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Abstract
This review summarizes patent applications from 2010 for small molecules for which there is a claim of antibacterial activity. The primary criterion for inclusion in this analysis was reporting of cellular antibacterial activity data (MICs) for at least one compound. Patent applications are reviewed according to their biological target and antibacterial class. Protein synthesis inhibitors disclosed in this period include inhibitors of the 50S ribosome subunit (oxazolidinones, macrolides/ketolides and pleuromutilins), 30S ribosome subunit (aminoglycosides and tetracyclines) and nonribosomal targets (PDF inhibitors). DNA synthesis inhibitors include inhibitors of GyrA/ParC and GyrB/ParE. Cell envelope disruptors disclosed in 2010 cover both inhibitors of cell-envelope synthesis (LpxC inhibitors, β-lactams and glycopeptides), as well as membrane disruptors (lipopeptides and polymyxins). Other antibacterial classes covered in this review include rifamycins and antibacterial peptides. Patent applications for compounds aimed at overcoming resistance mechanisms (efflux inhibitors and β-lactamase inhibitors) are also described.
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54
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Bourne CR, Wakeham N, Bunce RA, Berlin KD, Barrow WW. Classifying compound mechanism of action for linking whole cell phenotypes to molecular targets. J Mol Recognit 2012; 25:216-23. [PMID: 22434711 PMCID: PMC3703735 DOI: 10.1002/jmr.2174] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Drug development programs have proven successful when performed at a whole cell level, thus incorporating solubility and permeability into the primary screen. However, linking those results to the target within the cell has been a major setback. The Phenotype Microarray system, marketed and sold by Biolog, seeks to address this need by assessing the phenotype in combination with a variety of chemicals with known mechanism of action (MOA). We have evaluated this system for usefulness in deducing the MOA for three test compounds. To achieve this, we constructed a database with 21 known antimicrobials, which served as a comparison for grouping our unknown MOA compounds. Pearson correlation and Ward linkage calculations were used to generate a dendrogram that produced clustering largely by known MOA, although there were exceptions. Of the three unknown compounds, one was definitively placed as an antifolate. The second and third compounds' MOA were not clearly identified, likely because the unique MOA was not represented within the database. The availability of the database generated in this report for Staphylococcus aureus ATCC 29213 will increase the accessibility of this technique to other investigators. From our analysis, the Phenotype Microarray system can group compounds with clear MOA, but the distinction of unique or broadly acting MOA at this time is less clear.
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Affiliation(s)
- Christina R. Bourne
- Department of Veterinary Pathobiology, Oklahoma State University, 250 McElroy Hall, Stillwater OK 74078
| | - Nancy Wakeham
- Department of Veterinary Pathobiology, Oklahoma State University, 250 McElroy Hall, Stillwater OK 74078
| | - Richard A. Bunce
- Department of Chemistry, Oklahoma State University, 107 Physical Sciences 1, Stillwater OK 74078
| | - K. Darrell Berlin
- Department of Chemistry, Oklahoma State University, 107 Physical Sciences 1, Stillwater OK 74078
| | - William W. Barrow
- Department of Veterinary Pathobiology, Oklahoma State University, 250 McElroy Hall, Stillwater OK 74078
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Sanyal G, Doig P. Bacterial DNA replication enzymes as targets for antibacterial drug discovery. Expert Opin Drug Discov 2012; 7:327-39. [PMID: 22458504 DOI: 10.1517/17460441.2012.660478] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
INTRODUCTION The bacterial replisome is composed of a large number of enzymes, which work in exquisite coordination to accomplish chromosomal replication. Effective inhibition inside the bacterial cell of any of the 'essential' enzymes of the DNA replication pathway should be detrimental to cell survival. AREAS COVERED This review covers DNA replication enzymes that have been shown to have a potential for delivering antibacterial compounds or drug candidates including: type II topoisomerases, a clinically validated target family, and DNA ligase, which has yielded inhibitors with in vivo efficacy. A few of the 'replisome' enzymes that are structurally and functionally well characterized and have been subjects of antibacterial discovery efforts are also discussed. EXPERT OPINION Identification of several essential genes in the bacterial replication pathway raised hopes that targeting these gene products would lead to novel antibacterials. However, none of these novel, single gene targets have delivered antibacterial drug candidates into clinical trials. This lack of productivity may be due to the target properties and inhibitor identification approaches employed. For DNA primase, DNA helicase and other replisome targets, with the exception of DNA ligase, the exploitation of structure for lead generation has not been tested to the same extent that it has for DNA gyrase. Utilization of structural information should be considered to augment HTS efforts and initiate fragment-based lead generation. The complex protein-protein interactions involved in regulation of replication may explain why biochemical approaches have been less productive for some replisome targets than more independently functioning targets such as DNA ligase or DNA gyrase.
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Affiliation(s)
- Gautam Sanyal
- Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Dr, Waltham, MA 02451, USA.
