1
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Hafeez S, Zafar Paracha R, Adnan F. Designing of fragment based inhibitors with improved activity against E. coli AmpC β-lactamase compared to the conventional antibiotics. Saudi J Biol Sci 2024; 31:103884. [PMID: 38125736 PMCID: PMC10730856 DOI: 10.1016/j.sjbs.2023.103884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 11/19/2023] [Accepted: 11/24/2023] [Indexed: 12/23/2023] Open
Abstract
One of the most common primary resistance mechanism of multi-drug resistant (MDR) Gram negative pathogenic bacteria to combat β-lactam antibiotics, such as penicillins, cephalosporins and carbapenems is the generation of β- lactamases. The uropathogenic E. coli is mostly getting multi-drug resistance due to the synthesis of AmpC β-lactamases and therefore new antibiotics and inhibitors are needed to treat the evolving infections. The current study was designed for targetting AmpC β-lactamase of E. coli using molecular docking based virtual screening, linking fragments for designing novel compounds and binding mode analysis using molecular dynamic simulation with target protein. The FCH group all-purpose fragment library consisting of 9388 fragments has been screened against AmpC β-lactamase protein of E. coli and the antibiotics and anti-infectives used in treatment of Urinary tract Infections (UTIs) were also screened with AmpC β-lactamase protein. Among the 9388 fragments, 339 fragment candidates were selected and linked with cefepime antibiotic having maximum binding affinity for AmpC target protein. Computational analysis of interactions as well as molecular dynamics (MD) simulations were also conducted for identifying the most promising ligand-pocket complexes from docking investigations to comprehend their thermodynamic properties and verify the docking outcomes as well. Overall, the linked complexes (LCs) showed good binding interactions with AmpC β-lactamase. Interestingly, our fragment-based LCs remained relatively stable in comparison with cefepime antibiotic. Moreover, S12 fragment linked complex remained the most stable during 50 ns with remarkable number of interactions indicating it as promising candidate in novel lead discovery against MDR E. coli infections.
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Affiliation(s)
- Sidrah Hafeez
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| | - Rehan Zafar Paracha
- School of Interdisciplinary Engineering and Sciences (SINES), National University of Science and Technology (NUST), Islamabad 44000, Pakistan
| | - Fazal Adnan
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
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2
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Taylor DM, Anglin J, Hu L, Wang L, Sankaran B, Wang J, Matzuk MM, Prasad BV, Palzkill T. Unique Diacidic Fragments Inhibit the OXA-48 Carbapenemase and Enhance the Killing of Escherichia coli Producing OXA-48. ACS Infect Dis 2021; 7:3345-3354. [PMID: 34817169 PMCID: PMC9677231 DOI: 10.1021/acsinfecdis.1c00501] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Despite the advances in β-lactamase inhibitor development, limited options exist for the class D carbapenemase known as OXA-48. OXA-48 is one of the most prevalent carbapenemases in carbapenem-resistant Enterobacteriaceae infections and is not susceptible to most available β-lactamase inhibitors. Here, we screened various low-molecular-weight compounds (fragments) against OXA-48 to identify functional scaffolds for inhibitor development. Several biphenyl-, naphthalene-, fluorene-, anthraquinone-, and azobenzene-based compounds were found to inhibit OXA-48 with low micromolar potency despite their small size. Co-crystal structures of OXA-48 with several of these compounds revealed key interactions with the carboxylate-binding pocket, Arg214, and various hydrophobic residues of β-lactamase that can be exploited in future inhibitor development. A number of the low-micromolar-potency inhibitors, across different scaffolds, synergize with ampicillin to kill Escherichia coli expressing OXA-48, albeit at high concentrations of the respective inhibitors. Additionally, several compounds demonstrated micromolar potency toward the OXA-24 and OXA-58 class D carbapenemases that are prevalent in Acinetobacter baumannii. This work provides foundational information on a variety of chemical scaffolds that can guide the design of effective OXA-48 inhibitors that maintain efficacy as well as potency toward other major class D carbapenemases.
