 9, France
| | - Jean-Pierre Simorre
- RMN, UMR 5075,
Université Grenoble 1, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des Martyrs, CS 10090, 38044 Grenoble Cedex 9, France
| | - Michel Arthur
- Centre de Recherche
des Cordeliers, Equipe 12, UMR S 872, Université Pierre et
Marie Curie-Paris 6, INSERM, Université Paris Descartes, Sorbonne
Paris Cité, 15 rue de l’Ecole
de Médecine, 75006 Paris, France
| | - Catherine M. Bougault
- RMN, UMR 5075,
Université Grenoble 1, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des Martyrs, CS 10090, 38044 Grenoble Cedex 9, France
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10
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Tripathi R, Nair NN. Deacylation Mechanism and Kinetics of Acyl-Enzyme Complex of Class C β-Lactamase and Cephalothin. J Phys Chem B 2016; 120:2681-90. [PMID: 26918257 DOI: 10.1021/acs.jpcb.5b11623] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Understanding the molecular details of antibiotic resistance by the bacterial enzymes β-lactamases is vital for the development of novel antibiotics and inhibitors. In this spirit, the detailed mechanism of deacylation of the acyl-enzyme complex formed by cephalothin and class C β-lactamase is investigated here using hybrid quantum-mechanical/molecular-mechanical molecular dynamics methods. The roles of various active-site residues and substrate in the deacylation reaction are elucidated. We identify the base that activates the hydrolyzing water molecule and the residue that protonates the catalytic serine (Ser64). Conformational changes in the active sites and proton transfers that potentiate the efficiency of the deacylation reaction are presented. We have also characterized the oxyanion holes and other H-bonding interactions that stabilize the reaction intermediates. Together with the kinetic and mechanistic details of the acylation reaction, we analyze the complete mechanism and the overall kinetics of the drug hydrolysis. Finally, the apparent rate-determining step in the drug hydrolysis is scrutinized.
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Affiliation(s)
- Ravi Tripathi
- Department of Chemistry, Indian Institute of Technology Kanpur , Kanpur 208016, India
| | - Nisanth N Nair
- Department of Chemistry, Indian Institute of Technology Kanpur , Kanpur 208016, India
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11
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Grigorenko BL, Khrenova MG, Nilov DK, Nemukhin AV, Švedas VK. Catalytic Cycle of Penicillin Acylase from Escherichia coli: QM/MM Modeling of Chemical Transformations in the Enzyme Active Site upon Penicillin G Hydrolysis. ACS Catal 2014. [DOI: 10.1021/cs5002898] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Bella L. Grigorenko
- Chemistry
Department, Lomonosov Moscow State University, 1-3 Leninskiye Gory, Moscow 119991, Russia
- Emanuel
Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygin Street, Moscow 119991, Russia
| | - Maria G. Khrenova
- Chemistry
Department, Lomonosov Moscow State University, 1-3 Leninskiye Gory, Moscow 119991, Russia
| | - Dmitry K. Nilov
- Belozersky
Institute of Physicochemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
| | - Alexander V. Nemukhin
- Chemistry
Department, Lomonosov Moscow State University, 1-3 Leninskiye Gory, Moscow 119991, Russia
- Emanuel
Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygin Street, Moscow 119991, Russia
| | - Vytas K. Švedas
- Belozersky
Institute of Physicochemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
- Faculty
of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 1-73 Leninskie Gory, Moscow 119991, Russia
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12
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Reclaiming the efficacy of β-lactam-β-lactamase inhibitor combinations: avibactam restores the susceptibility of CMY-2-producing Escherichia coli to ceftazidime. Antimicrob Agents Chemother 2014; 58:4290-7. [PMID: 24820081 DOI: 10.1128/aac.02625-14] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
CMY-2 is a plasmid-encoded Ambler class C cephalosporinase that is widely disseminated in Enterobacteriaceae and is responsible for expanded-spectrum cephalosporin resistance. As a result of resistance to both ceftazidime and β-lactamase inhibitors in strains carrying blaCMY, novel β-lactam-β-lactamase inhibitor combinations are sought to combat this significant threat to β-lactam therapy. Avibactam is a bridged diazabicyclo [3.2.1]octanone non-β-lactam β-lactamase inhibitor in clinical development that reversibly inactivates serine β-lactamases. To define the spectrum of activity of ceftazidime-avibactam, we tested the susceptibilities of Escherichia coli clinical isolates that carry bla(CMY-2) or bla(CMY-69) and investigated the inactivation kinetics of CMY-2. Our analysis showed that CMY-2-containing clinical isolates of E. coli were highly susceptible to ceftazidime-avibactam (MIC(90), ≤ 0.5 mg/liter); in comparison, ceftazidime had a MIC90 of >128 mg/liter. More importantly, avibactam was an extremely potent inhibitor of CMY-2 β-lactamase, as demonstrated by a second-order onset of acylation rate constant (k2/K) of (4.9 ± 0.5) × 10(4) M(-1) s(-1) and the off-rate constant (k(off)) of (3.7 ± 0.4) × 10(-4) s(-1). Analysis of the reaction of avibactam with CMY-2 using mass spectrometry to capture reaction intermediates revealed that the CMY-2-avibactam acyl-enzyme complex was stable for as long as 24 h. Molecular modeling studies raise the hypothesis that a series of successive hydrogen-bonding interactions occur as avibactam proceeds through the reaction coordinate with CMY-2 (e.g., T316, G317, S318, T319, S343, N346, and R349). Our findings support the microbiological and biochemical efficacy of ceftazidime-avibactam against E. coli containing plasmid-borne CMY-2 and CMY-69.
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Hargis JC, White JK, Chen Y, Woodcock HL. Can molecular dynamics and QM/MM solve the penicillin binding protein protonation puzzle? J Chem Inf Model 2014; 54:1412-24. [PMID: 24697903 PMCID: PMC4036751 DOI: 10.1021/ci5000517] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
![]()
Benzylpenicillin, a member of the
β-lactam antibiotic class, has been widely used to combat bacterial
infections since 1947. The general mechanism is well-known: a serine
protease enzyme (i.e., DD-peptidase) forms a long lasting intermediate
with the lactam ring of the antibiotic known as acylation, effectively
preventing biosynthesis of the bacterial cell wall. Despite this overall
mechanistic understanding, many details of binding and catalysis are
unclear. Specifically, there is ongoing debate about active site protonation
states and the role of general acids/bases in the reaction. Herein,
a unique combination of MD simulations, QM/MM minimizations, and QM/MM
orbital analyses is combined with systematic variation of active site
residue protonation states. Critical interactions that maximize the
stability of the bound inhibitor are examined and used as metrics.
This approach was validated by examining cefoxitin interactions in
the CTX-M β-lactamase from E. coli and compared to an ultra high-resolution (0.88 Å) crystal structure.
Upon confirming the approach used, an investigation of the preacylated Streptomyces R61 active site with bound benzylpenicillin
was performed, varying the protonation states of His298 and Lys65.
We concluded that protonated His298 and deprotonated Lys65 are most
likely to exist in the R61 active site.
