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Dutta A, Sharma P, Dass D, Yarlagadda V. Exploring the Darobactin Class of Antibiotics: A Comprehensive Review from Discovery to Recent Advancements. ACS Infect Dis 2024. [PMID: 39028949 DOI: 10.1021/acsinfecdis.4c00412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2024]
Abstract
The prevalence of antimicrobial resistance in Gram-negative bacteria poses a greater challenge due to their intrinsic resistance to many antibiotics. Recently, darobactins have emerged as a novel class of antibiotics originating from previously unexplored Gram-negative bacterial species such as Photorhabdus, Vibrio, Pseudoalteromonas and Yersinia. Darobactins belong to the ribosomally synthesized and post-translationally modified peptide (RiPP) class of antibiotics, exhibiting selective activity against Gram-negative bacteria. They target the β-barrel assembly machinery (BAM), which is crucial for the maturation and insertion of outer membrane proteins in Gram-negative bacteria. The dar operon in the producer's genome encodes for the synthesis of darobactins, which are characterized by a fused ring system connected via an alkyl-aryl ether linkage (C-O-C) and a C-C cross-link. The enzyme DarE, using the radical S-adenosyl-l-methionine (rSAM), facilitates the formation of these bonds. Biosynthetic manipulation of the darobactin gene cluster, along with its expression in a surrogate host, has enabled access to diverse darobactin analogues with variable antibiotic activities. Recently, two independent research groups successfully achieved the total synthesis of darobactin, employing Larock heteroannulation to construct the bicyclic structure. This paper presents a comprehensive review of darobactins, encompassing their discovery through to the most recent advancements.
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Affiliation(s)
- Akash Dutta
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Peehu Sharma
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Dharam Dass
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
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2
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Matias LLR, Damasceno KSFDSC, Pereira AS, Passos TS, Morais AHDA. Innovative Biomedical and Technological Strategies for the Control of Bacterial Growth and Infections. Biomedicines 2024; 12:176. [PMID: 38255281 PMCID: PMC10813423 DOI: 10.3390/biomedicines12010176] [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: 11/28/2023] [Revised: 01/05/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
Antibiotics comprise one of the most successful groups of pharmaceutical products. Still, they have been associated with developing bacterial resistance, which has become one of the most severe problems threatening human health today. This context has prompted the development of new antibiotics or co-treatments using innovative tools to reverse the resistance context, combat infections, and offer promising antibacterial therapy. For the development of new alternatives, strategies, and/or antibiotics for controlling bacterial growth, it is necessary to know the target bacteria, their classification, morphological characteristics, the antibiotics currently used for therapies, and their respective mechanisms of action. In this regard, genomics, through the sequencing of bacterial genomes, has generated information on diverse genetic resources, aiding in the discovery of new molecules or antibiotic compounds. Nanotechnology has been applied to propose new antimicrobials, revitalize existing drug options, and use strategic encapsulating agents with their biochemical characteristics, making them more effective against various bacteria. Advanced knowledge in bacterial sequencing contributes to the construction of databases, resulting in advances in bioinformatics and the development of new antimicrobials. Moreover, it enables in silico antimicrobial susceptibility testing without the need to cultivate the pathogen, reducing costs and time. This review presents new antibiotics and biomedical and technological innovations studied in recent years to develop or improve natural or synthetic antimicrobial agents to reduce bacterial growth, promote well-being, and benefit users.
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Affiliation(s)
- Lídia Leonize Rodrigues Matias
- Biochemistry and Molecular Biology Postgraduate Program, Biosciences Center, Federal University of Rio Grande do Norte, Natal 59078-970, RN, Brazil;
| | | | - Annemberg Salvino Pereira
- Nutrition Course, Center for Health Sciences, Federal University of Rio Grande do Norte, Natal 59078-970, RN, Brazil;
| | - Thaís Souza Passos
- Nutrition Postgraduate Program, Center for Health Sciences, Federal University of Rio Grande do Norte, Natal 59078-970, RN, Brazil; (K.S.F.d.S.C.D.); (T.S.P.)
| | - Ana Heloneida de Araujo Morais
- Biochemistry and Molecular Biology Postgraduate Program, Biosciences Center, Federal University of Rio Grande do Norte, Natal 59078-970, RN, Brazil;
- Nutrition Postgraduate Program, Center for Health Sciences, Federal University of Rio Grande do Norte, Natal 59078-970, RN, Brazil; (K.S.F.d.S.C.D.); (T.S.P.)
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3
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Koteva K, Xu M, Wang W, Fiebig-Comyn AA, Cook MA, Coombes BK, Wright GD. Synthetic Biology Facilitates Semisynthetic Development of Type V Glycopeptide Antibiotics Targeting Vancomycin-Resistant Enterococcus. J Med Chem 2023. [PMID: 37315221 DOI: 10.1021/acs.jmedchem.3c00633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The continued efficacy of glycopeptide antibiotics (GPAs) against Gram-positive bacteria is challenged by the emergence and spread of GPA-resistant pathogens, particularly vancomycin-resistant enterococci (VRE). The growing frequency of GPA resistance propels the need for innovative development of more effective antibiotics. Unlike canonical GPAs like vancomycin, Type V GPAs adopt a distinct mode of action by binding peptidoglycan and blocking the activity of autolysins essential for cell division, rendering them a promising class of antibiotics for further development. In this study, the Type V GPA, rimomycin A, was modified to generate 32 new analogues. Compound 17, derived from rimomycin A through N-terminal acylation and C-terminal amidation, exhibited improved anti-VRE activity and solubility. In a VRE-A neutropenic thigh infection mouse model, compound 17 significantly lowered the bacterial load by 3-4 orders of magnitude. This study sets the stage to develop next-generation GPAs in response to growing VRE infections.
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Affiliation(s)
- Kalinka Koteva
- David Braley Centre for Antibiotic Discovery, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Min Xu
- David Braley Centre for Antibiotic Discovery, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, West 7th Avenue No. 32, 300308 Tianjin, China
- Haihe Laboratory of Synthetic Biology, West 15th Avenue No. 21, 300308 Tianjin, China
| | - Wenliang Wang
- David Braley Centre for Antibiotic Discovery, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Aline A Fiebig-Comyn
- David Braley Centre for Antibiotic Discovery, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Michael A Cook
- David Braley Centre for Antibiotic Discovery, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Brian K Coombes
- David Braley Centre for Antibiotic Discovery, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Gerard D Wright
- David Braley Centre for Antibiotic Discovery, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada
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Díaz-Puertas R, Adamek M, Mallavia R, Falco A. Fish Skin Mucus Extracts: An Underexplored Source of Antimicrobial Agents. Mar Drugs 2023; 21:350. [PMID: 37367675 DOI: 10.3390/md21060350] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 06/28/2023] Open
Abstract
The slow discovery of new antibiotics combined with the alarming emergence of antibiotic-resistant bacteria underscores the need for alternative treatments. In this regard, fish skin mucus has been demonstrated to contain a diverse array of bioactive molecules with antimicrobial properties, including peptides, proteins, and other metabolites. This review aims to provide an overview of the antimicrobial molecules found in fish skin mucus and its reported in vitro antimicrobial capacity against bacteria, fungi, and viruses. Additionally, the different methods of mucus extraction, which can be grouped as aqueous, organic, and acidic extractions, are presented. Finally, omic techniques (genomics, transcriptomics, proteomics, metabolomics, and multiomics) are described as key tools for the identification and isolation of new antimicrobial compounds. Overall, this study provides valuable insight into the potential of fish skin mucus as a promising source for the discovery of new antimicrobial agents.
