1
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Zhong R, Xu Z, Zhang S, Zeng M, Li H, Liu S, Lin S. Development of novel bisphenol derivatives with a membrane-targeting mechanism as potent gram-positive antibacterial agents. Eur J Med Chem 2024; 274:116544. [PMID: 38850855 DOI: 10.1016/j.ejmech.2024.116544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/18/2024] [Accepted: 05/28/2024] [Indexed: 06/10/2024]
Abstract
Antibiotic resistance is becoming increasingly severe. The development of small molecular antimicrobial peptides is regarded as a promising design strategy for antibiotics. Here, a series of bisphenol derivatives with amphiphilic structures were designed and synthesized as antibacterial agents by imitating the design strategy of antimicrobial peptides. After a series of structural optimizations, lead compound 43 was identified, which exhibited excellent antibacterial activity against Gram-positive bacterial strains (MICs = 0.78-1.56 μg/mL), poor hemolytic activity (HC50 > 200 μg/mL), and low cytotoxicity (CC50 > 100 μg/mL). Further biological evaluation results indicated that 43 exerted antibacterial effects by directly destroying bacterial cell membranes and displayed rapid bactericidal properties (within 0.5-1 h), leading to a very low probability of drug resistance. Moreover, in a murine model of corneal infection, 43 exhibited a strong in vivo antibacterial efficacy. These findings indicate that 43 is a promising candidate compound for the treatment of bacterial infections.
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Affiliation(s)
- Rongcui Zhong
- Affiliated Qingyuan Hospital, Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, State Key Laboratory of Respiratory Disease, and School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Zikai Xu
- Affiliated Qingyuan Hospital, Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, State Key Laboratory of Respiratory Disease, and School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Shujun Zhang
- Affiliated Qingyuan Hospital, Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, State Key Laboratory of Respiratory Disease, and School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Minghui Zeng
- Affiliated Qingyuan Hospital, Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, State Key Laboratory of Respiratory Disease, and School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Haizhou Li
- Affiliated Qingyuan Hospital, Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, State Key Laboratory of Respiratory Disease, and School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Shouping Liu
- Affiliated Qingyuan Hospital, Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, State Key Laboratory of Respiratory Disease, and School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 511436, China.
| | - Shuimu Lin
- Affiliated Qingyuan Hospital, Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, State Key Laboratory of Respiratory Disease, and School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 511436, China.
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2
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Yehorova D, Crean RM, Kasson PM, Kamerlin SCL. Key interaction networks: Identifying evolutionarily conserved non-covalent interaction networks across protein families. Protein Sci 2024; 33:e4911. [PMID: 38358258 PMCID: PMC10868456 DOI: 10.1002/pro.4911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/08/2024] [Accepted: 01/10/2024] [Indexed: 02/16/2024]
Abstract
Protein structure (and thus function) is dictated by non-covalent interaction networks. These can be highly evolutionarily conserved across protein families, the members of which can diverge in sequence and evolutionary history. Here we present KIN, a tool to identify and analyze conserved non-covalent interaction networks across evolutionarily related groups of proteins. KIN is available for download under a GNU General Public License, version 2, from https://www.github.com/kamerlinlab/KIN. KIN can operate on experimentally determined structures, predicted structures, or molecular dynamics trajectories, providing insight into both conserved and missing interactions across evolutionarily related proteins. This provides useful insight both into protein evolution, as well as a tool that can be exploited for protein engineering efforts. As a showcase system, we demonstrate applications of this tool to understanding the evolutionary-relevant conserved interaction networks across the class A β-lactamases.
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Affiliation(s)
- Dariia Yehorova
- School of Chemistry and Biochemistry, Georgia Institute of TechnologyAtlantaGeorgiaUSA
| | - Rory M. Crean
- Department of Chemistry—BMCUppsala UniversityUppsalaSweden
| | - Peter M. Kasson
- Department of Molecular PhysiologyUniversity of VirginiaCharlottesvilleVirginiaUSA
- Department Biomedical EngineeringUniversity of VirginiaCharlottesvilleVirginiaUSA
- Department of Cell and Molecular BiologyUppsala UniversityUppsalaSweden
| | - Shina C. L. Kamerlin
- School of Chemistry and Biochemistry, Georgia Institute of TechnologyAtlantaGeorgiaUSA
- Department of Chemistry—BMCUppsala UniversityUppsalaSweden
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3
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Bellini R, Guedes IA, Ciapina LP, de Vasconcelos ATR, Dardenne LE, Nicolás MF. Analysis of a novel class A β-lactamase OKP-B-6 of Klebsiella quasipneumoniae: structural characterisation and interaction with commercially available drugs. Mem Inst Oswaldo Cruz 2022; 117:e220102. [PMID: 36169569 PMCID: PMC9506704 DOI: 10.1590/0074-02760220102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 08/22/2022] [Indexed: 08/30/2023] Open
Abstract
BACKGROUND Gram-negative and Gram-positive bacteria produce beta-lactamase as factors to overcome beta-lactam antibiotics, causing their hydrolysis and impaired antimicrobial action. Class A beta-lactamase contains the chromosomal sulfhydryl reagent variable (SHV, point mutation variants of SHV-1), LEN (Klebsiella pneumoniae strain LEN-1), and other K. pneumoniae beta-lactamase (OKP) found mostly in Klebsiella’s phylogroups. The SHV known as extended-spectrum β-lactamase can inactivate most beta-lactam antibiotics. Class A also includes the worrisome plasmid-encoded Klebsiella pneumoniae carbapenemase (KPC-2), a carbapenemase that can inactivate most beta-lactam antibiotics, carbapenems, and some beta-lactamase inhibitors. OBJECTIVES So far, there is no 3D crystal structure for OKP-B, so our goal was to perform structural characterisation and molecular docking studies of this new enzyme. METHODS We applied a homology modelling method to build the OKP-B-6 structure, which was compared with SHV-1 and KPC-2 according to their electrostatic potentials at the active site. Using the DockThor-VS, we performed molecular docking of the SHV-1 inhibitors commercially available as sulbactam, tazobactam, and avibactam against the constructed model of OKP-B-6. FINDINGS From the point of view of enzyme inhibition, our results indicate that OKP-B-6 should be an extended-spectrum beta-lactamase (ESBL) susceptible to the same drugs as SHV-1. MAIN CONCLUSIONS This conclusion advantageously impacts the clinical control of the bacterial pathogens encoding OKP-B in their genome by using any effective, broad-spectrum, and multitarget inhibitor against SHV-containing bacteria.
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Affiliation(s)
- Reinaldo Bellini
- Laboratório Nacional de Computação Científica, Petrópolis, RJ, Brasil
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4
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Malla TR, Brewitz L, Muntean DG, Aslam H, Owen CD, Salah E, Tumber A, Lukacik P, Strain-Damerell C, Mikolajek H, Walsh MA, Schofield CJ. Penicillin Derivatives Inhibit the SARS-CoV-2 Main Protease by Reaction with Its Nucleophilic Cysteine. J Med Chem 2022; 65:7682-7696. [PMID: 35549342 PMCID: PMC9115881 DOI: 10.1021/acs.jmedchem.1c02214] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Indexed: 12/05/2022]
Abstract
The SARS-CoV-2 main protease (Mpro) is a medicinal chemistry target for COVID-19 treatment. Given the clinical efficacy of β-lactams as inhibitors of bacterial nucleophilic enzymes, they are of interest as inhibitors of viral nucleophilic serine and cysteine proteases. We describe the synthesis of penicillin derivatives which are potent Mpro inhibitors and investigate their mechanism of inhibition using mass spectrometric and crystallographic analyses. The results suggest that β-lactams have considerable potential as Mpro inhibitors via a mechanism involving reaction with the nucleophilic cysteine to form a stable acyl-enzyme complex as shown by crystallographic analysis. The results highlight the potential for inhibition of viral proteases employing nucleophilic catalysis by β-lactams and related acylating agents.
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Affiliation(s)
- Tika R. Malla
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Lennart Brewitz
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Dorian-Gabriel Muntean
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Hiba Aslam
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - C. David Owen
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom
- Research
Complex at Harwell, Harwell
Science and Innovation Campus, OX11
0FA Didcot, United Kingdom
| | - Eidarus Salah
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Anthony Tumber
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Petra Lukacik
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom
- Research
Complex at Harwell, Harwell
Science and Innovation Campus, OX11
0FA Didcot, United Kingdom
| | - Claire Strain-Damerell
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom
- Research
Complex at Harwell, Harwell
Science and Innovation Campus, OX11
0FA Didcot, United Kingdom
| | - Halina Mikolajek
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom
- Research
Complex at Harwell, Harwell
Science and Innovation Campus, OX11
0FA Didcot, United Kingdom
| | - Martin A. Walsh
- Diamond
Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom
- Research
Complex at Harwell, Harwell
Science and Innovation Campus, OX11
0FA Didcot, United Kingdom
| | - Christopher J. Schofield
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
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5
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Grigorenko VG, Petrova TE, Carolan C, Rubtsova MY, Uporov IV, Pereira J, Chojnowski G, Samygina VR, Lamzin VS, Egorov AM. Crystal structures of the molecular class A β-lactamase TEM-171 and its complexes with tazobactam. Acta Crystallogr D Struct Biol 2022; 78:825-834. [DOI: 10.1107/s2059798322004879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 05/06/2022] [Indexed: 11/10/2022] Open
Abstract
The resistance of bacteria to β-lactam antibiotics is primarily caused by the production of β-lactamases. Here, novel crystal structures of the native β-lactamase TEM-171 and two complexes with the widely used inhibitor tazobactam are presented, alongside complementary data from UV spectroscopy and fluorescence quenching. The six chemically identical β-lactamase molecules in the crystallographic asymmetric unit displayed different degrees of disorder. The tazobactam intermediate was covalently bound to the catalytic Ser70 in the trans-enamine configuration. While the conformation of tazobactam in the first complex resembled that in published β-lactamase–tazobactam structures, in the second complex, which was obtained after longer soaking of the native crystals in the inhibitor solution, a new and previously unreported tazobactam conformation was observed. It is proposed that the two complexes correspond to different stages along the deacylation path of the acyl-enzyme intermediate. The results provide a novel structural basis for the rational design of new β-lactamase inhibitors.
