1
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Mitku ML, Simegn W, Chanie GS, Mohammed Seid A, Beyna AT, Kebad Mengesha A, Melese M, Esubalew D, Gela YY, Ayenew W, Limenh LW. 3D-QSAR, ADMET, and molecular docking studies of aztreonam analogs as E. colis inhibitors. SAGE Open Med 2024; 12:20503121241271810. [PMID: 39206230 PMCID: PMC11350533 DOI: 10.1177/20503121241271810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 07/03/2024] [Indexed: 09/04/2024] Open
Abstract
Background The development of multidrug resistant strains of extended-spectrum β-lactamase-producing Escherichia coli has become a global problem; therefore, the discovery of new antibacterial agents is the only available solution. Objective To improve and propose new compounds with antibacterial activity, the three-dimensional quantitative structure-activity relationship and molecular docking studies were carried out on Aztreonam analogs as E. coli inhibitors in DNA gyrase B. Method This study's 3D-Quantitative structure-activity relationship model was created using on the Comparative Molecular Field Analysis and the Comparative Molecular Similarity Indices Analysis. Using the Comparative Molecular Field Analysis (Q 2 = 0.73; R 2 = 0.82), excellent predictability was achieved, and the best Comparative Molecular Similarity Indices Analysis model (Q 2 = 0.88; R 2 = 0.9). The generated model's ability to predict outcomes was assessed through external validation using a test set compound and an applicability domain technique. In this study, the steric, electrostatic, and hydrogen bond acceptor fields played a key role in antibacterial activity. Results The results of the molecular docking revealed that the newly generated compound A6 has the highest binding affinity with DNA gyrase B. It forms 10 hydrogen bonds with amino acid residues of Asn104, Asn274, Asn132, Ser70, Ser237, Thr105, Glu273, and 2 salt bridges with amino acid residues of Ser70 and Glu273 and one pi-pi interacting with Gys271 amino acid residue in the binding site of 5G1, and this result was validated by a new assessment method. We created some novel, highly effective DNA gyrase B inhibitors based on the earlier findings, and the most accurate model predicted their inhibitory actions. The ADMET characteristics and pharmacological similarity of these novel inhibitors were also examined. Conclusion These findings would be very beneficial in guiding the optimization process for the identification of novel drugs that can address the issue of multiple drug resistance.
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Affiliation(s)
- Melese Legesse Mitku
- Department of Pharmaceutical Chemistry, School of Pharmacy, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Wudneh Simegn
- Department of Social and Administrative Pharmacy, School of Pharmacy, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Gashaw Sisay Chanie
- Department of Clinical Pharmacy, School of Pharmacy, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Abdulwase Mohammed Seid
- Department of Clinical Pharmacy, School of Pharmacy, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Alemante Tafese Beyna
- Department of Pharmacology, School of Pharmacy, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Assefa Kebad Mengesha
- Department of Pharmacology, School of Pharmacy, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Mihret Melese
- Department of Human Physiology, School of Medicine, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Dereje Esubalew
- Department of Human Physiology, School of Medicine, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Yibeltal Yismaw Gela
- Department of Human Physiology, School of Medicine, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Wondim Ayenew
- Department of Social and Administrative Pharmacy, School of Pharmacy, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Liknaw Workie Limenh
- Department of Pharmaceutics, School of Pharmacy, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
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2
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Fram B, Su Y, Truebridge I, Riesselman AJ, Ingraham JB, Passera A, Napier E, Thadani NN, Lim S, Roberts K, Kaur G, Stiffler MA, Marks DS, Bahl CD, Khan AR, Sander C, Gauthier NP. Simultaneous enhancement of multiple functional properties using evolution-informed protein design. Nat Commun 2024; 15:5141. [PMID: 38902262 PMCID: PMC11190266 DOI: 10.1038/s41467-024-49119-x] [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: 09/28/2023] [Accepted: 05/24/2024] [Indexed: 06/22/2024] Open
Abstract
A major challenge in protein design is to augment existing functional proteins with multiple property enhancements. Altering several properties likely necessitates numerous primary sequence changes, and novel methods are needed to accurately predict combinations of mutations that maintain or enhance function. Models of sequence co-variation (e.g., EVcouplings), which leverage extensive information about various protein properties and activities from homologous protein sequences, have proven effective for many applications including structure determination and mutation effect prediction. We apply EVcouplings to computationally design variants of the model protein TEM-1 β-lactamase. Nearly all the 14 experimentally characterized designs were functional, including one with 84 mutations from the nearest natural homolog. The designs also had large increases in thermostability, increased activity on multiple substrates, and nearly identical structure to the wild type enzyme. This study highlights the efficacy of evolutionary models in guiding large sequence alterations to generate functional diversity for protein design applications.