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Affiliation(s)
- Jacqueline C Hargis
- Department of Chemistry, University of South Florida , Tampa, Florida 33620, United States
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14
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Hargis JC, Vankayala SL, White JK, Woodcock HL. Identification and Characterization of Noncovalent Interactions That Drive Binding and Specificity in DD-Peptidases and β-Lactamases. J Chem Theory Comput 2014; 10:855-864. [PMID: 24803854 PMCID: PMC3985439 DOI: 10.1021/ct400968v] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Indexed: 11/29/2022]
Abstract
![]()
Bacterial
resistance to standard (i.e., β-lactam-based) antibiotics
has become a global pandemic. Simultaneously, research into the underlying
causes of resistance has slowed substantially, although its importance
is universally recognized. Key to unraveling critical details is characterization
of the noncovalent interactions that govern binding and specificity
(DD-peptidases, antibiotic targets, versus β-lactamases, the
evolutionarily
derived enzymes that play a major role in resistance) and ultimately
resistance as a whole. Herein, we describe a detailed investigation
that elicits new chemical insights into these underlying intermolecular
interactions. Benzylpenicillin and a novel β-lactam peptidomimetic
complexed to the Stremptomyces R61
peptidase are examined using an arsenal of computational techniques:
MD simulations, QM/MM calculations, charge perturbation analysis,
QM/MM orbital analysis, bioinformatics, flexible receptor/flexible
ligand docking, and computational ADME predictions. Several key molecular
level interactions are identified that not only shed light onto fundamental
resistance mechanisms, but also offer explanations for observed specificity.
Specifically, an extended π–π network is elucidated
that suggests antibacterial resistance has evolved, in part, due to
stabilizing aromatic interactions. Additionally, interactions between
the protein and peptidomimetic substrate are identified and characterized.
Of particular interest is a water-mediated salt bridge between Asp217
and the positively charged N-terminus of the peptidomimetic, revealing
an interaction that may significantly contribute to β-lactam
specificity. Finally, interaction information is used to suggest modifications
to current β-lactam compounds that should both improve binding
and specificity in DD-peptidases and their physiochemical properties.
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Affiliation(s)
- Jacqueline C Hargis
- Department of Chemistry, University of South Florida , 4202 East Fowler Avenue, CHE205, Tampa, Florida 33620-5250, United States
| | - Sai Lakshmana Vankayala
- Department of Chemistry, University of South Florida , 4202 East Fowler Avenue, CHE205, Tampa, Florida 33620-5250, United States
| | - Justin K White
- Department of Chemistry, University of South Florida , 4202 East Fowler Avenue, CHE205, Tampa, Florida 33620-5250, United States
| | - H Lee Woodcock
- Department of Chemistry, University of South Florida , 4202 East Fowler Avenue, CHE205, Tampa, Florida 33620-5250, United States
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15
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Tripathi R, Nair NN. Mechanism of acyl-enzyme complex formation from the Henry-Michaelis complex of class C β-lactamases with β-lactam antibiotics. J Am Chem Soc 2013; 135:14679-90. [PMID: 24010547 DOI: 10.1021/ja405319n] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Bacteria that cause most of the hospital-acquired infections make use of class C β-lactamase (CBL) among other enzymes to resist a wide spectrum of modern antibiotics and pose a major public health concern. Other than the general features, details of the defensive mechanism by CBL, leading to the hydrolysis of drug molecules, remain a matter of debate, in particular the identification of the general base and role of the active site residues and substrate. In an attempt to unravel the detailed molecular mechanism, we carried out extensive hybrid quantum mechanical/molecular mechanical Car-Parrinello molecular dynamics simulation of the reaction with the aid of the metadynamics technique. On this basis, we report here the mechanism of the formation of the acyl-enzyme complex from the Henry-Michaelis complex formed by β-lactam antibiotics and CBL. We considered two β-lactam antibiotics, namely, cephalothin and aztreonam, belonging to two different subfamilies. A general mechanism for the formation of a β-lactam antibiotic-CBL acyl-enzyme complex is elicited, and the individual roles of the active site residues and substrate are probed. The general base in the acylation step has been identified as Lys67, while Tyr150 aids the protonation of the β-lactam nitrogen through either the substrate carboxylate group or a water molecule.
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Affiliation(s)
- Ravi Tripathi
- Department of Chemistry, Indian Institute of Technology Kanpur , 208016 Kanpur, India
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van der Kamp MW, Mulholland AJ. Combined quantum mechanics/molecular mechanics (QM/MM) methods in computational enzymology. Biochemistry 2013; 52:2708-28. [PMID: 23557014 DOI: 10.1021/bi400215w] [Citation(s) in RCA: 402] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Computational enzymology is a rapidly maturing field that is increasingly integral to understanding mechanisms of enzyme-catalyzed reactions and their practical applications. Combined quantum mechanics/molecular mechanics (QM/MM) methods are important in this field. By treating the reacting species with a quantum mechanical method (i.e., a method that calculates the electronic structure of the active site) and including the enzyme environment with simpler molecular mechanical methods, enzyme reactions can be modeled. Here, we review QM/MM methods and their application to enzyme-catalyzed reactions to investigate fundamental and practical problems in enzymology. A range of QM/MM methods is available, from cheaper and more approximate methods, which can be used for molecular dynamics simulations, to highly accurate electronic structure methods. We discuss how modeling of reactions using such methods can provide detailed insight into enzyme mechanisms and illustrate this by reviewing some recent applications. We outline some practical considerations for such simulations. Further, we highlight applications that show how QM/MM methods can contribute to the practical development and application of enzymology, e.g., in the interpretation and prediction of the effects of mutagenesis and in drug and catalyst design.
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Affiliation(s)
- Marc W van der Kamp
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.
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17
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Fu G, Liu H, Doerksen RJ. Molecular modeling to provide insight into the substrate binding and catalytic mechanism of human biliverdin-IXα reductase. J Phys Chem B 2012; 116:9580-94. [PMID: 22823425 DOI: 10.1021/jp301456j] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human biliverdin-IXα reductase (hBVR-A) catalyzes the conversion of biliverdin-IXα to bilirubin-IXα in the last step of heme degradation and is a key enzyme in regulating a wide range of cellular responses. Though the X-ray structure of hBVR-A is available including cofactor, a crystal structure with a bound substrate would be even more useful as a starting point for protein-structure-based inhibitor design, but none have been reported. The present study employed induced fit docking (IFD) to study the substrate binding modes to hBVR-A of biliverdin-IXα and four analogues. The proposed substrate binding modes were examined further by performing molecular dynamics (MD) simulations followed by molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) calculations. The predicted binding free energies for the five biliverdin-IXα analogues match well with the relative potency of their reported experimental binding affinities, supporting that the proposed binding modes are reasonable. Furthermore, the ternary complex structure of hBVR-A binding with biliverdin-IXα and the electron donor cofactor NADPH obtained from MD simulations was exploited to investigate the catalytic mechanism, by calculating the reaction energy profile using the quantum mechanics/molecular mechanics (QM/MM) method. On the basis of our calculations, the energetically preferred pathway consists of an initial protonation of the pyrrolic nitrogen on the biliverdin substrate followed by hydride transfer to yield the reduction product. This conclusion is consistent with a previous mechanistic study on human biliverdin IXβ reductase (hBVR-B).
