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Mhaidat I, Banidomi S, Wedian F, Badarneh R, Tashtoush H, Almomani W, Al-Mazaideh GM, Alharbi NS, Thiruvengadam M. Antioxidant and antibacterial activities of 5-mercapto(substitutedthio)-4-substituted-1,2,4-triazol based on nalidixic acid: A comprehensive study on its synthesis, characterization, and In silico evaluation. Heliyon 2024; 10:e28204. [PMID: 38571635 PMCID: PMC10987910 DOI: 10.1016/j.heliyon.2024.e28204] [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: 12/28/2023] [Revised: 03/13/2024] [Accepted: 03/13/2024] [Indexed: 04/05/2024] Open
Abstract
This study introduces a series of novel Alkyl thio-1,2,4-triazole (4a-p) and mercapto-1,2,4-triazole (3a-d) compounds derived from nalidixic acid. The synthesis was streamlined, involving interactions between nalidixic acid hydrazide and various isothiocyanates to yield cyclic and alkyl(aryl) sulfide compounds, characterized using 1H NMR, 13C NMR, IR, and elemental analysis. Antioxidant capabilities were quantified through DPPH and ABTS assays, highlighting significant potential, especially for compound 3d, which demonstrated an ABTS IC50 value of 0.397 μM, on par with ascorbic acid (IC50 = 0.87 μM). Antibacterial efficacy was established through MIC assessments against a broad spectrum of Gram-positive and Gram-negative bacteria, including Candida albicans. Compounds 3b, 4e, 4h, 4j, 4i, 4m, and 4o showed broad-spectrum activity, with 4k and 4m exhibiting pronounced potency against E. coli. Molecular docking studies validated the antibacterial potential, with compounds 4f and 4h showing high binding affinities (docking scores of -9.8 and -9.6 kcal/mol, respectively), indicating robust interactions with the bacterial enzyme targets. These scores underscore the compounds' mechanistic basis for their antibacterial action and support their therapeutic promise. Furthermore, compounds 3b, 4i, and 4m, identified through drug-likeness and toxicity predictions, were highlighted for their favorable profiles, suggesting their suitability for oral antibiotic therapies. This comprehensive study, blending synthetic, in vitro, and in silico approaches, emphasizes the triazole derivatives' potential as future candidates for antibiotic and antioxidant applications, particularly spotlighting compounds 3b, 4i, and 4m due to their promising efficacy and safety profiles.
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Affiliation(s)
- Ibrahim Mhaidat
- Department of Chemistry, Faculty of Sciences, Yarmouk University, Irbid, 21163, Jordan
| | - Sojoud Banidomi
- Department of Chemistry, Faculty of Sciences, Yarmouk University, Irbid, 21163, Jordan
| | - Fadel Wedian
- Department of Chemistry, Faculty of Sciences, Yarmouk University, Irbid, 21163, Jordan
| | - Rahaf Badarneh
- Department of Chemistry, Faculty of Sciences, Yarmouk University, Irbid, 21163, Jordan
| | - Hasan Tashtoush
- Department of Chemistry, Faculty of Sciences, Yarmouk University, Irbid, 21163, Jordan
| | - Waleed Almomani
- Department of Basic Medical Sciences, Faculty of Medicine, Yarmouk University, Irbid, 21163, Jordan
| | - Ghassab M. Al-Mazaideh
- Department of Chemistry and Chemical Technology, Tafila Technical University, Tafila, Jordan
| | - Naiyf S. Alharbi
- Department of Botany and Microbiology, College of Science, King Saud University, P. O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Muthu Thiruvengadam
- Department of Crop Science, College of Sanghuh Life Sciences, Konkuk University, Seoul, 05029, South Korea
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2
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Kongkham B, Yadav A, Ojha MD, Prabakaran D, P H. In vitro and computational studies of the β-lactamase inhibition and β-lactam potentiating properties of plant secondary metabolites. J Biomol Struct Dyn 2023; 41:10326-10346. [PMID: 36510677 DOI: 10.1080/07391102.2022.2154843] [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: 07/05/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022]
Abstract
β-lactam resistance in bacteria is primarily mediated through the production of β-lactamases. Among the several strategies explored to mitigate the issue of β-lactam resistance, the use of plant secondary metabolites in combination with existing β-lactams seem promising. The present study aims to identify possible β-lactam potentiating plant secondary metabolites following in vitro and in silico approaches. Among 180 extracts from selected 30 medicinal plants, acetone extract of Ficus religiosa (FRAE) bark recorded the least IC50 value of 3.9 mg/ml. Under in vitro conditions, FRAE potentiated the activity of ampicillin, which was evidenced by the significant reduction in IC50 values of ampicillin against multidrug resistant bacteria. Metabolic profiling following HR-LCMS analysis revealed the presence of diverse metabolites viz. flavonoids, alkaloids, terpenoids, etc. in FRAE. Further, ensemble docking of the FRAE metabolites against four Class A β-lactamase (SHV1, TEM1, KPC2 and CTX-M-27) showed quercetin, taxifolin, myricetin, luteolin, and miquelianin as potential inhibitors with the least average binding energy. In molecular dynamic simulation studies, myricetin formed the most stable complex with SHV1 and KPC-2 while miquelianin with TEM1 and CTX-M-27. Further, all five metabolites interacted with amino acid residue Glu166 in Ω loop of β-lactamase, interfering with the deacylation step, thereby disrupting the enzyme activity. The pharmacokinetics and ADMET profile indicate their drug-likeness and non-toxic nature, making them ideal β-lactam potentiators. This study highlights the ability of metabolites present in FRAE to act as β-lactamase inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bhani Kongkham
- Environmental Biotechnology Lab, Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, India
| | - Ajay Yadav
- Environmental Biotechnology Lab, Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, India
| | - Monu Dinesh Ojha
- Environmental Biotechnology Lab, Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, India
| | - Duraivadivel Prabakaran
- Environmental Biotechnology Lab, Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, India
| | - Hariprasad P
- Environmental Biotechnology Lab, Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, India
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3
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Gato E, Guijarro-Sánchez P, Alonso-García I, Pedraza-Merino R, Conde A, Lence E, Rumbo-Feal S, Peña-Escolano A, Lasarte-Monterrubio C, Blanco-Martín T, Fernández-González A, Fernández-López MDC, Maceiras R, Martínez-Guitián M, Vázquez-Ucha JC, Martínez-Martínez L, González-Bello C, Arca-Suárez J, Beceiro A, Bou G. In vitro development of imipenem/relebactam resistance in KPC-producing Klebsiella pneumoniae involves multiple mutations including OmpK36 disruption and KPC modification. Int J Antimicrob Agents 2023; 62:106935. [PMID: 37541530 DOI: 10.1016/j.ijantimicag.2023.106935] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 05/08/2023] [Accepted: 07/21/2023] [Indexed: 08/06/2023]
Abstract
OBJECTIVES In order to inform and anticipate potential strategies aimed at combating KPC-producing Klebsiella pneumoniae infections, we analysed imipenem/relebactam and ceftazidime/avibactam single-step mutant frequencies, resistance development trajectories, differentially selected resistance mechanisms and their associated fitness cost using four representative high-risk K. pneumoniae clones. METHODS Mutant frequencies and mutant preventive concentrations were determined using agar plates containing incremental concentrations of β-lactam/β-lactamase inhibitor. Resistance dynamics were determined through incubation for 7 days in 10 mL MH tubes containing incremental concentrations of each antibiotic combination up to their 64 × baseline MIC. Two colonies per strain from each experiment were characterized by antimicrobial susceptibility testing, whole genome sequencing and competitive growth assays (to determine in vitro fitness). KPC variants associated with imipenem/relebactam resistance were characterized by cloning and biochemical experiments, atomic models and molecular dynamics simulation studies. RESULTS Imipenem/relebactam prevented the emergence of single-step resistance mutants at lower concentrations than ceftazidime/avibactam. In three of the four strains evaluated, imipenem/relebactam resistance development emerged more rapidly, and in the ST512/KPC-3 clone reached higher levels compared to baseline MICs than for ceftazidime/avibactam. Lineages evolved in the presence of ceftazidime/avibactam showed KPC substitutions associated with high-level ceftazidime/avibactam resistance, increased imipenem/relebactam susceptibility and low fitness costs. Lineages that evolved in the presence of imipenem/relebactam showed OmpK36 disruption, KPC modifications (S106L, N132S, L167R) and strain-specific substitutions associated with imipenem/relebactam resistance and high fitness costs. Imipenem/relebactam-selected KPC derivatives demonstrated enhanced relebactam resistance through important changes affecting relebactam recognition and positioning. CONCLUSIONS Our findings anticipate potential resistance mechanisms affecting imipenem/relebactam during treatment of KPC-producing K. pneumoniae infections.
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Affiliation(s)
- Eva Gato
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario, Universitario A Coruña, A Coruña, Spain
| | - Paula Guijarro-Sánchez
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario, Universitario A Coruña, A Coruña, Spain
| | - Isaac Alonso-García
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario, Universitario A Coruña, A Coruña, Spain
| | - Rosa Pedraza-Merino
- Unidad de Microbiología, Hospital Universitario Reina Sofía, Departamento de Química Agrícola, Edafología y Microbiología, Universidad de Córdoba, e Instituto Maimonides de Investigación Biomédica de Córdoba (IMIBIC), España
| | - Adrian Conde
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Emilio Lence
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Soraya Rumbo-Feal
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario, Universitario A Coruña, A Coruña, Spain
| | - Andrea Peña-Escolano
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario, Universitario A Coruña, A Coruña, Spain
| | - Cristina Lasarte-Monterrubio
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario, Universitario A Coruña, A Coruña, Spain
| | - Tania Blanco-Martín
- Unidad de Microbiología, Hospital Universitario Reina Sofía, Departamento de Química Agrícola, Edafología y Microbiología, Universidad de Córdoba, e Instituto Maimonides de Investigación Biomédica de Córdoba (IMIBIC), España
| | - Ana Fernández-González
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario, Universitario A Coruña, A Coruña, Spain
| | - M Del Carmen Fernández-López
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario, Universitario A Coruña, A Coruña, Spain
| | - Romina Maceiras
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario, Universitario A Coruña, A Coruña, Spain
| | - Marta Martínez-Guitián
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario, Universitario A Coruña, A Coruña, Spain; NANOBIOFAR, Centro de Investigación en Medicina Molecular y Enfermedades Crónicas (CiMUS), Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Juan Carlos Vázquez-Ucha
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario, Universitario A Coruña, A Coruña, Spain; Ciber de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Luis Martínez-Martínez
- Unidad de Microbiología, Hospital Universitario Reina Sofía, Departamento de Química Agrícola, Edafología y Microbiología, Universidad de Córdoba, e Instituto Maimonides de Investigación Biomédica de Córdoba (IMIBIC), España; Ciber de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Jorge Arca-Suárez
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario, Universitario A Coruña, A Coruña, Spain; Ciber de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain.
