1
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Zhang L, Yang J, Xu X, Zhang J, Qiu Z, Ju Y, Luo B, Liu Y, Gou X, Sui J, Chen B, Wang Y, Tao T, He L, Yang T, Luo Y. Discovery and Optimization of Novel SaFabI Inhibitors as Specific Therapeutic Agents for MRSA Infection. J Med Chem 2024; 67:10096-10134. [PMID: 38845361 DOI: 10.1021/acs.jmedchem.4c00320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
As the rate-limiting enzyme in fatty acid biosynthesis, Staphylococcus aureus enoyl-acyl carrier protein reductase (SaFabI) emerges as a compelling target for combating methicillin-resistant S. aureus (MRSA) infections. Herein, compound 1, featuring a 4-(1H-benzo[d]imidazol-2-yl)pyrrolidin-2-one scaffold, was identified as a potent SaFabI inhibitor (IC50 = 976.8 nM) from an in-house library. Subsequent optimization yielded compound n31, with improved inhibitory efficacy on enzymatic activity (IC50 = 174.2 nM) and selective potency against S. aureus (MIC = 1-2 μg/mL). Mechanistically, n31 directly inhibited SaFabI in cellular contexts. Moreover, n31 exhibited favorable safety and pharmacokinetic profiles, and dose-dependently treated MRSA-induced skin infections, outperforming the approved drug, linezolid. The chiral separation of n31 resulted in (S)-n31, with superior activities (IC50 = 94.0 nM, MIC = 0.25-1 μg/mL) and in vivo therapeutic efficacy. In brief, our research proposes (S)-n31 as a promising candidate for SaFabI-targeted therapy, offering specific anti-S. aureus efficacy and potential for further development.
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Affiliation(s)
- Laiying Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jiaxing Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xin Xu
- Editorial Office of Chinese Journal of Medical Genetics, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Jiangnan Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Zhiqiang Qiu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yuan Ju
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Baozhu Luo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yan Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xupeng Gou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jing Sui
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Baoyi Chen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yanmei Wang
- Institute of traditional Chinese medicine, Sichuan College of Traditional Chinese Medicine, The Second Hospital of Traditional Chinese Medicine in Sichuan Province, Chengdu 610041, China
| | - Tao Tao
- Institute of traditional Chinese medicine, Sichuan College of Traditional Chinese Medicine, The Second Hospital of Traditional Chinese Medicine in Sichuan Province, Chengdu 610041, China
| | - Lei He
- Institute of traditional Chinese medicine, Sichuan College of Traditional Chinese Medicine, The Second Hospital of Traditional Chinese Medicine in Sichuan Province, Chengdu 610041, China
| | - Tao Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
- Laboratory of Human Diseases and Immunotherapies, West China Hospital, Sichuan University, Chengdu 610041, China
- Institute of Immunology and Inflammation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Youfu Luo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
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2
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Castaldo N, Vena A, Limongelli A, Giacobbe DR, Bassetti M. Emerging treatment options for skin and soft tissue infections tailoring drug selection to individual patients. Curr Opin Infect Dis 2024; 37:80-86. [PMID: 38277175 DOI: 10.1097/qco.0000000000001003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
PURPOSE OF REVIEW To provide a brief overview of drugs in Phase II and III of development for the treatment of acute bacterial skin and skin structure infections (ABSSSI), offering insights into potential customized treatment options. RECENT FINDINGS Several drugs are currently in advanced stages of evaluation for the treatment of ABSSSI, and numerous molecules are entering in the early development phases. Notably, many of these drugs exhibit unique mechanisms of action and interesting antimicrobial spectrum. SUMMARY Tailoring antibiotic therapy based on patient characteristics, likely pathogens, type, site and severity of ABSSSI is crucial. Given the inherent limitations of available treatments, the development of novel agents is a pivotal avenue. Such advancements hold promise for enhancing treatment efficacy and simplifying drug selection for ABSSSI in everyday clinical practice.
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Affiliation(s)
- Nadia Castaldo
- Department of Pulmonology, University of Udine and Azienda Sanitaria Universitaria Integrata di Udine, Udine
| | - Antonio Vena
- Department of Health Sciences (DISSAL), University of Genoa
- Clinica Malattie Infettive, IRCCS San Martino polyclinic Hospital, Genoa, Italy
| | - Alessandro Limongelli
- Department of Health Sciences (DISSAL), University of Genoa
- Clinica Malattie Infettive, IRCCS San Martino polyclinic Hospital, Genoa, Italy
| | - Daniele Roberto Giacobbe
- Department of Health Sciences (DISSAL), University of Genoa
- Clinica Malattie Infettive, IRCCS San Martino polyclinic Hospital, Genoa, Italy
| | - Matteo Bassetti
- Department of Health Sciences (DISSAL), University of Genoa
- Clinica Malattie Infettive, IRCCS San Martino polyclinic Hospital, Genoa, Italy
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3
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Nawrot D, Ambrożkiewicz-Mosler W, Doležal M, Bouz G. Antistaphylococcal discovery pipeline; where are we now? Eur J Med Chem 2024; 266:116077. [PMID: 38219657 DOI: 10.1016/j.ejmech.2023.116077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/01/2023] [Accepted: 12/18/2023] [Indexed: 01/16/2024]
Abstract
The serious spread of antibiotic-resistant Staphylococcal aureus strains is alarming. This is reflected by the measures governments and health-related bodies are offering to ease antibiotic drug development. Finding new active agents, preferably with novel mechanism of action, or even finding new targets for drug development are essential. In this review, we summarize the current status of novel antistaphylococcal agents undergoing clinical trials. We mainly discuss antistaphylococcal small molecules and peptides in the text with a special focus on their chemistry, while antistaphylococcal immunotherapy (antibodies) are mentioned in a summative table. This review shall serve as a summary that influences future synthetic efforts in the antistaphyloccocals development field.
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Affiliation(s)
- Daria Nawrot
- Faculty of Pharmacy in Hradec Králové, Charles University, 50005, Hradec Králové, Czech Republic.
| | | | - Martin Doležal
- Faculty of Pharmacy in Hradec Králové, Charles University, 50005, Hradec Králové, Czech Republic
| | - Ghada Bouz
- Faculty of Pharmacy in Hradec Králové, Charles University, 50005, Hradec Králové, Czech Republic.
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4
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Nazli A, Tao W, You H, He X, He Y. Treatment of MRSA Infection: Where are We? Curr Med Chem 2024; 31:4425-4460. [PMID: 38310393 DOI: 10.2174/0109298673249381231130111352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 07/10/2023] [Accepted: 10/10/2023] [Indexed: 02/05/2024]
Abstract
Staphylococcus aureus is a leading cause of septicemia, endocarditis, pneumonia, skin and soft tissue infections, bone and joint infections, and hospital-acquired infections. In particular, methicillin-resistant Staphylococcus aureus (MRSA) is associated with high morbidity and mortality, and continues to be a major public health problem. The emergence of multidrug-resistant MRSA strains along with the wide consumption of antibiotics has made anti-MRSA treatment a huge challenge. Novel treatment strategies (e.g., novel antimicrobials and new administrations) against MRSA are urgently needed. In the past decade, pharmaceutical companies have invested more in the research and development (R&D) of new antimicrobials and strategies, spurred by favorable policies. All research articles were collected from authentic online databases, including Google Scholar, PubMed, Scopus, and Web of Science, by using different combinations of keywords, including 'anti-MRSA', 'antibiotic', 'antimicrobial', 'clinical trial', 'clinical phase', clinical studies', and 'pipeline'. The information extracted from articles was compared to information provided on the drug manufacturer's website and Clinical Trials.gov (https://clinicaltrials.gov/) to confirm the latest development phase of anti-MRSA agents. The present review focuses on the current development status of new anti-MRSA strategies concerning chemistry, pharmacological target(s), indications, route of administration, efficacy and safety, pharmacokinetics, and pharmacodynamics, and aims to discuss the challenges and opportunities in developing drugs for anti-MRSA infections.
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Affiliation(s)
- Adila Nazli
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China
| | - Wenlan Tao
- Chongqing School, University of Chinese Academy of Sciences (UCAS Chongqing), Chongqing, 400714, China
| | - Hengyao You
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China
| | - Xiaoli He
- Chongqing School, University of Chinese Academy of Sciences (UCAS Chongqing), Chongqing, 400714, China
| | - Yun He
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China
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5
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Ostroumova OS, Efimova SS. Lipid-Centric Approaches in Combating Infectious Diseases: Antibacterials, Antifungals and Antivirals with Lipid-Associated Mechanisms of Action. Antibiotics (Basel) 2023; 12:1716. [PMID: 38136750 PMCID: PMC10741038 DOI: 10.3390/antibiotics12121716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/05/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
One of the global challenges of the 21st century is the increase in mortality from infectious diseases against the backdrop of the spread of antibiotic-resistant pathogenic microorganisms. In this regard, it is worth targeting antibacterials towards the membranes of pathogens that are quite conservative and not amenable to elimination. This review is an attempt to critically analyze the possibilities of targeting antimicrobial agents towards enzymes involved in pathogen lipid biosynthesis or towards bacterial, fungal, and viral lipid membranes, to increase the permeability via pore formation and to modulate the membranes' properties in a manner that makes them incompatible with the pathogen's life cycle. This review discusses the advantages and disadvantages of each approach in the search for highly effective but nontoxic antimicrobial agents. Examples of compounds with a proven molecular mechanism of action are presented, and the types of the most promising pharmacophores for further research and the improvement of the characteristics of antibiotics are discussed. The strategies that pathogens use for survival in terms of modulating the lipid composition and physical properties of the membrane, achieving a balance between resistance to antibiotics and the ability to facilitate all necessary transport and signaling processes, are also considered.
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Affiliation(s)
- Olga S. Ostroumova
- Laboratory of Membrane and Ion Channel Modeling, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, St. Petersburg 194064, Russia;
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6
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Douglas EA, Marshall B, Alghamadi A, Joseph EA, Duggan S, Vittorio S, De Luca L, Serpi M, Laabei M. Improved Antibacterial Activity of 1,3,4-Oxadiazole-Based Compounds That Restrict Staphylococcus aureus Growth Independent of LtaS Function. ACS Infect Dis 2023; 9:2141-2159. [PMID: 37828912 PMCID: PMC10644342 DOI: 10.1021/acsinfecdis.3c00250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Indexed: 10/14/2023]
Abstract
The lipoteichoic acid (LTA) biosynthesis pathway has emerged as a promising antimicrobial therapeutic target. Previous studies identified the 1,3,4 oxadiazole compound 1771 as an LTA inhibitor with activity against Gram-positive pathogens. We have succeeded in making six 1771 derivatives and, through subsequent hit validation, identified the incorporation of a pentafluorosulfanyl substituent as central in enhancing activity. Our newly described derivative, compound 13, showed a 16- to 32-fold increase in activity compared to 1771 when tested against a cohort of multidrug-resistant Staphylococcus aureus strains while simultaneously exhibiting an improved toxicity profile against mammalian cells. Molecular techniques were employed in which the assumed target, lipoteichoic acid synthase (LtaS), was both deleted and overexpressed. Neither deletion nor overexpression of LtaS altered 1771 or compound 13 susceptibility; however, overexpression of LtaS increased the MIC of Congo red, a previously identified LtaS inhibitor. These data were further supported by comparing the docking poses of 1771 and derivatives in the LtaS active site, which indicated the possibility of an additional target(s). Finally, we show that both 1771 and compound 13 have activity that is independent of LtaS, extending to cover Gram-negative species if the outer membrane is first permeabilized, challenging the classification that these compounds are strict LtaS inhibitors.