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Affiliation(s)
- Rocío Díaz-Puertas
- Institute of Research, Development and Innovation in Healthcare Biotechnology in Elche (IDiBE), Miguel Hernández University, 03202 Elche, Spain
| | - Mikolaj Adamek
- Fish Disease Research Unit, Institute for Parasitology, University of Veterinary Medicine, 30559 Hannover, Germany
| | - Ricardo Mallavia
- Institute of Research, Development and Innovation in Healthcare Biotechnology in Elche (IDiBE), Miguel Hernández University, 03202 Elche, Spain
| | - Alberto Falco
- Institute of Research, Development and Innovation in Healthcare Biotechnology in Elche (IDiBE), Miguel Hernández University, 03202 Elche, Spain
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5
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Lipase-activated glycopeptide nano-assemblies as an antibiotic nano-adjuvant to inhibit Pseudomonas aeruginosa biofilm and enhance antibacterial activity. Sci China Chem 2022. [DOI: 10.1007/s11426-022-1348-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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6
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Monteiro KLC, Silva ON, Dos Santos Nascimento IJ, Mendonça Júnior FJB, Aquino PGV, da Silva-Júnior EF, de Aquino TM. Medicinal Chemistry of Inhibitors Targeting Resistant Bacteria. Curr Top Med Chem 2022; 22:1983-2028. [PMID: 35319372 DOI: 10.2174/1568026622666220321124452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 02/01/2022] [Accepted: 02/13/2022] [Indexed: 12/15/2022]
Abstract
The discovery of antibiotics was a revolutionary feat that provided countless health benefits. The identification of penicillin by Alexander Fleming initiated the era of antibiotics, represented by constant discoveries that enabled effective treatments for the different classes of diseases caused by bacteria. However, the indiscriminate use of these drugs allowed the emergence of resistance mechanisms of these microorganisms against the available drugs. In addition, the constant discoveries in the 20th century generated a shortage of new molecules, worrying health agencies and professionals about the appearance of multidrug-resistant strains against available drugs. In this context, the advances of recent years in molecular biology and microbiology have allowed new perspectives in drug design and development, using the findings related to the mechanisms of bacterial resistance to generate new drugs that are not affected by such mechanisms and supply new molecules to be used to treat resistant bacterial infections. Besides, a promising strategy against bacterial resistance is the combination of drugs through adjuvants, providing new expectations in designing new antibiotics and new antimicrobial therapies. Thus, this manuscript will address the main mechanisms of bacterial resistance under the understanding of medicinal chemistry, showing the main active compounds against efflux mechanisms, and also the application of the use of drug delivery systems, and finally, the main potential natural products as adjuvants or with promising activity against resistant strains.
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Affiliation(s)
- Kadja Luana Chagas Monteiro
- Research Group on Therapeutic Strategies - GPET, Laboratory of Synthesis and Research in Medicinal Chemistry - LSPMED, Institute of Chemistry and Biotechnology, Federal University of Alagoas, 57072-970, Maceió, Alagoas, Brazil
| | - Osmar Nascimento Silva
- Faculty of Pharmacy, University Center of Anápolis, Unievangélica, 75083-515, Anápolis, Goiás, Brazil
| | - Igor José Dos Santos Nascimento
- Research Group on Therapeutic Strategies - GPET, Laboratory of Synthesis and Research in Medicinal Chemistry - LSPMED, Institute of Chemistry and Biotechnology, Federal University of Alagoas, 57072-970, Maceió, Alagoas, Brazil
| | | | | | - Edeildo Ferreira da Silva-Júnior
- Laboratory of Medicinal Chemistry, Institute of Pharmaceutical Sciences, Federal University of Alagoas, 57072-970, Maceió, Alagoas, Brazil
| | - Thiago Mendonça de Aquino
- Research Group on Therapeutic Strategies - GPET, Laboratory of Synthesis and Research in Medicinal Chemistry - LSPMED, Institute of Chemistry and Biotechnology, Federal University of Alagoas, 57072-970, Maceió, Alagoas, Brazil
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7
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Liu G, Stokes JM. A brief guide to machine learning for antibiotic discovery. Curr Opin Microbiol 2022; 69:102190. [PMID: 35963098 DOI: 10.1016/j.mib.2022.102190] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/11/2022] [Accepted: 07/12/2022] [Indexed: 11/03/2022]
Abstract
Rising antibiotic resistance and an alarmingly lean antibiotic pipeline require the adoption of novel approaches to rapidly discover new structural and functional classes of antibiotics. Excitingly, algorithmic approaches to antibiotic discovery are sufficiently advanced to meaningfully influence the antibiotic discovery process. Indeed, once trained on high-quality datasets, contemporary machine-learning and deep-learning models can be used to perform predictions for new antibiotics across vast chemical spaces, orders of magnitude more rapidly than compounds can be screened in the laboratory. This increases the probability of discovering new antibiotics with desirable properties. In this short review, we briefly describe the utility of contemporary machine-learning and deep-learning approaches to guide the discovery of new small-molecule antibiotics and unidentified natural products. We then propose a call to action for more open sharing of high-quality screening datasets to accelerate the rate at which forthcoming antibiotic-prediction models can be trained. Together, we aim to introduce antibiotic discoverers to a sample of recent applications of contemporary algorithmic methods to facilitate the wider adoption of these powerful computational approaches.
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Affiliation(s)
- Gary Liu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
| | - Jonathan M Stokes
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
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Falco A, Adamek M, Pereiro P, Hoole D, Encinar JA, Novoa B, Mallavia R. The Immune System of Marine Organisms as Source for Drugs against Infectious Diseases. Mar Drugs 2022; 20:md20060363. [PMID: 35736166 PMCID: PMC9230875 DOI: 10.3390/md20060363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 05/23/2022] [Accepted: 05/26/2022] [Indexed: 11/16/2022] Open
Abstract
The high proliferation of microorganisms in aquatic environments has allowed their coevolution for billions of years with other living beings that also inhabit these niches. Among the different existing types of interaction, the eternal competition for supremacy between the susceptible species and their pathogens has selected, as part of the effector division of the immune system of the former ones, a vast and varied arsenal of efficient antimicrobial molecules, which is highly amplified by the broad biodiversity radiated, above any others, at the marine habitats. At present, the great recent scientific and technological advances already allow the massive discovery and exploitation of these defense compounds for therapeutic purposes against infectious diseases of our interest. Among them, antimicrobial peptides and antimicrobial metabolites stand out because of the wide dimensions of their structural diversities, mechanisms of action, and target pathogen ranges. This revision work contextualizes the research in this field and serves as a presentation and scope identification of the Special Issue from Marine Drugs journal “The Immune System of Marine Organisms as Source for Drugs against Infectious Diseases”.