| | - Alejandro Beceiro
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario, Universitario A Coruña, A Coruña, Spain; Ciber de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Germán Bou
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario, Universitario A Coruña, A Coruña, Spain; Ciber de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
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4
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Tooke C, Hinchliffe P, Beer M, Zinovjev K, Colenso CK, Schofield CJ, Mulholland AJ, Spencer J. Tautomer-Specific Deacylation and Ω-Loop Flexibility Explain the Carbapenem-Hydrolyzing Broad-Spectrum Activity of the KPC-2 β-Lactamase. J Am Chem Soc 2023; 145:7166-7180. [PMID: 36972204 PMCID: PMC10080687 DOI: 10.1021/jacs.2c12123] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Indexed: 03/29/2023]
Abstract
KPC-2 (Klebsiella pneumoniae carbapenemase-2) is a globally disseminated serine-β-lactamase (SBL) responsible for extensive β-lactam antibiotic resistance in Gram-negative pathogens. SBLs inactivate β-lactams via a mechanism involving a hydrolytically labile covalent acyl-enzyme intermediate. Carbapenems, the most potent β-lactams, evade the activity of many SBLs by forming long-lived inhibitory acyl-enzymes; however, carbapenemases such as KPC-2 efficiently deacylate carbapenem acyl-enzymes. We present high-resolution (1.25-1.4 Å) crystal structures of KPC-2 acyl-enzymes with representative penicillins (ampicillin), cephalosporins (cefalothin), and carbapenems (imipenem, meropenem, and ertapenem) obtained utilizing an isosteric deacylation-deficient mutant (E166Q). The mobility of the Ω-loop (residues 165-170) negatively correlates with antibiotic turnover rates (kcat), highlighting the role of this region in positioning catalytic residues for efficient hydrolysis of different β-lactams. Carbapenem-derived acyl-enzyme structures reveal the predominance of the Δ1-(2R) imine rather than the Δ2 enamine tautomer. Quantum mechanics/molecular mechanics molecular dynamics simulations of KPC-2:meropenem acyl-enzyme deacylation used an adaptive string method to differentiate the reactivity of the two isomers. These identify the Δ1-(2R) isomer as having a significantly (7 kcal/mol) higher barrier than the Δ2 tautomer for the (rate-determining) formation of the tetrahedral deacylation intermediate. Deacylation is therefore likely to proceed predominantly from the Δ2, rather than the Δ1-(2R) acyl-enzyme, facilitated by tautomer-specific differences in hydrogen-bonding networks involving the carbapenem C-3 carboxylate and the deacylating water and stabilization by protonated N-4, accumulating a negative charge on the Δ2 enamine-derived oxyanion. Taken together, our data show how the flexible Ω-loop helps confer broad-spectrum activity upon KPC-2, while carbapenemase activity stems from efficient deacylation of the Δ2-enamine acyl-enzyme tautomer.
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Affiliation(s)
- Catherine
L. Tooke
- School
of Cellular and Molecular Medicine, Biomedical Sciences
Building, University Walk, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Philip Hinchliffe
- School
of Cellular and Molecular Medicine, Biomedical Sciences
Building, University Walk, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Michael Beer
- School
of Cellular and Molecular Medicine, Biomedical Sciences
Building, University Walk, University of Bristol, Bristol BS8 1TD, United Kingdom
- Centre
for Computational Chemistry, School of Chemistry, Cantock’s
Close, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Kirill Zinovjev
- School
of Biochemistry, Biomedical Sciences Building, University
Walk, University of Bristol, Bristol BS8 1TD, United Kingdom
- Departamento
de Química Física, Universitat
de València, Burjassot 46100, Comunitat Valenciana, Spain
| | - Charlotte K. Colenso
- School
of Cellular and Molecular Medicine, Biomedical Sciences
Building, University Walk, University of Bristol, Bristol BS8 1TD, United Kingdom
- Centre
for Computational Chemistry, School of Chemistry, Cantock’s
Close, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Christopher J. Schofield
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, Mansfield Road, University of Oxford, Oxford OX1 3TA United
Kingdom
| | - Adrian J. Mulholland
- Centre
for Computational Chemistry, School of Chemistry, Cantock’s
Close, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - James Spencer
- School
of Cellular and Molecular Medicine, Biomedical Sciences
Building, University Walk, University of Bristol, Bristol BS8 1TD, United Kingdom
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5
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Yin C, Song Z, Tian H, Palzkill T, Tao P. Unveiling the structural features that regulate carbapenem deacylation in KPC-2 through QM/MM and interpretable machine learning. Phys Chem Chem Phys 2023; 25:1349-1362. [PMID: 36537692 PMCID: PMC11162551 DOI: 10.1039/d2cp03724f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Resistance to carbapenem β-lactams presents major clinical and economical challenges for the treatment of pathogen infections. The fast hydrolysis of carbapenems by carbapenemase-producing bacterial strains enables the effective deactivation of carbapenem antibiotics. In this study, we aim to unravel the structural features that distinguish the notable deacylation activity of carbapenemases. The deacylation reactions between imipenem (IPM) and the KPC-2 class A serine-based β-lactamases (ASβLs) are modeled with combined quantum mechanical/molecular mechanical (QM/MM) minimum energy pathway (MEP) calculations and interpretable machine-learning (ML) methods. We first applied a dual-level computational protocol to achieve fast sampling of QM/MM MEPs. A tree-based ensemble ML model was employed to learn the MEP activation barriers from the conformational features of the KPC-2/IPM active site. The barrier-predicting model was then unboxed using the Shapley additive explanation (SHAP) importance attribution methods to derive mechanistic insights, which were also verified by additional QM/MM wavefunction analysis. Essentially, we show that potential hydrogen bonding interactions of the general base and the tautomerization states of the carbapenem pyrroline ring could concertedly regulate the activation barrier of KPC-2/IPM deacylation. Nonetheless, we demonstrate the efficacy of interpretable ML to assist the analysis of QM/MM simulation data for robust extraction of human-interpretable mechanistic insights.
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Affiliation(s)
- Chao Yin
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, 75205, USA.
| | - Zilin Song
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, 75205, USA.
| | - Hao Tian
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, 75205, USA.
| | - Timothy Palzkill
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Peng Tao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, 75205, USA.
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6
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Zhou J, Stapleton P, Xavier-Junior FH, Schatzlein A, Haider S, Healy J, Wells G. Triazole-substituted phenylboronic acids as tunable lead inhibitors of KPC-2 antibiotic resistance. Eur J Med Chem 2022; 240:114571. [DOI: 10.1016/j.ejmech.2022.114571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 11/04/2022]
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7
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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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8
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Amereh S, Kelishomi FZ, Ghayaz F, Javadi A, Peymani A, Fardsanei F, Aali E, Nikkhahi F. Activity of meropenem-vaborbactam against different beta-lactamase producing Klebsiella pneumoniae and Escherichia coli isolates in Iran. Acta Microbiol Immunol Hung 2022; 69:201-208. [PMID: 35895481 DOI: 10.1556/030.2022.01782] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 06/01/2022] [Indexed: 11/19/2022]
Abstract
We evaluated the activity of meropenem-vaborbactam against different beta-lactamase producing Klebsiella pneumoniae and Escherichia coli isolates. In our study antibiotic susceptibility testing, double disk synergy test, modified Hodge test were applied. Detection of ESBL, AmpC, and carbapenemase genes was performed by PCR. Multilocus sequence typing (MLST) analysis was done on OXA-48 producing K. pneumoniae strains. Our results showed that among E. coli and K. pneumoniae isolates, 41.1% and 40% of strains produced ESBL, respectively. Additionally, the prevalence of AmpC producing K. pneumoniae and E. coli was 4% and 45.5%, respectively. Altogether 64.2% of K. pneumoniae strains and one E. coli isolate produced carbapenemase. Among OXA-48 producing K. pneumoniae strains ST3500 and ST2528 were detected by MLST. Based on the phenotypic results of this study, vaborbactam was an effective inhibitor on the third-generation cephalosporin-resistant isolates (P < 0.0001). Meropenem-vaborbactam combination had the highest efficacy on KPC producing strains, and it had limited activity on isolates producing OXA-48 type beta-lactamases, whereas no effect was observed on NDM-1 producing isolates. Our study provided valuable information regarding the vaborbactam inhibitory effect on β-lactamase-producing strains.
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Affiliation(s)
- Samira Amereh
- 1 Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | | | - Fatemeh Ghayaz
- 1 Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Amir Javadi
- 2 Community Medicine Department, School of Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Amir Peymani
- 1 Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Fatemeh Fardsanei
- 1 Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Ehsan Aali
- 3 Social Determinants of Health Research Center, Research Institute for Prevention of Non-Communicable Diseases, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Farhad Nikkhahi
- 1 Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
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9
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Penicillanic Acid Sulfones Inactivate the Extended-Spectrum β-Lactamase CTX-M-15 through Formation of a Serine-Lysine Cross-Link: an Alternative Mechanism of β-Lactamase Inhibition. mBio 2022; 13:e0179321. [PMID: 35612361 PMCID: PMC9239225 DOI: 10.1128/mbio.01793-21] [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] [Indexed: 11/21/2022] Open
Abstract
β-Lactamases hydrolyze β-lactam antibiotics and are major determinants of antibiotic resistance in Gram-negative pathogens. Enmetazobactam (formerly AAI101) and tazobactam are penicillanic acid sulfone (PAS) β-lactamase inhibitors that differ by an additional methyl group on the triazole ring of enmetazobactam, rendering it zwitterionic. In this study, ultrahigh-resolution X-ray crystal structures and mass spectrometry revealed the mechanism of PAS inhibition of CTX-M-15, an extended-spectrum β-lactamase (ESBL) globally disseminated among Enterobacterales. CTX-M-15 crystals grown in the presence of enmetazobactam or tazobactam revealed loss of the Ser70 hydroxyl group and formation of a lysinoalanine cross-link between Lys73 and Ser70, two residues critical for catalysis. Moreover, the residue at position 70 undergoes epimerization, resulting in formation of a d-amino acid. Cocrystallization of enmetazobactam or tazobactam with CTX-M-15 with a Glu166Gln mutant revealed the same cross-link, indicating that this modification is not dependent on Glu166-catalyzed deacylation of the PAS-acylenzyme. A cocrystal structure of enmetazobactam with CTX-M-15 with a Lys73Ala mutation indicates that epimerization can occur without cross-link formation and positions the Ser70 Cβ closer to Lys73, likely facilitating formation of the Ser70-Lys73 cross-link. A crystal structure of a tazobactam-derived imine intermediate covalently linked to Ser70, obtained after 30 min of exposure of CTX-M-15 crystals to tazobactam, supports formation of an initial acylenzyme by PAS inhibitors on reaction with CTX-M-15. These data rationalize earlier results showing CTX-M-15 deactivation by PAS inhibitors to involve loss of protein mass, and they identify a distinct mechanism of β-lactamase inhibition by these agents.
