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Akkoc S, Karatas H, Muhammed MT, Kökbudak Z, Ceylan A, Almalki F, Laaroussi H, Ben Hadda T. Drug design of new therapeutic agents: molecular docking, molecular dynamics simulation, DFT and POM analyses of new Schiff base ligands and impact of substituents on bioactivity of their potential antifungal pharmacophore site. J Biomol Struct Dyn 2022:1-14. [DOI: 10.1080/07391102.2022.2111360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
- Senem Akkoc
- Department of Basic Pharmaceutical Sciences, Faculty of Pharmacy, Süleyman Demirel University, Isparta, Türkiye
- Faculty of Engineering and Natural Sciences, Bahçeşehir University, Istanbul, Türkiye
| | - Halis Karatas
- Department of Chemistry, Faculty of Science, Erciyes University, Kayseri, Türkiye
| | - Muhammed Tilahun Muhammed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Süleyman Demirel University, Isparta, Türkiye
| | - Zülbiye Kökbudak
- Department of Chemistry, Faculty of Science, Erciyes University, Kayseri, Türkiye
| | - Ahmet Ceylan
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Erciyes University, Kayseri, Türkiye
| | - Faisal Almalki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah Almukkarramah, Saudi Arabia
| | - Hamid Laaroussi
- Laboratory of Applied Chemistry & Environment, Faculty of Science, Mohammed Premier University, Oujda, Morocco
| | - Taibi Ben Hadda
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah Almukkarramah, Saudi Arabia
- Laboratory of Applied Chemistry & Environment, Faculty of Science, Mohammed Premier University, Oujda, Morocco
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Lucic A, Malla TR, Calvopiña K, Tooke CL, Brem J, McDonough MA, Spencer J, Schofield CJ. Studies on the Reactions of Biapenem with VIM Metallo β-Lactamases and the Serine β-Lactamase KPC-2. Antibiotics (Basel) 2022; 11:396. [PMID: 35326858 PMCID: PMC8944426 DOI: 10.3390/antibiotics11030396] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 02/06/2023] Open
Abstract
Carbapenems are important antibacterials and are both substrates and inhibitors of some β-lactamases. We report studies on the reaction of the unusual carbapenem biapenem, with the subclass B1 metallo-β-lactamases VIM-1 and VIM-2 and the class A serine-β-lactamase KPC-2. X-ray diffraction studies with VIM-2 crystals treated with biapenem reveal the opening of the β-lactam ring to form a mixture of the (2S)-imine and enamine complexed at the active site. NMR studies on the reactions of biapenem with VIM-1, VIM-2, and KPC-2 reveal the formation of hydrolysed enamine and (2R)- and (2S)-imine products. The combined results support the proposal that SBL/MBL-mediated carbapenem hydrolysis results in a mixture of tautomerizing enamine and (2R)- and (2S)-imine products, with the thermodynamically favoured (2S)-imine being the major observed species over a relatively long-time scale. The results suggest that prolonging the lifetimes of β-lactamase carbapenem complexes by optimising tautomerisation of the nascently formed enamine to the (2R)-imine and likely more stable (2S)-imine tautomer is of interest in developing improved carbapenems.
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Affiliation(s)
- Anka Lucic
- Chemistry Research Laboratory, The Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford OX1 3TA, UK; (A.L.); (T.R.M.); (K.C.); (J.B.); (M.A.M.)
| | - Tika R. Malla
- Chemistry Research Laboratory, The Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford OX1 3TA, UK; (A.L.); (T.R.M.); (K.C.); (J.B.); (M.A.M.)
| | - Karina Calvopiña
- Chemistry Research Laboratory, The Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford OX1 3TA, UK; (A.L.); (T.R.M.); (K.C.); (J.B.); (M.A.M.)
| | - Catherine L. Tooke
- Biomedical Sciences Building, School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, University Walk, Bristol BS8 1TD, UK; (C.L.T.); (J.S.)
| | - Jürgen Brem
- Chemistry Research Laboratory, The Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford OX1 3TA, UK; (A.L.); (T.R.M.); (K.C.); (J.B.); (M.A.M.)
| | - Michael A. McDonough
- Chemistry Research Laboratory, The Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford OX1 3TA, UK; (A.L.); (T.R.M.); (K.C.); (J.B.); (M.A.M.)
| | - James Spencer
- Biomedical Sciences Building, School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, University Walk, Bristol BS8 1TD, UK; (C.L.T.); (J.S.)
| | - Christopher J. Schofield
- Chemistry Research Laboratory, The Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford OX1 3TA, UK; (A.L.); (T.R.M.); (K.C.); (J.B.); (M.A.M.)
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3
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Gold B, Zhang J, Quezada LL, Roberts J, Ling Y, Wood M, Shinwari W, Goullieux L, Roubert C, Fraisse L, Bacqué E, Lagrange S, Filoche-Rommé B, Vieth M, Hipskind PA, Jungheim LN, Aubé J, Scarry SM, McDonald SL, Li K, Perkowski A, Nguyen Q, Dartois V, Zimmerman M, Olsen DB, Young K, Bonnett S, Joerss D, Parish T, Boshoff HI, Arora K, Barry CE, Guijarro L, Anca S, Rullas J, Rodríguez-Salguero B, Martínez-Martínez MS, Porras-De Francisco E, Cacho M, Barros-Aguirre D, Smith P, Berthel SJ, Nathan C, Bates RH. Identification of β-Lactams Active against Mycobacterium tuberculosis by a Consortium of Pharmaceutical Companies and Academic Institutions. ACS Infect Dis 2022; 8:557-573. [PMID: 35192346 PMCID: PMC8922279 DOI: 10.1021/acsinfecdis.1c00570] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Indexed: 11/28/2022]
Abstract
Rising antimicrobial resistance challenges our ability to combat bacterial infections. The problem is acute for tuberculosis (TB), the leading cause of death from infection before COVID-19. Here, we developed a framework for multiple pharmaceutical companies to share proprietary information and compounds with multiple laboratories in the academic and government sectors for a broad examination of the ability of β-lactams to kill Mycobacterium tuberculosis (Mtb). In the TB Drug Accelerator (TBDA), a consortium organized by the Bill & Melinda Gates Foundation, individual pharmaceutical companies collaborate with academic screening laboratories. We developed a higher order consortium within the TBDA in which four pharmaceutical companies (GlaxoSmithKline, Sanofi, MSD, and Lilly) collectively collaborated with screeners at Weill Cornell Medicine, the Infectious Disease Research Institute (IDRI), and the National Institute of Allergy and Infectious Diseases (NIAID), pharmacologists at Rutgers University, and medicinal chemists at the University of North Carolina to screen ∼8900 β-lactams, predominantly cephalosporins, and characterize active compounds. In a striking contrast to historical expectation, 18% of β-lactams screened were active against Mtb, many without a β-lactamase inhibitor. One potent cephaloporin was active in Mtb-infected mice. The steps outlined here can serve as a blueprint for multiparty, intra- and intersector collaboration in the development of anti-infective agents.