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Collin F, Karkare S, Maxwell A. Exploiting bacterial DNA gyrase as a drug target: current state and perspectives. Appl Microbiol Biotechnol 2011; 92:479-97. [PMID: 21904817 PMCID: PMC3189412 DOI: 10.1007/s00253-011-3557-z] [Citation(s) in RCA: 364] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 08/08/2011] [Accepted: 08/18/2011] [Indexed: 12/17/2022]
Abstract
DNA gyrase is a type II topoisomerase that can introduce negative supercoils into DNA at the expense of ATP hydrolysis. It is essential in all bacteria but absent from higher eukaryotes, making it an attractive target for antibacterials. The fluoroquinolones are examples of very successful gyrase-targeted drugs, but the rise in bacterial resistance to these agents means that we not only need to seek new compounds, but also new modes of inhibition of this enzyme. We review known gyrase-specific drugs and toxins and assess the prospects for developing new antibacterials targeted to this enzyme.
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Affiliation(s)
- Frédéric Collin
- Department Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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58
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Fabbretti A, Gualerzi CO, Brandi L. How to cope with the quest for new antibiotics. FEBS Lett 2011; 585:1673-81. [PMID: 21513713 DOI: 10.1016/j.febslet.2011.04.029] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 04/11/2011] [Accepted: 04/12/2011] [Indexed: 10/18/2022]
Abstract
Since their introduction in therapy, antibiotics have played an essential role in human society, saving millions of lives, allowing safe surgery, organ transplants, cancer therapy. Antibiotics have also helped to elucidate several biological mechanisms and boosted the birth and growth of pharmaceutical companies, generating profits and royalties. The golden era of antibiotics and the scientific and economical drive of big pharma towards these molecules is long gone, but the need for effective antibiotics is increased as their pipelines dwindle and multi-resistant pathogenic strains spread. Here we outline some strategies that could help meet this emergency and list promising new targets.
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Affiliation(s)
- Attilio Fabbretti
- Laboratory of Genetics, Department of Biosciences and Biotechnology, University of Camerino, Camerino (MC), Italy
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59
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Abstract
Although there has been a relentless increase in resistance to antimicrobial agents amongst important bacterial pathogens throughout the world, it is well known that the number of new antimicrobial agents being brought to the market has undergone a steady decline in the past several decades. There are a number of reasons for this, which are detailed in this article, but there is also a great deal of continuing research to find new effective antimicrobials, much of it now being carried out in academic centres and especially in small biotechnology companies, rather than by large pharma. Whilst classic screening methods and chemical modification of known antimicrobial agents continue to produce potential leads for new antimicrobial agents, a number of other approaches are being investigated. These include the search for potentiators of the activity of known antimicrobial agents and the development of hybrid agents, novel membrane-active drugs, and inhibitors of bacterial virulence and pathogenesis. A number of new bacterial targets are also being exploited, as are bacteriophages and their lytic enzymes. Given the amount of investigation presently underway, it is clear that although the antibiotic pipeline is not as promising as it was half a century ago, it is far from dry.
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60
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Gwynn MN, Portnoy A, Rittenhouse SF, Payne DJ. Challenges of antibacterial discovery revisited. Ann N Y Acad Sci 2010; 1213:5-19. [PMID: 21058956 DOI: 10.1111/j.1749-6632.2010.05828.x] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The discovery of novel antibiotic classes has not kept pace with the growing threat of bacterial resistance. Antibiotic candidates that act at new targets or via distinct mechanisms have the greatest potential to overcome resistance; however, novel approaches are also associated with higher attrition and longer timelines. This uncertainty has contributed to the withdrawal from antibiotic programs by many pharmaceutical companies. Genomic approaches have not yielded satisfactory results, in part due to nascent knowledge about unprecedented molecular targets, the challenge of achieving antibacterial activity by lead optimization of enzyme inhibitors, and the limitations of compound screening libraries for antibacterial discovery. Enhanced diversity of compound screening banks, entry into new chemical space, and new screening technologies are currently being exploited to improve hit rates for antibacterial discovery. Antibacterial compound lead optimization faces hurdles associated with the high plasma exposures required for efficacy. Lead optimization would be enhanced by the identification of new antibiotic classes with improved tractability and by expanding the predictability of in vitro safety assays. Implementing multiple screening and target identification strategies is recommended for improving the likelihood of discovering new antibacterial compounds that address unmet needs.
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Affiliation(s)
- Michael N Gwynn
- Antibacterial Discovery Performance Unit, Infectious Diseases Center of Excellence for Drug Discovery, GlaxoSmithKline, Collegeville, Pennsylvania, USA
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61
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Sissi C, Palumbo M. In front of and behind the replication fork: bacterial type IIA topoisomerases. Cell Mol Life Sci 2010; 67:2001-24. [PMID: 20165898 PMCID: PMC11115839 DOI: 10.1007/s00018-010-0299-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Revised: 01/26/2010] [Accepted: 02/01/2010] [Indexed: 01/03/2023]
Abstract
Topoisomerases are vital enzymes specialized in controlling DNA topology, in particular supercoiling and decatenation, to properly handle nucleic acid packing and cell dynamics. The type IIA enzymes act by cleaving both strands of a double helix and having another strand from the same or another molecule cross the DNA gate before a re-sealing event completes the catalytic cycle. Here, we will consider the two types of IIA prokaryotic topoisomerases, DNA Gyrase and Topoisomerase IV, as crucial regulators of bacterial cell cycle progression. Their synergistic action allows control of chromosome packing and grants occurrence of functional transcription and replication processes. In addition to displaying a fascinating molecular mechanism of action, which transduces chemical energy into mechanical energy by means of large conformational changes, these enzymes represent attractive pharmacological targets for antibacterial chemotherapy.