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Affiliation(s)
- Benjamin Fram
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Yang Su
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Ian Truebridge
- Institute for Protein Innovation, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- AI Proteins, Boston, MA, USA
| | - Adam J Riesselman
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Program in Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - John B Ingraham
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Alessandro Passera
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030, Vienna, Austria
| | - Eve Napier
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
| | - Nicole N Thadani
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Apriori Bio, Cambridge, MA, USA
| | - Samuel Lim
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Kristen Roberts
- Selux Diagnostics Inc., 56 Roland Street, Charlestown, MA, USA
| | - Gurleen Kaur
- Selux Diagnostics Inc., 56 Roland Street, Charlestown, MA, USA
| | - Michael A Stiffler
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Dyno Therapeutics, 343 Arsenal Street, Watertown, MA, USA
| | - Debora S Marks
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christopher D Bahl
- Institute for Protein Innovation, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- AI Proteins, Boston, MA, USA
| | - Amir R Khan
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Chris Sander
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nicholas P Gauthier
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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3
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Jeong BG, Kim MY, Jeong CS, Do H, Hwang J, Lee JH, Cha SS. Characterization of the extended substrate spectrum of the class A β-lactamase CESS-1 from Stenotrophomonas sp. and structure-based investigation into its substrate preference. Int J Antimicrob Agents 2024; 63:107171. [PMID: 38588869 DOI: 10.1016/j.ijantimicag.2024.107171] [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: 04/03/2023] [Revised: 03/10/2024] [Accepted: 04/03/2024] [Indexed: 04/10/2024]
Abstract
OBJECTIVES Stenotrophomonas spp. intrinsically resistant to many β-lactam antibiotics are found throughout the environment. CESS-1 identified in Stenotrophomonas sp. KCTC 12332 is an uncharacterized class A β-lactamase. The goal of this study was to reveal biochemical and structural characteristics of CESS-1. METHODS The hydrolytic activities of CESS-1 towards penicillins (penicillin G and ampicillin), cephalosporins (cephalexin, cefaclor, and cefotaxime), and carbapenems (imipenem and meropenem) was spectrophotometrically monitored. Structural information on E166Q mutants of CESS-1 acylated by cefaclor, cephalexin, or ampicillin were determined by X-ray crystallography. RESULTS CESS-1 displayed hydrolytic activities toward penicillins and cephalosporins, with negligible activity toward carbapenems. Although cefaclor, cephalexin, and ampicillin have similar structures with identical R1 side chains, the catalytic parameters of CESS-1 toward them were distinct. The kcat values for cefaclor, cephalexin, and ampicillin were 1249.6 s-1, 204.3 s-1, and 69.8 s-1, respectively, with the accompanying KM values of 287.6 μM, 236.7 μM, and 28.8 μM, respectively. CONCLUSIONS CESS-1 was able to discriminate between cefaclor and cephalexin with a single structural difference at C3 position: -Cl (cefaclor) and -CH3 (cephalexin). Structural comparisons among three E166Q mutants of CESS-1 acylated by cefaclor, cephalexin, or ampicillin, revealed that cooperative positional changes in the R1 side chain of substrates and their interaction with the β5-β6 loop affect the distance between Asn170 and the deacylating water at the acyl-enzyme intermediate state. This is directly associated with the differential hydrolytic activities of CESS-1 toward the three structurally similar β-lactam antibiotics.
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Affiliation(s)
- Bo-Gyeong Jeong
- Department of Chemistry & Nanoscience, Ewha Womans University, Seoul, Republic of Korea
| | - Myeong-Yeon Kim
- Department of Chemistry & Nanoscience, Ewha Womans University, Seoul, Republic of Korea
| | - Chang-Sook Jeong
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon, Republic of Korea
| | - Hackwon Do
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon, Republic of Korea
| | - Jisub Hwang
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon, Republic of Korea
| | - Jun Hyuck Lee
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon, Republic of Korea.
| | - Sun-Shin Cha
- Department of Chemistry & Nanoscience, Ewha Womans University, Seoul, Republic of Korea.
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4
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Johnson CL, Setterfield MA, Hassanain WA, Wipat A, Pocock M, Faulds K, Graham D, Keegan N. Multiplex detection of the big five carbapenemase genes using solid-phase recombinase polymerase amplification. Analyst 2024; 149:1527-1536. [PMID: 38265775 DOI: 10.1039/d3an01747h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
Five carbapenemase enzymes, coined the 'big five', have been identified as the biggest threat to worldwide antibiotic resistance based on their broad substrate affinity and global prevalence. Here we show the development of a molecular detection method for the gene sequences from the five carbapenemases utilising the isothermal amplification method of recombinase polymerase amplification (RPA). We demonstrate the successful detection of each of the big five carbapenemase genes with femtomolar detection limits using a spatially separated multiplex amplification strategy. The approach uses tailed oligonucleotides for hybridisation, reducing the complexity and cost of the assay compared to classical RPA detection strategies. The reporter probe, horseradish peroxidase, generates the measureable output on a benchtop microplate reader, but more notably, our study leverages the power of a portable Raman spectrometer, enabling up to a 19-fold enhancement in the limit of detection. Significantly, the development approach employed a solid-phase RPA format, wherein the forward primers targeting each of the five carbapenemase genes are immobilised to a streptavidin-coated microplate. The adoption of this solid-phase methodology is pivotal for achieving a successful developmental pathway when employing this streamlined approach. The assay takes 2 hours until result, including a 40 minutes RPA amplification step at 37 °C. This is the first example of using solid-phase RPA for the detection of the big five and represents a milestone towards the developments of an automated point-of-care diagnostic for the big five using RPA.
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Affiliation(s)
- Christopher L Johnson
- Diagnostic and Therapeutic Technologies, Translational and Clinical Research Institute, Newcastle University, Newcastle-Upon-Tyne, UK.
| | - Matthew A Setterfield
- Diagnostic and Therapeutic Technologies, Translational and Clinical Research Institute, Newcastle University, Newcastle-Upon-Tyne, UK.
| | - Waleed A Hassanain
- Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, Glasgow, UK
| | - Anil Wipat
- ICOS, School of Computing, Urban Sciences Building, Newcastle University, Newcastle-Upon-Tyne, UK
| | - Matthew Pocock
- ICOS, School of Computing, Urban Sciences Building, Newcastle University, Newcastle-Upon-Tyne, UK
| | - Karen Faulds
- Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, Glasgow, UK
| | - Duncan Graham
- Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, Glasgow, UK
| | - Neil Keegan
- Diagnostic and Therapeutic Technologies, Translational and Clinical Research Institute, Newcastle University, Newcastle-Upon-Tyne, UK.
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5
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Fram B, Truebridge I, Su Y, Riesselman AJ, Ingraham JB, Passera A, Napier E, Thadani NN, Lim S, Roberts K, Kaur G, Stiffler M, Marks DS, Bahl CD, Khan AR, Sander C, Gauthier NP. Simultaneous enhancement of multiple functional properties using evolution-informed protein design. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.539914. [PMID: 37214973 PMCID: PMC10197589 DOI: 10.1101/2023.05.09.539914] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Designing optimized proteins is important for a range of practical applications. Protein design is a rapidly developing field that would benefit from approaches that enable many changes in the amino acid primary sequence, rather than a small number of mutations, while maintaining structure and enhancing function. Homologous protein sequences contain extensive information about various protein properties and activities that have emerged over billions of years of evolution. Evolutionary models of sequence co-variation, derived from a set of homologous sequences, have proven effective in a range of applications including structure determination and mutation effect prediction. In this work we apply one of these models (EVcouplings) to computationally design highly divergent variants of the model protein TEM-1 β-lactamase, and characterize these designs experimentally using multiple biochemical and biophysical assays. Nearly all designed variants were functional, including one with 84 mutations from the nearest natural homolog. Surprisingly, all functional designs had large increases in thermostability and most had a broadening of available substrates. These property enhancements occurred while maintaining a nearly identical structure to the wild type enzyme. Collectively, this work demonstrates that evolutionary models of sequence co-variation (1) are able to capture complex epistatic interactions that successfully guide large sequence departures from natural contexts, and (2) can be applied to generate functional diversity useful for many applications in protein design.