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Affiliation(s)
| | - Brandon Marshall
- School
of Chemistry, Cardiff University, Cardiff CF10 3AT, Wales, U.K.
| | - Arwa Alghamadi
- School
of Chemistry, Cardiff University, Cardiff CF10 3AT, Wales, U.K.
| | - Erin A. Joseph
- School
of Chemistry, Cardiff University, Cardiff CF10 3AT, Wales, U.K.
| | - Seána Duggan
- Medical
Research Council Centre for Medical Mycology at the University of
Exeter, University of Exeter, Exeter EX4 4DQ, U.K.
| | - Serena Vittorio
- Department
of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina I-98125, Italy
| | - Laura De Luca
- Department
of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina I-98125, Italy
| | - Michaela Serpi
- School
of Chemistry, Cardiff University, Cardiff CF10 3AT, Wales, U.K.
| | - Maisem Laabei
- Department
of Life Sciences, University of Bath, Bath BA2 7AY, U.K.
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7
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Douglas EJ, Laabei M. Staph wars: the antibiotic pipeline strikes back. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001387. [PMID: 37656158 PMCID: PMC10569064 DOI: 10.1099/mic.0.001387] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/14/2023] [Indexed: 09/02/2023]
Abstract
Antibiotic chemotherapy is widely regarded as one of the most significant medical advancements in history. However, the continued misuse of antibiotics has contributed to the rapid rise of antimicrobial resistance (AMR) globally. Staphylococcus aureus, a major human pathogen, has become synonymous with multidrug resistance and is a leading antimicrobial-resistant pathogen causing significant morbidity and mortality worldwide. This review focuses on (1) the targets of current anti-staphylococcal antibiotics and the specific mechanisms that confirm resistance; (2) an in-depth analysis of recently licensed antibiotics approved for the treatment of S. aureus infections; and (3) an examination of the pre-clinical pipeline of anti-staphylococcal compounds. In addition, we examine the molecular mechanism of action of novel antimicrobials and derivatives of existing classes of antibiotics, collate data on the emergence of resistance to new compounds and provide an overview of key data from clinical trials evaluating anti-staphylococcal compounds. We present several successful cases in the development of alternative forms of existing antibiotics that have activity against multidrug-resistant S. aureus. Pre-clinical antimicrobials show promise, but more focus and funding are required to develop novel classes of compounds that can curtail the spread of and sustainably control antimicrobial-resistant S. aureus infections.
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Affiliation(s)
| | - Maisem Laabei
- Department of Life Sciences, University of Bath, Bath BA2 7AY, UK
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8
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Douglas EJA, Wulandari SW, Lovell SD, Laabei M. Novel antimicrobial strategies to treat multi-drug resistant Staphylococcus aureus infections. Microb Biotechnol 2023; 16:1456-1474. [PMID: 37178319 PMCID: PMC10281381 DOI: 10.1111/1751-7915.14268] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/12/2023] [Accepted: 04/18/2023] [Indexed: 05/15/2023] Open
Abstract
Antimicrobial resistance is a major obstacle for the treatment of infectious diseases and currently represents one of the most significant threats to global health. Staphylococcus aureus remains a formidable human pathogen with high mortality rates associated with severe systemic infections. S. aureus has become notorious as a multidrug resistant bacterium, which when combined with its extensive arsenal of virulence factors that exacerbate disease, culminates in an incredibly challenging pathogen to treat clinically. Compounding this major health issue is the lack of antibiotic discovery and development, with only two new classes of antibiotics approved for clinical use in the last 20 years. Combined efforts from the scientific community have reacted to the threat of dwindling treatment options to combat S. aureus disease in several innovative and exciting developments. This review describes current and future antimicrobial strategies aimed at treating staphylococcal colonization and/or disease, examining therapies that show significant promise at the preclinical development stage to approaches that are currently being investigated in clinical trials.
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9
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Essential Paralogous Proteins as Potential Antibiotic Multitargets in Escherichia coli. Microbiol Spectr 2022; 10:e0204322. [PMID: 36445138 PMCID: PMC9769728 DOI: 10.1128/spectrum.02043-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Antimicrobial resistance threatens our current standards of care for the treatment and prevention of infectious disease. Antibiotics that have multiple targets have a lower propensity for the development of antibiotic resistance than those that have single targets and therefore represent an important tool in the fight against antimicrobial resistance. In this work, groups of essential paralogous proteins were identified in the important Gram-negative pathogen Escherichia coli that could represent novel targets for multitargeting antibiotics. These groups include targets from a broad range of essential macromolecular and biosynthetic pathways, including cell wall synthesis, membrane biogenesis, transcription, translation, DNA replication, fatty acid biosynthesis, and riboflavin and isoprenoid biosynthesis. Importantly, three groups of clinically validated antibiotic multitargets were identified using this method: the two subunits of the essential topoisomerases, DNA gyrase and topoisomerase IV, and one pair of penicillin-binding proteins. An additional eighteen protein groups represent potentially novel multitargets that could be explored in drug discovery efforts aimed at developing compounds having multiple targets in E. coli and other bacterial pathogens. IMPORTANCE Many types of bacteria have gained resistance to existing antibiotics used in medicine today. Therefore, new antibiotics with novel mechanisms must continue to be developed. One tool to prevent the development of antibiotic resistance is for a single drug to target multiple processes in a bacterium so that more than one change must arise for resistance to develop. The work described here provides a comprehensive search for proteins in the bacterium Escherichia coli that could be targets for such multitargeting antibiotics. Several groups of proteins that are already targets of clinically used antibiotics were identified, indicating that this approach can uncover clinically relevant antibiotic targets. In addition, eighteen currently unexploited groups of proteins were identified, representing new multitargets that could be explored in antibiotic research and development.
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10
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Muhaj FF, George SJ, Tyring SK. Bacterial resistance and dermatological ramifications. Br J Dermatol 2022; 187:12-20. [PMID: 35083740 DOI: 10.1111/bjd.21033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 01/18/2022] [Accepted: 01/18/2022] [Indexed: 11/28/2022]
Abstract
The spread of COVID-19 serves as a reminder of the might of microbes in the era of modern medicine. For years, another threat has preoccupied infectious disease experts and public health officials alike: rising antimicrobial resistance (AMR). Resistance is exceeding stewardship efforts and the rates of new drug development and approval in the market. A dry antimicrobial pipeline is threatening our regression to a pre-antibiotic era. While the consequences of resistance may seem far removed from daily clinical practices, awareness of AMR is significant to dermatological care given that dermatologists prescribe more antibiotics per physician than other providers. Antibiotics in dermatology are often used for prolonged courses, with a significant potential for microbiome alteration and antibiotic-related adverse effects. Through this review we hope to contribute to efforts of bringing the crisis of AMR to the forefront of daily dermatological practice.
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Affiliation(s)
- F F Muhaj
- Department of Dermatology, MD Anderson Cancer Center, Houston, Texas, USA
| | - S J George
- Department of Dermatology, MD Anderson Cancer Center, Houston, Texas, USA
| | - S K Tyring
- Department of Dermatology, University of Texas McGovern Medical School at Houston, Houston, Texas, USA.,Center for Clinical Studies, Houston, Texas, USA
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11
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Eltschkner S, Kehrein J, Le TA, Davoodi S, Merget B, Basak S, Weinrich JD, Schiebel J, Tonge PJ, Engels B, Sotriffer C, Kisker C. A Long Residence Time Enoyl-Reductase Inhibitor Explores an Extended Binding Region with Isoenzyme-Dependent Tautomer Adaptation and Differential Substrate-Binding Loop Closure. ACS Infect Dis 2021; 7:746-758. [PMID: 33710875 DOI: 10.1021/acsinfecdis.0c00437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The enoyl-acyl carrier protein (ACP) reductase (ENR) is a key enzyme within the bacterial fatty-acid synthesis pathway. It has been demonstrated that small-molecule inhibitors carrying the diphenylether (DPE) scaffold bear a great potential for the development of highly specific and effective drugs against this enzyme class. Interestingly, different substitution patterns of the DPE scaffold have been shown to lead to varying effects on the kinetic and thermodynamic behavior toward ENRs from different organisms. Here, we investigated the effect of a 4'-pyridone substituent in the context of the slow tight-binding inhibitor SKTS1 on the inhibition of the Staphylococcus aureus enoyl-ACP-reductase saFabI and the closely related isoenzyme from Mycobacterium tuberculosis, InhA, and explored a new interaction site of DPE inhibitors within the substrate-binding pocket. Using high-resolution crystal structures of both complexes in combination with molecular dynamics (MD) simulations, kinetic measurements, and quantum mechanical (QM) calculations, we provide evidence that the 4'-pyridone substituent adopts different tautomeric forms when bound to the two ENRs. We furthermore elucidate the structural determinants leading to significant differences in the residence time of SKTS1 on both enzymes.
