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Theuretzbacher U, Blasco B, Duffey M, Piddock LJV. Unrealized targets in the discovery of antibiotics for Gram-negative bacterial infections. Nat Rev Drug Discov 2023; 22:957-975. [PMID: 37833553 DOI: 10.1038/s41573-023-00791-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2023] [Indexed: 10/15/2023]
Abstract
Advances in areas that include genomics, systems biology, protein structure determination and artificial intelligence provide new opportunities for target-based antibacterial drug discovery. The selection of a 'good' new target for direct-acting antibacterial compounds is the first decision, for which multiple criteria must be explored, integrated and re-evaluated as drug discovery programmes progress. Criteria include essentiality of the target for bacterial survival, its conservation across different strains of the same species, bacterial species and growth conditions (which determines the spectrum of activity of a potential antibiotic) and the level of homology with human genes (which influences the potential for selective inhibition). Additionally, a bacterial target should have the potential to bind to drug-like molecules, and its subcellular location will govern the need for inhibitors to penetrate one or two bacterial membranes, which is a key challenge in targeting Gram-negative bacteria. The risk of the emergence of target-based drug resistance for drugs with single targets also requires consideration. This Review describes promising but as-yet-unrealized targets for antibacterial drugs against Gram-negative bacteria and examples of cognate inhibitors, and highlights lessons learned from past drug discovery programmes.
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Affiliation(s)
| | - Benjamin Blasco
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Maëlle Duffey
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Laura J V Piddock
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland.
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2
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Calvo-Peña C, Cobos R, Sánchez-López JM, Ibañez A, Coque JJR. Albocycline Is the Main Bioactive Antifungal Compound Produced by Streptomyces sp. OR6 against Verticillium dahliae. PLANTS (BASEL, SWITZERLAND) 2023; 12:3612. [PMID: 37896074 PMCID: PMC10610244 DOI: 10.3390/plants12203612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/11/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023]
Abstract
Verticillium wilt is a soil-borne fungal disease that affects olive trees (Olea europaea) and poses a serious threat to their cultivation. The causal agent of this disease is Verticillium dahliae, a pathogen that is difficult to control with conventional methods. Therefore, there is a need to explore alternative strategies for the management of Verticillium wilt. In this study, we aimed to isolate and characterize actinobacteria from the rhizosphere of olive trees that could act as potential biocontrol agents against V. dahliae. We selected a Streptomyces sp. OR6 strain based on its in vitro antifungal activity and its ability to suppress the pathogen growth in soil samples. We identified the main active compound produced by this strain as albocycline, a macrolide polyketide with known antibacterial properties and some antifungal activity. Albocycline was able to efficiently suppress the germination of conidiospores. To our knowledge, this is the first report of albocycline as an effective agent against V. dahliae. Our results suggest that Streptomyces sp. OR6, or other albocycline-producing strains, could be used as a promising tool for the biological control of Verticillium wilt.
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Affiliation(s)
- Carla Calvo-Peña
- Instituto de Investigación de la Viña y el Vino, Escuela de Ingeniería Agraria, Universidad de León, 24009 León, Spain; (C.C.-P.); (A.I.)
| | - Rebeca Cobos
- Instituto de Investigación de la Viña y el Vino, Escuela de Ingeniería Agraria, Universidad de León, 24009 León, Spain; (C.C.-P.); (A.I.)
| | | | - Ana Ibañez
- Instituto de Investigación de la Viña y el Vino, Escuela de Ingeniería Agraria, Universidad de León, 24009 León, Spain; (C.C.-P.); (A.I.)
| | - Juan José R. Coque
- Instituto de Investigación de la Viña y el Vino, Escuela de Ingeniería Agraria, Universidad de León, 24009 León, Spain; (C.C.-P.); (A.I.)
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3
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Kumar G, Engle K. Natural products acting against S. aureus through membrane and cell wall disruption. Nat Prod Rep 2023; 40:1608-1646. [PMID: 37326041 DOI: 10.1039/d2np00084a] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Covering: 2015 to 2022Staphylococcus aureus (S. aureus) is responsible for several community and hospital-acquired infections with life-threatening complications such as bacteraemia, endocarditis, meningitis, liver abscess, and spinal cord epidural abscess. In recent decades, the abuse and misuse of antibiotics in humans, animals, plants, and fungi and the treatment of nonmicrobial diseases have led to the rapid emergence of multidrug-resistant pathogens. The bacterial wall is a complex structure consisting of the cell membrane, peptidoglycan cell wall, and various associated polymers. The enzymes involved in bacterial cell wall synthesis are established antibiotic targets and continue to be a central focus for antibiotic development. Natural products play a vital role in drug discovery and development. Importantly, natural products provide a starting point for active/lead compounds that sometimes need modification based on structural and biological properties to meet the drug criteria. Notably, microorganisms and plant metabolites have contributed as antibiotics for noninfectious diseases. In this study, we have summarized the recent advances in understanding the activity of the drugs or agents of natural origin that directly inhibit the bacterial membrane, membrane components, and membrane biosynthetic enzymes by targeting membrane-embedded proteins. We also discussed the unique aspects of the active mechanisms of established antibiotics or new agents.