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Affiliation(s)
- Benjamin Fram
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Ian Truebridge
- Institute for Protein Innovation, Boston, Massachusetts, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School; Boston, MA, USA
- current address: AI Proteins; Boston, MA, USA
| | - Yang Su
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Adam J. Riesselman
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Program in Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - John B. Ingraham
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Alessandro Passera
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- current address: Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Eve Napier
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
| | - Nicole N. Thadani
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Samuel Lim
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Kristen Roberts
- Selux Diagnostics, Inc., 56 Roland Street, Charlestown, MA, USA
| | - Gurleen Kaur
- Selux Diagnostics, Inc., 56 Roland Street, Charlestown, MA, USA
| | - Michael Stiffler
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Debora S. Marks
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Christopher D. Bahl
- Institute for Protein Innovation, Boston, Massachusetts, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School; Boston, MA, USA
- current address: AI Proteins; Boston, MA, USA
| | - Amir R. Khan
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
- Division of Newborn Medicine, Boston Children’s Hospital, Boston, MA, USA
| | - Chris Sander
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Nicholas P. Gauthier
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
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6
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Chudyk EI, Beer M, Limb MAL, Jones CA, Spencer J, van der Kamp MW, Mulholland AJ. QM/MM Simulations Reveal the Determinants of Carbapenemase Activity in Class A β-Lactamases. ACS Infect Dis 2022; 8:1521-1532. [PMID: 35877936 PMCID: PMC9379904 DOI: 10.1021/acsinfecdis.2c00152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Indexed: 11/28/2022]
Abstract
β-lactam antibiotic resistance in Gram-negative bacteria, primarily caused by β-lactamase enzymes that hydrolyze the β-lactam ring, has become a serious clinical problem. Carbapenems were formerly considered "last resort" antibiotics because they escaped breakdown by most β-lactamases, due to slow deacylation of the acyl-enzyme intermediate. However, an increasing number of Gram-negative bacteria now produce β-lactamases with carbapenemase activity: these efficiently hydrolyze the carbapenem β-lactam ring, severely limiting the treatment of some bacterial infections. Here, we use quantum mechanics/molecular mechanics (QM/MM) simulations of the deacylation reactions of acyl-enzyme complexes of eight β-lactamases of class A (the most widely distributed β-lactamase group) with the carbapenem meropenem to investigate differences between those inhibited by carbapenems (TEM-1, SHV-1, BlaC, and CTX-M-16) and those that hydrolyze them (SFC-1, KPC-2, NMC-A, and SME-1). QM/MM molecular dynamics simulations confirm the two enzyme groups to differ in the preferred acyl-enzyme orientation: carbapenem-inhibited enzymes favor hydrogen bonding of the carbapenem hydroxyethyl group to deacylating water (DW). QM/MM simulations of deacylation give activation free energies in good agreement with experimental hydrolysis rates, correctly distinguishing carbapenemases. For the carbapenem-inhibited enzymes, free energies for deacylation are significantly higher than for the carbapenemases, even when the hydroxyethyl group was restrained to prevent interaction with the DW. Analysis of these simulations, and additional simulations of mutant enzymes, shows how factors including the hydroxyethyl orientation, the active site volume, and architecture (conformations of Asn170 and Asn132; organization of the oxyanion hole; and the Cys69-Cys238 disulfide bond) collectively determine catalytic efficiency toward carbapenems.
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Affiliation(s)
- Ewa I. Chudyk
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Michael Beer
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
- School
of Cellular and Molecular Medicine, University
of Bristol Medical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Michael A. L. Limb
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Charlotte A. Jones
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - James Spencer
- School
of Cellular and Molecular Medicine, University
of Bristol Medical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Marc W. van der Kamp
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
- School
of Biochemistry, University of Bristol Medical
Sciences Building, University Walk, Bristol BS8 1TD, United
Kingdom
| | - Adrian J. Mulholland
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
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7
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Kaderabkova N, Bharathwaj M, Furniss RCD, Gonzalez D, Palmer T, Mavridou DAI. The biogenesis of β-lactamase enzymes. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35943884 DOI: 10.1099/mic.0.001217] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The discovery of penicillin by Alexander Fleming marked a new era for modern medicine, allowing not only the treatment of infectious diseases, but also the safe performance of life-saving interventions, like surgery and chemotherapy. Unfortunately, resistance against penicillin, as well as more complex β-lactam antibiotics, has rapidly emerged since the introduction of these drugs in the clinic, and is largely driven by a single type of extra-cytoplasmic proteins, hydrolytic enzymes called β-lactamases. While the structures, biochemistry and epidemiology of these resistance determinants have been extensively characterized, their biogenesis, a complex process including multiple steps and involving several fundamental biochemical pathways, is rarely discussed. In this review, we provide a comprehensive overview of the journey of β-lactamases, from the moment they exit the ribosomal channel until they reach their final cellular destination as folded and active enzymes.
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Affiliation(s)
- Nikol Kaderabkova
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Manasa Bharathwaj
- Centre to Impact AMR, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - R Christopher D Furniss
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Diego Gonzalez
- Laboratoire de Microbiologie, Institut de Biologie, Université de Neuchâtel, Neuchâtel, 2000, Switzerland
| | - Tracy Palmer
- Microbes in Health and Disease, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Despoina A I Mavridou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA.,John Ring LaMontagne Center for Infectious Diseases, The University of Texas at Austin, Austin, Texas, USA
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8
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Kemp MT, Nichols DA, Zhang X, Defrees K, Na I, Renslo AR, Chen Y. Mutation of the conserved Asp-Asp pair impairs the structure, function, and inhibition of CTX-M Class A β-lactamase. FEBS Lett 2021; 595:2981-2994. [PMID: 34704263 DOI: 10.1002/1873-3468.14215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/07/2021] [Accepted: 10/21/2021] [Indexed: 11/07/2022]
Abstract
The Asp233-Asp246 pair is highly conserved in Class A β-lactamases, which hydrolyze β-lactam antibiotics. Here, we characterize its function using CTX-M-14 β-lactamase. The D233N mutant displayed decreased activity that is substrate-dependent, with reductions in kcat /Km ranging from 20% for nitrocefin to 6-fold for cefotaxime. In comparison, the mutation reduced the binding of a known reversible inhibitor by 10-fold. The mutant structures showed movement of the 213-219 loop and the loss of the Thr216-Thr235 hydrogen bond, which was restored by inhibitor binding. Mutagenesis of Thr216 further highlighted its contribution to CTX-M activity. These results demonstrate the importance of the aspartate pair to CTX-M hydrolysis of substrates with bulky side chains, while suggesting increased protein flexibility as a means to evolve drug resistance.