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Affiliation(s)
- Alberto Falco
- Institute of Research, Development, and Innovation in Healthcare Biotechnology in Elche (IDiBE), Miguel Hernández University (UMH), 03202 Elche, Spain; (J.A.E.); (R.M.)
- Correspondence: (A.F.); (M.A.)
| | - Mikolaj Adamek
- Fish Disease Research Unit, Institute for Parasitology, University of Veterinary Medicine, 30559 Hannover, Germany
- Correspondence: (A.F.); (M.A.)
| | - Patricia Pereiro
- Institute of Marine Research, Consejo Superior de Investigaciones Científicas (IIM-CSIC), 36208 Vigo, Spain; (P.P.); (B.N.)
| | - David Hoole
- School of Life Sciences, Keele University, Keele ST5 5BG, UK;
| | - José Antonio Encinar
- Institute of Research, Development, and Innovation in Healthcare Biotechnology in Elche (IDiBE), Miguel Hernández University (UMH), 03202 Elche, Spain; (J.A.E.); (R.M.)
| | - Beatriz Novoa
- Institute of Marine Research, Consejo Superior de Investigaciones Científicas (IIM-CSIC), 36208 Vigo, Spain; (P.P.); (B.N.)
| | - Ricardo Mallavia
- Institute of Research, Development, and Innovation in Healthcare Biotechnology in Elche (IDiBE), Miguel Hernández University (UMH), 03202 Elche, Spain; (J.A.E.); (R.M.)
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9
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Modi G, Marqus GM, Vippila MR, Gollapalli DR, Kim Y, Manna AC, Chacko S, Maltseva N, Wang X, Cullinane RT, Zhang Y, Kotler JLM, Kuzmic P, Zhang M, Lawson AP, Joachimiak A, Cheung A, Snider BB, Rothstein DM, Cuny GD, Hedstrom L. The Enzymatic Activity of Inosine 5'-Monophosphate Dehydrogenase May Not Be a Vulnerable Target for Staphylococcus aureus Infections. ACS Infect Dis 2021; 7:3062-3076. [PMID: 34590817 DOI: 10.1021/acsinfecdis.1c00342] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many bacterial pathogens, including Staphylococcus aureus, require inosine 5'-monophosphate dehydrogenase (IMPDH) for infection, making this enzyme a promising new target for antibiotics. Although potent selective inhibitors of bacterial IMPDHs have been reported, relatively few have displayed antibacterial activity. Here we use structure-informed design to obtain inhibitors of S. aureus IMPDH (SaIMPDH) that have potent antibacterial activity (minimal inhibitory concentrations less than 2 μM) and low cytotoxicity in mammalian cells. The physicochemical properties of the most active compounds were within typical Lipinski/Veber space, suggesting that polarity is not a general requirement for achieving antibacterial activity. Five compounds failed to display activity in mouse models of septicemia and abscess infection. Inhibitor-resistant S. aureus strains readily emerged in vitro. Resistance resulted from substitutions in the cofactor/inhibitor binding site of SaIMPDH, confirming on-target antibacterial activity. These mutations decreased the binding of all inhibitors tested, but also decreased catalytic activity. Nonetheless, the resistant strains had comparable virulence to wild-type bacteria. Surprisingly, strains expressing catalytically inactive SaIMPDH displayed only a mild virulence defect. Collectively these observations question the vulnerability of the enzymatic activity of SaIMPDH as a target for the treatment of S. aureus infections, suggesting other functions of this protein may be responsible for its role in infection.
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Affiliation(s)
- Gyan Modi
- Department of Biology, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Gary M. Marqus
- Graduate Program in Chemistry, Brandeis University, Waltham Massachusetts 02453, United States
| | - Mohana Rao Vippila
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Health Building 2, 4849 Calhoun Rd., Houston, Texas 77204, United States
| | | | - Youngchang Kim
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois 60667, United States
- The Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Adhar C. Manna
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, United States
| | - Shibin Chacko
- Department of Biology, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Natalia Maltseva
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois 60667, United States
- The Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Xingyou Wang
- Graduate Program in Chemistry, Brandeis University, Waltham Massachusetts 02453, United States
| | - Ryan T. Cullinane
- Department of Biochemistry, Brandeis University, Massachusetts 02453, United States
| | - Yubo Zhang
- Department of Biochemistry, Brandeis University, Massachusetts 02453, United States
| | - Judy L. M. Kotler
- Graduate Program in Biochemistry and Biophysics, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Petr Kuzmic
- BioKin Ltd., Watertown, Massachusetts 02472, United States
| | - Minjia Zhang
- Department of Biology, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Ann P. Lawson
- Department of Biology, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois 60667, United States
- The Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60367, United States
| | - Ambrose Cheung
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, United States
| | - Barry B. Snider
- Department of Chemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - David M. Rothstein
- David Rothstein Consulting, LLC, Lexington, Massachusetts 02421, United States
| | - Gregory D. Cuny
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Health Building 2, 4849 Calhoun Rd., Houston, Texas 77204, United States
| | - Lizbeth Hedstrom
- Department of Biology, Brandeis University, Waltham, Massachusetts 02453, United States
- Department of Chemistry, Brandeis University, Waltham, Massachusetts 02453, United States
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Sambyal K, Singh RV. Exploitation of E. coli for the production of penicillin G amidase: a tool for the synthesis of semisynthetic β-lactam antibiotics. J Genet Eng Biotechnol 2021; 19:156. [PMID: 34652570 PMCID: PMC8521562 DOI: 10.1186/s43141-021-00263-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/04/2021] [Indexed: 11/10/2022]
Abstract
BACKGROUND Penicillin G amidase/acylases from microbial sources is a unique enzyme that belongs to the N-terminal nucleophilic hydrolase structural superfamily. It catalyzes the selective hydrolysis of side chain amide/acyl bond of penicillins and cephalosporins whereas the labile amide/acyl bond in the β-lactam ring remains intact. This review summarizes the production aspects of PGA from various microbial sources at optimized conditions. The minimal yield from wild strains has been extensively improved using varying strain improvement techniques like recombination and mutagenesis; further applied for the subsequent synthesis of 6-aminopenicillanic acid, which is an intermediate molecule for synthesis of a wide range of novel β-lactam antibiotics. Immobilization of PGA has also been attempted to enhance the durability of enzyme for the industrial purposes. SHORT CONCLUSION The present review provides an emphasis on exploitation of E. coli to enhance the microbial production of PGA. The latest achievements in the production of recombinant enzymes have also been discussed. Besides E. coli, other potent microbial strains with PGA activity must be explored to enhance the yields.
