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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. [PMID: 38651516 DOI: 10.1039/d4np00002a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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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Tran TTP, Huynh NNT, Pham NT, Nguyen DT, Tran CV, Nguyen UQ, Ho AN, Suh JW, Cheng J, Nguyen TKN, Tran SV, Nguyen DM. Metabolites from Streptomyces aureus (VTCC43181) and Their Inhibition of Mycobacterium tuberculosis ClpC1 Protein. Molecules 2024; 29:720. [PMID: 38338462 PMCID: PMC10856564 DOI: 10.3390/molecules29030720] [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: 12/22/2023] [Revised: 01/19/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
Tuberculosis is one of the most common infectious diseases in the world, caused by Mycobacterium tuberculosis. The outbreak of multiple drug-resistant tuberculosis has become a major challenge to prevent this disease worldwide. ClpC1 is a Clp ATPase protein of Mycobacterium tuberculosis, functioning as a chaperon when combined with the Clp complex. ClpC1 has emerged as a new target to discover anti-tuberculosis drugs. This study aimed to explore the ClpC1 inhibitors from actinomycetes, which have been known to provide abundant sources of antibiotics. Two cyclic peptides, including nocardamin (1), halolitoralin A (3), and a lactone pleurone (2), were isolated from the culture of Streptomyces aureus (VTCC43181). The structures of these compounds were determined based on the detailed analysis of their spectral data and comparison with references. This is the first time these compounds have been isolated from S. aureus. Compounds 1-3 were evaluated for their affection of ATPase activity of the recombinant ClpC1 protein. Of these compounds, halolitoralin A (1), a macrocyclic peptide, was effective for the ATPase hydrolysis of the ClpC1 protein.
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Affiliation(s)
- Thao Thi Phuong Tran
- Institute of Chemistry, Vietnam Academy of Science and Technology (VAST),18 Hoang Quoc Viet Road, Cau Giay, Hanoi 10000, Vietnam; (N.T.P.); (D.T.N.); (C.V.T.); (S.V.T.)
- Faculty of Chemistry, Graduate University of Science and Technology, VAST, 18 Hoang Quoc Viet Road, Cau Giay, Hanoi 10000, Vietnam;
| | - Ni Ngoc Thi Huynh
- Faculty of Chemistry, Graduate University of Science and Technology, VAST, 18 Hoang Quoc Viet Road, Cau Giay, Hanoi 10000, Vietnam;
- Faculty of Natural Sciences, Phu Yen University, 01 Nguyen Van Huyen Road, Tuy Hoa City 56000, Vietnam
| | - Ninh Thi Pham
- Institute of Chemistry, Vietnam Academy of Science and Technology (VAST),18 Hoang Quoc Viet Road, Cau Giay, Hanoi 10000, Vietnam; (N.T.P.); (D.T.N.); (C.V.T.); (S.V.T.)
| | - Dung Thi Nguyen
- Institute of Chemistry, Vietnam Academy of Science and Technology (VAST),18 Hoang Quoc Viet Road, Cau Giay, Hanoi 10000, Vietnam; (N.T.P.); (D.T.N.); (C.V.T.); (S.V.T.)
| | - Chien Van Tran
- Institute of Chemistry, Vietnam Academy of Science and Technology (VAST),18 Hoang Quoc Viet Road, Cau Giay, Hanoi 10000, Vietnam; (N.T.P.); (D.T.N.); (C.V.T.); (S.V.T.)
| | - Uyen Quynh Nguyen
- Institute of Microbiology and Biotechnology, Vietnam National University Hanoi, 44, Xuan Thuy Road, Cau Giay, Hanoi 10000, Vietnam;
| | - Anh Ngoc Ho
- Institute of Biotechnology, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet Road, Cau Giay, Hanoi 10000, Vietnam;
| | - Joo-Won Suh
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University, Yongin 17058, Republic of Korea (J.C.)
| | - Jinhua Cheng
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University, Yongin 17058, Republic of Korea (J.C.)
| | - Thao Kim Nu Nguyen
- Faculty of Biology, University of Natural Sciences, Vietnam National University, Hanoi, 334 Nguyen Trai Road, Thanh Xuân, Hanoi 10000, Vietnam
| | - Sung Van Tran
- Institute of Chemistry, Vietnam Academy of Science and Technology (VAST),18 Hoang Quoc Viet Road, Cau Giay, Hanoi 10000, Vietnam; (N.T.P.); (D.T.N.); (C.V.T.); (S.V.T.)
- Faculty of Chemistry, Graduate University of Science and Technology, VAST, 18 Hoang Quoc Viet Road, Cau Giay, Hanoi 10000, Vietnam;
| | - Duc Minh Nguyen
- Institute of Genome Research, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet Road, Cau Giay, Hanoi 10000, Vietnam
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Wang W, Gu L, Wang J, Hu X, Wei B, Zhang H, Wang H, Chen J. Recent Advances in Polypeptide Antibiotics Derived from Marine Microorganisms. Mar Drugs 2023; 21:547. [PMID: 37888482 PMCID: PMC10608164 DOI: 10.3390/md21100547] [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: 09/19/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 10/28/2023] Open
Abstract
In the post-antibiotic era, the rapid development of antibiotic resistance and the shortage of available antibiotics are triggering a new health-care crisis. The discovery of novel and potent antibiotics to extend the antibiotic pipeline is urgent. Small-molecule antimicrobial peptides have a wide variety of antimicrobial spectra and multiple innovative antimicrobial mechanisms due to their rich structural diversity. Consequently, they have become a new research hotspot and are considered to be promising candidates for next-generation antibiotics. Therefore, we have compiled a collection of small-molecule antimicrobial peptides derived from marine microorganisms from the last fifteen years to show the recent advances in this field. We categorize these compounds into three classes-cyclic oligopeptides, cyclic depsipeptides, and cyclic lipopeptides-according to their structural features, and present their sources, structures, and antimicrobial spectrums, with a discussion of the structure activity relationships and mechanisms of action of some compounds.
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Affiliation(s)
| | | | | | | | | | | | - Hong Wang
- Key Laboratory for Green Pharmaceutical Technologies and Related Equipment of Ministry of Education & Key Laboratory Pharmaceutical Engineering of Zhejiang Province & College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jianwei Chen
- Key Laboratory for Green Pharmaceutical Technologies and Related Equipment of Ministry of Education & Key Laboratory Pharmaceutical Engineering of Zhejiang Province & 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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4
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Paquette AR, Boddy CN. Macrocyclization strategies for the total synthesis of cyclic depsipeptides. Org Biomol Chem 2023; 21:8043-8053. [PMID: 37750186 DOI: 10.1039/d3ob01229h] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Cyclic depsipeptides are an important class of peptide natural products that are defined by the presence of ester and amide bonds within the macrocycle. The structural diversity of depsipeptides has required the development of a broad range of synthetic strategies to access these biologically active compounds. Solid phase peptide synthesis (SPPS) strategies have been an invaluable tool in their synthesis. The key aspect of their synthesis is the macrocyclization strategy. Three main strategies are used, solution phase macrolactamization of acyclic ester containing peptide, on-resin macrolactamization of a sidechain-anchored peptide, and the solution phase macrolactonization of a linear peptide. Additionally, biocatalysts have been used to produce these compounds in a regio- and chemo-selective manner. Each compound offers unique challenges, requiring careful synthetic design to avoid undesirable side reactivity or unwanted epimerization during the esterification and macrocyclizing steps. This focused review analyzes these three strategies for cyclic depsipeptide natural product total synthesis with selected examples from the literature between 2001-2023.
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Affiliation(s)
- André R Paquette
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, K1N 6N5, Canada.
| | - Christopher N Boddy
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, K1N 6N5, Canada.
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5
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Jacobo-Delgado YM, Rodríguez-Carlos A, Serrano CJ, Rivas-Santiago B. Mycobacterium tuberculosis cell-wall and antimicrobial peptides: a mission impossible? Front Immunol 2023; 14:1194923. [PMID: 37266428 PMCID: PMC10230078 DOI: 10.3389/fimmu.2023.1194923] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 04/25/2023] [Indexed: 06/03/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) is one of the most important infectious agents worldwide and causes more than 1.5 million deaths annually. To make matters worse, the drug resistance among Mtb strains has risen substantially in the last few decades. Nowadays, it is not uncommon to find patients infected with Mtb strains that are virtually resistant to all antibiotics, which has led to the urgent search for new molecules and therapies. Over previous decades, several studies have demonstrated the efficiency of antimicrobial peptides to eliminate even multidrug-resistant bacteria, making them outstanding candidates to counterattack this growing health problem. Nevertheless, the complexity of the Mtb cell wall makes us wonder whether antimicrobial peptides can effectively kill this persistent Mycobacterium. In the present review, we explore the complexity of the Mtb cell wall and analyze the effectiveness of antimicrobial peptides to eliminate the bacilli.
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6
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Chowdhury A, Bandyopadhyay A. Compelling Cyclic Peptide Scaffolds for Antitubercular Action: An Account (2011-21) of the Natural Source. Curr Protein Pept Sci 2022; 23:823-836. [PMID: 36200246 DOI: 10.2174/1389203723666220930111259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/01/2022] [Accepted: 09/06/2022] [Indexed: 01/20/2023]
Abstract
Natural cyclic peptide scaffolds are indispensable in medicinal chemistry, chemical biology, and drug discovery platforms due to their chemical diversity, structural integrity, proteolytic stability and biocompatibility. Historically, their isolation and profound understanding of target engagement have been identified as lead pharmacophore discovery. Natural cyclic peptides are the largest class of pharmacologically active scaffold, in which most show activity against drug-resistant Mycobacterium tuberculosis (Mtb). Nevertheless, eight recently discovered cyclic peptide scaffolds exhibit promising antitubercular activity among numerous naturally occurring antitubercular peptides, and they are amenable scaffolds to drug development. We examined their biological origin, scaffolds, isolations, chemical synthesis, and reasons for biological actions against Mtb. Understanding these peptide scaffold details will further allow synthetic and medicinal chemists to develop novel peptide therapeutics against tuberculosis-infected deadly diseases. This review emphasizes these cyclic peptides' in vitro and in vivo activity profiles, including their structural and chemical features.