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10
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Zhang NN, Bai X, Zhao SS, Zheng XM, Tang L, Yang SG, Zhang JQ. Computational study reveals substituted benzimidazole derivatives' binding selectivity to PI3Kδ and PI3Kγ. J Mol Model 2022; 28:123. [PMID: 35438328 DOI: 10.1007/s00894-022-05096-w] [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: 08/27/2021] [Accepted: 03/15/2022] [Indexed: 11/27/2022]
Abstract
Phosphatidylinositol 3-kinase (PI3K) is a key regulatory kinase in the PI3K/AKT/mTOR signaling pathway, which is involved in the regulation of cell proliferation, differentiation, apoptosis, and angiogenesis. Class IA PI3K isoforms γ and δ share a highly homologous ATP binding site and are distinguished by only a few residues around the binding site. Subtype-selective inhibitors have been proven to have great advantages in tumor treatment. Preliminary studies have obtained PI3K inhibitors bearing a benzimidazole structural motif with a certain selectivity for PI3Kδ and PI3Kγ subtypes. On this basis, we investigated the selective inhibitory mechanism of PI3Kδ and PI3Kγ using four developed inhibitors via molecular docking, molecular dynamics, binding free energy calculations, and residue energy decomposition. This study could provide references for the further development of PI3K-isoform-selective inhibitors.
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Affiliation(s)
- Na-Na Zhang
- State Key Laboratory of Functions and Applications of Medicinal Plants, College of Pharmacy, Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, Guizhou Medical University, Guiyang, 550025, China
| | - Xue Bai
- Pharmacy Department of Guizhou Provincial People's Hospital, Guiyang, 55000, China
| | - Shan-Shan Zhao
- State Key Laboratory of Functions and Applications of Medicinal Plants, College of Pharmacy, Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, Guizhou Medical University, Guiyang, 550025, China
| | - Xue-Mei Zheng
- State Key Laboratory of Functions and Applications of Medicinal Plants, College of Pharmacy, Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, Guizhou Medical University, Guiyang, 550025, China
| | - Lei Tang
- State Key Laboratory of Functions and Applications of Medicinal Plants, College of Pharmacy, Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, Guizhou Medical University, Guiyang, 550025, China
| | - Sheng-Gang Yang
- State Key Laboratory of Functions and Applications of Medicinal Plants, College of Pharmacy, Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, Guizhou Medical University, Guiyang, 550025, China.
| | - Ji-Quan Zhang
- State Key Laboratory of Functions and Applications of Medicinal Plants, College of Pharmacy, Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, Guizhou Medical University, Guiyang, 550025, China.
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11
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Structural Characterization of the D179N and D179Y Variants of KPC-2 β-Lactamase: Ω-Loop Destabilization as a Mechanism of Resistance to Ceftazidime-Avibactam. Antimicrob Agents Chemother 2022; 66:e0241421. [PMID: 35341315 DOI: 10.1128/aac.02414-21] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Klebsiella pneumoniae carbapenemases (KPC-2 and KPC-3) present a global clinical threat, as these β-lactamases confer resistance to carbapenems and oxyimino-cephalosporins. Recent clinically identified KPC variants with substitutions at Ambler position D179, located in the Ω loop, are resistant to the β-lactam/β-lactamase inhibitor combination ceftazidime-avibactam, but susceptible to meropenem-vaborbactam. To gain insights into ceftazidime-avibactam resistance conferred by D179N/Y variants of KPC-2, crystal structures of these variants were determined. The D179N KPC-2 structure revealed that the change of the carboxyl to an amide moiety at position 179 disrupted the salt bridge with R164 present in wild-type KPC-2. Additional interactions were disrupted in the Ω loop, causing a decrease in the melting temperature. Shifts originating from N179 were also transmitted toward the active site, including ∼1-Å shifts of the deacylation water and interacting residue N170. The structure of the D179Y KPC-2 β-lactamase revealed more drastic changes, as this variant exhibited disorder of the Ω loop, with other flanking regions also being disordered. We postulate that the KPC-2 variants can accommodate ceftazidime because the Ω loop is displaced in D179Y or can be more readily displaced in D179N KPC-2. To understand why the β-lactamase inhibitor vaborbactam is less affected by the D179 variants than avibactam, we determined the crystal structure of D179N KPC-2 in complex with vaborbactam, which revealed wild-type KPC-2-like vaborbactam-active site interactions. Overall, the structural results regarding KPC-2 D179 variants revealed various degrees of destabilization of the Ω loop that contribute to ceftazidime-avibactam resistance, possible substrate-assisted catalysis of ceftazidime, and meropenem and meropenem-vaborbactam susceptibility.
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12
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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: 0] [Impact Index Per Article: 0] [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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13
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Olehnovics E, Yin J, Pérez A, De Fabritiis G, Bonomo RA, Bhowmik D, Haider S. The Role of Hydrophobic Nodes in the Dynamics of Class A β-Lactamases. Front Microbiol 2021; 12:720991. [PMID: 34621251 PMCID: PMC8490755 DOI: 10.3389/fmicb.2021.720991] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 08/09/2021] [Indexed: 11/16/2022] Open
Abstract
Class A β-lactamases are known for being able to rapidly gain broad spectrum catalytic efficiency against most β-lactamase inhibitor combinations as a result of elusively minor point mutations. The evolution in class A β-lactamases occurs through optimisation of their dynamic phenotypes at different timescales. At long-timescales, certain conformations are more catalytically permissive than others while at the short timescales, fine-grained optimisation of free energy barriers can improve efficiency in ligand processing by the active site. Free energy barriers, which define all coordinated movements, depend on the flexibility of the secondary structural elements. The most highly conserved residues in class A β-lactamases are hydrophobic nodes that stabilize the core. To assess how the stable hydrophobic core is linked to the structural dynamics of the active site, we carried out adaptively sampled molecular dynamics (MD) simulations in four representative class A β-lactamases (KPC-2, SME-1, TEM-1, and SHV-1). Using Markov State Models (MSM) and unsupervised deep learning, we show that the dynamics of the hydrophobic nodes is used as a metastable relay of kinetic information within the core and is coupled with the catalytically permissive conformation of the active site environment. Our results collectively demonstrate that the class A enzymes described here, share several important dynamic similarities and the hydrophobic nodes comprise of an informative set of dynamic variables in representative class A β-lactamases.
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Affiliation(s)
- Edgar Olehnovics
- Pharmaceutical and Biological Chemistry, University College London School of Pharmacy, London, United Kingdom
| | - Junqi Yin
- Oak Ridge National Laboratory, National Center for Computational Sciences, Oak Ridge, TN, United States
| | - Adrià Pérez
- Computational Science Laboratory, Barcelona Biomedical Research Park, Universitat Pompeu Fabra, Barcelona, Spain
| | - Gianni De Fabritiis
- Computational Science Laboratory, Barcelona Biomedical Research Park, Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Robert A. Bonomo
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, United States
- Department of Medicine, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, United States
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, United States
- Department of Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH, United States
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH, United States
- Veterans Affairs Northeast Ohio Healthcare System, Research Service, Cleveland, OH, United States
| | - Debsindhu Bhowmik
- Computer Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Shozeb Haider
- Pharmaceutical and Biological Chemistry, University College London School of Pharmacy, London, United Kingdom
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14
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Li X, Quan J, Ke H, Wu W, Feng Y, Yu Y, Jiang Y. Emergence of a KPC Variant Conferring Resistance to Ceftazidime-Avibactam in a Widespread ST11 Carbapenem-Resistant Klebsiella pneumoniae Clone in China. Front Microbiol 2021; 12:724272. [PMID: 34484166 PMCID: PMC8415713 DOI: 10.3389/fmicb.2021.724272] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 07/30/2021] [Indexed: 11/24/2022] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP) infection poses a great threat to public health worldwide, and KPC-2-producing strains are the main factors responsible for resistance to carbapenems in China. Ceftazidime/avibactam (CZA) is a novel β-lactam/β-lactamase inhibitor combination with good activity against KPC-2 carbapenemase and is becoming the most important option for treating KPC-producing CRKP infection. Here, we report the emergence of a novel KPC-2 variant, designated KPC-74, produced by K. pneumoniae strain KP55, that conferred CZA resistance in a patient after CZA exposure. The novel blaKPC–74 variant showed a deletion of 6 nucleotides at positions 712–717 compared with blaKPC–2, and this deletion resulted in the consequent deletion of glycine and valine at positions 239 and 240. Antimicrobial susceptibility testing showed that KP55 presents multidrug resistance, including resistance to CZA and ertapenem, but is susceptible to imipenem, meropenem, and colistin. The blaKPC–74 gene was located on a plasmid, as determined by S1-nuclease pulsed-field gel electrophoresis followed by southern blotting, and confirmed to be 133,766 bp in length by whole-genome sequencing on both the Illumina and MinION platforms. The CZA resistance phenotype of the novel KPC variant was confirmed by both transformation of the blaKPC–74-harboring plasmid and a blaKPC–74 gene cloning assay, showing a 64-fold higher CZA minimum inhibitory concentration (MIC) than the recipient strains. The G239_V240del observed in KPC-74 was outside the omega-loop region but was still close to the active site Ser70 and omega-loop in the protein tertiary structure. The enzyme kinetic parameters and IC50 values further indicated that the hydrolytic activity of the KPC-74 enzyme against ceftazidime was potentiated twofold and that the affinity between KPC-74 and avibactam was alleviated 17-fold compared with that of the KPC-2 allele. This CZA resistance mediated by KPC-74 could be selected after CZA therapy and evolved to be more diverse and heterogeneous. Surveillance of CZA resistance is urgently needed in clinical settings.
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Affiliation(s)
- Xi Li
- Centre of Laboratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Jingjing Quan
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Huanhuan Ke
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, China.,Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wenhao Wu
- Centre of Laboratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Yu Feng
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, China.,Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Yan Jiang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
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15
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Yang Y, Hu B, Yang Y, Gong K, Wang H, Guo Q, Tang X, Li Y, Wang J. Rational design of selective HDAC2 inhibitors for liver cancer treatment: computational insights into the selectivity mechanism through molecular dynamics simulations and QM/MM calculations. Phys Chem Chem Phys 2021; 23:17576-17590. [PMID: 34369509 DOI: 10.1039/d1cp02264d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The rational design of selective histone deacetylase 2 (HDAC2) inhibitors is beneficial for the therapeutic treatment of liver cancer, though HDAC2 is highly homologous to HDAC8, which may lead to undesired side effects due to the pan-inhibition towards HDAC2 and HDAC8. To clarify the structural basis of selective inhibition towards HDAC2 over HDAC8, we utilized multiple in silico strategies, including sequence alignment, structural comparison, molecular docking, molecular dynamics simulations, free energy calculations, alanine scanning mutagenesis, pharmacophore modeling, protein contacts atlas analysis and QM/MM calculations to study the binding patterns of HDAC2/8 selective inhibitors. Through the whole process described above, it is found that although HDAC2 has conserved GLY154 and PHE210 that also exist within HDAC8, namely GLY151 and PHE208, the two isoforms exhibit diverse binding modes towards their inhibitors. Typically, HDAC2 inhibitors interact with the Zn2+ ions through the core chelate group, while HDAC8 inhibitors adopt a bent conformation within the HDAC8 pocket that inclines to be in contact with the Zn2+ ions through the terminal hydroxamic acid group. In summary, our data comprehensively elucidate the selectivity mechanism towards HDAC2 over HDAC8, which would guide the rational design of selective HDAC2 inhibitors for liver cancer treatment.