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Affiliation(s)
- Gang Fu
- Department of Medicinal Chemistry, School of Pharmacy, University of Mississippi, University, Mississippi 38677, United States
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18
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Tripathi R, Nair NN. Thermodynamic and Kinetic Stabilities of Active Site Protonation States of Class C β-Lactamase. J Phys Chem B 2012; 116:4741-53. [DOI: 10.1021/jp212186q] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Ravi Tripathi
- Department of Chemistry, Indian Institute of Technology, Kanpur, 208016 Kanpur,
India
| | - Nisanth N. Nair
- Department of Chemistry, Indian Institute of Technology, Kanpur, 208016 Kanpur,
India
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Kotsakis SD, Tzouvelekis LS, Petinaki E, Tzelepi E, Miriagou V. Effects of the Val211Gly substitution on molecular dynamics of the CMY-2 cephalosporinase: implications on hydrolysis of expanded-spectrum cephalosporins. Proteins 2011; 79:3180-92. [PMID: 21989938 DOI: 10.1002/prot.23150] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Revised: 07/04/2011] [Accepted: 07/14/2011] [Indexed: 11/05/2022]
Abstract
CMY-30, a naturally occurring class C β-lactamase differing from the Citrobacter freundii-derived CMY-2 by a Val211Gly substitution in the Ω-loop, exhibits increased hydrolytic efficiency against ceftazidime and cefotaxime. Kinetic constants of CMY-2 and CMY-30 against the latter substrates suggested that the improved efficiency of the Gly211 variant was due to an increase in k(cat). The structural basis of the increased turn-over rates of oxyimino-cephalosporins caused by Val211Gly was studied using 5 ns molecular dynamics simulations of CMY-2 and CMY-30 in their free forms and in covalent complexes with ceftazidime (acyl-enzyme) as well as a boronic acid analogue of ceftazidime (deacylation transition state). Analysis of thermal factors indicated that Val211Gly increased the flexibility of the Ω-loop/H7-helix and the Q120-loop formed by amino acids 112-125, and also altered the vibrations of the H10-helix/R2-loop. Structural elements containing the catalytic residues remained relatively rigid except Tyr150 in acyl-enzyme species. Regions exhibiting altered flexibility due to the substitution appear to move in a concerted manner in both enzymes. This movement was more intense in CMY-30 and also at directions different to those observed for CMY-2. Additionally, it appeared that the Val211Gly increased the available space for the accommodation of the R1 side chain of ceftazidime. These findings are likely associated with the significantly increased vibrations of the bound compounds observed in CMY-30 complexes. Therefore, the extended spectrum properties of CMY-30 seem to arise through a complex process implicating changes in protein movement and in the mode of substrate accommodation.
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Affiliation(s)
- Stathis D Kotsakis
- Laboratory of Bacteriology, Hellenic Pasteur Institute, 11521 Athens, Greece
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20
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Dzhekieva L, Rocaboy M, Kerff F, Charlier P, Sauvage E, Pratt RF. Crystal Structure of a Complex between the Actinomadura R39 dd-Peptidase and a Peptidoglycan-mimetic Boronate Inhibitor: Interpretation of a Transition State Analogue in Terms of Catalytic Mechanism. Biochemistry 2010; 49:6411-9. [DOI: 10.1021/bi100757c] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Liudmila Dzhekieva
- Department of Chemistry, Wesleyan University, Lawn Avenue, Middletown, Connecticut 06459
| | - Mathieu Rocaboy
- Centre d’Ingéniere des Proteines, Université de Liège, B-4000 Sart Tilman, Liège, Belgium
| | - Frédéric Kerff
- Centre d’Ingéniere des Proteines, Université de Liège, B-4000 Sart Tilman, Liège, Belgium
| | - Paulette Charlier
- Centre d’Ingéniere des Proteines, Université de Liège, B-4000 Sart Tilman, Liège, Belgium
| | - Eric Sauvage
- Centre d’Ingéniere des Proteines, Université de Liège, B-4000 Sart Tilman, Liège, Belgium
| | - R. F. Pratt
- Department of Chemistry, Wesleyan University, Lawn Avenue, Middletown, Connecticut 06459
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21
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Rodríguez A, Oliva C, González M. A comparative QM/MM study of the reaction mechanism of the Hepatitis C virus NS3/NS4A protease with the three main natural substrates NS5A/5B, NS4B/5A and NS4A/4B. Phys Chem Chem Phys 2010; 12:8001-15. [PMID: 20520921 DOI: 10.1039/c002116d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The reaction mechanism of the NS3/NS4A protease with the NS4B/5A and NS4A/4B natural substrates has been investigated using the QM/MM (quantum mechanics/molecular mechanics) approach, and some calculations have been performed on the reaction with the NS5A/5B natural substrate. This study widely extends a previous contribution of our group on the reaction mechanism with the NS5A/5B substrate, the main goal here being to understand the differences found between the reaction mechanism of each natural substrate and the role played by the enzymatic residues in the catalytic cycle. This knowledge will ultimately help in developing new NS3/NS4A protease inhibitors. The two first steps of the mechanism have been considered: Acylation and breaking of the peptide bond, with emphasis on the former one (rate limiting process). Energy and free energy profiles for both steps have been calculated at the AM1/MM level and corrected by means of MP2 ab initio calculations, being evident the importance of correlation energy. Acylation is the rate limiting step in all cases and occurs through a tetracoordinated intermediate, as previously suggested for other serine proteases. Specificities in the NS4B/5A mechanism can be attributed to the presence of a Proline residue in the substrate P2 position. The analysis of structures and energies confirm the importance of the oxyanion hole in the electrostatic stabilization of the tetracoordinated intermediate. Finally, the role of other residues, e.g., Arg-155 and Asp-79, has been explained, and the viability of Arg-155 mutants and its resistance to some protease inhibitors has been understood thanks to virtual mutation studies.
