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Nguyen VT, Birhanu BT, Miguel-Ruano V, Kim C, Batuecas M, Yang J, El-Araby AM, Jiménez-Faraco E, Schroeder VA, Alba A, Rana N, Sader S, Thomas CA, Feltzer R, Lee M, Fisher JF, Hermoso JA, Chang M, Mobashery S. Restoring susceptibility to β-lactam antibiotics in methicillin-resistant Staphylococcus aureus. Nat Chem Biol 2024:10.1038/s41589-024-01688-0. [PMID: 39060390 DOI: 10.1038/s41589-024-01688-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 06/26/2024] [Indexed: 07/28/2024]
Abstract
Infections by Staphylococcus aureus have been treated historically with β-lactam antibiotics. However, these antibiotics have become obsolete in methicillin-resistant S. aureus by acquisition of the bla and mec operons. The presence of the β-lactam antibiotic is detected by the sensor domains of BlaR and/or MecR, and the information is transmitted to the cytoplasm, resulting in derepression of the antibiotic-resistance genes. We hypothesized that inhibition of the sensor domain would shut down this response system, and β-lactam susceptibility would be restored. An in silico search of 11 million compounds led to a benzimidazole-based hit and, ultimately, to the boronate 4. The X-ray structure of 4 is covalently engaged with the active-site serine of BlaR. Compound 4 potentiates by 16- to 4,096-fold the activities of oxacillin and of meropenem against methicillin-resistant S. aureus strains. The combination of 4 with oxacillin or meropenem shows efficacy in infected mice, validating the strategy.
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Affiliation(s)
- Van T Nguyen
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Biruk T Birhanu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Vega Miguel-Ruano
- Department of Crystallography and Structural Biology, Instituto de Química-Física 'Blas Cabrera', Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Choon Kim
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Mayte Batuecas
- Department of Crystallography and Structural Biology, Instituto de Química-Física 'Blas Cabrera', Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Jingdong Yang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Amr M El-Araby
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Eva Jiménez-Faraco
- Department of Crystallography and Structural Biology, Instituto de Química-Física 'Blas Cabrera', Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Valerie A Schroeder
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Alejandra Alba
- Department of Crystallography and Structural Biology, Instituto de Química-Física 'Blas Cabrera', Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Neha Rana
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Safaa Sader
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Caitlyn A Thomas
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Rhona Feltzer
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Mijoon Lee
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Jed F Fisher
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Instituto de Química-Física 'Blas Cabrera', Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Mayland Chang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA.
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2
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Liang J, Ling J, Sun D, Wu G, Ouyang XK, Wang N, Yang G. Dextran-Based Antibacterial Hydrogel Dressings for Accelerating Infected Wound Healing by Reducing Inflammation Levels. Adv Healthc Mater 2024:e2400494. [PMID: 38801122 DOI: 10.1002/adhm.202400494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 05/23/2024] [Indexed: 05/29/2024]
Abstract
Infected wounds pose challenges such as exudate management, bacterial infections, and persistent inflammation, making them a significant challenge for modern dressings. To address these issues in infected wounds more effectively, aerogel-hydrogel biphase gels based on dextran are developed. The gel introduced in this study exhibits antibacterial and anti-inflammatory properties in the process of wound therapy, contributing to accelerated wound healing. The aerogel phase exhibits exceptional water-absorption capabilities, rapidly soaking up exudate from infected wound, thereby fostering a clean and hygienic wound healing microenvironment. Concurrently, the aerogel phase is enriched with hydrogen sulfide donors. Following water absorption and the formation of the hydrogel phase, it enables the sustained release of hydrogen sulfide around the wound sites. The experiments confirm that hydrogen sulfide, by promoting M2 macrophage differentiation and reducing the levels of inflammatory factors, effectively diminishes local inflammation levels at the wound site. Furthermore, the sodium copper chlorophyllin component within the hydrogel phase demonstrates effective antibacterial properties through photodynamic antimicrobial therapy, providing a viable solution to wound infection challenges.
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Affiliation(s)
- Jianhao Liang
- School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan, 310622, P. R. China
| | - Junhong Ling
- School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan, 310622, P. R. China
| | - Deguan Sun
- Department of Cardiothoracic Surgery, Zhoushan Hospital, Wenzhou Medical University, Zhoushan, 316000, P. R. China
| | - Guanhuai Wu
- Department of Cardiothoracic Surgery, Zhoushan Hospital, Wenzhou Medical University, Zhoushan, 316000, P. R. China
| | - Xiao-Kun Ouyang
- School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan, 310622, P. R. China
| | - Nan Wang
- School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan, 310622, P. R. China
| | - Guocai Yang
- Department of Cardiothoracic Surgery, Zhoushan Hospital, Wenzhou Medical University, Zhoushan, 316000, P. R. China
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3
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Wang H, Yang Y, Wang S, Badawy S, Ares I, Martínez M, Lopez-Torres B, Martínez-Larrañaga MR, Wang X, Anadón A, Martínez MA. Antimicrobial sensitisers: Gatekeepers to avoid the development of multidrug-resistant bacteria. J Control Release 2024; 369:25-38. [PMID: 38508527 DOI: 10.1016/j.jconrel.2024.03.031] [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: 10/24/2023] [Revised: 02/23/2024] [Accepted: 03/16/2024] [Indexed: 03/22/2024]
Abstract
The resistance of multidrug-resistant bacteria to existing antibiotics forces the continued development of new antibiotics and antibacterial agents, but the high costs and long timeframe involved in the development of new agents renders the hope that existing antibiotics may again play a part. The "antibiotic adjuvant" is an indirect antibacterial strategy, but its vague concept has, in the past, limited the development speed of related drugs. In this review article, we put forward an accurate concept of a "non-self-antimicrobial sensitisers (NSAS)", to distinguish it from an "antibiotic adjuvant", and then discuss several scientific methods to restore bacterial sensitivity to antibiotics, and the sources and action mechanism of existing NSAS, in order to guide the development and further research of NSAS.