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Affiliation(s)
- Ye Yang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning 110016, China.
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16
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Furey IM, Mehta SC, Sankaran B, Hu L, Prasad BVV, Palzkill T. Local interactions with the Glu166 base and the conformation of an active site loop play key roles in carbapenem hydrolysis by the KPC-2 β-lactamase. J Biol Chem 2021; 296:100799. [PMID: 34022225 PMCID: PMC8189571 DOI: 10.1016/j.jbc.2021.100799] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/06/2021] [Accepted: 05/17/2021] [Indexed: 01/05/2023] Open
Abstract
The Klebsiella pneumoniae carbapenemase-2 (KPC-2) is a common source of antibiotic resistance in Gram-negative bacterial infections. KPC-2 is a class A β-lactamase that exhibits a broad substrate profile and hydrolyzes most β-lactam antibiotics including carbapenems owing to rapid deacylation of the covalent acyl-enzyme intermediate. However, the features that allow KPC-2 to deacylate substrates more rapidly than non-carbapenemase enzymes are not clear. The active-site residues in KPC-2 are largely conserved in sequence and structure compared with non-carbapenemases, suggesting that subtle alterations may collectively facilitate hydrolysis of carbapenems. We utilized a nonbiased genetic approach to identify mutants deficient in carbapenem hydrolysis but competent for ampicillin hydrolysis. Subsequent pre–steady-state enzyme kinetics analyses showed that the substitutions slow the rate of deacylation of carbapenems. Structure determination via X-ray diffraction indicated that a F72Y mutant forms a hydrogen bond between the tyrosine hydroxyl group and Glu166, which may lower basicity and impair the activation of the catalytic water for deacylation, whereas several mutants impact the structure of the Q214-R220 active site loop. A T215P substitution lowers the deacylation rate and drastically alters the conformation of the loop, thereby disrupting interactions between the enzyme and the carbapenem acyl-enzyme intermediate. Thus, the environment of the Glu166 general base and the precise placement and conformational stability of the Q214-R220 loop are critical for efficient deacylation of carbapenems by the KPC-2 enzyme. Therefore, the design of carbapenem antibiotics that interact with Glu166 or alter the Q214-R220 loop conformation may disrupt enzyme function and overcome resistance.
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Affiliation(s)
- Ian M Furey
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Shrenik C Mehta
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Banumathi Sankaran
- Department of Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Liya Hu
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston Texas, USA
| | - B V Venkataram Prasad
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston Texas, USA
| | - Timothy Palzkill
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston Texas, USA.
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17
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Lucic A, Hinchliffe P, Malla TR, Tooke CL, Brem J, Calvopiña K, Lohans CT, Rabe P, McDonough MA, Armistead T, Orville AM, Spencer J, Schofield CJ. Faropenem reacts with serine and metallo-β-lactamases to give multiple products. Eur J Med Chem 2021; 215:113257. [PMID: 33618159 PMCID: PMC7614720 DOI: 10.1016/j.ejmech.2021.113257] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/23/2021] [Accepted: 01/30/2021] [Indexed: 11/30/2022]
Abstract
Penems have demonstrated potential as antibacterials and β-lactamase inhibitors; however, their clinical use has been limited, especially in comparison with the structurally related carbapenems. Faropenem is an orally active antibiotic with a C-2 tetrahydrofuran (THF) ring, which is resistant to hydrolysis by some β-lactamases. We report studies on the reactions of faropenem with carbapenem-hydrolysing β-lactamases, focusing on the class A serine β-lactamase KPC-2 and the metallo β-lactamases (MBLs) VIM-2 (a subclass B1 MBL) and L1 (a B3 MBL). Kinetic studies show that faropenem is a substrate for all three β-lactamases, though it is less efficiently hydrolysed by KPC-2. Crystallographic analyses on faropenem-derived complexes reveal opening of the β-lactam ring with formation of an imine with KPC-2, VIM-2, and L1. In the cases of the KPC-2 and VIM-2 structures, the THF ring is opened to give an alkene, but with L1 the THF ring remains intact. Solution state studies, employing NMR, were performed on L1, KPC-2, VIM-2, VIM-1, NDM-1, OXA-23, OXA-10, and OXA-48. The solution results reveal, in all cases, formation of imine products in which the THF ring is opened; formation of a THF ring-closed imine product was only observed with VIM-1 and VIM-2. An enamine product with a closed THF ring was also observed in all cases, at varying levels. Combined with previous reports, the results exemplify the potential for different outcomes in the reactions of penems with MBLs and SBLs and imply further structure-activity relationship studies are worthwhile to optimise the interactions of penems with β-lactamases. They also exemplify how crystal structures of β-lactamase substrate/inhibitor complexes do not always reflect reaction outcomes in solution.
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Affiliation(s)
- Anka Lucic
- Chemistry Research Laboratory, The Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Philip Hinchliffe
- Cellular and Molecular Medicine, Biomedical Sciences Building, University Walk, Bristol, BS8 1TD, United Kingdom
| | - Tika R Malla
- Chemistry Research Laboratory, The Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Catherine L Tooke
- Cellular and Molecular Medicine, Biomedical Sciences Building, University Walk, Bristol, BS8 1TD, United Kingdom
| | - Jürgen Brem
- Chemistry Research Laboratory, The Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Karina Calvopiña
- Chemistry Research Laboratory, The Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | | | - Patrick Rabe
- Chemistry Research Laboratory, The Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Michael A McDonough
- Chemistry Research Laboratory, The Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Timothy Armistead
- Cellular and Molecular Medicine, Biomedical Sciences Building, University Walk, Bristol, BS8 1TD, United Kingdom
| | - Allen M Orville
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, United Kingdom.
| | - James Spencer
- Cellular and Molecular Medicine, Biomedical Sciences Building, University Walk, Bristol, BS8 1TD, United Kingdom.
| | - Christopher J Schofield
- Chemistry Research Laboratory, The Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom.
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18
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Wang H, Wang Y, Li C, Wang H, Geng X, Hu B, Wen R, Wang J, Zhang F. Structural basis for tailor-made selective PI3K α/β inhibitors: a computational perspective. NEW J CHEM 2021. [DOI: 10.1039/d0nj04216a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
PI3K α and β are Class IA PI3K isoforms that share a highly homologous ATP binding site, differing only in a few residues around the binding site.
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Affiliation(s)
- Huibin Wang
- School of Pharmacy
- Shenyang Pharmaceutical University
- Shenyang 110016
- People's Republic of China
| | - Ying Wang
- Wuya College of Innovation
- Shenyang Pharmaceutical University
- Shenyang 110016
- People's Republic of China
| | - Chunshi Li
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education
- Shenyang Pharmaceutical University
- Shenyang 110016
- People's Republic of China
- School of Pharmaceutical Engineering
| | - Hanxun Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education
- Shenyang Pharmaceutical University
- Shenyang 110016
- People's Republic of China
- School of Pharmaceutical Engineering
| | - Xiaohui Geng
- School of Pharmacy
- Shenyang Pharmaceutical University
- Shenyang 110016
- People's Republic of China
| | - Baichun Hu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education
- Shenyang Pharmaceutical University
- Shenyang 110016
- People's Republic of China
- School of Pharmaceutical Engineering
| | - Rui Wen
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education
- Shenyang Pharmaceutical University
- Shenyang 110016
- People's Republic of China
- School of Pharmaceutical Engineering
| | - Jian Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education
- Shenyang Pharmaceutical University
- Shenyang 110016
- People's Republic of China
- School of Pharmaceutical Engineering
| | - Fengjiao Zhang
- Wuya College of Innovation
- Shenyang Pharmaceutical University
- Shenyang 110016
- People's Republic of China
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19
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Tooke CL, Hinchliffe P, Bonomo RA, Schofield CJ, Mulholland AJ, Spencer J. Natural variants modify Klebsiella pneumoniae carbapenemase (KPC) acyl-enzyme conformational dynamics to extend antibiotic resistance. J Biol Chem 2021; 296:100126. [PMID: 33257320 PMCID: PMC7949053 DOI: 10.1074/jbc.ra120.016461] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 11/21/2020] [Accepted: 11/30/2020] [Indexed: 12/11/2022] Open
Abstract
Class A serine β-lactamases (SBLs) are key antibiotic resistance determinants in Gram-negative bacteria. SBLs neutralize β-lactams via a hydrolytically labile covalent acyl-enzyme intermediate. Klebsiella pneumoniae carbapenemase (KPC) is a widespread SBL that hydrolyzes carbapenems, the most potent β-lactams; known KPC variants differ in turnover of expanded-spectrum oxyimino-cephalosporins (ESOCs), for example, cefotaxime and ceftazidime. Here, we compare ESOC hydrolysis by the parent enzyme KPC-2 and its clinically observed double variant (P104R/V240G) KPC-4. Kinetic analyses show that KPC-2 hydrolyzes cefotaxime more efficiently than the bulkier ceftazidime, with improved ESOC turnover by KPC-4 resulting from enhanced turnover (kcat), rather than altered KM values. High-resolution crystal structures of ESOC acyl-enzyme complexes with deacylation-deficient (E166Q) KPC-2 and KPC-4 mutants show that ceftazidime acylation causes rearrangement of three loops; the Ω, 240, and 270 loops, which border the active site. However, these rearrangements are less pronounced in the KPC-4 than the KPC-2 ceftazidime acyl-enzyme and are not observed in the KPC-2:cefotaxime acyl-enzyme. Molecular dynamics simulations of KPC:ceftazidime acyl-enyzmes reveal that the deacylation general base E166, located on the Ω loop, adopts two distinct conformations in KPC-2, either pointing "in" or "out" of the active site; with only the "in" form compatible with deacylation. The "out" conformation was not sampled in the KPC-4 acyl-enzyme, indicating that efficient ESOC breakdown is dependent upon the ordering and conformation of the KPC Ω loop. The results explain how point mutations expand the activity spectrum of the clinically important KPC SBLs to include ESOCs through their effects on the conformational dynamics of the acyl-enzyme intermediate.
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Affiliation(s)
- Catherine L Tooke
- School of Cellular and Molecular Medicine, Biomedical Sciences Building, University of Bristol, Bristol, United Kingdom; Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, United Kingdom
| | - Philip Hinchliffe
- School of Cellular and Molecular Medicine, Biomedical Sciences Building, University of Bristol, Bristol, United Kingdom
| | - Robert A Bonomo
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA; Departments of Medicine, Pharmacology, Molecular Biology and Microbiology, Biochemistry, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA; CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES) Cleveland, Ohio, USA
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, United Kingdom
| | - James Spencer
- School of Cellular and Molecular Medicine, Biomedical Sciences Building, University of Bristol, Bristol, United Kingdom.