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6
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Lang PA, Raj R, Tumber A, Lohans CT, Rabe P, Robinson CV, Brem J, Schofield CJ. Studies on enmetazobactam clarify mechanisms of widely used β-lactamase inhibitors. Proc Natl Acad Sci U S A 2022; 119:e2117310119. [PMID: 35486701 PMCID: PMC9170034 DOI: 10.1073/pnas.2117310119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 03/14/2022] [Indexed: 11/18/2022] Open
Abstract
β-Lactams are the most important class of antibacterials, but their use is increasingly compromised by resistance, most importantly via serine β-lactamase (SBL)-catalyzed hydrolysis. The scope of β-lactam antibacterial activity can be substantially extended by coadministration with a penicillin-derived SBL inhibitor (SBLi), i.e., the penam sulfones tazobactam and sulbactam, which are mechanism-based inhibitors working by acylation of the nucleophilic serine. The new SBLi enmetazobactam, an N-methylated tazobactam derivative, has recently completed clinical trials. Biophysical studies on the mechanism of SBL inhibition by enmetazobactam reveal that it inhibits representatives of all SBL classes without undergoing substantial scaffold fragmentation, a finding that contrasts with previous reports on SBL inhibition by tazobactam and sulbactam. We therefore reinvestigated the mechanisms of tazobactam and sulbactam using mass spectrometry under denaturing and nondenaturing conditions, X-ray crystallography, and NMR spectroscopy. The results imply that the reported extensive fragmentation of penam sulfone–derived acyl–enzyme complexes does not substantially contribute to SBL inhibition. In addition to observation of previously identified inhibitor-induced SBL modifications, the results reveal that prolonged reaction of penam sulfones with SBLs can induce dehydration of the nucleophilic serine to give a dehydroalanine residue that undergoes reaction to give a previously unobserved lysinoalanine cross-link. The results clarify the mechanisms of action of widely clinically used SBLi, reveal limitations on the interpretation of mass spectrometry studies concerning mechanisms of SBLi, and will inform the development of new SBLi working by reaction to form hydrolytically stable acyl–enzyme complexes.
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Affiliation(s)
- Pauline A. Lang
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
- Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Ritu Raj
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Anthony Tumber
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
- Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Christopher T. Lohans
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
- Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Patrick Rabe
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
- Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Carol V. Robinson
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Jürgen Brem
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
- Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Christopher J. Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
- Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford OX1 3TA, United Kingdom
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7
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Tassoni R, Blok A, Pannu NS, Ubbink M. New Conformations of Acylation Adducts of Inhibitors of β-Lactamase from Mycobacterium tuberculosis. Biochemistry 2019; 58:997-1009. [PMID: 30632739 PMCID: PMC6383187 DOI: 10.1021/acs.biochem.8b01085] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Mycobacterium tuberculosis (Mtb), the main causative
agent of tuberculosis (TB), is naturally resistant to β-lactam
antibiotics due to the production of the extended spectrum β-lactamase
BlaC. β-Lactam/β-lactamase inhibitor combination therapies
can circumvent the BlaC-mediated resistance of Mtb and are promising
treatment options against TB. However, still little is known of the
exact mechanism of BlaC inhibition by the β-lactamase inhibitors
currently approved for clinical use, clavulanic acid, sulbactam, tazobactam,
and avibactam. Here, we present the X-ray diffraction crystal structures
of the acyl-enzyme adducts of wild-type BlaC with the four inhibitors.
The +70 Da adduct derived from clavulanate and the trans-enamine acylation adducts of sulbactam and tazobactam are reported.
BlaC in complex with avibactam revealed two inhibitor conformations.
Preacylation binding could not be observed because inhibitor binding
was not detected in BlaC variants carrying a substitution of the active
site serine 70 to either alanine or cysteine, by crystallography,
ITC or NMR. These results suggest that the catalytic serine 70 is
necessary not only for enzyme acylation but also for increasing BlaC
affinity for inhibitors in the preacylation state. The structure of
BlaC with the serine to cysteine mutation showed a covalent linkage
of the cysteine 70 Sγ atom to the nearby amino group of lysine
73. The differences of adduct conformations between BlaC and other
β-lactamases are discussed.
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Affiliation(s)
- Raffaella Tassoni
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , Leiden 2333CC , The Netherlands
| | - Anneloes Blok
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , Leiden 2333CC , The Netherlands
| | - Navraj S Pannu
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , Leiden 2333CC , The Netherlands
| | - Marcellus Ubbink
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , Leiden 2333CC , The Netherlands
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8
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Krauß J, Bracher F. Pharmacokinetic Enhancers (Boosters)-Escort for Drugs against Degrading Enzymes and Beyond. Sci Pharm 2018; 86:scipharm86040043. [PMID: 30262788 DOI: 10.3390/scipharm86040043] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 09/19/2018] [Accepted: 09/20/2018] [Indexed: 02/04/2023] Open
Abstract
Pharmacokinetic enhancers (boosters) are compounds used in combination with a primary therapeutic agent (drug) and are not used for their direct effects on the disease but because they enhance or restore the activity of the primary agent. Hence, in certain cases, they represent an indispensable escort for enzyme-labile drugs. Pharmacokinetic enhancers can exert their activity on different ways. In the most common case, they inhibit enzymes such as human cytochrome P450 enzymes in the liver or other organs and, thereby, block or reduce undesired metabolism and inactivation of the primary drug. In this review, an overview will be given on the therapeutically most important classes of pharmacokinetic enhancers like β-lactamase inhibitors, inhibitors of CYP (cytochrome P450) enzymes in HIV therapy and hepatitis C, boosters for fluoropyrimidine-type anticancer agents, compounds utilized for enabling therapy of Parkinson's disease with levodopa, and others. Inhibitors of efflux pumps in both pathogenic bacteria and tumor cells will be addresses shortly.
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Affiliation(s)
- Jürgen Krauß
- Department of Pharmacy-Center for Drug Research, Ludwig-Maximilians University, Butenandtstr. 5-13, 81377 Munich, Germany.
| | - Franz Bracher
- Department of Pharmacy-Center for Drug Research, Ludwig-Maximilians University, Butenandtstr. 5-13, 81377 Munich, Germany.
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9
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Pereira R, Rabelo VWH, Sibajev A, Abreu PA, Castro HC. Class A β-lactamases and inhibitors: In silico analysis of the binding mode and the relationship with resistance. J Biotechnol 2018; 279:37-46. [PMID: 29753682 DOI: 10.1016/j.jbiotec.2018.05.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 04/22/2018] [Accepted: 05/03/2018] [Indexed: 02/01/2023]
Abstract
β-lactams are one of the most common antimicrobials used to treat bacterial infections. However, bacterial resistance has compromised their efficacy, mainly due to the β-lactamase enzyme production. To overcome this resistance, β-lactamase inhibitors can be used in association with these antimicrobials. Herein, we analyzed the structural characteristics of β-lactamases and their interactions with classical inhibitors, such as clavulanic acid (CA), sulbactam (SB) and tazobactam (TZ) to gain insights into resistance. The homology models of five class A β-lactamases, namely CARB-3, IMI-1, SFO-1, SHV-5 and TEM-10, were constructed and validated and revealed an overall 3D structural conservation, but with significant differences in the electrostatic potential maps, especially at important regions in the catalytic site. Molecular dockings of CA, SB and TZ with these enzymes revealed a covalent bond with the S70 in all complexes, except Carb-3 which is in agreement with experimental data reported so far. This is likely related to the less voluminous active site of Carb-3 model. Although few specific contacts were observed in the β-lactamase-inhibitor complexes, all compounds interacted with the residues in positions 73, 130, 132, 236 and 237. Therefore, this study provides new perspectives for the design of innovative compounds with broad-spectrum inhibitory profiles against β-lactamases.
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Affiliation(s)
- Rebeca Pereira
- Programa de Pós-graduação em Ciências e Biotecnologia - Instituto de Biologia, Universidade Federal Fluminense, Campus do Valonguinho, Niterói, RJ, CEP 24210-130, Brazil
| | - Vitor Won-Held Rabelo
- Programa de Pós-graduação em Ciências e Biotecnologia - Instituto de Biologia, Universidade Federal Fluminense, Campus do Valonguinho, Niterói, RJ, CEP 24210-130, Brazil; Laboratório de Modelagem Molecular e Pesquisa em Ciências Farmacêuticas, Universidade Federal do Rio de Janeiro, Campus Macaé, RJ, CEP 27965-045, Brazil
| | - Alexander Sibajev
- Centro de Ciências da Saúde - Curso de Medicina, Universidade Federal de Roraima, Campus do Paricarana, Boa Vista, RR, CEP 69304-000, Brazil
| | - Paula Alvarez Abreu
- Laboratório de Modelagem Molecular e Pesquisa em Ciências Farmacêuticas, Universidade Federal do Rio de Janeiro, Campus Macaé, RJ, CEP 27965-045, Brazil.
| | - Helena Carla Castro
- Programa de Pós-graduação em Ciências e Biotecnologia - Instituto de Biologia, Universidade Federal Fluminense, Campus do Valonguinho, Niterói, RJ, CEP 24210-130, Brazil.
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10
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Fritz RA, Alzate-Morales JH, Spencer J, Mulholland AJ, van der Kamp MW. Multiscale Simulations of Clavulanate Inhibition Identify the Reactive Complex in Class A β-Lactamases and Predict the Efficiency of Inhibition. Biochemistry 2018; 57:3560-3563. [PMID: 29812917 DOI: 10.1021/acs.biochem.8b00480] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Clavulanate is used as an effective drug in combination with β-lactam antibiotics to treat infections of some antibiotic resistant bacteria. Here, we perform combined quantum mechanics/molecular mechanics simulations of several covalent complexes of clavulanate with class A β-lactamases KPC-2 and TEM-1. Simulations of the deacylation reactions identify the decarboxylated trans-enamine complex as being responsible for inhibition. Further, the obtained free energy barriers discriminate clinically relevant inhibition (TEM-1) from less effective inhibition (KPC-2).