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Affiliation(s)
- Sandra Eltschkner
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, 97080 Würzburg, Germany
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, 223 62 Lund, Sweden
| | - Josef Kehrein
- Institute of Pharmacy and Food Chemistry, University of Würzburg, 97074 Würzburg, Germany
| | - Thien Anh Le
- Institute of Physical and Theoretical Chemistry, University of Würzburg, 97074 Würzburg, Germany
- Department of Experimental Physics 5 (Biophysics), University of Würzburg, 97074 Würzburg, Germany
| | - Shabnam Davoodi
- Institute for Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Benjamin Merget
- Institute of Pharmacy and Food Chemistry, University of Würzburg, 97074 Würzburg, Germany
| | - Sneha Basak
- Institute for Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Jonas D. Weinrich
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, 97080 Würzburg, Germany
- Department of Microbiology, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Johannes Schiebel
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Peter J. Tonge
- Institute for Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States
| | - Bernd Engels
- Institute of Physical and Theoretical Chemistry, University of Würzburg, 97074 Würzburg, Germany
| | - Christoph Sotriffer
- Institute of Pharmacy and Food Chemistry, University of Würzburg, 97074 Würzburg, Germany
| | - Caroline Kisker
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, 97080 Würzburg, Germany
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12
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Yogiara, Mordukhova EA, Kim D, Kim WG, Hwang JK, Pan JG. The food-grade antimicrobial xanthorrhizol targets the enoyl-ACP reductase (FabI) in Escherichia coli. Bioorg Med Chem Lett 2020; 30:127651. [PMID: 33130290 DOI: 10.1016/j.bmcl.2020.127651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 10/14/2020] [Accepted: 10/24/2020] [Indexed: 11/28/2022]
Abstract
Xanthorrhizol, isolated from the Indonesian Java turmeric Curcuma xanthorrhiza, displays broad-spectrum antibacterial activity. We report herein the evidence that mechanism of action of xanthorrhizol may involve FabI, an enoyl-(ACP) reductase, inhibition. The predicted Y156V substitution in the FabI enzyme promoted xanthorrhizol resistance, while the G93V mutation originally known for triclosan resistance was not effective against xanthorrhizol. Two other mutations, F203L and F203V, conferred FabI enzyme resistance to both xanthorrhizol and triclosan. These results showed that xanthorrhizol is a food-grade antimicrobial compound targeting FabI but with a different mode of binding from triclosan.
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Affiliation(s)
- Yogiara
- Department of Biotechnology, Yonsei University, 50-Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea; Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jalan Jenderal Sudirman 51, Jakarta 12930, Indonesia.
| | - Elena A Mordukhova
- GenoFocus Inc., 65 Techno 1-ro, Gwanpyeong-dong, Yuseong-gu, Daejeon 34014, Republic of Korea.
| | - Dooil Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 111 Gwahangno, Yuseong, Daejeon 34141, Republic of Korea.
| | - Won-Gon Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 111 Gwahangno, Yuseong, Daejeon 34141, Republic of Korea.
| | - Jae-Kwan Hwang
- Department of Biotechnology, Yonsei University, 50-Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea.
| | - Jae-Gu Pan
- GenoFocus Inc., 65 Techno 1-ro, Gwanpyeong-dong, Yuseong-gu, Daejeon 34014, Republic of Korea; Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 111 Gwahangno, Yuseong, Daejeon 34141, Republic of Korea.
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13
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Antimicrobial innovation: a current update and perspective on the antibiotic drug development pipeline. Future Med Chem 2020; 12:2035-2065. [DOI: 10.4155/fmc-2020-0225] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
As bacteria continue to develop resistance to our existing treatment options, antibiotic innovation remains overlooked. If current trends continue, then we could face the stark reality of a postantibiotic era, whereby routine bacterial infections could once again become deadly. In light of a warning signaled by the WHO, a number of new initiatives have been established in the hope of reinvigorating the antibiotic drug development pipeline. In this perspective, we aim to summarize some of these initiatives and funding options, as well as providing an insight into the predicament that we face. Using clinical trials data, company website information and the most recent press releases, a current update of the antibiotic drug development pipeline is also included.
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Rana P, Ghouse SM, Akunuri R, Madhavi YV, Chopra S, Nanduri S. FabI (enoyl acyl carrier protein reductase) - A potential broad spectrum therapeutic target and its inhibitors. Eur J Med Chem 2020; 208:112757. [PMID: 32883635 DOI: 10.1016/j.ejmech.2020.112757] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 07/30/2020] [Accepted: 08/11/2020] [Indexed: 12/11/2022]
Abstract
Development of new anti-bacterial agents acting upon underexploited targets and thus evading known mechanisms of resistance is the need of the hour. The highly conserved and distinct bacterial fatty acid biosynthesis pathway (FAS-II), presents a validated and yet relatively underexploited target for drug discovery. FabI and its isoforms (FabL, FabK, FabV and InhA) are essential enoyl-ACP reductases present in several microorganisms. In addition, the components of the FAS-II pathway are distinct from the multi-enzyme FAS-I complex found in mammals. Thus, inhibition of FabI and its isoforms is anticipated to result in broad-spectrum antibacterial activity. Several research groups from industry and academic laboratories have devoted significant efforts to develop effective FabI-targeting antibiotics, which are currently in various stages of clinical development for the treatment of multi-drug resistant bacterial infections. This review summarizes all the natural as well as synthetic inhibitors of gram-positive and gram-negative enoyl ACP reductases (FabI). The knowledge of the reported inhibitors can aid in the development of broad-spectrum antibacterials specifically targeting FabI enzymes from S. aureus, S. epidermidis, B. anthracis, B. cereus, E. coli, P. aeruginosa, P. falciparum and M. tuberculosis.
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Affiliation(s)
- Preeti Rana
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, 500 037, India
| | - Shaik Mahammad Ghouse
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, 500 037, India
| | - Ravikumar Akunuri
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, 500 037, India
| | - Y V Madhavi
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, 500 037, India
| | - Sidharth Chopra
- Division of Microbiology, CSIR-Central Drug Research Institute, Sitapur Road, Sector 10, Janakipuram Extension, Lucknow, 226 031, Uttar Pradesh, India.
| | - Srinivas Nanduri
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, 500 037, India.
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Wang J, Ye X, Yang X, Cai Y, Wang S, Tang J, Sachdeva M, Qian Y, Hu W, Leeds JA, Yuan Y. Discovery of Novel Antibiotics as Covalent Inhibitors of Fatty Acid Synthesis. ACS Chem Biol 2020; 15:1826-1834. [PMID: 32568510 DOI: 10.1021/acschembio.9b00982] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The steady increase in the prevalence of multidrug-resistant Staphylococcus aureus has made the search for novel antibiotics to combat this clinically important pathogen an urgent matter. In an effort to discover antibacterials with new chemical structures and mechanisms, we performed a growth inhibition screen of a synthetic library against S. aureus and discovered a promising scaffold with a 1,3,5-oxadiazin-2-one core. These compounds are potent against both methicillin-sensitive and methicillin-resistant S. aureus strains. Isolation of compound-resistant strains followed by whole genome sequencing revealed its cellular target as FabH, a key enzyme in bacterial fatty acid synthesis. Detailed mechanism of action studies suggested the compounds inhibit FabH activity by covalently modifying its active site cysteine residue with high selectivity. A crystal structure of FabH protein modified by a selected compound Oxa1 further confirmed covalency and suggested a possible mechanism for reaction. Moreover, the structural snapshot provided an explanation for compound selectivity. On the basis of the structure, we designed and synthesized Oxa1 derivatives and evaluated their antibacterial activity. The structure-activity relationship supports the hypothesis that noncovalent recognition between compounds and FabH is critical for the activity of these covalent inhibitors. We believe further optimization of the current scaffold could lead to an antibacterial with potential to treat drug-resistant bacteria in the clinic.
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Affiliation(s)
- Jia Wang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Xiaoping Ye
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Xiaohan Yang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Youyan Cai
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Shengjun Wang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jieyu Tang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Meena Sachdeva
- Novartis Institutes for Biomedical Research, Inc., Infectious Diseases Area, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Yu Qian
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Wenhao Hu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jennifer A. Leeds
- Novartis Institutes for Biomedical Research, Inc., Infectious Diseases Area, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Yanqiu Yuan
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Drug Non-Clinical Evaluation and Research, Guangzhou 510990, China
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Chung PY. Novel targets of pentacyclic triterpenoids in Staphylococcus aureus: A systematic review. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2020; 73:152933. [PMID: 31103429 DOI: 10.1016/j.phymed.2019.152933] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 04/15/2019] [Accepted: 04/16/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Staphylococcus aureus is an important pathogen both in community-acquired and healthcare-associated infections, and has successfully evolved numerous strategies for resisting the action to practically all antibiotics. Resistance to methicillin is now widely described in the community setting (CMRSA), thus the development of new drugs or alternative therapies is urgently necessary. Plants and their secondary metabolites have been a major alternative source in providing structurally diverse bioactive compounds as potential therapeutic agents for the treatment of bacterial infections. One of the classes of natural secondary metabolites from plants with the most bioactive compounds are the triterpenoids, which comprises structurally diverse organic compounds. In nature, triterpenoids are often found as tetra- or penta-cyclic structures. AIM This review highlights the anti-staphylococcal activities of pentacyclic triterpenoids, particularly α-amyrin (AM), betulinic acid (BA) and betulinaldehyde (BE). These compounds are based on a 30-carbon skeleton comprising five six-membered rings (ursanes and lanostanes) or four six-membered rings and one five-membered ring (lupanes and hopanes). METHODS Electronic databases such as ScienceDirect, PubMed and Scopus were used to search scientific contributions until March 2018, using relevant keywords. Literature focusing on the antimicrobial and antibiofilms of effects of pentacyclic triterpenoids on S. aureus were identified and summarized. RESULTS Pentacyclic triterpenoids can be divided into three representative classes, namely ursane, lupane and oleananes. This class of compounds have been shown to exhibit analgesic, immunomodulatory, anti-inflammatory, anticancer, antioxidant, antifungal and antibacterial activities. In studies of the antimicrobial activities and targets of AM, BA and BE in sensitive and multidrug-resistant S. aureus, these compounds acted synergistically and have different targets from the conventional antibiotics. CONCLUSION The inhibitory mechanisms of S. aureus in novel targets and pathways should stimulate further researches to develop AM, BA and BE as therapeutic agents for infections caused by S. aureus. Continued efforts to identify and exploit synergistic combinations by the three compounds and peptidoglycan inhibitors, are also necessary as alternative treatment options for S. aureus infections.
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Affiliation(s)
- Pooi Yin Chung
- Department of Pathology, School of Medicine, International Medical University, Bukit Jalil, Kuala Lumpur 57000, Malaysia.
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17
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Searching for mechanisms of action of antimicrobials. Arch Microbiol 2020; 202:2347-2354. [DOI: 10.1007/s00203-020-01959-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 06/05/2020] [Accepted: 06/15/2020] [Indexed: 01/21/2023]
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18
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Johnson ME, Fung LWM. Structural approaches to pathway-specific antimicrobial agents. Transl Res 2020; 220:114-121. [PMID: 32105648 PMCID: PMC7293926 DOI: 10.1016/j.trsl.2020.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/31/2020] [Accepted: 02/03/2020] [Indexed: 10/25/2022]
Abstract
This perspective provides an overview of the evolution of antibiotic discovery from a largely phenotypic-based effort, through an intensive structure-based design focus, to a more holistic approach today. The current focus on antibiotic development incorporates assay and discovery conditions that replicate the host environment as much as feasible. They also incorporate several strategies, including target identification and validation within the whole cell environment, a variety of target deconvolution methods, and continued refinement of structure-based design approaches.
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Affiliation(s)
- Michael E Johnson
- Department of Pharmaceutical Sciences, Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois.
| | - Leslie W-M Fung
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois.