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Affiliation(s)
- Arnab Chowdhury
- Biomimetic Peptide Engineering Laboratory, Department of Chemistry, Indian Institute of Technology, Ropar, Punjab- 140001, India
| | - Anupam Bandyopadhyay
- Biomimetic Peptide Engineering Laboratory, Department of Chemistry, Indian Institute of Technology, Ropar, Punjab- 140001, India
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7
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An JS, Kim MS, Han J, Jang SC, Im JH, Cui J, Lee Y, Nam SJ, Shin J, Lee SK, Yoon YJ, Oh DC. Nyuzenamide C, an Antiangiogenic Epoxy Cinnamic Acid-Containing Bicyclic Peptide from a Riverine Streptomyces sp. JOURNAL OF NATURAL PRODUCTS 2022; 85:804-814. [PMID: 35294831 DOI: 10.1021/acs.jnatprod.1c00837] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A new nonribosomal peptide, nyuzenamide C (1), was discovered from riverine sediment-derived Streptomyces sp. DM14. Comprehensive analysis of the spectroscopic data of nyuzenamide C (1) revealed that 1 has a bicyclic backbone composed of six common amino acid residues (Asn, Leu, Pro, Gly, Val, and Thr) and four nonproteinogenic amino acid units, including hydroxyglycine, β-hydroxyphenylalanine, p-hydroxyphenylglycine, and 3,β-dihydroxytyrosine, along with 1,2-epoxypropyl cinnamic acid. The absolute configuration of 1 was proposed by J-based configuration analysis, the advanced Marfey's method, quantum mechanics-based DP4 calculations, and bioinformatic analysis of its nonribosomal peptide synthetase biosynthetic gene cluster. Nyuzenamide C (1) displayed antiangiogenic activity in human umbilical vein endothelial cells and induced quinone reductase in murine Hepa-1c1c7 cells.
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Affiliation(s)
- Joon Soo An
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Myoun-Su Kim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jaeho Han
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sung Chul Jang
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Ji Hyeon Im
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jinsheng Cui
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yeonjin Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Jongheon Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yeo Joon Yoon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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8
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Hawkins PME, Hoi DM, Cheung CY, Wang T, Quan D, Sasi VM, Liu DY, Linington RG, Jackson CJ, Oehlers SH, Cook GM, Britton WJ, Clausen T, Payne RJ. Potent Bactericidal Antimycobacterials Targeting the Chaperone ClpC1 Based on the Depsipeptide Natural Products Ecumicin and Ohmyungsamycin A. J Med Chem 2022; 65:4893-4908. [PMID: 35293761 DOI: 10.1021/acs.jmedchem.1c02122] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ohmyungsamycin A and ecumicin are structurally related cyclic depsipeptide natural products that possess activity against Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB). Herein, we describe the design and synthesis of a library of analogues of these two natural products using an efficient solid-phase synthesis and late-stage macrolactamization strategy. Lead analogues possessed potent activity against Mtb in vitro (minimum inhibitory concentration 125-500 nM) and were shown to inhibit protein degradation by the mycobacterial ClpC1-ClpP1P2 protease with an associated enhancement of ClpC1 ATPase activity. The most promising analogue from the series exhibited rapid bactericidal killing activity against Mtb, capable of sterilizing cultures after 7 days, and retained bactericidal activity against hypoxic non-replicating Mtb. This natural product analogue was also active in an in vivo zebrafish model of infection.
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Affiliation(s)
- Paige M E Hawkins
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - David M Hoi
- Research Institute of Molecular Pathology (IMP), Dr-Bohr-Gasse 7, Vienna 1030, Austria
| | - Chen-Yi Cheung
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin 9016, New Zealand
| | - Trixie Wang
- Tuberculosis Research Program at the Centenary Institute, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Diana Quan
- Tuberculosis Research Program at the Centenary Institute, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Vishnu Mini Sasi
- Research School of Chemistry, Australian National University, Acton, 2601 Australian Capital Territory, Australia
| | - Dennis Y Liu
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Roger G Linington
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Acton, 2601 Australian Capital Territory, Australia
| | - Stefan H Oehlers
- Tuberculosis Research Program at the Centenary Institute, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Gregory M Cook
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin 9016, New Zealand
| | - Warwick J Britton
- Tuberculosis Research Program at the Centenary Institute, The University of Sydney, Sydney, New South Wales 2006, Australia.,Central Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Tim Clausen
- Research Institute of Molecular Pathology (IMP), Dr-Bohr-Gasse 7, Vienna 1030, Austria
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales 2006, Australia
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9
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In Vitro Profiling of Antitubercular Compounds by Rapid, Efficient, and Nondestructive Assays Using Autoluminescent Mycobacterium tuberculosis. Antimicrob Agents Chemother 2021; 65:e0028221. [PMID: 34097493 PMCID: PMC8284454 DOI: 10.1128/aac.00282-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Anti-infective drug discovery is greatly facilitated by the availability of in vitro assays that are more proficient at predicting the preclinical success of screening hits. Tuberculosis (TB) drug discovery is hindered by the relatively slow growth rate of Mycobacterium tuberculosis and the use of whole-cell-based in vitro assays that are inherently time-consuming, and for these reasons, rapid, noninvasive bioluminescence-based assays have been widely used in anti-TB drug discovery and development. In this study, in vitro assays that employ autoluminescent M. tuberculosis were optimized to determine MIC, minimum bactericidal concentration (MBC), time-kill curves, activity against macrophage internalized M. tuberculosis (90% effective concentration [EC90]), and postantibiotic effect (PAE) to provide rapid and dynamic biological information. Standardization of the luminescence-based MIC, MBC, time-kill, EC90, and PAE assays was accomplished by comparing results of established TB drugs and two ClpC1-targeting TB leads, ecumicin and rufomycin, to those obtained from conventional assays and/or to previous studies. Cumulatively, the use of the various streamlined luminescence-based in vitro assays has reduced the time for comprehensive in vitro profiling (MIC, MBC, time-kill, EC90, and PAE) by 2 months. The luminescence-based in vitro MBC and EC90 assays yield time and concentration-dependent kill information that can be used for pharmacokinetic-pharmacodynamic (PK-PD) modeling. The MBC and EC90 time-kill graphs revealed a significantly more rapid bactericidal activity for ecumicin than rufomycin. The PAEs of both ecumicin and rufomycin were comparable to that of the first-line TB drug rifampin. The optimization of several nondestructive, luminescence-based TB assays facilitates the in vitro profiling of TB drug leads in an efficient manner.
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Han J, Liu X, Zhang L, Quinn RJ, Feng Y. Anti-mycobacterial natural products and mechanisms of action. Nat Prod Rep 2021; 39:77-89. [PMID: 34226909 DOI: 10.1039/d1np00011j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Covering: up to June, 2020Tuberculosis (TB) continues to be a major disease with high mortality and morbidity globally. Drug resistance and long duration of treatment make antituberculosis drug discovery more challenging. In this review, we summarize recent advances on anti-TB natural products (NPs) and their potential molecular targets in cell wall synthesis, protein production, energy generation, nucleic acid synthesis and other emerging areas. We highlight compounds with activity against drug-resistant TB, and reveal several novel targets including Mtb biotin synthase, ATP synthase, 1,4-dihydroxy-2-naphthoate prenyltransferase and biofilms. These anti-TB NPs and their targets could facilitate target-based screening and accelerate TB drug discovery.
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Affiliation(s)
- Jianying Han
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia.
| | - Xueting Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Ronald J Quinn
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia.
| | - Yunjiang Feng
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia.
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Ahangarpour M, Kavianinia I, Harris PWR, Brimble MA. Photo-induced radical thiol-ene chemistry: a versatile toolbox for peptide-based drug design. Chem Soc Rev 2021; 50:898-944. [PMID: 33404559 DOI: 10.1039/d0cs00354a] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
While the global market for peptide/protein-based therapeutics is witnessing significant growth, the development of peptide drugs remains challenging due to their low oral bioavailability, poor membrane permeability, and reduced metabolic stability. However, a toolbox of chemical approaches has been explored for peptide modification to overcome these obstacles. In recent years, there has been a revival of interest in photoinduced radical thiol-ene chemistry as a powerful tool for the construction of therapeutic peptides.
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Affiliation(s)
- Marzieh Ahangarpour
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand.
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12
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Su C, Tuan NQ, Lee MJ, Zhang XY, Cheng JH, Jin YY, Zhao XQ, Suh JW. Enhanced Production of Active Ecumicin Component with Higher Antituberculosis Activity by the Rare Actinomycete Nonomuraea sp. MJM5123 Using a Novel Promoter-Engineering Strategy. ACS Synth Biol 2020; 9:3019-3029. [PMID: 32916055 DOI: 10.1021/acssynbio.0c00248] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Ecumicins are potent antituberculosis natural compounds produced by the rare actinomycete Nonomuraea sp. MJM5123. Here, we report an efficient genetic manipulation platform of this rare actinomycete. CRISPR/Cas9-based genome editing was achieved based on successful sporulation. Two genes in the ecumicin gene cluster were further investigated, ecuN and ecuE, which potentially encode a pretailoring cytochrome P450 hydroxylase and the core peptide synthase, respectively. Deletion of ecuN led to an enhanced ratio of the ecumicin compound EcuH16 relative to that of EcuH14, indicating that EcuN is indeed a P450 hydroxylase, and there is catalyzed hydroxylation at the C-3 position in unit12 phenylalanine to transform EcuH16 to the compound EcuH14. Furthermore, promoter engineering of ecuE by employing the strong promoter kasO*P was performed and optimized. We found that integrating the endogenous ribosome-binding site (RBS) of ecuE together with the RBS from kasO*P led to improved ecumicin production and resulted in a remarkably high EcuH16/EcuH14 ratio. Importantly, production of the more active component EcuH16 was considerably increased in the double RBSs engineered strain EPR1 compared to that in the wild-type strain, reaching 310 mg/L. At the same time, this production level was 2.3 times higher than that of the control strain EPA1 with only one RBS from kasO*P. To the best of our knowledge, this is the first report of genome editing and promoter engineering on the rare actinomycete Nonomuraea.