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Affiliation(s)
- M Trent Kemp
- Department of Molecular Medicine, University of South Florida College of Medicine, Tampa, FL, USA
| | - Derek A Nichols
- Department of Molecular Medicine, University of South Florida College of Medicine, Tampa, FL, USA
| | - Xiujun Zhang
- Department of Molecular Medicine, University of South Florida College of Medicine, Tampa, FL, USA
| | - Kyle Defrees
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Insung Na
- Department of Molecular Medicine, University of South Florida College of Medicine, Tampa, FL, USA
| | - Adam R Renslo
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Yu Chen
- Department of Molecular Medicine, University of South Florida College of Medicine, Tampa, FL, USA
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9
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Bahr G, González LJ, Vila AJ. Metallo-β-lactamases in the Age of Multidrug Resistance: From Structure and Mechanism to Evolution, Dissemination, and Inhibitor Design. Chem Rev 2021; 121:7957-8094. [PMID: 34129337 PMCID: PMC9062786 DOI: 10.1021/acs.chemrev.1c00138] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Antimicrobial resistance is one of the major problems in current practical medicine. The spread of genes coding for resistance determinants among bacteria challenges the use of approved antibiotics, narrowing the options for treatment. Resistance to carbapenems, last resort antibiotics, is a major concern. Metallo-β-lactamases (MBLs) hydrolyze carbapenems, penicillins, and cephalosporins, becoming central to this problem. These enzymes diverge with respect to serine-β-lactamases by exhibiting a different fold, active site, and catalytic features. Elucidating their catalytic mechanism has been a big challenge in the field that has limited the development of useful inhibitors. This review covers exhaustively the details of the active-site chemistries, the diversity of MBL alleles, the catalytic mechanism against different substrates, and how this information has helped developing inhibitors. We also discuss here different aspects critical to understand the success of MBLs in conferring resistance: the molecular determinants of their dissemination, their cell physiology, from the biogenesis to the processing involved in the transit to the periplasm, and the uptake of the Zn(II) ions upon metal starvation conditions, such as those encountered during an infection. In this regard, the chemical, biochemical and microbiological aspects provide an integrative view of the current knowledge of MBLs.
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Affiliation(s)
- Guillermo Bahr
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Lisandro J. González
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Alejandro J. Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
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10
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Lizana I, Uribe EA, Delgado EJ. A theoretical approach for the acylation/deacylation mechanisms of avibactam in the reversible inhibition of KPC-2. J Comput Aided Mol Des 2021; 35:943-952. [PMID: 34236545 PMCID: PMC8264174 DOI: 10.1007/s10822-021-00408-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/30/2021] [Indexed: 11/28/2022]
Abstract
Klebsiella pneumoniae carbapenemase (KPC-2) is the most commonly encountered class A β-lactamase variant worldwide, which confer high-level resistance to most available antibiotics. In this article we address the issue by a combined approach involving molecular dynamics simulations and hybrid quantum mechanics/molecular mechanics calculations. The study contributes to improve the understanding, at molecular level, of the acylation and deacylation stages of avibactam involved in the inhibition of KPC-2. The results show that both mechanisms, acylation and deacylation, the reaction occur via the formation of a tetrahedral intermediate. The formation of this intermediate corresponds to the rate limiting stage. The activation barriers are 19.5 kcal/mol and 23.0 kcal/mol for the acylation and deacylation stages, respectively. The associated rate constants calculated, using the Eyring equation, are 1.2 × 10−1 and 3.9 × 10−4 (s−1). These values allow estimating a value of 3.3 × 10−3 for the inhibition constant, in good agreement with the experimental value.
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Affiliation(s)
- Ignacio Lizana
- Grupo QTC, Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile.,Millennium Nucleus on Catalytic Processes Towards Sustainable Chemistry, 4070386, Santiago, Chile
| | - Elena A Uribe
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Eduardo J Delgado
- Grupo QTC, Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile. .,Millennium Nucleus on Catalytic Processes Towards Sustainable Chemistry, 4070386, Santiago, Chile.
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11
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Li QQ, Kang OH, Kwon DY. Study on Demethoxycurcumin as a Promising Approach to Reverse Methicillin-Resistance of Staphylococcus aureus. Int J Mol Sci 2021; 22:ijms22073778. [PMID: 33917423 PMCID: PMC8038695 DOI: 10.3390/ijms22073778] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/31/2021] [Accepted: 04/03/2021] [Indexed: 12/19/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) has always been a threatening pathogen. Research on phytochemical components that can replace antibiotics with limited efficacy may be an innovative method to solve intractable MRSA infections. The present study was devoted to investigate the antibacterial activity of the natural compound demethoxycurcumin (DMC) against MRSA and explore its possible mechanism for eliminating MRSA. The minimum inhibitory concentrations (MICs) of DMC against MRSA strains was determined by the broth microdilution method, and the results showed that the MIC of DMC was 62.5 μg/mL. The synergistic effects of DMC and antibiotics were investigated by the checkerboard method and the time–kill assay. The ATP synthase inhibitors were employed to block the metabolic ability of bacteria to explore their synergistic effect on the antibacterial ability of DMC. In addition, western blot analysis and qRT-PCR were performed to detect the proteins and genes related to drug resistance and S. aureus exotoxins. As results, DMC hindered the translation of penicillin-binding protein 2a (PBP2a) and staphylococcal enterotoxin and reduced the transcription of related genes. This study provides experimental evidences that DMC has the potential to be a candidate substance for the treatment of MRSA infections.