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Affiliation(s)
- Gautam Kumar
- Department of Natural Products, Chemical Sciences, National Institute of Pharmaceutical Education and Research-Hyderabad, Hyderabad, Balanagar, 500037, India.
| | - Kritika Engle
- Department of Natural Products, Chemical Sciences, National Institute of Pharmaceutical Education and Research-Hyderabad, Hyderabad, Balanagar, 500037, India.
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Stojković D, Petrović J, Carević T, Soković M, Liaras K. Synthetic and Semisynthetic Compounds as Antibacterials Targeting Virulence Traits in Resistant Strains: A Narrative Updated Review. Antibiotics (Basel) 2023; 12:963. [PMID: 37370282 PMCID: PMC10295040 DOI: 10.3390/antibiotics12060963] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 05/24/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
This narrative review paper provides an up-to-date overview of the potential of novel synthetic and semisynthetic compounds as antibacterials that target virulence traits in resistant strains. The review focused on research conducted in the last five years and investigated a range of compounds including azoles, indoles, thiophenes, glycopeptides, pleuromutilin derivatives, lactone derivatives, and chalcones. The emergence and spread of antibiotic-resistant bacterial strains is a growing public health concern, and new approaches are urgently needed to combat this threat. One promising approach is to target virulence factors, which are essential for bacterial survival and pathogenesis, but not for bacterial growth. By targeting virulence factors, it may be possible to reduce the severity of bacterial infections without promoting the development of resistance. We discuss the mechanisms of action of the various compounds investigated and their potential as antibacterials. The review highlights the potential of targeting virulence factors as a promising strategy to combat antibiotic resistance and suggests that further research is needed to identify new compounds and optimize their efficacy. The findings of this review suggest that novel synthetic and semisynthetic compounds that target virulence factors have great potential as antibacterials in the fight against antibiotic resistance.
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Affiliation(s)
- Dejan Stojković
- Department of Plant Physiology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11000 Belgrade, Serbia; (D.S.); (J.P.); (T.C.); (M.S.)
| | - Jovana Petrović
- Department of Plant Physiology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11000 Belgrade, Serbia; (D.S.); (J.P.); (T.C.); (M.S.)
| | - Tamara Carević
- Department of Plant Physiology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11000 Belgrade, Serbia; (D.S.); (J.P.); (T.C.); (M.S.)
| | - Marina Soković
- Department of Plant Physiology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11000 Belgrade, Serbia; (D.S.); (J.P.); (T.C.); (M.S.)
| | - Konstantinos Liaras
- Department of Life and Health Sciences, School of Sciences and Engineering, University of Nicosia, 2417 Nicosia, Cyprus
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Kumar G, Kiran Tudu A. Tackling multidrug-resistant Staphylococcus aureus by natural products and their analogues acting as NorA efflux pump inhibitors. Bioorg Med Chem 2023; 80:117187. [PMID: 36731248 DOI: 10.1016/j.bmc.2023.117187] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 01/29/2023]
Abstract
Staphylococcus aureus (S. aureus) is a pathogen responsible for various community and hospital-acquired infections with life-threatening complications like bacteraemia, endocarditis, meningitis, liver abscess, and spinal cord epidural abscess. Antibiotics have been used to treat microbial infections since the introduction of penicillin in 1940. In recent decades, the abuse and misuse of antibiotics in humans, animals, plants, and fungi, including the treatment of non-microbial diseases, have led to the rapid emergence of multidrug-resistant pathogens with increased virulence. Bacteria have developed several complementary mechanisms to avoid the effects of antibiotics. These mechanisms include chemical transformations and enzymatic inactivation of antibiotics, modification of antibiotics' target site, and reduction of intracellular antibiotics concentration by changes in membrane permeability or by the overexpression of efflux pumps (EPs). The strategy to check antibiotic resistance includes synthesis of the antibiotic analogues, or antibiotics are given in combination with the adjuvant. The inhibitors of multidrug EPs are considered promising alternative therapeutic options with the potential to revive the effects of antibiotics and reduce bacterial virulence. Natural products played a vital role in drug discovery and significantly contributed to the area of infectious diseases. Also, natural products provide lead compounds that sometimes need modification based on structural and biological properties to meet the drug criteria. This review discusses natural products and their derived compounds as NorA efflux pump inhibitors (EPIs).