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Affiliation(s)
- Claudia Sissi
- Department of Pharmaceutical Sciences, University of Padova, Via Marzolo 5, 35131, Padua, Italy.
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63
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Ruble JC, Hurd AR, Johnson TA, Sherry DA, Barbachyn MR, Toogood PL, Bundy GL, Graber DR, Kamilar GM. Synthesis of (−)-PNU-286607 by Asymmetric Cyclization of Alkylidene Barbiturates. J Am Chem Soc 2009; 131:3991-7. [DOI: 10.1021/ja808014h] [Citation(s) in RCA: 143] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- J. Craig Ruble
- Infectious Diseases Medicinal Chemistry, Pharmacia Corporation, 301 Henrietta Street, Kalamazoo, Michigan 49001, Antibacterial Chemistry, Pfizer Global Research and Development, 2800 Plymouth Road, Ann Arbor Michigan 48105, and Antibacterial Chemistry, Pfizer Global Research and Development, Eastern Point Road, Groton, Connecticut 06340
| | - Alexander R. Hurd
- Infectious Diseases Medicinal Chemistry, Pharmacia Corporation, 301 Henrietta Street, Kalamazoo, Michigan 49001, Antibacterial Chemistry, Pfizer Global Research and Development, 2800 Plymouth Road, Ann Arbor Michigan 48105, and Antibacterial Chemistry, Pfizer Global Research and Development, Eastern Point Road, Groton, Connecticut 06340
| | - Timothy A. Johnson
- Infectious Diseases Medicinal Chemistry, Pharmacia Corporation, 301 Henrietta Street, Kalamazoo, Michigan 49001, Antibacterial Chemistry, Pfizer Global Research and Development, 2800 Plymouth Road, Ann Arbor Michigan 48105, and Antibacterial Chemistry, Pfizer Global Research and Development, Eastern Point Road, Groton, Connecticut 06340
| | - Debra A. Sherry
- Infectious Diseases Medicinal Chemistry, Pharmacia Corporation, 301 Henrietta Street, Kalamazoo, Michigan 49001, Antibacterial Chemistry, Pfizer Global Research and Development, 2800 Plymouth Road, Ann Arbor Michigan 48105, and Antibacterial Chemistry, Pfizer Global Research and Development, Eastern Point Road, Groton, Connecticut 06340
| | - Michael R. Barbachyn
- Infectious Diseases Medicinal Chemistry, Pharmacia Corporation, 301 Henrietta Street, Kalamazoo, Michigan 49001, Antibacterial Chemistry, Pfizer Global Research and Development, 2800 Plymouth Road, Ann Arbor Michigan 48105, and Antibacterial Chemistry, Pfizer Global Research and Development, Eastern Point Road, Groton, Connecticut 06340
| | - Peter L. Toogood
- Infectious Diseases Medicinal Chemistry, Pharmacia Corporation, 301 Henrietta Street, Kalamazoo, Michigan 49001, Antibacterial Chemistry, Pfizer Global Research and Development, 2800 Plymouth Road, Ann Arbor Michigan 48105, and Antibacterial Chemistry, Pfizer Global Research and Development, Eastern Point Road, Groton, Connecticut 06340
| | - Gordon L. Bundy
- Infectious Diseases Medicinal Chemistry, Pharmacia Corporation, 301 Henrietta Street, Kalamazoo, Michigan 49001, Antibacterial Chemistry, Pfizer Global Research and Development, 2800 Plymouth Road, Ann Arbor Michigan 48105, and Antibacterial Chemistry, Pfizer Global Research and Development, Eastern Point Road, Groton, Connecticut 06340
| | - David R. Graber
- Infectious Diseases Medicinal Chemistry, Pharmacia Corporation, 301 Henrietta Street, Kalamazoo, Michigan 49001, Antibacterial Chemistry, Pfizer Global Research and Development, 2800 Plymouth Road, Ann Arbor Michigan 48105, and Antibacterial Chemistry, Pfizer Global Research and Development, Eastern Point Road, Groton, Connecticut 06340
| | - Gregg M. Kamilar
- Infectious Diseases Medicinal Chemistry, Pharmacia Corporation, 301 Henrietta Street, Kalamazoo, Michigan 49001, Antibacterial Chemistry, Pfizer Global Research and Development, 2800 Plymouth Road, Ann Arbor Michigan 48105, and Antibacterial Chemistry, Pfizer Global Research and Development, Eastern Point Road, Groton, Connecticut 06340
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