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Affiliation(s)
| | - Ok-Hwa Kang
- Correspondence: (O.-H.K.); (D.-Y.K.); Tel.: +82-63-850-6802 (O.-H.K. & D.-Y.K.)
| | - Dong-Yeul Kwon
- Correspondence: (O.-H.K.); (D.-Y.K.); Tel.: +82-63-850-6802 (O.-H.K. & D.-Y.K.)
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12
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Structural Basis and Binding Kinetics of Vaborbactam in Class A β-Lactamase Inhibition. Antimicrob Agents Chemother 2020; 64:AAC.00398-20. [PMID: 32778546 DOI: 10.1128/aac.00398-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 07/31/2020] [Indexed: 12/20/2022] Open
Abstract
Class A β-lactamases are a major cause of β-lactam resistance in Gram-negative bacteria. The recently FDA-approved cyclic boronate vaborbactam is a reversible covalent inhibitor of class A β-lactamases, including CTX-M extended-spectrum β-lactamase and KPC carbapenemase, both frequently observed in the clinic. Intriguingly, vaborbactam displayed different binding kinetics and cell-based activity for these two enzymes, despite their similarity. A 1.0-Å crystal structure of CTX-M-14 demonstrated that two catalytic residues, K73 and E166, are positively charged and neutral, respectively. Meanwhile, a 1.25-Å crystal structure of KPC-2 revealed a more compact binding mode of vaborbactam versus CTX-M-14, as well as alternative conformations of W105. Together with kinetic analysis of W105 mutants, the structures demonstrate the influence of this residue and the unusual conformation of the β3 strand on the inactivation rate, as well as the stability of the reversible covalent bond with S70. Furthermore, studies of KPC-2 S130G mutant shed light on the different impacts of S130 in the binding of vaborbactam versus avibactam, another recently approved β-lactamase inhibitor. Taken together, these new data provide valuable insights into the inhibition mechanism of vaborbactam and future development of cyclic boronate inhibitors.
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13
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Das CK, Nair NN. Elucidating the Molecular Basis of Avibactam‐Mediated Inhibition of Class A β‐Lactamases. Chemistry 2020; 26:9639-9651. [DOI: 10.1002/chem.202001261] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/10/2020] [Indexed: 12/25/2022]
Affiliation(s)
- Chandan Kumar Das
- Department of ChemistryIndian Institute of Technology Kanpur Kanpur 208016 India
- Current Address: Lehrstuhl für Theoretische ChemieRuhr Universität Bochum 44780 Bochum Germany
| | - Nisanth N. Nair
- Department of ChemistryIndian Institute of Technology Kanpur Kanpur 208016 India
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14
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Mechanism of proton transfer in class A β-lactamase catalysis and inhibition by avibactam. Proc Natl Acad Sci U S A 2020; 117:5818-5825. [PMID: 32123084 DOI: 10.1073/pnas.1922203117] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Gram-negative bacteria expressing class A β-lactamases pose a serious health threat due to their ability to inactivate all β-lactam antibiotics. The acyl-enzyme intermediate is a central milestone in the hydrolysis reaction catalyzed by these enzymes. However, the protonation states of the catalytic residues in this complex have never been fully analyzed experimentally due to inherent difficulties. To help unravel the ambiguity surrounding class A β-lactamase catalysis, we have used ultrahigh-resolution X-ray crystallography and the recently approved β-lactamase inhibitor avibactam to trap the acyl-enzyme complex of class A β-lactamase CTX-M-14 at varying pHs. A 0.83-Å-resolution CTX-M-14 complex structure at pH 7.9 revealed a neutral state for both Lys73 and Glu166. Furthermore, the avibactam hydroxylamine-O-sulfonate group conformation varied according to pH, and this conformational switch appeared to correspond to a change in the Lys73 protonation state at low pH. In conjunction with computational analyses, our structures suggest that Lys73 has a perturbed acid dissociation constant (pKa) compared with acyl-enzyme complexes with β-lactams, hindering its function to deprotonate Glu166 and the initiation of the deacylation reaction. Further NMR analysis demonstrated Lys73 pKa to be ∼5.2 to 5.6. Together with previous ultrahigh-resolution crystal structures, these findings enable us to follow the proton transfer process of the entire acylation reaction and reveal the critical role of Lys73. They also shed light on the stability and reversibility of the avibactam carbamoyl acyl-enzyme complex, highlighting the effect of substrate functional groups in influencing the protonation states of catalytic residues and subsequently the progression of the reaction.
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15
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β-Lactamase of Mycobacterium tuberculosis Shows Dynamics in the Active Site That Increase upon Inhibitor Binding. Antimicrob Agents Chemother 2020; 64:AAC.02025-19. [PMID: 31871087 DOI: 10.1128/aac.02025-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 12/19/2019] [Indexed: 12/11/2022] Open
Abstract
The Mycobacterium tuberculosis β-lactamase BlaC is a broad-spectrum β-lactamase that can convert a range of β-lactam antibiotics. Enzymes with low specificity are expected to exhibit active-site flexibility. To probe the motions in BlaC, we studied the dynamic behavior in solution using nuclear magnetic resonance (NMR) spectroscopy. 15N relaxation experiments show that BlaC is mostly rigid on the pico- to nanosecond timescale. Saturation transfer experiments indicate that also on the high-millisecond timescale BlaC is not dynamic. Using relaxation dispersion experiments, clear evidence was obtained for dynamics in the low-millisecond range, with an exchange rate of ca. 860 s-1 The dynamic amide groups are localized in the active site. Upon formation of an adduct with the inhibitor avibactam, extensive line broadening occurs, indicating an increase in magnitude of the active-site dynamics. Furthermore, the rate of the motions increases significantly. Upon reaction with the inhibitor clavulanic acid, similar line broadening is accompanied by duplication of NMR signals, indicative of at least one additional, slower exchange process (exchange rate, k ex, of <100 s-1), while for this inhibitor also loss of pico- to nanosecond timescale rigidity is observed for some amides in the α domain. Possible sources of the observed dynamics, such as motions in the omega loop and rearrangements of active-site residues, are discussed. The increase in dynamics upon ligand binding argues against a model of inhibitor binding through conformational selection. Rather, the induced dynamics may serve to maximize the likelihood of sampling the optimal conformation for hydrolysis of the bound ligand.