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Affiliation(s)
- Ben Gold
- Department
of Microbiology & Immunology, Weill
Cornell Medicine, 413 East 69th Street, New York, New York 10021, United
States
| | - Jun Zhang
- Department
of Microbiology & Immunology, Weill
Cornell Medicine, 413 East 69th Street, New York, New York 10021, United
States
| | - Landys Lopez Quezada
- Department
of Microbiology & Immunology, Weill
Cornell Medicine, 413 East 69th Street, New York, New York 10021, United
States
| | - Julia Roberts
- Department
of Microbiology & Immunology, Weill
Cornell Medicine, 413 East 69th Street, New York, New York 10021, United
States
| | - Yan Ling
- Department
of Microbiology & Immunology, Weill
Cornell Medicine, 413 East 69th Street, New York, New York 10021, United
States
| | - Madeleine Wood
- Department
of Microbiology & Immunology, Weill
Cornell Medicine, 413 East 69th Street, New York, New York 10021, United
States
| | - Wasima Shinwari
- Department
of Microbiology & Immunology, Weill
Cornell Medicine, 413 East 69th Street, New York, New York 10021, United
States
| | - Laurent Goullieux
- Sanofi,
Infectious Diseases Therapeutic Area, 69280 Marcy l’Étoile, France
- Evotec
(Lyon) SAS, 69007 Lyon, France
| | - Christine Roubert
- Sanofi,
Infectious Diseases Therapeutic Area, 69280 Marcy l’Étoile, France
- Evotec
(Lyon) SAS, 69007 Lyon, France
| | - Laurent Fraisse
- Sanofi,
Infectious Diseases Therapeutic Area, 69280 Marcy l’Étoile, France
| | - Eric Bacqué
- Sanofi,
Infectious Diseases Therapeutic Area, 69280 Marcy l’Étoile, France
- Evotec
(Lyon) SAS, 69007 Lyon, France
| | - Sophie Lagrange
- Sanofi,
Infectious Diseases Therapeutic Area, 69280 Marcy l’Étoile, France
- Evotec
(Lyon) SAS, 69007 Lyon, France
| | | | - Michal Vieth
- Lilly
Biotechnology Center, Eli Lilly and Company, 10290 Campus Point Dr, San Diego, California 92121, United States
| | - Philip A. Hipskind
- Lilly
Research Laboratories, Lilly Corporate Center, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Louis N. Jungheim
- YourEncore, 20 North Meridian Street, Indianapolis, Indiana 46204, United States
| | - Jeffrey Aubé
- Division
of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of
Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Sarah M. Scarry
- Division
of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of
Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Stacey L. McDonald
- Division
of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of
Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Kelin Li
- Division
of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of
Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Andrew Perkowski
- Division
of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of
Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Quyen Nguyen
- Division
of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of
Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Véronique Dartois
- Public
Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey 07103, United States
| | - Matthew Zimmerman
- Public
Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey 07103, United States
| | - David B. Olsen
- Merck
& Co., Inc., Infectious Diseases, 770 Sumneytown Pike, West Point, Pennsylvania 19486, United States
| | - Katherine Young
- Merck
& Co., Inc., Infectious Diseases, 770 Sumneytown Pike, West Point, Pennsylvania 19486, United States
| | - Shilah Bonnett
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Ave E, Suite 400, Seattle, Washington 98102, United States
| | - Douglas Joerss
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Ave E, Suite 400, Seattle, Washington 98102, United States
| | - Tanya Parish
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Ave E, Suite 400, Seattle, Washington 98102, United States
| | - Helena I. Boshoff
- Tuberculosis Research Section, Laboratory
of Clinical Immunology and Microbiology, Bethesda, Maryland 20892, United States
| | - Kriti Arora
- Tuberculosis Research Section, Laboratory
of Clinical Immunology and Microbiology, Bethesda, Maryland 20892, United States
| | - Clifton E. Barry
- Tuberculosis Research Section, Laboratory
of Clinical Immunology and Microbiology, Bethesda, Maryland 20892, United States
| | - Laura Guijarro
- Global Health Pharma R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Sara Anca
- Global Health Pharma R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Joaquín Rullas
- Global Health Pharma R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | | | | | | | - Monica Cacho
- Global Health Pharma R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - David Barros-Aguirre
- Global Health Pharma R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Paul Smith
- Independent Consultant, Global Health Pharma R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Steven J. Berthel
- Panorama Global, 2101
4th Avenue, Suite 2100, Seattle, Washington 98121, United States
| | - Carl Nathan
- Department
of Microbiology & Immunology, Weill
Cornell Medicine, 413 East 69th Street, New York, New York 10021, United
States
| | - Robert H. Bates
- Global Health Pharma R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
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Anti-Metatype Antibody Screening, Sandwich Immunoassay Development, and Structural Insights for β-Lactams Based on Penicillin Binding Protein. Molecules 2021; 26:molecules26185569. [PMID: 34577037 PMCID: PMC8470104 DOI: 10.3390/molecules26185569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/06/2021] [Accepted: 09/08/2021] [Indexed: 11/29/2022] Open
Abstract
Theoretically, sandwich immunoassay is more sensitive and has a wider working range than that of competitive format. However, it has been thought that small molecules cannot be detected by the sandwich format due to their limited size. In the present study, we proposed a novel strategy for achieving sandwich immunoassay of β-lactams with low molecular weights. Firstly, five β-lactam antibiotics were selected to bind with penicillin binding protein (PBP)2x* to form complexes. Then, monoclonal and polyclonal antibodies against PBP2x*-β-lactams complexes were produced by animal immunization. Subsequently, the optimal pairing antibodies were utilized to establish sandwich immunoassay for detection of 18 PBP2x*-β-lactam complexes. Among them, ceftriaxone could be detected at as low as 1.65 ng/mL with working range of 1–1000 ng/mL in milk. To reveal the detection mechanism, computational chemistry and molecular recognition study were carried out. The results showed that β-lactams with a large size and complex structures maybe conducive to induce conformational changes of PBP2x*, and then exhibit greater possibility of being detected by sandwich immunoassay after combination with PBP2x*. This study provides insights for subsequent investigations of anti-metatype antibody screening and sandwich immunoassay establishment for small-molecule detection.
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Xi P, Cao W, Li L, Shi W, Li F, Xu H, Xu X, Ke Y, Zhang J. Identification of related impurities in an oral pharmaceutical formulation of tebipenem pivoxil using ultra-high-performance liquid chromatography/electrospray ionization quadrupole time-of-flight tandem mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2021; 35:e9129. [PMID: 34097785 DOI: 10.1002/rcm.9129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/29/2021] [Accepted: 05/21/2021] [Indexed: 06/12/2023]
Abstract
RATIONALE Tebipenem pivoxil (TBPM-PI) has been developed as the first oral carbapenem drug in the world to treat otolaryngological and respiratory infections in pediatric patients. Due to its structural properties and external factors, some related impurities, which may cause side effects in patients, might be formed during the synthesis and storage of TBPM-PI. It was vital to rapidly separate and identify the related impurities to guarantee the safe use of TBPM-PI. METHODS A method using ultra-high-performance liquid chromatography (UHPLC) coupled with quadrupole time-of-flight tandem mass spectrometry (QTOF-MS/MS) was developed to separate and detect TBPM-PI and related impurities in an oral pharmaceutical formulation. LC/MS and MS/MS spectra of these compounds in the formulation were acquired to confirm their elemental compositions and propose their structures based on LC/MS data and fragmentation pathways of available reference substances. RESULTS LC/MS parameters and MS/MS fragmentation pathways of reference substances of TBPM-PI and related impurities were summarized in detail. Based on this, a total of 23 related impurities were found and characterized in the oral pharmaceutical formulation. Eight of these were verified by comparison with reference substances and the structures of the other 15 were proposed for the first time. In addition, four of these compounds were produced by the reaction of excipients and pre-existing related impurities. CONCLUSIONS A UHPLC/QTOF-MS method was established and used for the separation and identification of 23 related impurities in a TBPM-PI oral pharmaceutical formulation. Moreover, it was proved that new related impurities could be produced by the reaction of excipients in the pharmaceutical formulation and related impurities in the corresponding active pharmaceutical ingredient (API).
