1
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Caso C, Altmann K. Cyclization by Intramolecular Suzuki-Miyaura Cross-Coupling-A Review. Chemistry 2025; 31:e202402664. [PMID: 39385337 PMCID: PMC11711311 DOI: 10.1002/chem.202402664] [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: 07/13/2024] [Revised: 10/03/2024] [Accepted: 10/08/2024] [Indexed: 10/12/2024]
Abstract
Ring systems of all sizes are frequent core or substructures in natural products and they are important elements of many drug molecules, as they often confer high binding affinity to and selectivity for disease-relevant biological targets. A uniform key transformation in the synthesis of such structures is the cyclization step. Among the various approaches that have been developed for ring closure, the intramolecular Suzuki-Miyaura reaction has emerged as a powerful option for the construction of normal- and medium-sized rings as well as macrocycles, due to its stereospecificity, the mild reaction conditions, and the non-toxic nature of the boron by-products. In this review, we summarize the state-of-the-art of the application of intramolecular Suzuki-Miyaura cross-coupling reactions in the construction of (macro)cyclic frameworks of natural products and bioactive molecules of synthetic origin, covering (mostly) examples that have been reported since 2015. Target molecules prepared via intramolecular Suzuki-Miyaura cross-coupling as a key step range from natural products/natural product analogs to synthetic drug candidates, featuring ring sizes from 4 to ≫12. We highlight the utility, scope, and limitations of the reaction for different ring sizes and arrays of functional groups. Where possible, comparisons with other methods of cyclization are provided.
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Affiliation(s)
- Carolina Caso
- Department of Chemistry and Applied BiosciencesInstitute of Pharmaceutical SciencesETH ZürichHCI H429, Vladimir-Prelog-Weg 1–5/108093ZürichSwitzerland
| | - Karl‐Heinz Altmann
- Department of Chemistry and Applied BiosciencesInstitute of Pharmaceutical SciencesETH ZürichHCI H429, Vladimir-Prelog-Weg 1–5/108093ZürichSwitzerland
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2
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Butler MS, Vollmer W, Goodall ECA, Capon RJ, Henderson IR, Blaskovich MAT. A Review of Antibacterial Candidates with New Modes of Action. ACS Infect Dis 2024; 10:3440-3474. [PMID: 39018341 PMCID: PMC11474978 DOI: 10.1021/acsinfecdis.4c00218] [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: 03/17/2024] [Revised: 06/15/2024] [Accepted: 06/17/2024] [Indexed: 07/19/2024]
Abstract
There is a lack of new antibiotics to combat drug-resistant bacterial infections that increasingly threaten global health. The current pipeline of clinical-stage antimicrobials is primarily populated by "new and improved" versions of existing antibiotic classes, supplemented by several novel chemical scaffolds that act on traditional targets. The lack of fresh chemotypes acting on previously unexploited targets (the "holy grail" for new antimicrobials due to their scarcity) is particularly unfortunate as these offer the greatest opportunity for innovative breakthroughs to overcome existing resistance. In recognition of their potential, this review focuses on this subset of high value antibiotics, providing chemical structures where available. This review focuses on candidates that have progressed to clinical trials, as well as selected examples of promising pioneering approaches in advanced stages of development, in order to stimulate additional research aimed at combating drug-resistant infections.
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Affiliation(s)
- Mark S. Butler
- Centre
for Superbug Solutions and ARC Training Centre for Environmental and
Agricultural Solutions to Antimicrobial Resistance, Institute for
Molecular Bioscience, The University of
Queensland, St. Lucia, Queensland 4072, Australia
| | - Waldemar Vollmer
- Centre
for Superbug Solutions and ARC Training Centre for Environmental and
Agricultural Solutions to Antimicrobial Resistance, Institute for
Molecular Bioscience, The University of
Queensland, St. Lucia, Queensland 4072, Australia
| | - Emily C. A. Goodall
- Centre
for Superbug Solutions and ARC Training Centre for Environmental and
Agricultural Solutions to Antimicrobial Resistance, Institute for
Molecular Bioscience, The University of
Queensland, St. Lucia, Queensland 4072, Australia
| | - Robert J. Capon
- Centre
for Superbug Solutions and ARC Training Centre for Environmental and
Agricultural Solutions to Antimicrobial Resistance, Institute for
Molecular Bioscience, The University of
Queensland, St. Lucia, Queensland 4072, Australia
| | - Ian R. Henderson
- Centre
for Superbug Solutions and ARC Training Centre for Environmental and
Agricultural Solutions to Antimicrobial Resistance, Institute for
Molecular Bioscience, The University of
Queensland, St. Lucia, Queensland 4072, Australia
| | - Mark A. T. Blaskovich
- Centre
for Superbug Solutions and ARC Training Centre for Environmental and
Agricultural Solutions to Antimicrobial Resistance, Institute for
Molecular Bioscience, The University of
Queensland, St. Lucia, Queensland 4072, Australia
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3
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Schum D, Elsen FAV, Ruddell S, Schorpp K, Junca H, Müsken M, Chen SY, Fiedler MK, Pickl T, Pieper DH, Hadian K, Zacharias M, Sieber SA. Screening Privileged Alkyl Guanidinium Motifs under Host-Mimicking Conditions Reveals a Novel Antibiotic with an Unconventional Mode of Action. JACS AU 2024; 4:3125-3134. [PMID: 39211621 PMCID: PMC11350587 DOI: 10.1021/jacsau.4c00449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 06/20/2024] [Accepted: 06/24/2024] [Indexed: 09/04/2024]
Abstract
Screening large molecule libraries against pathogenic bacteria is often challenged by a low hit rate due to limited uptake, underrepresentation of antibiotic structural motifs, and assays that do not resemble the infection conditions. To address these limitations, we present a screen of a focused library of alkyl guanidinium compounds, a structural motif associated with antibiotic activity and enhanced uptake, under host-mimicking infection conditions against a panel of disease-associated bacteria. Several hit molecules were identified with activities against Gram-positive and Gram-negative bacteria, highlighting the fidelity of the general concept. We selected one compound (L15) for in-depth mode of action studies that exhibited bactericidal activity against methicillin-resistant Staphylococcus aureus USA300 with a minimum inhibitory concentration of 1.5 μM. Structure-activity relationship studies confirmed the necessity of the guanidinium motif for antibiotic activity. The mode of action was investigated using affinity-based protein profiling with an L15 probe and identified the signal peptidase IB (SpsB) as the most promising hit. Validation by activity assays, binding site identification, docking, and molecular dynamics simulations demonstrated SpsB activation by L15, a recently described mechanism leading to the dysregulation of protein secretion and cell death. Overall, this study highlights the need for unconventional screening strategies to identify novel antibiotics.
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Affiliation(s)
- Dominik Schum
- TUM
School of Natural Sciences, Department of Bioscience, Chair of Organic Chemistry II, Center for Functional Protein Assemblies
(CPA), Technical University of Munich (TUM), Ernst-Otto-Fischer Str. 8, Garching 85748, Germany
| | - Franziska A. V. Elsen
- TUM
School of Natural Sciences, Department of Bioscience, Chair of Organic Chemistry II, Center for Functional Protein Assemblies
(CPA), Technical University of Munich (TUM), Ernst-Otto-Fischer Str. 8, Garching 85748, Germany
| | - Stuart Ruddell
- TUM
School of Natural Sciences, Department of Bioscience, Chair of Organic Chemistry II, Center for Functional Protein Assemblies
(CPA), Technical University of Munich (TUM), Ernst-Otto-Fischer Str. 8, Garching 85748, Germany
| | - Kenji Schorpp
- Helmholtz
Zentrum München, Research Unit Signaling and Translation, Ingolstädter Landstraße
1, Neuherberg, Munich 85764, Germany
| | - Howard Junca
- Helmholtz
Centre for Infection Research, Microbial Interactions and Processes, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Mathias Müsken
- Helmholtz
Centre for Infection Research, Central Facility for Microscopy, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Shu-Yu Chen
- TUM
School of Natural Sciences, Department of Bioscience, Theoretical Biophysics (T38), Center for Functional Protein Assemblies
(CPA), Technical University of Munich (TUM), Ernst-Otto-Fischer Str. 8, Garching 85748, Germany
| | - Michaela K. Fiedler
- TUM
School of Natural Sciences, Department of Bioscience, Chair of Organic Chemistry II, Center for Functional Protein Assemblies
(CPA), Technical University of Munich (TUM), Ernst-Otto-Fischer Str. 8, Garching 85748, Germany
| | - Thomas Pickl
- TUM School
of Natural Sciences, Department of Chemistry, Catalysis Research Center (CRC), Technical University of Munich (TUM), Ernst-Otto-Fischer Str. 1, Garching 85748, Germany
| | - Dietmar H. Pieper
- Helmholtz
Centre for Infection Research, Microbial Interactions and Processes, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Kamyar Hadian
- Helmholtz
Zentrum München, Research Unit Signaling and Translation, Ingolstädter Landstraße
1, Neuherberg, Munich 85764, Germany
| | - Martin Zacharias
- TUM
School of Natural Sciences, Department of Bioscience, Theoretical Biophysics (T38), Center for Functional Protein Assemblies
(CPA), Technical University of Munich (TUM), Ernst-Otto-Fischer Str. 8, Garching 85748, Germany
| | - Stephan A. Sieber
- TUM
School of Natural Sciences, Department of Bioscience, Chair of Organic Chemistry II, Center for Functional Protein Assemblies
(CPA), Technical University of Munich (TUM), Ernst-Otto-Fischer Str. 8, Garching 85748, Germany
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4
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Chen J, Wang W, Hu X, Yue Y, Lu X, Wang C, Wei B, Zhang H, Wang H. Medium-sized peptides from microbial sources with potential for antibacterial drug development. Nat Prod Rep 2024; 41:1235-1263. [PMID: 38651516 DOI: 10.1039/d4np00002a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Covering: 1993 to the end of 2022As the rapid development of antibiotic resistance shrinks the number of clinically available antibiotics, there is an urgent need for novel options to fill the existing antibiotic pipeline. In recent years, antimicrobial peptides have attracted increased interest due to their impressive broad-spectrum antimicrobial activity and low probability of antibiotic resistance. However, macromolecular antimicrobial peptides of plant and animal origin face obstacles in antibiotic development because of their extremely short elimination half-life and poor chemical stability. Herein, we focus on medium-sized antibacterial peptides (MAPs) of microbial origin with molecular weights below 2000 Da. The low molecular weight is not sufficient to form complex protein conformations and is also associated to a better chemical stability and easier modifications. Microbially-produced peptides are often composed of a variety of non-protein amino acids and terminal modifications, which contribute to improving the elimination half-life of compounds. Therefore, MAPs have great potential for drug discovery and are likely to become key players in the development of next-generation antibiotics. In this review, we provide a detailed exploration of the modes of action demonstrated by 45 MAPs and offer a concise summary of the structure-activity relationships observed in these MAPs.