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Affiliation(s)
- Rubén A Fritz
- Center for Bioinformatics and Molecular Simulations, Faculty of Engineering , University of Talca , Talca , Chile
| | - Jans H Alzate-Morales
- Center for Bioinformatics and Molecular Simulations, Faculty of Engineering , University of Talca , Talca , Chile
| | - James Spencer
- School of Cellular and Molecular Medicine , 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
| | - Marc W van der Kamp
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , U.K
- School of Biochemistry , University of Bristol , University Walk , Bristol BS8 1TD , U.K
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11
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van den Akker F, Bonomo RA. Exploring Additional Dimensions of Complexity in Inhibitor Design for Serine β-Lactamases: Mechanistic and Intra- and Inter-molecular Chemistry Approaches. Front Microbiol 2018; 9:622. [PMID: 29675000 PMCID: PMC5895744 DOI: 10.3389/fmicb.2018.00622] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 03/19/2018] [Indexed: 01/14/2023] Open
Abstract
As a bacterial resistance strategy, serine β-lactamases have evolved from cell wall synthesizing enzymes known as penicillin-binding proteins (PBP), by not only covalently binding β-lactam antibiotics but, also acquiring mechanisms of deacylating these antibiotics. This critical deacylation step leads to release of hydrolyzed and inactivated β-lactams, thereby providing resistance for the bacteria against these antibiotics targeting the cell wall. To combat β-lactamase-mediated antibiotic resistance, numerous β-lactamase inhibitors were developed that utilize various strategies to inactivate the β-lactamase. Most of these compounds are “mechanism-based” inhibitors that in some manner mimic the β-lactam substrate, having a carbonyl moiety and a negatively charged carboxyl or sulfate group. These compounds form a covalent adduct with the catalytic serine via an initial acylation step. To increase the life-time of the inhibitory covalent adduct intermediates, a remarkable array of different strategies was employed to improve inhibition potency. Such approaches include post-acylation intra- and intermolecular chemical rearrangements as well as affecting the deacylation water. These approaches transform the inhibitor design process from a 3-dimensional problem (i.e., XYZ coordinates) to one with additional dimensions of complexity as the reaction coordinate and time spent at each chemical state need to be taken into consideration. This review highlights the mechanistic intricacies of the design efforts of the β-lactamase inhibitors which so far have resulted in the development of “two generations” and 5 clinically available inhibitors.
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Affiliation(s)
- Focco van den Akker
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, United States
| | - Robert A Bonomo
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, United States.,Medicine, Pharmacology, Molecular Biology and Microbiology, Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH, United States.,Medical Service and Geriatric Research, Education, and Clinical Centers (GRECC), Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, United States.,Case Western Reserve University-VA Medical Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH, United States
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12
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Lewandowski EM, Lethbridge KG, Sanishvili R, Skiba J, Kowalski K, Chen Y. Mechanisms of proton relay and product release by Class A β-lactamase at ultrahigh resolution. FEBS J 2017; 285:87-100. [PMID: 29095570 DOI: 10.1111/febs.14315] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 09/15/2017] [Accepted: 10/28/2017] [Indexed: 01/25/2023]
Abstract
The β-lactam antibiotics inhibit penicillin-binding proteins (PBPs) by forming a stable, covalent, acyl-enzyme complex. During the evolution from PBPs to Class A β-lactamases, the β-lactamases acquired Glu166 to activate a catalytic water and cleave the acyl-enzyme bond. Here we present three product complex crystal structures of CTX-M-14 Class A β-lactamase with a ruthenocene-conjugated penicillin-a 0.85 Å resolution structure of E166A mutant complexed with the penilloate product, a 1.30 Å resolution complex structure of the same mutant with the penicilloate product, and a 1.18 Å resolution complex structure of S70G mutant with a penicilloate product epimer-shedding light on the catalytic mechanisms and product inhibition of PBPs and Class A β-lactamases. The E166A-penilloate complex captured the hydrogen bonding network following the protonation of the leaving group and, for the first time, unambiguously show that the ring nitrogen donates a proton to Ser130, which in turn donates a proton to Lys73. These observations indicate that in the absence of Glu166, the equivalent lysine would be neutral in PBPs and therefore capable of serving as the general base to activate the catalytic serine. Together with previous results, this structure suggests a common proton relay network shared by Class A β-lactamases and PBPs, from the catalytic serine to the lysine, and ultimately to the ring nitrogen. Additionally, the E166A-penicilloate complex reveals previously unseen conformational changes of key catalytic residues during the release of the product, and is the first structure to capture the hydrolyzed product in the presence of an unmutated catalytic serine. DATABASE Structural data are available in the PDB database under the accession numbers 5TOP, 5TOY, and 5VLE.
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Affiliation(s)
- Eric M Lewandowski
- Department of Molecular Medicine, University of South Florida College of Medicine, Tampa, FL, USA
| | - Kathryn G Lethbridge
- Department of Molecular Medicine, University of South Florida College of Medicine, Tampa, FL, USA
| | - Ruslan Sanishvili
- GMCA@APS, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, IL, USA
| | - Joanna Skiba
- Department of Organic Chemistry, Faculty of Chemistry, University of Lodz, Poland
| | - Konrad Kowalski
- Department of Organic Chemistry, Faculty of Chemistry, University of Lodz, Poland
| | - Yu Chen
- Department of Molecular Medicine, University of South Florida College of Medicine, Tampa, FL, USA
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13
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Wang DY, Abboud MI, Markoulides MS, Brem J, Schofield CJ. The road to avibactam: the first clinically useful non-β-lactam working somewhat like a β-lactam. Future Med Chem 2016; 8:1063-84. [PMID: 27327972 DOI: 10.4155/fmc-2016-0078] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023] Open
Abstract
Avibactam, which is the first non-β-lactam β-lactamase inhibitor to be introduced for clinical use, is a broad-spectrum serine β-lactamase inhibitor with activity against class A, class C, and, some, class D β-lactamases. We provide an overview of efforts, which extend to the period soon after the discovery of the penicillins, to develop clinically useful non-β-lactam compounds as antibacterials, and, subsequently, penicillin-binding protein and β-lactamase inhibitors. Like the β-lactam inhibitors, avibactam works via a mechanism involving covalent modification of a catalytically important nucleophilic serine residue. However, unlike the β-lactam inhibitors, avibactam reacts reversibly with its β-lactamase targets. We discuss chemical factors that may account for the apparently special nature of β-lactams and related compounds as antibacterials and β-lactamase inhibitors, including with respect to resistance. Avenues for future research including non-β-lactam antibacterials acting similarly to β-lactams are discussed.
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Affiliation(s)
| | | | | | - Jürgen Brem
- Department of Chemistry, University of Oxford, UK
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14
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Crystal Structures of KPC-2 and SHV-1 β-Lactamases in Complex with the Boronic Acid Transition State Analog S02030. Antimicrob Agents Chemother 2016; 60:1760-6. [PMID: 26729491 DOI: 10.1128/aac.02643-15] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Accepted: 12/27/2015] [Indexed: 01/29/2023] Open
Abstract
Resistance to expanded-spectrum cephalosporins and carbapenems has rendered certain strains of Klebsiella pneumoniae the most problematic pathogens infecting patients in the hospital and community. This broad-spectrum resistance to β-lactamases emerges in part via the expression of KPC-2 and SHV-1 β-lactamases and variants thereof. KPC-2 carbapenemase is particularly worrisome, as the genetic determinant encoding this β-lactamase is rapidly spread via plasmids. Moreover, KPC-2, a class A enzyme, is difficult to inhibit with mechanism-based inactivators (e.g., clavulanate). In order to develop new β-lactamase inhibitors (BLIs) to add to the limited available armamentarium that can inhibit KPC-2, we have structurally probed the boronic acid transition state analog S02030 for its inhibition of KPC-2 and SHV-1. S02030 contains a boronic acid, a thiophene, and a carboxyl triazole moiety. We present here the 1.54- and 1.87-Å resolution crystal structures of S02030 bound to SHV-1 and KPC-2 β-lactamases, respectively, as well as a comparative analysis of the S02030 binding modes, including a previously determined S02030 class C ADC-7 β-lactamase complex. S02030 is able to inhibit vastly different serine β-lactamases by interacting with the conserved features of these active sites, which includes (i) forming the bond with catalytic serine via the boron atom, (ii) positioning one of the boronic acid oxygens in the oxyanion hole, and (iii) utilizing its amide moiety to make conserved interactions across the width of the active site. In addition, S02030 is able to overcome more distantly located structural differences between the β-lactamases. This unique feature is achieved by repositioning the more polar carboxyl-triazole moiety, generated by click chemistry, to create polar interactions as well as reorient the more hydrophobic thiophene moiety. The former is aided by the unusual polar nature of the triazole ring, allowing it to potentially form a unique C-H…O 2.9-Å hydrogen bond with S130 in KPC-2.
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15
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Heidari-Torkabadi H, Bethel CR, Ding Z, Pusztai-Carey M, Bonnet R, Bonomo RA, Carey PR. “Mind the Gap”: Raman Evidence for Rapid Inactivation of CTX-M-9 β-Lactamase Using Mechanism-Based Inhibitors that Bridge the Active Site. J Am Chem Soc 2015; 137:12760-3. [DOI: 10.1021/jacs.5b10007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Christopher R. Bethel
- Research
Service, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States
| | | | | | - Richard Bonnet
- Clermont Université, UMR 1071 INSERM/Université d’Auvergne, Clermont-Ferrand, France
| | - Robert A. Bonomo
- Research
Service, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States
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16
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Krishnan NP, Nguyen NQ, Papp-Wallace KM, Bonomo RA, van den Akker F. Inhibition of Klebsiella β-Lactamases (SHV-1 and KPC-2) by Avibactam: A Structural Study. PLoS One 2015; 10:e0136813. [PMID: 26340563 PMCID: PMC4560403 DOI: 10.1371/journal.pone.0136813] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 08/07/2015] [Indexed: 11/18/2022] Open
Abstract
β-Lactamase inhibition is an important clinical strategy in overcoming β-lactamase-mediated resistance to β-lactam antibiotics in Gram negative bacteria. A new β-lactamase inhibitor, avibactam, is entering the clinical arena and promising to be a major step forward in our antibiotic armamentarium. Avibactam has remarkable broad-spectrum activity in being able to inhibit classes A, C, and some class D β-lactamases. We present here structural investigations into class A β-lactamase inhibition by avibactam as we report the crystal structures of SHV-1, the chromosomal penicillinase of Klebsiella pneumoniae, and KPC-2, an acquired carbapenemase found in the same pathogen, complexed with avibactam. The 1.80 Å KPC-2 and 1.42 Å resolution SHV-1 β-lactamase avibactam complex structures reveal avibactam covalently bonded to the catalytic S70 residue. Analysis of the interactions and chair-shaped conformation of avibactam bound to the active sites of KPC-2 and SHV-1 provides structural insights into recently laboratory-generated amino acid substitutions that result in resistance to avibactam in KPC-2 and SHV-1. Furthermore, we observed several important differences in the interactions with amino acid residues, in particular that avibactam forms hydrogen bonds to S130 in KPC-2 but not in SHV-1, that can possibly explain some of the different kinetic constants of inhibition. Our observations provide a possible reason for the ability of KPC-2 β-lactamase to slowly desulfate avibactam with a potential role for the stereochemistry around the N1 atom of avibactam and/or the presence of an active site water molecule that could aid in avibactam desulfation, an unexpected consequence of novel inhibition chemistry.