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Affiliation(s)
- Chun Su
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University, Yongin, Gyeonggi, 17058, Republic of Korea
| | - Nguyen-Quang Tuan
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University, Yongin, Gyeonggi, 17058, Republic of Korea
| | - Mi-Jin Lee
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University, Yongin, Gyeonggi, 17058, Republic of Korea
| | - Xia-Ying Zhang
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China
| | - Jin-Hua Cheng
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University, Yongin, Gyeonggi, 17058, Republic of Korea
| | - Ying-Yu Jin
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University, Yongin, Gyeonggi, 17058, Republic of Korea
- R&D Center, MANBANGBIO CO., LTD, Cheoingu, Yongin, Gyeonggi-Do 17058, Republic of Korea
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Joo-Won Suh
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University, Yongin, Gyeonggi, 17058, Republic of Korea
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Hawkins PME, Tran W, Nagalingam G, Cheung CY, Giltrap AM, Cook GM, Britton WJ, Payne RJ. Total Synthesis and Antimycobacterial Activity of Ohmyungsamycin A, Deoxyecumicin, and Ecumicin. Chemistry 2020; 26:15200-15205. [PMID: 32567168 DOI: 10.1002/chem.202002408] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/15/2020] [Indexed: 12/24/2022]
Abstract
The ohmyungsamycin and ecumicin natural product families are structurally related cyclic depsipeptides that display potent antimycobacterial activity. Herein the total syntheses of ohmyungsamycin A, deoxyecumicin, and ecumicin are reported, together with the direct biological comparison of members of these natural product families against Mycobacterium tuberculosis (Mtb), the etiological agent of tuberculosis (TB). The synthesis of each of the natural products employed a solid-phase strategy to assemble the linear peptide precursor, involving a key on-resin esterification and an optional on-resin dimethylation step, before a final solution-phase macrolactamization between the non-proteinogenic N-methyl-4-methoxy-l-tryptophan amino acid and a bulky N-methyl-l-valine residue. The synthetic natural products possessed potent antimycobacterial activity against Mtb with MIC90 's ranging from 110-360 nm and retained activity against Mtb in Mtb-infected macrophages. Deoxyecumicin also exhibited rapid bactericidal killing against Mtb, sterilizing cultures after 21 days.
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Affiliation(s)
- Paige M E Hawkins
- School of Chemistry, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Wendy Tran
- School of Chemistry, The University of Sydney, Sydney, NSW, 2006, Australia
| | | | - Chen-Yi Cheung
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, PO Box 56, 9016, Dunedin, New Zealand
| | - Andrew M Giltrap
- School of Chemistry, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Gregory M Cook
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, PO Box 56, 9016, Dunedin, New Zealand
| | - Warwick J Britton
- Centenary Institute, The University of Sydney, Sydney, NSW, 2006, Australia.,Central Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Sydney, NSW, 2006, Australia
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14
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Di Natale C, De Benedictis I, De Benedictis A, Marasco D. Metal-Peptide Complexes as Promising Antibiotics to Fight Emerging Drug Resistance: New Perspectives in Tuberculosis. Antibiotics (Basel) 2020; 9:antibiotics9060337. [PMID: 32570779 PMCID: PMC7344629 DOI: 10.3390/antibiotics9060337] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/14/2020] [Accepted: 06/16/2020] [Indexed: 12/21/2022] Open
Abstract
In metal-peptide interactions, cations form stable complexes through bonds with coordinating groups as side chains of amino acids. These compounds, among other things, exert a wide variety of antimicrobial activities through structural changes of peptides upon metal binding and redox chemistry. They exhibit different mechanisms of action (MOA), including the modification of DNA/RNA, protein and cell wall synthesis, permeabilization and modulation of gradients of cellular membranes. Nowadays, the large increase in antibiotic resistance represents a crucial problem to limit progression at the pandemic level of the diseases that seemed nearly eradicated, such as tuberculosis (Tb). Mycobacterium tuberculosis (Mtb) is intrinsically resistant to many antibiotics due to chromosomal mutations which can lead to the onset of novel strains. Consequently, the maximum pharmaceutical effort should be focused on the development of new therapeutic agents and antimicrobial peptides can represent a valuable option as a copious source of potential bioactive compounds. The introduction of a metal center can improve chemical diversity and hence specificity and bioavailability while, in turn, the coordination to peptides of metal complexes can protect them and enhance their poor water solubility and air stability: the optimization of these parameters is strictly required for drug prioritization and to obtain potent inhibitors of Mtb infections with novel MOAs. Here, we present a panoramic review of the most recent findings in the field of metal complex-peptide conjugates and their delivery systems with the potential pharmaceutical application as novel antibiotics in Mtb infections.
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Affiliation(s)
- Concetta Di Natale
- Department of Pharmacy, University of Naples “Federico II”, 80134 Napoli NA, Italy; (C.D.N.); (I.D.B.); (A.D.B.)
- Center for Advanced Biomaterial for Health Care (CABHC), Istituto Italiano di Tecnologia, 80125 Naples, Italy
- Interdisciplinary Research Centre on Biomaterials (CRIB) and Dipartimento di Ingegneria Chimica, dei Materiali e della Produzione Industriale, University of Naples Federico II, Piazzale Tecchio 80, 80125 Naples, Italy
| | - Ilaria De Benedictis
- Department of Pharmacy, University of Naples “Federico II”, 80134 Napoli NA, Italy; (C.D.N.); (I.D.B.); (A.D.B.)
| | - Arianna De Benedictis
- Department of Pharmacy, University of Naples “Federico II”, 80134 Napoli NA, Italy; (C.D.N.); (I.D.B.); (A.D.B.)
| | - Daniela Marasco
- Department of Pharmacy, University of Naples “Federico II”, 80134 Napoli NA, Italy; (C.D.N.); (I.D.B.); (A.D.B.)
- Correspondence:
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15
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Wolf NM, Lee H, Zagal D, Nam JW, Oh DC, Lee H, Suh JW, Pauli GF, Cho S, Abad-Zapatero C. Structure of the N-terminal domain of ClpC1 in complex with the antituberculosis natural product ecumicin reveals unique binding interactions. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020; 76:458-471. [PMID: 32355042 PMCID: PMC7193532 DOI: 10.1107/s2059798320004027] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 03/22/2020] [Indexed: 11/10/2022]
Abstract
The biological processes related to protein homeostasis in Mycobacterium tuberculosis, the etiologic agent of tuberculosis, have recently been established as critical pathways for therapeutic intervention. Proteins of particular interest are ClpC1 and the ClpC1-ClpP1-ClpP2 proteasome complex. The structure of the potent antituberculosis macrocyclic depsipeptide ecumicin complexed with the N-terminal domain of ClpC1 (ClpC1-NTD) is presented here. Crystals of the ClpC1-NTD-ecumicin complex were monoclinic (unit-cell parameters a = 80.0, b = 130.0, c = 112.0 Å, β = 90.07°; space group P21; 12 complexes per asymmetric unit) and diffracted to 2.5 Å resolution. The structure was solved by molecular replacement using the self-rotation function to resolve space-group ambiguities. The new structure of the ecumicin complex showed a unique 1:2 (target:ligand) stoichiometry exploiting the intramolecular dyad in the α-helical fold of the target N-terminal domain. The structure of the ecumicin complex unveiled extensive interactions in the uniquely extended N-terminus, a critical binding site for the known cyclopeptide complexes. This structure, in comparison with the previously reported rufomycin I complex, revealed unique features that could be relevant for understanding the mechanism of action of these potential antituberculosis drug leads. Comparison of the ecumicin complex and the ClpC1-NTD-L92S/L96P double-mutant structure with the available structures of rufomycin I and cyclomarin A complexes revealed a range of conformational changes available to this small N-terminal helical domain and the minor helical alterations involved in the antibiotic-resistance mechanism. The different modes of binding and structural alterations could be related to distinct modes of action.
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Affiliation(s)
- Nina M Wolf
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Hyun Lee
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Daniel Zagal
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Joo Won Nam
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Dong Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Hanki Lee
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University, Cheoin-gu, Yongin-si, Gyeonggi-do 17058, Republic of Korea
| | - Joo Won Suh
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University, Cheoin-gu, Yongin-si, Gyeonggi-do 17058, Republic of Korea
| | - Guido F Pauli
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Sanghyun Cho
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Celerino Abad-Zapatero
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
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16
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17
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Yathursan S, Wiles S, Read H, Sarojini V. A review on anti-tuberculosis peptides: Impact of peptide structure on anti-tuberculosis activity. J Pept Sci 2019; 25:e3213. [PMID: 31515916 DOI: 10.1002/psc.3213] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 08/03/2019] [Accepted: 08/07/2019] [Indexed: 12/18/2022]
Abstract
Antibiotic resistance is a major public health problem globally. Particularly concerning amongst drug-resistant human pathogens is Mycobacterium tuberculosis that causes the deadly infectious tuberculosis (TB) disease. Significant issues associated with current treatment options for drug-resistant TB and the high rate of mortality from the disease makes the development of novel treatment options against this pathogen an urgent need. Antimicrobial peptides are part of innate immunity in all forms of life and could provide a potential solution against drug-resistant TB. This review is a critical analysis of antimicrobial peptides that are reported to be active against the M tuberculosis complex exclusively. However, activity on non-TB strains such as Mycobacterium avium and Mycobacterium intracellulare, whenever available, have been included at appropriate sections for these anti-TB peptides. Natural and synthetic antimicrobial peptides of diverse sequences, along with their chemical structures, are presented, discussed, and correlated to their observed antimycobacterial activities. Critical analyses of the structure allied to the anti-mycobacterial activity have allowed us to draw important conclusions and ideas for research and development on these promising molecules to realise their full potential. Even though the review is focussed on peptides, we have briefly summarised the structures and potency of the various small molecule drugs that are available and under development, for TB treatment.