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16
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Langan PS, Sullivan B, Weiss KL, Coates L. Probing the role of the conserved residue Glu166 in a class A β-lactamase using neutron and X-ray protein crystallography. Acta Crystallogr D Struct Biol 2020; 76:118-123. [PMID: 32038042 PMCID: PMC7008513 DOI: 10.1107/s2059798319016334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 12/03/2019] [Indexed: 11/10/2022] Open
Abstract
The amino-acid sequence of the Toho-1 β-lactamase contains several conserved residues in the active site, including Ser70, Lys73, Ser130 and Glu166, some of which coordinate a catalytic water molecule. This catalytic water molecule is essential in the acylation and deacylation parts of the reaction mechanism through which Toho-1 inactivates specific antibiotics and provides resistance to its expressing bacterial strains. To investigate the function of Glu166 in the acylation part of the catalytic mechanism, neutron and X-ray crystallographic studies were performed on a Glu166Gln mutant. The structure of this class A β-lactamase mutant provides several insights into its previously reported reduced drug-binding kinetic rates. A joint refinement of both X-ray and neutron diffraction data was used to study the effects of the Glu166Gln mutation on the active site of Toho-1. This structure reveals that while the Glu166Gln mutation has a somewhat limited impact on the positions of the conserved amino acids within the active site, it displaces the catalytic water molecule from the active site. These subtle changes offer a structural explanation for the previously observed decreases in the binding of non-β-lactam inhibitors such as the recently developed diazobicyclooctane inhibitor avibactam.
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Affiliation(s)
- Patricia S. Langan
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Brendan Sullivan
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Kevin L. Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Leighton Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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17
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18
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Tooke CL, Hinchliffe P, Bragginton EC, Colenso CK, Hirvonen VHA, Takebayashi Y, Spencer J. β-Lactamases and β-Lactamase Inhibitors in the 21st Century. J Mol Biol 2019; 431:3472-3500. [PMID: 30959050 PMCID: PMC6723624 DOI: 10.1016/j.jmb.2019.04.002] [Citation(s) in RCA: 440] [Impact Index Per Article: 88.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 03/27/2019] [Accepted: 04/01/2019] [Indexed: 12/31/2022]
Abstract
The β-lactams retain a central place in the antibacterial armamentarium. In Gram-negative bacteria, β-lactamase enzymes that hydrolyze the amide bond of the four-membered β-lactam ring are the primary resistance mechanism, with multiple enzymes disseminating on mobile genetic elements across opportunistic pathogens such as Enterobacteriaceae (e.g., Escherichia coli) and non-fermenting organisms (e.g., Pseudomonas aeruginosa). β-Lactamases divide into four classes; the active-site serine β-lactamases (classes A, C and D) and the zinc-dependent or metallo-β-lactamases (MBLs; class B). Here we review recent advances in mechanistic understanding of each class, focusing upon how growing numbers of crystal structures, in particular for β-lactam complexes, and methods such as neutron diffraction and molecular simulations, have improved understanding of the biochemistry of β-lactam breakdown. A second focus is β-lactamase interactions with carbapenems, as carbapenem-resistant bacteria are of grave clinical concern and carbapenem-hydrolyzing enzymes such as KPC (class A) NDM (class B) and OXA-48 (class D) are proliferating worldwide. An overview is provided of the changing landscape of β-lactamase inhibitors, exemplified by the introduction to the clinic of combinations of β-lactams with diazabicyclooctanone and cyclic boronate serine β-lactamase inhibitors, and of progress and strategies toward clinically useful MBL inhibitors. Despite the long history of β-lactamase research, we contend that issues including continuing unresolved questions around mechanism; opportunities afforded by new technologies such as serial femtosecond crystallography; the need for new inhibitors, particularly for MBLs; the likely impact of new β-lactam:inhibitor combinations and the continuing clinical importance of β-lactams mean that this remains a rewarding research area.
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Affiliation(s)
- Catherine L Tooke
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Philip Hinchliffe
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Eilis C Bragginton
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Charlotte K Colenso
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Viivi H A Hirvonen
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Yuiko Takebayashi
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom.
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19
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Structural Insights into the Inhibition of the Extended-Spectrum β-Lactamase PER-2 by Avibactam. Antimicrob Agents Chemother 2019; 63:AAC.00487-19. [PMID: 31235626 DOI: 10.1128/aac.00487-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 06/17/2019] [Indexed: 02/07/2023] Open
Abstract
The diazabicyclooctane (DBO) avibactam (AVI) reversibly inactivates most serine-β-lactamases. Previous investigations showed that inhibition constants of AVI toward class A PER-2 are reminiscent of values observed for class C and D β-lactamases (i.e., k 2/K of ≈103 M-1 s-1) but lower than other class A β-lactamases (i.e., k 2/K = 104 to 105 M-1 s-1). Herein, biochemical and structural studies were conducted with PER-2 and AVI to explore these differences. Furthermore, biochemical studies on Arg220 and Thr237 variants with AVI were conducted to gain deeper insight into the mechanism of PER-2 inactivation. The main biochemical and structural observations revealed the following: (i) both amino-acid substitutions in Arg220 and the rich hydrophobic content in the active site hinder the binding of catalytic waters and acylation, impairing AVI inhibition; (ii) movement of Ser130 upon binding of AVI favors the formation of a hydrogen bond with the sulfate group of AVI; and (iii) the Thr237Ala substitution alters the AVI inhibition constants. The acylation constant (k 2/K) of PER-2 by AVI is primarily influenced by stabilizing hydrogen bonds involving AVI and important residues such as Thr237 and Arg220. (Variants in Arg220 demonstrate a dramatic reduction in k 2/K) We also observed that displacement of Ser130 side chain impairs AVI acylation, an observation not made in other extended-spectrum β-lactamases (ESBLs). Comparatively, relebactam combined with a β-lactam is more potent against Escherichia coli producing PER-2 variants than β-lactam-AVI combinations. Our findings provide a rationale for evaluating the utility of the currently available DBO inhibitors against unique ESBLs like PER-2 and anticipate the effectiveness of these inhibitors toward variants that may eventually be selected upon AVI usage.