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Affiliation(s)
- Hanfei Wang
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yingying Yang
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Simeng Wang
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Sara Badawy
- MAO Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Pathology Department of Animal Medicine, Faculty of Veterinary Medicine, Benha University, Egypt
| | - Irma Ares
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Universidad Complutense de Madrid (UCM), and Research Institute Hospital, 12 de Octubre (i+12), 28040 Madrid, Spain
| | - Marta Martínez
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Universidad Complutense de Madrid (UCM), and Research Institute Hospital, 12 de Octubre (i+12), 28040 Madrid, Spain
| | - Bernardo Lopez-Torres
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Universidad Complutense de Madrid (UCM), and Research Institute Hospital, 12 de Octubre (i+12), 28040 Madrid, Spain
| | - María-Rosa Martínez-Larrañaga
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Universidad Complutense de Madrid (UCM), and Research Institute Hospital, 12 de Octubre (i+12), 28040 Madrid, Spain
| | - Xu Wang
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China; MAO Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Arturo Anadón
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Universidad Complutense de Madrid (UCM), and Research Institute Hospital, 12 de Octubre (i+12), 28040 Madrid, Spain.
| | - María-Aránzazu Martínez
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Universidad Complutense de Madrid (UCM), and Research Institute Hospital, 12 de Octubre (i+12), 28040 Madrid, Spain
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4
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Introvigne ML, Beardsley TJ, Fernando MC, Leonard DA, Wallar BJ, Rudin SD, Taracila MA, Rather PN, Colquhoun JM, Song S, Fini F, Hujer KM, Hujer AM, Prati F, Powers RA, Bonomo RA, Caselli E. Sulfonamidoboronic Acids as "Cross-Class" Inhibitors of an Expanded-Spectrum Class C Cephalosporinase, ADC-33, and a Class D Carbapenemase, OXA-24/40: Strategic Compound Design to Combat Resistance in Acinetobacter baumannii. Antibiotics (Basel) 2023; 12:antibiotics12040644. [PMID: 37107006 PMCID: PMC10135033 DOI: 10.3390/antibiotics12040644] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/17/2023] [Accepted: 03/18/2023] [Indexed: 04/29/2023] Open
Abstract
Acinetobacter baumannii is a Gram-negative organism listed as an urgent threat pathogen by the World Health Organization (WHO). Carbapenem-resistant A. baumannii (CRAB), especially, present therapeutic challenges due to complex mechanisms of resistance to β-lactams. One of the most important mechanisms is the production of β-lactamase enzymes capable of hydrolyzing β-lactam antibiotics. Co-expression of multiple classes of β-lactamases is present in CRAB; therefore, the design and synthesis of "cross-class" inhibitors is an important strategy to preserve the efficacy of currently available antibiotics. To identify new, nonclassical β-lactamase inhibitors, we previously identified a sulfonamidomethaneboronic acid CR167 active against Acinetobacter-derived class C β-lactamases (ADC-7). The compound demonstrated affinity for ADC-7 with a Ki = 160 nM and proved to be able to decrease MIC values of ceftazidime and cefotaxime in different bacterial strains. Herein, we describe the activity of CR167 against other β-lactamases in A. baumannii: the cefepime-hydrolysing class C extended-spectrum β-lactamase (ESAC) ADC-33 and the carbapenem-hydrolyzing OXA-24/40 (class D). These investigations demonstrate CR167 as a valuable cross-class (C and D) inhibitor, and the paper describes our attempts to further improve its activity. Five chiral analogues of CR167 were rationally designed and synthesized. The structures of OXA-24/40 and ADC-33 in complex with CR167 and select chiral analogues were obtained. The structure activity relationships (SARs) are highlighted, offering insights into the main determinants for cross-class C/D inhibitors and impetus for novel drug design.
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Affiliation(s)
- Maria Luisa Introvigne
- Department of Life Sciences, Università di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Trevor J Beardsley
- Department of Chemistry, Grand Valley State University, Allendale, MI 49401, USA
| | - Micah C Fernando
- Department of Chemistry, Grand Valley State University, Allendale, MI 49401, USA
| | - David A Leonard
- Department of Chemistry, Grand Valley State University, Allendale, MI 49401, USA
| | - Bradley J Wallar
- Department of Chemistry, Grand Valley State University, Allendale, MI 49401, USA
| | - Susan D Rudin
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, USA
| | - Magdalena A Taracila
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, USA
| | - Philip N Rather
- Research Service, Atlanta Veterans Medical Center, Decatur, GA 30033, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30307, USA
- Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA 30307, USA
| | - Jennifer M Colquhoun
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30307, USA
| | - Shaina Song
- Research Service, Atlanta Veterans Medical Center, Decatur, GA 30033, USA
| | - Francesco Fini
- Department of Life Sciences, Università di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Kristine M Hujer
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, USA
| | - Andrea M Hujer
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, USA
| | - Fabio Prati
- Department of Life Sciences, Università di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Rachel A Powers
- Department of Chemistry, Grand Valley State University, Allendale, MI 49401, USA
| | - Robert A Bonomo
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, USA
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, USA
- Departments of Medicine, Pharmacology, Molecular Biology and Microbiology, Biochemistry, Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH 44106, USA
| | - Emilia Caselli
- Department of Life Sciences, Università di Modena e Reggio Emilia, Via Campi 103, 41125 Modena, Italy
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5
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Wen X, Wu X, Jin R, Lu X. Privileged heterocycles for DNA-encoded library design and hit-to-lead optimization. Eur J Med Chem 2023; 248:115079. [PMID: 36669370 DOI: 10.1016/j.ejmech.2022.115079] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 12/22/2022] [Accepted: 12/29/2022] [Indexed: 01/15/2023]
Abstract
It is well known that heterocyclic compounds play a key role in improving drug activity, target selectivity, physicochemical properties as well as reducing toxicity. In this review, we summarized the representative heterocyclic structures involved in hit compounds which were obtained from DNA-encoded library from 2013 to 2021. In some examples, the state of the art in heterocycle-based DEL synthesis and hit-to-lead optimization are highlighted. We hope that more and more novel heterocycle-based DEL toolboxes and in-depth pharmaceutical research on these lead compounds can be developed to accelerate the discovery of new drugs.
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Affiliation(s)
- Xin Wen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai, 201203, China.
| | - Xinyuan Wu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai, 201203, China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China.
| | - Rui Jin
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai, 201203, China.
| | - Xiaojie Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai, 201203, China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China.