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Affiliation(s)
- Alejandro Rodríguez
- Departament de Química Física i IQTC, Universitat de Barcelona, C/Martí i Franquès 1, 08028 Barcelona, Spain
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22
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Abiram A, Kolandaivel P. Effect of piratoxin II and acutohaemolysin phospholipase (PLA2) proteins on myristic fatty acid—An ONIOM and DFT study. J Mol Model 2010; 16:1853-65. [DOI: 10.1007/s00894-010-0681-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2009] [Accepted: 01/29/2010] [Indexed: 12/14/2022]
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Drawz SM, Babic M, Bethel CR, Taracila M, Distler AM, Ori C, Caselli E, Prati F, Bonomo RA. Inhibition of the class C beta-lactamase from Acinetobacter spp.: insights into effective inhibitor design. Biochemistry 2010; 49:329-40. [PMID: 19925018 DOI: 10.1021/bi9015988] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The need to develop beta-lactamase inhibitors against class C cephalosporinases of Gram-negative pathogens represents an urgent clinical priority. To respond to this challenge, five boronic acid derivatives, including a new cefoperazone analogue, were synthesized and tested against the class C cephalosporinase of Acinetobacter baumannii [Acinetobacter-derived cephalosporinase (ADC)]. The commercially available carbapenem antibiotics were also assayed. In the boronic acid series, a chiral cephalothin analogue with a meta-carboxyphenyl moiety corresponding to the C(3)/C(4) carboxylate of beta-lactams showed the lowest K(i) (11 +/- 1 nM). In antimicrobial susceptibility tests, this cephalothin analogue lowered the ceftazidime and cefotaxime minimum inhibitory concentrations (MICs) of Escherichia coli DH10B cells carrying bla(ADC) from 16 to 4 microg/mL and from 8 to 1 microg/mL, respectively. On the other hand, each carbapenem exhibited a K(i) of <20 microM, and timed electrospray ionization mass spectrometry (ESI-MS) demonstrated the formation of adducts corresponding to acyl-enzyme intermediates with both intact carbapenem and carbapenem lacking the C(6) hydroxyethyl group. To improve our understanding of the interactions between the beta-lactamase and the inhibitors, we constructed models of ADC as an acyl-enzyme intermediate with (i) the meta-carboxyphenyl cephalothin analogue and (ii) the carbapenems, imipenem and meropenem. Our first model suggests that this chiral cephalothin analogue adopts a novel conformation in the beta-lactamase active site. Further, the addition of the substituent mimicking the cephalosporin dihydrothiazine ring may significantly improve affinity for the ADC beta-lactamase. In contrast, the ADC-carbapenem models offer a novel role for the R(2) side group and also suggest that elimination of the C(6) hydroxyethyl group by retroaldolic reaction leads to a significant conformational change in the acyl-enzyme intermediate. Lessons from the diverse mechanisms and structures of the boronic acid derivatives and carbapenems provide insights for the development of new beta-lactamase inhibitors against these critical drug resistance targets.
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Affiliation(s)
- Sarah M Drawz
- Department of Pathology, Case Western Reserve UniversitySchool of Medicine, Cleveland, Ohio 44106, USA
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24
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Kawai F, Clarke TB, Roper DI, Han GJ, Hwang KY, Unzai S, Obayashi E, Park SY, Tame JR. Crystal Structures of Penicillin-Binding Proteins 4 and 5 from Haemophilus influenzae. J Mol Biol 2010; 396:634-45. [DOI: 10.1016/j.jmb.2009.11.055] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Revised: 11/20/2009] [Accepted: 11/22/2009] [Indexed: 10/20/2022]
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25
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Ranaghan KE, Mulholland AJ. Investigations of enzyme-catalysed reactions with combined quantum mechanics/molecular mechanics (QM/MM) methods. INT REV PHYS CHEM 2010. [DOI: 10.1080/01442350903495417] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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26
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Zhang R, Lev B, Cuervo JE, Noskov SY, Salahub DR. A Guide to QM/MM Methodology and Applications. ADVANCES IN QUANTUM CHEMISTRY 2010. [DOI: 10.1016/s0065-3276(10)59010-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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Abstract
Since the introduction of penicillin, beta-lactam antibiotics have been the antimicrobial agents of choice. Unfortunately, the efficacy of these life-saving antibiotics is significantly threatened by bacterial beta-lactamases. beta-Lactamases are now responsible for resistance to penicillins, extended-spectrum cephalosporins, monobactams, and carbapenems. In order to overcome beta-lactamase-mediated resistance, beta-lactamase inhibitors (clavulanate, sulbactam, and tazobactam) were introduced into clinical practice. These inhibitors greatly enhance the efficacy of their partner beta-lactams (amoxicillin, ampicillin, piperacillin, and ticarcillin) in the treatment of serious Enterobacteriaceae and penicillin-resistant staphylococcal infections. However, selective pressure from excess antibiotic use accelerated the emergence of resistance to beta-lactam-beta-lactamase inhibitor combinations. Furthermore, the prevalence of clinically relevant beta-lactamases from other classes that are resistant to inhibition is rapidly increasing. There is an urgent need for effective inhibitors that can restore the activity of beta-lactams. Here, we review the catalytic mechanisms of each beta-lactamase class. We then discuss approaches for circumventing beta-lactamase-mediated resistance, including properties and characteristics of mechanism-based inactivators. We next highlight the mechanisms of action and salient clinical and microbiological features of beta-lactamase inhibitors. We also emphasize their therapeutic applications. We close by focusing on novel compounds and the chemical features of these agents that may contribute to a "second generation" of inhibitors. The goal for the next 3 decades will be to design inhibitors that will be effective for more than a single class of beta-lactamases.
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Affiliation(s)
- Sarah M. Drawz
- Departments of Pathology, Medicine, Pharmacology, Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
| | - Robert A. Bonomo
- Departments of Pathology, Medicine, Pharmacology, Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
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28
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Chen Y, Zhang W, Shi Q, Hesek D, Lee M, Mobashery S, Shoichet BK. Crystal structures of penicillin-binding protein 6 from Escherichia coli. J Am Chem Soc 2009; 131:14345-54. [PMID: 19807181 PMCID: PMC3697005 DOI: 10.1021/ja903773f] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Penicillin-binding protein 6 (PBP6) is one of the two main DD-carboxypeptidases in Escherichia coli, which are implicated in maturation of bacterial cell wall and formation of cell shape. Here, we report the first X-ray crystal structures of PBP6, capturing its apo state (2.1 A), an acyl-enzyme intermediate with the antibiotic ampicillin (1.8 A), and for the first time for a PBP, a preacylation complex (a "Michaelis complex", determined at 1.8 A) with a peptidoglycan substrate fragment containing the full pentapeptide, NAM-(L-Ala-D-isoGlu-L-Lys-D-Ala-D-Ala). These structures illuminate the molecular interactions essential for ligand recognition and catalysis by DD-carboxypeptidases, and suggest a coupling of conformational flexibility of active site loops to the reaction coordinate. The substrate fragment complex structure, in particular, provides templates for models of cell wall recognition by PBPs, as well as substantiating evidence for the molecular mimicry by beta-lactam antibiotics of the peptidoglycan acyl-D-Ala-D-Ala moiety.