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Affiliation(s)
- Pengxuan Xi
- Green Catalysis Center, College of Chemistry, Zhengzhou University, 100 Science Road, Zhengzhou, 450001, China
| | - Wanxue Cao
- Green Catalysis Center, College of Chemistry, Zhengzhou University, 100 Science Road, Zhengzhou, 450001, China
| | - Li Li
- Green Catalysis Center, College of Chemistry, Zhengzhou University, 100 Science Road, Zhengzhou, 450001, China
| | - Weimin Shi
- Green Catalysis Center, College of Chemistry, Zhengzhou University, 100 Science Road, Zhengzhou, 450001, China
| | - Fuxin Li
- Jiyuan Branch, Henan Tobacco Corporation, 38 Huanghe Road, Jiyuan, 459000, China
| | - Haitao Xu
- Zhengzhou Mingze Pharmaceutical Technology Co., Ltd., 369 Xisihuan Road, Zhengzhou, 450000, China
| | - Xiaojie Xu
- Zhengzhou Mingze Pharmaceutical Technology Co., Ltd., 369 Xisihuan Road, Zhengzhou, 450000, China
| | - Yu Ke
- School of Pharmaceutical Sciences, Zhengzhou University, 100 Science Road, Zhengzhou, 450001, China
| | - Jianye Zhang
- Green Catalysis Center, College of Chemistry, Zhengzhou University, 100 Science Road, Zhengzhou, 450001, China
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6
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Brown NW, Shirley JD, Marshall AP, Carlson EE. Comparison of Bioorthogonal β-Lactone Activity-Based Probes for Selective Labeling of Penicillin-Binding Proteins. Chembiochem 2021; 22:193-202. [PMID: 32964667 PMCID: PMC7790944 DOI: 10.1002/cbic.202000556] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/21/2020] [Indexed: 01/20/2023]
Abstract
Penicillin-binding proteins (PBPs) are a family of bacterial enzymes that are key components of cell-wall biosynthesis and the target of β-lactam antibiotics. Most microbial pathogens contain multiple structurally homologous PBP isoforms, making it difficult to target individual PBPs. To study the roles and regulation of specific PBP isoforms, a panel of bioorthogonal β-lactone probes was synthesized and compared. Fluorescent labeling confirmed selectivity, and PBPs were selectively enriched from Streptococcus pneumoniae lysates. Comparisons between fluorescent labeling of probes revealed that the accessibility of bioorthogonal reporter molecules to the bound probe in the native protein environment exerts a more significant effect on labeling intensity than the bioorthogonal reaction used, observations that are likely applicable beyond this class of probes or proteins. Selective, bioorthogonal activity-based probes for PBPs will facilitate the activity-based determination of the roles and regulation of specific PBP isoforms, a key gap in knowledge that has yet to be filled.
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Affiliation(s)
- Nathaniel W Brown
- Department of Chemistry, University of Minnesota-Twin Cities 139 Smith Hall, Pleasant Street SE, Minneapolis, MN, 55455, USA
| | - Joshua D Shirley
- Department of Medicinal Chemistry, University of Minnesota-Twin Cities, 308 Harvard Street SE, Minneapolis, MN, 55455, USA
| | - Andrew P Marshall
- Department of Chemistry, University of Minnesota-Twin Cities 139 Smith Hall, Pleasant Street SE, Minneapolis, MN, 55455, USA
| | - Erin E Carlson
- Department of Chemistry, University of Minnesota-Twin Cities 139 Smith Hall, Pleasant Street SE, Minneapolis, MN, 55455, USA
- Department of Medicinal Chemistry, University of Minnesota-Twin Cities, 308 Harvard Street SE, Minneapolis, MN, 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota-Twin Cities, 321 Church Street SE, Minneapolis, MN, 55455, USA
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Issakhanian L, Behzadi P. Antimicrobial Agents and Urinary Tract Infections. Curr Pharm Des 2020; 25:1409-1423. [PMID: 31218955 DOI: 10.2174/1381612825999190619130216] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 06/12/2019] [Indexed: 02/06/2023]
Abstract
Urinary Tract Infections (UTIs); second-ranking infectious diseases are regarded as a significant global health care problem. The UTIs annually cost tens of millions of dollars for governments worldwide. The main reason behind these costs is incorrect or indefinite treatment. There are a wide range of gram-negative and grampositive bacteria which may cause UTIs in males and females, children and adults. Among gram-negative bacteria, some members of Enterobacteriaceae such as Escherichia coli (E.coli) strains have significant contribution in UTIs. Uropathogenic E.coli (UPEC) strains are recognized as typical bacterial agents for UTIs. Thus, sharp and accurate diagnostic tools are needed for detection and identification of the microbial causative agents of UTIs. In parallel with the utilization of suitable diagnostic methods-to reduce the number of UTIs, effective and definite treatment procedures are needed. Therefore, the prescription of accurate, specific and effective antibiotics and drugs may lead to a definite treatment. However, there are many cases related to UTIs which can be relapsed. Due to a diversity of opportunistic and pathogenic causative microbial agents of UTIs, the treatment procedures should be achieved by the related antimicrobial agents. In this review, common and effective antimicrobial agents which are often prescribed for UTIs caused by UPEC will be discussed. Moreover, we will have a sharp look at their (antimicrobials) molecular treatment mechanisms.
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Affiliation(s)
| | - Payam Behzadi
- Department of Microbiology, College of Basic Sciences, Shahr-e-Qods Branch, Islamic Azad University, Tehran, Iran
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In Vitro Activity of Tebipenem (SPR859) against Penicillin-Binding Proteins of Gram-Negative and Gram-Positive Bacteria. Antimicrob Agents Chemother 2019; 63:AAC.02181-18. [PMID: 30718255 DOI: 10.1128/aac.02181-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/29/2019] [Indexed: 12/25/2022] Open
Abstract
Tebipenem (SPR859) is the microbiologically active form of SPR994 (tebipenem-pivoxil), an orally available carbapenem with activity against extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae Measurement of the relative binding of SPR859 to the bacterial cell targets revealed that it is a potent inhibitor of multiple penicillin-binding proteins (PBPs) but primarily a Gram-negative PBP 2 inhibitor, similar to other compounds in this class. These data support further clinical development of SPR994.