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Koulenti D, Xu E, Song A, Sum Mok IY, Karageorgopoulos DE, Armaganidis A, Tsiodras S, Lipman J. Emerging Treatment Options for Infections by Multidrug-Resistant Gram-Positive Microorganisms. Microorganisms 2020; 8:E191. [PMID: 32019171 PMCID: PMC7074912 DOI: 10.3390/microorganisms8020191] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 01/26/2020] [Accepted: 01/28/2020] [Indexed: 12/22/2022] Open
Abstract
Antimicrobial agents are currently the mainstay of treatment for bacterial infections worldwide. However, due to the increased use of antimicrobials in both human and animal medicine, pathogens have now evolved to possess high levels of multi-drug resistance, leading to the persistence and spread of difficult-to-treat infections. Several current antibacterial agents active against Gram-positive bacteria will be rendered useless in the face of increasing resistance rates. There are several emerging antibiotics under development, some of which have been shown to be more effective with an improved safety profile than current treatment regimens against Gram-positive bacteria. We will extensively discuss these antibiotics under clinical development (phase I-III clinical trials) to combat Gram-positive bacteria, such as Staphylococcus aureus, Enterococcus faecium and Streptococcus pneumoniae. We will delve into the mechanism of actions, microbiological spectrum, and, where available, the pharmacokinetics, safety profile, and efficacy of these drugs, aiming to provide a comprehensive review to the involved stakeholders.
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Affiliation(s)
- Despoina Koulenti
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4072, Australia; (E.X.); (A.S.); (I.Y.S.M.); (J.L.)
- 2nd Critical Care Department, Attikon University Hospital, 12462 Athens, Greece;
| | - Elena Xu
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4072, Australia; (E.X.); (A.S.); (I.Y.S.M.); (J.L.)
| | - Andrew Song
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4072, Australia; (E.X.); (A.S.); (I.Y.S.M.); (J.L.)
| | - Isaac Yin Sum Mok
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4072, Australia; (E.X.); (A.S.); (I.Y.S.M.); (J.L.)
| | - Drosos E. Karageorgopoulos
- 4th Department of Internal Medicine, Attikon University Hospital, 12462 Athens, Greece; (D.E.K.); (S.T.)
| | | | - Sotirios Tsiodras
- 4th Department of Internal Medicine, Attikon University Hospital, 12462 Athens, Greece; (D.E.K.); (S.T.)
| | - Jeffrey Lipman
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4072, Australia; (E.X.); (A.S.); (I.Y.S.M.); (J.L.)
- Department of Intensive Care Medicine, Royal Brisbane and Women’s Hospital, Brisbane, QLD 4029, Australia
- Anesthesiology and Critical Care, Centre Hospitalier Universitaire De Nîmes (CHU), University of Montpellier, 30029 Nîmes, France
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20
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Carro L. Recent Progress in the Development of Small-Molecule FtsZ Inhibitors as Chemical Tools for the Development of Novel Antibiotics. Antibiotics (Basel) 2019; 8:E217. [PMID: 31717975 PMCID: PMC6963470 DOI: 10.3390/antibiotics8040217] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/26/2019] [Accepted: 11/05/2019] [Indexed: 01/20/2023] Open
Abstract
Antibiotics are potent pharmacological weapons against bacterial pathogens, nevertheless their efficacy is becoming compromised due to the worldwide emergence and spread of multidrug-resistant bacteria or "superbugs". Antibiotic resistance is rising to such dangerous levels that the treatment of bacterial infections is becoming a clinical challenge. Therefore, urgent action is needed to develop new generations of antibiotics that will help tackle this increasing and serious public health problem. Due to its essential role in bacterial cell division, the tubulin-like protein FtsZ has emerged as a promising target for the development of novel antibiotics with new mechanisms of action. This review highlights the medicinal chemistry efforts towards the identification of small-molecule FtsZ inhibitors with antibacterial activity in the last three years.
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Affiliation(s)
- Laura Carro
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain;
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
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21
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Richie DL, Wang L, Chan H, De Pascale G, Six DA, Wei JR, Dean CR. A pathway-directed positive growth restoration assay to facilitate the discovery of lipid A and fatty acid biosynthesis inhibitors in Acinetobacter baumannii. PLoS One 2018; 13:e0193851. [PMID: 29505586 PMCID: PMC5837183 DOI: 10.1371/journal.pone.0193851] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Accepted: 02/19/2018] [Indexed: 11/19/2022] Open
Abstract
Acinetobacter baumannii ATCC 19606 can grow without lipooligosaccharide (LOS). Lack of LOS can result from disruption of the early lipid A biosynthetic pathway genes lpxA, lpxC or lpxD. Although LOS itself is not essential for growth of A. baumannii ATCC 19606, it was previously shown that depletion of the lipid A biosynthetic enzyme LpxK in cells inhibited growth due to the toxic accumulation of lipid A pathway intermediates. Growth of LpxK-depleted cells was restored by chemical inhibition of LOS biosynthesis using CHIR-090 (LpxC) and fatty acid biosynthesis using cerulenin (FabB/F) and pyridopyrimidine (acetyl-CoA-carboxylase). Here, we expand on this by showing that inhibition of enoyl-acyl carrier protein reductase (FabI), responsible for converting trans-2-enoyl-ACP into acyl-ACP during the fatty acid elongation cycle also restored growth during LpxK depletion. Inhibition of fatty acid biosynthesis during LpxK depletion rescued growth at 37°C, but not at 30°C, whereas rescue by LpxC inhibition was temperature independent. We exploited these observations to demonstrate proof of concept for a targeted medium-throughput growth restoration screening assay to identify small molecule inhibitors of LOS and fatty acid biosynthesis. The differential temperature dependence of fatty acid and LpxC inhibition provides a simple means by which to separate growth stimulating compounds by pathway. Targeted cell-based screening platforms such as this are important for faster identification of compounds inhibiting pathways of interest in antibacterial discovery for clinically relevant Gram-negative pathogens.
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Affiliation(s)
- Daryl L. Richie
- Novartis Institutes for BioMedical Research, Emeryville, CA, United States of America
| | - Lisha Wang
- Novartis Institutes for BioMedical Research, Emeryville, CA, United States of America
| | - Helen Chan
- Novartis Institutes for BioMedical Research, Emeryville, CA, United States of America
| | - Gianfranco De Pascale
- Novartis Institutes for BioMedical Research, Emeryville, CA, United States of America
| | - David A. Six
- Novartis Institutes for BioMedical Research, Emeryville, CA, United States of America
| | - Jun-Rong Wei
- Novartis Institutes for BioMedical Research, Emeryville, CA, United States of America
| | - Charles R. Dean
- Novartis Institutes for BioMedical Research, Emeryville, CA, United States of America
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22
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Foster TJ. Antibiotic resistance in Staphylococcus aureus. Current status and future prospects. FEMS Microbiol Rev 2018; 41:430-449. [PMID: 28419231 DOI: 10.1093/femsre/fux007] [Citation(s) in RCA: 406] [Impact Index Per Article: 67.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 02/12/2017] [Indexed: 12/11/2022] Open
Abstract
The major targets for antibiotics in staphylococci are (i) the cell envelope, (ii) the ribosome and (iii) nucleic acids. Several novel targets emerged from recent targeted drug discovery programmes including the ClpP protease and FtsZ from the cell division machinery. Resistance can either develop by horizontal transfer of resistance determinants encoded by mobile genetic elements viz plasmids, transposons and the staphylococcal cassette chromosome or by mutations in chromosomal genes. Horizontally acquired resistance can occur by one of the following mechanisms: (i) enzymatic drug modification and inactivation, (ii) enzymatic modification of the drug binding site, (iii) drug efflux, (iv) bypass mechanisms involving acquisition of a novel drug-resistant target, (v) displacement of the drug to protect the target. Acquisition of resistance by mutation can result from (i) alteration of the drug target that prevents the inhibitor from binding, (ii) derepression of chromosomally encoded multidrug resistance efflux pumps and (iii) multiple stepwise mutations that alter the structure and composition of the cell wall and/or membrane to reduce drug access to its target. This review focuses on development of resistance to currently used antibiotics and examines future prospects for new antibiotics and informed use of drug combinations.
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Abstract
PURPOSE OF REVIEW Skin and soft tissue infections (SSTIs) are the most frequent infectious cause of referrals to emergency departments and hospital admissions in developed world, contributing to significant morbidity and healthcare expenditures. We sought to review recent literature covering epidemiology and management of SSTIs. RECENT FINDINGS Incidence trends of SSTIs were increasing worldwide with Staphylococcus aureus and streptococci predominating and methicillin-resistant S. aureus (MRSA) posing additional challenges, because of high rates of treatment failure and relapse. Development of new antimicrobials was associated with an appraisal of regulatory definitions and endpoints. Prediction of clinical response can be very tricky, because of variable risk factors for recurrence or treatment failure, depending mostly on the host. Precise indications for new antimicrobials should be established; their integration into clinical practice algorithms may serve reduction of unnecessary admissions, overtreatment and total costs. SUMMARY New antimicrobials with activity against MRSA have been recently launched. Long-acting agents, mainly oritavancin and dalbavancin, provide the opportunity of single-dose treatment and early discharge. Further outpatient treatment options include new per os antibiotics such as oxazolidinones. Validated assessment tools are urgently needed to support decision-making toward rational resource utilization and delivery of optimal treatment.
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Kim HT, Kim S, Na BK, Chung J, Hwang E, Hwang KY. Structural insights into the dimer-tetramer transition of FabI from Bacillus anthracis. Biochem Biophys Res Commun 2017; 493:28-33. [PMID: 28935372 DOI: 10.1016/j.bbrc.2017.09.084] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 09/15/2017] [Indexed: 11/30/2022]
Abstract
Enoyl-ACP reductase (ENR, also known as FabI) has received considerable interest as an anti-bacterial target due to its essentiality in fatty acid synthesis. All the FabI structures reported to date, regardless of the organism, are composed of homo-tetramers, except for two structures: Bacillus cereus and Staphylococcus aureus FabI (bcFabI and saFabI, respectively), which have been reported as dimers. However, the reason for the existence of the dimeric form in these organisms and the biological meaning of dimeric and tetrameric forms of FabI are ambiguous. Herein, we report the high-resolution crystal structure of a dimeric form of Bacillus anthracis FabI (baFabI) and the crystal structures of tetrameric forms of baFabI in the apo state and in complex with NAD+ and with NAD+-triclosan, at 1.7 Å, 1.85 Å, 1.96 Å, and 1.95 Å, respectively. Interestingly, we found that baFabI with a His6-tag at its C-terminus exists as a dimer, whereas untagged-baFabI exists as a tetramer. The His6-tag may block the dimer-tetramer transition, since baFabI has relatively short-length amino acids (255LG256) after the 310-helix η7 compared to those of FabI of other organisms. The dimeric form of baFabI is catalytically inactive, because the α-helix α5 occupies the NADH-binding site. During the process of dimer-tetramer transition, this α5 helix rotates about 55° toward the tetramer interface and the active site is established. Therefore, tetramerization of baFabI is required for cofactor binding and catalytic activity.