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Affiliation(s)
- Jianwei Chen
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Wei Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xubin Hu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yujie Yue
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xingyue Lu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Chenjie Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Bin Wei
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Huawei Zhang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Hong Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
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5
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Zhang Y, Zhang D, Zhao W, Li H, Lu Z, Guo B, Meng X, Zhou X, Yang Y. Design, Synthesis, and Biological Evaluation of Novel Arylomycins against Multidrug-Resistant Gram-Negative Bacteria. J Med Chem 2024; 67:6585-6609. [PMID: 38598362 DOI: 10.1021/acs.jmedchem.4c00018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
G0775, an arylomycin-type SPase I inhibitor that is being evaluated in a preclinical study, exhibited potent antibacterial activities against some Gram-negative bacteria but meanwhile suffered defects such as a narrow antibacterial spectrum and poor pharmacokinetic properties. Herein, systematic structural modifications were carried out, including optimization of the macrocyclic skeleton, warheads, and lipophilic regions. The optimization culminated in the discovery of 138f, which showed more potent activity and a broader spectrum against clinically isolated carbapenem-resistant Gram-negative bacteria, especially against Acinetobacter baumannii and Pseudomonas aeruginosa. 162, the free amine of 138f, exhibited an excellent pharmacokinetic profile in rats. In a neutropenic mouse thigh model of infection with multidrug-resistant P. aeruginosa, the potent in vivo antibacterial efficacy of 162 was confirmed and superior to that of G0775 (3.5-log decrease vs 1.1-log decrease in colony-forming unit (CFU)). These results support 162 as a potential antimicrobial agent for further research.
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Affiliation(s)
- Yinyong Zhang
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, Sichuan China
- Key Laboratory of Advanced Technologies of Material, Minister of Education, School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu 610031, Sichuan China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dan Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenhao Zhao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongyuan Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhengyu Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bin Guo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Meng
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xianli Zhou
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, Sichuan China
- Key Laboratory of Advanced Technologies of Material, Minister of Education, School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu 610031, Sichuan China
- Affiliated Hospital, The Third People's Hospital of Chengdu, Southwest Jiaotong University, Chengdu 610000, Sichuan, China
| | - Yushe Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, Beijing 100049, China
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6
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Koehler MFT, Chen YC, Chen Y, Chen Y, Crawford JJ, Durk MR, Garland K, Hanan EJ, Higuchi RI, Hu H, Ly CQ, Paraselli PG, Roberts TC, Schwarz JB, Smith PA, Yu Z, Heise CE. Lipid Tales: Optimizing Arylomycin Membrane Anchors. ACS Med Chem Lett 2023; 14:1524-1530. [PMID: 37974942 PMCID: PMC10641904 DOI: 10.1021/acsmedchemlett.3c00327] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/22/2023] [Indexed: 11/19/2023] Open
Abstract
Multidrug-resistant bacteria are spreading at alarming rates, and despite extensive efforts, no new antibiotic class with activity against Gram-negative bacteria has been approved in over 50 years. LepB inhibitors (LepBi) based on the arylomycin class of natural products are a novel class of antibiotics and function by inhibiting the bacterial type I signal peptidase (SPase) in Gram-negative bacteria. One critical aspect of LepBi development involves optimization of the membrane-anchored lipophilic portion of the molecule. We therefore developed an approach that assesses the effect of this portion on the complicated equilibria of plasma protein binding, crossing the outer membrane of Gram-negative bacteria and anchoring in the bacterial inner membrane to facilitate SPase binding. Our findings provide important insights into the development of antibacterial agents where the target is associated with the inner membrane of Gram-negative bacteria.
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Affiliation(s)
- Michael F. T. Koehler
- Department
of Discovery Chemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | - Yi-Chen Chen
- Department
of Drug Metabolism and Pharmacokinetics, Genentech, Inc., South San Francisco, California 94080, United States
| | - Yongsheng Chen
- Department
of Chemistry, WuXi AppTec, Shanghai 200131, China
| | - Yuan Chen
- Department
of Drug Metabolism and Pharmacokinetics, Genentech, Inc., South San Francisco, California 94080, United States
| | - James J. Crawford
- Department
of Discovery Chemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | - Matthew R. Durk
- Department
of Drug Metabolism and Pharmacokinetics, Genentech, Inc., South San Francisco, California 94080, United States
| | - Keira Garland
- Department
of Discovery Chemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | - Emily J. Hanan
- Department
of Discovery Chemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | | | - Huiyong Hu
- Department
of Discovery Chemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | - Cuong Q. Ly
- Department
of Discovery Chemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | | | | | - Jacob B. Schwarz
- Department
of Discovery Chemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | - Peter A. Smith
- Department
of Infectious Disease, Genentech, Inc., South San Francisco, California 94080, United States
| | - Zhiyong Yu
- Department
of Chemistry, WuXi AppTec, Shanghai 200131, China
| | - Christopher E. Heise
- Department
of Biochemical and Cellular Pharmacology, Genentech, Inc., 1 DNA
Way, South San Francisco, California 94080, United States
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7
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Stone MC, Mychack A, Coe KA, Walker S. Combining Signal Peptidase and Lipoprotein Processing Inhibitors Overcomes Ayr Resistance in Staphylococcus aureus. Antimicrob Agents Chemother 2023; 67:e0011523. [PMID: 37097175 PMCID: PMC10190671 DOI: 10.1128/aac.00115-23] [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: 02/02/2023] [Accepted: 03/30/2023] [Indexed: 04/26/2023] Open
Abstract
Antibiotic resistance in bacterial pathogens is an ongoing public health concern. The arylomycins are a class of natural product antibiotics that target the type I signal peptidase, which carries out the terminal step in protein secretion. Here, we used transposon sequencing (Tn-Seq) to profile the effects of the optimized arylomycin derivative G0775 in Staphylococcus aureus. Our transposon libraries include both upregulation and inactivation mutants, allowing us to identify resistance mechanisms and targets for synergism. We identified several cell envelope pathways that, when inactivated, sensitize S. aureus to the arylomycin G0775. These pathways include the lipoprotein processing pathway, and we have shown that inhibitors of this pathway synergize with G0775 even though lipoprotein processing is nonessential in S. aureus. Moreover, we found that blocking this pathway completely reverses Ayr resistance, which is a major resistance mechanism to arylomycins, including G0775. Our Tn-Seq data also showed that upregulation of mprF and several other genes is protective against G0775. Because a subset of these genes was previously found in a Tn-Seq profile of the clinically important antibiotic daptomycin, we tested a set of daptomycin-nonsusceptible clinical isolates with gain-of-function mutations in mprF for susceptibility to arylomycin G0775. Despite structural and mechanistic differences between these antibiotics, we observed similar decreases in susceptibility. Taken together, our results highlight how Tn-Seq profiles that include both gene inactivation and upregulation can identify targets, antibiotic resistance mechanisms, and strategies to overcome resistance.
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Affiliation(s)
- Madeleine C. Stone
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Aaron Mychack
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Kathryn A. Coe
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Suzanne Walker
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
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8
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Adams Z, Silvestri AP, Chiorean S, Flood DT, Balo BP, Shi Y, Holcomb M, Walsh SI, Maillie CA, Pierens GK, Forli S, Rosengren KJ, Dawson PE. Stretching Peptides to Generate Small Molecule β-Strand Mimics. ACS CENTRAL SCIENCE 2023; 9:648-656. [PMID: 37122474 PMCID: PMC10141592 DOI: 10.1021/acscentsci.2c01462] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Indexed: 05/03/2023]
Abstract
Advances in the modulation of protein-protein interactions (PPIs) enable both characterization of PPI networks that govern diseases and design of therapeutics and probes. The shallow protein surfaces that dominate PPIs are challenging to target using standard methods, and approaches for accessing extended backbone structures are limited. Here, we incorporate a rigid, linear, diyne brace between side chains at the i to i+2 positions to generate a family of low-molecular-weight, extended-backbone peptide macrocycles. NMR and density functional theory studies show that these stretched peptides adopt stable, rigid conformations in solution and can be tuned to explore extended peptide conformational space. The diyne brace is formed in excellent conversions (>95%) and amenable to high-throughput synthesis. The minimalist structure-inducing tripeptide core (<300 Da) is amenable to further synthetic elaboration. Diyne-braced inhibitors of bacterial type 1 signal peptidase demonstrate the utility of the technique.