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Affiliation(s)
- Yu Chen
- Department of Pharmaceutical Chemistry, University of California San Francisco, Byers Hall, Room 508D, 1700 Fourth Street, San Francisco, California 94158-2550
| | - Weilie Zhang
- Department of Chemistry and Biochemistry, 423 Nieuwland Science Center, UniVersity of Notre Dame, Notre Dame, Indiana 46556
| | - Qicun Shi
- Department of Chemistry and Biochemistry, 423 Nieuwland Science Center, UniVersity of Notre Dame, Notre Dame, Indiana 46556
| | - Dusan Hesek
- Department of Chemistry and Biochemistry, 423 Nieuwland Science Center, UniVersity of Notre Dame, Notre Dame, Indiana 46556
| | - Mijoon Lee
- Department of Chemistry and Biochemistry, 423 Nieuwland Science Center, UniVersity of Notre Dame, Notre Dame, Indiana 46556
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, 423 Nieuwland Science Center, UniVersity of Notre Dame, Notre Dame, Indiana 46556
| | - Brian K. Shoichet
- Department of Pharmaceutical Chemistry, University of California San Francisco, Byers Hall, Room 508D, 1700 Fourth Street, San Francisco, California 94158-2550
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29
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Chen Y, McReynolds A, Shoichet BK. Re-examining the role of Lys67 in class C beta-lactamase catalysis. Protein Sci 2009; 18:662-9. [PMID: 19241376 DOI: 10.1002/pro.60] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Lys67 is essential for the hydrolysis reaction mediated by class C beta-lactamases. Its exact catalytic role lies at the center of several different proposed reaction mechanisms, particularly for the deacylation step, and has been intensely debated. Whereas a conjugate base hypothesis postulates that a neutral Lys67 and Tyr150 act together to deprotonate the deacylating water, previous experiments on the K67R mutants of class C beta-lactamases suggested that the role of Lys67 in deacylation is mainly electrostatic, with only a 2- to 3-fold decrease in the rate of the mutant vs the wild type enzyme. Using the Class C beta-lactamase AmpC, we have reinvestigated the activity of this K67R mutant enzyme, using biochemical and structural studies. Both the rates of acylation and deacylation were affected in the AmpC K67R mutant, with a 61-fold decrease in k(cat), the deacylation rate. We have determined the structure of the K67R mutant by X-ray crystallography both in apo and transition state-analog complexed forms, and observed only minimal conformational changes in the catalytic residues relative to the wild type. These results suggest that the arginine side chain is unable to play the same catalytic role as Lys67 in either the acylation or deacylation reactions catalyzed by AmpC. Therefore, the activity of this mutant can not be used to discredit the conjugate base hypothesis as previously concluded, although the reaction catalyzed by the K67R mutant itself likely proceeds by an alternative mechanism. Indeed, a manifold of mechanisms may contribute to hydrolysis in class C beta-lactamases, depending on the enzyme (wt or mutant) and the substrate, explaining why different mutants and substrates seem to support different pathways. For the WT enzyme itself, the conjugate base mechanism may be well favored.
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Affiliation(s)
- Yu Chen
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94158-2550, USA
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Schneider KD, Bethel CR, Distler AM, Hujer AM, Bonomo RA, Leonard DA. Mutation of the active site carboxy-lysine (K70) of OXA-1 beta-lactamase results in a deacylation-deficient enzyme. Biochemistry 2009; 48:6136-45. [PMID: 19485421 DOI: 10.1021/bi900448u] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Class D beta-lactamases hydrolyze beta-lactam antibiotics by using an active site serine nucleophile to form a covalent acyl-enzyme intermediate and subsequently employ water to deacylate the beta-lactam and release product. Class D beta-lactamases are carboxylated on the epsilon-amino group of an active site lysine, with the resulting carbamate functional group serving as a general base. We discovered that substitutions of the active site serine and lysine in OXA-1 beta-lactamase, a monomeric class D enzyme, significantly disrupt catalytic turnover. Substitution of glycine for the nucleophilic serine (S67G) results in an enzyme that can still bind substrate but is unable to form a covalent acyl-enzyme intermediate. Substitution of the carboxylated lysine (K70), on the other hand, results in enzyme that can be acylated by substrate but is impaired with respect to deacylation. We employed the fluorescent penicillin BOCILLIN FL to show that three different substitutions for K70 (alanine, aspartate, and glutamate) lead to the accumulation of significant acyl-enzyme intermediate. Interestingly, BOCILLIN FL deacylation rates (t(1/2)) vary depending on the identity of the substituting residue, from approximately 60 min for K70A to undetectable deacylation for K70D. Tryptophan fluorescence spectroscopy was used to confirm that these results are applicable to natural (i.e., nonfluorescent) substrates. Deacylation by K70A, but not K70D or K70E, can be partially restored by the addition of short-chain carboxylic acid mimetics of the lysine carbamate. In conclusion, we establish the functional role of the carboxylated lysine in OXA-1 and highlight its specific role in acylation and deacylation.
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Affiliation(s)
- Kyle D Schneider
- Department of Chemistry, Grand Valley State University, Allendale, Michigan 49401, USA
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31
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Roca M, Vardi-Kilshtain A, Warshel A. Toward accurate screening in computer-aided enzyme design. Biochemistry 2009; 48:3046-56. [PMID: 19161327 DOI: 10.1021/bi802191b] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The ability to design effective enzymes is one of the most fundamental challenges in biotechnology and in some respects in biochemistry. In fact, such ability would be one of the most convincing manifestations of a full understanding of the origin of enzyme catalysis. In this work, we explore the reliability of different simulation approaches, in terms of their ability to rank different possible active site constructs. This validation is done by comparing the ability of different approaches to evaluate the catalytic contributions of various residues in chorismate mutase. It is demonstrated that the empirical valence bond (EVB) model can serve as a practical yet accurate tool in the final stages of computer-aided enzyme design (CAED). Other approaches for fast screening are also examined and found to be less accurate and mainly useful for qualitative screening of ionized residues. It is pointed out that accurate ranking of different options for enzyme design cannot be accomplished by approaches that cannot capture the electrostatic preorganization effect. This is in particular true with regard to current design approaches that use gas phase or small cluster calculations and then estimate the interaction between the enzyme and the transition state (TS) model rather than the TS binding free energy or the relevant activation free energy. The ability of the EVB model to provide a tool for quantitative ranking in the final stage of CAED may help in progressing toward the design of enzymes whose catalytic power is closer to that of native enzymes than to that of the current generation of designer enzymes.
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Affiliation(s)
- Maite Roca
- Department of Chemistry, UniVersity of Southern California, Los Angeles, California 90089-1062, USA
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32
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Tian L, Friesner RA. QM/MM Simulation on P450 BM3 Enzyme Catalysis Mechanism. J Chem Theory Comput 2009; 5:1421-1431. [PMID: 20046929 DOI: 10.1021/ct900040n] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Using a structure generated by induced fit modeling of the protein-ligand complex, the reaction path for hydrogen atom abstraction in P450 BM3 is studied by means of mixed QM/MM methods to determine the structures and energetics along the reaction path. The IFD structure is suitable for hydrogen atom abstraction at the ω-1 position. The electronic structures obtained are similar to those observed in P450 cam. We show that the barrier for the hydrogen abstraction step from QM/MM modeling is 13.3 kcal/mol in quartet and 15.6 kcal/mol in doublet. Although there is some strain energy present in the ligand, the activation barrier is not dramatically affected. A crystal water molecule, HOH502, plays a role as catalyst and decreases the activation barrier by about 2 kcal/mol and reaction energy by about 3-4 kcal/mol. In order to achieve reactive chemistry at the remaining experimentally observed positions in the hydrocarbon tail of the ligand, other structures would have to be utilized as a starting point for the reaction. Finally, the present results still leave open the question of whether DFT methods provide an accurate computation of the barrier height in the P450 hydrogen atom abstraction reaction.