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Affiliation(s)
- Krishika Sambyal
- University Institute of Biotechnology, Chandigarh University, Gharuan, Punjab, India
| | - Rahul Vikram Singh
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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11
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Swietnicki W. Secretory System Components as Potential Prophylactic Targets for Bacterial Pathogens. Biomolecules 2021; 11:892. [PMID: 34203937 PMCID: PMC8232601 DOI: 10.3390/biom11060892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 06/13/2021] [Accepted: 06/14/2021] [Indexed: 01/18/2023] Open
Abstract
Bacterial secretory systems are essential for virulence in human pathogens. The systems have become a target of alternative antibacterial strategies based on small molecules and antibodies. Strategies to use components of the systems to design prophylactics have been less publicized despite vaccines being the preferred solution to dealing with bacterial infections. In the current review, strategies to design vaccines against selected pathogens are presented and connected to the biology of the system. The examples are given for Y. pestis, S. enterica, B. anthracis, S. flexneri, and other human pathogens, and discussed in terms of effectiveness and long-term protection.
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Affiliation(s)
- Wieslaw Swietnicki
- Department of Immunology of Infectious Diseases, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, ul. R. Weigla 12, 53-114 Wroclaw, Poland
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12
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Wei F, Zhang X, Cui P, Gou X, Wang S. Cell-based 3D bionic screening by mimicking the drug-receptor interaction environment in vivo. J Mater Chem B 2021; 9:683-693. [PMID: 33367374 DOI: 10.1039/d0tb02661a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Most small-molecule drugs influence cell behavior through their interaction with one or more cellular proteins. The efficacy is unanticipated in the later stages of drug development if small-molecule drugs are discovered in the absence of a biological context. Bionic screening is an in vivo drug-receptor interaction platform that can identify small molecules with recognized activity, improving the likelihood of drug efficacy in the clinic. Here, we report the design of an innovative cell-based bionic screening system using 3D microcarrier cultures to simulate in vivo conditions and facilitate small-molecule drug discovery. Through its combination with HPLC/MS, the method can comprehensively identify small-molecule lead compounds in arbitrarily complex systems in an unbiased manner. In particular, cell-covered microcarriers provide a high-density of cells for affinity performance assessments in the absence of appreciable cell damage and maintain immunogenicity, the 3D structure of which is similar to tissue morphology in vivo, thereby mimicking in vivo drug-receptor interactions. The method is scalable, easy to handle, and requires minimal optimization across a range of different cell lines to realize high-throughput drug screening for the corresponding diseases. This provides a valuable tool for lead compound discovery in more physiologically relevant systems and may address the lack of clinically available drugs.
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Affiliation(s)
- Fen Wei
- Health Science Center, School of Pharmacy, Xi'an Jiaotong University, 76# Yanta West Road, Xi'an, 710061, China.
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13
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Zhou S, Chen X, Ni X, Liu Y, Zhang H, Dong M, Xia H. Pyridoxal-5'-phosphate-dependent enzyme GenB3 Catalyzes C-3',4'-dideoxygenation in gentamicin biosynthesis. Microb Cell Fact 2021; 20:65. [PMID: 33750386 PMCID: PMC7941887 DOI: 10.1186/s12934-021-01558-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/03/2021] [Indexed: 11/20/2022] Open
Abstract
Background The C-3′,4′-dideoxygenation structure in gentamicin can prevent deactivation by aminoglycoside 3′-phosphotransferase (APH(3′)) in drug-resistant pathogens. However, the enzyme catalyzing the dideoxygenation step in the gentamicin biosynthesis pathway remains unknown. Results Here, we report that GenP catalyzes 3′ phosphorylation of the gentamicin biosynthesis intermediates JI-20A, JI-20Ba, and JI-20B. We further demonstrate that the pyridoxal-5′-phosphate (PLP)-dependent enzyme GenB3 uses these phosphorylated substrates to form 3′,4′-dideoxy-4′,5′-ene-6′-oxo products. The following C-6′-transamination and the GenB4-catalyzed reduction of 4′,5′-olefin lead to the formation of gentamicin C. To the best of our knowledge, GenB3 is the first PLP-dependent enzyme catalyzing dideoxygenation in aminoglycoside biosynthesis. Conclusions This discovery solves a long-standing puzzle in gentamicin biosynthesis and enriches our knowledge of the chemistry of PLP-dependent enzymes. Interestingly, these results demonstrate that to evade APH(3′) deactivation by pathogens, the gentamicin producers evolved a smart strategy, which utilized their own APH(3′) to activate hydroxyls as leaving groups for the 3′,4′-dideoxygenation in gentamicin biosynthesis. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01558-7.
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Affiliation(s)
- Shaotong Zhou
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Benxi, 117004, China
| | - Xiaotang Chen
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Benxi, 117004, China
| | - Xianpu Ni
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Benxi, 117004, China.
| | - Yu Liu
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Benxi, 117004, China
| | - Hui Zhang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Benxi, 117004, China
| | - Min Dong
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Huanzhang Xia
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Benxi, 117004, China.
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14
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Zagui GS, Tonani KAA, Fregonesi BM, Machado GP, Silva TV, Andrade LN, Andrade D, Segura-Muñoz SI. Tertiary hospital sewage as reservoir of bacteria expressing MDR phenotype in Brazil. BRAZ J BIOL 2021; 82:e234471. [PMID: 33681897 DOI: 10.1590/1519-6984.234471] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 07/21/2020] [Indexed: 11/22/2022] Open
Abstract
High doses of antibiotics used in hospitals can affect the microbial composition of sewers, selecting resistant bacteria. In this sense, we evaluated the antibiotic resistance profile and the multiresistant phenotype of bacteria isolated in sewage from a tertiary hospital in the interior São Paulo state, Brazil. For bacteria isolation, 10 µL of sewage samples were sown in selective culture media and the isolates were identified using VITEK-2 automatized system. The antibiotic sensitivity test was performed by disk diffusion. High percentages of resistance were found for amoxicillin, ampicillin, ceftazidime, clindamycin, vancomycin and the multidrug-resistant phenotype (MDR) was attributed to 60.7% of the isolates. Our results show bacteria classified as critical/high priority by WHO List of Priority Pathogens (Enterococcus and Staphylococcus aureus resistant to vancomycin and Enterobacteriaceae resistant to carbapenems) in hospital sewage. Therefore, the implementation of disinfection technologies for hospital sewage would reduce the bacterial load in the sewage that will reach urban wastewater treatment plants, minimizing superficial water contamination and bacterial resistance spread in the environment.