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Affiliation(s)
- Zoë
C. Adams
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Anthony P. Silvestri
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- Unnatural
Products, Inc., 2161
Delaware Ave, Suite A., Santa Cruz, California 95060, United States
| | - Sorina Chiorean
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Dillon T. Flood
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Brian P. Balo
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yifan Shi
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Matthew Holcomb
- Department
of Integrated Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Shawn I. Walsh
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Colleen A. Maillie
- Department
of Integrated Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Gregory K. Pierens
- Centre
for Advanced Imaging, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Stefano Forli
- Department
of Integrated Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - K. Johan Rosengren
- Institute
for Molecular Bioscience and School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Philip E. Dawson
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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9
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Molinaro C, Kawasaki Y, Wanyoike G, Nishioka T, Yamamoto T, Snedecor B, Robinson SJ, Gosselin F. Engineered Cytochrome P450-Catalyzed Oxidative Biaryl Coupling Reaction Provides a Scalable Entry into Arylomycin Antibiotics. J Am Chem Soc 2022; 144:14838-14845. [PMID: 35905381 DOI: 10.1021/jacs.2c06019] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We report herein the first example of a cytochrome P450-catalyzed oxidative carbon-carbon coupling process for a scalable entry into arylomycin antibiotic cores. Starting from wild-type hydroxylating cytochrome P450 enzymes and engineered Escherichia coli, a combination of enzyme engineering, random mutagenesis, and optimization of reaction conditions generated a P450 variant that affords the desired arylomycin core 2d in 84% assay yield. Furthermore, this process was demonstrated as a viable route for the production of the arylomycin antibiotic core on the gram scale. Finally, this new entry affords a viable, scalable, and practical route for the synthesis of novel Gram-negative antibiotics.
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Affiliation(s)
- Carmela Molinaro
- Department of Small Molecule Process Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Yukie Kawasaki
- Applied Microbiotechnology Department, MicroBiopharm Japan Co. Ltd., 156 Nakagawara, Kiyosu, Aichi 452-0915, Japan
| | - George Wanyoike
- Production Technology Department, MicroBiopharm Japan Co. Ltd., 1808 Nakaizumi, Iwata, Shizuoka 438-0078, Japan
| | - Taiki Nishioka
- Applied Microbiotechnology Department, MicroBiopharm Japan Co. Ltd., 156 Nakagawara, Kiyosu, Aichi 452-0915, Japan
| | - Tsuyoshi Yamamoto
- Applied Microbiotechnology Department, MicroBiopharm Japan Co. Ltd., 156 Nakagawara, Kiyosu, Aichi 452-0915, Japan
| | - Brad Snedecor
- Department of Cell Culture and Bioprocess Operations, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Sarah J Robinson
- Department of Discovery Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Francis Gosselin
- Department of Small Molecule Process Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
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10
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Kaushik S, He H, Dalbey RE. Bacterial Signal Peptides- Navigating the Journey of Proteins. Front Physiol 2022; 13:933153. [PMID: 35957980 PMCID: PMC9360617 DOI: 10.3389/fphys.2022.933153] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/21/2022] [Indexed: 11/18/2022] Open
Abstract
In 1971, Blobel proposed the first statement of the Signal Hypothesis which suggested that proteins have amino-terminal sequences that dictate their export and localization in the cell. A cytosolic binding factor was predicted, and later the protein conducting channel was discovered that was proposed in 1975 to align with the large ribosomal tunnel. The 1975 Signal Hypothesis also predicted that proteins targeted to different intracellular membranes would possess distinct signals and integral membrane proteins contained uncleaved signal sequences which initiate translocation of the polypeptide chain. This review summarizes the central role that the signal peptides play as address codes for proteins, their decisive role as targeting factors for delivery to the membrane and their function to activate the translocation machinery for export and membrane protein insertion. After shedding light on the navigation of proteins, the importance of removal of signal peptide and their degradation are addressed. Furthermore, the emerging work on signal peptidases as novel targets for antibiotic development is described.
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11
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Johnston CW, Badran AH. Natural and engineered precision antibiotics in the context of resistance. Curr Opin Chem Biol 2022; 69:102160. [PMID: 35660248 DOI: 10.1016/j.cbpa.2022.102160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 04/18/2022] [Accepted: 04/22/2022] [Indexed: 12/14/2022]
Abstract
Antibiotics are essential weapons in our fight against infectious disease, yet the consequences of broad-spectrum antibiotic use on microbiome stability and pathogen resistance are prompting investigations into more selective alternatives. Echoing the advent of precision medicine in oncology, precision antibiotics with focused activities are emerging as a means of addressing infections without damaging microbiomes or incentivizing resistance. Historically, antibiotic design principles have been gleaned from Nature, and reinvestigation of overlooked antibacterials is now providing scaffolds and targets for the design of pathogen-specific drugs. In this perspective, we summarize the biosynthetic and antibacterial mechanisms used to access these activities, and discuss how such strategies may be co-opted through engineering approaches to afford precision antibiotics.
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Affiliation(s)
- Chad W Johnston
- Department of Pharmacology & Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Ahmed H Badran
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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12
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Szałaj N, Benediktsdottir A, Rusin D, Karlén A, Mowbray SL, Więckowska A. Bacterial type I signal peptidase inhibitors - Optimized hits from nature. Eur J Med Chem 2022; 238:114490. [DOI: 10.1016/j.ejmech.2022.114490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 05/20/2022] [Accepted: 05/21/2022] [Indexed: 11/04/2022]
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13
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López C, Delmonti J, Bonomo RA, Vila AJ. Deciphering the evolution of metallo-β-lactamases: a journey from the test tube to the bacterial periplasm. J Biol Chem 2022; 298:101665. [PMID: 35120928 DOI: 10.1016/j.jbc.2022.101665] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 01/13/2022] [Accepted: 01/16/2022] [Indexed: 12/20/2022] Open
Abstract
Understanding the evolution of metallo-β-lactamases (MBLs) is fundamental to deciphering the mechanistic basis of resistance to carbapenems in pathogenic and opportunistic bacteria. Presently, these MBL producing pathogens are linked to high rates of morbidity and mortality worldwide. However, the study of the biochemical and biophysical features of MBLs in vitro provides an incomplete picture of their evolutionary potential, since this limited and artificial environment disregards the physiological context where evolution and selection take place. Herein, we describe recent efforts aimed to address the evolutionary traits acquired by different clinical variants of MBLs in conditions mimicking their native environment (the bacterial periplasm) and considering whether they are soluble or membrane-bound proteins. This includes addressing the metal content of MBLs within the cell under zinc starvation conditions, and the context provided by different bacterial hosts that result in particular resistance phenotypes. Our analysis highlights recent progress bridging the gap between in vitro and in-cell studies.
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Affiliation(s)
- Carolina López
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), S2000EXF Rosario, Argentina
| | - Juliana Delmonti
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), S2000EXF Rosario, Argentina
| | - Robert A Bonomo
- Research Service, Veterans Affairs Northeast Ohio Healthcare System, Cleveland, Ohio, USA; Departments of Medicine, Pharmacology, Molecular Biology and Microbiology, Biochemistry, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA; Medical Service and GRECC, Veterans Affairs Northeast Ohio Healthcare System, Cleveland, Ohio, USA; CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
| | - Alejandro J Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), S2000EXF Rosario, Argentina; CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA; Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, S2002LRK Rosario, Argentina.
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14
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Aldemir H, Shu S, Schaefers F, Hong H, Richarz R, Harteis S, Einsiedler M, Milzarek TM, Schneider S, Gulder TAM. Carrier Protein-Free Enzymatic Biaryl Coupling in Arylomycin A2 Assembly and Structure of the Cytochrome P450 AryC. Chemistry 2022; 28:e202103389. [PMID: 34725865 PMCID: PMC9299028 DOI: 10.1002/chem.202103389] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Indexed: 12/16/2022]
Abstract
The arylomycin antibiotics are potent inhibitors of bacterial type I signal peptidase. These lipohexapeptides contain a biaryl structural motif reminiscent of glycopeptide antibiotics. We herein describe the functional and structural evaluation of AryC, the cytochrome P450 performing biaryl coupling in biosynthetic arylomycin assembly. Unlike its enzymatic counterparts in glycopeptide biosynthesis, AryC converts free substrates without the requirement of any protein interaction partner, likely enabled by a strongly hydrophobic cavity at the surface of AryC pointing to the substrate tunnel. This activity enables chemo-enzymatic assembly of arylomycin A2 that combines the advantages of liquid- and solid-phase peptide synthesis with late-stage enzymatic cross-coupling. The reactivity of AryC is unprecedented in cytochrome P450-mediated biaryl construction in non-ribosomal peptides, in which peptidyl carrier protein (PCP)-tethering so far was shown crucial both in vivo and in vitro.
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Affiliation(s)
- Hülya Aldemir
- Chair of Technical BiochemistryTechnical University of DresdenBergstraße 6601069DresdenGermany
- Biosystems Chemistry, Faculty of ChemistryTechnical University of MunichLichtenbergstraße 485748GarchingGermany
| | - Shuangjie Shu
- Chair of Technical BiochemistryTechnical University of DresdenBergstraße 6601069DresdenGermany
- Biosystems Chemistry, Faculty of ChemistryTechnical University of MunichLichtenbergstraße 485748GarchingGermany
| | - Francoise Schaefers
- Biosystems Chemistry, Faculty of ChemistryTechnical University of MunichLichtenbergstraße 485748GarchingGermany
| | - Hanna Hong
- Biosystems Chemistry, Faculty of ChemistryTechnical University of MunichLichtenbergstraße 485748GarchingGermany
| | - René Richarz
- Biosystems Chemistry, Faculty of ChemistryTechnical University of MunichLichtenbergstraße 485748GarchingGermany
| | - Sabrina Harteis
- Biosystems Chemistry, Faculty of ChemistryTechnical University of MunichLichtenbergstraße 485748GarchingGermany
| | - Manuel Einsiedler
- Chair of Technical BiochemistryTechnical University of DresdenBergstraße 6601069DresdenGermany
| | - Tobias M. Milzarek
- Chair of Technical BiochemistryTechnical University of DresdenBergstraße 6601069DresdenGermany
| | - Sabine Schneider
- Department of ChemistryLudwig-Maximillians-University MunichButenandtstraße 5–1381377MunichGermany
| | - Tobias A. M. Gulder
- Chair of Technical BiochemistryTechnical University of DresdenBergstraße 6601069DresdenGermany
- Biosystems Chemistry, Faculty of ChemistryTechnical University of MunichLichtenbergstraße 485748GarchingGermany
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15
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Zhu F, Powell WC, Jing R, Walczak MA. Organometallic Ala M Reagents for Umpolung Peptide Diversification. CHEM CATALYSIS 2021; 1:870-884. [PMID: 34738092 PMCID: PMC8562471 DOI: 10.1016/j.checat.2021.05.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Selective modifications of peptides and proteins have emerged as a promising strategy to develop novel mechanistic probes and prepare compounds with translational potentials. Here, we report alanine carbastannatranes AlaSn as a universal synthon in various C-C and C-heteroatom bond-forming reactions. These reagents are compatible with peptide manipulation techniques and can undergo chemoselective conjugation in minutes when promoted by Pd(0). Despite their increased nucleophilicity and propensity to transfer the alkyl group, C(sp3)-C(sp2) coupling with AlaSn can be accomplished at room temperature under buffered conditions (pH 6.5-8.5). We also show that AlaSn can be easily transformed into several canonical L- and D-amino acids in arylation, acylation, and etherification reactions. Furthermore, AlaSn can partake in macrocyclizations exemplified by the synthesis of medium size cyclic peptides with various topologies. Taken together, metalated alanine AlaSn demonstrates unparalleled scope and represents a new type of umpolung reagents suitable for structure-activity relationship studies and peptide diversification.