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Affiliation(s)
- Li Tian
- Department of Chemistry, Columbia University, New York, New York 10027
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33
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Roy D, Sunoj RB. Water catalysis in the Morita-Baylis-Hillman reaction: a mechanistic perspective. Chemistry 2008; 14:10530-4. [PMID: 18988243 DOI: 10.1002/chem.200801822] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Dipankar Roy
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
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34
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Fenollar-Ferrer C, Frau J, Donoso J, Muñoz F. Evolution of class C β-lactamases: factors influencing their hydrolysis and recognition mechanisms. Theor Chem Acc 2008. [DOI: 10.1007/s00214-008-0463-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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35
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Mukherjee P, Desai PV, Srivastava A, Tekwani BL, Avery MA. Probing the structures of leishmanial farnesyl pyrophosphate synthases: homology modeling and docking studies. J Chem Inf Model 2008; 48:1026-40. [PMID: 18419114 DOI: 10.1021/ci700355z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Leishmania donovani and Leishmania major farnesyl pyrophosphate synthase ( LdFPPS and LmFPPS) are potential targets for the development of antileishmanial therapy. The protein sequence for LdFPPS was recently elucidated in our laboratory. Highly refined homology models were generated using the protein sequences of LdFPPS and the closely related LmFPPS enzyme. A ligand-refined model of LmFPPS with a bound bisphosphonate ligand was generated using restraint-guided molecular mechanics followed by quantum mechanics/molecular mechanics refinement. The ligand-refined model of LmFPPS was further validated through extensive pose validation, enrichment, and other docking studies involving known bisphosphonate inhibitors. The model was able to explain the critical binding site interactions and site-directed mutagenesis data obtained from experimental studies on related FPPS enzymes. The ligand-refined model in conjunction with the validated docking protocol could be utilized in the future for structure-based virtual screening and rational drug design studies against these targets.
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Affiliation(s)
- Prasenjit Mukherjee
- Department of Medicinal Chemistry, School of Pharmacy, University of Mississippi, University, Mississippi 38677, USA
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36
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Rinaldo D, Philipp DM, Lippard SJ, Friesner RA. Intermediates in dioxygen activation by methane monooxygenase: a QM/MM study. J Am Chem Soc 2007; 129:3135-47. [PMID: 17326634 PMCID: PMC2517126 DOI: 10.1021/ja0654074] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein effects in the activation of dioxygen by methane monooxygenase (MMO) were investigated by using combined QM/MM and broken-symmetry Density Functional Theory (DFT) methods. The effects of a novel empirical scheme recently developed by our group on the relative DFT energies of the various intermediates in the catalytic cycle are investigated. Inclusion of the protein leads to much better agreement between the experimental and computed geometric structures for the reduced form (MMOH(red)). Analysis of the electronic structure of MMOH(red) reveals that the two iron atoms have distinct environments. Different coordination geometries tested for the MMOH(peroxo) intermediate reveal that, in the protein environment, the mu-eta2,eta2 structure is more stable than the others. Our analysis also shows that the protein helps to drive reactants toward products along the reaction path. Furthermore, these results demonstrate the importance of including the protein environment in our models and the usefulness of the QM/MM approach for accurate modeling of enzymatic reactions. A discrepancy remains in our calculation of the Fe-Fe distance in our model of HQ as compared to EXAFS data obtained several years ago, for which we currently do not have an explanation.
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37
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Hata M, Fujii Y, Tanaka Y, Ishikawa H, Ishii M, Neya S, Tsuda M, Hoshino T. Substrate deacylation mechanisms of serine-beta-lactamases. Biol Pharm Bull 2007; 29:2151-9. [PMID: 17077507 DOI: 10.1248/bpb.29.2151] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The substrate deacylation mechanisms of serine-beta-lactamases (classes A, C and D) were investigated by theoretical calculations. The deacylation of class A proceeds via four elementary reactions. The rate-determining process is the tetrahedral intermediate (TI) formation and the activation energy is 24.6 kcal/mol at the DFT level. The deacylation does not proceed only by Glu166, which acts as a general base, but Lys73 also participates in the reaction. The C3-carboxyl group of the substrate reduces the barrier height at the TI formation (substrate-assisted catalysis). In the case of class C, the deacylation consists of two elementary processes. The activation energy of the TI formation has been estimated to be 30.5 kcal/mol. Tyr150Oeta is stabilized in the deprotonated state in the acyl-enzyme complex and works as a general base. This situation can exist due to the interaction with two positively charged side chains of lysine (Lys67 and Lys315). The deacylation of class D also consists of two elementary reaction processes. The activation energy of the TI formation is ca. 30 kcal/mol. It is thought that the side chain of Lys70 is deprotonated and acts as a general base. When Lys70 is carbamylated, the activation energy is reduced to less than 20 kcal/mol. This suggests that the high hydrolysis activity of class D with carbamylated Lys70 is due to the reduction of activation energy for deacylation. From these results, it is concluded that the contribution of the lysine residue adjacent to the serine residue is indispensable for the enzymatic reactions by serine-beta-lactamases.
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Affiliation(s)
- Masayuki Hata
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Japan.
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38
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Substrate-Enzyme Interactions from Modeling and Isotope Effects. ACTA ACUST UNITED AC 2007. [DOI: 10.1007/1-4020-5372-x_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
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39
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Coto PB, Strambi A, Ferré N, Olivucci M. The color of rhodopsins at the ab initio multiconfigurational perturbation theory resolution. Proc Natl Acad Sci U S A 2006; 103:17154-9. [PMID: 17090682 PMCID: PMC1859901 DOI: 10.1073/pnas.0604048103] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2006] [Indexed: 11/18/2022] Open
Abstract
We demonstrate that "brute force" quantum-mechanics/molecular-mechanics computations based on ab initio (i.e., first principles) multiconfigurational perturbation theory can reproduce the absorption maxima of a set of modified bovine rhodopsins with an accuracy allowing for the analysis of the factors determining their colors. In particular, we show that the theory accounts for the changes in excitation energy even when the proteins display the same charge distribution. Three color-tuning mechanisms, leading to changes of close magnitude, are demonstrated to operate in these conditions. The first is based on the change of the conformation of the conjugated backbone of the retinal chromophore. The second operates through the control of the distance between the positive charge residing on the chromophore and the carboxylate counterion. Finally, the third mechanism operates through the changes in orientation of the chromophore relative to the protein. These results offer perspectives for the unbiased computational design of mutants or chemically modified proteins with wanted optical properties.