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Affiliation(s)
- Nikhil P. Krishnan
- Department of Biochemistry, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH, 44106, United States of America
| | - Nhu Q. Nguyen
- Department of Biochemistry, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH, 44106, United States of America
| | - Krisztina M. Papp-Wallace
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, 10701 East Boulevard, Cleveland, OH, 44106, United States of America
| | - Robert A. Bonomo
- Department of Biochemistry, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH, 44106, United States of America
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, 10701 East Boulevard, Cleveland, OH, 44106, United States of America
- Department of Medicine, Case Western Reserve University, Cleveland, OH, United States of America
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, United States of America
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, United States of America
| | - Focco van den Akker
- Department of Biochemistry, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH, 44106, United States of America
- * E-mail:
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17
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Antonopoulos IH, Warner BA, Carey PR. Concerted Protein and Nucleic Acid Conformational Changes Observed Prior to Nucleotide Incorporation in a Bacterial RNA Polymerase: Raman Crystallographic Evidence. Biochemistry 2015. [PMID: 26222797 DOI: 10.1021/acs.biochem.5b00484] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Transcription elongation requires the continuous incorporation of ribonucleotide triphosphates into a growing transcript. RNA polymerases (RNAPs) are able to processively synthesize a growing RNA chain via translocation of the RNAP enzyme along its nucleic acid template strand after each nucleotide addition cycle. In this work, a time-resolved Raman spectroscopic analysis of nucleotide addition in single crystals of the Thermus thermophilus elongation complex (TthEC) is reported. When [(13)C,(15)N]GTP (*GTP) is soaked into crystals of the TthEC, large reversible changes in the Raman spectrum that are assigned to protein and nucleic acid conformational events during a single-nucleotide incorporation are observed. The *GTP population in the TthEC crystal reaches a stable population at 37 min, while substantial and reversible protein conformational changes (mainly ascribed to changes in α-helical Raman features) maximize at approximately 50 min. At the same time, changes in nucleic acid bases and phosphodiester backbone Raman marker bands occur. Catalysis begins at approximately 65-70 min, soon after the maximal protein and DNA changes, and is monitored via the decline in a triphosphate vibrational Raman mode from *GTP. The Raman data indicate that approximately 40% of the total triphosphate population, present as *GTP, reacts in the crystal. This may suggest that a second population of noncovalently bound *GTP resides in a site distinct from the catalytic site. The data reported here are an extension of our recent work on the elongation complex (EC) of a bacterial RNAP, Thermus thermophilus (Tth), where Raman spectroscopy and polyacrylamide gel electrophoresis were employed to monitor incorporation and misincorporation in single TthEC crystals [Antonopoulos, I. H., et al. (2015) Biochemistry 54, 652-665]. Therefore, the initial study establishes the groundwork for this study. In contrast to our previous study, in which incorporation takes place very rapidly inside the crystals, the data on this single crystal exhibit a slower time regime, which allows the dissection of the structural dynamics associated with GMP incorporation within the TthEC crystal.
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Affiliation(s)
- Ioanna H Antonopoulos
- Department of Biochemistry, Case Western Reserve University School of Medicine , Cleveland, Ohio 44106, United States
| | - Brittany A Warner
- Department of Biochemistry and Molecular Biology, The Center of RNA Molecular Biology, Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Paul R Carey
- Department of Biochemistry, Case Western Reserve University School of Medicine , Cleveland, Ohio 44106, United States
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18
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Carey PR, Heidari-Torkabadi H. New techniques in antibiotic discovery and resistance: Raman spectroscopy. Ann N Y Acad Sci 2015; 1354:67-81. [PMID: 26275225 DOI: 10.1111/nyas.12847] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 06/15/2015] [Accepted: 06/18/2015] [Indexed: 11/29/2022]
Abstract
Raman spectroscopy can play a role in both antibiotic discovery and understanding the molecular basis of resistance. A major challenge in drug development is to measure the population of the drug molecules inside a cell line and to follow the chemistry of their reactions with intracellular targets. Recently, a protocol based on Raman microscopy has been developed that achieves these goals. Drug candidates are soaked into live bacterial cells and subsequently the cells are frozen and freeze-dried. The samples yield exemplary (nonresonance) Raman data that provide a measure of the number of drug molecules within each cell, as well as details of drug-target interactions. Results are discussed for two classes of compounds inhibiting either β-lactamase or dihydrofolate reductase enzymes in a number of Gram-positive or Gram-negative cell lines. The advantages of the present protocol are that it does not use labels and it can measure the kinetics of cell-compound uptake on the time scale of minutes. Spectroscopic interpretation is supported by in vitro Raman experiments. Studying drug-target interactions in aqueous solution and in single crystals can provide molecular level insights into drug-target interactions, which, in turn, provide the underpinnings of our understanding of data from bacterial cells. Thus, the applicability of X-ray crystallographic-derived data to in-cell chemistry can be tested.
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Affiliation(s)
- Paul R Carey
- Department of Biochemistry.,Department of Chemistry, Case Western Reserve University, Cleveland, Ohio
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19
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Che T, Rodkey E, Bethel CR, Shanmugam S, Ding Z, Pusztai-Carey M, Nottingham M, Chai W, Buynak JD, Bonomo RA, van den Akker F, Carey PR. Detecting a quasi-stable imine species on the reaction pathway of SHV-1 β-lactamase and 6β-(hydroxymethyl)penicillanic acid sulfone. Biochemistry 2015; 54:734-43. [PMID: 25536850 PMCID: PMC4310624 DOI: 10.1021/bi501197t] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 12/22/2014] [Indexed: 11/30/2022]
Abstract
For the class A β-lactamase SHV-1, the kinetic and mechanistic properties of the clinically used inhibitor sulbactam are compared with the sulbactam analog substituted in its 6β position by a CH2OH group (6β-(hydroxymethyl)penicillanic acid). The 6β substitution improves both in vitro and microbiological inhibitory properties of sulbactam. Base hydrolysis of both compounds was studied by Raman and NMR spectroscopies and showed that lactam ring opening is followed by fragmentation of the dioxothiazolidine ring leading to formation of the iminium ion within 3 min. The iminium ion slowly loses a proton and converts to cis-enamine (which is a β-aminoacrylate) in 1 h for sulbactam and in 4 h for 6β-(hydroxymethyl) sulbactam. Rapid mix-rapid freeze Raman spectroscopy was used to follow the reactions between the two sulfones and SHV-1. Within 23 ms, a 10-fold excess of sulbactam was entirely hydrolyzed to give a cis-enamine product. In contrast, the 6β-(hydroxymethyl) sulbactam formed longer-lived acyl-enzyme intermediates that are a mixture of imine and enamines. Single crystal Raman studies, soaking in and washing out unreacted substrates, revealed stable populations of imine and trans-enamine acyl enzymes. The corresponding X-ray crystallographic data are consonant with the Raman data and also reveal the role played by the 6β-hydroxymethyl group in retarding hydrolysis of the acyl enzymes. The 6β-hydroxymethyl group sterically hinders approach of the water molecule as well as restraining the side chain of E166 that facilitates hydrolysis.
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Affiliation(s)
- Tao Che
- Department of Biochemistry, Department of Molecular
Biology and Microbiology, Department of Pharmacology, and Department of
Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Elizabeth
A. Rodkey
- Department of Biochemistry, Department of Molecular
Biology and Microbiology, Department of Pharmacology, and Department of
Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Christopher R. Bethel
- Research
Service, Louis Stokes Cleveland Veterans
Affairs Medical Center, Cleveland, Ohio 44106, United States
| | - Sivaprakash Shanmugam
- Department of Biochemistry, Department of Molecular
Biology and Microbiology, Department of Pharmacology, and Department of
Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Zhe Ding
- Department of Biochemistry, Department of Molecular
Biology and Microbiology, Department of Pharmacology, and Department of
Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Marianne Pusztai-Carey
- Department of Biochemistry, Department of Molecular
Biology and Microbiology, Department of Pharmacology, and Department of
Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Michael Nottingham
- Department
of Chemistry, Southern Methodist University, Dallas, Texas 75275, United States
| | - Weirui Chai
- Department
of Chemistry, Southern Methodist University, Dallas, Texas 75275, United States
| | - John D. Buynak
- Department
of Chemistry, Southern Methodist University, Dallas, Texas 75275, United States
| | - Robert A. Bonomo
- Department of Biochemistry, Department of Molecular
Biology and Microbiology, Department of Pharmacology, and Department of
Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
- Research
Service, Louis Stokes Cleveland Veterans
Affairs Medical Center, Cleveland, Ohio 44106, United States
| | - Focco van den Akker
- Department of Biochemistry, Department of Molecular
Biology and Microbiology, Department of Pharmacology, and Department of
Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Paul R. Carey
- Department of Biochemistry, Department of Molecular
Biology and Microbiology, Department of Pharmacology, and Department of
Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
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20
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Kumar KM, Lavanya P, Anbarasu A, Ramaiah S. Molecular dynamics and molecular docking studies on E166A point mutant, R274N/R276N double mutant, and E166A/R274N/R276N triple mutant forms of class A β-lactamases. J Biomol Struct Dyn 2014; 32:1953-68. [PMID: 24261683 DOI: 10.1080/07391102.2013.847804] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Bacterial resistance to β-lactams antibiotics is a serious threat to human health. The most common cause of resistance to the β-lactams is the production of β-lactamase that inactivates β-lactams. Specifically, class A extended-spectrum β-lactamase produced by antibiotic resistant bacteria is capable of hydrolyzing extended-spectrum Cephalosporins and Monobactams. Mutations in class A β-lactamases play a crucial role in substrate and inhibitor specificity. In this present study, the E166A point mutant, R274N/R276N double mutant, and E166A/R274N/R276N triple mutant class A β-lactamases are analyzed. Molecular dynamics (MD) simulations are done to understand the consequences of mutations in class A β-lactamases. Root mean square deviation, root mean square fluctuation, radius of gyration, solvent accessibility surface area, hydrogen bond, and essential dynamics analysis results indicate notable loss in stability for mutant class A β-lactamases. MD simulations of native and mutant structures clearly confirm that the substitution of alanine at the position of 166, Asparagine at 274 and 276 causes more flexibility in 3D space. Molecular docking results indicate the mutation in class A β-lactamases which decrease the binding affinity of Cefpirome and Ceftobiprole which are third and fifth generation Cephalosporins, respectively. MD simulation of Ceftobiprole-native and mutant type Class A β-lactamases complexes reveal that E166A/R274N/R276N mutations alter the structure and notable loss in the stability for Ceftobirole-mutant type Class A β-lactamases complexes. Ceftobiprole is currently prescribed for patients with serious bacterial infections; this phenomenon is the probable cause for the effectiveness of Ceftobiprole in controlling bacterial infections.