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9
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Cascade reactions as efficient and universal tools for construction and modification of 6-, 5-, 4- and 3-membered sulfur heterocycles of biological relevance. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.09.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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10
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Jain A, Utley L, Parr TR, Zabawa T, Pucci MJ. Tebipenem, the first oral carbapenem antibiotic. Expert Rev Anti Infect Ther 2018; 16:513-522. [DOI: 10.1080/14787210.2018.1496821] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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11
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Adediran SA, Sarkar KS, Pratt RF. Kinetic Evidence for a Second Ligand Binding Site on Streptococcus pneumoniae Penicillin-Binding Protein 2x. Biochemistry 2018; 57:1758-1766. [PMID: 29485264 DOI: 10.1021/acs.biochem.7b01209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
High molecular mass penicillin-binding proteins (PBPs, DD-peptidases) of class B, such as Streptococcus pneumoniae PBP2x, catalyze the cross-linking of peptidoglycan in bacterial cell wall biosynthesis and are thus important antibiotic targets. Despite their importance in this regard, structure-function studies of ligands of these enzymes have been impeded by the absence of useful substrates. In vitro, these enzymes do not catalyze peptide hydrolysis or aminolysis, their in vivo reaction, but some, such as PBP2x, do catalyze these reactions of certain thioesters such as PhCH2CONHCH2COSCH(D-Me)CO2- (2). We have now prepared several peptidoglycan-mimetic thioesters that we expected to more closely resemble the natural substrates of these enzymes. To our surprise, however, these compounds, although indeed substrates of PBP2x, did not, unlike 2, appear to form an acyl-enzyme intermediate during hydrolysis, and their turnover was inhibited by certain peptides and N-acylamino acids much more weakly than that of 2. An inhibitor of this type, N-benzyloxycarbonyl-d-glutamic acid, also quenched the fluorescence of PBP2x that had been labeled at the DD-peptidase active site by 6-dansylamidopenicillanic acid. These results were interpreted in terms of a model where the peptidoglycan-mimetic thioesters preferentially bound to and hydrolyzed at a site other than the classical DD-peptidase active site. This second site is likely to represent part of an extended binding site that accommodates a peptidoglycan substrate or regulator in vivo. Such a site may be a target for future inhibitor/antibiotic design.
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Affiliation(s)
- S A Adediran
- Department of Chemistry , Wesleyan University , Lawn Avenue , Middletown , Connecticut 06459 , United States
| | - Kumar Subarno Sarkar
- Department of Chemistry , Wesleyan University , Lawn Avenue , Middletown , Connecticut 06459 , United States
| | - R F Pratt
- Department of Chemistry , Wesleyan University , Lawn Avenue , Middletown , Connecticut 06459 , United States
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12
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Sharifzadeh S, Boersma MJ, Kocaoglu O, Shokri A, Brown CL, Shirley JD, Winkler ME, Carlson EE. Novel Electrophilic Scaffold for Imaging of Essential Penicillin-Binding Proteins in Streptococcus pneumoniae. ACS Chem Biol 2017; 12:2849-2857. [PMID: 28990753 DOI: 10.1021/acschembio.7b00614] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptidoglycan (PG) is a mesh-like heteropolymer made up of glycan chains cross-linked by short peptides and is the major scaffold of eubacterial cell walls, determining cell shape, size, and chaining. This structure, which is required for growth and survival, is located outside of the cytoplasmic membrane of bacterial cells, making it highly accessible to antibiotics. Penicillin-binding proteins (PBPs) are essential for construction of PG and perform transglycosylase activities to generate the glycan strands and transpeptidation to cross-link the appended peptides. The β-lactam antibiotics, which are among the most clinically effective antibiotics for the treatment of bacterial infections, inhibit PBP transpeptidation, ultimately leading to cell lysis. Despite this importance, the discrete functions of individual PBP homologues have been difficult to determine. These major gaps in understanding of PBP activation and macromolecular interactions largely result from a lack of tools to assess the functional state of specific PBPs in bacterial cells. We have identified β-lactones as a privileged scaffold for the generation of PBP-selective probes and utilized these compounds for imaging of the essential proteins, PBP2x and PBP2b, in Streptococcus pneumoniae. We demonstrated that while PBP2b activity is restricted to a ring surrounding the division sites, PBP2x activity is present both at the septal center and at the surrounding ring. These spatially separate regions of PBP2x activity could not be detected by previous activity-based approaches, which highlights a critical strength of our PBP-selective imaging strategy.
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Affiliation(s)
- Shabnam Sharifzadeh
- Departments
of Chemistry, ‡Medicinal Chemistry, and Biochemistry, §Molecular Biology
and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Departments of Biology, ⊥Molecular and Cellular Biochemistry,
and #Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Michael J. Boersma
- Departments
of Chemistry, ‡Medicinal Chemistry, and Biochemistry, §Molecular Biology
and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Departments of Biology, ⊥Molecular and Cellular Biochemistry,
and #Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Ozden Kocaoglu
- Departments
of Chemistry, ‡Medicinal Chemistry, and Biochemistry, §Molecular Biology
and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Departments of Biology, ⊥Molecular and Cellular Biochemistry,
and #Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Alireza Shokri
- Departments
of Chemistry, ‡Medicinal Chemistry, and Biochemistry, §Molecular Biology
and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Departments of Biology, ⊥Molecular and Cellular Biochemistry,
and #Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Clayton L. Brown
- Departments
of Chemistry, ‡Medicinal Chemistry, and Biochemistry, §Molecular Biology
and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Departments of Biology, ⊥Molecular and Cellular Biochemistry,
and #Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Joshua D. Shirley
- Departments
of Chemistry, ‡Medicinal Chemistry, and Biochemistry, §Molecular Biology
and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Departments of Biology, ⊥Molecular and Cellular Biochemistry,
and #Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Malcolm E. Winkler
- Departments
of Chemistry, ‡Medicinal Chemistry, and Biochemistry, §Molecular Biology
and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Departments of Biology, ⊥Molecular and Cellular Biochemistry,
and #Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Erin E. Carlson
- Departments
of Chemistry, ‡Medicinal Chemistry, and Biochemistry, §Molecular Biology
and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Departments of Biology, ⊥Molecular and Cellular Biochemistry,
and #Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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13
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Paczkowska M, Mizera M, Dzitko J, Lewandowska K, Zalewski P, Cielecka-Piontek J. Vibrational (FT-IR, Raman) and DFT analysis on the structure of labile drugs. The case of crystalline tebipenem and its ester. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.12.074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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14
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Sakata H, Kuroki H, Ouchi K, Tajima T, Iwata S. Pediatric community-acquired pneumonia treated with a three-day course of tebipenem pivoxil. J Infect Chemother 2017; 23:307-311. [PMID: 28238680 DOI: 10.1016/j.jiac.2017.01.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 01/28/2017] [Indexed: 02/06/2023]
Abstract
We evaluated the efficacy and safety of a 3-day treatment regimen of tebipenem pivoxil for pediatric community-acquired pneumonia. Tebipenem pivoxil was administered to 49 patients, and its effectiveness was evaluated in 36 patients 2-4 days after initiation of treatment. Thirty-two patients were cured 7-15 days after initiation of treatment. Body temperature was significantly lower on the day following initial administration (median 38.8 to 37.0 °C, n = 33). Leukocyte counts and C-reactive protein levels were significantly reduced by Day 2-4 of treatment (median 16,100 to 7800 white blood cells/μL, and 5.6 to 1.5 mg/dL, respectively; n = 28). Six of the 49 patients had mild diarrhea. Thus, we concluded that 3-day treatment with tebipenem pivoxil was safe and efficacious for treating pediatric community-acquired pneumonia.