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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
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Lingfei Wang
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Advanced Light Source, Lawrence Berkeley National Laboratory, CA, 94720, USA
| | - Jin Wang
- 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
| | - B.V. Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular 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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3
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Bahr G, González LJ, Vila AJ. Metallo-β-lactamases in the Age of Multidrug Resistance: From Structure and Mechanism to Evolution, Dissemination, and Inhibitor Design. Chem Rev 2021; 121:7957-8094. [PMID: 34129337 PMCID: PMC9062786 DOI: 10.1021/acs.chemrev.1c00138] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Antimicrobial resistance is one of the major problems in current practical medicine. The spread of genes coding for resistance determinants among bacteria challenges the use of approved antibiotics, narrowing the options for treatment. Resistance to carbapenems, last resort antibiotics, is a major concern. Metallo-β-lactamases (MBLs) hydrolyze carbapenems, penicillins, and cephalosporins, becoming central to this problem. These enzymes diverge with respect to serine-β-lactamases by exhibiting a different fold, active site, and catalytic features. Elucidating their catalytic mechanism has been a big challenge in the field that has limited the development of useful inhibitors. This review covers exhaustively the details of the active-site chemistries, the diversity of MBL alleles, the catalytic mechanism against different substrates, and how this information has helped developing inhibitors. We also discuss here different aspects critical to understand the success of MBLs in conferring resistance: the molecular determinants of their dissemination, their cell physiology, from the biogenesis to the processing involved in the transit to the periplasm, and the uptake of the Zn(II) ions upon metal starvation conditions, such as those encountered during an infection. In this regard, the chemical, biochemical and microbiological aspects provide an integrative view of the current knowledge of MBLs.
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Affiliation(s)
- Guillermo Bahr
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Lisandro J. González
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Alejandro J. Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
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4
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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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5
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Liu X, Dong S, Ma Y, Xu H, Zhao H, Gao Q. N-(Sulfamoylbenzoyl)-L-proline Derivatives as Potential Non-β-lactam ESBL Inhibitors: Structure-Based Lead Identification, Medicinal Chemistry and Synergistic Antibacterial Activities. Med Chem 2019; 15:196-206. [DOI: 10.2174/1573406414666180816123232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 05/01/2018] [Accepted: 06/04/2018] [Indexed: 11/22/2022]
Abstract
Background:
There is an urgent need to develop novel inhibitors against clinically
widespread extended-spectrum β-lactamases (ESBLs) to meet the challenges of the ever-evolving
threat of antibiotic resistances. Most existing ESBL inhibitors sharing a common chemical feature
of β-lactam ring in their molecule, this structural characteristic makes them intrinsically susceptible
to enzymatic breakdown by the resistance mechanisms employed by the bacteria.
Objective:
The aim of this study was to screen and discover novel lead compounds by using Lproline
as initial scaffold to create a “non-sulfur, non-β-lactam” new chemotypes for potential
ESBL inhibitors.
Methods:
Structure-based molecular docking and virtual screening were employed in the novel
inhibitor generation process for lead compound screening and SAR analysis. Evaluation of the
ESBL inhibitory activity of the lead compounds was performed in combination with three of the
most susceptible antibiotics: ceftazidime, meropenem and ampicillin, against thirteen ESBL enzymes
including four new CTX-M harboring strains and four KPC-2 producing species.
Results:
L-proline derived (S)-1-(2-sulfamoylbenzoyl)pyrrolidine-2-carboxylic acid (compound
6) as a “non-sulfur, non-β-lactam” and the most potential ESBL inhibitor was identified. Compound
6 possesses ideal anti-resistance activities by reducing MICs of ceftazidime, meropenem
and ampicillin by 16-133, 32-133 and 67-267 fold respectiveily. The inhibitory mechanism of 6
with CTX-M, KPC-2 and penicillinase were proposed and probed with molecular docking analysis.
Conclusion:
Given that the simple proline derivative but promising synergistic antibacterial
properties of compound 6 augers well for further investigations into its in vivo efficacy.
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Affiliation(s)
- Xinyu Liu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Shengjie Dong
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Yuru Ma
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Hu Xu
- Department of Medicinal Chemistry, Gudui BioPharma Technology Inc., 5 Lanyuan Road, Huayuan Industrial Park, Tianjin 300384, China
| | - Hongxia Zhao
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Qingzhi Gao
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
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6
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Lakemeyer M, Zhao W, Mandl FA, Hammann P, Sieber SA. Thinking Outside the Box-Novel Antibacterials To Tackle the Resistance Crisis. Angew Chem Int Ed Engl 2018; 57:14440-14475. [PMID: 29939462 DOI: 10.1002/anie.201804971] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Indexed: 12/13/2022]
Abstract
The public view on antibiotics as reliable medicines changed when reports about "resistant superbugs" appeared in the news. While reasons for this resistance development are easily spotted, solutions for re-establishing effective antibiotics are still in their infancy. This Review encompasses several aspects of the antibiotic development pipeline from very early strategies to mature drugs. An interdisciplinary overview is given of methods suitable for mining novel antibiotics and strategies discussed to unravel their modes of action. Select examples of antibiotics recently identified by using these platforms not only illustrate the efficiency of these measures, but also highlight promising clinical candidates with therapeutic potential. Furthermore, the concept of molecules that disarm pathogens by addressing gatekeepers of virulence will be covered. The Review concludes with an evaluation of antibacterials currently in clinical development. Overall, this Review aims to connect select innovative antimicrobial approaches to stimulate interdisciplinary partnerships between chemists from academia and industry.