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20
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Mehta SC, Furey IM, Pemberton OA, Boragine DM, Chen Y, Palzkill T. KPC-2 β-lactamase enables carbapenem antibiotic resistance through fast deacylation of the covalent intermediate. J Biol Chem 2021; 296:100155. [PMID: 33273017 PMCID: PMC7895804 DOI: 10.1074/jbc.ra120.015050] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 11/24/2020] [Accepted: 12/03/2020] [Indexed: 01/23/2023] Open
Abstract
Serine active-site β-lactamases hydrolyze β-lactam antibiotics through the formation of a covalent acyl-enzyme intermediate followed by deacylation via an activated water molecule. Carbapenem antibiotics are poorly hydrolyzed by most β-lactamases owing to slow hydrolysis of the acyl-enzyme intermediate. However, the emergence of the KPC-2 carbapenemase has resulted in widespread resistance to these drugs, suggesting it operates more efficiently. Here, we investigated the unusual features of KPC-2 that enable this resistance. We show that KPC-2 has a 20,000-fold increased deacylation rate compared with the common TEM-1 β-lactamase. Furthermore, kinetic analysis of active site alanine mutants indicates that carbapenem hydrolysis is a concerted effort involving multiple residues. Substitution of Asn170 greatly decreases the deacylation rate, but this residue is conserved in both KPC-2 and non-carbapenemase β-lactamases, suggesting it promotes carbapenem hydrolysis only in the context of KPC-2. X-ray structure determination of the N170A enzyme in complex with hydrolyzed imipenem suggests Asn170 may prevent the inactivation of the deacylating water by the 6α-hydroxyethyl substituent of carbapenems. In addition, the Thr235 residue, which interacts with the C3 carboxylate of carbapenems, also contributes strongly to the deacylation reaction. In contrast, mutation of the Arg220 and Thr237 residues decreases the acylation rate and, paradoxically, improves binding affinity for carbapenems. Thus, the role of these residues may be ground state destabilization of the enzyme-substrate complex or, alternatively, to ensure proper alignment of the substrate with key catalytic residues to facilitate acylation. These findings suggest modifications of the carbapenem scaffold to avoid hydrolysis by KPC-2 β-lactamase.
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Affiliation(s)
- Shrenik C Mehta
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Ian M Furey
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Orville A Pemberton
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, Tampa, Florida, USA
| | - David M Boragine
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Yu Chen
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, Tampa, Florida, USA
| | - Timothy Palzkill
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA.
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21
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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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22
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Oueslati S, Iorga BI, Tlili L, Exilie C, Zavala A, Dortet L, Jousset AB, Bernabeu S, Bonnin RA, Naas T. Unravelling ceftazidime/avibactam resistance of KPC-28, a KPC-2 variant lacking carbapenemase activity. J Antimicrob Chemother 2020; 74:2239-2246. [PMID: 31127297 DOI: 10.1093/jac/dkz209] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 04/09/2019] [Accepted: 04/18/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND KPC-like carbapenemases have spread worldwide with more than 30 variants identified that differ by single or double amino-acid substitutions. OBJECTIVES To describe the steady-state kinetic parameters of KPC-28, which differs from KPC-2 by a H274Y substitution and the deletion of two amino acids (Δ242-GT-243). METHODS The blaKPC-2, blaKPC-3, blaKPC-14 and blaKPC-28 genes were cloned into a pTOPO vector for susceptibility testing or into pET41b for overexpression, purification and subsequent kinetic parameter (Km, kcat) determination. Molecular docking experiments were performed to explore the role of the amino-acid changes in the carbapenemase activity. RESULTS Susceptibility testing revealed that Escherichia coli producing KPC-28 displayed MICs that were lower for carbapenems and higher for ceftazidime and ceftazidime/avibactam as compared with KPC-2. The catalytic efficiencies of KPC-28 and KPC-14 for imipenem were 700-fold and 200-fold lower, respectively, than those of KPC-2, suggesting that Δ242-GT-243 in KPC-28 and KPC-14 is responsible for reduced carbapenem hydrolysis. Similarly, the H274Y substitution resulted in KPC-28 in a 50-fold increase in ceftazidime hydrolysis that was strongly reversed by clavulanate. CONCLUSIONS We have shown that KPC-28 lacks carbapenemase activity, has increased ceftazidime hydrolytic activity and is strongly inhibited by clavulanate. KPC-28-producing E. coli isolates display an avibactam-resistant ESBL profile, which may be wrongly identified by molecular and immunochromatographic assays as the presence of a carbapenemase. Accordingly, confirmation of carbapenem hydrolysis will be mandatory with assays based solely on blaKPC gene or gene product detection.
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Affiliation(s)
- Saoussen Oueslati
- EA7361 'Structure, Dynamic, Function and Expression of Broad Spectrum β-Lactamases', Faculty of Medicine, Université Paris-Sud, LabEx Lermit, Université Paris-Saclay, Le Kremlin-Bicêtre, France
| | - Bogdan I Iorga
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, LabEx LERMIT, Gif-sur-Yvette, France
| | - Linda Tlili
- EA7361 'Structure, Dynamic, Function and Expression of Broad Spectrum β-Lactamases', Faculty of Medicine, Université Paris-Sud, LabEx Lermit, Université Paris-Saclay, Le Kremlin-Bicêtre, France
| | - Cynthia Exilie
- EA7361 'Structure, Dynamic, Function and Expression of Broad Spectrum β-Lactamases', Faculty of Medicine, Université Paris-Sud, LabEx Lermit, Université Paris-Saclay, Le Kremlin-Bicêtre, France
| | - Agustin Zavala
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, LabEx LERMIT, Gif-sur-Yvette, France
| | - Laurent Dortet
- EA7361 'Structure, Dynamic, Function and Expression of Broad Spectrum β-Lactamases', Faculty of Medicine, Université Paris-Sud, LabEx Lermit, Université Paris-Saclay, Le Kremlin-Bicêtre, France.,Bacteriology-Hygiene Unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France.,Associated French National Reference Centre for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | - Agnès B Jousset
- EA7361 'Structure, Dynamic, Function and Expression of Broad Spectrum β-Lactamases', Faculty of Medicine, Université Paris-Sud, LabEx Lermit, Université Paris-Saclay, Le Kremlin-Bicêtre, France.,Bacteriology-Hygiene Unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France.,Associated French National Reference Centre for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | - Sandrine Bernabeu
- EA7361 'Structure, Dynamic, Function and Expression of Broad Spectrum β-Lactamases', Faculty of Medicine, Université Paris-Sud, LabEx Lermit, Université Paris-Saclay, Le Kremlin-Bicêtre, France.,Bacteriology-Hygiene Unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Rémy A Bonnin
- EA7361 'Structure, Dynamic, Function and Expression of Broad Spectrum β-Lactamases', Faculty of Medicine, Université Paris-Sud, LabEx Lermit, Université Paris-Saclay, Le Kremlin-Bicêtre, France.,Associated French National Reference Centre for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | - Thierry Naas
- EA7361 'Structure, Dynamic, Function and Expression of Broad Spectrum β-Lactamases', Faculty of Medicine, Université Paris-Sud, LabEx Lermit, Université Paris-Saclay, Le Kremlin-Bicêtre, France.,Bacteriology-Hygiene Unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France.,Associated French National Reference Centre for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
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23
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Zhou Y, Lv X, Chen M, Guo Y, Ding R, Liu B, Deng X, Wang J. Characterization of Corosolic Acid as a KPC-2 Inhibitor That Increases the Susceptibility of KPC-2-Positive Bacteria to Carbapenems. Front Pharmacol 2020; 11:1047. [PMID: 32733256 PMCID: PMC7363806 DOI: 10.3389/fphar.2020.01047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/26/2020] [Indexed: 12/18/2022] Open
Abstract
The emergence of KPC-producing Gram-negative bacteria in clinical practice highlights the need to search for novel antimicrobials and new anti-infection strategies. In this study, we constructed a laboratory KPC-2-positive strain, E. coli BL21(DE3) (pET28a-KPC-2) and identified the activity of KPC-2 in this strain. Using enzyme inhibition assays, checkerboard MIC assays, growth curves, time-killing assays and combined disk test, we found that the natural compound corosolic acid (CA) significantly inhibited the activity of the class A β-lactamase KPC-2, which is common among clinical isolates. CA treatment increased the antibacterial or bactericidal activity of imipenem and meropenem against E. coli BL21(DE3) (pET28a-KPC-2) in vitro (FIC index = 0.17 ± 0.03 for both carbapenems). In addition, the mouse intraperitoneal infection model confirmed that the combination therapy significantly reduced the bacterial load in the livers and spleens following subcutaneous administration. Our results showed that CA can be used to extend the life of carbapenems, providing a viable strategy for severe infections caused by KPC-2-positive bacteria.
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Affiliation(s)
- Yonglin Zhou
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, China.,Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, China
| | - Xiaohong Lv
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, China
| | - Meishan Chen
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, China
| | - Yan Guo
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, China
| | - Rui Ding
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, China
| | - Bin Liu
- Jilin Institute for Food Control, Changchun, China
| | - Xuming Deng
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, China.,Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, China
| | - Jianfeng Wang
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, China.,Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, China
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24
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Tooke CL, Hinchliffe P, Krajnc A, Mulholland AJ, Brem J, Schofield CJ, Spencer J. Cyclic boronates as versatile scaffolds for KPC-2 β-lactamase inhibition. RSC Med Chem 2020; 11:491-496. [PMID: 33479650 PMCID: PMC7536818 DOI: 10.1039/c9md00557a] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 01/08/2020] [Indexed: 12/14/2022] Open
Abstract
Klebsiella pneumoniae carbapenemase-2 (KPC-2) is a serine-β-lactamase (SBL) capable of hydrolysing almost all β-lactam antibiotics. We compare KPC-2 inhibition by vaborbactam, a clinically-approved monocyclic boronate, and VNRX-5133 (taniborbactam), a bicyclic boronate in late-stage clinical development. Vaborbactam inhibition is slowly reversible, whereas taniborbactam has an off-rate indicating essentially irreversible complex formation and a 15-fold higher on-rate, although both potentiate β-lactam activity against KPC-2-expressing K. pneumoniae. High resolution X-ray crystal structures reveal closely related binding modes for both inhibitors to KPC-2, with differences apparent only in positioning of the endocyclic boronate ester oxygen. The results indicate the bicyclic boronate scaffold as both an efficient, long-lasting, KPC-2 inhibitor and capable of supporting further iterations that may improve potency against specific enzyme targets and pre-empt the emergence of inhibitor resistant KPC-2 variants.
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Affiliation(s)
- Catherine L Tooke
- School of Cellular and Molecular Medicine , Biomedical Sciences Building , University of Bristol , Bristol , BS8 1TD , UK .