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Affiliation(s)
- Hyun Tae Kim
- Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, South Korea; Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea
| | - Sulhee Kim
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea
| | - Byeong Kwan Na
- Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, South Korea
| | - Jiwoung Chung
- Crystalgenomics, Inc., 5F, Tower A, Korea Bio Park 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13524, South Korea
| | - Eunha Hwang
- Division of Bioconvergence Analysis, Korea Basic Science Institute, 162 Yeongudangiro Ochang, Cheongwongu, Cheongju, Chungbuk 28119, South Korea
| | - Kwang Yeon Hwang
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea.
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Morvan C, Halpern D, Kénanian G, Pathania A, Anba-Mondoloni J, Lamberet G, Gruss A, Gloux K. The Staphylococcus aureus FASII bypass escape route from FASII inhibitors. Biochimie 2017; 141:40-46. [PMID: 28728970 DOI: 10.1016/j.biochi.2017.07.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 07/13/2017] [Indexed: 01/05/2023]
Abstract
Antimicrobials targeting the fatty acid synthesis (FASII) pathway are being developed as alternative treatments for bacterial infections. Emergence of resistance to FASII inhibitors was mainly considered as a consequence of mutations in the FASII target genes. However, an alternative and efficient anti-FASII resistance strategy, called here FASII bypass, was uncovered. Bacteria that bypass FASII incorporate exogenous fatty acids in membrane lipids, and thus dispense with the need for FASII. This strategy is used by numerous Gram-positive low GC % bacteria, including streptococci, enterococci, and staphylococci. Some bacteria repress FASII genes once fatty acids are available, and "constitutively" shift to FASII bypass. Others, such as the major pathogen Staphylococcus aureus, can undergo high frequency mutations that favor FASII bypass. This capacity is particularly relevant during infection, as the host supplies the fatty acids needed for bacteria to bypass FASII and thus become resistant to FASII inhibitors. Screenings for anti-FASII resistance in the presence of exogenous fatty acids confirmed that FASII bypass confers anti-FASII resistance among clinical and veterinary isolates. Polymorphisms in S. aureus FASII initiation enzymes favor FASII bypass, possibly by increasing availability of acyl-carrier protein, a required intermediate. Here we review FASII bypass and consequences in light of proposed uses of anti-FASII to treat infections, with a focus on FASII bypass in S. aureus.
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Affiliation(s)
- Claire Morvan
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - David Halpern
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Gérald Kénanian
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Amit Pathania
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Jamila Anba-Mondoloni
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Gilles Lamberet
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Alexandra Gruss
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
| | - Karine Gloux
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
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Yao J, Rock CO. Exogenous fatty acid metabolism in bacteria. Biochimie 2017; 141:30-39. [PMID: 28668270 DOI: 10.1016/j.biochi.2017.06.015] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 06/26/2017] [Indexed: 10/19/2022]
Abstract
Bacterial type II fatty acid synthesis (FASII) is a target for novel antibiotic development. All bacteria encode for mechanisms to incorporate exogenous fatty acids, and some bacteria can use exogenous fatty acids to bypass FASII inhibition. Bacteria encode three different mechanisms for activating exogenous fatty acids for incorporation into phospholipid synthesis. Exogenous fatty acids are converted into acyl-CoA in Gammaproteobacteria such as E. coli. Acyl-CoA molecules constitute a separate pool from endogenously synthesized acyl-ACP. Acyl-CoA can be used for phospholipid synthesis or broken down by β-oxidation, but cannot be used for lipopolysaccharide synthesis. Exogenous fatty acids are converted into acyl-ACP in some Gram-negative bacteria. The resulting acyl-ACP undergoes the same fates as endogenously synthesized acyl-ACP. Exogenous fatty acids are converted into acyl-phosphates in Gram-positive bacteria, and can be used for phospholipid synthesis or become acyl-ACP. Only the order Lactobacillales can use exogenous fatty acids to bypass FASII inhibition. FASII shuts down completely in presence of exogenous fatty acids in Lactobacillales, allowing Lactobacillales to synthesize phospholipids entirely from exogenous fatty acids. Inhibition of FASII cannot be bypassed in other bacteria because FASII is only partially down-regulated in presence of exogenous fatty acid or FASII is required to synthesize essential metabolites such as β-hydroxyacyl-ACP. Certain selective pressures such as FASII inhibition or growth in biofilms can select for naturally occurring one step mutations that attenuate endogenous fatty acid synthesis. Although attempts have been made to estimate the natural prevalence of these mutants, culture-independent metagenomic methods would provide a better estimate.
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Affiliation(s)
- Jiangwei Yao
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Charles O Rock
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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Bush K, Page MGP. What we may expect from novel antibacterial agents in the pipeline with respect to resistance and pharmacodynamic principles. J Pharmacokinet Pharmacodyn 2017; 44:113-132. [DOI: 10.1007/s10928-017-9506-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 01/20/2017] [Indexed: 12/25/2022]
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Mistry TL, Truong L, Ghosh AK, Johnson ME, Mehboob S. Benzimidazole-Based FabI Inhibitors: A Promising Novel Scaffold for Anti-staphylococcal Drug Development. ACS Infect Dis 2017; 3:54-61. [PMID: 27756129 DOI: 10.1021/acsinfecdis.6b00123] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The enoyl-ACP reductase (FabI) enzyme is a well validated target for anti-staphylococcal drug discovery and development. With the goal of finding alternate therapeutics for drug-resistant strains of Staphylococcus aureus, such as methicillin-resistant S. aureus (MRSA), our previously published series of benzimidazole-based inhibitors of the FabI enzyme from Francisella tularensis (FtFabI) have been evaluated against FabI from S. aureus (SaFabI). We report here the preliminary structure-activity relationship of this series and the prioritization of compounds toward lead optimization. Mutational studies have identified key residues that contribute toward stabilizing the inhibitors in the active site of FabI. Mutations that do not significantly impact enzyme function but destabilize inhibitor binding are more likely to occur in nature as organisms evolve to evade the action of antibiotics leading to resistance. Identifying these residues provides guidance for minimizing susceptibility to resistance. Additionally, we have identified compounds that elicit antibacterial activity through off-target effects and observe that close analogs can display differing modes of action (on-target vs off-target) and need to be individually evaluated early on to prioritize compounds for lead optimization. Overall, our data suggest that the benzimidazole scaffold is a promising scaffold for anti-staphylococcal drug development.
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Affiliation(s)
- Tina L. Mistry
- Center
for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Lena Truong
- Center
for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Arun K. Ghosh
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Michael E. Johnson
- Center
for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois 60607, United States
- Novalex Therapeutics, 2242 W. Harrison, Chicago, Illinois 60612, United States
| | - Shahila Mehboob
- Novalex Therapeutics, 2242 W. Harrison, Chicago, Illinois 60612, United States
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Environmental fatty acids enable emergence of infectious Staphylococcus aureus resistant to FASII-targeted antimicrobials. Nat Commun 2016; 7:12944. [PMID: 27703138 PMCID: PMC5059476 DOI: 10.1038/ncomms12944] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 08/16/2016] [Indexed: 01/11/2023] Open
Abstract
The bacterial pathway for fatty acid biosynthesis, FASII, is a target for development of new anti-staphylococcal drugs. This strategy is based on previous reports indicating that self-synthesized fatty acids appear to be indispensable for Staphylococcus aureus growth and virulence, although other bacteria can use exogenous fatty acids to compensate FASII inhibition. Here we report that staphylococci can become resistant to the FASII-targeted inhibitor triclosan via high frequency mutations in fabD, one of the FASII genes. The fabD mutants can be conditional for FASII and not require exogenous fatty acids for normal growth, and can use diverse fatty acid combinations (including host fatty acids) when FASII is blocked. These mutants show cross-resistance to inhibitors of other FASII enzymes and are infectious in mice. Clinical isolates bearing fabD polymorphisms also bypass FASII inhibition. We propose that fatty acid-rich environments within the host, in the presence of FASII inhibitors, might favour the emergence of staphylococcal strains displaying resistance to multiple FASII inhibitors. The bacterial pathway for fatty acid biosynthesis, FASII, is a target for development of new anti-staphylococcal drugs. Here, Morvan et al. show that exogenous fatty acids can favour the emergence of staphylococcal strains displaying resistance to multiple FASII inhibitors.
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Bacterial fatty acid metabolism in modern antibiotic discovery. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1862:1300-1309. [PMID: 27668701 DOI: 10.1016/j.bbalip.2016.09.014] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 09/12/2016] [Accepted: 09/19/2016] [Indexed: 12/28/2022]
Abstract
Bacterial fatty acid synthesis is essential for many pathogens and different from the mammalian counterpart. These features make bacterial fatty acid synthesis a desirable target for antibiotic discovery. The structural divergence of the conserved enzymes and the presence of different isozymes catalyzing the same reactions in the pathway make bacterial fatty acid synthesis a narrow spectrum target rather than the traditional broad spectrum target. Furthermore, bacterial fatty acid synthesis inhibitors are single-targeting, rather than multi-targeting like traditional monotherapeutic, broad-spectrum antibiotics. The single-targeting nature of bacterial fatty acid synthesis inhibitors makes overcoming fast-developing, target-based resistance a necessary consideration for antibiotic development. Target-based resistance can be overcome through multi-targeting inhibitors, a cocktail of single-targeting inhibitors, or by making the single targeting inhibitor sufficiently high affinity through a pathogen selective approach such that target-based mutants are still susceptible to therapeutic concentrations of drug. Many of the pathogens requiring new antibiotic treatment options encode for essential bacterial fatty acid synthesis enzymes. This review will evaluate the most promising targets in bacterial fatty acid metabolism for antibiotic therapeutics development and review the potential and challenges in advancing each of these targets to the clinic and circumventing target-based resistance. This article is part of a Special Issue entitled: Bacterial Lipids edited by Russell E. Bishop.