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Affiliation(s)
- Markus Lakemeyer
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Weining Zhao
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Franziska A Mandl
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Peter Hammann
- R&D Therapeutic Area Infectious Diseases, Sanofi-Aventis (Deutschland) GmbH, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Stephan A Sieber
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
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7
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Lakemeyer M, Zhao W, Mandl FA, Hammann P, Sieber SA. Über bisherige Denkweisen hinaus - neue Wirkstoffe zur Überwindung der Antibiotika-Krise. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804971] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Markus Lakemeyer
- Fakultät für Chemie; Lehrstuhl für Organische Chemie II, Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Weining Zhao
- Fakultät für Chemie; Lehrstuhl für Organische Chemie II, Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Franziska A. Mandl
- Fakultät für Chemie; Lehrstuhl für Organische Chemie II, Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Peter Hammann
- R&D Therapeutic Area Infectious Diseases; Sanofi-Aventis (Deutschland) GmbH; Industriepark Höchst 65926 Frankfurt am Main Deutschland
| | - Stephan A. Sieber
- Fakultät für Chemie; Lehrstuhl für Organische Chemie II, Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
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8
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Swain SS, Paidesetty SK, Padhy RN. Synthesis of novel thymol derivatives against MRSA and ESBL producing pathogenic bacteria. Nat Prod Res 2018; 33:3181-3189. [DOI: 10.1080/14786419.2018.1474465] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Shasank S. Swain
- Central Research Laboratory, IMS and Sum Hospital, Siksha ‘O’ Anusandhan (Deemed to be University), Bhubaneswar, India
| | - Sudhir K. Paidesetty
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Siksha ‘O’ Anusandhan (Deemed to be University), Bhubaneswar, India
| | - Rabindra N. Padhy
- Central Research Laboratory, IMS and Sum Hospital, Siksha ‘O’ Anusandhan (Deemed to be University), Bhubaneswar, India
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9
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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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10
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Activity of the β-Lactamase Inhibitor LN-1-255 against Carbapenem-Hydrolyzing Class D β-Lactamases from Acinetobacter baumannii. Antimicrob Agents Chemother 2017; 61:AAC.01172-17. [PMID: 28807908 DOI: 10.1128/aac.01172-17] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 08/02/2017] [Indexed: 12/21/2022] Open
Abstract
The number of infections caused by Gram-negative pathogens carrying carbapenemases is increasing, and the group of carbapenem-hydrolyzing class D β-lactamases (CHDLs) is especially problematic. Several clinically important CHDLs have been identified in Acinetobacter baumannii, including OXA-23, OXA-24/40, OXA-58, OXA-143, OXA-235, and the chromosomally encoded OXA-51. The selection and dissemination of carbapenem-resistant A. baumannii strains constitutes a serious global threat. Carbapenems have been successfully utilized as last-resort antibiotics for the treatment of multidrug-resistant A. baumannii infections. However, the spread of OXA carbapenemases is compromising the continued use of these antimicrobials. In response to this clinical issue, it is necessary and urgent to design and develop new specific inhibitors with efficacy against these enzymes. The aim of this work was to characterize the inhibitory activity of LN-1-255 (a 6-alkylidene-2-substituted penicillin sulfone) and compare it to that of two established inhibitors (avibactam and tazobactam) against the most relevant enzymes of each group of class D carbapenemases in A. baumannii The β-lactamase inhibitor LN-1-255 demonstrated excellent microbiological synergy and inhibition kinetics parameters against all tested CHDLs and a significantly higher activity than tazobactam and avibactam. A combination of carbapenems and LN-1-255 was effective against A. baumannii class D carbapenemases. Docking assays confirmed the affinity of LN-1-255 for the active site of these enzymes. LN-1-255 represents a potential new β-lactamase inhibitor that may have a significant role in eradicating infections caused by A. baumannii isolates carrying CHDLs.
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11
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Korczynska M, Le DD, Younger N, Gregori-Puigjané E, Tumber A, Krojer T, Velupillai S, Gileadi C, Nowak RP, Iwasa E, Pollock SB, Torres IO, Oppermann U, Shoichet BK, Fujimori DG. Docking and Linking of Fragments To Discover Jumonji Histone Demethylase Inhibitors. J Med Chem 2016; 59:1580-98. [PMID: 26699912 PMCID: PMC5080985 DOI: 10.1021/acs.jmedchem.5b01527] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Development of tool molecules that inhibit Jumonji demethylases allows for the investigation of cancer-associated transcription. While scaffolds such as 2,4-pyridinedicarboxylic acid (2,4-PDCA) are potent inhibitors, they exhibit limited selectivity. To discover new inhibitors for the KDM4 demethylases, enzymes overexpressed in several cancers, we docked a library of 600,000 fragments into the high-resolution structure of KDM4A. Among the most interesting chemotypes were the 5-aminosalicylates, which docked in two distinct but overlapping orientations. Docking poses informed the design of covalently linked fragment compounds, which were further derivatized. This combined approach improved affinity by ∼ 3 log-orders to yield compound 35 (Ki = 43 nM). Several hybrid inhibitors were selective for KDM4C over the related enzymes FIH, KDM2A, and KDM6B while lacking selectivity against the KDM3 and KDM5 subfamilies. Cocrystal structures corroborated the docking predictions. This study extends the use of structure-based docking from fragment discovery to fragment linking optimization, yielding novel KDM4 inhibitors.