- Centre for Computational Chemistry , School of Chemistry , University of Bristol , Bristol , BS8 1TS , UK
| | - Philip Hinchliffe
- School of Cellular and Molecular Medicine , Biomedical Sciences Building , University of Bristol , Bristol , BS8 1TD , UK .
| | - Alen Krajnc
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK
| | - Adrian J Mulholland
- Centre for Computational Chemistry , School of Chemistry , University of Bristol , Bristol , BS8 1TS , UK
| | - Jürgen Brem
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK
| | - Christopher J Schofield
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK
| | - James Spencer
- School of Cellular and Molecular Medicine , Biomedical Sciences Building , University of Bristol , Bristol , BS8 1TD , UK .
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25
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Linciano P, Gianquinto E, Montanari M, Maso L, Bellio P, Cebrián-Sastre E, Celenza G, Blázquez J, Cendron L, Spyrakis F, Tondi D. 4-Amino-1,2,4-triazole-3-thione as a Promising Scaffold for the Inhibition of Serine and Metallo- β-Lactamases. Pharmaceuticals (Basel) 2020; 13:E52. [PMID: 32213902 PMCID: PMC7151704 DOI: 10.3390/ph13030052] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/05/2020] [Accepted: 03/21/2020] [Indexed: 02/04/2023] Open
Abstract
The emergence of bacteria that co-express serine- and metallo- carbapenemases is a threat to the efficacy of the available β-lactam antibiotic armamentarium. The 4-amino-1,2,4-triazole-3-thione scaffold has been selected as the starting chemical moiety in the design of a small library of β-Lactamase inhibitors (BLIs) with extended activity profiles. The synthesised compounds have been validated in vitro against class A serine β-Lactamase (SBLs) KPC-2 and class B1 metallo β-Lactamases (MBLs) VIM-1 and IMP-1. Of the synthesised derivatives, four compounds showed cross-class micromolar inhibition potency and therefore underwent in silico analyses to elucidate their binding mode within the catalytic pockets of serine- and metallo-BLs. Moreover, several members of the synthesised library have been evaluated, in combination with meropenem (MEM), against clinical strains that overexpress BLs for their ability to synergise carbapenems.
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Affiliation(s)
- Pasquale Linciano
- Department of Life Sciences, University of Modena and Reggio Emilia, Via G. Campi 103, 41125 Modena, Italy; (P.L.); (M.M.)
| | - Eleonora Gianquinto
- Department of Drug Science and Technology, University of Turin, Via P. Giuria 9, 10125 Turin, Italy;
| | - Martina Montanari
- Department of Life Sciences, University of Modena and Reggio Emilia, Via G. Campi 103, 41125 Modena, Italy; (P.L.); (M.M.)
| | - Lorenzo Maso
- Department of Biology, University of Padua, Viale G. Colombo 3, 35121 Padua, Italy; (L.M.); (L.C.)
| | - Pierangelo Bellio
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, via Vetoio 1, 67100 L’Aquila, Italy; (P.B.); (G.C.)
| | | | - Giuseppe Celenza
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, via Vetoio 1, 67100 L’Aquila, Italy; (P.B.); (G.C.)
| | - Jesús Blázquez
- National Center of Biotechnology-CSIC, Calle Darwin 3, 28049 Madrid, Spain; (E.C.-S.); (J.B.)
| | - Laura Cendron
- Department of Biology, University of Padua, Viale G. Colombo 3, 35121 Padua, Italy; (L.M.); (L.C.)
| | - Francesca Spyrakis
- Department of Drug Science and Technology, University of Turin, Via P. Giuria 9, 10125 Turin, Italy;
| | - Donatella Tondi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via G. Campi 103, 41125 Modena, Italy; (P.L.); (M.M.)
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26
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Hecker SJ, Reddy KR, Lomovskaya O, Griffith DC, Rubio-Aparicio D, Nelson K, Tsivkovski R, Sun D, Sabet M, Tarazi Z, Parkinson J, Totrov M, Boyer SH, Glinka TW, Pemberton OA, Chen Y, Dudley MN. Discovery of Cyclic Boronic Acid QPX7728, an Ultrabroad-Spectrum Inhibitor of Serine and Metallo-β-lactamases. J Med Chem 2020; 63:7491-7507. [DOI: 10.1021/acs.jmedchem.9b01976] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Scott J. Hecker
- Qpex Biopharma, Inc., 6275 Nancy Ridge Drive, Suite 100, San Diego, California 92121, United States
| | - K. Raja Reddy
- Qpex Biopharma, Inc., 6275 Nancy Ridge Drive, Suite 100, San Diego, California 92121, United States
| | - Olga Lomovskaya
- Qpex Biopharma, Inc., 6275 Nancy Ridge Drive, Suite 100, San Diego, California 92121, United States
| | - David C. Griffith
- Qpex Biopharma, Inc., 6275 Nancy Ridge Drive, Suite 100, San Diego, California 92121, United States
| | - Debora Rubio-Aparicio
- Qpex Biopharma, Inc., 6275 Nancy Ridge Drive, Suite 100, San Diego, California 92121, United States
| | - Kirk Nelson
- Qpex Biopharma, Inc., 6275 Nancy Ridge Drive, Suite 100, San Diego, California 92121, United States
| | - Ruslan Tsivkovski
- Qpex Biopharma, Inc., 6275 Nancy Ridge Drive, Suite 100, San Diego, California 92121, United States
| | - Dongxu Sun
- Qpex Biopharma, Inc., 6275 Nancy Ridge Drive, Suite 100, San Diego, California 92121, United States
| | - Mojgan Sabet
- Qpex Biopharma, Inc., 6275 Nancy Ridge Drive, Suite 100, San Diego, California 92121, United States
| | - Ziad Tarazi
- Qpex Biopharma, Inc., 6275 Nancy Ridge Drive, Suite 100, San Diego, California 92121, United States
| | - Jonathan Parkinson
- Qpex Biopharma, Inc., 6275 Nancy Ridge Drive, Suite 100, San Diego, California 92121, United States
| | - Maxim Totrov
- Molsoft LLC, 11199 Sorrento Valley Road, San Diego, California 92121, United States
| | - Serge H. Boyer
- Qpex Biopharma, Inc., 6275 Nancy Ridge Drive, Suite 100, San Diego, California 92121, United States
| | - Tomasz W. Glinka
- Qpex Biopharma, Inc., 6275 Nancy Ridge Drive, Suite 100, San Diego, California 92121, United States
| | - Orville A. Pemberton
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, 12901 Bruce B. Downs Boulevard, Tampa, Florida 33612, United States
| | - Yu Chen
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, 12901 Bruce B. Downs Boulevard, Tampa, Florida 33612, United States
| | - Michael N. Dudley
- Qpex Biopharma, Inc., 6275 Nancy Ridge Drive, Suite 100, San Diego, California 92121, United States
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27
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Akhtar A, Pemberton OA, Chen Y. Structural Basis for Substrate Specificity and Carbapenemase Activity of OXA-48 Class D β-Lactamase. ACS Infect Dis 2020; 6:261-271. [PMID: 31872762 DOI: 10.1021/acsinfecdis.9b00304] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Carbapenem-hydrolyzing class D β-lactamases (CHDLs) are a diverse family of enzymes that are rapidly becoming the predominant cause of bacterial resistance against β-lactam antibiotics in many regions of the world. OXA-48, an atypical member of CHDLs, is one of the most frequently observed in the clinic and exhibits a unique substrate profile. We applied X-ray crystallography to OXA-48 complexes with multiple β-lactam antibiotics to elucidate this enzyme's carbapenemase activity and its preference of imipenem over meropenem and other substrates such as cefotaxime. In particular, we obtained acyl-enzyme complexes of OXA-48 with imipenem, meropenem, faropenem, cefotaxime, and cefoxitin, and a product complex with imipenem. Importantly, the product complex captures a key reaction milestone with the newly generated carboxylate group still in the oxyanion hole, and represents the first such complex with a wild-type serine β-lactamase. A potential hydrogen bond is observed between the two carboxylate groups from the product and the carbamylated Lys73, representing the stage immediately after the breakage of the acyl-enzyme bond where the product carboxylate would be neutral. The placement of the product carboxylate also illustrates the approximate transient location of the deacylation water that has long eluded structural characterization in class D β-lactamases. Additionally, comparing the product complex with the acyl-enzyme intermediates provides new insights into the various mechanisms by which specific side chain groups hinder the access of the deacylation water to the acyl-enzyme linkage, especially in meropenem. Taken together, these data offer valuable information on the substrate specificity of OXA-48 and the catalytic mechanism of CHDLs.
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Affiliation(s)
- Afroza Akhtar
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, 12901 Bruce B. Downs Boulevard, MDC 3522, Tampa, Florida 33612, United States
| | - Orville A. Pemberton
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, 12901 Bruce B. Downs Boulevard, MDC 3522, Tampa, Florida 33612, United States
| | - Yu Chen
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, 12901 Bruce B. Downs Boulevard, MDC 3522, Tampa, Florida 33612, United States
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Kroeck KG, Sacco MD, Smith EW, Zhang X, Shoun D, Akhtar A, Darch SE, Cohen F, Andrews LD, Knox JE, Chen Y. Discovery of dual-activity small-molecule ligands of Pseudomonas aeruginosa LpxA and LpxD using SPR and X-ray crystallography. Sci Rep 2019; 9:15450. [PMID: 31664082 PMCID: PMC6820557 DOI: 10.1038/s41598-019-51844-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 10/09/2019] [Indexed: 11/09/2022] Open
Abstract
The lipid A biosynthesis pathway is essential in Pseudomonas aeruginosa. LpxA and LpxD are the first and third enzymes in this pathway respectively, and are regarded as promising antibiotic targets. The unique structural similarities between these two enzymes make them suitable targets for dual-binding inhibitors, a characteristic that would decrease the likelihood of mutational resistance and increase cell-based activity. We report the discovery of multiple small molecule ligands that bind to P. aeruginosa LpxA and LpxD, including dual-binding ligands. Binding poses were determined for select compounds by X-ray crystallography. The new structures reveal a previously uncharacterized magnesium ion residing at the core of the LpxD trimer. In addition, ligand binding in the LpxD active site resulted in conformational changes in the distal C-terminal helix-bundle, which forms extensive contacts with acyl carrier protein (ACP) during catalysis. These ligand-dependent conformational changes suggest a potential allosteric influence of reaction intermediates on ACP binding, and vice versa. Taken together, the novel small molecule ligands and their crystal structures provide new chemical scaffolds for ligand discovery targeting lipid A biosynthesis, while revealing structural features of interest for future investigation of LpxD function.
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Affiliation(s)
- Kyle G Kroeck
- Department of Molecular Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida, 33612, United States
| | - Michael D Sacco
- Department of Molecular Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida, 33612, United States
| | - Emmanuel W Smith
- Department of Molecular Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida, 33612, United States
| | - Xiujun Zhang
- Department of Molecular Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida, 33612, United States
| | - Daniel Shoun
- Department of Molecular Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida, 33612, United States
| | - Afroza Akhtar
- Department of Molecular Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida, 33612, United States
| | - Sophie E Darch
- Department of Molecular Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida, 33612, United States
| | - Frederick Cohen
- Former employees of ACHAOGEN Inc., 1 Tower Place, Suite 400, South San Francisco, California, 94080, United States
| | - Logan D Andrews
- Former employees of ACHAOGEN Inc., 1 Tower Place, Suite 400, South San Francisco, California, 94080, United States
| | - John E Knox
- Former employees of ACHAOGEN Inc., 1 Tower Place, Suite 400, South San Francisco, California, 94080, United States
| | - Yu Chen
- Department of Molecular Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida, 33612, United States.