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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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Mitchell JM, June CM, Baggett VL, Lowe BC, Ruble JF, Bonomo RA, Leonard DA, Powers RA. Conformational flexibility in carbapenem hydrolysis drives substrate specificity of the class D carbapenemase OXA-24/40. J Biol Chem 2022; 298:102127. [PMID: 35709986 PMCID: PMC9293634 DOI: 10.1016/j.jbc.2022.102127] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 12/03/2022] Open
Abstract
The evolution of multidrug resistance in Acinetobacter spp. increases the risk of our best antibiotics losing their efficacy. From a clinical perspective, the carbapenem-hydrolyzing class D β-lactamase subfamily present in Acinetobacter spp. is particularly concerning because of its ability to confer resistance to carbapenems. The kinetic profiles of class D β-lactamases exhibit variability in carbapenem hydrolysis, suggesting functional differences. To better understand the structure–function relationship between the carbapenem-hydrolyzing class D β-lactamase OXA-24/40 found in Acinetobacter baumannii and carbapenem substrates, we analyzed steady-state kinetics with the carbapenem antibiotics meropenem and ertapenem and determined the structures of complexes of OXA-24/40 bound to imipenem, meropenem, doripenem, and ertapenem, as well as the expanded-spectrum cephalosporin cefotaxime, using X-ray crystallography. We show that OXA-24/40 exhibits a preference for ertapenem compared with meropenem, imipenem, and doripenem, with an increase in catalytic efficiency of up to fourfold. We suggest that superposition of the nine OXA-24/40 complexes will better inform future inhibitor design efforts by providing insight into the complicated and varying ways in which carbapenems are selected and bound by class D β-lactamases.
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Affiliation(s)
- Joshua M Mitchell
- Department of Chemistry, Grand Valley State University, Allendale, MI
| | - Cynthia M June
- Department of Chemistry, Grand Valley State University, Allendale, MI
| | - Vincent L Baggett
- Department of Chemistry, Grand Valley State University, Allendale, MI
| | - Beth C Lowe
- Department of Chemistry, Grand Valley State University, Allendale, MI
| | - James F Ruble
- Department of Chemistry, Grand Valley State University, Allendale, MI
| | - Robert A Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, 10701 East Boulevard, Cleveland, OH; Departments of Medicine, Biochemistry, Molecular Biology and Microbiology, Pharmacology, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH; CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES) Cleveland, OH.
| | - David A Leonard
- Department of Chemistry, Grand Valley State University, Allendale, MI
| | - Rachel A Powers
- Department of Chemistry, Grand Valley State University, Allendale, MI.
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8
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Jiang J, Xu Z, Chen J, Xu Z, Huang Y, Xi J, Fan L. Staphylococcus aureus-targeting peptide/surfactant assemblies for antibacterial therapy. Colloids Surf B Biointerfaces 2022; 214:112444. [PMID: 35278861 DOI: 10.1016/j.colsurfb.2022.112444] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 02/01/2022] [Accepted: 03/02/2022] [Indexed: 01/03/2023]
Abstract
To address the challenge from microbial resistance, this work developed a surfactant with 18-carbon single hydrocarbon chain and multi-amine head groups (C18N3). After assembling with Staphylococcus aureus-targeting peptide (CARG), the obtained C18N3/CARG assemblies exhibited excellent antimicrobial activities against Staphylococcus aureus and methicillin-resistant Staphylococcus aureus in vitro and in vivo, in which the targeting peptide CARG bonded specifically to Staphylococcus aureus and C18N3 killed bacteria with a mechanism of membrane disruption. Importantly, C18N3 could also work as a β-lactamase inhibitor to overcome the bacterial resistance to β-lactam antibiotics through noncompetitive inhibition. The combination of β-lactam antibiotic and C18N3/CARG assemblies more effectively suppressed methicillin-resistant Staphylococcus aureus in vitro and in vivo relative to equivalent dose of free antibiotic or C18N3. Thus, the antibacterial platform of antibiotic-carrying surfactant assemblies bearing bacteria-targeted peptides, in which C18N3 performed dual function, antibacterial agent and β-lactamase inhibitor, may help fight against the difficult-to-treat infections.
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Affiliation(s)
- Jian Jiang
- Department of Pharmacology, Institute of Translational Medicine, School of Medicine, Yangzhou University, Yangzhou 225009, China
| | - Zhilong Xu
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002, China
| | - Jie Chen
- Department of Pharmacology, Institute of Translational Medicine, School of Medicine, Yangzhou University, Yangzhou 225009, China
| | - Ze Xu
- Department of Pharmacology, Institute of Translational Medicine, School of Medicine, Yangzhou University, Yangzhou 225009, China
| | - Ying Huang
- Department of Pharmacology, Institute of Translational Medicine, School of Medicine, Yangzhou University, Yangzhou 225009, China
| | - Juqun Xi
- Department of Pharmacology, Institute of Translational Medicine, School of Medicine, Yangzhou University, Yangzhou 225009, China; Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou 225009, China.
| | - Lei Fan
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002, China.
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9
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Yadav TC, Agarwal V, Srivastava AK, Raghuwanshi N, Varadwaj P, Prasad R, Pruthi V. Insight into Structure-Function Relationships of β-Lactamase and BLIPs Interface Plasticity using Protein-Protein Interactions. Curr Pharm Des 2020; 25:3378-3389. [PMID: 31544712 DOI: 10.2174/1381612825666190911154650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 09/05/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Mostly BLIPs are identified in soil bacteria Streptomyces and originally isolated from Streptomyces clavuligerus and can be utilized as a model system for biophysical, structural, mutagenic and computational studies. BLIP possess homology with two proteins viz., BLIP-I (Streptomyces exofoliatus) and BLP (beta-lactamase inhibitory protein like protein from S. clavuligerus). BLIP consists of 165 amino acid, possessing two homologues domains comprising helix-loop-helix motif packed against four stranded beta-sheet resulting into solvent exposed concave surface with extended four stranded beta-sheet. BLIP-I is a 157 amino acid long protein obtained from S. exofoliatus having 37% sequence identity to BLIP and inhibits beta-lactamase. METHODS This review is intended to briefly illustrate the beta-lactamase inhibitory activity of BLIP via proteinprotein interaction and aims to open up a new avenue to combat antimicrobial resistance using peptide based inhibition. RESULTS D49A mutation in BLIP-I results in a decrease in affinity for TEM-1 from 0.5 nM to 10 nM (Ki). It is capable of inhibiting TEM-1 and bactopenemase and differs from BLIP only in modulating cell wall synthesis enzyme. Whereas, BLP is a 154 amino acid long protein isolated from S. clavuligerus via DNA sequencing analysis of Cephamycin-Clavulanate gene bunch. It shares 32% sequence similarity with BLIP and 42% with BLIP-I. Its biological function is unclear and lacks beta-lactamase inhibitory activity. CONCLUSION Protein-protein interactions mediate a significant role in regulation and modulation of cellular developments and processes. Specific biological markers and geometric characteristics are manifested by active site binding clefts of protein surfaces which determines the specificity and affinity for their targets. TEM1.BLIP is a classical model to study protein-protein interaction. β-Lactamase inhibitory proteins (BLIPs) interacts and inhibits various β-lactamases with extensive range of affinities.