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Affiliation(s)
- Feng Zhu
- Department of Chemistry, University of Colorado, Boulder, CO 80309, United States
- Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai, 200240, P. R. C
- These authors contributed equally
| | - Wyatt C. Powell
- Department of Chemistry, University of Colorado, Boulder, CO 80309, United States
- These authors contributed equally
| | - Ruiheng Jing
- Department of Chemistry, University of Colorado, Boulder, CO 80309, United States
| | - Maciej A. Walczak
- Department of Chemistry, University of Colorado, Boulder, CO 80309, United States
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16
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Effective Small Molecule Antibacterials from a Novel Anti-Protein Secretion Screen. Microorganisms 2021; 9:microorganisms9030592. [PMID: 33805695 PMCID: PMC8000395 DOI: 10.3390/microorganisms9030592] [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: 02/18/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 12/03/2022] Open
Abstract
The increasing problem of bacterial resistance to antibiotics underscores the urgent need for new antibacterials. Protein export pathways are attractive potential targets. The Sec pathway is essential for bacterial viability and includes components that are absent from eukaryotes. Here, we used a new high-throughput in vivo screen based on the secretion and activity of alkaline phosphatase (PhoA), a Sec-dependent secreted enzyme that becomes active in the periplasm. The assay was optimized for a luminescence-based substrate and was used to screen a ~240K small molecule compound library. After hit confirmation and analoging, 14 HTS secretion inhibitors (HSI), belonging to eight structural classes, were identified with IC50 < 60 µM. The inhibitors were evaluated as antibacterials against 19 Gram-negative and Gram-positive bacterial species (including those from the WHO’s top pathogens list). Seven of them—HSI#6, 9; HSI#1, 5, 10; and HSI#12, 14—representing three structural families, were bacteriocidal. HSI#6 was the most potent hit against 13 species of both Gram-negative and Gram-positive bacteria with IC50 of 0.4 to 8.7 μM. HSI#1, 5, 9 and 10 inhibited the viability of Gram-positive bacteria with IC50 ~6.9–77.8 μM. HSI#9, 12, and 14 inhibited the viability of E. coli strains with IC50 < 65 μM. Moreover, HSI#1, 5 and 10 inhibited the viability of an E. coli strain missing TolC to improve permeability with IC50 4 to 14 μM, indicating their inability to penetrate the outer membrane. The antimicrobial activity was not related to the inhibition of the SecA component of the translocase in vitro, and hence, HSI molecules may target new unknown components that directly or indirectly affect protein secretion. The results provided proof of the principle that the new broad HTS approach can yield attractive nanomolar inhibitors that have potential as new starting compounds for optimization to derive potential antibiotics.
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17
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Upert G, Luther A, Obrecht D, Ermert P. Emerging peptide antibiotics with therapeutic potential. MEDICINE IN DRUG DISCOVERY 2021; 9:100078. [PMID: 33398258 PMCID: PMC7773004 DOI: 10.1016/j.medidd.2020.100078] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/15/2020] [Accepted: 12/27/2020] [Indexed: 02/09/2023] Open
Abstract
This review covers some of the recent progress in the field of peptide antibiotics with a focus on compounds with novel or established mode of action and with demonstrated efficacy in animal infection models. Novel drug discovery approaches, linear and macrocyclic peptide antibiotics, lipopeptides like the polymyxins as well as peptides addressing targets located in the plasma membrane or in the outer membrane of bacterial cells are discussed.
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Key Words
- ADMET, absorption, distribution, metabolism and excretion – toxicity in pharmacokinetics
- AMP, antimicrobial peptide
- AMR, antimicrobial resistance
- ATCC, ATCC cell collection
- Antibiotic
- BAM, β-barrel assembly machinery
- CC50, cytotoxic concentration to kill 50% of cells
- CD, circular dichroism
- CFU, colony forming unit
- CLSI, clinical and laboratory standards institute
- CMS, colistin methane sulfonate
- DMPC, 1,2-dimyristoyl-sn-glycero-3-phosphocholine
- ESKAPE, acronym encompassing six bacterial pathogens (often carrying antibiotic resistance): Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumonia, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp
- FDA, U. S. Food and Drug Administration
- HABP, hospital acquired bacterial pneumonia
- HDP, host-defense peptide
- HEK293, human embryonic kidney 293 cells
- HK-2, human kidney 2 cells (proximal tubular cell line)
- HepG2, human hepatocellular carcinoma cell line
- Hpg, 4-hydroxy-phenyl glycine
- ITC, isothermal titration calorimetry
- KPC, Klebsiella pneumoniae metallo-β-lactamase C resistant
- LPS, lipopolysaccharide
- LptA, lipopolysaccharide transport protein A
- LptC, lipopolysaccharide transport protein C
- LptD, lipopolysaccharide transport protein D
- MDR, multidrug-resistant
- MH-I, Müller-Hinton broth I
- MH-II, Müller-Hinton broth II (cation adjusted)
- MIC, minimal inhibitory concentration
- MRSA, methicilline-resistant S. aureus
- MSSA, methicilline-sensitive S. aureus
- MoA, mechanism (mode) of action
- NDM-1, New Delhi metallo-β-lactamase resistant
- NOAEL, no adverse effect level
- ODL, odilorhabdin
- OMPTA (outer membrane targeting antibiotic)
- OMPTA, outer membrane targeting antibiotic
- Omp, outer membrane protein
- PBMC, peripheral mononuclear blood cell
- PBP, penicillin-binding protein
- PBS, phosphate-buffered saline
- PK, pharmacokinetics
- POPC, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
- POPG, 2-oleoyl-1-palmitoyl-sn-glycero-3-phospho-(1-glycerol)
- PrAMPs, polyproline antimicrobial peptides
- RBC, red blood cell
- SAR, structure-activity relationship
- SPR, surface plasmon resonance
- SPase I, signal peptidase I
- VABP, ventilator associated bacterial pneumonia
- VIM-1, beta-lactamase 2 (K. pneumoniae)
- VISA, vancomycin-intermediate S. aureus
- VRE, vancomycin-resistant enterococcus
- WHO, World Health Organization
- WT, wild type
- WTA, wall teichoic acid
- XDR, extremely drug-resistant
- antimicrobial peptide
- antimicrobial resistance
- bid, bis in die (two times a day)
- i.p., intraperitoneal
- i.v., intravenous
- lipopeptide
- mITT population, minimal intend-to-treat population
- peptide antibiotic
- s.c., subcutaneous
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Affiliation(s)
- Gregory Upert
- Polyphor Ltd, Hegenheimermattweg 125, 4123 Allschwil, Switzerland
| | - Anatol Luther
- Bachem AG, Hauptstrasse 114, 4416 Bubendorf, Switzerland
| | - Daniel Obrecht
- Polyphor Ltd, Hegenheimermattweg 125, 4123 Allschwil, Switzerland
| | - Philipp Ermert
- Polyphor Ltd, Hegenheimermattweg 125, 4123 Allschwil, Switzerland
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18
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Emmerich CH, Gamboa LM, Hofmann MCJ, Bonin-Andresen M, Arbach O, Schendel P, Gerlach B, Hempel K, Bespalov A, Dirnagl U, Parnham MJ. Improving target assessment in biomedical research: the GOT-IT recommendations. Nat Rev Drug Discov 2021; 20:64-81. [PMID: 33199880 PMCID: PMC7667479 DOI: 10.1038/s41573-020-0087-3] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2020] [Indexed: 02/06/2023]
Abstract
Academic research plays a key role in identifying new drug targets, including understanding target biology and links between targets and disease states. To lead to new drugs, however, research must progress from purely academic exploration to the initiation of efforts to identify and test a drug candidate in clinical trials, which are typically conducted by the biopharma industry. This transition can be facilitated by a timely focus on target assessment aspects such as target-related safety issues, druggability and assayability, as well as the potential for target modulation to achieve differentiation from established therapies. Here, we present recommendations from the GOT-IT working group, which have been designed to support academic scientists and funders of translational research in identifying and prioritizing target assessment activities and in defining a critical path to reach scientific goals as well as goals related to licensing, partnering with industry or initiating clinical development programmes. Based on sets of guiding questions for different areas of target assessment, the GOT-IT framework is intended to stimulate academic scientists' awareness of factors that make translational research more robust and efficient, and to facilitate academia-industry collaboration.