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Affiliation(s)
- Gautam Kumar
- Department of Natural Products, Chemical Sciences, National Institute of Pharmaceutical Education and Research-Hyderabad, Hyderabad, Balanagar, Telangana 500037, India.
| | - Asha Kiran Tudu
- Department of Natural Products, Chemical Sciences, National Institute of Pharmaceutical Education and Research-Hyderabad, Hyderabad, Balanagar, Telangana 500037, India
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A novel milk-derived peptide effectively inhibits Staphylococcus aureus: Interferes with cell wall synthesis, peptidoglycan biosynthesis disruption reaction mechanism, and its application in real milk system. Food Control 2023. [DOI: 10.1016/j.foodcont.2022.109374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Raina D, Kumar C, Kumar V, Khan IA, Saran S. Potential Inhibitors Targeting Escherichia coli UDP-N-Acetylglucosamine Enolpyruvyl Transferase (MurA): An Overview. Indian J Microbiol 2022; 62:11-22. [PMID: 35068599 PMCID: PMC8758813 DOI: 10.1007/s12088-021-00988-6] [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: 06/06/2021] [Accepted: 10/12/2021] [Indexed: 11/28/2022] Open
Abstract
Antibiotic resistance is one of the biggest challenges that is escalating and affecting humanity across the globe. To overcome this increasing burden of resistance, discovering novel hits by targeting the enzymes involved in peptidoglycan (murein) biosynthesis has always been considered better in antimicrobial drug discovery. UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) enzyme has been identified as essential for Escherichia coli survival and catalyzes the early-stage step in bacterial cell wall synthesis. The present article gives a brief overview of the role of enzymes in peptidoglycan synthesis and MurA enzyme (previously known as MurZ in E. coli), in particular, including its structural and active site features. This review also provides an insight into the current knowledge of the reported MurA inhibitors, their mechanism of action and drawbacks of these hits that hinder their clinical trials, which would be helpful for synthesis and discovering potent molecules. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12088-021-00988-6.
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Affiliation(s)
- Diksha Raina
- Fermentation and Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001 India ,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Chetan Kumar
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India ,Natural Product and Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001 India
| | - Vinod Kumar
- Fermentation and Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001 India ,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Inshad Ali Khan
- Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan 305817 India
| | - Saurabh Saran
- Fermentation and Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001 India ,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
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Sun M, Qin J, Kang Y, Zhang Y, Ba M, Yang H, Duan Y, Yao Y. 2-Methoxydiol derivatives as new tubulin and HDAC dual-targeting inhibitors, displaying antitumor and antiangiogenic response. Bioorg Chem 2022; 120:105625. [DOI: 10.1016/j.bioorg.2022.105625] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/29/2021] [Accepted: 01/11/2022] [Indexed: 12/22/2022]
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Hurley MFD, Northrup JD, Ge Y, Schafmeister CE, Voelz VA. Metal Cation-Binding Mechanisms of Q-Proline Peptoid Macrocycles in Solution. J Chem Inf Model 2021; 61:2818-2828. [PMID: 34125519 DOI: 10.1021/acs.jcim.1c00447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The rational design of foldable and functionalizable peptidomimetic scaffolds requires the concerted application of both computational and experimental methods. Recently, a new class of designed peptoid macrocycle incorporating spiroligomer proline mimics (Q-prolines) has been found to preorganize when bound by monovalent metal cations. To determine the solution-state structure of these cation-bound macrocycles, we employ a Bayesian inference method (BICePs) to reconcile enhanced-sampling molecular simulations with sparse ROESY correlations from experimental NMR studies to predict and design conformational and binding properties of macrocycles as functional scaffolds for peptidomimetics. Conformations predicted to be most populated in solution were then simulated in the presence of explicit cations to yield trajectories with observed binding events, revealing a highly preorganized all-trans amide conformation, whose formation is likely limited by the slow rate of cis/trans isomerization. Interestingly, this conformation differs from a racemic crystal structure solved in the absence of cation. Free energies of cation binding computed from distance-dependent potentials of mean force suggest Na+ has a higher affinity to the macrocycle than K+, with both cations binding much more strongly in acetonitrile than water. The simulated affinities are able to correctly rank the extent to which different macrocycle sequences exhibit preorganization in the presence of different metal cations and solvents, suggesting our approach is suitable for solution-state computational design.