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Affiliation(s)
- Hiroshi Sakata
- Department of Pediatrics, Asahikawa Kosei Hospital, Japan.
| | - Haruo Kuroki
- Sotobo Children's Clinic, Medical Corporation Shigyo-no-kai, Japan
| | - Kazunobu Ouchi
- Department of Pediatrics, Kawasaki Medical School, Japan
| | - Takeshi Tajima
- Department of Pediatrics, Hakujikai Memorial Hospital, Japan
| | - Satoshi Iwata
- Center for Infectious Diseases and Infection Control, Keio University School of Medicine, Japan
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15
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Filippova EV, Kieser KJ, Luan CH, Wawrzak Z, Kiryukhina O, Rubin EJ, Anderson WF. Crystal structures of the transpeptidase domain of the Mycobacterium tuberculosis penicillin-binding protein PonA1 reveal potential mechanisms of antibiotic resistance. FEBS J 2016; 283:2206-18. [PMID: 27101811 PMCID: PMC5245116 DOI: 10.1111/febs.13738] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 03/30/2016] [Accepted: 04/15/2016] [Indexed: 01/21/2023]
Abstract
UNLABELLED Mycobacterium tuberculosis is a human respiratory pathogen that causes the deadly disease tuberculosis. The rapid global spread of antibiotic-resistant M. tuberculosis makes tuberculosis infections difficult to treat. To overcome this problem new effective antimicrobial strategies are urgently needed. One promising target for new therapeutic approaches is PonA1, a class A penicillin-binding protein, which is required for maintaining physiological cell wall synthesis and cell shape during growth in mycobacteria. Here, crystal structures of the transpeptidase domain, the enzymatic domain responsible for penicillin binding, of PonA1 from M. tuberculosis in the inhibitor-free form and in complex with penicillin V are reported. We used site-directed mutagenesis, antibiotic profiling experiments, and fluorescence thermal shift assays to measure PonA1's sensitivity to different classes of β-lactams. Structural comparison of the PonA1 apo-form and the antibiotic-bound form shows that binding of penicillin V induces conformational changes in the position of the loop β4'-α3 surrounding the penicillin-binding site. We have also found that binding of different antibiotics including penicillin V positively impacts protein stability, while other tested β-lactams such as clavulanate or meropenem resulted in destabilization of PonA1. Our antibiotic profiling experiments indicate that the transpeptidase activity of PonA1 in both M. tuberculosis and M. smegmatis mediates tolerance to specific cell wall-targeting antibiotics, particularly to penicillin V and meropenem. Because M. tuberculosis is an important human pathogen, these structural data provide a template to design novel transpeptidase inhibitors to treat tuberculosis infections. DATABASE Structural data are available in the PDB database under the accession numbers 5CRF and 5CXW.
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Affiliation(s)
- Ekaterina V Filippova
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Midwest Center for Structural Genomics (MCSG), Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Karen J Kieser
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Chi-Hao Luan
- Midwest Center for Structural Genomics (MCSG), Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
- High Throughput Analysis Laboratory and Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Zdzislaw Wawrzak
- Life Science Collaborative Access Team, Synchrotron Research Center, Northwestern University, Evanston, IL, USA
| | - Olga Kiryukhina
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Midwest Center for Structural Genomics (MCSG), Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Eric J Rubin
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Wayne F Anderson
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Midwest Center for Structural Genomics (MCSG), Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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16
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Fisher JF, Mobashery S. β-Lactam Resistance Mechanisms: Gram-Positive Bacteria and Mycobacterium tuberculosis. Cold Spring Harb Perspect Med 2016; 6:cshperspect.a025221. [PMID: 27091943 DOI: 10.1101/cshperspect.a025221] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The value of the β-lactam antibiotics for the control of bacterial infection has eroded with time. Three Gram-positive human pathogens that were once routinely susceptible to β-lactam chemotherapy-Streptococcus pneumoniae, Enterococcus faecium, and Staphylococcus aureus-now are not. Although a fourth bacterium, the acid-fast (but not Gram-positive-staining) Mycobacterium tuberculosis, has intrinsic resistance to earlier β-lactams, the emergence of strains of this bacterium resistant to virtually all other antibiotics has compelled the evaluation of newer β-lactam combinations as possible contributors to the multidrug chemotherapy required to control tubercular infection. The emerging molecular-level understanding of these resistance mechanisms used by these four bacteria provides the conceptual framework for bringing forward new β-lactams, and new β-lactam strategies, for the future control of their infections.
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Affiliation(s)
- Jed F Fisher
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556-5670
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556-5670
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17
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Fungal naphtho-γ-pyrones: Potent antibiotics for drug-resistant microbial pathogens. Sci Rep 2016; 6:24291. [PMID: 27063778 PMCID: PMC4827027 DOI: 10.1038/srep24291] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 03/24/2016] [Indexed: 12/26/2022] Open
Abstract
Four naphtho-γ-pyrones (fonsecinones A and C and aurasperones A and E) were identified as potential antibacterial agents against Escherichia coli, extended-spectrum β-lactamase (ESBL)-producing E. coli, Pseudomonas aeruginosa, Enterococcus faecalis, and methicillin-resistant Staphylococcus aureus (MRSA) in an in vitro antibacterial screen of 218 fungal metabolites. Fonsecinone A (2) exhibited the most potent antibacterial activity, with minimum inhibitory concentrations (MICs) of 4.26, 17.04, and 4.26 μg/mL against ESBL-producing E. coli, P. aeruginosa, and E. faecalis, respectively. The inhibitory effects of fonsecinones A (2) and C (3) against E. coli and ESBL-producing E. coli were comparable to those of amikacin. Molecular docking-based target identification of naphtho-γ-pyrones 1–8 revealed bacterial enoyl-acyl carrier protein reductase (FabI) as an antibacterial target, which was further validated by FabI affinity and inhibition assays. Fonsecinones A (2) and C (3) and aurasperones A (6) and E (7) bound FabI specifically and produced concentration-dependent inhibition effects. This work is the first report of anti-drug-resistant bacterial activities of naphtho-γ-pyrones 1–8 and their possible antibacterial mechanism of action and provides an example of the successful application of in silico methods for drug target identification and validation and the identification of new lead antibiotic compounds against drug-resistant pathogens.
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18
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Talaczyńska A, Lewandowska K, Garbacki P, Zalewski P, Skibiński R, Miklaszewski A, Mizera M, Cielecka-Piontek J. Solid-state stability studies of crystal form of tebipenem. Drug Dev Ind Pharm 2015; 42:238-44. [DOI: 10.3109/03639045.2015.1044902] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Alicja Talaczyńska
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Poznan University of Medical Sciences, Poznań, Poland,
| | | | - Piotr Garbacki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Poznan University of Medical Sciences, Poznań, Poland,
| | - Przemysław Zalewski
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Poznan University of Medical Sciences, Poznań, Poland,
| | - Robert Skibiński
- Department of Medicinal Chemistry, Medical University of Lublin, Lublin, Poland, and
| | - Andrzej Miklaszewski
- Institute of Materials Science and Engineering, Poznan University of Technology, Poznan, Poland
| | - Mikołaj Mizera
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Poznan University of Medical Sciences, Poznań, Poland,
| | - Judyta Cielecka-Piontek
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Poznan University of Medical Sciences, Poznań, Poland,
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19
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Penicillin-binding proteins: evergreen drug targets. Curr Opin Pharmacol 2014; 18:112-9. [DOI: 10.1016/j.coph.2014.09.012] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 09/12/2014] [Indexed: 02/07/2023]
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20
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Gogoi RR, Gogoi D, Bezbaruah RL. Virtual Screening of compounds from Tabernaemontana divaricata for potential anti-bacterial activity. Bioinformation 2014; 10:152-6. [PMID: 24748755 PMCID: PMC3974242 DOI: 10.6026/97320630010152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 12/18/2013] [Accepted: 12/19/2013] [Indexed: 11/29/2022] Open
Abstract
Virtual Screening and Molecular Docking analysis for Tabernaemontana divaricata derived 66 Law Molecular Weight Compounds
(LMW) was conducted and to identified and predicted novel molecules as a inhibitor of Streptococcus pneumonia. The investigation
has revealed several compounds with optimum binding towards Penicillin-binding proteins, Sialidases, Aspartate betasemialdehide
dehydrogenase cell membrane protein of Streptococcus pneumonia. Docking results were computed in term of
binding energy, ligand efficiency and number of hydrogen bonding. Apparicine (-5.14), 5-Hydroxyvoaphylline (-4.78), Voacangine
(-4.7), 19-Hydroxycoronaridine (-4.44) and Coronaridine (-4.72) are identified as most suitable to bind with N-acetylglucosamine-1-
phosphate uridyltransferase receptor. Ervaticine (-6.33), Ibogamine (-6.15), Methylvoaphylline (-5.74) and Coronaridine
hydroxyindolenine (-5.32) has showed novel binding against the penicillin-binding proteins. Ervaticine (-6.42), 5-oxo-11-hydroxy
voaphylline (-6.18), Conolobine B (-6.02) has found optimum binding against the active site of NanB sialidase of Streptococcus
pneumonia. The compounds 3S-Cyanocoronaridine (-6.71), 19-Epivoacristine (-5.48) and Ervaticine(-5.45) interacting with aspartate
beta-semialdehide and found suitable with least docking score.