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Affiliation(s)
- Sutharsana Yathursan
- School of Chemical Sciences, University of Auckland, Private Bag, 92019, Auckland, New Zealand
| | - Siouxsie Wiles
- Bioluminescent Superbugs Lab, Department of Molecular Medicine and Pathology, University of Auckland, Private Bag, 92019, Auckland, New Zealand
| | - Hannah Read
- Bioluminescent Superbugs Lab, Department of Molecular Medicine and Pathology, University of Auckland, Private Bag, 92019, Auckland, New Zealand
| | - Vijayalekshmi Sarojini
- School of Chemical Sciences, University of Auckland, Private Bag, 92019, Auckland, New Zealand.,The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, 6140, New Zealand
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18
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Strategies in anti-Mycobacterium tuberculosis drug discovery based on phenotypic screening. J Antibiot (Tokyo) 2019; 72:719-728. [PMID: 31292530 PMCID: PMC6760628 DOI: 10.1038/s41429-019-0205-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 06/05/2019] [Accepted: 06/11/2019] [Indexed: 11/20/2022]
Abstract
The rise of multi- and extensively drug-resistant Mycobacterium tuberculosis (M. tb) strains and co-infection with human immunodeficiency virus has escalated the need for new anti-M. tb drugs. Numerous challenges associated with the M. tb, in particular slow growth and pathogenicity level 3, discouraged use of this organism in past primary screening efforts. From current knowledge of the physiology and drug susceptibility of mycobacteria in general and M. tb specifically, it can be assumed that many potentially useful drug leads were missed by failing to screen directly against this pathogen. This review discusses recent high-throughput phenotypic screening strategies for anti-M. tb drug discovery. Emphasis is placed on prioritization of hits, including their extensive biological and chemical profiling, as well as the development status of promising drug candidates discovered with phenotypic screening.
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19
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Wolf NM, Lee H, Choules MP, Pauli GF, Phansalkar R, Anderson JR, Gao W, Ren J, Santarsiero BD, Lee H, Cheng J, Jin YY, Ho NA, Duc NM, Suh JW, Abad-Zapatero C, Cho S. High-Resolution Structure of ClpC1-Rufomycin and Ligand Binding Studies Provide a Framework to Design and Optimize Anti-Tuberculosis Leads. ACS Infect Dis 2019; 5:829-840. [PMID: 30990022 DOI: 10.1021/acsinfecdis.8b00276] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Addressing the urgent need to develop novel drugs against drug-resistant Mycobacterium tuberculosis ( M. tb) strains, ecumicin (ECU) and rufomycin I (RUFI) are being explored as promising new leads targeting cellular proteostasis via the caseinolytic protein ClpC1. Details of the binding topology and chemical mode of (inter)action of these cyclopeptides help drive further development of novel potency-optimized entities as tuberculosis drugs. ClpC1 M. tb protein constructs with mutations driving resistance to ECU and RUFI show reduced binding affinity by surface plasmon resonance (SPR). Despite certain structural similarities, ECU and RUFI resistant mutation sites did not overlap in their SPR binding patterns. SPR competition experiments show ECU prevents RUFI binding, whereas RUFI partially inhibits ECU binding. The X-ray structure of the ClpC1-NTD-RUFI complex reveals distinct differences compared to the previously reported ClpC1-NTD-cyclomarin A structure. Surprisingly, the complex structure revealed that the epoxide moiety of RUFI opened and covalently bound to ClpC1-NTD via the sulfur atom of Met1. Furthermore, RUFI analogues indicate that the epoxy group of RUFI is critical for binding and bactericidal activity. The outcomes demonstrate the significance of ClpC1 as a novel target and the importance of SAR analysis of identified macrocyclic peptides for drug discovery.
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Affiliation(s)
- Nina M. Wolf
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Hyun Lee
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Biophysics Core at the Research Resource Center, University of Illinois at Chicago, 1100 S. Ashland Street, Chicago, Illinois 60612, United States
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Mary P. Choules
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Guido F. Pauli
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Rasika Phansalkar
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Jeffrey R. Anderson
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Wei Gao
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Jinhong Ren
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, 900 S. Ashland Street, Chicago, Illinois 60612, United States
| | - Bernard D. Santarsiero
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, 900 S. Ashland Street, Chicago, Illinois 60612, United States
| | - Hanki Lee
- Center for Nutraceutical and Pharmaceutical Materials, College of Natural Sciences, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin-si, Gyeonggi-do 17058, Republic of Korea
| | - Jinhua Cheng
- Center for Nutraceutical and Pharmaceutical Materials, College of Natural Sciences, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin-si, Gyeonggi-do 17058, Republic of Korea
- Division of Bioscience and Bioinformatics, College of Natural Sciences, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin-si, Gyeonggi-do 17058, Republic of Korea
| | - Ying-Yu Jin
- Center for Nutraceutical and Pharmaceutical Materials, College of Natural Sciences, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin-si, Gyeonggi-do 17058, Republic of Korea
- Division of Bioscience and Bioinformatics, College of Natural Sciences, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin-si, Gyeonggi-do 17058, Republic of Korea
| | - Ngoc Anh Ho
- Center for Nutraceutical and Pharmaceutical Materials, College of Natural Sciences, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin-si, Gyeonggi-do 17058, Republic of Korea
| | - Nguyen Minh Duc
- Center for Nutraceutical and Pharmaceutical Materials, College of Natural Sciences, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin-si, Gyeonggi-do 17058, Republic of Korea
| | - Joo-Won Suh
- Center for Nutraceutical and Pharmaceutical Materials, College of Natural Sciences, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin-si, Gyeonggi-do 17058, Republic of Korea
- Division of Bioscience and Bioinformatics, College of Natural Sciences, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin-si, Gyeonggi-do 17058, Republic of Korea
| | - Celerino Abad-Zapatero
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, 900 S. Ashland Street, Chicago, Illinois 60612, United States
| | - Sanghyun Cho
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
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Schrey H, Spiteller P. E- and Z-Proxamidines, Unprecedented 1,3-Diazacyclooct-1-ene Alkaloids from Fruiting Bodies of Laccaria proxima. Chemistry 2019; 25:8035-8042. [PMID: 31033066 DOI: 10.1002/chem.201900566] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Indexed: 11/07/2022]
Abstract
Fruiting bodies of Laccaria proxima were screened for the presence of new secondary metabolites by means of HPLC-UV and LC-HR-(+)-ESIMS. Thus, two isomeric alkaloids with a highly unusual core structure, E-proxamidine and its Z-isomer, were isolated from Laccaria proxima. The proxamidines consist of an eight-membered heterocyclic ring system with a formamidine unit. The structures were established by 2D NMR spectroscopic methods, HR-(+)-ESIMS, and HR-(+)-ESIMS/MS. The proxamidines are probably biosynthetically derived from tryptophan, dimethylallyl pyrophosphate, and S-adenosylmethionine and the eight-membered ring of the proxamidines is likely to be generated by a rearrangement of the tryptophan sceleton. Metabolic profiling of fruiting bodies of some other Laccaria species revealed that the proxamidines appear in significant amounts only in L. proxima making the compounds suitable as chemotaxonomic markers. E-Proxamidine exhibits herbicidal activity against Lepidium sativum.
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Affiliation(s)
- Hedda Schrey
- Institut für Organische und Analytische Chemie, Universität Bremen, Leobener Straße 7, 28359, Bremen, Germany
| | - Peter Spiteller
- Institut für Organische und Analytische Chemie, Universität Bremen, Leobener Straße 7, 28359, Bremen, Germany
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21
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Synthesis and exploration of in-silico and in-vitro α-glucosidase and α-amylase inhibitory activities of N-(3-acetyl-2-methyl-4-phenylquinolin-6-yl)arylamides. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2019. [DOI: 10.1007/s13738-018-01580-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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22
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Using chemical inhibitors to probe AAA protein conformational dynamics and cellular functions. Curr Opin Chem Biol 2019; 50:45-54. [PMID: 30913482 DOI: 10.1016/j.cbpa.2019.02.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/18/2019] [Accepted: 02/19/2019] [Indexed: 01/24/2023]
Abstract
The AAA proteins are a family of enzymes that play key roles in diverse dynamic cellular processes, ranging from proteostasis to directional intracellular transport. Dysregulation of AAA proteins has been linked to several diseases, including cancer, suggesting a possible therapeutic role for inhibitors of these enzymes. In the past decade, new chemical probes have been developed for AAA proteins including p97, dynein, midasin, and ClpC1. In this review, we discuss how these compounds have been used to study the cellular functions and conformational dynamics of AAA proteins. We discuss future directions for inhibitor development and early efforts to utilize AAA protein inhibitors in the clinical setting.
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23
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Zhao P, Xue Y, Gao W, Li J, Zu X, Fu D, Feng S, Bai X, Zuo Y, Li P. Actinobacteria-Derived peptide antibiotics since 2000. Peptides 2018; 103:48-59. [PMID: 29567053 DOI: 10.1016/j.peptides.2018.03.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 03/16/2018] [Accepted: 03/18/2018] [Indexed: 11/23/2022]
Abstract
Members of the Actinobacteria, including Streptomyces spp., Kutzneria sp. Actinoplanes spp., Actinomycete sp., Nocardia sp., Brevibacteriumsp.,Actinomadura spp., Micromonospora sp., Amycolatopsis spp., Nonomuraea spp., Nocardiopsis spp., Marinactinospora sp., Rhodococcus sp., Lentzea sp., Actinokineospora sp., Planomonospora sp., Streptomonospora sp., and Microbacterium sp., are an important source of structurally diverse classes of short peptides of ∼30 residues or fewer that will likely play an important role in new antibiotic development and discovery. Additionally, many have unique structures that make them recalcitrant to traditional modes of drug resistance via novel mechanisms, and these are ideal therapeutic tools and potential alternatives to current antibiotics. The need for novel antibiotic is urgent, and this review summarizes 199 Actinobacteria compounds published since 2000, including 35 cyclic lipopeptides containing piperazic or pipecolic acids, eight aromatic peptides, five glycopeptides, 21 bicyclic peptides, 44 other cyclic lipopeptides, five linear lipopeptides, six 2,5-diketopiperazines, one dimeric peptide, four nucleosidyl peptides, two thioamide-containing peptides, 25 thiopeptides, nine lasso peptides, and 34 typical cyclic peptides. The current and potential therapeutic applications of these peptides, including their structure, antituberculotic, antibacterial, antifungal, antiviral, anti-brugia, anti-plasmodial, and anti-trypanosomal activities, are discussed.
