1
|
Xu X, Zhang L, Yang T, Qiu Z, Bai L, Luo Y. Targeting caseinolytic protease P and its AAA1 chaperone for tuberculosis treatment. Drug Discov Today 2023; 28:103508. [PMID: 36706830 DOI: 10.1016/j.drudis.2023.103508] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 01/11/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023]
Abstract
Caseinolytic protease P with its AAA1 chaperone, known as Mycobacterium tuberculosis (Mtb)ClpP1P2 proteolytic machinery, maintains protein homeostasis in Mtb cells and is essential for bacterial survival. It is regarded as an important biological target with the potential to address the increasingly serious issue of multidrug-resistant (MDR) TB. Over the past 10 years, many MtbClpP1P2-targeted modulators have been identified and characterized, some of which have shown potent anti-TB activity. In this review, we describe current understanding of the substrates, structure and function of MtbClpP1P2, classify the modulators of this important protein machine into several categories based on their binding subunits or pockets, and discuss their binding details; Such information provides insights for use in candidate drug research and development of TB treatments by targeting MtbClpP1P2 proteolytic machinery.
Collapse
Affiliation(s)
- Xin Xu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Laiying Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Tao Yang
- Laboratory of Human Diseases and Immunotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Zhiqiang Qiu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Lang Bai
- Center of Infectious Diseases and State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China.
| | - Youfu Luo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China.
| |
Collapse
|
2
|
Hwang J, Strange N, Mazraani R, Phillips MJ, Gamble AB, Huston WM, Tyndall JDA. Design, synthesis and biological evaluation of P2-modified proline analogues targeting the HtrA serine protease in Chlamydia. Eur J Med Chem 2021; 230:114064. [PMID: 35007862 DOI: 10.1016/j.ejmech.2021.114064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/07/2021] [Accepted: 12/18/2021] [Indexed: 11/19/2022]
Abstract
High temperature requirement A (HtrA) serine proteases have emerged as a novel class of antibacterial target, which are crucial in protein quality control and are involved in the pathogenesis of a wide array of bacterial infections. Previously, we demonstrated that HtrA in Chlamydia is essential for bacterial survival, replication and virulence. Here, we report a new series of proline (P2)-modified inhibitors of Chlamydia trachomatis HtrA (CtHtrA) developed by proline ring expansion and Cγ-substitutions. The structure-based drug optimization process was guided by molecular modelling and in vitro pharmacological evaluation of inhibitory potency, selectivity and cytotoxicity. Compound 25 from the first-generation 4-substituted proline analogues increased antiCtHtrA potency and selectivity over human neutrophil elastase (HNE) by approximately 6- and 12-fold, respectively, relative to the peptidic lead compound 1. Based on this compound, second-generation substituted proline residues containing 1,2,3-triazole moieties were synthesized by regioselective azide-alkyne click chemistry. Compound 49 demonstrated significantly improved antichlamydial activity in whole cell assays, diminishing the bacterial infectious progeny below the detection limit at the lowest dose tested. Compound 49 resulted in approximately 9- and 22-fold improvement in the inhibitory potency and selectivity relative to 1, respectively. To date, compound 49 is the most potent HtrA inhibitor developed against Chlamydia spp.
Collapse
Affiliation(s)
- Jimin Hwang
- School of Pharmacy, University of Otago, Dunedin, New Zealand
| | - Natalie Strange
- School of Life Sciences, Faculty of Science, University of Technology Sydney, New South Wales, Australia
| | - Rami Mazraani
- School of Life Sciences, Faculty of Science, University of Technology Sydney, New South Wales, Australia
| | - Matthew J Phillips
- School of Life Sciences, Faculty of Science, University of Technology Sydney, New South Wales, Australia
| | - Allan B Gamble
- School of Pharmacy, University of Otago, Dunedin, New Zealand.
| | - Wilhelmina M Huston
- School of Life Sciences, Faculty of Science, University of Technology Sydney, New South Wales, Australia.
| | | |
Collapse
|
3
|
Structures of prokaryotic ubiquitin-like protein Pup in complex with depupylase Dop reveal the mechanism of catalytic phosphate formation. Nat Commun 2021; 12:6635. [PMID: 34789727 PMCID: PMC8599861 DOI: 10.1038/s41467-021-26848-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 10/27/2021] [Indexed: 02/06/2023] Open
Abstract
Pupylation is the post-translational modification of lysine side chains with prokaryotic ubiquitin-like protein (Pup) that targets proteins for proteasomal degradation in mycobacteria and other members of Actinobacteria. Pup ligase PafA and depupylase Dop are the two enzymes acting in this pathway. Although they share close structural and sequence homology indicative of a common evolutionary origin, they catalyze opposing reactions. Here, we report a series of high-resolution crystal structures of Dop in different functional states along the reaction pathway, including Pup-bound states in distinct conformations. In combination with biochemical analysis, the structures explain the role of the C-terminal residue of Pup in ATP hydrolysis, the process that generates the catalytic phosphate in the active site, and suggest a role for the Dop-loop as an allosteric sensor for Pup-binding and ATP cleavage. Pupylation is a bacterial post-translational protein modification, where the small ubiquitin-like protein Pup is covalently attached to lysine side chains of target proteins, which is a reversible process and depupylation is catalysed by the depupylase enzyme, Dop. Here, the authors present crystal structures of Dop in different functional states, which together with biochemical experiments provide insights into the catalytic mechanism of this enzyme.