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Affiliation(s)
- Rashmi Rekha Gogoi
- Centre for Bioinformatics Studies, Dibrugarh University, Dibrugarh, Assam
| | - Dhrubajyoti Gogoi
- DBT-Bioinformatics Infrastructure Facility, Biotechnology Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam
| | - Rajib Lochan Bezbaruah
- DBT-Bioinformatics Infrastructure Facility, Biotechnology Division, CSIR-North East Institute of Science and Technology, Jorhat, Assam
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21
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Butler MS, Robertson AAB, Cooper MA. Natural product and natural product derived drugs in clinical trials. Nat Prod Rep 2014; 31:1612-61. [DOI: 10.1039/c4np00064a] [Citation(s) in RCA: 383] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The 25 Natural Product (NP)-derived drugs launched since 2008 and the 100 NP-derived compounds and 33 Antibody Drug Conjugates (ADCs) in clinical trials or in registration at the end of 2013 are reviewed.
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Affiliation(s)
- Mark S. Butler
- Division of Chemistry and Structural Biology
- Institute for Molecular Bioscience
- The University of Queensland
- Brisbane, Australia
| | - Avril A. B. Robertson
- Division of Chemistry and Structural Biology
- Institute for Molecular Bioscience
- The University of Queensland
- Brisbane, Australia
| | - Matthew A. Cooper
- Division of Chemistry and Structural Biology
- Institute for Molecular Bioscience
- The University of Queensland
- Brisbane, Australia
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22
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Cielecka-Piontek J, Zalewski P, Barszcz B, Lewandowska K, Paczkowska M. Stress Degradation Studies of Tebipenem and a Validated Stability-Indicating LC Method. Chromatographia 2013; 76:381-386. [PMID: 23555151 PMCID: PMC3612176 DOI: 10.1007/s10337-012-2331-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2012] [Revised: 09/05/2012] [Accepted: 09/18/2012] [Indexed: 10/27/2022]
Abstract
A inexpensive and rapid isocratic LC method has been developed for the quantitative determination of tebipenem-a new β-lactam antibiotic. Stress degradation studies were performed on tebipenem in acidic (0.2 N hydrochloric acid) and basic (0.02 N sodium hydroxide) solutions, in a solution with oxidizing agent (3 % hydrogen peroxide), and in the solid state, during thermolysis and photolysis. For a chromatographic separation of tebipenem and its degradation products, a C-18 stationary phase and 12 mM ammonium acetate-acetonitrile (96:4 v/v) were used. A quantitative determination of tebipenem was carried out by using a PDA detector at 298 nm, with a flow rate of 1.2 mL min-1. The linear regression analysis for the calibration plots showed a good linear relationship (r = 0.999) in the concentration range 0.041-0.240 mg mL-1. The method demonstrated good precision (1.14-1.96 % RSD) and recovery (99.60-101.90 %). The limits of detection and quantitation were 9.69 and 29.36 μg mL-1, respectively. The analysis of tebipenem reactivity was supported by quantum chemical calculations based on the density functional theory (DFT). The analysis of the electron density of the HOMO and LUMO of tebipenem suggested the possibility of electron transport in the molecule during the degradation of bi-cyclic 4:5 fused penem rings.
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Affiliation(s)
- Judyta Cielecka-Piontek
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Poznan University of Medical Sciences, Grunwaldzka 6, 60-780 Poznań, Poland
| | - Przemysław Zalewski
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Poznan University of Medical Sciences, Grunwaldzka 6, 60-780 Poznań, Poland
| | - Bolesław Barszcz
- Department of Molecular Crystals, Institute of Molecular Physics Polish Academy Sciences, Smoluchowskiego 17, 60-179 Poznań, Poland
| | - Kornelia Lewandowska
- Department of Molecular Crystals, Institute of Molecular Physics Polish Academy Sciences, Smoluchowskiego 17, 60-179 Poznań, Poland
| | - Magdalena Paczkowska
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Poznan University of Medical Sciences, Grunwaldzka 6, 60-780 Poznań, Poland
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23
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Yamachika S, Sugihara C, Kamai Y, Yamashita M. Correlation between penicillin-binding protein 2 mutations and carbapenem resistance in Escherichia coli. J Med Microbiol 2013; 62:429-436. [DOI: 10.1099/jmm.0.051631-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Shinichiro Yamachika
- Oncology Research Laboratories, Daiichi Sankyo Co. Ltd, 1-16-13 Kitakasai, Edogawa-ku, Tokyo 134-8630, Japan
| | - Chika Sugihara
- Lead Discovery & Optimization Research Laboratories II, Daiichi Sankyo Co. Ltd, 1-16-13 Kitakasai, Edogawa-ku, Tokyo 134-8630, Japan
| | - Yasuki Kamai
- Oncology Research Laboratories, Daiichi Sankyo Co. Ltd, 1-16-13 Kitakasai, Edogawa-ku, Tokyo 134-8630, Japan
| | - Makoto Yamashita
- Biological Research Laboratories, Daiichi Sankyo Co. Ltd, 1-16-13 Kitakasai, Edogawa-ku, Tokyo 134-8630, Japan
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24
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Ouyang X, Zhou S, Su CTT, Ge Z, Li R, Kwoh CK. CovalentDock: automated covalent docking with parameterized covalent linkage energy estimation and molecular geometry constraints. J Comput Chem 2012; 34:326-36. [PMID: 23034731 DOI: 10.1002/jcc.23136] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 08/06/2012] [Accepted: 09/05/2012] [Indexed: 12/21/2022]
Abstract
Covalent linkage formation is a very important mechanism for many covalent drugs to work. However, partly due to the limitations of proper computational tools for covalent docking, most covalent drugs are not discovered systematically. In this article, we present a new covalent docking package, the CovalentDock, built on the top of the source code of Autodock. We developed an empirical model of free energy change estimation for covalent linkage formation, which is compatible with existing scoring functions used in docking, while handling the molecular geometry constrains of the covalent linkage with special atom types and directional grid maps. Integrated preparation scripts are also written for the automation of the whole covalent docking workflow. The result tested on existing crystal structures with covalent linkage shows that CovalentDock can reproduce the native covalent complexes with significant improved accuracy when compared with the default covalent docking method in Autodock. Experiments also suggest that CovalentDock is capable of covalent virtual screening with satisfactory enrichment performance. In addition, the investigation on the results also shows that the chirality and target selectivity along with the molecular geometry constrains are well preserved by CovalentDock, showing great capability of this method in the application for covalent drug discovery.