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Jones JA, Virga KG, Gumina G, Hevener KE. Recent Advances in the Rational Design and Optimization of Antibacterial Agents. MEDCHEMCOMM 2016; 7:1694-1715. [PMID: 27642504 DOI: 10.1039/c6md00232c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
This review discusses next-generation antibacterial agents developed using rational, or targeted, drug design strategies. The focus of this review is on small-molecule compounds that have been designed to bypass developing bacterial resistance, improve the antibacterial spectrum of activity, and/or to optimize other properties, including physicochemical and pharmacokinetic properties. Agents are discussed that affect known antibacterial targets, such as the bacterial ribosome, nucleic acid binding proteins, and proteins involved in cell-wall biosynthesis; as well as some affecting novel bacterial targets which do not have currently marketed agents. The discussion of the agents focuses on the rational design strategies employed and the synthetic medicinal chemistry and structure-based design techniques utilized by the scientists involved in the discoveries, including such methods as ligand- and structure-based strategies, structure-activity relationship (SAR) expansion strategies, and novel synthetic organic chemistry methods. As such, the discussion is limited to small-molecule therapeutics that have confirmed macromolecular targets and encompasses only a fraction of all antibacterial agents recently approved or in late-stage clinical trials. The antibacterial agents selected have been recently approved for use on the U.S. or European markets or have shown promising results in phase 2 or phase 3 U.S. CLINICAL TRIALS
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Affiliation(s)
- Jesse A Jones
- Department of Biomedical and Pharmaceutical Sciences, Idaho State University, 1311 E. Central Drive, Meridian, ID 83642-7991 (USA)
| | - Kristopher G Virga
- Department of Pharmaceutical Sciences, Presbyterian College School of Pharmacy, 307 North Broad Street, Clinton, SC 29325 (USA)
| | - Giuseppe Gumina
- Department of Pharmaceutical Sciences, Presbyterian College School of Pharmacy, 307 North Broad Street, Clinton, SC 29325 (USA)
| | - Kirk E Hevener
- Department of Biomedical and Pharmaceutical Sciences, Idaho State University, 1311 E. Central Drive, Meridian, ID 83642-7991 (USA)
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Furi L, Haigh R, Al Jabri ZJH, Morrissey I, Ou HY, León-Sampedro R, Martinez JL, Coque TM, Oggioni MR. Dissemination of Novel Antimicrobial Resistance Mechanisms through the Insertion Sequence Mediated Spread of Metabolic Genes. Front Microbiol 2016; 7:1008. [PMID: 27446047 PMCID: PMC4923244 DOI: 10.3389/fmicb.2016.01008] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 06/13/2016] [Indexed: 12/14/2022] Open
Abstract
The widely used biocide triclosan selectively targets FabI, the NADH-dependent trans-2-enoyl-acyl carrier protein (ACP) reductase, which is also an important target for the development of narrow spectrum antibiotics. The analysis of triclosan resistant Staphylococcus aureus isolates had previously shown that in about half of the strains, the mechanism of triclosan resistance consists on the heterologous duplication of the triclosan target gene due to the acquisition of an additional fabI allele derived from Staphylococcus haemolyticus (sh-fabI). In the current work, the genomic sequencing of 10 of these strains allowed the characterization of two novel composite transposons TnSha1 and TnSha2 involved in the spread of sh-fabI. TnSha1 harbors one copy of IS1272, whereas TnSha2 is a 11.7 kb plasmid carrying TnSha1 present either as plasmid or in an integrated form generally flanked by two IS1272 elements. The target and mechanism of integration for IS1272 and TnSha1 are novel and include targeting of DNA secondary structures, generation of blunt-end deletions of the stem-loop and absence of target duplication. Database analyses showed widespread occurrence of these two elements in chromosomes and plasmids, with TnSha1 mainly in S. aureus and with TnSha2 mainly in S. haemolyticus and S. epidermidis. The acquisition of resistance by means of an insertion sequence-based mobilization and consequent duplication of drug-target metabolic genes, as observed here for sh-fabI, is highly reminiscent of the situation with the ileS2 gene conferring mupirocin resistance, and the dfrA and dfrG genes conferring trimethoprim resistance both of which are mobilized by IS257. These three examples, which show similar mechanisms and levels of spread of metabolic genes linked to IS elements, highlight the importance of this genetic strategy for recruitment and rapid distribution of novel resistance mechanisms in staphylococci.
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Affiliation(s)
- Leonardo Furi
- Department of Genetics, University of LeicesterLeicester, UK; Dipartimento di Biotecnologie Mediche, Universita di SienaSiena, Italy
| | - Richard Haigh
- Department of Genetics, University of Leicester Leicester, UK
| | | | | | - Hong-Yu Ou
- State Key Laboratory for Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiaotong University Shanghai, China
| | - Ricardo León-Sampedro
- Departamento de Microbiología, Instituto Ramón y Cajal de Investigación Sanitaria, Hospital Universitario Ramón y CajalMadrid, Spain; Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP)Spain
| | - Jose L Martinez
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones CientíficasMadrid, Spain; Unidad de Resistencia a Antibióticos y Virulencia Bacteriana (RYC-Consejo Superior de Investigaciones Científicas)Madrid, Spain
| | - Teresa M Coque
- Departamento de Microbiología, Instituto Ramón y Cajal de Investigación Sanitaria, Hospital Universitario Ramón y CajalMadrid, Spain; Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP)Spain; Unidad de Resistencia a Antibióticos y Virulencia Bacteriana (RYC-Consejo Superior de Investigaciones Científicas)Madrid, Spain
| | - Marco R Oggioni
- Department of Genetics, University of LeicesterLeicester, UK; Dipartimento di Biotecnologie Mediche, Universita di SienaSiena, Italy
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Yao J, Rock CO. Resistance Mechanisms and the Future of Bacterial Enoyl-Acyl Carrier Protein Reductase (FabI) Antibiotics. Cold Spring Harb Perspect Med 2016; 6:a027045. [PMID: 26931811 DOI: 10.1101/cshperspect.a027045] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Missense mutations leading to clinical antibiotic resistance are a liability of single-target inhibitors. The enoyl-acyl carrier protein reductase (FabI) inhibitors have one intracellular protein target and drug resistance is increased by the acquisition of single-base-pair mutations that alter drug binding. The spectrum of resistance mechanisms to FabI inhibitors suggests criteria that should be considered during the development of single-target antibiotics that would minimize the impact of missense mutations on their clinical usefulness. These criteria include high-affinity, fast on/off kinetics, few drug contacts with residue side chains, and no toxicity. These stringent criteria are achievable by structure-guided design, but this approach will only yield pathogen-specific drugs. Single-step acquisition of resistance may limit the clinical application of broad-spectrum, single-target antibiotics, but appropriately designed pathogen-specific antibiotics have the potential to overcome this liability.
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Affiliation(s)
- Jiangwei Yao
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Charles O Rock
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
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34
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Design and development of pyrrole carbaldehyde: an effective pharmacophore for enoyl-ACP reductase. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1517-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Vuong C, Yeh AJ, Cheung GYC, Otto M. Investigational drugs to treat methicillin-resistant Staphylococcus aureus. Expert Opin Investig Drugs 2015; 25:73-93. [PMID: 26536498 DOI: 10.1517/13543784.2016.1109077] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
INTRODUCTION Staphylococcus aureus remains one of the leading causes of morbidity and mortality worldwide. This is to a large extent due to antibiotic-resistant strains, in particular methicillin-resistant S. aureus (MRSA). While the toll of invasive MRSA infections appears to decrease in U.S. hospitals, the rate of community-associated MRSA infections remains constant and there is a surge of MRSA in many other countries, a situation that calls for continuing if not increased efforts to find novel strategies to combat MRSA infections. AREAS COVERED This review provides an overview of current investigational drugs and therapeutic antibodies against S. aureus in early clinical development (up to phase II clinical development). It includes a short description of the mechanism of action and a presentation of microbiological and clinical data. EXPERT OPINION Increased recent antibiotic development efforts and results from pathogenesis research have led to several new antibiotics and therapies, such as anti-virulence drugs, as well as a more informed selection of targets for vaccination efforts against MRSA. This developing portfolio of novel anti-staphylococcal drugs will hopefully provide us with additional and more efficient ways to combat MRSA infections in the near future and prevent us from running out of treatment options, even if new resistances arise.
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Affiliation(s)
- Cuong Vuong
- a Principal Scientist/Laboratory Head, Bacteriology , AiCuris GmbH & Co. KG, Friedrich-Ebert-Str. 475/Geb. 302, 42117 Wuppertal , Germany
| | - Anthony J Yeh
- b Post-baccalaureate IRTA, Laboratory of Bacteriology , National Institute of Allergy and Infectious Diseases, National Institutes of Health , Bldg. 33, 1W10, 9000 Rockville Pike, Bethesda , MD 20892 , USA
| | - Gordon Y C Cheung
- c Staff Scientist, National Institute of Allergy and Infectious Diseases , National Institutes of Health, Laboratory of Bacteriology , Bldg. 33, 1W10, 9000 Rockville Pike, Bethesda , MD 20892 , USA
| | - Michael Otto
- d Senior Investigator, National Institute of Allergy and Infectious Diseases , National Institutes of Health, Laboratory of Bacteriology , Bldg. 33, 1W10, 9000 Rockville Pike, Bethesda , MD 20892 , USA
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Yogiara, Kim D, Hwang JK, Pan JG. Escherichia coli ASKA Clone Library Harboring tRNA-Specific Adenosine Deaminase (tadA) Reveals Resistance towards Xanthorrhizol. Molecules 2015; 20:16290-305. [PMID: 26370953 PMCID: PMC6331797 DOI: 10.3390/molecules200916290] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 08/27/2015] [Accepted: 08/31/2015] [Indexed: 11/16/2022] Open
Abstract
Xanthorrhizol is a potent antimicrobial compound isolated from the rhizome of Curcuma xanthorrhiza. However, the mechanism of xanthorrhizol action is unknown. To screen for probable target(s), we introduced the ASKA pooled-plasmid library into Escherichia coli W3110 imp4213 and enriched the library for resistant clones with increasing concentrations of xanthorrhizol. After three rounds of enrichment, we found nine genes that increased xanthorrhizol resistance. The resistant clones were able to grow in LB medium containing 256 µg/mL xanthorrhizol, representing a 16-fold increase in the minimum inhibitory concentration. Subsequent DNA sequence analysis revealed that overexpression of tadA, galU, fucU, ydeA, ydaC, soxS, nrdH, yiiD, and mltF genes conferred increased resistance towards xanthorrhizol. Among these nine genes, tadA is the only essential gene. tadA encodes a tRNA-specific adenosine deaminase. Overexpression of E. coli W3110 imp4213 (pCA24N-tadA) conferred resistance to xanthorrhizol up to 128 µg/mL. Moreover, overexpression of two tadA mutant enzymes (A143V and F149G) led to a twofold increase in the MIC. These results suggest that the targets of xanthorrhizol may include tadA, which has never before been explored as an antibiotic target.
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Affiliation(s)
- Yogiara
- Department of Biotechnology, Yonsei University, 50-Yonsei-ro Seodaemun-gu, Seoul 120-749, Korea.
- Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jalan Jenderal Sudirman 51, Jakarta 12930, Indonesia.
| | - Dooil Kim
- Superbacteria Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 111 Gwahangno, Yuseong, Daejeon 305-806, Korea.
| | - Jae-Kwan Hwang
- Department of Biotechnology, Yonsei University, 50-Yonsei-ro Seodaemun-gu, Seoul 120-749, Korea.
| | - Jae-Gu Pan
- Superbacteria Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 111 Gwahangno, Yuseong, Daejeon 305-806, Korea.
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Mutations upstream of fabI in triclosan resistant Staphylococcus aureus strains are associated with elevated fabI gene expression. BMC Genomics 2015; 16:345. [PMID: 25924916 PMCID: PMC4415318 DOI: 10.1186/s12864-015-1544-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 04/17/2015] [Indexed: 01/30/2023] Open
Abstract
Background The enoyl-acyl carrier protein (ACP) reductase enzyme (FabI) is the target for a series of antimicrobial agents including novel compounds in clinical trial and the biocide triclosan. Mutations in fabI and heterodiploidy for fabI have been shown to confer resistance in S. aureus strains in a previous study. Here we further determined the fabI upstream sequence of a selection of these strains and the gene expression levels in strains with promoter region mutations. Results Mutations in the fabI promoter were found in 18% of triclosan resistant clinical isolates, regardless the previously identified molecular mechanism conferring resistance. Although not significant, a higher rate of promoter mutations were found in strains without previously described mechanisms of resistance. Some of the mutations identified in the clinical isolates were also detected in a series of laboratory mutants. Microarray analysis of selected laboratory mutants with fabI promoter region mutations, grown in the absence of triclosan, revealed increased fabI expression in three out of four tested strains. In two of these strains, only few genes other than fabI were upregulated. Consistently with these data, whole genome sequencing of in vitro selected mutants identified only few mutations except the upstream and coding regions of fabI, with the promoter mutation as the most probable cause of fabI overexpression. Importantly the gene expression profiling of clinical isolates containing similar mutations in the fabI promoter also showed, when compared to unrelated non-mutated isolates, a significant up-regulation of fabI. Conclusions In conclusion, we have demonstrated the presence of C34T, T109G, and A101C mutations in the fabI promoter region of strains with fabI up-regulation, both in clinical isolates and/or laboratory mutants. These data provide further observations linking mutations upstream fabI with up-regulated expression of the fabI gene. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1544-y) contains supplementary material, which is available to authorized users.
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Wang H, Lu Y, Liu L, Kim SW, Hooker JM, Fowler JS, Tonge PJ. Radiosynthesis and biological evaluation of a novel enoyl-ACP reductase inhibitor for Staphylococcus aureus. Eur J Med Chem 2014; 88:66-73. [PMID: 25217335 DOI: 10.1016/j.ejmech.2014.09.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 08/27/2014] [Accepted: 09/03/2014] [Indexed: 11/18/2022]
Abstract
The pharmacokinetics (PK) and pharmacodynamics (PD) of PT119, a potent Staphylococcus aureus enoyl-ACP reductase (saFabI) inhibitor with a Ki value of 0.01 nM and a residence time of 750 min on the enzyme target, has been evaluated in mice. PT119 was found to have promising antibacterial activity in two different S. aureus infection models: it caused a 3 log reduction in the CFU's in a mouse thigh muscle infection model and increased the survival rate from 0% to 50% in a mouse systemic infection model. PT119 was then radiolabeled with carbon-11 to evaluate its biodistribution and PK in both healthy and S. aureus infected mice using positron emission tomography (PET). The biodistribution of [11C]PT119 and/or its labeled metabolites did not differ significantly between the healthy group and the infected group, and PT119 was found to distribute equally between serum and tissue during the ∼1 h of analysis permitted by the carbon-11 half life. This approach provides important data for PK/PD modeling and is the first step in identifying radiotracers that can non-invasively image bacterial infection in vivo.
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Affiliation(s)
- Hui Wang
- Institute of Chemical Biology & Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA
| | - Yang Lu
- Institute of Chemical Biology & Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA
| | - Li Liu
- Institute of Chemical Biology & Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA
| | - Sung Won Kim
- Biosciences Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Jacob M Hooker
- Biosciences Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Joanna S Fowler
- Biosciences Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Peter J Tonge
- Institute of Chemical Biology & Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA.
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Wang L, Le X, Li L, Ju Y, Lin Z, Gu Q, Xu J. Discovering New Agents Active against Methicillin-Resistant Staphylococcus aureus with Ligand-Based Approaches. J Chem Inf Model 2014; 54:3186-97. [DOI: 10.1021/ci500253q] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Ling Wang
- Research
Center for Drug Discovery and Institute of Human Virology, School
of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Xiu Le
- Research
Center for Drug Discovery and Institute of Human Virology, School
of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Long Li
- Research
Center for Drug Discovery and Institute of Human Virology, School
of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Yingchen Ju
- Research
Center for Drug Discovery and Institute of Human Virology, School
of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Zhongxiang Lin
- College
of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Qiong Gu
- Research
Center for Drug Discovery and Institute of Human Virology, School
of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Jun Xu
- Research
Center for Drug Discovery and Institute of Human Virology, School
of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
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Schiebel J, Chang A, Shah S, Lu Y, Liu L, Pan P, Hirschbeck MW, Tareilus M, Eltschkner S, Yu W, Cummings JE, Knudson SE, Bommineni GR, Walker SG, Slayden RA, Sotriffer CA, Tonge PJ, Kisker C. Rational design of broad spectrum antibacterial activity based on a clinically relevant enoyl-acyl carrier protein (ACP) reductase inhibitor. J Biol Chem 2014; 289:15987-6005. [PMID: 24739388 DOI: 10.1074/jbc.m113.532804] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Determining the molecular basis for target selectivity is of particular importance in drug discovery. The ideal antibiotic should be active against a broad spectrum of pathogenic organisms with a minimal effect on human targets. CG400549, a Staphylococcus-specific 2-pyridone compound that inhibits the enoyl-acyl carrier protein reductase (FabI), has recently been shown to possess human efficacy for the treatment of methicillin-resistant Staphylococcus aureus infections, which constitute a serious threat to human health. In this study, we solved the structures of three different FabI homologues in complex with several pyridone inhibitors, including CG400549. Based on these structures, we rationalize the 65-fold reduced affinity of CG400549 toward Escherichia coli versus S. aureus FabI and implement concepts to improve the spectrum of antibacterial activity. The identification of different conformational states along the reaction coordinate of the enzymatic hydride transfer provides an elegant visual depiction of the relationship between catalysis and inhibition, which facilitates rational inhibitor design. Ultimately, we developed the novel 4-pyridone-based FabI inhibitor PT166 that retained favorable pharmacokinetics and efficacy in a mouse model of S. aureus infection with extended activity against Gram-negative and mycobacterial organisms.
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Affiliation(s)
- Johannes Schiebel
- From the Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Wuerzburg, D-97080 Wuerzburg, Germany, the Institute of Pharmacy and Food Chemistry, University of Wuerzburg, Am Hubland, D-97074 Wuerzburg, Germany
| | - Andrew Chang
- the Institute for Chemical Biology and Drug Discovery, Department of Chemistry, and School of Dental Medicine, Department of Oral Biology and Pathology, Stony Brook University, Stony Brook, New York 11794-3400, and
| | - Sonam Shah
- the Institute for Chemical Biology and Drug Discovery, Department of Chemistry, and
| | - Yang Lu
- the Institute for Chemical Biology and Drug Discovery, Department of Chemistry, and School of Dental Medicine, Department of Oral Biology and Pathology, Stony Brook University, Stony Brook, New York 11794-3400, and
| | - Li Liu
- the Institute for Chemical Biology and Drug Discovery, Department of Chemistry, and
| | - Pan Pan
- the Institute for Chemical Biology and Drug Discovery, Department of Chemistry, and
| | - Maria W Hirschbeck
- From the Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Wuerzburg, D-97080 Wuerzburg, Germany
| | - Mona Tareilus
- From the Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Wuerzburg, D-97080 Wuerzburg, Germany
| | - Sandra Eltschkner
- From the Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Wuerzburg, D-97080 Wuerzburg, Germany
| | - Weixuan Yu
- the Institute for Chemical Biology and Drug Discovery, Department of Chemistry, and
| | - Jason E Cummings
- the Rocky Mountain Regional Center of Excellence and Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682
| | - Susan E Knudson
- the Rocky Mountain Regional Center of Excellence and Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682
| | - Gopal R Bommineni
- the Institute for Chemical Biology and Drug Discovery, Department of Chemistry, and
| | - Stephen G Walker
- School of Dental Medicine, Department of Oral Biology and Pathology, Stony Brook University, Stony Brook, New York 11794-3400, and
| | - Richard A Slayden
- the Rocky Mountain Regional Center of Excellence and Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682
| | - Christoph A Sotriffer
- the Institute of Pharmacy and Food Chemistry, University of Wuerzburg, Am Hubland, D-97074 Wuerzburg, Germany
| | - Peter J Tonge
- the Institute for Chemical Biology and Drug Discovery, Department of Chemistry, and
| | - Caroline Kisker
- From the Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Wuerzburg, D-97080 Wuerzburg, Germany,
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41
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Yao J, Maxwell JB, Rock CO. Resistance to AFN-1252 arises from missense mutations in Staphylococcus aureus enoyl-acyl carrier protein reductase (FabI). J Biol Chem 2013; 288:36261-71. [PMID: 24189061 DOI: 10.1074/jbc.m113.512905] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
AFN-1252 is a potent antibiotic against Staphylococcus aureus that targets the enoyl-acyl carrier protein reductase (FabI). A thorough screen for AFN-1252-resistant strains was undertaken to identify the spectrum of mechanisms for acquired resistance. A missense mutation in fabI predicted to encode FabI(M99T) was isolated 49 times, and a single isolate was predicted to encode FabI(Y147H). AFN-1252 only bound to the NADPH form of FabI, and the close interactions between the drug and Met-99 and Tyr-147 explained how the mutations would result in resistant enzymes. The clone expressing FabI(Y147H) had a pronounced growth defect that was rescued by exogenous fatty acid supplementation, and the purified protein had less than 5% of the enzymatic activity of FabI. FabI(Y147F) was also catalytically defective but retained its sensitivity to AFN-1252, illustrating the importance of the conserved Tyr-147 hydroxyl group in FabI function. The strains expressing FabI(M99T) exhibited normal growth, and the biochemical properties of the purified protein were indistinguishable from those of FabI. The AFN-1252 Ki(app) increased from 4 nm in FabI to 69 nm in FabI(M99T), accounting for the increased resistance of the corresponding mutant strain. The low activity of FabI(Y147H) precluded an accurate Ki measurement. The strain expressing FabI(Y147H) was also resistant to triclosan; however, the strain expressing FabI(M99T) was more susceptible. Strains with higher levels of AFN-1252 resistance were not obtained. The AFN-1252-resistant strains remained sensitive to submicromolar concentrations of AFN-1252, which blocked growth through inhibition of fatty acid biosynthesis at the FabI step.