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Affiliation(s)
| | - Lorena Martinez Gamboa
- Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- QUEST Center for Transforming Biomedical Research, Berlin Institute of Health, Berlin, Germany
| | - Martine C J Hofmann
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine & Pharmacology TMP, Frankfurt am Main, Germany
| | - Marc Bonin-Andresen
- Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Olga Arbach
- Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- SPARK-Validation Fund, Berlin Institute of Health, Berlin, Germany
| | - Pascal Schendel
- Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Katja Hempel
- Boehringer-Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Anton Bespalov
- PAASP GmbH, Heidelberg, Germany
- Valdman Institute of Pharmacology, Pavlov Medical University, St. Petersburg, Russia
| | - Ulrich Dirnagl
- Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- QUEST Center for Transforming Biomedical Research, Berlin Institute of Health, Berlin, Germany
| | - Michael J Parnham
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine & Pharmacology TMP, Frankfurt am Main, Germany
- Faculty of Biochemistry, Chemistry & Pharmacy, J.W. Goethe University Frankfurt, Frankfurt am Main, Germany
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Wu ZC, Boger DL. The quest for supernatural products: the impact of total synthesis in complex natural products medicinal chemistry. Nat Prod Rep 2020; 37:1511-1531. [PMID: 33169762 PMCID: PMC7678878 DOI: 10.1039/d0np00060d] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Covering: 2000 up to 2020This review presents select recent advances in the medicinal chemistry of complex natural products that are prepared by total synthesis. The underlying studies highlight enabling divergent synthetic strategies and methods that permit the systematic medicinal chemistry studies of key analogues bearing deep-seated structural changes not readily accessible by semisynthetic or biosynthetic means. Select and recent examples are detailed where the key structural changes are designed to improve defined properties or to overcome an intrinsic limitation of the natural product itself. In the examples presented, the synthetic efforts provided supernatural products, a term first introduced by our colleague Ryan Shenvi (Synlett, 2016, 27, 1145-1164), with properties superseding the parent natural product. The design principles and approaches for creating the supernatural products are highlighted with an emphasis on the properties addressed that include those that improve activity or potency, increase selectivity, enhance durability, broaden the spectrum of activity, improve chemical or metabolic stability, overcome limiting physical properties, add mechanisms of action, enhance PK properties, overcome drug resistance, and/or improve in vivo efficacy. Some such improvements may be regarded by some as iterative enhancements whereas others, we believe, truly live up to their characterization as supernatural products. Most such efforts are also accompanied by advances in synthetic organic chemistry, inspiring the development of new synthetic methodology and providing supernatural products with improved synthetic accessibility.
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Affiliation(s)
- Zhi-Chen Wu
- Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA.
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Tan YX, Peters DS, Walsh SI, Holcomb M, Santos-Martins D, Forli S, Romesberg FE. Initial Analysis of the Arylomycin D Antibiotics. JOURNAL OF NATURAL PRODUCTS 2020; 83:2112-2121. [PMID: 32614583 DOI: 10.1021/acs.jnatprod.9b01174] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The arylomycins are a class of natural product antibiotics that inhibit bacterial type I signal peptidase and are under development as therapeutics. Four classes of arylomycins are known, arylomycins A-D. Previously, we reported the synthesis and analysis of representatives of the A, B, and C classes and showed that their spectrum of activity has the potential to be much broader than originally assumed. Along with a comparison of the mechanism of acquired and innate resistance, this led us to suggest that the arylomycins are latent antibiotics, antibiotics that once possessed broad-spectrum activity, but which upon examination today, have only narrow spectrum activity due to prior selection for resistance in the course of the competition with other microorganisms that drove their evolution in the first place. Interestingly, actinocarbasin, the only identified member of the arylomycin D class, has been reported to have activity against MRSA. To confirm and understand this activity, several actinocarbasin derivatives were synthesized. We demonstrate that the previously reported structure of actinocarbasin is incorrect, identify what is likely the correct scaffold, confirm that scaffold has activity against MRSA, and determine the origin of this activity.
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Affiliation(s)
- Yun Xuan Tan
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - David S Peters
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Shawn I Walsh
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Matthew Holcomb
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Diogo Santos-Martins
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Floyd E Romesberg
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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21
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Sengupta S, Mehta G. Macrocyclization via C-H functionalization: a new paradigm in macrocycle synthesis. Org Biomol Chem 2020; 18:1851-1876. [PMID: 32101232 DOI: 10.1039/c9ob02765c] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The growing emphasis on macrocycles in engaging difficult therapeutic targets such as protein-protein interactions and GPCRs via preferential adaptation of bioactive and cell penetrating conformations has provided impetus to the search for de novo macrocyclization strategies that are efficient, chemically robust and amenable to diversity creation. An emerging macrocyclization paradigm based on the C-H activation logic, of particular promise in the macrocyclization of complex peptides, has added a new dimension to this pursuit, enabling efficacious access to macrocycles of various sizes and topologies with high atom and step economy. Significant achievements in macrocyclization methodologies and their applications in the synthesis of bioactive natural products and drug-like molecules, employing strategic variations of C-H activation are captured in this review. It is expected that this timely account will foster interest in newer ways of macrocycle construction among practitioners of organic synthesis and chemical biology to advance the field.
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Affiliation(s)
- Saumitra Sengupta
- School of Chemistry, University of Hyderabad, Gachibowli, Hyderabad-5000 046, Telengana, India.
| | - Goverdhan Mehta
- School of Chemistry, University of Hyderabad, Gachibowli, Hyderabad-5000 046, Telengana, India.
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22
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Liu K, Huigens RW. Instructive Advances in Chemical Microbiology Inspired by Nature's Diverse Inventory of Molecules. ACS Infect Dis 2020; 6:541-562. [PMID: 31842540 PMCID: PMC7346871 DOI: 10.1021/acsinfecdis.9b00413] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Natural product antibiotics have played an essential role in the treatment of bacterial infection in addition to serving as useful tools to explore the intricate biology of bacteria. Our current arsenal of antibiotics operate through the inhibition of well-defined bacterial targets critical for replication and growth. Pathogenic bacteria effectively utilize a diversity of mechanisms that lead to acquired resistance and/or innate tolerance toward antibiotic therapies, which can result in devastating consequences to human life. Several research groups have established innovative programs that work at the chemistry-biology interface to develop new molecules that aim to define and address concerns related to antibiotic resistance and tolerance. In this Review, we present recent progress by select research groups that highlight a diversity of integrated chemical biology and medicinal chemistry approaches aimed at the development and utilization of chemical tools that have led to promising new microbiological insights that may lead to significant clinical advances regarding the treatment of pathogenic bacteria.
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Affiliation(s)
- Ke Liu
- 1345 Center Drive, Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | - Robert W. Huigens
- 1345 Center Drive, Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
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23
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Gupta K, Daroch P, Harjai K, Chhibber S. Parallels among natural and synthetically modified quorum-quenching strategies as convoy to future therapy. Microbiology (Reading) 2019; 165:1265-1281. [DOI: 10.1099/mic.0.000826] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Kshitiz Gupta
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Priya Daroch
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Kusum Harjai
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Sanjay Chhibber
- Department of Microbiology, Panjab University, Chandigarh, India
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Lehman KM, Grabowicz M. Countering Gram-Negative Antibiotic Resistance: Recent Progress in Disrupting the Outer Membrane with Novel Therapeutics. Antibiotics (Basel) 2019; 8:antibiotics8040163. [PMID: 31554212 PMCID: PMC6963605 DOI: 10.3390/antibiotics8040163] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 09/19/2019] [Accepted: 09/20/2019] [Indexed: 10/27/2022] Open
Abstract
Gram-negative bacteria shield themselves from antibiotics by producing an outer membrane (OM) that forms a formidable permeability barrier. Multidrug resistance among these organisms is a particularly acute problem that is exacerbated by the OM. The poor penetrance of many available antibiotics prevents their clinical use, and efforts to discover novel classes of antibiotics against Gram-negative bacteria have been unsuccessful for almost 50 years. Recent insights into how the OM is built offer new hope. Several essential multiprotein molecular machines (Bam, Lpt, and Lol) work in concert to assemble the barrier and offer a swathe of new targets for novel therapeutic development. Murepavadin has been at the vanguard of these efforts, but its recently reported phase III clinical trial toxicity has tempered the anticipation of imminent new clinical options. Nonetheless, the many concerted efforts aimed at breaking down the OM barrier provide a source of ongoing optimism for what may soon come through the development pipeline. We will review the current state of drug development against the OM assembly targets, highlighting insightful new discovery approaches and strategies.
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Affiliation(s)
- Kelly M Lehman
- Microbiology and Molecular Genetics Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, GA 30322, USA.
- Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA 30322, USA.
- Department of Microbiology & Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA.
| | - Marcin Grabowicz
- Microbiology and Molecular Genetics Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, GA 30322, USA.
- Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA 30322, USA.
- Department of Microbiology & Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA.
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA.
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25
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Optimized arylomycins are a new class of Gram-negative antibiotics. Nature 2018; 561:189-194. [PMID: 30209367 DOI: 10.1038/s41586-018-0483-6] [Citation(s) in RCA: 251] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 06/26/2018] [Indexed: 11/08/2022]
Abstract
Multidrug-resistant bacteria are spreading at alarming rates, and despite extensive efforts no new class of antibiotic with activity against Gram-negative bacteria has been approved in over fifty years. Natural products and their derivatives have a key role in combating Gram-negative pathogens. Here we report chemical optimization of the arylomycins-a class of natural products with weak activity and limited spectrum-to obtain G0775, a molecule with potent, broad-spectrum activity against Gram-negative bacteria. G0775 inhibits the essential bacterial type I signal peptidase, a new antibiotic target, through an unprecedented molecular mechanism. It circumvents existing antibiotic resistance mechanisms and retains activity against contemporary multidrug-resistant Gram-negative clinical isolates in vitro and in several in vivo infection models. These findings demonstrate that optimized arylomycin analogues such as G0775 could translate into new therapies to address the growing threat of multidrug-resistant Gram-negative infections.