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Affiliation(s)
- K M Kumar
- a School of Biosciences and Technology, VIT University , Vellore 632014 , Tamil Nadu , India
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21
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Rodkey EA, Winkler ML, Bethel CR, Pagadala SRR, Buynak JD, Bonomo RA, van den Akker F. Penam sulfones and β-lactamase inhibition: SA2-13 and the importance of the C2 side chain length and composition. PLoS One 2014; 9:e85892. [PMID: 24454944 PMCID: PMC3894197 DOI: 10.1371/journal.pone.0085892] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 12/03/2013] [Indexed: 02/01/2023] Open
Abstract
β-Lactamases are the major reason β-lactam resistance is seen in Gram-negative bacteria. To combat this resistance mechanism, β-lactamase inhibitors are currently being developed. Presently, there are only three that are in clinical use (clavulanate, sulbactam and tazobactam). In order to address this important medical need, we explored a new inhibition strategy that takes advantage of a long-lived inhibitory trans-enamine intermediate. SA2-13 was previously synthesized and shown to have a lower k(react) than tazobactam. We investigated here the importance of the carboxyl linker length and composition by synthesizing three analogs of SA2-13 (PSR-4-157, PSR-4-155, and PSR-3-226). All SA2-13 analogs yielded higher turnover numbers and k(react) compared to SA2-13. We next demonstrated using protein crystallography that increasing the linker length by one carbon allowed for better capture of a trans-enamine intermediate; in contrast, this trans-enamine intermediate did not occur when the C2 linker length was decreased by one carbon. If the linker was altered by both shortening it and changing the carboxyl moiety into a neutral amide moiety, the stable trans-enamine intermediate in wt SHV-1 did not form; this intermediate could only be observed when a deacylation deficient E166A variant was studied. We subsequently studied SA2-13 against a relatively recently discovered inhibitor-resistant (IR) variant of SHV-1, SHV K234R. Despite the alteration in the mechanism of resistance due to the K→R change in this variant, SA2-13 was effective at inhibiting this IR enzyme and formed a trans-enamine inhibitory intermediate similar to the intermediate seen in the wt SHV-1 structure. Taken together, our data reveals that the C2 side chain linker length and composition profoundly affect the formation of the trans-enamine intermediate of penam sulfones. We also show that the design of SA2-13 derivatives offers promise against IR SHV β-lactamases that possess the K234R substitution.
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Affiliation(s)
- Elizabeth A. Rodkey
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Marisa L. Winkler
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio, United States of America
- Research Division, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio, United States of America
| | - Christopher R. Bethel
- Research Division, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio, United States of America
| | | | - John D. Buynak
- Department of Chemistry, Southern Methodist University, Dallas, Texas, United States of America
| | - Robert A. Bonomo
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio, United States of America
- Research Division, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio, United States of America
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, United States of America
- * E-mail: (RAB); (FVDA)
| | - Focco van den Akker
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio, United States of America
- * E-mail: (RAB); (FVDA)
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22
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Rodkey EA, McLeod DC, Bethel CR, Smith KM, Xu Y, Chai W, Che T, Carey PR, Bonomo RA, van den Akker F, Buynak JD. β-Lactamase inhibition by 7-alkylidenecephalosporin sulfones: allylic transposition and formation of an unprecedented stabilized acyl-enzyme. J Am Chem Soc 2013; 135:18358-69. [PMID: 24219313 PMCID: PMC4042847 DOI: 10.1021/ja403598g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The inhibition of the class A SHV-1 β-lactamase by 7-(tert-butoxycarbonyl)methylidenecephalosporin sulfone was examined kinetically, spectroscopically, and crystallographically. An 1.14 Å X-ray crystal structure shows that the stable acyl-enzyme, which incorporates an eight-membered ring, is a covalent derivative of Ser70 linked to the 7-carboxy group of 2-H-5,8-dihydro-1,1-dioxo-1,5-thiazocine-4,7-dicarboxylic acid. A cephalosporin-derived enzyme complex of this type is unprecedented, and the rearrangement leading to its formation may offer new possibilities for inhibitor design. The observed acyl-enzyme derives its stability from the resonance stabilization conveyed by the β-aminoacrylate (i.e., vinylogous urethane) functionality as there is relatively little interaction of the eight-membered ring with active site residues. Two mechanistic schemes are proposed, differing in whether, subsequent to acylation of the active site serine and opening of the β-lactam, the resultant dihydrothiazine fragments on its own or is assisted by an adjacent nucleophilic atom, in the form of the carbonyl oxygen of the C7 tert-butyloxycarbonyl group. This compound was also found to be a submicromolar inhibitor of the class C ADC-7 and PDC-3 β-lactamases.
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Affiliation(s)
- Elizabeth A. Rodkey
- Department of Biochemistry, Case Western Reserve University, 10900 Euclid Ave., Cleveland, Ohio 44106, United States
| | - David C. McLeod
- Department of Chemistry, Southern Methodist University, 3215 Daniel Ave., Dallas, Texas 75275, United States
| | - Christopher R. Bethel
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, 10701 East Boulevard, Cleveland, Ohio 44106, United States
| | - Kerri M. Smith
- Department of Chemistry, Cleveland State University, 2121 Euclid Ave., Cleveland, Ohio 44115, United States
| | - Yan Xu
- Department of Chemistry, Cleveland State University, 2121 Euclid Ave., Cleveland, Ohio 44115, United States
| | - Weirui Chai
- Department of Chemistry, Southern Methodist University, 3215 Daniel Ave., Dallas, Texas 75275, United States
| | - Tao Che
- Department of Biochemistry, Case Western Reserve University, 10900 Euclid Ave., Cleveland, Ohio 44106, United States
| | - Paul R. Carey
- Department of Biochemistry, Case Western Reserve University, 10900 Euclid Ave., Cleveland, Ohio 44106, United States
| | - Robert A. Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, 10701 East Boulevard, Cleveland, Ohio 44106, United States
| | - Focco van den Akker
- Department of Biochemistry, Case Western Reserve University, 10900 Euclid Ave., Cleveland, Ohio 44106, United States
| | - John D. Buynak
- Department of Chemistry, Southern Methodist University, 3215 Daniel Ave., Dallas, Texas 75275, United States
- Center for Drug Discovery, Design, and Development, Southern Methodist University, Dallas, Texas 75275, United States
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Espinoza-Herrera SJ, Gaur V, Suo Z, Carey PR. Following DNA chain extension and protein conformational changes in crystals of a Y-family DNA polymerase via Raman crystallography. Biochemistry 2013; 52:4881-90. [PMID: 23855392 DOI: 10.1021/bi400524h] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Y-Family DNA polymerases are known to bypass DNA lesions in vitro and in vivo. Sulfolobus solfataricus DNA polymerase (Dpo4) was chosen as a model Y-family enzyme for investigating the mechanism of DNA synthesis in single crystals. Crystals of Dpo4 in complexes with DNA (the binary complex) in the presence or absence of an incoming nucleotide were analyzed by Raman microscopy. (13)C- and (15)N-labeled d*CTP, or unlabeled dCTP, were soaked into the binary crystals with G as the templating base. In the presence of the catalytic metal ions, Mg(2+) and Mn(2+), nucleotide incorporation was detected by the disappearance of the triphosphate band of dCTP and the retention of *C modes in the crystal following soaking out of noncovalently bound C(or *C)TP. The addition of the second coded base, thymine, was observed by adding cognate dTTP to the crystal following a single d*CTP addition. Adding these two bases caused visible damage to the crystal that was possibly caused by protein and/or DNA conformational change within the crystal. When d*CTP is soaked into the Dpo4 crystal in the absence of Mn(2+) or Mg(2+), the primer extension reaction did not occur; instead, a ternary protein·template·d*CTP complex was formed. In the Raman difference spectra of both binary and ternary complexes, in addition to the modes of d(*C)CTP, features caused by ring modes from the template/primer bases being perturbed and from the DNA backbone appear, as well as features from perturbed peptide and amino acid side chain modes. These effects are more pronounced in the ternary complex than in the binary complex. Using standardized Raman intensities followed as a function of time, the C(*C)TP population in the crystal was maximal at ∼20 min. These remained unchanged in the ternary complex but declined in the binary complexes as chain incorporation occurred.
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Li R, Wang YT, Chen CL. Why tazobactam and sulbactam have different intermediates population with SHV-1 β-lactamase: a molecular dynamics study. J Mol Model 2013; 19:2519-24. [DOI: 10.1007/s00894-013-1802-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2012] [Accepted: 02/08/2013] [Indexed: 10/27/2022]
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Computer modeling on the tautomerization of sulbactam intermediate in SHV-1 β-lactamases: E166A mutant vs. wild type. J Mol Graph Model 2013; 40:131-9. [DOI: 10.1016/j.jmgm.2012.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2012] [Revised: 12/09/2012] [Accepted: 12/10/2012] [Indexed: 10/27/2022]
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26
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Heidari Torkabadi H, Che T, Shou J, Shanmugam S, Crowder MW, Bonomo RA, Pusztai-Carey M, Carey PR. Raman spectra of interchanging β-lactamase inhibitor intermediates on the millisecond time scale. J Am Chem Soc 2013; 135:2895-8. [PMID: 23406484 DOI: 10.1021/ja311440p] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rapid mix-rapid freeze is a powerful method to study the mechanisms of enzyme-substrate reactions in solution. Here we report a protocol that combines this method with normal (non-resonance) Raman microscopy to enable us to define molecular details of intermediates at early time points. With this combined method, SHV-1, a class A β-lactamase, and tazobactam, a commercially available β-lactamase inhibitor, were rapidly mixed on the millisecond time scale and then were flash-frozen by injection into an isopentane solution surrounded by liquid nitrogen. The "ice" was finally freeze-dried and characterized by Raman microscopy. We found that the reaction is almost complete in solution at 25 ms, giving rise to a major population composed of the trans-enamine intermediate. Between 25 and 500 ms, minor populations of protonated imine are detected that have previously been postulated to precede enamine intermediates. However, within 1 s, the imines are converted entirely to enamines. Interestingly, with this method, we can measure directly the turnover number of SHV-1 and tazobactam. The enzyme is completely inhibited at 1:4 ratio (enzyme:inhibitor) or greater, a number that agrees with the turnover number derived from steady-state kinetic methods. This application, employing non-intensity-enhanced Raman spectroscopy, provides a general and effective route to study the early events in enzyme-substrate reactions.