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Affiliation(s)
- Pedro B. Coto
- Dipartimento di Chimica, Università di Siena, via Aldo Moro 2, I-53100 Siena, Italy
| | - Angela Strambi
- Dipartimento di Chimica, Università di Siena, via Aldo Moro 2, I-53100 Siena, Italy
| | - Nicolas Ferré
- Laboratoire de Chimie Théorique et de Modélisation Moléculaire, Unite Mixte de Recherche 6517, Centre National de la Recherche Scientifique, Université de Provence, Case 521 Faculté de Saint-Jérôme, Avenue Esc. Normandie Niemen, 13397 Marseille Cedex 20, France; and
| | - Massimo Olivucci
- Dipartimento di Chimica, Università di Siena, via Aldo Moro 2, I-53100 Siena, Italy
- Chemistry Department, Bowling Green State University, Bowling Green, OH 43403
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40
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Okazaki S, Suzuki A, Komeda H, Yamaguchi S, Asano Y, Yamane T. Crystal structure and functional characterization of a D-stereospecific amino acid amidase from Ochrobactrum anthropi SV3, a new member of the penicillin-recognizing proteins. J Mol Biol 2006; 368:79-91. [PMID: 17331533 DOI: 10.1016/j.jmb.2006.10.070] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2006] [Revised: 10/19/2006] [Accepted: 10/20/2006] [Indexed: 11/28/2022]
Abstract
D-amino acid amidase (DAA) from Ochrobactrum anthropi SV3, which catalyzes the stereospecific hydrolysis of D-amino acid amides to yield the D-amino acid and ammonia, has attracted increasing attention as a catalyst for the stereospecific production of D-amino acids. In order to clarify the structure-function relationships of DAA, the crystal structures of native DAA, and of the D-phenylalanine/DAA complex, were determined at 2.1 and at 2.4 A resolution, respectively. Both crystals contain six subunits (A-F) in the asymmetric unit. The fold of DAA is similar to that of the penicillin-recognizing proteins, especially D-alanyl-D-alanine-carboxypeptidase from Streptomyces R61, and class C beta-lactamase from Enterobacter cloacae strain GC1. The catalytic residues of DAA and the nucleophilic water molecule for deacylation were assigned based on these structures. DAA has a flexible Omega-loop, similar to class C beta-lactamase. DAA forms a pseudo acyl-enzyme intermediate between Ser60 O(gamma) and the carbonyl moiety of d-phenylalanine in subunits A, B, C, D, and E, but not in subunit F. The difference between subunit F and the other subunits (A, B, C, D and E) might be attributed to the order/disorder structure of the Omega-loop: the structure of this loop cannot assigned in subunit F. Deacylation of subunit F may be facilitated by the relative movement of deprotonated His307 toward Tyr149. His307 N(epsilon2) extracts the proton from Tyr149 O(eta), then Tyr149 O(eta) attacks a nucleophilic water molecule as a general base. Gln214 on the Omega-loop is essential for forming a network of water molecules that contains the nucleophilic water needed for deacylation. Although peptidase activity is found in almost all penicillin-recognizing proteins, DAA lacks peptidase activity. The lack of transpeptidase and carboxypeptidase activities may be attributed to steric hindrance of the substrate-binding pocket by a loop comprised of residues 278-290 and the Omega-loop.
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Affiliation(s)
- Seiji Okazaki
- Department of Biotechnology, School of Engineering, Nagoya University, Chikusa, Nagoya 464-8603, Japan
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41
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Abstract
Researchers in the post-genome era are confronted with the daunting task of assigning structure and function to tens of thousands of encoded proteins. To realize this goal, new technologies are emerging for the analysis of protein function on a global scale, such as activity-based protein profiling (ABPP), which aims to develop active site-directed chemical probes for enzyme analysis in whole proteomes. For the pursuit of such chemical proteomic technologies, it is helpful to derive inspiration from protein-reactive natural products. Natural products use a remarkably diverse set of mechanisms to covalently modify enzymes from distinct mechanistic classes, thus providing a wellspring of chemical concepts that can be exploited for the design of active-site-directed proteomic probes. Herein, we highlight several examples of protein-reactive natural products and illustrate how their mechanisms of action have influenced and continue to shape the progression of chemical proteomic technologies like ABPP.
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Affiliation(s)
- Carmen Drahl
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
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42
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Cavalli A, Carloni P, Recanatini M. Target-Related Applications of First Principles Quantum Chemical Methods in Drug Design. Chem Rev 2006; 106:3497-519. [PMID: 16967914 DOI: 10.1021/cr050579p] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Andrea Cavalli
- Department of Pharmaceutical Sciences, University of Bologna, Via Belmeloro 6, I-40126 Bologna, Italy
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43
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Chen Y, Minasov G, Roth TA, Prati F, Shoichet BK. The deacylation mechanism of AmpC beta-lactamase at ultrahigh resolution. J Am Chem Soc 2006; 128:2970-6. [PMID: 16506777 PMCID: PMC1544378 DOI: 10.1021/ja056806m] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Beta-lactamases confer bacterial resistance to beta-lactam antibiotics, such as penicillins. The characteristic class C beta-lactamase AmpC catalyzes the reaction with several key residues including Ser64, Tyr150, and Lys67. Here, we describe a 1.07 A X-ray crystallographic structure of AmpC beta-lactamase in complex with a boronic acid deacylation transition-state analogue. The high quality of the electron density map allows the determination of many proton positions. The proton on the Tyr150 hydroxyl group is clearly visible and is donated to the boronic oxygen mimicking the deacylation water. Meanwhile, Lys67 hydrogen bonds with Ser64Ogamma, Asn152Odelta1, and the backbone oxygen of Ala220. This suggests that this residue is positively charged and has relinquished the hydrogen bond with Tyr150 observed in acyl-enzyme complex structures. Together with previous biochemical and NMR studies, these observations indicate that Tyr150 is protonated throughout the reaction coordinate, disfavoring mechanisms that involve a stable tyrosinate as the general base for deacylation. Rather, the hydroxyl of Tyr150 appears to be well positioned to electrostatically stabilize the negative charge buildup in the tetrahedral high-energy intermediate. This structure, in itself, appears consistent with a mechanism involving either Tyr150 acting as a transient catalytic base in conjunction with a neutral Lys67 or the lactam nitrogen as the general base. Whereas mutagenesis studies suggest that Lys67 may be replaced by an arginine, disfavoring the conjugate base mechanism, distinguishing between these two hypotheses may ultimately depend on direct determination of the pK(a) of Lys67 along the reaction coordinate.
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Affiliation(s)
- Yu Chen
- Department of Pharmaceutical Chemistry, University of California-San Francisco, QB3 Building Room 508D, 1700 4th Street, San Francisco, CA 94143-2550, USA
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44
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Barker JJ. Antibacterial drug discovery and structure-based design. Drug Discov Today 2006; 11:391-404. [PMID: 16635801 DOI: 10.1016/j.drudis.2006.03.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2005] [Revised: 12/06/2005] [Accepted: 03/14/2006] [Indexed: 10/24/2022]
Abstract
Bacterial resistance continues to develop and pose a significant threat, both in hospitals and, more recently, in the community. A focus on other therapeutic areas by the larger pharmaceutical companies has left a shortfall in the pipeline of novel antibacterials. Recently, many new structures have been studied by structure-genomics initiatives, delivering a wealth of targets to consider. Using the tools of structure-based design, antibacterial discovery must exploit these targets to accelerate the process of drug discovery.
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Affiliation(s)
- John J Barker
- Evotec UK, 111 Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK.