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Szałaj N, Lu L, Benediktsdottir A, Zamaratski E, Cao S, Olanders G, Hedgecock C, Karlén A, Erdélyi M, Hughes D, Mowbray SL, Brandt P. Boronic ester-linked macrocyclic lipopeptides as serine protease inhibitors targeting Escherichia coli type I signal peptidase. Eur J Med Chem 2018; 157:1346-1360. [DOI: 10.1016/j.ejmech.2018.08.086] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/22/2018] [Accepted: 08/29/2018] [Indexed: 12/22/2022]
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Yeh CH, Walsh SI, Craney A, Tabor MG, Voica AF, Adhikary R, Morris SE, Romesberg FE. Optimization of a β-Lactam Scaffold for Antibacterial Activity via the Inhibition of Bacterial Type I Signal Peptidase. ACS Med Chem Lett 2018; 9:376-380. [PMID: 29670704 DOI: 10.1021/acsmedchemlett.8b00064] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 03/07/2018] [Indexed: 11/30/2022] Open
Abstract
β-Lactam antibiotics, one of the most important class of human therapeutics, act via the inhibition of penicillin-binding proteins (PBPs). The unparalleled success in their development has inspired efforts to develop them as inhibitors of other targets. Bacterial type I signal peptidase is evolutionarily related to the PBPs, but the stereochemistry of its substrates and its catalytic mechanism suggest that β-lactams with the 5S stereochemistry, as opposed to the 5R stereochemistry of the traditional β-lactams, would be required for inhibition. We report the synthesis and evaluation of a variety of 5S penem derivatives and identify several with promising activity against both a Gram-positive and a Gram-negative bacterial pathogen. To our knowledge these are the first 5S β-lactams to possess significant antibacterial activity and the first β-lactams imparted with antibacterial activity via optimization of the inhibition of a target other than a PBP. Along with the privileged status of their scaffold and the promise of bacterial signal peptidase I (SPase) as a target, this activity makes these compounds promising leads for development as novel therapeutics.
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Affiliation(s)
- Chien-Hung Yeh
- Department of Chemistry, The Scripps Research Institute, La Jolla California 92037 United States
| | - Shawn I. Walsh
- Department of Chemistry, The Scripps Research Institute, La Jolla California 92037 United States
| | - Arryn Craney
- Department of Chemistry, The Scripps Research Institute, La Jolla California 92037 United States
| | - M. Greg Tabor
- Department of Chemistry, The Scripps Research Institute, La Jolla California 92037 United States
| | - Ana-Florina Voica
- Department of Chemistry, The Scripps Research Institute, La Jolla California 92037 United States
| | - Ramkrishna Adhikary
- Department of Chemistry, The Scripps Research Institute, La Jolla California 92037 United States
| | - Sydney E. Morris
- Department of Chemistry, The Scripps Research Institute, La Jolla California 92037 United States
| | - Floyd E. Romesberg
- Department of Chemistry, The Scripps Research Institute, La Jolla California 92037 United States
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Peters DS, Romesberg FE, Baran PS. Scalable Access to Arylomycins via C-H Functionalization Logic. J Am Chem Soc 2018; 140:2072-2075. [PMID: 29381350 PMCID: PMC5817625 DOI: 10.1021/jacs.8b00087] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
Arylomycins
are a promising class of “latent” antibacterial
natural products currently in preclinical development. Access to analogues
within this family has previously required a lengthy route involving
multiple functional group manipulations that is costly and time-intensive
on scale. This study presents a simplified route predicated on simple
C–H functionalization logic that is enabled by a Cu-mediated
oxidative phenol coupling that mimics the putative biosynthesis. This
operationally simple macrocyclization is the largest of its
kind and can be easily performed on gram scale. The application of
this new route to a formal synthesis of the natural product and a
collection of new analogues along with their biological evaluation
is also reported.
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Affiliation(s)
- David S Peters
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Floyd E Romesberg
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Phil S Baran
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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29
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Quorum sensing inhibitors: can endophytes be prospective sources? Arch Microbiol 2017; 200:355-369. [PMID: 29026943 DOI: 10.1007/s00203-017-1437-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 09/02/2017] [Accepted: 10/05/2017] [Indexed: 01/16/2023]
Abstract
Endophytes are microbes which reside inside the plant tissues asymptomatically or causing pathogenicity to the host plant for a brief period. Owing to their presence in a specialized niche, endophytes are capable of synthesizing diverse types of bioactive molecules. Continuous development of resistance mechanism by pathogens to the currently available health treatments and pharmaceuticals has led researchers to explore new therapeutic agents. Quorum sensing has a role in the development of microbial pathogenic traits including biofilm formation. Utilization of quorum sensing (QS) inhibitors in antivirulence approach against pathogenesis is one of the innovative strategies. Endophytic microbes provide a plethora of such required bioactive molecules. This review summarizes the bioprospecting of endophytic microbes for production of novel QS inhibitors. At the outset, an overview is presented about the QS and QS inhibition followed by a summary on the endophytes as a treasure trove of bioactive metabolites, particularly the QS inhibitors. Next, we have outlined screening, purification, production, and application of QS inhibitors starting from the isolation of endophytic microbes. There is huge prospect for endophytes in the domain of human healthcare and food industry, provided that we develop a comprehensive understanding of the biology of endophyte and its ecosystem.
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30
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Blaskovich MAT, Butler MS, Cooper MA. Polishing the tarnished silver bullet: the quest for new antibiotics. Essays Biochem 2017; 61:103-114. [PMID: 28258234 PMCID: PMC5869247 DOI: 10.1042/ebc20160077] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 01/23/2017] [Accepted: 01/24/2017] [Indexed: 11/29/2022]
Abstract
We are facing a potential catastrophe of untreatable bacterial infections, driven by the inexorable rise of extensively drug-resistant bacteria, coupled with a market failure of pharmaceutical and biotech companies to deliver new therapeutic options. While global recognition of the problem is finally apparent, solutions are still a long way from being implemented. In addition to drug stewardship programmes and better diagnostics, new antibiotics are desperately needed. The question remains as to how to achieve this goal. This review will examine the different strategies being applied to discover new antibiotics.
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Affiliation(s)
- Mark A T Blaskovich
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane 4072, Australia
| | - Mark S Butler
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane 4072, Australia
| | - Matthew A Cooper
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane 4072, Australia
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31
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Walsh SI, Craney A, Romesberg FE. Not just an antibiotic target: Exploring the role of type I signal peptidase in bacterial virulence. Bioorg Med Chem 2016; 24:6370-6378. [PMID: 27769673 PMCID: PMC5279723 DOI: 10.1016/j.bmc.2016.09.048] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 09/17/2016] [Accepted: 09/19/2016] [Indexed: 01/23/2023]
Abstract
The looming antibiotic crisis has prompted the development of new strategies towards fighting infection. Traditional antibiotics target bacterial processes essential for viability, whereas proposed antivirulence approaches rely on the inhibition of factors that are required only for the initiation and propagation of infection within a host. Although antivirulence compounds have yet to prove their efficacy in the clinic, bacterial signal peptidase I (SPase) represents an attractive target in that SPase inhibitors exhibit broad-spectrum antibiotic activity, but even at sub-MIC doses also impair the secretion of essential virulence factors. The potential consequences of SPase inhibition on bacterial virulence have not been thoroughly examined, and are explored within this review. In addition, we review growing evidence that SPase has relevant biological functions outside of mediating secretion, and discuss how the inhibition of these functions may be clinically significant.
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Affiliation(s)
- Shawn I Walsh
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Arryn Craney
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Floyd E Romesberg
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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32
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Abstract
Signal peptidases are membrane proteases that play crucial roles in the protein transport pathway of bacteria. They cleave off the signal peptide from precursor proteins that are membrane inserted by the SecYEG or Tat translocons. Signal peptide cleavage releases the translocated protein from the inner membrane allowing the protein to be exported to the periplasm, outer membrane, or secreted into the medium. Signal peptidases are very important proteins to study. They are unique serine proteases with a Ser-Lys dyad, catalyze cleavage at the membrane surface, and are promising potential antibacterial drug targets. This chapter will focus on the isolation of signal peptidases and the preprotein substrates, as well as describe a peptide library approach for characterizing the substrate specificity.
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Affiliation(s)
- R E Dalbey
- The Ohio State University, Columbus, OH, United States.
| | - D Pei
- The Ohio State University, Columbus, OH, United States
| | - Ö D Ekici
- The Ohio State University, Newark, OH, United States
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33
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Farha MA, Brown ED. Strategies for target identification of antimicrobial natural products. Nat Prod Rep 2016; 33:668-80. [DOI: 10.1039/c5np00127g] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Despite a pervasive decline in natural product research at many pharmaceutical companies over the last two decades, natural products have undeniably been a prolific and unsurpassed source for new lead antibacterial compounds.
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Affiliation(s)
- Maya A. Farha
- M.G. DeGroote Institute for Infectious Disease Research and Department of Biochemistry and Biomedical Sciences
- McMaster University
- Hamilton
- Canada
| | - Eric D. Brown
- M.G. DeGroote Institute for Infectious Disease Research and Department of Biochemistry and Biomedical Sciences
- McMaster University
- Hamilton
- Canada
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34
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Balibar CJ, Roemer T. Yeast: a microbe with macro-implications to antimicrobial drug discovery. Brief Funct Genomics 2015; 15:147-54. [PMID: 26443612 DOI: 10.1093/bfgp/elv038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Paramount to any rational discovery of new antibiotics displaying novel mechanisms of action is a deep knowledge of the genetic basis of microbial growth, division and virulence. The bakers' yeast,Saccharomyces cerevisiae, illustrates the highest understanding of the genetic underpinnings of microbial life, and from this framework, a systems biology paradigm has evolved, begging to be emulated in antibacterial discovery. Here, we review landmark events in the history of yeast genomics that provide this new foundation for antibacterial drug discovery.