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Affiliation(s)
- G S Zagui
- Universidade de São Paulo - USP, Escola de Enfermagem de Ribeirão Preto, Departamento de Enfermagem Materno-Infantil e Saúde Pública, Ribeirão Preto, SP, Brasil
| | - K A A Tonani
- Universidade de São Paulo - USP, Escola de Enfermagem de Ribeirão Preto, Departamento de Enfermagem Materno-Infantil e Saúde Pública, Ribeirão Preto, SP, Brasil
| | - B M Fregonesi
- Universidade de São Paulo - USP, Escola de Enfermagem de Ribeirão Preto, Departamento de Enfermagem Materno-Infantil e Saúde Pública, Ribeirão Preto, SP, Brasil
| | - G P Machado
- Universidade de São Paulo - USP, Escola de Enfermagem de Ribeirão Preto, Departamento de Enfermagem Materno-Infantil e Saúde Pública, Ribeirão Preto, SP, Brasil
| | - T V Silva
- Universidade de São Paulo - USP, Escola de Enfermagem de Ribeirão Preto, Departamento de Enfermagem Materno-Infantil e Saúde Pública, Ribeirão Preto, SP, Brasil
| | - L N Andrade
- Universidade de São Paulo - USP, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Ribeirão Preto, SP, Brasil
| | - D Andrade
- Universidade de Ribeirão Preto, Escola de Enfermagem de Ribeirão Preto, Departamento de Enfermagem Geral e Especializada, Ribeirão Preto, SP, Brasil
| | - S I Segura-Muñoz
- Universidade de São Paulo - USP, Escola de Enfermagem de Ribeirão Preto, Departamento de Enfermagem Materno-Infantil e Saúde Pública, Ribeirão Preto, SP, Brasil
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15
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Fullam E, Young RJ. Physicochemical properties and Mycobacterium tuberculosis transporters: keys to efficacious antitubercular drugs? RSC Med Chem 2020; 12:43-56. [PMID: 34041481 PMCID: PMC8130550 DOI: 10.1039/d0md00265h] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/15/2020] [Indexed: 12/14/2022] Open
Abstract
Securing novel, safe, and effective medicines to treat Mycobacterium tuberculosis remains an elusive goal, particularly influenced by the largely impervious Mtb envelope that limits exposure and thus efficacy of inhibitors at their cellular and periplasmic targets. The impact of physicochemical properties on pharmacokinetic parameters that govern oral absorption and exposure at sites of infection is considered alongside how these properties influence penetration of the Mtb envelope, with the likely influence of transporter proteins. The findings are discussed to benchmark current drugs and the emerging pipeline, whilst considering tactics for future rational and targeted design strategies, based around emerging data on Mtb transporters and their structures and functions.
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Affiliation(s)
- Elizabeth Fullam
- School of Life Sciences, University of Warwick Coventry CV4 7AL UK
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16
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Cruz CD, Wrigstedt P, Moslova K, Iashin V, Mäkkylä H, Ghemtio L, Heikkinen S, Tammela P, Perea-Buceta JE. Installation of an aryl boronic acid function into the external section of N-aryl-oxazolidinones: Synthesis and antimicrobial evaluation. Eur J Med Chem 2020; 211:113002. [PMID: 33223262 DOI: 10.1016/j.ejmech.2020.113002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/02/2020] [Accepted: 11/04/2020] [Indexed: 10/23/2022]
Abstract
N-aryl-oxazolidinones is a prominent family of antimicrobials used for treating infections caused by clinically prevalent Gram-positive bacteria. Recently, boron-containing compounds have displayed intriguing potential in the antibiotic discovery setting. Herein, we report the unprecedented introduction of a boron-containing moiety such as an aryl boronic acid in the external region of the oxazolidinone structure via a chemoselective acyl coupling reaction. As a result, we accessed a series of analogues with a distal aryl boronic pharmacophore on the oxazolidinone scaffold. We identified that a peripheric linear conformation coupled with freedom of rotation and no further substitution on the external aryl boronic ring, an amido linkage with hydrogen bonding character, in addition to a para-relative disposition between boronic group and linker, are the optimal combination of structural features in this series for antimicrobial activity. In comparison to linezolid, the analogue comprising all those features, compound 20b, displayed levels of antimicrobial activity augmented by an eight-fold to a thirty-two-fold against a panel of Gram-positive strains, and a near one hundred-fold against Escherichia coli JW5503, a Gram-negative mutant strain with a defective efflux capability.
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Affiliation(s)
- Cristina D Cruz
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, 00014, Finland
| | - Pauli Wrigstedt
- Department of Chemistry, Faculty of Science, University of Helsinki, P.O. Box 55, 00014, Finland
| | - Karina Moslova
- Department of Chemistry, Faculty of Science, University of Helsinki, P.O. Box 55, 00014, Finland
| | - Vladimir Iashin
- Department of Chemistry, Faculty of Science, University of Helsinki, P.O. Box 55, 00014, Finland
| | - Heidi Mäkkylä
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, 00014, Finland
| | - Léo Ghemtio
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, 00014, Finland
| | - Sami Heikkinen
- Department of Chemistry, Faculty of Science, University of Helsinki, P.O. Box 55, 00014, Finland
| | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, 00014, Finland
| | - Jesus E Perea-Buceta
- Department of Chemistry, Faculty of Science, University of Helsinki, P.O. Box 55, 00014, Finland.
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17
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Mansbach RA, Leus IV, Mehla J, Lopez CA, Walker JK, Rybenkov VV, Hengartner NW, Zgurskaya HI, Gnanakaran S. Machine Learning Algorithm Identifies an Antibiotic Vocabulary for Permeating Gram-Negative Bacteria. J Chem Inf Model 2020; 60:2838-2847. [PMID: 32453589 DOI: 10.1021/acs.jcim.0c00352] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Drug discovery faces a crisis. The industry has used up the "obvious" space in which to find novel drugs for biomedical applications, and productivity is declining. One strategy to combat this is rational approaches to expand the search space without relying on chemical intuition, to avoid rediscovery of similar spaces. In this work, we present proof of concept of an approach to rationally identify a "chemical vocabulary" related to a specific drug activity of interest without employing known rules. We focus on the pressing concern of multidrug resistance in Pseudomonas aeruginosa by searching for submolecules that promote compound entry into this bacterium. By synergizing theory, computation, and experiment, we validate our approach, explain the molecular mechanism behind identified fragments promoting compound entry, and select candidate compounds from an external library that display good permeation ability.