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Rodkey EA, Drawz SM, Sampson JM, Bethel CR, Bonomo RA, van den Akker F. Crystal structure of a preacylation complex of the β-lactamase inhibitor sulbactam bound to a sulfenamide bond-containing thiol-β-lactamase. J Am Chem Soc 2012; 134:16798-804. [PMID: 22974281 DOI: 10.1021/ja3073676] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The rise of inhibitor-resistant and other β-lactamase variants is generating an interest in developing new β-lactamase inhibitors to complement currently available antibiotics. To gain insight into the chemistry of inhibitor recognition, we determined the crystal structure of the inhibitor preacylation complex of sulbactam, a clinical β-lactamase inhibitor, bound in the active site of the S70C variant of SHV-1 β-lactamase, a resistance enzyme that is normally present in Klebsiella pneumoniae. The S70C mutation was designed to affect the reactivity of that catalytic residue to allow for capture of the preacylation complex. Unexpectedly, the 1.45 Å resolution inhibitor complex structure revealed that residue C70 is involved in a sulfenamide bond with K73. Such a covalent bond is not present in the wild-type SHV-1 or in an apo S70C structure also determined in this study. This bond likely contributed significantly to obtaining the preacylation complex with sulbactam due to further decreased reactivity toward substrates. The intact sulbactam is positioned in the active site such that its carboxyl moiety interacts with R244, S130, and T235 and its carbonyl moiety is situated in the oxyanion hole. To our knowledge, in addition to being the first preacylation inhibitor β-lactamase complex, this is also the first observation of a sulfenamide bond between a cysteine and lysine in an active site. Not only could our results aid, therefore, structure-based inhibitor design efforts in class A β-lactamases, but the sulfenamide-bond forming approach to yield preacylation complexes could also be applied to other classes of β-lactamases and penicillin-binding proteins with the SXXK motif.
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Affiliation(s)
- Elizabeth A Rodkey
- Department of Biochemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
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28
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Li R, Liao JM, Gu CR, Wang YT, Chen CL. Theoretical investigation on reaction of sulbactam with wild-type SHV-1 β-lactamase: acylation, tautomerization, and deacylation. J Phys Chem B 2011; 115:10298-310. [PMID: 21797222 DOI: 10.1021/jp111572v] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular dynamics (MD) simulation and quantum mechanical (QM) calculations were used to investigate the reaction mechanism of sulbactam with class A wild-type SHV-1 β-lactamase including acylation, tautomerization, and deacylation. Five different sulbactam-enzyme configurations were investigated by MD simulations. In the acylation step, we found that Glu166 cannot activate Ser70 directly for attacking on the carbonyl carbon, and Lys73 would participate in the reaction acting as a relay. Additionally, we found that sulbactam carboxyl can also act as a general base. QM calculations were performed on the formation mechanism of linear intermediates. We suggest that both imine and trans-enamine intermediates can be obtained in the opening of a five-membered thiazolidine ring. By MD simulation, we found that imine intermediate can exist in two conformations, which can generate subsequent trans- and cis-enamine intermediates, respectively. The QM calculations revealed that trans-enamine intermediate is much more stable than other intermediates. The deacylation mechanism of three linear intermediates (imine, trans-enamine, cis-enamine) was investigated separately. It is remarkably noted that, in cis-enamine intermediate, Glu166 cannot activate water for attacking on the carbonyl carbon directly. This leads to a decreasing of the deacylation rate of cis-enamine. These findings will be potentially useful in the development of new inhibitors.
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Affiliation(s)
- Rui Li
- The Department of Chemistry, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan
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Frase H, Smith CA, Toth M, Champion MM, Mobashery S, Vakulenko SB. Identification of products of inhibition of GES-2 beta-lactamase by tazobactam by x-ray crystallography and spectrometry. J Biol Chem 2011; 286:14396-409. [PMID: 21345789 PMCID: PMC3077639 DOI: 10.1074/jbc.m110.208744] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Revised: 01/19/2011] [Indexed: 01/28/2023] Open
Abstract
The GES-2 β-lactamase is a class A carbapenemase, the emergence of which in clinically important bacterial pathogens is a disconcerting development as the enzyme confers resistance to carbapenem antibiotics. Tazobactam is a clinically used inhibitor of class A β-lactamases, which inhibits the GES-2 enzyme effectively, restoring susceptibility to β-lactam antibiotics. We have investigated the details of the mechanism of inhibition of the GES-2 enzyme by tazobactam. By the use of UV spectrometry, mass spectroscopy, and x-ray crystallography, we have documented and identified the involvement of a total of seven distinct GES-2·tazobactam complexes and one product of the hydrolysis of tazobactam that contribute to the inhibition profile. The x-ray structures for the GES-2 enzyme are for both the native (1.45 Å) and the inhibited complex with tazobactam (1.65 Å). This is the first such structure of a carbapenemase in complex with a clinically important β-lactam inhibitor, shedding light on the structural implications for the inhibition process.
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Affiliation(s)
- Hilary Frase
- From the Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556 and
| | - Clyde A. Smith
- the Stanford Synchrotron Radiation Laboratory, Stanford University, Menlo Park, California 94025
| | - Marta Toth
- From the Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556 and
| | - Matthew M. Champion
- From the Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556 and
| | - Shahriar Mobashery
- From the Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556 and
| | - Sergei B. Vakulenko
- From the Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556 and
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Ligand-dependent disorder of the Omega loop observed in extended-spectrum SHV-type beta-lactamase. Antimicrob Agents Chemother 2011; 55:2303-9. [PMID: 21357298 DOI: 10.1128/aac.01360-10] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Among Gram-negative bacteria, resistance to β-lactams is mediated primarily by β-lactamases (EC 3.2.6.5), periplasmic enzymes that inactivate β-lactam antibiotics. Substitutions at critical amino acid positions in the class A β-lactamase families result in enzymes that can hydrolyze extended-spectrum cephalosporins, thus demonstrating an "extended-spectrum" β-lactamase (ESBL) phenotype. Using SHV ESBLs with substitutions in the Ω loop (R164H and R164S) as target enzymes to understand this enhanced biochemical capability and to serve as a basis for novel β-lactamase inhibitor development, we determined the spectra of activity and crystal structures of these variants. We also studied the inactivation of the R164H and R164S mutants with tazobactam and SA2-13, a unique β-lactamase inhibitor that undergoes a distinctive reaction chemistry in the active site. We noted that the reduced Ki values for the R164H and R164S mutants with SA2-13 are comparable to those with tazobactam (submicromolar). The apo enzyme crystal structures of the R164H and R164S SHV variants revealed an ordered Ω loop architecture that became disordered when SA2-13 was bound. Important structural alterations that result from the binding of SA2-13 explain the enhanced susceptibility of these ESBL enzymes to this inhibitor and highlight ligand-dependent Ω loop flexibility as a mechanism for accommodating and hydrolyzing β-lactam substrates.
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31
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Carey PR, Chen Y, Gong B, Kalp M. Kinetic crystallography by Raman microscopy. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:742-9. [PMID: 20797452 DOI: 10.1016/j.bbapap.2010.08.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Revised: 08/12/2010] [Accepted: 08/16/2010] [Indexed: 11/16/2022]
Abstract
Raman spectra, obtained using a Raman microscope, offer a unique and incisive approach to follow interactions and reactions inside a single crystal under soak-in or soak-out conditions. The utility of this approach derives from the finding that the Raman spectra from single macromolecular crystals, under normal (non-resonance) conditions, are extremely stable, with a low "light background," and provide ideal platforms for Raman difference spectroscopy. In turn, this allows the interrogation of sub-molecular changes in very large and complex macromolecular environments. There is often great synergy with X-ray crystallography, with the Raman spectroscopist providing crystallography colleagues with the best soak-in conditions to generate a targeted intermediate for flash freezing and X-ray analysis. On the other hand, X-ray structures at points along a reaction pathway provide invaluable benchmarks for interpreting the Raman data from populations seen by Raman to be changing in real-time. These principles will be illustrated by two reactions: the first involves a complex, branching reaction pathway underlying the inhibition of β-lactamases by clinically important pharmaceutical compounds, where different combinations of drug and enzyme function in different regions of the pathway. The second shows how temporal data can be derived for several events in the initiation step of RNA synthesis-more specifically, when one GTP molecule is joined to one ATP molecule to form a G∙A dimer in the active site of a 115,000 Dalton crystalline RNA polymerase. Finally, we will summarize the extension of Raman microscopy to nucleic acid crystals and the information that has been obtained for RNA-based enzymes. This article is part of a Special Issue entitled: Protein Structure and Function in the Crystalline State.
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Affiliation(s)
- Paul R Carey
- Case Western Reserve University, Department of Biochemistry, 10900 Euclid Avenue, Cleveland, OH 44106, USA.
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32
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Raman-assisted crystallography of biomolecules at the synchrotron: instrumentation, methods and applications. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:750-9. [PMID: 20691814 DOI: 10.1016/j.bbapap.2010.07.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Revised: 07/25/2010] [Accepted: 07/28/2010] [Indexed: 11/23/2022]
Abstract
Raman spectroscopy is a powerful technique that, in recent years, has been successfully coupled to X-ray crystallography for the analysis of biological macromolecular systems. The complementarity between both techniques is illustrated at multiple stages, including sample preparation, data collection and structural interpretation with a mechanistic perspective. The current state of instrumentation is described, focusing on synchrotron based setups. Present and future applications of Raman microspectrophotometry are reviewed with reference to recent examples dealing with metallo-, photosensitive-, and redox-proteins. The added value of Raman microspectrophotometry to assess X-radiation damage is discussed, and its applicability to investigate crystalline DNA molecules is also emphasized. This article is part of a Special Issue entitled: Protein Structure and Function in the Crystalline State.
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33
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Kluge AF, Petter RC. Acylating drugs: redesigning natural covalent inhibitors. Curr Opin Chem Biol 2010; 14:421-7. [PMID: 20457000 DOI: 10.1016/j.cbpa.2010.03.035] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Revised: 02/18/2010] [Accepted: 03/26/2010] [Indexed: 11/26/2022]
Abstract
Structural modification of naturally occurring beta-lactams and beta-lactones is a highly effective strategy for generating drugs for treating bacterial infections, cancer, obesity, and hyperlipidemia. These drugs acylate catalytic amino acids (serine, threonine, or cysteine) in enzyme targets such as penicillin-binding proteins (PBPs), beta-lactamases, lipases, HMG-CoA reductase, fatty acid synthetase, and the 20S proteasome. Optimally performing drugs combine features of high target affinity, chemoselective reactivity, and high stability of the acylated target protein. This review provides a perspective on these two classes of acylating agents and summarizes recent advances in mechanism and structure-based design of acylating drugs.