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Affiliation(s)
- Pengchao Zhao
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Yun Xue
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China.
| | - Weina Gao
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Jinghua Li
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Xiangyang Zu
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Dongliao Fu
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Shuxiao Feng
- College of Chemical Engineering and Pharmacy, Henan University of Science and Technology, Luoyang, 471023, China
| | - Xuefei Bai
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Yanjun Zuo
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Ping Li
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
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24
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Target discovery focused approaches to overcome bottlenecks in the exploitation of antimycobacterial natural products. Future Med Chem 2018; 10:811-822. [PMID: 29569936 DOI: 10.4155/fmc-2017-0273] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Tuberculosis is a major global health hazard. The search for new antimycobacterials has focused on such as screening combinational chemistry libraries or designing chemicals to target predefined pockets of essential bacterial proteins. The relative ineffectiveness of these has led to a reappraisal of natural products for new antimycobacterial drug leads. However, progress has been limited, we suggest through a failure in many cases to define the drug target and optimize the hits using this information. We highlight methods of target discovery needed to develop a drug into a candidate for clinical trials. We incorporate these into suggested analysis pipelines which could inform the research strategies to accelerate the development of new drug leads from natural products.
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25
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Hur J, Jang J, Sim J, Son WS, Ahn HC, Kim TS, Shin YH, Lim C, Lee S, An H, Kim SH, Oh DC, Jo EK, Jang J, Lee J, Suh YG. Conformation-Enabled Total Syntheses of Ohmyungsamycins A and B and Structural Revision of Ohmyungsamycin B. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201711286] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Joonseong Hur
- College of Pharmacy; Seoul National University; 1 Gwanak-ro Gwanak-gu Seoul 08826 Republic of Korea
| | - Jaebong Jang
- College of Pharmacy; Seoul National University; 1 Gwanak-ro Gwanak-gu Seoul 08826 Republic of Korea
| | - Jaehoon Sim
- College of Pharmacy; Seoul National University; 1 Gwanak-ro Gwanak-gu Seoul 08826 Republic of Korea
- College of Pharmacy; CHA University; 120 Haeryong-ro Pocheon Gyeonggi-do 11160 Republic of Korea
| | - Woo Sung Son
- College of Pharmacy; CHA University; 120 Haeryong-ro Pocheon Gyeonggi-do 11160 Republic of Korea
| | - Hee-Chul Ahn
- Department of Pharmacy; Dongguk University; Dongguk-ro 32 Ilsandong-gu, Goyang Geonggi-do 10326 Republic of Korea
| | - Tae Sung Kim
- Department of Microbiology; Chungnam National University School of Medicine; Munhwa-ro 266 Jungku Daejeon 35015 Republic of Korea
| | - Yern-Hyerk Shin
- Natural Products Research Institute; College of Pharmacy; Seoul National University; 1 Gwanak-ro Gwanak-gu Seoul 08826 Republic of Korea
| | - Changjin Lim
- College of Pharmacy; Seoul National University; 1 Gwanak-ro Gwanak-gu Seoul 08826 Republic of Korea
- College of Pharmacy; CHA University; 120 Haeryong-ro Pocheon Gyeonggi-do 11160 Republic of Korea
| | - Seungbeom Lee
- College of Pharmacy; Seoul National University; 1 Gwanak-ro Gwanak-gu Seoul 08826 Republic of Korea
| | - Hongchan An
- College of Pharmacy; Seoul National University; 1 Gwanak-ro Gwanak-gu Seoul 08826 Republic of Korea
| | - Seok-Ho Kim
- College of Pharmacy; CHA University; 120 Haeryong-ro Pocheon Gyeonggi-do 11160 Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute; College of Pharmacy; Seoul National University; 1 Gwanak-ro Gwanak-gu Seoul 08826 Republic of Korea
| | - Eun-Kyeong Jo
- Department of Microbiology; Chungnam National University School of Medicine; Munhwa-ro 266 Jungku Daejeon 35015 Republic of Korea
| | - Jichan Jang
- Division of Applied Life Science; Research Institute of Life Science; Gyeongsang National University; Jinju 52828 Republic of Korea
| | - Jeeyeon Lee
- College of Pharmacy; Seoul National University; 1 Gwanak-ro Gwanak-gu Seoul 08826 Republic of Korea
| | - Young-Ger Suh
- College of Pharmacy; Seoul National University; 1 Gwanak-ro Gwanak-gu Seoul 08826 Republic of Korea
- College of Pharmacy; CHA University; 120 Haeryong-ro Pocheon Gyeonggi-do 11160 Republic of Korea
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26
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Hur J, Jang J, Sim J, Son WS, Ahn HC, Kim TS, Shin YH, Lim C, Lee S, An H, Kim SH, Oh DC, Jo EK, Jang J, Lee J, Suh YG. Conformation-Enabled Total Syntheses of Ohmyungsamycins A and B and Structural Revision of Ohmyungsamycin B. Angew Chem Int Ed Engl 2018; 57:3069-3073. [PMID: 29380472 DOI: 10.1002/anie.201711286] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 12/28/2017] [Indexed: 01/06/2023]
Abstract
The first total syntheses of the bioactive cyclodepsipeptides ohmyungsamycin A and B are described. Key features of our synthesis include the concise preparation of a linear cyclization precursor that consists of N-methyl amides and non-proteinogenic amino acids, and its macrolactamization from a bent conformation. The proposed structure of ohmyungsamycin B was revised based on its synthesis. The cyclic core of the ohmyungsamycins was shown to be responsible for the excellent antituberculosis activity, and ohmyungsamycin variants with truncated chains were evaluated for their biological activity.
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Affiliation(s)
- Joonseong Hur
- College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Jaebong Jang
- College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Jaehoon Sim
- College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.,College of Pharmacy, CHA University, 120 Haeryong-ro, Pocheon, Gyeonggi-do, 11160, Republic of Korea
| | - Woo Sung Son
- College of Pharmacy, CHA University, 120 Haeryong-ro, Pocheon, Gyeonggi-do, 11160, Republic of Korea
| | - Hee-Chul Ahn
- Department of Pharmacy, Dongguk University, Dongguk-ro 32, Ilsandong-gu, Goyang, Geonggi-do, 10326, Republic of Korea
| | - Tae Sung Kim
- Department of Microbiology, Chungnam National University School of Medicine, Munhwa-ro 266, Jungku, Daejeon, 35015, Republic of Korea
| | - Yern-Hyerk Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Changjin Lim
- College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.,College of Pharmacy, CHA University, 120 Haeryong-ro, Pocheon, Gyeonggi-do, 11160, Republic of Korea
| | - Seungbeom Lee
- College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Hongchan An
- College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Seok-Ho Kim
- College of Pharmacy, CHA University, 120 Haeryong-ro, Pocheon, Gyeonggi-do, 11160, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Eun-Kyeong Jo
- Department of Microbiology, Chungnam National University School of Medicine, Munhwa-ro 266, Jungku, Daejeon, 35015, Republic of Korea
| | - Jichan Jang
- Division of Applied Life Science, Research Institute of Life Science, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Jeeyeon Lee
- College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Young-Ger Suh
- College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.,College of Pharmacy, CHA University, 120 Haeryong-ro, Pocheon, Gyeonggi-do, 11160, Republic of Korea
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27
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Abstract
The first total synthesis of the potent anti-mycobacterial cyclic depsipeptide natural product ecumicin is described. Synthesis was achieved via a solid-phase strategy, incorporating the synthetic non-proteinogenic amino acids N-methyl-4-methoxy-l-tryptophan and threo-β-hydroxy-l-phenylalanine into the growing linear peptide chain. The synthesis employed key on-resin esterification and dimethylation steps as well as a final macrolactamization between the unusual N-methyl-4-methoxy-l-tryptophan unit and a bulky N-methyl-l-valine residue. The synthetic natural product possessed potent antimycobacterial activity against the virulent H37Rv strain of Mycobacterium tuberculosis (MIC90 = 312 nM).
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Affiliation(s)
- Paige M E Hawkins
- School of Chemistry, The University of Sydney , Sydney, NSW 2006, Australia
| | - Andrew M Giltrap
- School of Chemistry, The University of Sydney , Sydney, NSW 2006, Australia
| | - Gayathri Nagalingam
- Tuberculosis Research Program, Centenary Institute, and Sydney Medical School, The University of Sydney , Sydney, NSW 2006, Australia
| | - Warwick J Britton
- Tuberculosis Research Program, Centenary Institute, and Sydney Medical School, The University of Sydney , Sydney, NSW 2006, Australia
| | - Richard J Payne
- School of Chemistry, The University of Sydney , Sydney, NSW 2006, Australia
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28
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Gao W, McAlpine JB, Choules MP, Napolitano JG, Lankin DC, Simmler C, Ho NA, Lee H, Suh JW, Burton IW, Cho S, Franzblau SG, Chen SN, Pauli GF. Structural Sequencing of Oligopeptides Aided by 1H Iterative Full-Spin Analysis. JOURNAL OF NATURAL PRODUCTS 2017; 80:2630-2643. [PMID: 29035048 DOI: 10.1021/acs.jnatprod.7b00207] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
This report describes an approach using 1H NMR iterative full-spin analysis (HiFSA) to extract definitive structural information on unknown peptides from 1D 1H NMR data. By comparing the experimental data and HiFSA fingerprint of a known analogue, it is possible to isolate the characteristic 1H subspectrum of the different amino acids and, thus, elucidate the structure of the peptide. To illustrate this methodology, a comprehensive analysis of five new anti-Mycobacterium tuberculosis peptides (2-6), all analogues of ecumicin (1), was carried out. The method was validated by demonstrating congruence of the HiFSA-based structures with all available data, including MS and 2D NMR. The highly reproducible HiFSA fingerprints of the new ∼1600 amu peptides were generated in this process. Besides oligo-peptides, the HiFSA sequencing approach could be extended to all oligomeric compounds consisting of chains of monomers lacking H-H spin-spin coupling across the moieties. HiFSA sequencing is capable of differentiating complex oligomers that exhibit minor structural differences such as shifted hydoxyl or methyl groups. Because it employs the basic and most sensitive 1D 1H NMR experiment, HiFSA sequencing enables the exploration of peptide analogues up to at least 2000 amu, even with basic contemporary spectrometers and when only sub-milligram amounts of isolates are available.