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Affiliation(s)
- Tara C Yadav
- Department of Biotechnology, Indian Institute of Technology, Roorkee-247667, Uttarakhand, India
| | - Vidhu Agarwal
- Department of Bioinformatics, Indian Institute of Information Technology, Allahabad 211015, India
| | - Amit K Srivastava
- Department of Biotechnology, Indian Institute of Technology, Roorkee-247667, Uttarakhand, India
| | - Navdeep Raghuwanshi
- Vaccine Formulation & Research Center, Gennova (Emcure) Biopharmaceuticals Limited, Pune - 11057, Maharashtra, India
| | - Pritish Varadwaj
- Department of Bioinformatics, Indian Institute of Information Technology, Allahabad 211015, India
| | - Ramasare Prasad
- Department of Biotechnology, Indian Institute of Technology, Roorkee-247667, Uttarakhand, India
| | - Vikas Pruthi
- Department of Biotechnology, Indian Institute of Technology, Roorkee-247667, Uttarakhand, India
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10
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Taylor DM, Anglin J, Park S, Ucisik MN, Faver JC, Simmons N, Jin Z, Palaniappan M, Nyshadham P, Li F, Campbell J, Hu L, Sankaran B, Prasad BV, Huang H, Matzuk MM, Palzkill T. Identifying Oxacillinase-48 Carbapenemase Inhibitors Using DNA-Encoded Chemical Libraries. ACS Infect Dis 2020; 6:1214-1227. [PMID: 32182432 PMCID: PMC7673237 DOI: 10.1021/acsinfecdis.0c00015] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Bacterial resistance to β-lactam antibiotics is largely mediated by β-lactamases, which catalyze the hydrolysis of these drugs and continue to emerge in response to antibiotic use. β-Lactamases that hydrolyze the last resort carbapenem class of β-lactam antibiotics (carbapenemases) are a growing global health threat. Inhibitors have been developed to prevent β-lactamase-mediated hydrolysis and restore the efficacy of these antibiotics. However, there are few inhibitors available for problematic carbapenemases such as oxacillinase-48 (OXA-48). A DNA-encoded chemical library approach was used to rapidly screen for compounds that bind and potentially inhibit OXA-48. Using this approach, a hit compound, CDD-97, was identified with submicromolar potency (Ki = 0.53 ± 0.08 μM) against OXA-48. X-ray crystallography showed that CDD-97 binds noncovalently in the active site of OXA-48. Synthesis and testing of derivatives of CDD-97 revealed structure-activity relationships and informed the design of a compound with a 2-fold increase in potency. CDD-97, however, synergizes poorly with β-lactam antibiotics to inhibit the growth of bacteria expressing OXA-48 due to poor accumulation into E. coli. Despite the low in vivo activity, CDD-97 provides new insights into OXA-48 inhibition and demonstrates the potential of using DNA-encoded chemistry technology to rapidly identify β-lactamase binders and to study β-lactamase inhibition, leading to clinically useful inhibitors.
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Affiliation(s)
- Doris Mia Taylor
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Justin Anglin
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Suhyeorn Park
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Melek N. Ucisik
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - John C. Faver
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Nicholas Simmons
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zhuang Jin
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Murugesan Palaniappan
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Pranavanand Nyshadham
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Feng Li
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - James Campbell
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Advanced Light Source, Lawrence Berkeley National Lab, CA, 94720, USA
| | - B.V. Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hongbing Huang
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Martin M. Matzuk
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Timothy Palzkill
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, 77030, USA
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11
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Lefurgy ST, Caselli E, Taracila MA, Malashkevich VN, Biju B, Papp-Wallace KM, Bonanno JB, Prati F, Almo SC, Bonomo RA. Structures of FOX-4 Cephamycinase in Complex with Transition-State Analog Inhibitors. Biomolecules 2020; 10:biom10050671. [PMID: 32349291 PMCID: PMC7277225 DOI: 10.3390/biom10050671] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/14/2020] [Accepted: 04/16/2020] [Indexed: 12/17/2022] Open
Abstract
Boronic acid transition-state analog inhibitors (BATSIs) are partners with β-lactam antibiotics for the treatment of complex bacterial infections. Herein, microbiological, biochemical, and structural findings on four BATSIs with the FOX-4 cephamycinase, a class C β-lactamase that rapidly hydrolyzes cefoxitin, are revealed. FOX-4 is an extended-spectrum class C cephalosporinase that demonstrates conformational flexibility when complexed with certain ligands. Like other β-lactamases of this class, studies on FOX-4 reveal important insights into structure–activity relationships. We show that SM23, a BATSI, shows both remarkable flexibility and affinity, binding similarly to other β-lactamases, yet retaining an IC50 value < 0.1 μM. Our analyses open up new opportunities for the design of novel transition-state analogs of class C enzymes.
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Affiliation(s)
- Scott T. Lefurgy
- Department of Chemistry, Hofstra University, Hempstead, NY 11549, USA
| | - Emilia Caselli
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Magdalena A. Taracila
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, USA
| | | | - Beena Biju
- Department of Chemistry, Hofstra University, Hempstead, NY 11549, USA
| | - Krisztina M. Papp-Wallace
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, USA
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Jeffrey B. Bonanno
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Fabio Prati
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Steven C. Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Robert A. Bonomo
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, USA
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Department of Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES) Cleveland, OH 44106, USA
- Correspondence: ; Tel.: +216-791-3800 (ext. 64801); Fax: +216-231-3482
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12
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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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13
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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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14
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Biochemical Activity of Vaborbactam. Antimicrob Agents Chemother 2020; 64:AAC.01935-19. [PMID: 31712199 PMCID: PMC6985712 DOI: 10.1128/aac.01935-19] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 10/30/2019] [Indexed: 11/20/2022] Open
Abstract
The most common mechanism of resistance to β-lactams antibiotics in Gram-negative bacteria is production of β-lactamase enzymes capable of cleaving the β-lactam ring. Inhibition of β-lactamase activity with small-molecule drugs is a proven strategy to restore the potency of many β-lactam antibiotics. Vaborbactam (formerly RPX7009) is a cyclic boronic acid β-lactamase inhibitor (BLI) with a broad spectrum of activity against various serine β-lactamases, including KPC carbapenemases. The combination of vaborbactam and meropenem is approved in the United States and Europe for the treatment of various nosocomial infections. We attempted to gain more insight into the mechanism of action of vaborbactam by conducting detailed kinetic characterization of its interaction with various recombinant His-tagged β-lactamases. Vaborbactam demonstrated potent inhibition of class A and class C enzymes with Ki values ranging from 0.022 to 0.18 μM, while inhibition of class D enzymes was rather poor, and no activity against class B β-lactamases was detected. Importantly, vaborbactam inhibited KPC-2, KPC-3, BKC-1, and SME-2 carbapenemases at 1:1 stoichiometry, while these numbers were higher for other class A and C enzymes. Vaborbactam was also shown to be a potent progressive inactivator of several enzymes, including KPCs with inactivation constants k 2/K in the range of 3.4 × 103 to 2.4 × 104 M-1 s-1 Finally, experiments on the recovery of enzyme activity demonstrated the high stability of the vaborbactam-KPC complex, with 0.000040 s-1 k off values and a corresponding residence time of 7 h, whereas the release of vaborbactam bound to other serine β-lactamases was substantially faster. The biochemical characteristics of vaborbactam described in this study may facilitate further chemical optimization efforts to develop boronic BLIs with improved affinity and broader spectrum of inhibition.