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Affiliation(s)
- Rachael A Mansbach
- Department of Theoretical Biology and Biophysics, Los Alamos National Lab, MS-K710, P.O. Box 1663, Los Alamos, New Mexico 87545-0001, United States
| | - Inga V Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, SLSRC, Rm 1000, Norman, Oklahoma 73019-5251, United States
| | - Jitender Mehla
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, SLSRC, Rm 1000, Norman, Oklahoma 73019-5251, United States
| | - Cesar A Lopez
- Department of Theoretical Biology and Biophysics, Los Alamos National Lab, MS-K710, P.O. Box 1663, Los Alamos, New Mexico 87545-0001, United States
| | - John K Walker
- Pharmacology and Physiological Science, School of Medicine, Saint Louis University, Schwitalla Hall, Room M362, St. Louis, Missouri 63104, United States
| | - Valentin V Rybenkov
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, SLSRC, Rm 1000, Norman, Oklahoma 73019-5251, United States
| | - Nicolas W Hengartner
- Department of Theoretical Biology and Biophysics, Los Alamos National Lab, MS-K710, P.O. Box 1663, Los Alamos, New Mexico 87545-0001, United States
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, SLSRC, Rm 1000, Norman, Oklahoma 73019-5251, United States
| | - S Gnanakaran
- Department of Theoretical Biology and Biophysics, Los Alamos National Lab, MS-K710, P.O. Box 1663, Los Alamos, New Mexico 87545-0001, United States
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18
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Recent Studies on the Antimicrobial Activity of Transition Metal Complexes of Groups 6–12. CHEMISTRY-SWITZERLAND 2020. [DOI: 10.3390/chemistry2020026] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Antimicrobial resistance is an increasingly serious threat to global public health that requires innovative solutions to counteract new resistance mechanisms emerging and spreading globally in infectious pathogens. Classic organic antibiotics are rapidly exhausting the structural variations available for an effective antimicrobial drug and new compounds emerging from the industrial pharmaceutical pipeline will likely have a short-term and limited impact before the pathogens can adapt. Inorganic and organometallic complexes offer the opportunity to discover and develop new active antimicrobial agents by exploiting their wide range of three-dimensional geometries and virtually infinite design possibilities that can affect their substitution kinetics, charge, lipophilicity, biological targets and modes of action. This review describes recent studies on the antimicrobial activity of transition metal complexes of groups 6–12. It focuses on the effectiveness of the metal complexes in relation to the rich structural chemical variations of the same. The aim is to provide a short vade mecum for the readers interested in the subject that can complement other reviews.
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19
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Frei A, Amado M, Cooper MA, Blaskovich MAT. Light-Activated Rhenium Complexes with Dual Mode of Action against Bacteria. Chemistry 2020; 26:2852-2858. [PMID: 31788867 PMCID: PMC7687258 DOI: 10.1002/chem.201904689] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/12/2019] [Indexed: 12/20/2022]
Abstract
New antibiotics and innovative approaches to kill drug-resistant bacteria are urgently needed. Metal complexes offer access to alternative modes of action but have only sparingly been investigated in antibacterial drug discovery. We have developed a light-activated rhenium complex with activity against drug-resistant S. aureus and E. coli. The activity profile against mutant strains combined with assessments of cellular uptake and synergy suggest two distinct modes of action.
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Affiliation(s)
- Angelo Frei
- Institute for Molecular BioscienceThe University of QueenslandSt. LuciaQueensland4072Australia
| | - Maite Amado
- Institute for Molecular BioscienceThe University of QueenslandSt. LuciaQueensland4072Australia
| | - Matthew A. Cooper
- Institute for Molecular BioscienceThe University of QueenslandSt. LuciaQueensland4072Australia
| | - Mark A. T. Blaskovich
- Institute for Molecular BioscienceThe University of QueenslandSt. LuciaQueensland4072Australia
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20
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Ban YH, Song MC, Park JW, Yoon YJ. Minor components of aminoglycosides: recent advances in their biosynthesis and therapeutic potential. Nat Prod Rep 2020; 37:301-311. [DOI: 10.1039/c9np00041k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
This Highlight covers the recent advances in the biosynthetic pathways of aminoglycosides including their minor components, together with the therapeutic potential for minor aminoglycoside components and semi-synthetic aminoglycosides.
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Affiliation(s)
- Yeon Hee Ban
- Department of Chemistry and Nanoscience
- Ewha Womans University
- Seoul 03760
- Republic of Korea
| | - Myoung Chong Song
- Department of Chemistry and Nanoscience
- Ewha Womans University
- Seoul 03760
- Republic of Korea
| | - Je Won Park
- School of Biosystems and Biomedical Sciences
- Korea University
- Seoul 02841
- Republic of Korea
| | - Yeo Joon Yoon
- Department of Chemistry and Nanoscience
- Ewha Womans University
- Seoul 03760
- Republic of Korea
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21
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Smitten KL, Southam HM, de la Serna JB, Gill MR, Jarman PJ, Smythe CGW, Poole RK, Thomas JA. Using Nanoscopy To Probe the Biological Activity of Antimicrobial Leads That Display Potent Activity against Pathogenic, Multidrug Resistant, Gram-Negative Bacteria. ACS NANO 2019; 13:5133-5146. [PMID: 30964642 DOI: 10.1021/acsnano.8b08440] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Medicinal leads that are also compatible with imaging technologies are attractive, as they facilitate the development of therapeutics through direct mechanistic observations at the molecular level. In this context, the uptake and antimicrobial activities of several luminescent dinuclear RuII complexes against E. coli were assessed and compared to results obtained for another ESKAPE pathogen, the Gram-positive major opportunistic pathogen Enterococcus faecalis, V583. The most promising lead displays potent activity, particularly against the Gram-negative bacteria, and potency is retained in the uropathogenic multidrug resistant EC958 ST131 strain. Exploiting the inherent luminescent properties of this complex, super-resolution STED nanoscopy was used to image its initial localization at/in cellular membranes and its subsequent transfer to the cell poles. Membrane damage assays confirm that the complex disrupts the bacterial membrane structure before internalization. Mammalian cell culture and animal model studies indicate that the complex is not toxic to eukaryotes, even at concentrations that are several orders of magnitude higher than its minimum inhibitory concentration (MIC). Taken together, these results have identified a lead molecular architecture for hard-to-treat, multiresistant, Gram-negative bacteria, which displays activities that are already comparable to optimized natural product-based leads.
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Affiliation(s)
- Kirsty L Smitten
- Department of Chemistry , The University of Sheffield , Western Bank , Sheffield S3 7HF , U.K
| | - Hannah M Southam
- Department of Molecular Biology and Biotechnology , The University of Sheffield , Western Bank , Sheffield S10 2TN , U.K
| | - Jorge Bernardino de la Serna
- Central Laser Facility, Rutherford Appleton Laboratory, Research Complex at Harwell , Science and Technology Facilities Council , Harwell-Oxford , Didcot OX11 0QX , U.K
- Department of Physics , King's College London , London WC2R 2LS , U.K
| | - Martin R Gill
- Department of Chemistry , The University of Sheffield , Western Bank , Sheffield S3 7HF , U.K
| | - Paul J Jarman
- Department of Biomedical Science , The University of Sheffield , Western Bank , Sheffield S10 2TN , U.K
| | - Carl G W Smythe
- Department of Biomedical Science , The University of Sheffield , Western Bank , Sheffield S10 2TN , U.K
| | - Robert K Poole
- Department of Molecular Biology and Biotechnology , The University of Sheffield , Western Bank , Sheffield S10 2TN , U.K
| | - Jim A Thomas
- Department of Chemistry , The University of Sheffield , Western Bank , Sheffield S3 7HF , U.K
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22
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Konaklieva MI. Addressing Antimicrobial Resistance through New Medicinal and Synthetic Chemistry Strategies. SLAS DISCOVERY 2018; 24:419-439. [PMID: 30523713 DOI: 10.1177/2472555218812657] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Over the past century, a multitude of derivatives of structural scaffolds with established antimicrobial potential have been prepared and tested, and a variety of new scaffolds have emerged. The effectiveness of antibiotics, however, is in sharp decline because of the emergence of drug-resistant microorganisms. The prevalence of drug resistance, both in clinical and community settings, is a consequence of bacterial ingenuity in altering pathways and/or cell morphology, making it a persistent threat to human health. The fundamental ability of pathogens to survive in a multitude of habitats can be triggered by recognition of chemical signals that warn organisms of exposure to a potentially harmful environment. Host immune defenses, including reactive oxygen intermediates and antibacterial substances, are among the multitude of chemical signals that can subsequently trigger expression of phenotypes better adapted for survival in that hostile environment. Thus, resistance development appears to be unavoidable, which leads to the conclusion that developing an alternative perspective for treatment options is vital. This review will discuss emerging medicinal chemistry approaches for addressing the global multidrug resistance in the 21st century.