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Affiliation(s)
- Wei Gao
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago , Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago , Chicago, Illinois 60612, United States
| | - James B McAlpine
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago , Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago , Chicago, Illinois 60612, United States
| | - Mary P Choules
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago , Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago , Chicago, Illinois 60612, United States
| | - José G Napolitano
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago , Chicago, Illinois 60612, United States
- Center for Natural Product Technologies, College of Pharmacy, University of Illinois at Chicago , Chicago, Illinois 60612, United States
| | - David C Lankin
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago , Chicago, Illinois 60612, United States
- Center for Natural Product Technologies, College of Pharmacy, University of Illinois at Chicago , Chicago, Illinois 60612, United States
| | - Charlotte Simmler
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago , Chicago, Illinois 60612, United States
- Center for Natural Product Technologies, College of Pharmacy, University of Illinois at Chicago , Chicago, Illinois 60612, United States
| | - Ngoc Anh Ho
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University , Yongin, Gyeonggi-do 17458, South Korea
| | - Hanki Lee
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University , Yongin, Gyeonggi-do 17458, South Korea
| | - Joo-Won Suh
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University , Yongin, Gyeonggi-do 17458, South Korea
- Division of Biosciences and Bioinformatics, Myongji University , Yongin, Gyeonggi-do 17458, South Korea
| | - Ian W Burton
- Institute for Aquatic and Crop Resource Development, National Research Council , Halifax, Nova Scotia B3H 3Z1, Canada
| | - Sanghyun Cho
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago , Chicago, Illinois 60612, United States
| | - Scott G Franzblau
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago , Chicago, Illinois 60612, United States
| | - Shao-Nong Chen
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago , Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago , Chicago, Illinois 60612, United States
- Center for Natural Product Technologies, College of Pharmacy, University of Illinois at Chicago , Chicago, Illinois 60612, United States
| | - Guido F Pauli
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago , Chicago, Illinois 60612, United States
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago , Chicago, Illinois 60612, United States
- Center for Natural Product Technologies, College of Pharmacy, University of Illinois at Chicago , Chicago, Illinois 60612, United States
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29
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Hussain A, Rather M, Shah A, Bhat Z, Shah A, Ahmad Z, Parvaiz Hassan Q. Antituberculotic activity of actinobacteria isolated from the rare habitats. Lett Appl Microbiol 2017; 65:256-264. [DOI: 10.1111/lam.12773] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 06/12/2017] [Accepted: 07/04/2017] [Indexed: 10/19/2022]
Affiliation(s)
- A. Hussain
- Microbial Biotechnology Division; CSIR-Indian Institute of Integrative Medicine; Srinagar India
- Academy of Scientific and Innovative Research; CSIR-Indian Institute of Integrative Medicine; Jammu Tawi India
| | - M.A. Rather
- Clinical Microbiology and PK/PD Division; CSIR-Indian Institute of Integrative Medicine; Srinagar India
| | - A.M. Shah
- Microbial Biotechnology Division; CSIR-Indian Institute of Integrative Medicine; Srinagar India
| | - Z.S. Bhat
- Clinical Microbiology and PK/PD Division; CSIR-Indian Institute of Integrative Medicine; Srinagar India
| | - A. Shah
- Microbial Biotechnology Division; CSIR-Indian Institute of Integrative Medicine; Srinagar India
| | - Z. Ahmad
- Clinical Microbiology and PK/PD Division; CSIR-Indian Institute of Integrative Medicine; Srinagar India
| | - Q. Parvaiz Hassan
- Microbial Biotechnology Division; CSIR-Indian Institute of Integrative Medicine; Srinagar India
- Academy of Scientific and Innovative Research; CSIR-Indian Institute of Integrative Medicine; Jammu Tawi India
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30
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Mycobacterial Caseinolytic Protease Gene Regulator ClgR Is a Substrate of Caseinolytic Protease. mSphere 2017; 2:mSphere00338-16. [PMID: 28317028 PMCID: PMC5352834 DOI: 10.1128/msphere.00338-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Accepted: 02/20/2017] [Indexed: 02/06/2023] Open
Abstract
With 9 million new cases and more than 1 million deaths per year, tuberculosis, caused by Mycobacterium tuberculosis, is the biggest infectious disease killer globally. New drugs for the treatment of the drug-resistant forms of the disease are needed. Recently, a new target-lead couple, the mycobacterial protease ClpP1P2 and the human anticancer drug bortezomib, was identified. However, we know little about how expression of this protease is regulated, which proteins in the bacterium it degrades, how the protease recognizes its target proteins, and how the inhibition of ClpP1P2 exerts whole-cell antimicrobial activity. Here, we show that the ClpP1P2 protease regulates its own expression, and we identified a new substrate and a new substrate recognition sequence and a mechanism for how ClpP1P2 inhibition causes bacterial growth inhibition. The mycobacterial caseinolytic protease ClpP1P2 is a degradative protease that recently gained interest as a genetically and pharmacologically validated drug target for tuberculosis. The first whole-cell active ClpP1P2 inhibitor, the human proteasome inhibitor bortezomib, is currently undergoing lead optimization to introduce selectivity for the bacterial target. How inhibition of ClpP1P2 translates into whole-cell antimicrobial activity is little understood. Previous work has shown that the caseinolytic protease gene regulator ClgR is an activator of the clpP1P2 genes and also suggested that this transcription factor may be a substrate of the protease. Here, we employ promoter activity reporters and direct mRNA level measurements showing that bortezomib treatment of Mycobacterium bovis BCG increased transcription of clpP1P2 and other ClgR-dependent promoters, suggesting that inhibition of ClpP1P2 increases cellular ClgR levels. Then, we carried out red fluorescent protein-ClgR fusion analyses to show that ClgR is indeed a substrate of ClpP1P2 and to identify ClgR’s C-terminal nonapeptide APVVSLAVA as the signal sufficient for recognition and efficient protein degradation by ClpP1P2. Interestingly, accumulation of ClgR appears to be toxic for bacilli, suggesting a mechanism for how pharmacological inhibition of ClpP1P2 protease activity by bortezomib translates into whole-cell antibacterial activity. IMPORTANCE With 9 million new cases and more than 1 million deaths per year, tuberculosis, caused by Mycobacterium tuberculosis, is the biggest infectious disease killer globally. New drugs for the treatment of the drug-resistant forms of the disease are needed. Recently, a new target-lead couple, the mycobacterial protease ClpP1P2 and the human anticancer drug bortezomib, was identified. However, we know little about how expression of this protease is regulated, which proteins in the bacterium it degrades, how the protease recognizes its target proteins, and how the inhibition of ClpP1P2 exerts whole-cell antimicrobial activity. Here, we show that the ClpP1P2 protease regulates its own expression, and we identified a new substrate and a new substrate recognition sequence and a mechanism for how ClpP1P2 inhibition causes bacterial growth inhibition.
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31
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Gao W, Napolitano JG, Lankin DC, Kim JY, Jin YY, Lee H, Suh JW, Chen SN, Pauli GF. Computer-assisted 1 H NMR analysis of the anti-tuberculosis drug lead ecumicin. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:239-244. [PMID: 27094011 PMCID: PMC5071145 DOI: 10.1002/mrc.4425] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 02/10/2016] [Indexed: 05/28/2023]
Affiliation(s)
- Wei Gao
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, 60612, USA
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - José G. Napolitano
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - David C. Lankin
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Jin-Yong Kim
- Division of Bioscience and Bioinformatics, College of Natural Science, Myongji University, Cheoin-gu, Yongin, Gyeonggi-Do, 17058, Korea
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University, Cheoin-gu, Yongin, Gyeonggi-Do, 17058, Korea
| | - Ying-Yu Jin
- Division of Bioscience and Bioinformatics, College of Natural Science, Myongji University, Cheoin-gu, Yongin, Gyeonggi-Do, 17058, Korea
| | - Hanki Lee
- Division of Bioscience and Bioinformatics, College of Natural Science, Myongji University, Cheoin-gu, Yongin, Gyeonggi-Do, 17058, Korea
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University, Cheoin-gu, Yongin, Gyeonggi-Do, 17058, Korea
| | - Joo-Won Suh
- Division of Bioscience and Bioinformatics, College of Natural Science, Myongji University, Cheoin-gu, Yongin, Gyeonggi-Do, 17058, Korea
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University, Cheoin-gu, Yongin, Gyeonggi-Do, 17058, Korea
| | - Shao-Nong Chen
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, 60612, USA
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Guido F. Pauli
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, 60612, USA
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, 60612, USA
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32
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Recent developments in natural product-based drug discovery for tuberculosis. Drug Discov Today 2017; 22:585-591. [DOI: 10.1016/j.drudis.2016.11.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/14/2016] [Accepted: 11/17/2016] [Indexed: 11/21/2022]
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33
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New tuberculosis drug leads from naturally occurring compounds. Int J Infect Dis 2017; 56:212-220. [PMID: 28062229 DOI: 10.1016/j.ijid.2016.12.024] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 12/21/2016] [Accepted: 12/22/2016] [Indexed: 12/21/2022] Open
Abstract
Tuberculosis (TB) continues to be a significant cause of mortality and morbidity worldwide. An estimated 2 billion individuals are infected with Mycobacterium tuberculosis and annually there are approximately 10 million new cases of clinical TB and 1.5 million deaths. Currently available drugs and vaccines have had no significant impact on TB control. In addition, the emergence of drug resistant TB is considered a public health crisis, with some strains now resistant to all available drugs. Unfortunately, the growing burden of antibiotic resistance is coupled with decreased effort in the development of new antibiotics. Natural sources are attractive starting points in the search for anti-tubercular drugs because they are extremely rich in chemical diversity and have privileged antimicrobial activity. This review will discuss recent advances in the development of TB drug leads from natural products, with a particular focus on anti-mycobacterial compounds in late-stage preclinical and clinical development.
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34
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Malik IT, Brötz-Oesterhelt H. Conformational control of the bacterial Clp protease by natural product antibiotics. Nat Prod Rep 2017; 34:815-831. [DOI: 10.1039/c6np00125d] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Natural products targeting the bacterial Clp protease unravel key interfaces for protein–protein–interaction and long-distance conformational control.