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Affiliation(s)
- Xuchang Ouyang
- BioInformatics Research Centre, School of Computer Engineering, Nanyang Technological University, Singapore 639798
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25
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Meletis G, Exindari M, Vavatsi N, Sofianou D, Diza E. Mechanisms responsible for the emergence of carbapenem resistance in Pseudomonas aeruginosa. Hippokratia 2012; 16:303-307. [PMID: 23935307 PMCID: PMC3738602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Pseudomonas aeruginosa (P. aeruginosa) is an opportunistic pathogen associated with a range of nosocomial infections. This microorganism is noted for its intrinsic resistance to antibiotics and for its ability to acquire genes encoding resistance determinants. Among the beta-lactam antibiotics, carbapenems with antipseudomonal activity are important agents for the therapy of infections due to P. aeruginosa. The development of carbapenem resistance among P. aeruginosa strains is multifactorial. Plasmid or integron-mediated carbapenemases, increased expression of efflux systems, reduced porin expression and increased chromosomal cephalosporinase activity have all been defined as contributory factors. Phenotypic tests and molecular techniques are used for the characterization of the resistance determinants. The isolation of carbapenem resistant strains is alarming and requires the implementation of strict infection control measures in order to prevent the spread of carbapenemase encoding genes to unrelated clones or to other bacterial species.
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Affiliation(s)
- G Meletis
- Department of Clinical Microbiology, Veroia G. Hospital, Veroia, Greece
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26
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Correlation of the antimicrobial activity of ME1036 with its binding affinities to the penicillin-binding proteins from Streptococcus pneumoniae strains. J Antibiot (Tokyo) 2011; 64:741-6. [DOI: 10.1038/ja.2011.76] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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27
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Bobba S, Gutheil WG. Multivariate geometrical analysis of catalytic residues in the penicillin-binding proteins. Int J Biochem Cell Biol 2011; 43:1490-9. [PMID: 21740978 DOI: 10.1016/j.biocel.2011.06.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Revised: 05/04/2011] [Accepted: 06/22/2011] [Indexed: 12/11/2022]
Abstract
Penicillin-binding proteins (PBPs) are bacterial enzymes involved in the final stages of cell wall biosynthesis, and are targets of the β-lactam antibiotics. They can be subdivided into essential high-molecular-mass (HMM) and non-essential low-molecular-mass (LMM) PBPs, and further divided into subclasses based on sequence homologies. PBPs can catalyze transpeptidase or hydrolase (carboxypeptidase and endopeptidase) reactions. The PBPs are of interest for their role in bacterial cell wall biosynthesis, and as mechanistically interesting enzymes which can catalyze alternative reaction pathways using the same catalytic machinery. A global catalytic residue comparison seemed likely to provide insight into structure-function correlations within the PBPs. More than 90 PBP structures were aligned, and a number (40) of active site geometrical parameters extracted. This dataset was analyzed using both univariate and multivariate statistical methods. Several interesting relationships were observed. (1) Distribution of the dihedral angle for the SXXK-motif Lys side chain (DA_1) was bimodal, and strongly correlated with HMM/transpeptidase vs LMM/hydrolase classification/activity (P<0.001). This structural feature may therefore be associated with the main functional difference between the HMM and LMM PBPs. (2) The distance between the SXXK-motif Lys-NZ atom and the Lys/His-nitrogen atom of the (K/H)T(S)G-motif was highly conserved, suggesting importance for PBP function, and a possibly conserved role in the catalytic mechanism of the PBPs. (3) Principal components-based cluster analysis revealed several distinct clusters, with the HMM Class A and B, LMM Class C, and LMM Class A K15 PBPs forming one "Main" cluster, and demonstrating a globally similar arrangement of catalytic residues within this group.
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Affiliation(s)
- Sudheer Bobba
- Division of Pharmaceutical Sciences, University of Missouri-Kansas City, Kansas City, MO 64108, United States
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Gautam A, Vyas R, Tewari R. Peptidoglycan biosynthesis machinery: a rich source of drug targets. Crit Rev Biotechnol 2010; 31:295-336. [PMID: 21091161 DOI: 10.3109/07388551.2010.525498] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The range of antibiotic therapy for the control of bacterial infections is becoming increasingly limited because of the rapid rise in multidrug resistance in clinical bacterial isolates. A few diseases, such as tuberculosis, which were once thought to be under control, have re-emerged as serious health threats. These problems have resulted in intensified research to look for new inhibitors for bacterial pathogens. Of late, the peptidoglycan (PG) layer, the most important component of the bacterial cell wall has been the subject of drug targeting because, first, it is essential for the survivability of eubacteria and secondly, it is absent in humans. The last decade has seen tremendous inputs in deciphering the 3-D structures of the PG biosynthetic enzymes. Many inhibitors against these enzymes have been developed using virtual and high throughput screening techniques. This review discusses the mechanistic and structural properties of the PG biosynthetic enzymes and inhibitors developed in the last decade.
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Affiliation(s)
- Ankur Gautam
- Department of Biotechnology, Panjab University, Chandigarh, India
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Sainsbury S, Bird L, Rao V, Shepherd SM, Stuart DI, Hunter WN, Owens RJ, Ren J. Crystal structures of penicillin-binding protein 3 from Pseudomonas aeruginosa: comparison of native and antibiotic-bound forms. J Mol Biol 2010; 405:173-84. [PMID: 20974151 PMCID: PMC3025346 DOI: 10.1016/j.jmb.2010.10.024] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Revised: 10/08/2010] [Accepted: 10/15/2010] [Indexed: 11/24/2022]
Abstract
We report the first crystal structures of a penicillin-binding protein (PBP), PBP3, from Pseudomonas aeruginosa in native form and covalently linked to two important β-lactam antibiotics, carbenicillin and ceftazidime. Overall, the structures of apo and acyl complexes are very similar; however, variations in the orientation of the amino-terminal membrane-proximal domain relative to that of the carboxy-terminal transpeptidase domain indicate interdomain flexibility. Binding of either carbenicillin or ceftazidime to purified PBP3 increases the thermostability of the enzyme significantly and is associated with local conformational changes, which lead to a narrowing of the substrate-binding cleft. The orientations of the two β-lactams in the active site and the key interactions formed between the ligands and PBP3 are similar despite differences in the two drugs, indicating a degree of flexibility in the binding site. The conserved binding mode of β-lactam-based inhibitors appears to extend to other PBPs, as suggested by a comparison of the PBP3/ceftazidime complex and the Escherichia coli PBP1b/ceftoxamine complex. Since P. aeruginosa is an important human pathogen, the structural data reveal the mode of action of the frontline antibiotic ceftazidime at the molecular level. Improved drugs to combat infections by P. aeruginosa and related Gram-negative bacteria are sought and our study provides templates to assist that process and allows us to discuss new ways of inhibiting PBPs.