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45
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Monajjemi M, Heshmata M, Haeria HH. QM/MM model study on properties and structure of some antibiotics in gas phase: Comparison of energy and NMR chemical shift. BIOCHEMISTRY (MOSCOW) 2006; 71 Suppl 1:S113-22. [PMID: 16487062 DOI: 10.1134/s0006297906130190] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
The combination of Quantum Mechanics (QM) and Molecular Mechanics (MM) methods has become an alternative tool for many applications for which pure QM and MM are not suitable. The QM/MM method has been used for different types of problems, for example: structural biology, surface phenomena, and liquid phase. In this paper, we have used these methods for antibiotics and then we compare results. The calculations were done by the full ab initio method (HF/3-21G) and the (HF/STO-3G) and QM/MM (ONIOM) method with HF (3-21G)/AM1/UFF and HF (STO-3G)/AM1/UFF. We found the geometry that has obtained by the QM/MM method to be very accurate, and we can use this rapid method in place of time consuming ab initio methods for large molecules. Comparison of energy values in the QM/MM and QM methods is given. In the present work, we compare chemical shifts and conclude that the QM/MM method is a perturbed full QM method. The work has been done on penicillin, streptomycin, benzyl penicillin, neomycin, kanamycin, gentamicin, and amoxicillin.
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Affiliation(s)
- M Monajjemi
- Science and Research Branch, Islamic Azad University, Tehran, Iran.
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46
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Banks JL, Beard HS, Cao Y, Cho AE, Damm W, Farid R, Felts AK, Halgren TA, Mainz DT, Maple JR, Murphy R, Philipp DM, Repasky MP, Zhang LY, Berne BJ, Friesner RA, Gallicchio E, Levy RM. Integrated Modeling Program, Applied Chemical Theory (IMPACT). J Comput Chem 2005; 26:1752-80. [PMID: 16211539 PMCID: PMC2742605 DOI: 10.1002/jcc.20292] [Citation(s) in RCA: 1053] [Impact Index Per Article: 55.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We provide an overview of the IMPACT molecular mechanics program with an emphasis on recent developments and a description of its current functionality. With respect to core molecular mechanics technologies we include a status report for the fixed charge and polarizable force fields that can be used with the program and illustrate how the force fields, when used together with new atom typing and parameter assignment modules, have greatly expanded the coverage of organic compounds and medicinally relevant ligands. As we discuss in this review, explicit solvent simulations have been used to guide our design of implicit solvent models based on the generalized Born framework and a novel nonpolar estimator that have recently been incorporated into the program. With IMPACT it is possible to use several different advanced conformational sampling algorithms based on combining features of molecular dynamics and Monte Carlo simulations. The program includes two specialized molecular mechanics modules: Glide, a high-throughput docking program, and QSite, a mixed quantum mechanics/molecular mechanics module. These modules employ the IMPACT infrastructure as a starting point for the construction of the protein model and assignment of molecular mechanics parameters, but have then been developed to meet specialized objectives with respect to sampling and the energy function.
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47
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48
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Reynolds AM, Gherman BF, Cramer CJ, Tolman WB. Characterization of a 1:1 Cu−O2 Adduct Supported by an Anilido Imine Ligand. Inorg Chem 2005; 44:6989-97. [PMID: 16180861 DOI: 10.1021/ic050280p] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Copper(I) complexes of sterically hindered anilido imine ligands o-C6H4{N(C6H3(i)Pr2)}{C(R)=NC6H3(i)Pr2}- (L(1), R = H; L(2), R = CH3) have been prepared and characterized by spectroscopic and X-ray crystallographic methods. These complexes are highly reactive with O2, and in the case of L2 the product of low-temperature oxygenation was fully characterized by spectroscopic, X-ray crystallographic, and computational methods. The resonance Raman spectrum features an isotope-sensitive vibration at 974 cm(-1) (Delta(18O) = 66 cm(-1)), consistent with assignment as an O-O stretch. Despite the asymmetric coordination environment provided by the supporting anilido imine ligand, the X-ray crystal structure confirms rather symmetric side-on binding of the O2 moiety to the copper center, and the O-O bond length of 1.392(2) Angstroms indicates that this intermediate has significant Cu(III)-peroxo character. Theoretical calculations support this interpretation and predict that while a fully optimized end-on singlet geometry can be obtained, it is higher in energy than the side-on isomer by 3.5 kcal mol(-1) at the CASPT2/TZP level.
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Affiliation(s)
- Anne M Reynolds
- Department of Chemistry, University of Minnesota, Minneapolis, 55455, USA
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49
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Chakrabarti R, Klibanov AM, Friesner RA. Sequence optimization and designability of enzyme active sites. Proc Natl Acad Sci U S A 2005; 102:12035-40. [PMID: 16103370 PMCID: PMC1189337 DOI: 10.1073/pnas.0505397102] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2005] [Indexed: 11/18/2022] Open
Abstract
We recently found that many residues in enzyme active sites can be computationally predicted by the optimization of scoring functions based on substrate binding affinity, subject to constraints on the geometry of catalytic residues and protein stability. Here, we explore the generality of this surprising observation. First, the impact of hydrogen-bonding networks necessary for catalysis on the accuracy of sequence optimization is assessed; incorporation of these networks, where relevant, into the set of catalytic constraints is found to be essential. Next, the impact of multiple substrate selectivity on sequence optimization is probed by carrying out independent calculations for complexes of deoxyribonucleoside kinases with various cognate ligands, revealing how simultaneous selection pressures determined active-site sequences of these enzymes. Including previous calculations on simpler enzymes, computational sequence optimization correctly predicts 76% of all active-site residues tested (86% correct, with 93% similar, for naturally conserved residues). In these studies, the ligand is fixed in its native conformation. To assess the applicability of these methods to de novo active-site design, the effect of small ligand motions around the native pose is also examined. Robustness of sequence accuracy for topologically similar poses is demonstrated for selected kinases, but not for a model peptidase. Based on these observations, we introduce the notion of the designability of an enzyme active site, a metric that may be used to guide the search for protein scaffolds suitable for the introduction of de novo activity for a desired chemical reaction.
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Affiliation(s)
- Raj Chakrabarti
- Department of Chemistry and Center for Biomolecular Simulation, Columbia University, New York, NY 10027, USA
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50
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Friesner RA. Ab initio quantum chemistry: methodology and applications. Proc Natl Acad Sci U S A 2005; 102:6648-53. [PMID: 15870212 PMCID: PMC1100737 DOI: 10.1073/pnas.0408036102] [Citation(s) in RCA: 173] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2004] [Indexed: 11/18/2022] Open
Abstract
This Perspective provides an overview of state-of-the-art ab initio quantum chemical methodology and applications. The methods that are discussed include coupled cluster theory, localized second-order Moller-Plesset perturbation theory, multireference perturbation approaches, and density functional theory. The accuracy of each approach for key chemical properties is summarized, and the computational performance is analyzed, emphasizing significant advances in algorithms and implementation over the past decade. Incorporation of a condensed-phase environment by means of mixed quantum mechanical/molecular mechanics or self-consistent reaction field techniques, is presented. A wide range of illustrative applications, focusing on materials science and biology, are discussed briefly.
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Affiliation(s)
- Richard A Friesner
- Department of Chemistry, Columbia University, 3000 Broadway, MC 3110, New York, NY 10025, USA.
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