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15
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Ma Y, Wang C, Li Y, Li J, Wan Q, Chen J, Tay FR, Niu L. Considerations and Caveats in Combating ESKAPE Pathogens against Nosocomial Infections. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1901872. [PMID: 31921562 PMCID: PMC6947519 DOI: 10.1002/advs.201901872] [Citation(s) in RCA: 139] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/04/2019] [Indexed: 05/19/2023]
Abstract
ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) are among the most common opportunistic pathogens in nosocomial infections. ESKAPE pathogens distinguish themselves from normal ones by developing a high level of antibiotic resistance that involves multiple mechanisms. Contemporary therapeutic strategies which are potential options in combating ESKAPE bacteria need further investigation. Herein, a broad overview of the antimicrobial research on ESKAPE pathogens over the past five years is provided with prospective clinical applications.
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Affiliation(s)
- Yu‐Xuan Ma
- State Key Laboratory of Military StomatologyNational Clinical Research Center for Oral DiseasesShaanxi Key Laboratory of StomatologyDepartment of ProsthodonticsSchool of StomatologyThe Fourth Military Medical University145 Changle West RoadXi'anShaanxi710032P. R. China
| | - Chen‐Yu Wang
- State Key Laboratory of Military StomatologyNational Clinical Research Center for Oral DiseasesShaanxi Key Laboratory of StomatologyDepartment of ProsthodonticsSchool of StomatologyThe Fourth Military Medical University145 Changle West RoadXi'anShaanxi710032P. R. China
| | - Yuan‐Yuan Li
- State Key Laboratory of Military StomatologyNational Clinical Research Center for Oral DiseasesShaanxi Key Laboratory of StomatologyDepartment of ProsthodonticsSchool of StomatologyThe Fourth Military Medical University145 Changle West RoadXi'anShaanxi710032P. R. China
| | - Jing Li
- State Key Laboratory of Military StomatologyNational Clinical Research Center for Oral DiseasesShaanxi Key Laboratory of StomatologyDepartment of ProsthodonticsSchool of StomatologyThe Fourth Military Medical University145 Changle West RoadXi'anShaanxi710032P. R. China
| | - Qian‐Qian Wan
- State Key Laboratory of Military StomatologyNational Clinical Research Center for Oral DiseasesShaanxi Key Laboratory of StomatologyDepartment of ProsthodonticsSchool of StomatologyThe Fourth Military Medical University145 Changle West RoadXi'anShaanxi710032P. R. China
| | - Ji‐Hua Chen
- State Key Laboratory of Military StomatologyNational Clinical Research Center for Oral DiseasesShaanxi Key Laboratory of StomatologyDepartment of ProsthodonticsSchool of StomatologyThe Fourth Military Medical University145 Changle West RoadXi'anShaanxi710032P. R. China
| | - Franklin R. Tay
- State Key Laboratory of Military StomatologyNational Clinical Research Center for Oral DiseasesShaanxi Key Laboratory of StomatologyDepartment of ProsthodonticsSchool of StomatologyThe Fourth Military Medical University145 Changle West RoadXi'anShaanxi710032P. R. China
- The Graduate SchoolAugusta University1430, John Wesley Gilbert DriveAugustaGA30912‐1129USA
| | - Li‐Na Niu
- State Key Laboratory of Military StomatologyNational Clinical Research Center for Oral DiseasesShaanxi Key Laboratory of StomatologyDepartment of ProsthodonticsSchool of StomatologyThe Fourth Military Medical University145 Changle West RoadXi'anShaanxi710032P. R. China
- The Graduate SchoolAugusta University1430, John Wesley Gilbert DriveAugustaGA30912‐1129USA
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16
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González-Bello C, Rodríguez D, Pernas M, Rodríguez Á, Colchón E. β-Lactamase Inhibitors To Restore the Efficacy of Antibiotics against Superbugs. J Med Chem 2019; 63:1859-1881. [PMID: 31663735 DOI: 10.1021/acs.jmedchem.9b01279] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Infections caused by resistant bacteria are nowadays too common, and some pathogens have even become resistant to multiple types of antibiotics, in which case few or even no treatments are available. In recent years, the most successful strategy in anti-infective drug discovery for the treatment of such problematic infections is the combination therapy "antibiotic + inhibitor of resistance". These inhibitors allow the repurposing of antibiotics that have already proven to be safe and effective for clinical use. Three main types of compounds have been developed to block the principal bacterial resistance mechanisms: (i) β-lactamase inhibitors; (ii) outer membrane permeabilizers; (iii) efflux pump inhibitors. This Perspective is focused on β-lactamase inhibitors that disable the most prevalent cause of antibiotic resistance in Gram-negative bacteria, i.e., the deactivation of the most widely used antibiotics, β-lactams (penicillins, cephalosporines, carbapenems, and monobactams), by the production of β-lactamases. An overview of the most recently identified β-lactamase inhibitors and of combination therapy is provided. The article also covers the mechanism of action of the different types of β-lactamase enzymes as a basis for inhibitor design and target inactivation.
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Affiliation(s)
- Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Diana Rodríguez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Marina Pernas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Ángela Rodríguez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Esther Colchón
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
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17
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Krajnc A, Brem J, Hinchliffe P, Calvopiña K, Panduwawala TD, Lang PA, Kamps JJAG, Tyrrell JM, Widlake E, Saward BG, Walsh TR, Spencer J, Schofield CJ. Bicyclic Boronate VNRX-5133 Inhibits Metallo- and Serine-β-Lactamases. J Med Chem 2019; 62:8544-8556. [PMID: 31454231 PMCID: PMC6767355 DOI: 10.1021/acs.jmedchem.9b00911] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
The
bicyclic boronate VNRX-5133 (taniborbactam) is a new type of
β-lactamase inhibitor in clinical development. We report that
VNRX-5133 inhibits serine-β-lactamases (SBLs) and some clinically
important metallo-β-lactamases (MBLs), including NDM-1 and VIM-1/2.