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Affiliation(s)
- Sarah Sainsbury
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Louise Bird
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
- Oxford Protein Production Facility UK, The Research Complex at Harwell, Rutherford Appleton Laboratory Harwell Science and Innovation Campus, Oxfordshire OX11 0FA, UK
| | - Vincenzo Rao
- Biological Chemistry and Drug Discovery, College of Life Sciences, The Wellcome Trust Building, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Sharon M. Shepherd
- Biological Chemistry and Drug Discovery, College of Life Sciences, The Wellcome Trust Building, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - David I. Stuart
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - William N. Hunter
- Biological Chemistry and Drug Discovery, College of Life Sciences, The Wellcome Trust Building, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Raymond J. Owens
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
- Oxford Protein Production Facility UK, The Research Complex at Harwell, Rutherford Appleton Laboratory Harwell Science and Innovation Campus, Oxfordshire OX11 0FA, UK
- Corresponding authors. R. J. Owens is to be contacted at: Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.
| | - Jingshan Ren
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
- Corresponding authors. R. J. Owens is to be contacted at: Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.
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Nicola G, Tomberg J, Pratt RF, Nicholas RA, Davies C. Crystal structures of covalent complexes of β-lactam antibiotics with Escherichia coli penicillin-binding protein 5: toward an understanding of antibiotic specificity. Biochemistry 2010; 49:8094-104. [PMID: 20726582 DOI: 10.1021/bi100879m] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Penicillin-binding proteins (PBPs) are the molecular targets for the widely used β-lactam class of antibiotics, but how these compounds act at the molecular level is not fully understood. We have determined crystal structures of Escherichia coli PBP 5 as covalent complexes with imipenem, cloxacillin, and cefoxitin. These antibiotics exhibit very different second-order rates of acylation for the enzyme. In all three structures, there is excellent electron density for the central portion of the β-lactam, but weak or absent density for the R1 or R2 side chains. Areas of contact between the antibiotics and PBP 5 do not correlate with the rates of acylation. The same is true for conformational changes, because although a shift of a loop leading to an electrostatic interaction between Arg248 and the β-lactam carboxylate, which occurs completely with cefoxitin and partially with imipenem and is absent with cloxacillin, is consistent with the different rates of acylation, mutagenesis of Arg248 decreased the level of cefoxitin acylation only 2-fold. Together, these data suggest that structures of postcovalent complexes of PBP 5 are unlikely to be useful vehicles for the design of new covalent inhibitors of PBPs. Finally, superimposition of the imipenem-acylated complex with PBP 5 in complex with a boronic acid peptidomimetic shows that the position corresponding to the hydrolytic water molecule is occluded by the ring nitrogen of the β-lactam. Because the ring nitrogen occupies a similar position in all three complexes, this supports the hypothesis that deacylation is blocked by the continued presence of the leaving group after opening of the β-lactam ring.
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Affiliation(s)
- George Nicola
- Department of Biochemistry, Medical University of South Carolina, Charleston, South Carolina 29425, USA
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Llarrull LI, Testero SA, Fisher JF, Mobashery S. The future of the β-lactams. Curr Opin Microbiol 2010; 13:551-7. [PMID: 20888287 DOI: 10.1016/j.mib.2010.09.008] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Revised: 09/08/2010] [Accepted: 09/09/2010] [Indexed: 11/15/2022]
Abstract
In the 80 years since their discovery the β-lactam antibiotics have progressed through structural generations, each in response to the progressive evolution of bacterial resistance mechanisms. The generational progression was driven by the ingenious, but largely empirical, manipulation of structure by medicinal chemists. Nonetheless, the true creative force in these efforts was Nature, and as the discovery of new β-lactams from Nature has atrophied while at the same time multi-resistant and opportunistic bacterial pathogens have burgeoned, the time for empirical drug discovery has passed. We concisely summarize recent developments with respect to bacterial resistance, the identity of the new β-lactams, and the emerging non-empirical strategies that will ensure that this incredible class of antibiotics has a future.
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Affiliation(s)
- Leticia I Llarrull
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
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Miguet L, Zervosen A, Gerards T, Pasha FA, Luxen A, Distèche-Nguyen M, Thomas A. Discovery of new inhibitors of resistant Streptococcus pneumoniae penicillin binding protein (PBP) 2x by structure-based virtual screening. J Med Chem 2009; 52:5926-36. [PMID: 19746934 DOI: 10.1021/jm900625q] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Penicillin binding proteins (PBPs) are involved in the biosynthesis of the peptidoglycan layer constitutive of the bacterial envelope. They have been targeted for more than half a century by extensively derived molecular scaffolds of penicillins and cephalosporins. Streptococcus pneumoniae resists the antibiotic pressure by inducing highly mutated PBPs that can no longer bind the beta-lactam containing agents. To find inhibitors of PBP2x from Streptococcus pneumoniae (spPBP2x) with novel chemical scaffold so as to circumvent the resistance problems, a hierarchical virtual screening procedure was performed on the NCI database containing approximately 260000 compounds. The calculations involved ligand-based pharmacophore mapping studies and molecular docking simulations in a homology model of spPBP2x from the highly resistant strain 5204. A total of 160 hits were found, and 55 were available for experimental tests. Three compounds harboring two novel chemical scaffolds were identified as inhibitors of the resistant strain 5204-spPBP2x at the micromolar range.
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Affiliation(s)
- Laurence Miguet
- Laboratoire de Dynamique Moleculaire, Institut de Biologie Structurale Jean-Pierre Ebel (CEA/CNRS/UJF), Grenoble, France
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Powell AJ, Tomberg J, Deacon AM, Nicholas RA, Davies C. Crystal structures of penicillin-binding protein 2 from penicillin-susceptible and -resistant strains of Neisseria gonorrhoeae reveal an unexpectedly subtle mechanism for antibiotic resistance. J Biol Chem 2009; 284:1202-12. [PMID: 18986991 PMCID: PMC2613624 DOI: 10.1074/jbc.m805761200] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2008] [Revised: 10/23/2008] [Indexed: 11/06/2022] Open
Abstract
Penicillin-binding protein 2 (PBP2) from N. gonorrhoeae is the major molecular target for beta-lactam antibiotics used to treat gonococcal infections. PBP2 from penicillin-resistant strains of N. gonorrhoeae harbors an aspartate insertion after position 345 (Asp-345a) and 4-8 additional mutations, but how these alter the architecture of the protein is unknown. We have determined the crystal structure of PBP2 derived from the penicillin-susceptible strain FA19, which shows that the likely effect of Asp-345a is to alter a hydrogen-bonding network involving Asp-346 and the SXN triad at the active site. We have also solved the crystal structure of PBP2 derived from the penicillin-resistant strain FA6140 that contains four mutations near the C terminus of the protein. Although these mutations lower the second order rate of acylation for penicillin by 5-fold relative to wild type, comparison of the two structures shows only minor structural differences, with the positions of the conserved residues in the active site essentially the same in both. Kinetic analyses indicate that two mutations, P551S and F504L, are mainly responsible for the decrease in acylation rate. Melting curves show that the four mutations lower the thermal stability of the enzyme. Overall, these data suggest that the molecular mechanism underlying antibiotic resistance contributed by the four mutations is subtle and involves a small but measurable disordering of residues in the active site region that either restricts the binding of antibiotic or impedes conformational changes that are required for acylation by beta-lactam antibiotics.
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Affiliation(s)
- Ailsa J Powell
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425, USA
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