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Affiliation(s)
- Jiangwei Yao
- From the Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
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42
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Tsuji BT, Harigaya Y, Lesse AJ, Forrest A, Ngo D. Activity of AFN-1252, a novel FabI inhibitor, against Staphylococcus aureus in an in vitro pharmacodynamic model simulating human pharmacokinetics. J Chemother 2013; 25:32-5. [PMID: 23433442 PMCID: PMC3558987 DOI: 10.1179/1973947812y.0000000060] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
AFN-1252, a potent enoyl-ACP reductase (FabI) inhibitor, is under development for the treatment of Staphylococcus aureus infections. The activity of AFN-1252 against two isolates of S. aureus, MSSA 26213 and MRSA S186, was studied in an in vitro pharmacodynamic model simulating AFN-1252 pharmacokinetics in man. Reductions in bacterial viable count over the first 6 hours were generally 1–2 logs and maximal reductions in viable count were generally achieved at fAUC/MIC ratios of 100–200. Maximum reductions in viable count against MSSA 29213 and MRSA S186 were approximately 4 logs, achieved by 450 mg q12h (fAUC/MIC = 1875) dosing at 28 hours. Staphylococcal resistance to AFN-1252 did not develop throughout the 48-hour experiments. As multidrug resistance continues to increase, these studies support the continued investigation of AFN-1252 as a targeted therapeutic for staphylococcal infections.
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Affiliation(s)
- Brian T Tsuji
- Laboratory for Antimicrobial Pharmacodynamics, The New York State Center of Excellence in Bioinformatics, University at Buffalo, State University of New York, NY14203, USA.
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43
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Butler MS, Blaskovich MA, Cooper MA. Antibiotics in the clinical pipeline in 2013. J Antibiot (Tokyo) 2013; 66:571-91. [PMID: 24002361 DOI: 10.1038/ja.2013.86] [Citation(s) in RCA: 309] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 07/31/2013] [Accepted: 08/02/2013] [Indexed: 12/17/2022]
Abstract
The continued emergence of multi-drug-resistant bacteria is a major public health concern. The identification and development of new antibiotics, especially those with new modes of action, is imperative to help treat these infections. This review lists the 22 new antibiotics launched since 2000 and details the two first-in-class antibiotics, fidaxomicin (1) and bedaquiline (2), launched in 2011 and 2012, respectively. The development status, mode of action, spectra of activity, historical discovery and origin of the drug pharmacophore (natural product, natural product derived, synthetic or protein/mammalian peptide) of the 49 compounds and 6 β-lactamase/β-lactam combinations in active clinical development are discussed, as well as compounds that have been discontinued from clinical development since 2011. New antibacterial pharmacophore templates are also reviewed and analyzed.
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Affiliation(s)
- Mark S Butler
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
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44
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Wang Y, Ma S. Recent Advances in Inhibitors of Bacterial Fatty Acid Synthesis Type II (FASII) System Enzymes as Potential Antibacterial Agents. ChemMedChem 2013; 8:1589-608. [DOI: 10.1002/cmdc.201300209] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Revised: 06/30/2013] [Indexed: 12/25/2022]
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45
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Chang A, Schiebel J, Yu W, Bommineni GR, Pan P, Baxter MV, Khanna A, Sotriffer CA, Kisker C, Tonge PJ. Rational optimization of drug-target residence time: insights from inhibitor binding to the Staphylococcus aureus FabI enzyme-product complex. Biochemistry 2013; 52:4217-28. [PMID: 23697754 DOI: 10.1021/bi400413c] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Drug-target kinetics has recently emerged as an especially important facet of the drug discovery process. In particular, prolonged drug-target residence times may confer enhanced efficacy and selectivity in the open in vivo system. However, the lack of accurate kinetic and structural data for a series of congeneric compounds hinders the rational design of inhibitors with decreased off-rates. Therefore, we chose the Staphylococcus aureus enoyl-ACP reductase (saFabI)--an important target for the development of new anti-staphylococcal drugs--as a model system to rationalize and optimize the drug-target residence time on a structural basis. Using our new, efficient, and widely applicable mechanistically informed kinetic approach, we obtained a full characterization of saFabI inhibition by a series of 20 diphenyl ethers complemented by a collection of 9 saFabI-inhibitor crystal structures. We identified a strong correlation between the affinities of the investigated saFabI diphenyl ether inhibitors and their corresponding residence times, which can be rationalized on a structural basis. Because of its favorable interactions with the enzyme, the residence time of our most potent compound exceeds 10 h. In addition, we found that affinity and residence time in this system can be significantly enhanced by modifications predictable by a careful consideration of catalysis. Our study provides a blueprint for investigating and prolonging drug-target kinetics and may aid in the rational design of long-residence-time inhibitors targeting the essential saFabI enzyme.
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Affiliation(s)
- Andrew Chang
- Institute for Chemical Biology & Drug Discovery, Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, USA
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Kumar K, Chopra S. New drugs for methicillin-resistant Staphylococcus aureus: an update. J Antimicrob Chemother 2013; 68:1465-70. [DOI: 10.1093/jac/dkt045] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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47
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Transcriptional profiles of the response of methicillin-resistant Staphylococcus aureus to pentacyclic triterpenoids. PLoS One 2013; 8:e56687. [PMID: 23437212 PMCID: PMC3577688 DOI: 10.1371/journal.pone.0056687] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 01/14/2013] [Indexed: 11/19/2022] Open
Abstract
Staphylococcus aureus is an important human pathogen in both hospital and the community that has demonstrated resistance to all currently available antibiotics over the last two decades. Multidrug-resistant isolates of methicillin-resistant S. aureus (MRSA) exhibiting decreased susceptibilities to glycopeptides has also emerged, representing a crucial challenge for antimicrobial therapy and infection control. The availability of complete whole-genome nucleotide sequence data of various strains of S. aureus presents an opportunity to explore novel compounds and their targets to address the challenges presented by antimicrobial drug resistance in this organism. Study compounds α-amyrin [3β-hydroxy-urs-12-en-3-ol (AM)], betulinic acid [3β-hydroxy-20(29)-lupaene-28-oic acid (BA)] and betulinaldehyde [3β-hydroxy-20(29)-lupen-28-al (BE)] belong to pentacyclic triterpenoids and were reported to exhibit antimicrobial activities against bacteria and fungi, including S. aureus. The MIC values of these compounds against a reference strain of methicillin-resistant S. aureus (MRSA) (ATCC 43300) ranged from 64 µg/ml to 512 µg/ml. However, the response mechanisms of S. aureus to these compounds are still poorly understood. The transcription profile of reference strain of MRSA treated with sub-inhibitory concentrations of the three compounds was determined using Affymetrix GeneChips. The findings showed that these compounds regulate multiple desirable targets in cell division, two-component system, ABC transporters, fatty acid biosynthesis, peptidoglycan biosynthesis, aminoacyl-tRNA synthetase, ribosome and β-lactam resistance pathways which could be further explored in the development of therapeutic agents for the treatment of S. aureus infections.
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The Francisella tularensis FabI enoyl-acyl carrier protein reductase gene is essential to bacterial viability and is expressed during infection. J Bacteriol 2012; 195:351-8. [PMID: 23144254 DOI: 10.1128/jb.01957-12] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Francisella tularensis is classified as a category A priority pathogen and causes fatal disseminated disease in humans upon inhalation of less than 50 bacteria. Although drugs are available for treatment, they are not ideal because of toxicity and route of delivery, and in some cases patients relapse upon withdrawal. We have an ongoing program to develop novel FAS-II FabI enoyl-ACP reductase enzyme inhibitors for Francisella and other select agents. To establish F. tularensis FabI (FtFabI) as a clinically relevant drug target, we demonstrated that fatty acid biosynthesis and FabI activity are essential for growth even in the presence of exogenous long-chain lipids and that FtfabI is not transcriptionally altered in the presence of exogenous long-chain lipids. Inhibition of FtFabI or fatty acid synthesis results in loss of viability that is not rescued by exogenous long-chain lipid supplementation. Importantly, whole-genome transcriptional profiling of F. tularensis with DNA microarrays from infected tissues revealed that FtfabI and de novo fatty acid biosynthetic genes are transcriptionally active during infection. This is the first demonstration that the FabI enoyl-ACP-reductase enzyme encoded by F. tularensis is essential and not bypassed by exogenous fatty acids and that de novo fatty acid biosynthetic components encoded in F. tularensis are transcriptionally active during infection in the mouse model of tularemia.
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49
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Gerusz V, Denis A, Faivre F, Bonvin Y, Oxoby M, Briet S, LeFralliec G, Oliveira C, Desroy N, Raymond C, Peltier L, Moreau F, Escaich S, Vongsouthi V, Floquet S, Drocourt E, Walton A, Prouvensier L, Saccomani M, Durant L, Genevard JM, Sam-Sambo V, Soulama-Mouze C. From triclosan toward the clinic: discovery of nonbiocidal, potent FabI inhibitors for the treatment of resistant bacteria. J Med Chem 2012; 55:9914-28. [PMID: 23092194 DOI: 10.1021/jm301113w] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
In this paper, we present some elements of our optimization program to decouple triclosan's specific FabI effect from its nonspecific cytotoxic component. The implementation of this strategy delivered highly specific, potent, and nonbiocidal new FabI inhibitors. We also disclose some preclinical data of one of their representatives, 83, a novel antibacterial compound active against resistant staphylococci and some clinically relevant Gram negative bacteria that is currently undergoing clinical trials.
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Affiliation(s)
- Vincent Gerusz
- Medicinal Chemistry and ‡Biology, Mutabilis, 102 Avenue Gaston Roussel, 93230 Romainville, France.
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50
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Inhibitors of fatty acid synthesis in prokaryotes and eukaryotes as anti-infective, anticancer and anti-obesity drugs. Future Med Chem 2012; 4:1113-51. [PMID: 22709254 DOI: 10.4155/fmc.12.62] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
There is a large range of diseases, such diabetes and cancer, which are connected to abnormal fatty acid metabolism in human cells. Therefore, inhibitors of human fatty acid synthase have great potential to manage or treat these diseases. In prokaryotes, fatty acid synthesis is important for signaling, as well as providing starting materials for the synthesis of phospholipids, which are required for the formation of the cell membrane. Recently, there has been renewed interest in the development of new molecules that target bacterial fatty acid synthases for the treatment of bacterial diseases. In this review, we look at the differences and similarities between fatty acid synthesis in humans and bacteria and highlight various small molecules that have been shown to inhibit either the mammalian or bacterial fatty acid synthase or both.
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