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Tooke CL, Hinchliffe P, Lang PA, Mulholland AJ, Brem J, Schofield CJ, Spencer J. Molecular Basis of Class A β-Lactamase Inhibition by Relebactam. Antimicrob Agents Chemother 2019; 63:AAC.00564-19. [PMID: 31383664 PMCID: PMC6761529 DOI: 10.1128/aac.00564-19] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 07/04/2019] [Indexed: 12/23/2022] Open
Abstract
β-Lactamase production is the major β-lactam resistance mechanism in Gram-negative bacteria. β-Lactamase inhibitors (BLIs) efficacious against serine β-lactamase (SBL) producers, especially strains carrying the widely disseminated class A enzymes, are required. Relebactam, a diazabicyclooctane (DBO) BLI, is in phase 3 clinical trials in combination with imipenem for the treatment of infections by multidrug-resistant Enterobacteriaceae We show that relebactam inhibits five clinically important class A SBLs (despite their differing spectra of activity), representing both chromosomal and plasmid-borne enzymes, i.e., the extended-spectrum β-lactamases L2 (inhibition constant 3 μM) and CTX-M-15 (21 μM) and the carbapenemases KPC-2, -3, and -4 (1 to 5 μM). Against purified class A SBLs, relebactam is an inferior inhibitor compared with the clinically approved DBO avibactam (9- to 120-fold differences in half maximal inhibitory concentration [IC50]). MIC assays indicate relebactam potentiates β-lactam (imipenem) activity against KPC-producing Klebsiella pneumoniae, with similar potency to avibactam (with ceftazidime). Relebactam is less effective than avibactam in combination with aztreonam against Stenotrophomonas maltophilia K279a. X-ray crystal structures of relebactam bound to CTX-M-15, L2, KPC-2, KPC-3, and KPC-4 reveal its C2-linked piperidine ring can sterically clash with Asn104 (CTX-M-15) or His/Trp105 (L2 and KPCs), rationalizing its poorer inhibition activity than that of avibactam, which has a smaller C2 carboxyamide group. Mass spectrometry and crystallographic data show slow, pH-dependent relebactam desulfation by KPC-2, -3, and -4. This comprehensive comparison of relebactam binding across five clinically important class A SBLs will inform the design of future DBOs, with the aim of improving clinical efficacy of BLI-β-lactam combinations.
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Affiliation(s)
- Catherine L Tooke
- School of Cellular and Molecular Medicine, Biomedical Sciences Building, University of Bristol, Bristol, United Kingdom
| | - Philip Hinchliffe
- School of Cellular and Molecular Medicine, Biomedical Sciences Building, University of Bristol, Bristol, United Kingdom
| | - Pauline A Lang
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, United Kingdom
| | - Jürgen Brem
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | | | - James Spencer
- School of Cellular and Molecular Medicine, Biomedical Sciences Building, University of Bristol, Bristol, United Kingdom
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Linciano P, Vicario M, Kekez I, Bellio P, Celenza G, Martín-Blecua I, Blázquez J, Cendron L, Tondi D. Phenylboronic Acids Probing Molecular Recognition against Class A and Class C β-lactamases. Antibiotics (Basel) 2019; 8:antibiotics8040171. [PMID: 31574990 PMCID: PMC6963673 DOI: 10.3390/antibiotics8040171] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 09/25/2019] [Accepted: 09/27/2019] [Indexed: 11/24/2022] Open
Abstract
Worldwide dissemination of pathogens resistant to almost all available antibiotics represent a real problem preventing efficient treatment of infectious diseases. Among antimicrobial used in therapy, β-lactam antibiotics represent 40% thus playing a crucial role in the management of infections treatment. We report a small series of phenylboronic acids derivatives (BAs) active against class A carbapenemases KPC-2 and GES-5, and class C cephalosporinases AmpC. The inhibitory profile of our BAs against class A and C was investigated by means of molecular docking, enzyme kinetics and X-ray crystallography. We were interested in the mechanism of recognition among class A and class C to direct the design of broad serine β-Lactamases (SBLs) inhibitors. Molecular modeling calculations vs GES-5 and crystallographic studies vs AmpC reasoned, respectively, the ortho derivative 2 and the meta derivative 3 binding affinity. The ability of our BAs to protect β-lactams from BLs hydrolysis was determined in biological assays conducted against clinical strains: Fractional inhibitory concentration index (FICI) tests confirmed their ability to be synergic with β-lactams thus restoring susceptibility to meropenem. Considering the obtained results and the lack of cytotoxicity, our derivatives represent validated probe for the design of SBLs inhibitors.
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Affiliation(s)
- Pasquale Linciano
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy.
| | - Mattia Vicario
- Department of Biology, University of Padova, Viale G. Colombo 3, 35121 Padova, Italy.
| | - Ivana Kekez
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia.
| | - Pierangelo Bellio
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, via Vetoio 1, 67100 L'Aquila, Italy.
| | - Giuseppe Celenza
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, via Vetoio 1, 67100 L'Aquila, Italy.
| | | | - Jesús Blázquez
- National Center of Biotechnology-CSIC, Calle Darwin 3, 28049 Madrid, Spain.
| | - Laura Cendron
- Department of Biology, University of Padova, Viale G. Colombo 3, 35121 Padova, Italy.
| | - Donatella Tondi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy.
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31
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Mechanistic Insights into β-Lactamase-Catalysed Carbapenem Degradation Through Product Characterisation. Sci Rep 2019; 9:13608. [PMID: 31541180 PMCID: PMC6754457 DOI: 10.1038/s41598-019-49264-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 08/15/2019] [Indexed: 01/20/2023] Open
Abstract
β-Lactamases are a major threat to the clinical use of carbapenems, which are often antibiotics of last resort. Despite this, the reaction outcomes and mechanisms by which β-lactamases degrade carbapenems are still not fully understood. The carbapenem bicyclic core consists of a β-lactam ring fused to a pyrroline ring. Following β-lactamase-mediated opening of the β-lactam, the pyrroline may interconvert between an enamine (2-pyrroline) form and two epimeric imine (1-pyrroline) forms; previous crystallographic and spectroscopic studies have reported all three of these forms in the contexts of hydrolysis by different β-lactamases. As we show by NMR spectroscopy, the serine β-lactamases (KPC-2, SFC-1, CMY-10, OXA-23, and OXA-48) and metallo-β-lactamases (NDM-1, VIM-1, BcII, CphA, and L1) tested all degrade carbapenems to preferentially give the Δ2 (enamine) and/or (R)-Δ1 (imine) products. Rapid non-enzymatic tautomerisation of the Δ2 product to the (R)-Δ1 product prevents assignment of the nascent enzymatic product by NMR. The observed stereoselectivity implies that carbapenemases control the form of their pyrroline ring intermediate(s)/product(s), thereby preventing pyrroline tautomerisation from inhibiting catalysis.
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Pemberton OA, Jaishankar P, Akhtar A, Adams JL, Shaw LN, Renslo AR, Chen Y. Heteroaryl Phosphonates as Noncovalent Inhibitors of Both Serine- and Metallocarbapenemases. J Med Chem 2019; 62:8480-8496. [PMID: 31483651 DOI: 10.1021/acs.jmedchem.9b00728] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Gram-negative pathogens expressing serine β-lactamases (SBLs) and metallo-β-lactamases (MBLs), especially those with carbapenemase activity, threaten the clinical utility of almost all β-lactam antibiotics. Here we describe the discovery of a heteroaryl phosphonate scaffold that exhibits noncovalent cross-class inhibition of representative carbapenemases, specifically the SBL KPC-2 and the MBLs NDM-1 and VIM-2. The most potent lead, compound 16, exhibited low nM to low μM inhibition of KPC-2, NDM-1, and VIM-2. Compound 16 potentiated imipenem efficacy against resistant clinical and laboratory bacterial strains expressing carbapenemases while showing some cytotoxicity toward human HEK293T cells only at concentrations above 100 μg/mL. Complex structures with KPC-2, NDM-1, and VIM-2 demonstrate how these inhibitors achieve high binding affinity to both enzyme classes. These findings provide a structurally and mechanistically new scaffold for drug discovery targeting multidrug resistant Gram-negative pathogens and more generally highlight the active site features of carbapenemases that can be leveraged for lead discovery.
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Affiliation(s)
- Orville A Pemberton
- Department of Molecular Medicine , University of South Florida Morsani College of Medicine , 12901 Bruce B. Downs Boulevard, MDC 3522 , Tampa , Florida 33612 , United States
| | - Priyadarshini Jaishankar
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center , University of California, San Francisco , 600 16th Street, Genentech Hall N574 , San Francisco , California 94158 , United States
| | - Afroza Akhtar
- Department of Molecular Medicine , University of South Florida Morsani College of Medicine , 12901 Bruce B. Downs Boulevard, MDC 3522 , Tampa , Florida 33612 , United States
| | - Jessie L Adams
- Department of Cell Biology, Microbiology & Molecular Biology , University of South Florida , 4202 E. Fowler Avenue , Tampa , Florida 33620 , United States
| | - Lindsey N Shaw
- Department of Cell Biology, Microbiology & Molecular Biology , University of South Florida , 4202 E. Fowler Avenue , Tampa , Florida 33620 , United States
| | - Adam R Renslo
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center , University of California, San Francisco , 600 16th Street, Genentech Hall N574 , San Francisco , California 94158 , United States
| | - Yu Chen
- Department of Molecular Medicine , University of South Florida Morsani College of Medicine , 12901 Bruce B. Downs Boulevard, MDC 3522 , Tampa , Florida 33612 , United States
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33
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Wang YL, Liu S, Yu ZJ, Lei Y, Huang MY, Yan YH, Ma Q, Zheng Y, Deng H, Sun Y, Wu C, Yu Y, Chen Q, Wang Z, Wu Y, Li GB. Structure-Based Development of (1-(3′-Mercaptopropanamido)methyl)boronic Acid Derived Broad-Spectrum, Dual-Action Inhibitors of Metallo- and Serine-β-lactamases. J Med Chem 2019; 62:7160-7184. [PMID: 31269398 DOI: 10.1021/acs.jmedchem.9b00735] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Yao-Ling Wang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
| | - Sha Liu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
| | - Zhu-Jun Yu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
| | - Yuan Lei
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
| | - Meng-Yi Huang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
| | - Yu-Hang Yan
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
| | - Qiang Ma
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
| | - Yang Zheng
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
| | - Hui Deng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Ying Sun
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Chengyong Wu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Yamei Yu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Qiang Chen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Zhenling Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Yong Wu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
| | - Guo-Bo Li
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
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Torelli NJ, Akhtar A, DeFrees K, Jaishankar P, Pemberton OA, Zhang X, Johnson C, Renslo AR, Chen Y. Active-Site Druggability of Carbapenemases and Broad-Spectrum Inhibitor Discovery. ACS Infect Dis 2019; 5:1013-1021. [PMID: 30942078 DOI: 10.1021/acsinfecdis.9b00052] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Serine and metallo-carbapenemases are a serious health concern due to their capability to hydrolyze nearly all β-lactam antibiotics. However, the molecular basis for their unique broad-spectrum substrate profile is poorly understood, particularly for serine carbapenemases, such as KPC-2. Using substrates and newly identified small molecules, we compared the ligand binding properties of KPC-2 with the noncarbapenemase CTX-M-14, both of which are Class A β-lactamases with highly similar active sites. Notably, compared to CTX-M-14, KPC-2 was more potently inhibited by hydrolyzed β-lactam products (product inhibition), as well as by a series of novel tetrazole-based inhibitors selected from molecular docking against CTX-M-14. Together with complex crystal structures, these data suggest that the KPC-2 active site has an enhanced ability to form favorable interactions with substrates and small molecule ligands due to its increased hydrophobicity and flexibility. Such properties are even more pronounced in metallo-carbapenemases, such as NDM-1, which was also inhibited by some of the novel tetrazole compounds, including one displaying comparable low μM affinities against both KPC-2 and NDM-1. Our results suggest that carbapenemase activity confers an evolutionary advantage on producers via a broad β-lactam substrate scope but also a mechanistic Achilles' heel that can be exploited for new inhibitor discovery. The complex structures demonstrate, for the first time, how noncovalent inhibitors can be engineered to simultaneously target both serine and metallo-carbapenemases. Despite the relatively modest activity of the current compounds, these studies also demonstrate that hydrolyzed products and tetrazole-based chemotypes can provide valuable starting points for broad-spectrum inhibitor discovery against carbapenemases.