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Affiliation(s)
- Arthur F Kluge
- Avila Therapeutics, 100 Beaver Street, Waltham, MA 02453, USA
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34
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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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Kalp M, Bethel CR, Bonomo RA, Carey PR. Why the extended-spectrum beta-lactamases SHV-2 and SHV-5 are "hypersusceptible" to mechanism-based inhibitors. Biochemistry 2009; 48:9912-20. [PMID: 19736945 DOI: 10.1021/bi9012098] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Extended-spectrum beta-lactamases (ESBLs) are derivatives of enzymes such as SHV-1 and TEM-1 that have undergone site-specific mutations that enable them to hydrolyze, and thus inactivate, oxyimino-cephalosporins, such as cefotaxime and ceftazidime. X-ray crystallographic data provide an explanation for this in that the mutations bring about an expansion of the binding pocket by moving a beta-strand that forms part of the active site wall. Another characteristic of ESBLs that has remained enigmatic is the fact that they are "hypersusceptible" to inhibition by the mechanism-based inactivators tazobactam, sulbactam, and clavulanic acid. Here, we provide a rationale for this "hypersusceptibility" based on a comparative analysis of the intermediates formed by these compounds with wild-type (WT) SHV-1 beta-lactamase and its ESBL variants SHV-2 and SHV-5, which carry the G238S and G238S/E240K substitutions, respectively. A Raman spectroscopic analysis of the reactions in single crystals shows that, compared to WT, the SHV-2 and SHV-5 variants have relatively higher populations of the stable trans-enamine intermediate over the less stable and more easily hydrolyzable cis-enamine and imine co-intermediates. In solution, SHV-2 and SHV-5 also form larger populations of an enamine species compared to SHV-1 as detected by stopped-flow kinetic experiments under single-turnover conditions. Moreover, a simple Raman band shape analysis predicts that the trans-enamine intermediates themselves in SHV-2 and SHV-5 are held in more stable, rigid conformations compared to their trans-enamine analogues in WT SHV-1. As a result of this stabilization, more of the trans-enamine intermediate is formed, which subsequently lowers the K(I) values of the mechanism-based inhibitors up to 50-fold in SHV-2 and SHV-5.
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Affiliation(s)
- Matthew Kalp
- Department of Biochemistry, Molecular Biology and Microbiology, and Medicine,Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
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36
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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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37
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Miani A, Helfand MS, Raugei S. Ab Initio Raman Spectra of β-Lactamase Inhibitor Intermediates Bound to E166A SHV β-Lactamase. J Chem Theory Comput 2009; 5:2158-72. [DOI: 10.1021/ct900131q] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Andrea Miani
- SISSA and INFM-DEMOCRITOS center via Beirut 2, I-34014, Trieste, Italy, and Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106
| | - Marion Skalweit Helfand
- SISSA and INFM-DEMOCRITOS center via Beirut 2, I-34014, Trieste, Italy, and Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106
| | - Simone Raugei
- SISSA and INFM-DEMOCRITOS center via Beirut 2, I-34014, Trieste, Italy, and Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106
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Kalp M, Totir MA, Buynak JD, Carey PR. Different intermediate populations formed by tazobactam, sulbactam, and clavulanate reacting with SHV-1 beta-lactamases: Raman crystallographic evidence. J Am Chem Soc 2009; 131:2338-47. [PMID: 19161282 DOI: 10.1021/ja808311s] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Tazobactam, sulbactam, and clavulanic acid are the only beta-lactamase inhibitors in clinical use. Comparative inhibitory activities of clavulanic acid, sulbactam, and tazobactam against clinically important beta-lactamases conclude that tazobactam is superior to both clavulanic acid and sulbactam. Thus far, the majority of explanations for this phenomenon have relied on kinetic studies, which report differences in the ligands' apparent dissociation constants and number of turnovers before inactivation. Due their innate limitations, these investigations do not examine the identity of intermediates on the reaction pathway and relate them to the efficacy of the inhibitors. In the present study, the reactions between the three inhibitors and SHV-1 beta-lactamase have been examined in single crystals using a Raman microscope. The results show that tazobactam forms a predominant population of trans-enamine, a chemically inert species, with SHV-1, while clavulanate and sulbactam form a mixture of trans-enamine and two labile species, the cis-enamine and imine. The same reactions are then reexamined using a deacylation-deficient variant, SHV E166A, that has been used to trap acyl-enzyme intermediates for X-ray crystallographic analysis. Our Raman data show that significant differences exist between the wild-type and SHV E166A acyl-enzyme populations. Namely, compared to SHV-1, sulbactam shows significantly smaller populations of cis-enamine and imine in the E166A variant, while clavulanate exists almost exclusively as trans-enamine in the E166A active site. Using clavulanate as an example, we also show that Raman crystallography can provide novel information on the presence of multiple conformers or tautomers for intermediates within a complex reaction pathway. These insights caution against the interpretation of experimental data obtained with deacylation-deficient beta-lactamases to make mechanistic conclusions about inhibitors within the enzyme.
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Affiliation(s)
- Matthew Kalp
- Department of Biochemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
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39
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Li R, Feng D, Feng S. Computational study on decarboxylation mechanism of β-lactamases inhibitors: Clavulanate vs. sulbactam. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.03.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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40
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Totir MA, Cha J, Ishiwata A, Wang B, Sheri A, Anderson VE, Buynak J, Mobashery S, Carey PR. Why clinically used tazobactam and sulbactam are poor inhibitors of OXA-10 beta-lactamase: Raman crystallographic evidence. Biochemistry 2008; 47:4094-101. [PMID: 18324783 DOI: 10.1021/bi702348w] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The clinically used inhibitors tazobactam and sulbactam are effective in the inhibition of activity of class A beta-lactamases, but not for class D beta-lactamases. The two inhibitors exhibit a complex multistep profile for their chemistry of inhibition with class A beta-lactamases. To compare the inhibition profiles for class A and D enzymes, the reactions were investigated within OXA-10 beta-lactamase (a class D enzyme) crystals using a Raman microscope. The favored reaction pathway appears to be distinctly different from that for class A beta-lactamases. In contrast to the case of class A enzymes that favor the formation of a key enamine species, the OXA-10 enzyme forms an alpha,beta-unsaturated acrylate (acid or ester). Quantum mechanical calculations support the likely product as the adduct of Ser115 to the acrylate. Few enamine-like species are formed by sulbactam or tazobactam with this enzyme. Taken together, our results show that the facile conversion of the initial imine, formed upon acylation of the active site Ser67, to the cis- and/or trans-enamine is disfavored. Instead, there is a significant population of the imine that could either experience cross-linking to a second nucleophile (e.g., Ser115) or give rise to the alpha,beta-unsaturated product and permanent inhibition. Alternatively, the imine can undergo hydrolysis to regenerate the catalytically active OXA-10 enzyme. This last process is the dominant one for class D beta-lactamases since the enzyme is not effectively inhibited. In contrast to sulbactam and tazobactam, the reactions between oxacillin or 6alpha-hydroxyisopropylpenicillinate (both substrates) and OXA-10 beta-lactamase appear much less complex. These compounds lead to a single acyl-enzyme species, the presence of which was confirmed by Raman and MALDI-TOF experiments.
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Affiliation(s)
- Monica A Totir
- Departments of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106, USA
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41
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Mansour TS, Bradford PA, Venkatesan AM. Recent Developments in β-Lactamases and Inhibitors. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2008. [DOI: 10.1016/s0065-7743(08)00015-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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42
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Padayatti PS, Sheri A, Totir MA, Helfand MS, Carey MP, Anderson VA, Carey PR, Bethel CR, Bonomo RA, Buynak JD, van den Akker F. Rational design of a beta-lactamase inhibitor achieved via stabilization of the trans-enamine intermediate: 1.28 A crystal structure of wt SHV-1 complex with a penam sulfone. J Am Chem Soc 2007; 128:13235-42. [PMID: 17017804 PMCID: PMC2593906 DOI: 10.1021/ja063715w] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
beta-Lactamases are one of the major causes of antibiotic resistance in Gram negative bacteria. The continuing evolution of beta-lactamases that are capable of hydrolyzing our most potent beta-lactams presents a vexing clinical problem, in particular since a number of them are resistant to inhibitors. The efficient inhibition of these enzymes is therefore of great clinical importance. Building upon our previous structural studies that examined tazobactam trapped as a trans-enamine intermediate in a deacylation deficient SHV variant, we designed a novel penam sulfone derivative that forms a more stable trans-enamine intermediate. We report here the 1.28 A resolution crystal structure of wt SHV-1 in complex with a rationally designed penam sulfone, SA2-13. The compound is covalently bound to the active site of wt SHV-1 similar to tazobactam yet forms an additional salt-bridge with K234 and hydrogen bonds with S130 and T235 to stabilize the trans-enamine intermediate. Kinetic measurements show that SA2-13, once reacted with SHV-1 beta-lactamase, is about 10-fold slower at being released from the enzyme compared to tazobactam. Stabilizing the trans-enamine intermediate represents a novel strategy for the rational design of mechanism-based class A beta-lactamase inhibitors.
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Affiliation(s)
- Pius S. Padayatti
- Department of Biochemistry, Case Western Reserve University, Cleveland Ohio 44106
| | - Anjaneyulu Sheri
- Department of Chemistry, Southern Methodist University, Dallas TX 75275-0314
| | - Monica A. Totir
- Department of Chemistry, Case Western Reserve University, Cleveland Ohio 44106
| | - Marion S. Helfand
- Research Division, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland Ohio 44106
| | - Marianne P. Carey
- Department of Biochemistry, Case Western Reserve University, Cleveland Ohio 44106
| | - Vernon A. Anderson
- Department of Biochemistry, Case Western Reserve University, Cleveland Ohio 44106
| | - Paul R. Carey
- Department of Biochemistry, Case Western Reserve University, Cleveland Ohio 44106
| | - Christopher R. Bethel
- Research Division, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland Ohio 44106
| | - Robert A. Bonomo
- Research Division, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland Ohio 44106
- Department of Pharmacology, Case Western Reserve University, Cleveland Ohio 44106
| | - John D. Buynak
- Department of Chemistry, Southern Methodist University, Dallas TX 75275-0314
| | - Focco van den Akker
- Department of Biochemistry, Case Western Reserve University, Cleveland Ohio 44106
- Corresponding author:
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Totir MA, Helfand MS, Carey MP, Sheri A, Buynak JD, Bonomo RA, Carey PR. Sulbactam forms only minimal amounts of irreversible acrylate-enzyme with SHV-1 beta-lactamase. Biochemistry 2007; 46:8980-7. [PMID: 17630699 PMCID: PMC2596720 DOI: 10.1021/bi7006146] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Sulbactam is a mechanism-based inhibitor of beta-lactamase enzymes used in clinical practice. It undergoes a complex series of chemical reactions in the active site that have been studied extensively in the past three decades. However, the actual species that gives rise to inhibition in a clinical setting has not been established. Recent studies by our group, using Raman microscopy and X-ray crystallography, have found that large quantities of enamine-based acyl-enzyme species are present within minutes in single crystals of SHV-1 beta-lactamases which can lead to significant inhibition. The enamines are formed by breakdown of the cyclic beta-lactam structures with further transformations leading to imine formation and subsequent isomerization to cis and/or trans enamines. Another favored form of inhibition arises from attack on the imine by a second nucleophilic amino acid side chain, e.g., from serine 130, to form a cross-linked species in the active site that can degrade to an acrylate-like species irreversibly bound to the enzyme. Thus, the imine is at a branch point on the reaction pathway. Using sulbactam and 6,6-dideuterated sulbactam we follow these alternate paths in WT and E166A SHV-1 beta-lactamase by means of Raman microscopic studies on single enzyme crystals. For the unlabeled sulbactam, the Raman data show the presence of an acrylate-like species, probably 3-serine acrylate, several hours after the reaction is started in the crystal. However, for the 6,6-dideutero analogue the acrylate signature appears on the time scale of minutes. The Raman signatures, principally an intense feature near 1530 cm-1, are assigned based on quantum mechanical calculations on model compounds that mimic acrylate species in the active site. The different time scales observed for acrylate-like product formation are ascribed to different rates of reaction involving the imine intermediate. It is proposed that for the unsubstituted sulbactam the conversion from imine to enamine, which involves breaking a C-H bond, is aided by quantum mechanical tunneling. For the 6,6-dideutero-sulbactam the same step involves breaking a C-D bond, which has little or no assistance from tunneling. Consequently the conversion to enamines is slower, and a higher population of imine results, presenting the opportunity for the competing reaction with the second nucleophile, serine 130 being the prime candidate. The hydrolysis of the resulting cross-linked intermediate leads to the observed rapid buildup of the acrylate product in the Raman spectra from the dideutero analogue. The protocol used here, essentially running the reactions with the two forms of sulbactam in parallel, provides an element of control and enables us to conclude that, for the unsubstituted sulbactam, the formation of the cross-linked intermediate and the final irreversible acrylate product is not a significant route to inhibition of SHV-1.