VNRX-5133 activity against IMP-1 and tested B2/B3 MBLs was lower/not
observed. Crystallography reveals how VNRX-5133 binds to the class
D SBL OXA-10 and MBL NDM-1. The crystallographic results highlight
the ability of bicyclic boronates to inhibit SBLs and MBLs via binding
of a tetrahedral (sp3) boron species. The structures imply
conserved binding of the bicyclic core with SBLs/MBLs. With NDM-1,
by crystallography, we observed an unanticipated VNRX-5133 binding
mode involving cyclization of its acylamino oxygen onto the boron
of the bicyclic core. Different side-chain binding modes for bicyclic
boronates for SBLs and MBLs imply scope for side-chain optimization.
The results further support the “high-energy-intermediate”
analogue approach for broad-spectrum β-lactamase inhibitor development
and highlight the ability of boron inhibitors to interchange between
different hybridization states/binding modes.
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Affiliation(s)
- Alen Krajnc
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Jürgen Brem
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Philip Hinchliffe
- School of Cellular and Molecular Medicine, Biomedical Sciences Building, University Walk , University of Bristol , Bristol BS8 1TD , United Kingdom
| | - Karina Calvopiña
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Tharindi D Panduwawala
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Pauline A Lang
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Jos J A G Kamps
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Jonathan M Tyrrell
- Department of Medical Microbiology & Infectious Disease , Institute of Infection & Immunity , UHW Main Building, Heath Park , Cardiff CF14 4XN , United Kingdom
| | - Emma Widlake
- Department of Medical Microbiology & Infectious Disease , Institute of Infection & Immunity , UHW Main Building, Heath Park , Cardiff CF14 4XN , United Kingdom
| | - Benjamin G Saward
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Timothy R Walsh
- Department of Medical Microbiology & Infectious Disease , Institute of Infection & Immunity , UHW Main Building, Heath Park , Cardiff CF14 4XN , United Kingdom
| | - James Spencer
- School of Cellular and Molecular Medicine, Biomedical Sciences Building, University Walk , University of Bristol , Bristol BS8 1TD , United Kingdom
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
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18
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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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19
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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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20
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Krajnc A, Lang PA, Panduwawala TD, Brem J, Schofield CJ. Will morphing boron-based inhibitors beat the β-lactamases? Curr Opin Chem Biol 2019; 50:101-110. [PMID: 31004962 PMCID: PMC6591701 DOI: 10.1016/j.cbpa.2019.03.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 02/28/2019] [Accepted: 03/01/2019] [Indexed: 01/13/2023]
Abstract
The β-lactams remain the most important antibacterials, but their use is increasingly compromised by resistance, importantly by β-lactamases. Although β-lactam and non-β-lactam inhibitors forming stable acyl-enzyme complexes with nucleophilic serine β-lactamases (SBLs) are widely used, these are increasingly susceptible to evolved SBLs and do not inhibit metallo-β-lactamases (MBLs). Boronic acids and boronate esters, especially cyclic ones, can potently inhibit both SBLs and MBLs. Vaborbactam, a monocyclic boronate, is approved for clinical use, but its β-lactamase coverage is limited. Bicyclic boronates rapidly react with SBLs and MBLs forming stable enzyme-inhibitor complexes that mimic the common anionic high-energy tetrahedral intermediates in SBL/MBL catalysis, as revealed by crystallography. The ability of boronic acids to 'morph' between sp2 and sp3 hybridisation states may help enable potent inhibition. There is limited structure-activity relationship information on the (bi)cyclic boronate inhibitors compared to β-lactams, hence scope for creativity towards new boron-based β-lactamase inhibitors/antibacterials.
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Affiliation(s)
- Alen Krajnc
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Pauline A Lang
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Tharindi D Panduwawala
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Jürgen Brem
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Christopher J Schofield
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom.
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21
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Tehrani KHME, Martin NI. β-lactam/β-lactamase inhibitor combinations: an update. MEDCHEMCOMM 2018; 9:1439-1456. [PMID: 30288219 PMCID: PMC6151480 DOI: 10.1039/c8md00342d] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 08/16/2018] [Indexed: 12/22/2022]
Abstract
Antibiotic resistance caused by β-lactamase production continues to present a growing challenge to the efficacy of β-lactams and their role as the most important class of clinically used antibiotics. In response to this threat however, only a handful of β-lactamase inhibitors have been introduced to the market over the past thirty years. The first-generation β-lactamase inhibitors (clavulanic acid, sulbactam and tazobactam) are all β-lactam derivatives and work primarily by inactivating class A and some class C serine β-lactamases. The newer generations of β-lactamase inhibitors including avibactam and vaborbactam are based on non-β-lactam structures and their spectrum of inhibition is extended to KPC as an important class A carbapenemase. Despite these advances several class D and virtually all important class B β-lactamases are resistant to existing inhibitors. The present review provides an overview of recent FDA-approved β-lactam/β-lactamase inhibitor combinations as well as an update on research efforts aimed at the discovery and development of novel β-lactamase inhibitors.
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Affiliation(s)
- Kamaleddin H M E Tehrani
- Department of Chemical Biology & Drug Discovery , Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Universiteitsweg 99 , 3584 CG Utrecht , The Netherlands
| | - Nathaniel I Martin
- Department of Chemical Biology & Drug Discovery , Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Universiteitsweg 99 , 3584 CG Utrecht , The Netherlands
- Biological Chemistry Group , Institute of Biology Leiden , Leiden University , Sylvius Laboratories, Sylviusweg 72 , 2333 BE Leiden , The Netherlands . ; Tel: +31 (0)6 1878 5274
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22
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Tackling the Antibiotic Resistance Caused by Class A β-Lactamases through the Use of β-Lactamase Inhibitory Protein. Int J Mol Sci 2018; 19:ijms19082222. [PMID: 30061509 PMCID: PMC6121496 DOI: 10.3390/ijms19082222] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 07/23/2018] [Accepted: 07/25/2018] [Indexed: 12/27/2022] Open
Abstract
β-Lactams are the most widely used and effective antibiotics for the treatment of infectious diseases. Unfortunately, bacteria have developed several mechanisms to combat these therapeutic agents. One of the major resistance mechanisms involves the production of β-lactamase that hydrolyzes the β-lactam ring thereby inactivating the drug. To overcome this threat, the small molecule β-lactamase inhibitors (e.g., clavulanic acid, sulbactam and tazobactam) have been used in combination with β-lactams for treatment. However, the bacterial resistance to this kind of combination therapy has evolved recently. Therefore, multiple attempts have been made to discover and develop novel broad-spectrum β-lactamase inhibitors that sufficiently work against β-lactamase producing bacteria. β-lactamase inhibitory proteins (BLIPs) (e.g., BLIP, BLIP-I and BLIP-II) are potential inhibitors that have been found from soil bacterium Streptomyces spp. BLIPs bind and inhibit a wide range of class A β-lactamases from a diverse set of Gram-positive and Gram-negative bacteria, including TEM-1, PC1, SME-1, SHV-1 and KPC-2. To the best of our knowledge, this article represents the first systematic review on β-lactamase inhibitors with a particular focus on BLIPs and their inherent properties that favorably position them as a source of biologically-inspired drugs to combat antimicrobial resistance. Furthermore, an extensive compilation of binding data from β-lactamase–BLIP interaction studies is presented herein. Such information help to provide key insights into the origin of interaction that may be useful for rationally guiding future drug design efforts.