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Affiliation(s)
- Magdalena Korczynska
- Department of Pharmaceutical Chemistry, University of California, San Francisco, Genentech Hall, 600 16th Street, MC2280, San Francisco, California 94158-2280, United States
| | - Daniel D. Le
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, Genentech Hall, 600 16th Street, MC2280, San Francisco, California 94158-2280, United States
| | - Noah Younger
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, Genentech Hall, 600 16th Street, MC2280, San Francisco, California 94158-2280, United States
| | - Elisabet Gregori-Puigjané
- Department of Pharmaceutical Chemistry, University of California, San Francisco, Genentech Hall, 600 16th Street, MC2280, San Francisco, California 94158-2280, United States
| | - Anthony Tumber
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, U.K
- Nuffield Department of Clinical Medicine, Target Discovery Institute (TDI), University of Oxford, Oxford OX3 7BN, U.K
| | - Tobias Krojer
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, U.K
| | | | - Carina Gileadi
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, U.K
| | - Radosław P. Nowak
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, U.K
| | - Eriko Iwasa
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, Genentech Hall, 600 16th Street, MC2280, San Francisco, California 94158-2280, United States
| | - Samuel B. Pollock
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, Genentech Hall, 600 16th Street, MC2280, San Francisco, California 94158-2280, United States
| | - Idelisse Ortiz Torres
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, Genentech Hall, 600 16th Street, MC2280, San Francisco, California 94158-2280, United States
| | - Udo Oppermann
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, U.K
- Botnar Research Center, University of Oxford, Oxford OX3 7LD, U.K
| | - Brian K. Shoichet
- Department of Pharmaceutical Chemistry, University of California, San Francisco, Genentech Hall, 600 16th Street, MC2280, San Francisco, California 94158-2280, United States
| | - Danica Galonić Fujimori
- Department of Pharmaceutical Chemistry, University of California, San Francisco, Genentech Hall, 600 16th Street, MC2280, San Francisco, California 94158-2280, United States
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, Genentech Hall, 600 16th Street, MC2280, San Francisco, California 94158-2280, United States
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Probing metallo-β-lactamases with molecular fragments identified by consensus docking. Bioorg Med Chem Lett 2015; 25:5243-6. [DOI: 10.1016/j.bmcl.2015.09.056] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 09/18/2015] [Accepted: 09/23/2015] [Indexed: 11/23/2022]
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High frequencies of antibiotic resistance genes in infants' meconium and early fecal samples. J Dev Orig Health Dis 2015; 7:35-44. [PMID: 26353938 DOI: 10.1017/s2040174415001506] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The gastrointestinal tract (GIT) microbiota has been identified as an important reservoir of antibiotic resistance genes (ARGs) that can be horizontally transferred to pathogenic species. Maternal GIT microbes can be transmitted to the offspring, and recent work indicates that such transfer starts before birth. We have used culture-independent genetic screenings to explore whether ARGs are already present in the meconium accumulated in the GIT during fetal life and in feces of 1-week-old infants. We have analyzed resistance to β-lactam antibiotics (BLr) and tetracycline (Tcr), screening for a variety of genes conferring each. To evaluate whether ARGs could have been inherited by maternal transmission, we have screened perinatal fecal samples of the 1-week-old babies' mothers, as well as a mother-infant series including meconium, fecal samples collected through the infant's 1st year, maternal fecal samples and colostrum. Our results reveal a high prevalence of BLr and Tcr in both meconium and early fecal samples, implying that the GIT resistance reservoir starts to accumulate even before birth. We show that ARGs present in the mother may reach the meconium and colostrum and establish in the infant GIT, but also that some ARGs were likely acquired from other sources. Alarmingly, we identified in both meconium and 1-week-olds' samples a particularly elevated prevalence of mecA (>45%), six-fold higher than that detected in the mothers. The mecA gene confers BLr to methicillin-resistant Staphylococcus aureus, and although its detection does not imply the presence of this pathogen, it does implicate the young infant's GIT as a noteworthy reservoir of this gene.
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