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20
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Lizana I, Delgado EJ. Molecular Insights on the Release of Avibactam from the Acyl-Enzyme Complex. Biophys J 2019; 116:1650-1657. [PMID: 31010666 DOI: 10.1016/j.bpj.2019.03.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 02/13/2019] [Accepted: 03/06/2019] [Indexed: 02/06/2023] Open
Abstract
Avibactam is a non-β-lactam β-lactamase inhibitor for treating complicated urinary tract and respiratory infections caused by multidrug-resistant bacterial pathogens, a serious public health threat. Despite its importance, the release mechanism of avibactam from the enzyme-inhibitor complex has been scarcely studied from first principles, considering the total protein environment. This information at the molecular level is essential for the rational design of new antibiotics and inhibitors. In this article, we addressed the release of avibactam from the complex CTX-M-15 by means of molecular dynamics simulations and quantum mechanics/molecular mechanics calculations. This study provides molecular information not available earlier, including exploration of the potential energy surfaces, characterization of the observed intermediate, and their critical points, as well. Our results show that unlike that observed in the acylation reaction, the residues Glu166 and Lys73 would be in their neutral forms. Release of avibactam follows a stepwise mechanism in which the first stage corresponds to the formation of a tetrahedral intermediate, whereas the second stage corresponds to the cleavage of the Ser70-C7 bond, mediated by Lys73, either directly or through Ser130.
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Affiliation(s)
- Ignacio Lizana
- Departament of Physical Chemistry, Universidad de Concepción, Concepción, Chile
| | - Eduardo J Delgado
- Departament of Physical Chemistry, Universidad de Concepción, Concepción, Chile; Millenium Nucleus on Catalytic Processes toward Sustainable Chemistry, Santiago, Chile.
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21
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The Neutron Macromolecular Crystallography Instruments at Oak Ridge National Laboratory: Advances, Challenges, and Opportunities. CRYSTALS 2018. [DOI: 10.3390/cryst8100388] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The IMAGINE and MaNDi instruments, located at Oak Ridge National Laboratory High Flux Isotope Reactor and Spallation Neutron Source, respectively, are powerful tools for determining the positions of hydrogen atoms in biological macromolecules and their ligands, orienting water molecules, and for differentiating chemical states in macromolecular structures. The possibility to model hydrogen and deuterium atoms in neutron structures arises from the strong interaction of neutrons with the nuclei of these isotopes. Positions can be unambiguously assigned from diffraction studies at the 1.5–2.5 Å resolutions, which are typical for protein crystals. Neutrons have the additional benefit for structural biology of not inducing radiation damage to protein crystals, which can be critical in the study of metalloproteins. Here we review the specifications of the IMAGINE and MaNDi beamlines and illustrate their complementarity. IMAGINE is suitable for crystals with unit cell edges up to 150 Å using a quasi-Laue technique, whereas MaNDi provides neutron crystallography resources for large unit cell samples with unit cell edges up to 300 Å using the time of flight (TOF) Laue technique. The microbial culture and crystal growth facilities which support the IMAGINE and MaNDi user programs are also described.
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22
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Kwon H, Langan PS, Coates L, Raven EL, Moody PCE. The rise of neutron cryo-crystallography. Acta Crystallogr D Struct Biol 2018; 74:792-799. [PMID: 30082515 PMCID: PMC6079629 DOI: 10.1107/s205979831800640x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 04/25/2018] [Indexed: 11/10/2022] Open
Abstract
The use of boiled-off liquid nitrogen to maintain protein crystals at 100 K during X-ray data collection has become almost universal. Applying this to neutron protein crystallography offers the opportunity to significantly broaden the scope of biochemical problems that can be addressed, although care must be taken in assuming that direct extrapolation to room temperature is always valid. Here, the history to date of neutron protein cryo-crystallography and the particular problems and solutions associated with the mounting and cryocooling of the larger crystals needed for neutron crystallography are reviewed. Finally, the outlook for further cryogenic neutron studies using existing and future neutron instrumentation is discussed.
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Affiliation(s)
- Hanna Kwon
- Henry Wellcome Laboratories for Structural Biology, Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Lancaster Road, Leicester LE1 7RH, England
| | - Patricia S. Langan
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Leighton Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Emma L. Raven
- Leicester Institute of Structural and Chemical Biology, Department of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, England
| | - Peter C. E. Moody
- Henry Wellcome Laboratories for Structural Biology, Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Lancaster Road, Leicester LE1 7RH, England
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23
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Neutron macromolecular crystallography. Emerg Top Life Sci 2018; 2:39-55. [DOI: 10.1042/etls20170083] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/12/2017] [Accepted: 12/19/2017] [Indexed: 01/02/2023]
Abstract
Neutron diffraction techniques permit direct determination of the hydrogen (H) and deuterium (D) positions in crystal structures of biological macromolecules at resolutions of ∼1.5 and 2.5 Å, respectively. In addition, neutron diffraction data can be collected from a single crystal at room temperature without radiation damage issues. By locating the positions of H/D-atoms, protonation states and water molecule orientations can be determined, leading to a more complete understanding of many biological processes and drug-binding. In the last ca. 5 years, new beamlines have come online at reactor neutron sources, such as BIODIFF at Heinz Maier-Leibnitz Zentrum and IMAGINE at Oak Ridge National Laboratory (ORNL), and at spallation neutron sources, such as MaNDi at ORNL and iBIX at the Japan Proton Accelerator Research Complex. In addition, significant improvements have been made to existing beamlines, such as LADI-III at the Institut Laue-Langevin. The new and improved instrumentations are allowing sub-mm3 crystals to be regularly used for data collection and permitting the study of larger systems (unit-cell edges >100 Å). Owing to this increase in capacity and capability, many more studies have been performed and for a wider range of macromolecules, including enzymes, signalling proteins, transport proteins, sugar-binding proteins, fluorescent proteins, hormones and oligonucleotides; of the 126 structures deposited in the Protein Data Bank, more than half have been released since 2013 (65/126, 52%). Although the overall number is still relatively small, there are a growing number of examples for which neutron macromolecular crystallography has provided the answers to questions that otherwise remained elusive.