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Affiliation(s)
- I. T. Malik
- Department of Microbial Bioactive Compounds
- Interfaculty Institute of Microbiology and Infection Medicine
- University of Tuebingen
- Germany
| | - H. Brötz-Oesterhelt
- Department of Microbial Bioactive Compounds
- Interfaculty Institute of Microbiology and Infection Medicine
- University of Tuebingen
- Germany
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35
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Grzelak EM, Hwang C, Cai G, Nam JW, Choules MP, Gao W, Lankin DC, McAlpine JB, Mulugeta SG, Napolitano JG, Suh JW, Yang SH, Cheng J, Lee H, Kim JY, Cho SH, Pauli GF, Franzblau SG, Jaki BU. Bioautography with TLC-MS/NMR for Rapid Discovery of Anti-tuberculosis Lead Compounds from Natural Sources. ACS Infect Dis 2016; 2:294-301. [PMID: 27478868 DOI: 10.1021/acsinfecdis.5b00150] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
While natural products constitute an established source of lead compounds, the classical iterative bioassay-guided isolation process is both time- and labor-intensive and prone to failing to identify active minor constituents. (HP)TLC-bioautography-MS/NMR, which combines cutting-edge microbiological, chromatographic, and spectrometric technologies, was developed to accelerate anti-tuberculosis (TB) drug discovery from natural sources by acquiring structural information at a very early stage of the isolation process. Using the avirulent, bioluminescent Mtb strain mc27000 luxABCDE, three variations of bioautography were evaluated and optimized for sensitivity in detecting anti-TB agents, including established clinical agents and new leads with novel mechanisms of action. Several exemplary applications of this approach to microbial extracts demonstrate its potential as a routine method in anti-TB drug discovery from natural sources.
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Affiliation(s)
- Edyta M. Grzelak
- Institute for Tuberculosis Research and ‡Department of
Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Changhwa Hwang
- Institute for Tuberculosis Research and ‡Department of
Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Geping Cai
- Institute for Tuberculosis Research and ‡Department of
Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Joo-Won Nam
- Institute for Tuberculosis Research and ‡Department of
Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Mary P. Choules
- Institute for Tuberculosis Research and ‡Department of
Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Wei Gao
- Institute for Tuberculosis Research and ‡Department of
Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - David C. Lankin
- Institute for Tuberculosis Research and ‡Department of
Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - James B. McAlpine
- Institute for Tuberculosis Research and ‡Department of
Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Surafel G. Mulugeta
- Institute for Tuberculosis Research and ‡Department of
Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | | | - Joo-Won Suh
- Center for
Nutraceutical and Pharmaceutical Materials and Division of Bioscience
and Bioinformatics, College of Natural Science, Myongji University, Cheoin-gu, Gyeonggi-Do 449-728, Republic of Korea
| | - Seung Hwan Yang
- Center for
Nutraceutical and Pharmaceutical Materials and Division of Bioscience
and Bioinformatics, College of Natural Science, Myongji University, Cheoin-gu, Gyeonggi-Do 449-728, Republic of Korea
| | - Jinhua Cheng
- Center for
Nutraceutical and Pharmaceutical Materials and Division of Bioscience
and Bioinformatics, College of Natural Science, Myongji University, Cheoin-gu, Gyeonggi-Do 449-728, Republic of Korea
| | - Hanki Lee
- Center for
Nutraceutical and Pharmaceutical Materials and Division of Bioscience
and Bioinformatics, College of Natural Science, Myongji University, Cheoin-gu, Gyeonggi-Do 449-728, Republic of Korea
| | - Jin-Yong Kim
- Center for
Nutraceutical and Pharmaceutical Materials and Division of Bioscience
and Bioinformatics, College of Natural Science, Myongji University, Cheoin-gu, Gyeonggi-Do 449-728, Republic of Korea
| | - Sang-Hyun Cho
- Institute for Tuberculosis Research and ‡Department of
Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Guido F. Pauli
- Institute for Tuberculosis Research and ‡Department of
Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Scott G. Franzblau
- Institute for Tuberculosis Research and ‡Department of
Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Birgit U. Jaki
- Institute for Tuberculosis Research and ‡Department of
Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
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36
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Famulla K, Sass P, Malik I, Akopian T, Kandror O, Alber M, Hinzen B, Ruebsamen-Schaeff H, Kalscheuer R, Goldberg AL, Brötz-Oesterhelt H. Acyldepsipeptide antibiotics kill mycobacteria by preventing the physiological functions of the ClpP1P2 protease. Mol Microbiol 2016; 101:194-209. [PMID: 26919556 DOI: 10.1111/mmi.13362] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2016] [Indexed: 01/06/2023]
Abstract
The Clp protease complex in Mycobacterium tuberculosis is unusual in its composition, functional importance and activation mechanism. Whilst most bacterial species contain a single ClpP protein that is dispensable for normal growth, mycobacteria have two ClpPs, ClpP1 and ClpP2, which are essential for viability and together form the ClpP1P2 tetradecamer. Acyldepsipeptide antibiotics of the ADEP class inhibit the growth of Gram-positive firmicutes by activating ClpP and causing unregulated protein degradation. Here we show that, in contrast, mycobacteria are killed by ADEP through inhibition of ClpP function. Although ADEPs can stimulate purified M. tuberculosis ClpP1P2 to degrade larger peptides and unstructured proteins, this effect is weaker than for ClpP from other bacteria and depends on the presence of an additional activating factor (e.g. the dipeptide benzyloxycarbonyl-leucyl-leucine in vitro) to form the active ClpP1P2 tetradecamer. The cell division protein FtsZ, which is a particularly sensitive target for ADEP-activated ClpP in firmicutes, is not degraded in mycobacteria. Depletion of the ClpP1P2 level in a conditional Mycobacterium bovis BCG mutant enhanced killing by ADEP unlike in other bacteria. In summary, ADEPs kill mycobacteria by preventing interaction of ClpP1P2 with the regulatory ATPases, ClpX or ClpC1, thus inhibiting essential ATP-dependent protein degradation.
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Affiliation(s)
- Kirsten Famulla
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany
| | - Peter Sass
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany
| | - Imran Malik
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany
| | - Tatos Akopian
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Olga Kandror
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Marina Alber
- Institute for Medical Microbiology and Hospital Hygiene, University of Duesseldorf, Duesseldorf, Germany
| | | | | | - Rainer Kalscheuer
- Institute for Medical Microbiology and Hospital Hygiene, University of Duesseldorf, Duesseldorf, Germany
| | | | - Heike Brötz-Oesterhelt
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Germany
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37
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Chang J, Kwon HJ. Discovery of novel drug targets and their functions using phenotypic screening of natural products. ACTA ACUST UNITED AC 2016; 43:221-31. [DOI: 10.1007/s10295-015-1681-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 08/27/2015] [Indexed: 12/27/2022]
Abstract
Abstract
Natural products are valuable resources that provide a variety of bioactive compounds and natural pharmacophores in modern drug discovery. Discovery of biologically active natural products and unraveling their target proteins to understand their mode of action have always been critical hurdles for their development into clinical drugs. For effective discovery and development of bioactive natural products into novel therapeutic drugs, comprehensive screening and identification of target proteins are indispensable. In this review, a systematic approach to understanding the mode of action of natural products isolated using phenotypic screening involving chemical proteomics-based target identification is introduced. This review highlights three natural products recently discovered via phenotypic screening, namely glucopiericidin A, ecumicin, and terpestacin, as representative case studies to revisit the pivotal role of natural products as powerful tools in discovering the novel functions and druggability of targets in biological systems and pathological diseases of interest.
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Affiliation(s)
- Junghwa Chang
- grid.15444.30 0000000404705454 Department of Biotechnology, Translational Research Center for Protein Function Control, College of Life Science and Biotechnology Yonsei University 120-749 Seoul Republic of Korea
| | - Ho Jeong Kwon
- grid.15444.30 0000000404705454 Department of Biotechnology, Translational Research Center for Protein Function Control, College of Life Science and Biotechnology Yonsei University 120-749 Seoul Republic of Korea
- grid.15444.30 0000000404705454 Department of Internal Medicine, College of Medicine Yonsei University 120-752 Seoul Republic of Korea
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38
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Pauli GF, Niemitz M, Bisson J, Lodewyk MW, Soldi C, Shaw JT, Tantillo DJ, Saya JM, Vos K, Kleinnijenhuis RA, Hiemstra H, Chen SN, McAlpine JB, Lankin DC, Friesen JB. Toward Structural Correctness: Aquatolide and the Importance of 1D Proton NMR FID Archiving. J Org Chem 2016; 81:878-89. [PMID: 26812443 PMCID: PMC4746703 DOI: 10.1021/acs.joc.5b02456] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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The revision of the structure of
the sesquiterpene aquatolide from
a bicyclo[2.2.0]hexane to a bicyclo[2.1.1]hexane structure using compelling
NMR data, X-ray crystallography, and the recent confirmation via full
synthesis exemplify that the achievement of “structural correctness”
depends on the completeness of the experimental evidence. Archived
FIDs and newly acquired aquatolide spectra demonstrate that archiving
and rigorous interpretation of 1D 1H NMR data may enhance
the reproducibility of (bio)chemical research and curb the growing
trend of structural misassignments. Despite being the most accessible
NMR experiment, 1D 1H spectra encode a wealth of information
about bonds and molecular geometry that may be fully mined by 1H iterative full spin analysis (HiFSA). Fully characterized
1D 1H spectra are unideterminant for a given structure.
The corresponding FIDs may be readily submitted with publications
and collected in databases. Proton NMR spectra are indispensable for
structural characterization even in conjunction with 2D data. Quantum
interaction and linkage tables (QuILTs) are introduced for a more
intuitive visualization of 1D J-coupling relationships,
NOESY correlations, and heteronuclear experiments. Overall, this study
represents a significant contribution to best practices in NMR-based
structural analysis and dereplication.