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23
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Papp-Wallace KM, Nguyen NQ, Jacobs MR, Bethel CR, Barnes MD, Kumar V, Bajaksouzian S, Rudin SD, Rather PN, Bhavsar S, Ravikumar T, Deshpande PK, Patil V, Yeole R, Bhagwat SS, Patel MV, van den Akker F, Bonomo RA. Strategic Approaches to Overcome Resistance against Gram-Negative Pathogens Using β-Lactamase Inhibitors and β-Lactam Enhancers: Activity of Three Novel Diazabicyclooctanes WCK 5153, Zidebactam (WCK 5107), and WCK 4234. J Med Chem 2018; 61:4067-4086. [PMID: 29627985 DOI: 10.1021/acs.jmedchem.8b00091] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Limited treatment options exist to combat infections caused by multidrug-resistant (MDR) Gram-negative bacteria possessing broad-spectrum β-lactamases. The design of novel β-lactamase inhibitors is of paramount importance. Here, three novel diazabicyclooctanes (DBOs), WCK 5153, zidebactam (WCK 5107), and WCK 4234 (compounds 1-3, respectively), were synthesized and biochemically characterized against clinically important bacteria. Compound 3 inhibited class A, C, and D β-lactamases with unprecedented k2/ K values against OXA carbapenemases. Compounds 1 and 2 acylated class A and C β-lactamses rapidly but not the tested OXAs. Compounds 1-3 formed highly stable acyl-complexes as demonstrated by mass spectrometry. Crystallography revealed that 1-3 complexed with KPC-2 adopted a "chair conformation" with the sulfate occupying the carboxylate binding region. The cefepime-2 and meropenem-3 combinations were effective in murine peritonitis and neutropenic lung infection models caused by MDR Acinetobacter baumannii. Compounds 1-3 are novel β-lactamase inhibitors that demonstate potent cross-class inhibition, and clinical studies targeting MDR infections are warranted.
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Affiliation(s)
- Krisztina M Papp-Wallace
- Research Service , Louis Stokes Cleveland Department of Veterans Affairs Medical Center , 10701 East Boulevard , Cleveland , Ohio 44106 , United States
| | | | - Michael R Jacobs
- Department of Pathology , University Hospitals, Cleveland Medical Center , Cleveland , Ohio 44106 , United States
| | - Christopher R Bethel
- Research Service , Louis Stokes Cleveland Department of Veterans Affairs Medical Center , 10701 East Boulevard , Cleveland , Ohio 44106 , United States
| | - Melissa D Barnes
- Research Service , Louis Stokes Cleveland Department of Veterans Affairs Medical Center , 10701 East Boulevard , Cleveland , Ohio 44106 , United States
| | | | - Saralee Bajaksouzian
- Department of Pathology , University Hospitals, Cleveland Medical Center , Cleveland , Ohio 44106 , United States
| | - Susan D Rudin
- Research Service , Louis Stokes Cleveland Department of Veterans Affairs Medical Center , 10701 East Boulevard , Cleveland , Ohio 44106 , United States
| | - Philip N Rather
- Department of Microbiology and Immunology , Emory University School of Medicine Atlanta , Georgia 30322 , United States.,Research Service , Atlanta VA Medical Center , Decatur , Georgia 30033 , United States
| | | | | | | | - Vijay Patil
- Wockhardt Research Centre , Aurangabad , India
| | | | | | | | | | - Robert A Bonomo
- Research Service , Louis Stokes Cleveland Department of Veterans Affairs Medical Center , 10701 East Boulevard , Cleveland , Ohio 44106 , United States
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24
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van den Akker F, Bonomo RA. Exploring Additional Dimensions of Complexity in Inhibitor Design for Serine β-Lactamases: Mechanistic and Intra- and Inter-molecular Chemistry Approaches. Front Microbiol 2018; 9:622. [PMID: 29675000 PMCID: PMC5895744 DOI: 10.3389/fmicb.2018.00622] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 03/19/2018] [Indexed: 01/14/2023] Open
Abstract
As a bacterial resistance strategy, serine β-lactamases have evolved from cell wall synthesizing enzymes known as penicillin-binding proteins (PBP), by not only covalently binding β-lactam antibiotics but, also acquiring mechanisms of deacylating these antibiotics. This critical deacylation step leads to release of hydrolyzed and inactivated β-lactams, thereby providing resistance for the bacteria against these antibiotics targeting the cell wall. To combat β-lactamase-mediated antibiotic resistance, numerous β-lactamase inhibitors were developed that utilize various strategies to inactivate the β-lactamase. Most of these compounds are “mechanism-based” inhibitors that in some manner mimic the β-lactam substrate, having a carbonyl moiety and a negatively charged carboxyl or sulfate group. These compounds form a covalent adduct with the catalytic serine via an initial acylation step. To increase the life-time of the inhibitory covalent adduct intermediates, a remarkable array of different strategies was employed to improve inhibition potency. Such approaches include post-acylation intra- and intermolecular chemical rearrangements as well as affecting the deacylation water. These approaches transform the inhibitor design process from a 3-dimensional problem (i.e., XYZ coordinates) to one with additional dimensions of complexity as the reaction coordinate and time spent at each chemical state need to be taken into consideration. This review highlights the mechanistic intricacies of the design efforts of the β-lactamase inhibitors which so far have resulted in the development of “two generations” and 5 clinically available inhibitors.