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Affiliation(s)
- Nicholas J. Torelli
- Department of Molecular Medicine, University of South Florida College of Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, Florida 33612, United States
| | - Afroza Akhtar
- Department of Molecular Medicine, University of South Florida College of Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, Florida 33612, United States
| | - Kyle DeFrees
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California San Francisco, 600 16th Street, Genentech Hall N572B, San Francisco, California 94158, United States
| | - Priyadarshini Jaishankar
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California San Francisco, 600 16th Street, Genentech Hall N572B, San Francisco, California 94158, United States
| | - Orville A. Pemberton
- Department of Molecular Medicine, University of South Florida College of Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, Florida 33612, United States
| | - Xiujun Zhang
- Department of Molecular Medicine, University of South Florida College of Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, Florida 33612, United States
| | - Cody Johnson
- Department of Molecular Medicine, University of South Florida College of Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, Florida 33612, United States
| | - Adam R. Renslo
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California San Francisco, 600 16th Street, Genentech Hall N572B, San Francisco, California 94158, United States
| | - Yu Chen
- Department of Molecular Medicine, University of South Florida College of Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, Florida 33612, United States
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Shurina BA, Page RC. Influence of substrates and inhibitors on the structure of Klebsiella pneumoniae carbapenemase-2. Exp Biol Med (Maywood) 2019; 244:1596-1604. [PMID: 31161945 DOI: 10.1177/1535370219854322] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The hydrolysis of last resort carbapenem antibiotics by Klebsiella pneumoniae carbapenemase-2 (KPC-2) presents a significant danger to global health. Combined with horizontal gene transfer, the emergence KPC-2 threatens to quickly expand carbapenemase activity to ever increasing numbers of pathogens. Our understanding of KPC-2 has greatly increased over the past decade thanks, in great part, to 20 crystal structures solved by groups around the world. These include apo KPC-2 structures, along with structures featuring a library of 10 different inhibitors representing diverse structural and functional classes. Herein we focus on cataloging the available KPC-2 structures and presenting a discussion of key aspects of each structure and important relationships between structures. Although the available structures do not provide information on dynamic motions with KPC-2, and the family of structures indicates small conformational changes across a wide array of bound inhibitors, substrates, and products, the structures provide a strong foundation for additional studies in the coming years to discover new KPC-2 inhibitors. Impact statement The work herein is important to the field as it provides a clear and succinct accounting of available KPC-2 structures. The work advances the field by collecting and analyzing differences and similarities across the available structures. This work features new analyses and interpretations of the existing structures which will impact the field in a positive way by making structural insights more widely available among the beta-lactamase community.
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Affiliation(s)
- Ben A Shurina
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Richard C Page
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
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36
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Amirkulova DB, White AD. Recent advances in maximum entropy biasing techniques for molecular dynamics. MOLECULAR SIMULATION 2019. [DOI: 10.1080/08927022.2019.1608988] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- D. B. Amirkulova
- Department of Chemical Engineering, University of Rochester, Rochester, NY, USA
| | - A. D. White
- Department of Chemical Engineering, University of Rochester, Rochester, NY, USA
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37
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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: 432] [Impact Index Per Article: 86.4] [Reference Citation Analysis] [Abstract] [Key Words] [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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38
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Klein R, Linciano P, Celenza G, Bellio P, Papaioannou S, Blazquez J, Cendron L, Brenk R, Tondi D. In silico identification and experimental validation of hits active against KPC-2 β-lactamase. PLoS One 2018; 13:e0203241. [PMID: 30496182 PMCID: PMC6264499 DOI: 10.1371/journal.pone.0203241] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 11/06/2018] [Indexed: 01/25/2023] Open
Abstract
Bacterial resistance has become a worldwide concern, particularly after the emergence of resistant strains overproducing carbapenemases. Among these, the KPC-2 carbapenemase represents a significant clinical challenge, being characterized by a broad substrate spectrum that includes aminothiazoleoxime and cephalosporins such as cefotaxime. Moreover, strains harboring KPC-type β-lactamases are often reported as resistant to available β-lactamase inhibitors (clavulanic acid, tazobactam and sulbactam). Therefore, the identification of novel non β-lactam KPC-2 inhibitors is strongly necessary to maintain treatment options. This study explored novel, non-covalent inhibitors active against KPC-2, as putative hit candidates. We performed a structure-based in silico screening of commercially available compounds for non-β-lactam KPC-2 inhibitors. Thirty-two commercially available high-scoring, fragment-like hits were selected for in vitro validation and their activity and mechanism of action vs the target was experimentally evaluated using recombinant KPC-2. N-(3-(1H-tetrazol-5-yl)phenyl)-3-fluorobenzamide (11a), in light of its ligand efficiency (LE = 0.28 kcal/mol/non-hydrogen atom) and chemistry, was selected as hit to be directed to chemical optimization to improve potency vs the enzyme and explore structural requirement for inhibition in KPC-2 binding site. Further, the compounds were evaluated against clinical strains overexpressing KPC-2 and the most promising compound reduced the MIC of the β-lactam antibiotic meropenem by four-fold.
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Affiliation(s)
- Raphael Klein
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, Mainz, Germany
| | - Pasquale Linciano
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Modena, Italy
| | - Giuseppe Celenza
- Dipartimento di Scienze Cliniche Applicate e Biotecnologie, Università dell’Aquila,L’Aquila, Italy
| | - Pierangelo Bellio
- Dipartimento di Scienze Cliniche Applicate e Biotecnologie, Università dell’Aquila,L’Aquila, Italy
| | - Sofia Papaioannou
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Modena, Italy
| | - Jesus Blazquez
- Department of Microbial Biotechnology, National Center for Biotechnology, Consejo Superior de Investigaciones Científicas (CSIC), Campus de la Universidad Autonoma-Cantoblanco, Madrid, Spain
| | - Laura Cendron
- Dipartimento di Biologia, Università di Padova, Padova, Italy
| | - Ruth Brenk
- Department of Biomedicine, University of Bergen, Bergen, Norway
- * E-mail: (DT); (RB)
| | - Donatella Tondi
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Modena, Italy
- * E-mail: (DT); (RB)
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Antibacterial Spectrum of a Tetrazole-Based Reversible Inhibitor of Serine β-Lactamases. Antimicrob Agents Chemother 2018; 62:AAC.02563-17. [PMID: 29844038 DOI: 10.1128/aac.02563-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 05/13/2018] [Indexed: 11/20/2022] Open
Abstract
CTX-M is the most prevalent family of extended-spectrum β-lactamases. We recently developed a tetrazole-derived noncovalent inhibitor of CTX-M-9. Here, we present the biochemical and microbiological activity of this inhibitor across a representative panel of serine β-lactamases and Gram-negative bacteria. The compound displayed significant activity against all major subgroups of CTX-M, including CTX-M-15, while it exhibited some low-level inhibition of other serine β-lactamases. Complex crystal structures with the CTX-M-14 S237A mutant and CTX-M-27 illustrate the binding contribution of specific active-site residues on the β3 strand. In vitro pharmacokinetic studies revealed drug-like properties and positive prospects for further optimization. These studies suggest that tetrazole-based compounds can provide novel chemotypes for future serine β-lactamase inhibitor discovery.
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Cortina GA, Hays JM, Kasson PM. Conformational Intermediate That Controls KPC-2 Catalysis and Beta-Lactam Drug Resistance. ACS Catal 2018; 8:2741-2747. [PMID: 30637173 DOI: 10.1021/acscatal.7b03832] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The KPC-2 carbapenemase enzyme is responsible for drug resistance in the majority of carbapenem-resistant gram-negative bacterial infections in the United States. A better understanding of what permits KPC-2 to hydrolyze carbapenem antibiotics and how this might be inhibited is thus of fundamental interest and great practical importance to development of better anti-infectives. By correlating molecular dynamics simulations with experimental enzyme kinetics, we have identified conformational changes that control KPC-2's ability to hydrolyze carbapenem antibiotics. Related beta-lactamase enzymes can interconvert between catalytically permissive and catalytically nonpermissive forms of an acylenzyme intermediate critical to drug hydrolysis. Using molecular dynamics simulations, we identify a similar equilibrium in KPC-2 and analyze the determinants of this conformational change. Because the conformational dynamics of KPC-2 are complex and sensitive to allosteric changes, we develop an information-theoretic approach to identify key determinants of this change. We measure unbiased estimators of the reaction coordinate between catalytically permissive and nonpermissive states, perform information-theoretic feature selection and, using restrained molecular dynamics simulations, validate the protein conformational changes predicted to control catalytically permissive geometry. We identify two binding-pocket residues that control the conformational transitions between catalytically active and inactive forms of KPC-2. Mutations to one of these residues, Trp105, lower the stability of the catalytically permissive state in simulations and have reduced experimental k cat values that show a strong linear correlation with the simulated catalytically permissive state lifetimes. This understanding can be leveraged to predict the drug resistance of further KPC-2 mutants and help design inhibitors to combat extreme drug resistance.
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Affiliation(s)
| | | | - Peter M. Kasson
- Laboratory of Molecular Biophysics, Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Box 596, Uppsala 75124, Sweden
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