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35
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Yang L, Ibrahim A, Johnston CW, Skinnider MA, Ma B, Magarvey NA. Exploration of Nonribosomal Peptide Families with an Automated Informatic Search Algorithm. ACTA ACUST UNITED AC 2015; 22:1259-69. [PMID: 26364933 DOI: 10.1016/j.chembiol.2015.08.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Revised: 07/30/2015] [Accepted: 08/10/2015] [Indexed: 02/02/2023]
Abstract
Microbial natural products are some of the most important pharmaceutical agents and possess unparalleled chemical diversity. Here we present an untargeted metabolomics algorithm that builds on our validated iSNAP platform to rapidly identify families of peptide natural products. By utilizing known or in silico-dereplicated seed structures, this algorithm screens tandem mass spectrometry data to elaborate extensive molecular families within crude microbial culture extracts with high confidence and statistical significance. Analysis of peptide natural product producers revealed an abundance of unreported congeners, revealing one of the largest families of natural products described to date, as well as a novel variant with greater potency. These findings demonstrate the effectiveness of the iSNAP platform as an accurate tool for rapidly profiling large families of nonribosomal peptides.
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Affiliation(s)
- Lian Yang
- The David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Ashraf Ibrahim
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Chad W Johnston
- The Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Michael A Skinnider
- The Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Bin Ma
- The David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Nathan A Magarvey
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON L8N 3Z5, Canada; The Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada.
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36
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Craney A, Romesberg FE. The inhibition of type I bacterial signal peptidase: Biological consequences and therapeutic potential. Bioorg Med Chem Lett 2015; 25:4761-4766. [PMID: 26276537 DOI: 10.1016/j.bmcl.2015.07.072] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 07/16/2015] [Accepted: 07/21/2015] [Indexed: 01/05/2023]
Abstract
The general secretory pathway has long been regarded as a potential antibiotic drug target. In particular, bacterial type I signal peptidase (SPase) is emerging as a strong candidate for therapeutic use. In this review, we focus on the information gained from the use of SPase inhibitors as probes of prokaryote biology. A thorough understanding of the consequences of SPase inhibition and the mechanisms of resistance that arise are essential to the success of SPase as an antibiotic target. In addition to the role of SPase in processing secreted proteins, the use of SPase inhibitors has elucidated a previously unknown function for SPase in regulating cleavage events of membrane proteins.
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Affiliation(s)
- Arryn Craney
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Floyd E Romesberg
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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37
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Origins of Yersinia pestis sensitivity to the arylomycin antibiotics and the inhibition of type I signal peptidase. Antimicrob Agents Chemother 2015; 59:3887-98. [PMID: 25896690 DOI: 10.1128/aac.00181-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 04/10/2015] [Indexed: 02/04/2023] Open
Abstract
Yersinia pestis is the etiologic agent of the plague. Reports of Y. pestis strains that are resistant to each of the currently approved first-line and prophylactic treatments point to the urgent need to develop novel antibiotics with activity against the pathogen. We previously reported that Y. pestis strain KIM6+, unlike most Enterobacteriaceae, is susceptible to the arylomycins, a novel class of natural-product lipopeptide antibiotics that inhibit signal peptidase I (SPase). In this study, we show that the arylomycin activity is conserved against a broad range of Y. pestis strains and confirm that it results from the inhibition of SPase. We next investigated the origins of this unique arylomycin sensitivity and found that it does not result from an increased affinity of the Y. pestis SPase for the antibiotic and that alterations to each component of the Y. pestis lipopolysaccharide-O antigen, core, and lipid A-make at most only a small contribution. Instead, the origins of the sensitivity can be traced to an increased dependence on SPase activity that results from high levels of protein secretion under physiological conditions. These results highlight the potential of targeting protein secretion in cases where there is a heavy reliance on this process and also have implications for the development of the arylomycins as an antibiotic with activity against Y. pestis and potentially other Gram-negative pathogens.
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38
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Craney A, Romesberg FE. A putative cro-like repressor contributes to arylomycin resistance in Staphylococcus aureus. Antimicrob Agents Chemother 2015; 59:3066-74. [PMID: 25753642 PMCID: PMC4432125 DOI: 10.1128/aac.04597-14] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 03/05/2015] [Indexed: 01/26/2023] Open
Abstract
Antibiotic-resistant bacteria are a significant public health concern and motivate efforts to develop new classes of antibiotics. One such class of antibiotics is the arylomycins, which target type I signal peptidase (SPase), the enzyme responsible for the release of secreted proteins from their N-terminal leader sequences. Despite the essentiality, conservation, and relative accessibility of SPase, the activity of the arylomycins is limited against some bacteria, including the important human pathogen Staphylococcus aureus. To understand the origins of the limited activity against S. aureus, we characterized the susceptibility of a panel of strains to two arylomycin derivatives, arylomycin A-C16 and its more potent analog arylomycin M131. We observed a wide range of susceptibilities to the two arylomycins and found that resistant strains were sensitized by cotreatment with tunicamycin, which inhibits the first step of wall teichoic acid synthesis. To further understand how S. aureus responds to the arylomycins, we profiled the transcriptional response of S. aureus NCTC 8325 to growth-inhibitory concentrations of arylomycin M131 and found that it upregulates the cell wall stress stimulon (CWSS) and an operon consisting of a putative transcriptional regulator and three hypothetical proteins. Interestingly, we found that mutations in the putative transcriptional regulator are correlated with resistance, and selection for resistance ex vivo demonstrated that mutations in this gene are sufficient for resistance. The results begin to elucidate how S. aureus copes with secretion stress and how it evolves resistance to the inhibition of SPase.
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Affiliation(s)
- Arryn Craney
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA
| | - Floyd E Romesberg
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA
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39
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Al Toma RS, Brieke C, Cryle MJ, Süssmuth RD. Structural aspects of phenylglycines, their biosynthesis and occurrence in peptide natural products. Nat Prod Rep 2015; 32:1207-35. [DOI: 10.1039/c5np00025d] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Phenylglycine-type amino acids occur in a wide variety of peptide natural products. Herein structures and properties of these peptides as well as the biosynthetic origin and incorporation of phenylglycines are discussed.
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Affiliation(s)
| | - Clara Brieke
- Max Planck Institute for Medical Research
- Department of Biomolecular Mechanisms
- 69120 Heidelberg
- Germany
| | - Max J. Cryle
- Max Planck Institute for Medical Research
- Department of Biomolecular Mechanisms
- 69120 Heidelberg
- Germany
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40
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Meredith TC, Wang H, Beaulieu P, Gründling A, Roemer T. Harnessing the power of transposon mutagenesis for antibacterial target identification and evaluation. Mob Genet Elements 2014; 2:171-178. [PMID: 23094235 PMCID: PMC3469428 DOI: 10.4161/mge.21647] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Determining the mechanism of action of bacterial growth inhibitors can be a formidable challenge in the progression of small molecules into antibacterial therapies. To help address this bottleneck, we have developed a robust transposon mutagenesis system using a suite of outward facing promoters in order to generate a comprehensive range of expression genotypes in Staphylococcus aureus from which to select defined compound-resistant transposon insertion mutants. Resistance stemming from either gene or operon over/under-expression, in addition to deletion, provides insight into multiple factors that contribute to a compound's observed activity, including means of cell envelope penetration and susceptibility to efflux. By profiling the entire resistome, the suitability of an antibacterial target itself is also evaluated, sometimes with unanticipated results. We herein show that for the staphylococcal signal peptidase (SpsB) inhibitors, modulating expression of lipoteichoic acid synthase (LtaS) confers up to a 100-fold increase in the minimal inhibitory concentration. As similarly efficient transposition systems are or will become established in other bacteria and cell types, we discuss the utility, limitations and future promise of Tnp mutagenesis for determining both a compound's mechanism of action and in the evaluation of novel targets.
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Affiliation(s)
- Timothy C Meredith
- Infectious Diseases Division; Merck Frosst Center for Therapeutic Research; Kirkland, Quebec, Canada
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41
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Personne Y, Curtis MA, Wareham DW, Waite RD. Activity of the type I signal peptidase inhibitor MD3 against multidrug-resistant Gram-negative bacteria alone and in combination with colistin. J Antimicrob Chemother 2014; 69:3236-43. [PMID: 25134721 DOI: 10.1093/jac/dku309] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVES Effective treatment of Gram-negative bacterial infections is increasingly challenging due to the spread of multidrug-resistant strains and a lack of new antimicrobials in development. Bacterial type I signal peptidases (SPases) represent a highly conserved and essential target for inhibition by novel compounds. SPases are required for the effective processing of membrane translocated proteins involved in core functions related to metabolism, virulence and resistance. In this study we assessed the biochemical and functional activity of a novel synthetic inhibitor (MD3) of SPases against a wide range of Gram-negative pathogens. METHODS The activity and specificity of MD3 for recombinant Pseudomonas aeruginosa SPase (LepB) and a genetically engineered LepB-regulatable strain were investigated. Antimicrobial activity of the compound alone and in combination with outer membrane-permeabilizing agents (sodium hexametaphosphate, colistin) was also determined against a collection of P. aeruginosa, Acinetobacter baumannii, Klebsiella pneumoniae and Stenotrophomonas maltophilia isolates. RESULTS MD3 was found to inactivate the P. aeruginosa LepB protein (IC50 10 μM), resulting in antimicrobial effects potentiated in the presence of colistin. MD3 also demonstrated potent activity against wild-type and multidrug-resistant strains of A. baumannii and S. maltophilia with MICs ranging from 0.5 to 14 mg/L in the presence of subinhibitory concentrations of colistin. CONCLUSIONS MD3 is a novel inhibitor of bacterial SPase in a range of non-fermentative Gram-negative bacteria. The antimicrobial activity is potentiated in combination with colistin and suggests that SPase inhibition warrants further exploration as a basis for future mono or combination therapies.