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Affiliation(s)
- Focco van den Akker
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, United States
| | - Robert A Bonomo
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, United States.,Medicine, Pharmacology, Molecular Biology and Microbiology, Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH, United States.,Medical Service and Geriatric Research, Education, and Clinical Centers (GRECC), Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, United States.,Case Western Reserve University-VA Medical Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH, United States
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25
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Caselli E, Romagnoli C, Powers RA, Taracila MA, Bouza AA, Swanson HC, Smolen KA, Fini F, Wallar BJ, Bonomo RA, Prati F. Inhibition of Acinetobacter-Derived Cephalosporinase: Exploring the Carboxylate Recognition Site Using Novel β-Lactamase Inhibitors. ACS Infect Dis 2018; 4:337-348. [PMID: 29144725 DOI: 10.1021/acsinfecdis.7b00153] [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: 12/17/2022]
Abstract
Boronic acids are attracting a lot of attention as β-lactamase inhibitors, and in particular, compound S02030 ( Ki = 44 nM) proved to be a good lead compound against ADC-7 ( Acinetobacter-derived cephalosporinase), one of the most significant resistance determinants in A. baumannii. The atomic structure of the ADC-7/S02030 complex highlighted the importance of critical structural determinants for recognition of the boronic acids. Herein, to elucidate the role in recognition of the R2-carboxylate, which mimics the C3/C4 found in β-lactams, we designed, synthesized, and characterized six derivatives of S02030 (3a). Out of the six compounds, the best inhibitors proved to be those with an explicit negative charge (compounds 3a-c, 3h, and 3j, Ki = 44-115 nM), which is in contrast to the derivatives where the negative charge is omitted, such as the amide derivative 3d ( Ki = 224 nM) and the hydroxyamide derivative 3e ( Ki = 155 nM). To develop a structural characterization of inhibitor binding in the active site, the X-ray crystal structures of ADC-7 in a complex with compounds 3c, SM23, and EC04 were determined. All three compounds share the same structural features as in S02030 but only differ in the carboxy-R2 side chain, thereby providing the opportunity of exploring the distinct binding mode of the negatively charged R2 side chain. This cephalosporinase demonstrates a high degree of versatility in recognition, employing different residues to directly interact with the carboxylate, thus suggesting the existence of a "carboxylate binding region" rather than a binding site in ADC enzymes. Furthermore, this class of compounds was tested against resistant clinical strains of A. baumannii and are effective at inhibiting bacterial growth in conjunction with a β-lactam antibiotic.
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Affiliation(s)
- Emilia Caselli
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 101, 41125, Modena, Italy
| | - Chiara Romagnoli
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 101, 41125, Modena, Italy
| | - Rachel A. Powers
- Department of Chemistry, Grand Valley State University, 1 Campus Drive, Allendale, Michigan 49401, United States
| | - Magdalena A. Taracila
- Departments of Medicine, Pharmacology, Biochemistry and Molecular Biology and Microbiology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Alexandra A. Bouza
- Department of Chemistry, Grand Valley State University, 1 Campus Drive, Allendale, Michigan 49401, United States
| | - Hollister C. Swanson
- Department of Chemistry, Grand Valley State University, 1 Campus Drive, Allendale, Michigan 49401, United States
| | - Kali A. Smolen
- Department of Chemistry, Grand Valley State University, 1 Campus Drive, Allendale, Michigan 49401, United States
| | - Francesco Fini
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 101, 41125, Modena, Italy
| | - Bradley J. Wallar
- Department of Chemistry, Grand Valley State University, 1 Campus Drive, Allendale, Michigan 49401, United States
| | - Robert A. Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs
Medical Center, 10701 East Boulevard, Cleveland, Ohio 44106, United States
- Departments of Medicine, Pharmacology, Biochemistry and Molecular Biology and Microbiology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Fabio Prati
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 101, 41125, Modena, Italy
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26
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Celenza G, Vicario M, Bellio P, Linciano P, Perilli M, Oliver A, Blazquez J, Cendron L, Tondi D. Phenylboronic Acid Derivatives as Validated Leads Active in Clinical Strains Overexpressing KPC-2: A Step against Bacterial Resistance. ChemMedChem 2018; 13:713-724. [PMID: 29356380 DOI: 10.1002/cmdc.201700788] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Indexed: 12/28/2022]
Abstract
The emergence and dissemination of multidrug resistant (MDR) pathogens resistant to nearly all available antibiotics poses a significant threat in clinical therapy. Among them, Klebsiella pneumoniae clinical isolates overexpressing KPC-2 carbapenemase are the most worrisome, extending bacterial resistance to last-resort carbapenems. In this study, we investigate the molecular recognition requirements in the KPC-2 active site by small phenylboronic acid derivatives. Four new phenylboronic acid derivatives were designed and tested against KPC-2. For the most active, despite their simple chemical structures, nanomolar affinity was achieved. The new derivatives restored susceptibility to meropenem in clinical strains overexpressing KPC-2. Moreover, no cytotoxicity was detected in cell-viability assays, which further validated the designed leads. Two crystallographic binary complexes of the best inhibitors binding KPC-2 were obtained at high resolution. Kinetic descriptions of slow binding, time-dependent inhibition, and interaction geometries in KPC-2 were fully investigated. This study will ultimately lead toward the optimization and development of more-effective KPC-2 inhibitors.
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Affiliation(s)
- Giuseppe Celenza
- Dipartimento di Scienze Cliniche Applicate e Biotecnologie, Università dell'Aquila, Via Vetoio 1, 67100, L'Aquila, Italy
| | - Mattia Vicario
- Dipartimento di Biologia, Università di Padova, Viale G. Colombo 3, 35121, Padova, Italy
| | - Pierangelo Bellio
- Dipartimento di Scienze Cliniche Applicate e Biotecnologie, Università dell'Aquila, Via Vetoio 1, 67100, L'Aquila, Italy
| | - Pasquale Linciano
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Via Campi 103, 41100, Modena, Italy
| | - Mariagrazia Perilli
- Dipartimento di Scienze Cliniche Applicate e Biotecnologie, Università dell'Aquila, Via Vetoio 1, 67100, L'Aquila, Italy
| | - Antonio Oliver
- Servicio de Microbiología and Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria de Mallorca, Palma de Mallorca, Spain
| | - Jesús Blazquez
- Department of Microbial Biotechnology, National Center for Biotechnology, Consejo Superior de Investigaciones Científicas (CSIC), C/ Darwin, 3, Campus de la Universidad Autonoma-Cantoblanco, 28049, Madrid, Spain
| | - Laura Cendron
- Dipartimento di Biologia, Università di Padova, Viale G. Colombo 3, 35121, Padova, Italy
| | - Donatella Tondi
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Via Campi 103, 41100, Modena, Italy
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