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24
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Langan PS, Vandavasi VG, Cooper CJ, Weiss KL, Ginell SL, Parks JM, Coates L. Substrate Binding Induces Conformational Changes in a Class A β-lactamase That Prime It for Catalysis. ACS Catal 2018. [DOI: 10.1021/acscatal.7b04114] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Patricia S. Langan
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Venu Gopal Vandavasi
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Connor J. Cooper
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Kevin L. Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Stephan L. Ginell
- Structural Biology Center, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - Jerry M. Parks
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, United States
| | - Leighton Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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25
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Hussein R, Ibrahim M, Chatterjee R, Coates L, Müh F, Yachandra VK, Yano J, Kern J, Dobbek H, Zouni A. Optimizing Crystal Size of Photosystem II by Macroseeding: Toward Neutron Protein Crystallography. CRYSTAL GROWTH & DESIGN 2018; 18:85-94. [PMID: 29962903 PMCID: PMC6020701 DOI: 10.1021/acs.cgd.7b00878] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Photosystem II (PSII) catalyzes the photo-oxidation of water to molecular oxygen and protons. The water splitting reaction occurs inside the oxygen-evolving complex (OEC) via a Mn4CaO5 cluster. To elucidate the reaction mechanism, detailed structural information for each intermediate state of the OEC is required. Despite the current high-resolution crystal structure of PSII at 1.85 Å and other efforts to follow the structural changes of the Mn4CaO5 cluster using X-ray free electron laser (XFEL) crystallography in addition to spectroscopic methods, many details about the reaction mechanism and conformational changes in the catalytic site during water oxidation still remain elusive. In this study, we present a rarely found successful application of the conventional macroseeding method to a large membrane protein like the dimeric PSII core complex (dPSIIcc). Combining microseeding with macroseeding crystallization techniques allowed us to reproducibly grow large dPSIIcc crystals with a size of ~3 mm. These large crystals will help improve the data collected from spectroscopic methods like polarized extended X-ray absorption fine structure (EXAFS) and single crystal electron paramagnetic resonance (EPR) techniques and are a prerequisite for determining a three-dimensional structure using neutron diffraction.
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Affiliation(s)
- Rana Hussein
- Institut für Biologie, Humboldt-Universität zu Berlin, Unter den Linden 6, D-10099 Berlin, Germany
- Corresponding Authors: (R.H.) Phone; +49 30 2093 47933; . (A.Z.) Phone: +49 30 2093 47930;
| | - Mohamed Ibrahim
- Institut für Biologie, Humboldt-Universität zu Berlin, Unter den Linden 6, D-10099 Berlin, Germany
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Leighton Coates
- Neutron Scattering Science Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Frank Müh
- Institute of Theoretical Physics, Johannes Kepler University Linz, Linz, Austria
| | - Vittal K. Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Holger Dobbek
- Institut für Biologie, Humboldt-Universität zu Berlin, Unter den Linden 6, D-10099 Berlin, Germany
| | - Athina Zouni
- Institut für Biologie, Humboldt-Universität zu Berlin, Unter den Linden 6, D-10099 Berlin, Germany
- Corresponding Authors: (R.H.) Phone; +49 30 2093 47933; . (A.Z.) Phone: +49 30 2093 47930;
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González-Bello C. Antibiotic adjuvants - A strategy to unlock bacterial resistance to antibiotics. Bioorg Med Chem Lett 2017; 27:4221-4228. [PMID: 28827113 DOI: 10.1016/j.bmcl.2017.08.027] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 08/08/2017] [Accepted: 08/13/2017] [Indexed: 12/11/2022]
Abstract
Resistance to available antibiotics in pathogenic bacteria is currently a global challenge since the number of strains that are resistant to multiple types of antibiotics has increased dramatically each year and has spread worldwide. To unlock this problem, the use of an 'antibiotic adjuvant' in combination with an antibiotic is now being exploited. This approach enables us to prolong the lifespan of these life-saving drugs. This digests review provides an overview of the main types of antibiotic adjuvants, the basis of their operation and the remaining issues to be tackled in this field. Particular emphasis is placed on those compounds that are already in clinical development, namely β-lactamase inhibitors.
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Affiliation(s)
- Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain.
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27
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Pan X, He Y, Lei J, Huang X, Zhao Y. Crystallographic Snapshots of Class A β-Lactamase Catalysis Reveal Structural Changes That Facilitate β-Lactam Hydrolysis. J Biol Chem 2017; 292:4022-4033. [PMID: 28100776 DOI: 10.1074/jbc.m116.764340] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 12/22/2016] [Indexed: 11/06/2022] Open
Abstract
β-Lactamases confer resistance to β-lactam-based antibiotics. There is great interest in understanding their mechanisms to enable the development of β-lactamase-specific inhibitors. The mechanism of class A β-lactamases has been studied extensively, revealing Lys-73 and Glu-166 as general bases that assist the catalytic residue Ser-70. However, the specific roles of these two residues within the catalytic cycle remain not fully understood. To help resolve this, we first identified an E166H mutant that is functional but is kinetically slow. We then carried out time-resolved crystallographic study of a full cycle of the catalytic reaction. We obtained structures that represent apo, ES*-acylation, and ES*-deacylation states and analyzed the conformational changes of His-166. The "in" conformation in the apo structure allows His-166 to form a hydrogen bond with Lys-73. The unexpected "flipped-out" conformation of His-166 in the ES*-acylation structure was further examined by molecular dynamics simulations, which suggested deprotonated Lys-73 serving as the general base for acylation. The "revert-in" conformation in the ES*-deacylation structure aligns His-166 toward the water molecule that hydrolyzes the acyl adduct. Finally, when the acyl adduct is fully hydrolyzed, His-166 rotates back to the "in" conformation of the apo-state, restoring the Lys-73/His-166 interaction. Using His-166 as surrogate, our study identifies distinct conformational changes within the active site during catalysis. We suggest that the native Glu-166 executes similar changes in a less constricted way. Taken together, this structural series improves our understanding of β-lactam hydrolysis in this important class of enzymes.
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Affiliation(s)
- Xuehua Pan
- From the Department of Applied Biology and Chemical Technology, State Key Laboratory of Chirosciences, Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong.,the Shenzhen Research Institute, Hong Kong Polytechnic University, Shenzhen, and
| | - Yunjiao He
- From the Department of Applied Biology and Chemical Technology, State Key Laboratory of Chirosciences, Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Jinping Lei
- the Department of Chemistry, Center of Systems Biology and Human Health, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Xuhui Huang
- the Department of Chemistry, Center of Systems Biology and Human Health, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Yanxiang Zhao
- From the Department of Applied Biology and Chemical Technology, State Key Laboratory of Chirosciences, Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong,
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