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23
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Jaggupilli A, Singh N, De Jesus VC, Gounni MS, Dhanaraj P, Chelikani P. Chemosensory bitter taste receptors (T2Rs) are activated by multiple antibiotics. FASEB J 2018; 33:501-517. [PMID: 30011231 DOI: 10.1096/fj.201800521rr] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Many medications including antibiotics taste bitter. The potency of these antibiotics on the 25 bitter taste receptors (T2Rs) in humans remains poorly understood. Here we characterize by sensory and structure-function analyses how antibiotics frequently used to treat airway infections in cystic fibrosis activate multiple human T2Rs. The potency of the broad-spectrum antibiotics, tobramycin, levofloxacin, and azithromycin on the highly expressed T2Rs in airways, T2R4, T2R14, and T2R20 was pursued. The amino acids and structural features of T2R4, T2R14, and T2R20 important for antibiotic binding were characterized by mutational analysis in heterologous cell-based assays. Strikingly, extracellular loop 2 in T2Rs performs a key function in binding to antibiotics with contribution from residues in transmembrane helices. Our results suggest that different antibiotics activate multiple T2Rs with different potencies. An understanding of the nonantibiotic and physiologic effects mediated through T2Rs on the host cells is much needed.-Jaggupilli, A., Singh, N., De Jesus, V. C., Gounni, M. S., Dhanaraj, P., Chelikani, P. Chemosensory bitter taste receptors (T2Rs) are activated by multiple antibiotics.
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Affiliation(s)
- Appalaraju Jaggupilli
- Manitoba Chemosensory Biology Research Group and Department of Oral Biology, University of Manitoba, Children's Hospital Research Institute of Manitoba (CHRIM), Winnipeg, Manitoba, Canada
| | - Nisha Singh
- Manitoba Chemosensory Biology Research Group and Department of Oral Biology, University of Manitoba, Children's Hospital Research Institute of Manitoba (CHRIM), Winnipeg, Manitoba, Canada
| | - Vivianne Cruz De Jesus
- Manitoba Chemosensory Biology Research Group and Department of Oral Biology, University of Manitoba, Children's Hospital Research Institute of Manitoba (CHRIM), Winnipeg, Manitoba, Canada
| | - Mohamed Soussi Gounni
- Manitoba Chemosensory Biology Research Group and Department of Oral Biology, University of Manitoba, Children's Hospital Research Institute of Manitoba (CHRIM), Winnipeg, Manitoba, Canada
| | - Premnath Dhanaraj
- Manitoba Chemosensory Biology Research Group and Department of Oral Biology, University of Manitoba, Children's Hospital Research Institute of Manitoba (CHRIM), Winnipeg, Manitoba, Canada
| | - Prashen Chelikani
- Manitoba Chemosensory Biology Research Group and Department of Oral Biology, University of Manitoba, Children's Hospital Research Institute of Manitoba (CHRIM), Winnipeg, Manitoba, Canada
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24
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Cox G, Ejim L, Stogios PJ, Koteva K, Bordeleau E, Evdokimova E, Sieron AO, Savchenko A, Serio AW, Krause KM, Wright GD. Plazomicin Retains Antibiotic Activity against Most Aminoglycoside Modifying Enzymes. ACS Infect Dis 2018; 4:980-987. [PMID: 29634241 DOI: 10.1021/acsinfecdis.8b00001] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Plazomicin is a next-generation, semisynthetic aminoglycoside antibiotic currently under development for the treatment of infections due to multidrug-resistant Enterobacteriaceae. The compound was designed by chemical modification of the natural product sisomicin to provide protection from common aminoglycoside modifying enzymes that chemically alter these drugs via N-acetylation, O-adenylylation, or O-phosphorylation. In this study, plazomicin was profiled against a panel of isogenic strains of Escherichia coli individually expressing twenty-one aminoglycoside resistance enzymes. Plazomicin retained antibacterial activity against 15 of the 17 modifying enzyme-expressing strains tested. Expression of only two of the modifying enzymes, aac(2')-Ia and aph(2″)-IVa, decreased plazomicin potency. On the other hand, expression of 16S rRNA ribosomal methyltransferases results in a complete lack of plazomicin potency. In vitro enzymatic assessment confirmed that AAC(2')-Ia and APH(2'')-IVa (aminoglycoside acetyltransferase, AAC; aminoglycoside phosphotransferase, APH) were able to utilize plazomicin as a substrate. AAC(2')-Ia and APH(2'')-IVa are limited in their distribution to Providencia stuartii and Enterococci, respectively. These data demonstrate that plazomicin is not modified by a broad spectrum of common aminoglycoside modifying enzymes including those commonly found in Enterobacteriaceae. However, plazomicin is inactive in the presence of 16S rRNA ribosomal methyltransferases, which should be monitored in future surveillance programs.