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Affiliation(s)
- Guido F Pauli
- Department of Medicinal Chemistry & Pharmacognosy and Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago , 833 South Wood Street, Chicago, Illinois 60612, United States
| | - Matthias Niemitz
- PERCH Solutions Limited , Puijonkatu 24B5, 70110 Kuopio, Finland
| | - Jonathan Bisson
- Department of Medicinal Chemistry & Pharmacognosy and Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago , 833 South Wood Street, Chicago, Illinois 60612, United States
| | - Michael W Lodewyk
- Physical Science Department, Butte College , Oroville, California 95965, United States
| | - Cristian Soldi
- Department of Chemistry, University of California-Davis , One Shields Avenue, Davis, California 95616, United States.,Federal University of Santa Catarina , Centro de Curitibanos, Rod. Ulysses Gaboardi, Km 3, Curitibanos, SC 89520-000, Brazil
| | - Jared T Shaw
- Department of Chemistry, University of California-Davis , One Shields Avenue, Davis, California 95616, United States
| | - Dean J Tantillo
- Department of Chemistry, University of California-Davis , One Shields Avenue, Davis, California 95616, United States
| | - Jordy M Saya
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Klaas Vos
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Roel A Kleinnijenhuis
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Henk Hiemstra
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Shao-Nong Chen
- Department of Medicinal Chemistry & Pharmacognosy and Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago , 833 South Wood Street, Chicago, Illinois 60612, United States
| | - James B McAlpine
- Department of Medicinal Chemistry & Pharmacognosy and Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago , 833 South Wood Street, Chicago, Illinois 60612, United States
| | - David C Lankin
- Department of Medicinal Chemistry & Pharmacognosy and Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago , 833 South Wood Street, Chicago, Illinois 60612, United States
| | - J Brent Friesen
- Physical Sciences Department, Rosary College of Arts and Sciences, Dominican University , 7900 West Division Street, River Forest, Illinois 60305, United States
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39
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De Leon Rodriguez LM, Kaur H, Brimble MA. Synthesis and bioactivity of antitubercular peptides and peptidomimetics: an update. Org Biomol Chem 2016; 14:1177-87. [DOI: 10.1039/c5ob02298c] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This mini-review provides an update on the synthesis and bioactivity of peptides and peptidomimetics that exhibit very potent antitubercular activity.
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Affiliation(s)
| | - Harveen Kaur
- School of Chemical Sciences
- The University of Auckland
- Auckland
- New Zealand
| | - Margaret A. Brimble
- School of Chemical Sciences
- The University of Auckland
- Auckland
- New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery
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40
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Jin YY, Kim JY, Yang SH, Lee H, Suh JW. Improvement of the productivity of ecumicin, a novel anti-tuberculosis agent, from new Nonomuraea sp. MJM5123. J Antibiot (Tokyo) 2015; 69:362-7. [PMID: 26648116 DOI: 10.1038/ja.2015.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 10/25/2015] [Accepted: 11/12/2015] [Indexed: 10/22/2022]
Abstract
Ecumicin is a novel anti-tuberculosis agent produced by Nonomuraea sp. MJM5123 as a new strain of actinomycetes. First, in order to increase the cell mass of Nonomuraea sp. MJM5123, we optimized the culture conditions with regard to carbon and nitrogen sources. The cell mass of Nonomuraea sp. MJM5123 increased by approximately twofold when glucose and soybean flour were used as carbon and nitrogen sources, respectively. For maximum production of ecumicin, we optimized the culture conditions by adding amino acids as building blocks for ecumicin, by adding vegetable oils and by controlling the temperature and pH. Ecumicin production was two times higher with the addition of valine as the building blocks for ecumicin compared with the production in the absence of valine. Interestingly, with the addition of 1% corn oil, the production of ecumicin increased by 4.6-fold compared with the production in the absence of corn oil. Finally, by controlling the pH and temperature, we established an optimized culture condition in which Nonomuraea sp. MJM5123 produced 576 mg ecumicin per litre of medium, which is about 50 times higher than in the control medium at 30 °C and pH 7.0.
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Affiliation(s)
- Ying-Yu Jin
- Center for Nurtaceutical and Pharmaceutical Materials, Yongin, Gyeonggi-do, Republic of Korea
| | - Jin-Yong Kim
- Division of Biosciences and Bioinformatics, Myongji University, Yongin, Gyeonggi-do, Republic of Korea
| | - Seung Hwan Yang
- Center for Nurtaceutical and Pharmaceutical Materials, Yongin, Gyeonggi-do, Republic of Korea
| | - Hanki Lee
- Center for Nurtaceutical and Pharmaceutical Materials, Yongin, Gyeonggi-do, Republic of Korea
| | - Joo-Won Suh
- Center for Nurtaceutical and Pharmaceutical Materials, Yongin, Gyeonggi-do, Republic of Korea.,Division of Biosciences and Bioinformatics, Myongji University, Yongin, Gyeonggi-do, Republic of Korea
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41
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Anti-tuberculosis lead molecules from natural products targeting Mycobacterium tuberculosis ClpC1. J Ind Microbiol Biotechnol 2015; 43:205-12. [PMID: 26586403 DOI: 10.1007/s10295-015-1709-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 10/31/2015] [Indexed: 02/06/2023]
Abstract
Tuberculosis (TB) is a serious and potentially fatal disease caused by Mycobacterium tuberculosis (M. tb). The occurrence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) M. tb is a significant public health concern because most of the anti-TB drugs that have been in use for over 40 years are no longer effective for the treatment of these infections. Recently, new anti-TB lead compounds such as cyclomarin A, lassomycin, and ecumicin, which are cyclic peptides from actinomycetes, have shown potent anti-TB activity against MDR and XDR M. tb as well as drug-susceptible M. tb in vitro. The target molecule of these antibiotics is ClpC1, a protein that is essential for the growth of M. tb. In this review, we introduce the three anti-TB lead compounds as potential anti-TB therapeutic agents targeting ClpC1 and compare them with the existing anti-TB drugs approved by the US Food and Drug Administration.
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42
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Natural products as probes in pharmaceutical research. J Ind Microbiol Biotechnol 2015; 43:249-60. [PMID: 26438431 DOI: 10.1007/s10295-015-1691-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 09/16/2015] [Indexed: 10/23/2022]
Abstract
From the start of the pharmaceutical research natural products played a key role in drug discovery and development. Over time many discoveries of fundamental new biology were triggered by the unique biological activity of natural products. Unprecedented chemical structures, novel chemotypes, often pave the way to investigate new biology and to explore new pathways and targets. This review summarizes the recent results in the area with a focus on research done in the laboratories of Novartis Institutes for BioMedical Research. We aim to put the technological advances in target identification techniques in the context to the current revival of phenotypic screening and the increasingly complex biological questions related to drug discovery.
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43
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Amos GCA, Borsetto C, Laskaris P, Krsek M, Berry AE, Newsham KK, Calvo-Bado L, Pearce DA, Vallin C, Wellington EMH. Designing and Implementing an Assay for the Detection of Rare and Divergent NRPS and PKS Clones in European, Antarctic and Cuban Soils. PLoS One 2015; 10:e0138327. [PMID: 26398766 PMCID: PMC4580463 DOI: 10.1371/journal.pone.0138327] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 08/28/2015] [Indexed: 11/28/2022] Open
Abstract
The ever increasing microbial resistome means there is an urgent need for new antibiotics. Metagenomics is an underexploited tool in the field of drug discovery. In this study we aimed to produce a new updated assay for the discovery of biosynthetic gene clusters encoding bioactive secondary metabolites. PCR assays targeting the polyketide synthases (PKS) and non-ribosomal peptide synthetases (NRPS) were developed. A range of European soils were tested for their biosynthetic potential using clone libraries developed from metagenomic DNA. Results revealed a surprising number of NRPS and PKS clones with similarity to rare Actinomycetes. Many of the clones tested were phylogenetically divergent suggesting they were fragments from novel NRPS and PKS gene clusters. Soils did not appear to cluster by location but did represent NRPS and PKS clones of diverse taxonomic origin. Fosmid libraries were constructed from Cuban and Antarctic soil samples; 17 fosmids were positive for NRPS domains suggesting a hit rate of less than 1 in 10 genomes. NRPS hits had low similarities to both rare Actinobacteria and Proteobacteria; they also clustered with known antibiotic producers suggesting they may encode for pathways producing novel bioactive compounds. In conclusion we designed an assay capable of detecting divergent NRPS and PKS gene clusters from the rare biosphere; when tested on soil samples results suggest the majority of NRPS and PKS pathways and hence bioactive metabolites are yet to be discovered.
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Affiliation(s)
- Gregory C. A. Amos
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Chiara Borsetto
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Paris Laskaris
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Martin Krsek
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Andrew E. Berry
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Kevin K. Newsham
- Ecosystem Programme, British Antarctic Survey, Natural Environment Research Council, High Cross, Cambridge, CB3 OET, United Kingdom
| | - Leo Calvo-Bado
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - David A. Pearce
- Ecosystem Programme, British Antarctic Survey, Natural Environment Research Council, High Cross, Cambridge, CB3 OET, United Kingdom
| | - Carlos Vallin
- Department of Biomedical Research, Center of Pharmaceutical Chemistry, Atabey, Playa, Havana, Cuba
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44
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The cyclic peptide ecumicin targeting ClpC1 is active against Mycobacterium tuberculosis in vivo. Antimicrob Agents Chemother 2014; 59:880-9. [PMID: 25421483 DOI: 10.1128/aac.04054-14] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Drug-resistant tuberculosis (TB) has lent urgency to finding new drug leads with novel modes of action. A high-throughput screening campaign of >65,000 actinomycete extracts for inhibition of Mycobacterium tuberculosis viability identified ecumicin, a macrocyclic tridecapeptide that exerts potent, selective bactericidal activity against M. tuberculosis in vitro, including nonreplicating cells. Ecumicin retains activity against isolated multiple-drug-resistant (MDR) and extensively drug-resistant (XDR) strains of M. tuberculosis. The subcutaneous administration to mice of ecumicin in a micellar formulation at 20 mg/kg body weight resulted in plasma and lung exposures exceeding the MIC. Complete inhibition of M. tuberculosis growth in the lungs of mice was achieved following 12 doses at 20 or 32 mg/kg. Genome mining of lab-generated, spontaneous ecumicin-resistant M. tuberculosis strains identified the ClpC1 ATPase complex as the putative target, and this was confirmed by a drug affinity response test. ClpC1 functions in protein breakdown with the ClpP1P2 protease complex. Ecumicin markedly enhanced the ATPase activity of wild-type (WT) ClpC1 but prevented activation of proteolysis by ClpC1. Less stimulation was observed with ClpC1 from ecumicin-resistant mutants. Thus, ClpC1 is a valid drug target against M. tuberculosis, and ecumicin may serve as a lead compound for anti-TB drug development.
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