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Affiliation(s)
- Yoann Personne
- Centre for Immunology and Infectious Disease, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London E1 2AT, UK
| | - Michael A Curtis
- Institute of Dentistry, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London E1 2AD, UK
| | - David W Wareham
- Centre for Immunology and Infectious Disease, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London E1 2AT, UK
| | - Richard D Waite
- Centre for Immunology and Infectious Disease, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London E1 2AT, UK
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Aldemir H, Richarz R, Gulder TAM. Das biokatalytische Repertoire natürlicher Biarylbildung. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201401075] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Aldemir H, Richarz R, Gulder TAM. The Biocatalytic Repertoire of Natural Biaryl Formation. Angew Chem Int Ed Engl 2014; 53:8286-93. [DOI: 10.1002/anie.201401075] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Indexed: 02/04/2023]
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Rao C V S, De Waelheyns E, Economou A, Anné J. Antibiotic targeting of the bacterial secretory pathway. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:1762-83. [PMID: 24534745 DOI: 10.1016/j.bbamcr.2014.02.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 01/27/2014] [Accepted: 02/06/2014] [Indexed: 02/06/2023]
Abstract
Finding new, effective antibiotics is a challenging research area driven by novel approaches required to tackle unconventional targets. In this review we focus on the bacterial protein secretion pathway as a target for eliminating or disarming pathogens. We discuss the latest developments in targeting the Sec-pathway for novel antibiotics focusing on two key components: SecA, the ATP-driven motor protein responsible for driving preproteins across the cytoplasmic membrane and the Type I signal peptidase that is responsible for the removal of the signal peptide allowing the release of the mature protein from the membrane. We take a bird's-eye view of other potential targets in the Sec-pathway as well as other Sec-dependent or Sec-independent protein secretion pathways as targets for the development of novel antibiotics. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
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Affiliation(s)
- Smitha Rao C V
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology, KU Leuven, O&N1, 6th floor, Herestraat 49, P.O. Box 1037, B-3000 Leuven, Belgium.
| | - Evelien De Waelheyns
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology, KU Leuven, O&N1, 6th floor, Herestraat 49, P.O. Box 1037, B-3000 Leuven, Belgium.
| | - Anastassios Economou
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology, KU Leuven, O&N1, 6th floor, Herestraat 49, P.O. Box 1037, B-3000 Leuven, Belgium; Institute of Molecular Biology and Biotechnology, FORTH, University of Crete, P.O. Box 1385, GR-711 10 Iraklio, Crete, Greece; Department of Biology, University of Crete, P.O. Box 1385, GR-71110 Iraklio, Crete, Greece.
| | - Jozef Anné
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology, KU Leuven, O&N1, 6th floor, Herestraat 49, P.O. Box 1037, B-3000 Leuven, Belgium.
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Use of Metagenomics and Isolation of Actinobacteria in Brazil's Atlantic Rainforest Soil for Antimicrobial Prospecting. ISRN BIOTECHNOLOGY 2014; 2014:909601. [PMID: 25937991 PMCID: PMC4393038 DOI: 10.1155/2014/909601] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 02/10/2014] [Indexed: 11/17/2022]
Abstract
Modern techniques involving molecular biology, such as metagenomics, have the advantage of exploiting a higher number of microorganisms; however, classic isolation and culture methods used to obtain antimicrobials continue to be promising, especially in the isolation of Actinobacteria, which are responsible for the production of many of these compounds. In this work, two methodologies were used to search for antimicrobial substances—isolation of Actinobacteria and metagenomics of the Atlantic Rainforest soil and of the cultivation of cocoa intercropped with acai berry in the Atlantic Rainforest. The metagenomic libraries were constructed with the CopyControl Fosmid Library kit EPICENTRE, resulting in a total of 2688 clones, 1344 of each soil sample. None of the clones presented antimicrobial activity against the microorganisms tested: S. aureus, Bacillus subtilis, and Salmonella choleraesuis. A total of 46 isolates were obtained from the isolation of soil Actinobacteria: 24 isolates from Atlantic Rainforest soil and 22 isolates from the intercrop cultivation soil. Of these, two Atlantic Rainforest soil isolates inhibited the growth of S. aureus including a clinical isolate of S. aureus MRSA—a promising result, since it is an important multidrug-resistant human pathogen.
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Abstract
Cell-cell communication, or quorum sensing, is a widespread phenomenon in bacteria that is used to coordinate gene expression among local populations. Its use by bacterial pathogens to regulate genes that promote invasion, defense, and spread has been particularly well documented. With the ongoing emergence of antibiotic-resistant pathogens, there is a current need for development of alternative therapeutic strategies. An antivirulence approach by which quorum sensing is impeded has caught on as a viable means to manipulate bacterial processes, especially pathogenic traits that are harmful to human and animal health and agricultural productivity. The identification and development of chemical compounds and enzymes that facilitate quorum-sensing inhibition (QSI) by targeting signaling molecules, signal biogenesis, or signal detection are reviewed here. Overall, the evidence suggests that QSI therapy may be efficacious against some, but not necessarily all, bacterial pathogens, and several failures and ongoing concerns that may steer future studies in productive directions are discussed. Nevertheless, various QSI successes have rightfully perpetuated excitement surrounding new potential therapies, and this review highlights promising QSI leads in disrupting pathogenesis in both plants and animals.
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Richardson MB, Williams SJ. A practical synthesis of long-chain iso-fatty acids (iso-C12-C19) and related natural products. Beilstein J Org Chem 2013; 9:1807-12. [PMID: 24062846 PMCID: PMC3778388 DOI: 10.3762/bjoc.9.210] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 08/15/2013] [Indexed: 11/23/2022] Open
Abstract
A gram-scale synthesis of terminally-branched iso-fatty acids (iso-C12–C19) was developed commencing with methyl undec-10-enoate (methyl undecylenate) (for iso-C12–C14) or the C15 and C16 lactones pentadecanolide (for iso-C15–C17) and hexadecanolide (for iso-C18–C19). Central to the approaches outlined is the two-step construction of the terminal isopropyl group through addition of methylmagnesium bromide to the ester/lactones and selective reduction of the resulting tertiary alcohols. Thus, the C12, C17 and C18 iso-fatty acids were obtained in three steps from commercially-available starting materials, and the remaining C13–C16 and C19 iso-fatty acids were prepared by homologation or recursive dehomologations of these fatty acids or through intercepting appropriate intermediates. Highlighting the synthetic potential of the iso-fatty acids and various intermediates prepared herein, we describe the synthesis of the natural products (S)-2,15-dimethylpalmitic acid, (S)-2-hydroxy-15-methylpalmitic acid, and 2-oxo-14-methylpentadecane.
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Affiliation(s)
- Mark B Richardson
- School of Chemistry, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
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Liu J, Smith PA, Steed DB, Romesberg F. Efforts toward broadening the spectrum of arylomycin antibiotic activity. Bioorg Med Chem Lett 2013; 23:5654-9. [PMID: 24012184 DOI: 10.1016/j.bmcl.2013.08.026] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 07/24/2013] [Accepted: 08/05/2013] [Indexed: 11/26/2022]
Abstract
New antibiotics are needed, and one source may be 'latent' antibiotics, natural products whose once broad-spectrum activity is currently limited by the evolution of resistance in nature. We have identified a potential class of latent antibiotics, the arylomycins, which are lipopeptides with a C-terminal macrocycle that target signal peptidase and whose spectrum is limited by a resistance-conferring mutation in many bacteria. Herein, we report the synthesis and evaluation of several arylomycin derivatives, and demonstrate that both C-terminal homologation with a glycyl aldehyde and addition of a positive charge to the macrocycle increase the activity and spectrum of the arylomycin scaffold.
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Affiliation(s)
- Jian Liu
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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Singh SB, Young K, Miesel L. Screening strategies for discovery of antibacterial natural products. Expert Rev Anti Infect Ther 2013; 9:589-613. [PMID: 21819327 DOI: 10.1586/eri.11.81] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Microbial-derived natural products have been a traditional source of antibiotics and antibiotic leads and continue to be effective sources of antibiotics today. The most important of these discoveries were made about 50 years ago. Chemical modifications of natural products discovered during those years continue to produce new clinical agents but their value is now, unfortunately, fading away owing to the exhaustion of opportunities of chemical modifications. The discovery of new natural antibiotics is directly linked to new screening technologies, particularly technologies that can help to eliminate the rediscovery of known antibiotics. In this article, we have reviewed the screening technologies from recent literature as well as originating from authors laboratories that were used for the screening of natural products. The article covers the entire spectrum of screening strategies, including classical empiric whole-cell assays to more sophisticated antisense based hypersensitive Staphylococcus aureus Fitness Test assays designed to screen all targets simultaneously. These technologies have led to the discovery of a series of natural product antibiotics, which have been summarized, including the discovery of platensimycin, platencin, nocathiacins, philipimycin, cyclothialidine and muryamycins. It is quite clear that natural products provide a tremendous opportunity to discover new antibiotics when combined with new hyper-sensitive whole-cell technologies.
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Affiliation(s)
- Sheo B Singh
- Merck Research Laboratories, Rahway, NJ 07065, USA.
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Hänchen A, Rausch S, Landmann B, Toti L, Nusser A, Süssmuth RD. Alanine scan of the peptide antibiotic feglymycin: assessment of amino acid side chains contributing to antimicrobial activity. Chembiochem 2013; 14:625-32. [PMID: 23447362 DOI: 10.1002/cbic.201300032] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Indexed: 01/08/2023]
Abstract
The antibiotic feglymycin is a linear 13-mer peptide synthesized by the bacterium Streptomyces sp. DSM 11171. It mainly consists of the nonproteinogenic amino acids 4-hydroxyphenylglycine and 3,5-dihydroxyphenylglycine. An alanine scan of feglymycin was performed by solution-phase peptide synthesis in order to assess the significance of individual amino acid side chains for biological activity. Hence, 13 peptides were synthesized from di- and tripeptide building blocks, and subsequently tested for antibacterial activity against Staphylococcus aureus strains. Furthermore we tested the inhibition of peptidoglycan biosynthesis enzymes MurA and MurC, which are inhibited by feglymycin. Whereas the antibacterial activity is significantly based on the three amino acids D-Hpg1, L-Hpg5, and L-Phe12, the inhibitory activity against MurA and MurC depends mainly on L-Asp13. The difference in the position dependence for antibacterial activity and enzyme inhibition suggests multiple molecular targets in the modes of action of feglymycin.
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Affiliation(s)
- Anne Hänchen
- Technische Universität Berlin, Fakultät II, Institut für Chemie, Strasse des 17. Juni 124, 10623 Berlin, Germany
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