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Affiliation(s)
- Monica A. Totir
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106
| | - Marion S. Helfand
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
- Research Division, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio 44106
| | - Marianne P. Carey
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106
| | - Anjaneyulu Sheri
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75205
| | - John D. Buynak
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75205
| | - Robert A. Bonomo
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106
- Research Division, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio 44106
| | - Paul R. Carey
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106
- * To whom correspondence should be addressed: . Department of Biochemistry, Case Western Reserve University, 10900 Euclid Avenue Cleveland, Ohio 44106 Tel. (216) 368 0031 Fax (216) 368 3419
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44
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Li R, Feng D, He M. Theoretical study of the reaction from 6-methylidene penem to seven-membered ring intermediates. J Phys Chem A 2007; 111:4720-5. [PMID: 17477514 DOI: 10.1021/jp070685q] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A sort of beta-lactamase inhibitor, 6-methylidene penem can inhibit both class A and class C serine beta-lactamase. Its inhibition mechanism involves yielding a seven-membered ring intermediate after acylation of the serine. Density functional theory (DFT) method was used on the molecular model to determine the mechanism of producing the seven-membered ring intermediate. Solvent effects were considered via polarizable continuum model (PCM). Moreover, a water-assisted process was considered in the hydrogen transfer process. The results show that the seven-membered ring intermediate can be obtained via two possible mechanisms, namely, concerted mechanism and stepwise mechanism. In stepwise mechanism, a new thiirane intermediate which has never been reported was found. The product of stepwise mechanism, e, has five tautomerics, and they can be tautomerized by hydrogen transfer.
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Affiliation(s)
- Rui Li
- Institute of Theoretical Chemistry and College of Life Science, Shandong University, Jinan 250100, People's Republic of China
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45
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Miani A, Raugei S, Carloni P, Helfand MS. Structure and Raman Spectrum of Clavulanic Acid in Aqueous Solution. J Phys Chem B 2007; 111:2621-30. [PMID: 17302447 DOI: 10.1021/jp066135u] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The calculation of the vibrational Raman spectrum of enzyme-bound beta-lactamase inhibitors may be of help to understand the mechanisms responsible for bacterial drug resistance. Here, we present a study of the solvation structure and the vibrational properties of clavulanate, an important beta-lactamase inhibitor, in aqueous solution as obtained from full quantum and hybrid empirical/quantum molecular dynamics simulations at ambient conditions. The analysis of the vibrational density of states indicates that hybrid empirical/quantum mechanical simulations are able to properly describe the vibrational levels of clavulanate in solution. In addition, we propose a computationally efficient protocol to calculate the vibrational Raman effect for large solute molecules in water, which is able to faithfully reproduce the experimentally recorded clavulanate Raman spectrum and discloses the possibility to employ hybrid simulations to assign the experimental Raman spectra of inhibitors bound to beta-lactamases.
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Affiliation(s)
- Andrea Miani
- SISSA/ISAS and INFM-DEMOCRITOS, Modeling Center for Research in Atomistic Simulation, via Beirut 2, I-34014, Trieste, Italy
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46
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Mulchande J, Martins L, Moreira R, Archer M, Oliveira TF, Iley J. The efficiency of C-4 substituents in activating the β-lactam scaffold towards serine proteases and hydroxide ion. Org Biomol Chem 2007; 5:2617-26. [DOI: 10.1039/b706622h] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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47
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Totir MA, Padayatti PS, Helfand MS, Carey MP, Bonomo RA, Carey PR, van den Akker F. Effect of the inhibitor-resistant M69V substitution on the structures and populations of trans-enamine beta-lactamase intermediates. Biochemistry 2006; 45:11895-904. [PMID: 17002290 PMCID: PMC2596060 DOI: 10.1021/bi060990m] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The objective of this study was to determine the molecular factors that lead to beta-lactamase inhibitor resistance for the M69V variant in SHV-1 beta-lactamase. With mechanism-based inhibitors, the beta-lactamase forms an acyl-enzyme intermediate that consists of a trans-enamine derivative in the active site. This study focuses on these intermediates by introducing the E166A mutation that greatly retards deacylation. Thus, by comparing the properties of the E166A and M69V/E166A forms, we can explore the consequences of the resistance mutation at the level of the enamine acyl-enzyme forms. The reactions between the beta-lactamase and the inhibitors tazobactam, sulbactam, and clavulanic acid are followed in single crystals of the enzymes by using a Raman microscope. The resulting Raman difference spectroscopic data provide detailed information about conformational events involving the enamine species as well as an estimate of their populations. The Raman difference spectra for each of the inhibitors in the E166A and M69V/E166A variants are very similar. In particular, detailed analysis of the main enamine Raman vibration near 1595 cm(-1) reveals that the structure and flexibility of the enamine fragments are essentially identical for each of the three inhibitors in E166A and in the M69V/E166A double mutant. This finding is in accord with the X-ray-derived structures, presented herein at 1.6-1.75 A resolution, of the trans-enamine intermediates formed by the three inhibitors in M69V/E166A. However, a comparison of Raman results for M69V/E166A and E166A shows that the M69V mutation results in a 40%, 25%, and negligible reductions in the enamine population when the beta-lactamase crystals are soaked in 5 mM tazobactam, clavulanic acid, and sulbactam solutions, respectively. The levels of enamine from tazobactam and clavulanic acid can be increased by increasing the concentrations of inhibitor in the mother liquor. Thus, the sensitivity of population levels to the inhibitor concentration in the mother liquor focuses attention on the properties of the encounter complex preceding acylation. It is proposed that for small ligands, such as tazobactam, sulbactam, and clavulanic acid, the positioning of the lactam ring in the active site in the correct orientation for acylation is only one of a number of poorly defined conformations. For tazobactam and clavulanic acid, the correctly oriented encounter complex is even less likely in the M69V variant, leading to a reduction in the level of inhibition of the enzyme via formation of the acyl-enzyme intermediate and the onset of resistance. Analysis of the X-ray structures of the three intermediates in M69V/E166A demonstrates that, compared to the structures for the E166A form, the oxyanion hole becomes smaller, providing one explanation for why acylation may be less efficient following the M69V substitution.
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Affiliation(s)
- Monica A Totir
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106, USA
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48
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Wang F, Cassidy C, Sacchettini JC. Crystal structure and activity studies of the Mycobacterium tuberculosis beta-lactamase reveal its critical role in resistance to beta-lactam antibiotics. Antimicrob Agents Chemother 2006; 50:2762-71. [PMID: 16870770 PMCID: PMC1538687 DOI: 10.1128/aac.00320-06] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
beta-Lactam antibiotics are extremely effective in disrupting the synthesis of the bacterial cell wall in both gram-positive and gram-negative bacteria. However, they are ineffective against Mycobacterium tuberculosis, due to the production of a beta-lactamase enzyme encoded on the chromosome of M. tuberculosis that degrades these antibiotics. Indeed, recent studies have demonstrated that deletion of the blaC gene, the only gene encoding a beta-lactamase in M. tuberculosis, or inhibition of the encoded enzyme resulted in significantly increased sensitivity to beta-lactam antibiotics. In this paper we present a biochemical and structural characterization of M. tuberculosis BlaC. Recombinant BlaC shows a broad range of specificity with almost equal penicillinase and cepholothinase activity. While clavulanate is a mechanism-based inhibitor to class A beta-lactamase with high potency (typically K(i) < 0.1 microM), it is a relatively poor inhibitor of the M. tuberculosis BlaC (K(i) = 2.4 microM). The crystal structure of the enzyme, determined at a resolution of 1.7 A, shows that the overall fold of the M. tuberculosis enzyme is similar to other class A beta-lactamases. There are, however, several distinct features of the active site, such as the amino acid substitutions N132G, R164A, R244A, and R276E, that explain the broad specificity of the enzyme, relatively low penicillinase activity, and resistance to clavulanate.
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Affiliation(s)
- Feng Wang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
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49
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Affiliation(s)
- Paul R Carey
- Department of Biochemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA.
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50
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Abstract
Recent studies using a Raman microscope have shown that single protein crystals provide an ideal platform to undertake Raman difference spectroscopic analyses under nonresonance conditions. This approach, termed Raman crystallography, provides a means of characterizing chemical events within the crystal such as ligand binding and enzyme reactions. In many cases Raman crystallography goes hand in hand with X-ray crystallographic studies because the Raman results can inform the X-ray crystallographer about the status of chemical events in the crystal prior to flash freezing and X-ray analysis. In turn, the combined data from the Raman and X-ray analyses are highly synergistic and offer novel perspectives on structure and dynamics in enzyme active sites. In a related area, protein misfolding, Raman microscopy can provide detailed insights into the chemistry of the amyloid plaques associated with Alzheimer's disease and into the intermediates on the alpha-synuclein protein misfolding pathway implicated in Parkinson's disease.
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Affiliation(s)
- Paul R Carey
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106, USA.
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