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Affiliation(s)
- Georgina Cox
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, Ontario L8N 4K1, Canada
| | - Linda Ejim
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, Ontario L8N 4K1, Canada
| | - Peter J. Stogios
- Center for Structural Genomics of Infectious Diseases (CSGID) and Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5G 1L6, Canada
| | - Kalinka Koteva
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, Ontario L8N 4K1, Canada
| | - Emily Bordeleau
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, Ontario L8N 4K1, Canada
| | - Elena Evdokimova
- Center for Structural Genomics of Infectious Diseases (CSGID) and Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5G 1L6, Canada
| | - Arthur O. Sieron
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, Ontario L8N 4K1, Canada
| | - Alexei Savchenko
- Center for Structural Genomics of Infectious Diseases (CSGID) and Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5G 1L6, Canada
- Department of Microbiology, Immunology and Infectious Diseases, Health Research Innovation Centre, University of Calgary, 3330 Hospital Drive NW, HRIC-2C66, Calgary, Alberta T2N 4N1, Canada
| | - Alisa W. Serio
- Achaogen, One Tower Place, Suite 300, South San Francisco, California 94080, United States
| | - Kevin M. Krause
- Achaogen, One Tower Place, Suite 300, South San Francisco, California 94080, United States
| | - Gerard D. Wright
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, Ontario L8N 4K1, Canada
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25
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Abstract
Our limited understanding of the molecular basis for compound entry into and efflux out of Gram-negative bacteria is now recognized as a key bottleneck for the rational discovery of novel antibacterial compounds. Traditional, large-scale biochemical or target-agnostic phenotypic antibacterial screening efforts have, as a result, not been very fruitful. A main driver of this knowledge gap has been the historical lack of predictive cellular assays, tools, and models that provide structure-activity relationships to inform optimization of compound accumulation. A variety of recent approaches has recently been described to address this conundrum. This Perspective explores these approaches and considers ways in which their integration could successfully redirect antibacterial drug discovery efforts.
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Affiliation(s)
- Rubén Tommasi
- Entasis Therapeutics, Inc., 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Ramkumar Iyer
- Entasis Therapeutics, Inc., 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Alita A. Miller
- Entasis Therapeutics, Inc., 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
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26
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The evolution of substrate discrimination in macrolide antibiotic resistance enzymes. Nat Commun 2018; 9:112. [PMID: 29317655 PMCID: PMC5760710 DOI: 10.1038/s41467-017-02680-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 12/19/2017] [Indexed: 12/13/2022] Open
Abstract
The production of antibiotics by microbes in the environment and their use in medicine and agriculture select for existing and emerging resistance. To address this inevitability, prudent development of antibiotic drugs requires careful consideration of resistance evolution. Here, we identify the molecular basis for expanded substrate specificity in MphI, a macrolide kinase (Mph) that does not confer resistance to erythromycin, in contrast to other known Mphs. Using a combination of phylogenetics, drug-resistance phenotypes, and in vitro enzyme assays, we find that MphI and MphK phosphorylate erythromycin poorly resulting in an antibiotic-sensitive phenotype. Using likelihood reconstruction of ancestral sequences and site-saturation combinatorial mutagenesis, supported by Mph crystal structures, we determine that two non-obvious mutations in combination expand the substrate range. This approach should be applicable for studying the functional evolution of any antibiotic resistance enzyme and for evaluating the evolvability of resistance enzymes to new generations of antibiotic scaffolds. New antibiotics with reduced potential for resistance are urgently needed. Here, the authors use a multidisciplinary approach to characterize substrate discrimination in macrolide resistance kinases and present a strategy for the prediction of mutations that expand the substrate range of antibiotic-inactivating enzymes.
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27
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Non-protein biologic therapeutics. Curr Opin Biotechnol 2017; 53:65-75. [PMID: 29289799 DOI: 10.1016/j.copbio.2017.12.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 12/10/2017] [Accepted: 12/11/2017] [Indexed: 01/15/2023]
Abstract
While the therapeutic biologics are dominated by therapeutic proteins, particularly monoclonal antibodies, a wide range of non-protein therapeutic biologics are rapidly gaining ground both in clinical studies and approved products. Many of these first-in-class therapies provide novel treatment modalities and address previously untreatable conditions or undruggable targets. In particular, novel treatments for rare genetic disorders and qualitatively different oncology therapeutics have been approved in the last two years. This review discusses recent advances in peptide, nucleic acid, carbohydrate, vaccine, and cell-based therapies as well as the manufacturing and commercialization challenges associated with these novel therapeutics.
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28
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Abstract
Natural products have served as powerful therapeutics against pathogenic bacteria since the golden age of antibiotics of the mid-20th century. However, the increasing frequency of antibiotic-resistant infections clearly demonstrates that new antibiotics are critical for modern medicine. Because combinatorial approaches have not yielded effective drugs, we propose that the development of new antibiotics around proven natural scaffolds is the best short-term solution to the rising crisis of antibiotic resistance. We analyze herein synthetic approaches aiming to reengineer natural products into potent antibiotics. Furthermore, we discuss approaches in modulating quorum sensing and biofilm formation as a nonlethal method, as well as narrow-spectrum pathogen-specific antibiotics, which are of interest given new insights into the implications of disrupting the microbiome.
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Affiliation(s)
- Sean E. Rossiter
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Madison H. Fletcher
- Department of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - William M. Wuest
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
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29
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McKerrow JH, Lipinski CA. The rule of five should not impede anti-parasitic drug development. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2017. [PMID: 28623818 PMCID: PMC5473536 DOI: 10.1016/j.ijpddr.2017.05.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
The “rule of 5” has become a mainstay of decision-making in the pharmaceutical industry as well as in nonindustrial (academic and institutional) drug development. However the authors of the original paper never intended for “double cutoffs” to preclude development of new drug leads for parasitic diseases. “rule of 5” is a mainstay of decision-making in drug screening efforts. Acts as an absorption-permeability alert procedure to guide medicinal chemists. Never intended to apply to parasitic infectious diseases. Should not impede anti-parasitic drug development.
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Affiliation(s)
- James H McKerrow
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, United States.
| | - Christopher A Lipinski
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, United States
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30
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Park JW, Ban YH, Nam SJ, Cha SS, Yoon YJ. Biosynthetic pathways of aminoglycosides and their engineering. Curr Opin Biotechnol 2017; 48:33-41. [PMID: 28365471 DOI: 10.1016/j.copbio.2017.03.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 02/27/2017] [Accepted: 03/15/2017] [Indexed: 11/30/2022]
Abstract
Despite decades long clinical usage, aminoglycosides still remain a valuable pharmaceutical source for fighting Gram-negative bacterial pathogens, and their newly identified bioactivities are also renewing interest in this old class of antibiotics. As Nature's gift, some aminoglycosides possess natural defensive structural elements that can circumvent drug resistance mechanisms. Thus, a detailed understanding of aminoglycoside biosynthesis will enable us to apply Nature's biosynthetic strategy towards expanding structural diversity in order to produce novel and more robust aminoglycoside analogs. The engineered biosynthesis of novel aminoglycosides is required not only to develop effective therapeutics against the emerging 'superbugs' but also to reinvigorate antibiotic lead discovery in readiness for the emerging post-antibiotic era.
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Affiliation(s)
- Je Won Park
- School of Biosystem and Biomedical Science, Korea University, Seoul 02841, Republic of Korea
| | - Yeon Hee Ban
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Sun-Shin Cha
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Yeo Joon Yoon
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea.
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31
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Cox G, Sieron A, King AM, De Pascale G, Pawlowski AC, Koteva K, Wright GD. A Common Platform for Antibiotic Dereplication and Adjuvant Discovery. Cell Chem Biol 2017; 24:98-109. [DOI: 10.1016/j.chembiol.2016.11.011] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/07/2016] [Accepted: 11/17/2016] [Indexed: 12/20/2022]
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