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Affiliation(s)
- Matthew F D Hurley
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Justin D Northrup
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Yunhui Ge
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | | | - Vincent A Voelz
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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10
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Voelz VA, Ge Y, Raddi RM. Reconciling Simulations and Experiments With BICePs: A Review. Front Mol Biosci 2021; 8:661520. [PMID: 34046431 PMCID: PMC8144449 DOI: 10.3389/fmolb.2021.661520] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 04/12/2021] [Indexed: 02/04/2023] Open
Abstract
Bayesian Inference of Conformational Populations (BICePs) is an algorithm developed to reconcile simulated ensembles with sparse experimental measurements. The Bayesian framework of BICePs enables population reweighting as a post-simulation processing step, with several advantages over existing methods, including the proper use of reference potentials, and the estimation of a Bayes factor-like quantity called the BICePs score for model selection. Here, we summarize the theory underlying this method in context with related algorithms, review the history of BICePs applications to date, and discuss current shortcomings along with future plans for improvement.
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Affiliation(s)
- Vincent A. Voelz
- Department of Chemistry, Temple University, Philadelphia, PA, United States
| | - Yunhui Ge
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, United States
| | - Robert M. Raddi
- Department of Chemistry, Temple University, Philadelphia, PA, United States
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Scherzi T, D'Ambrosio EA, Daher SS, Grimes CL, Dunman PM, Andrade RB. Staphylococcus aureus resistance to albocycline can be achieved by mutations that alter cellular NAD/PH pools. Bioorg Med Chem 2021; 32:115995. [PMID: 33477021 PMCID: PMC7891091 DOI: 10.1016/j.bmc.2021.115995] [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: 10/28/2020] [Accepted: 12/31/2020] [Indexed: 11/21/2022]
Abstract
Small molecule target identification is a critical step in modern antibacterial drug discovery, particularly against multi-drug resistant pathogens. Albocycline (ALB) is a macrolactone natural product with potent activity against methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant S. aureus (VRSA) whose mechanism of action has been elusive to date. Herein, we report biochemical and genomic studies that reveal ALB does not target bacterial peptidoglycan biosynthesis or the ribosome; rather, it appears to modulate NADPH ratios and upregulate redox sensing in the cell consistent with previous studies at Upjohn. Owing to the complexity inherent in biological pathways, further genomic assays are needed to identify the true molecular target(s) of albocycline.
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Affiliation(s)
- Tyler Scherzi
- Department of Microbiology and Immunology, University of Rochester, School of Medicine and Dentistry, Rochester, NY 14642, United States
| | - Elizabeth A D'Ambrosio
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Samer S Daher
- Department of Chemistry, Temple University, Philadelphia, PA 19122, United States
| | - Catherine L Grimes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Paul M Dunman
- Department of Microbiology and Immunology, University of Rochester, School of Medicine and Dentistry, Rochester, NY 14642, United States
| | - Rodrigo B Andrade
- Department of Chemistry, Temple University, Philadelphia, PA 19122, United States.
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Daher SS, Franklin KP, Scherzi T, Dunman PM, Andrade RB. Synthesis and biological evaluation of semi-synthetic albocycline analogs. Bioorg Med Chem Lett 2020; 30:127509. [PMID: 32827630 DOI: 10.1016/j.bmcl.2020.127509] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 12/18/2022]
Abstract
Albocycline (ALB) is a unique macrolactone natural product with potent, narrow-spectrum activity against methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-intermediate (VISA), and vancomycin-resistant S. aureus (VRSA) strains (MIC = 0.5-1.0 μg/mL). Described herein is the synthesis and evaluation of a novel series analogs derived from albocycline by functionalization at three specific sites: the C2-C3 enone, the tertiary carbinol at C4, and the allylic C16 methyl group. Exploration of the structure-activity relationships (SAR) by means of minimum inhibitory concentration assays (MICs) revealed that C4 ester analog 6 was twice as potent as ALB, which represents a class of lead compound that can be further studied to address multi-drug resistant pathogens.
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Affiliation(s)
- Samer S Daher
- Department of Chemistry, Temple University, Philadelphia, PA 19122, United States
| | - Kevin P Franklin
- Department of Chemistry, Temple University, Philadelphia, PA 19122, United States
| | - Tyler Scherzi
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, United States
| | - Paul M Dunman
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, United States
| | - Rodrigo B Andrade
- Department of Chemistry, Temple University, Philadelphia, PA 19122, United States.
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