Collapse
|
4
|
Brötz-Oesterhelt H, Vorbach A. Reprogramming of the Caseinolytic Protease by ADEP Antibiotics: Molecular Mechanism, Cellular Consequences, Therapeutic Potential. Front Mol Biosci 2021; 8:690902. [PMID: 34109219 PMCID: PMC8182300 DOI: 10.3389/fmolb.2021.690902] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 04/28/2021] [Indexed: 12/14/2022] Open
Abstract
Rising antibiotic resistance urgently calls for the discovery and evaluation of novel antibiotic classes and unique antibiotic targets. The caseinolytic protease Clp emerged as an unprecedented target for antibiotic therapy 15 years ago when it was observed that natural product-derived acyldepsipeptide antibiotics (ADEP) dysregulated its proteolytic core ClpP towards destructive proteolysis in bacterial cells. A substantial database has accumulated since on the interaction of ADEP with ClpP, which is comprehensively compiled in this review. On the molecular level, we describe the conformational control that ADEP exerts over ClpP, the nature of the protein substrates degraded, and the emerging structure-activity-relationship of the ADEP compound class. On the physiological level, we review the multi-faceted antibacterial mechanism, species-dependent killing modes, the activity against carcinogenic cells, and the therapeutic potential of the compound class.
Collapse
Affiliation(s)
- Heike Brötz-Oesterhelt
- Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tübingen, Germany.,Cluster of Excellence: Controlling Microbes to Fight Infection, Tübingen, Germany
| | - Andreas Vorbach
- Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tübingen, Germany
| |
Collapse
|
5
|
Wu J, Yan X, Weng P, Chen G, Wu Z. Homology- and cross-resistance of Lactobacillus plantarum to acid and osmotic stress and the influence of induction conditions on its proliferation by RNA-Seq. J Basic Microbiol 2021; 61:576-590. [PMID: 33945164 DOI: 10.1002/jobm.202100051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/23/2021] [Accepted: 04/18/2021] [Indexed: 12/27/2022]
Abstract
In this study, homology- and cross-resistance of Lactobacillus plantarum L1 and Lactobacillus plantarum L2 to acid and osmotic stress were investigated. Meanwhile, its proliferation mechanism was demonstrated by transcriptomic analysis using RNA sequencing. We found that the homologous-resistance and cross-resistance of L. plantarum L1 and L. plantarum L2 increased after acid and osmotic induction treatment by lactic acid and sodium lactate solution in advance, and the survival rate of live bacteria was improved. In addition, the count of viable bacteria of L. plantarum L2 significantly increased cultivated at a pH 5.0 with a 15% sodium lactate sublethal treatment, compared with the control group. Further study revealed that genes related to membrane transport, amino acid metabolism, nucleotide metabolism, and cell growth were significantly upregulated. These findings will contribute to promote high-density cell culture of starter cultures production in the fermented food industry.
Collapse
Affiliation(s)
- Jingyi Wu
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, China
| | - Xu Yan
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, China
| | - Peifang Weng
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, China
| | - Gong Chen
- Sichuan Food Fermentation Industry Research and Design Institute, Chengdu, Sichuan, China
| | - Zufang Wu
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, China
| |
Collapse
|
6
|
Bigi M, Vazquez CL, Castelão ABC, García EA, Cataldi AA, Jackson M, McNeil M, Soria M, Zumárraga MJ, Cabruja M, Gago G, Blanco FC, Nishibe C, Almeida NF, de Araújo FR, Bigi F. Analysing nonsynonymous mutations between two Mycobacterium bovis strains with contrasting pathogenic profiles. Vet Microbiol 2019; 239:108482. [PMID: 31759775 DOI: 10.1016/j.vetmic.2019.108482] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 10/22/2019] [Accepted: 10/24/2019] [Indexed: 01/03/2023]
Abstract
Mycobacterium bovis (M. bovis) is the causative agent of bovine tuberculosis, a chronic infectious disease that can affect cattle, other domesticated species, wild animals and humans. This disease produces important economic losses worldwide. Two M. bovis strains (04-303 and 534) have been isolated in Argentina. Whereas the 04-303 strain was isolated from a wild boar, the 534 strain was obtained from cattle. In a previous study, six weeks after infection, the 04-303 strain induced 100% mortality in mice. By contrast, mice infected with the 534 strain survived, with limited tissue damage, after four months. In this study we compared all predictive proteins encoded in both M. bovis genomes. The comparative analysis revealed 141 polymorphic proteins between both strains. From these proteins, nine virulence proteins showed polymorphisms in 04-303, whereas five did it in the 534 strain. Remarkably, both strains contained a high level of polymorphism in proteins related to phthiocerol dimycocerosate (PDIM) synthesis or transport. Further experimental evidence indicated that only mutations in the 534 strain have an impact on PDIM synthesis. The observed reduction in PDIM content in the 534 strain, together with its low capacity to induce phagosome arrest, may be associated with the reported deficiency of this strain to replicate and survive inside bovine macrophages. The findings of this study could contribute to a better understanding of pathogenicity and virulence aspects of M. bovis, which is essential for further studies aiming at developing new vaccines and diagnostic techniques for bovines.
Collapse
Affiliation(s)
- Mercedes Bigi
- Universidad de Buenos Aires, Facultad de Agronomía, Cátedra de Microbiología Agrícola, INBA-CONICET, Buenos Aires, Argentina.
| | | | - Ana Beatriz C Castelão
- Faculdade de Medicina Veterinária e Zootecnia, Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil.
| | | | | | - Mary Jackson
- Colorado State University, Dept. of Microbiology, Immunology and Pathology, USA.
| | - Michael McNeil
- Colorado State University, Dept. of Microbiology, Immunology and Pathology, USA.
| | - Marcelo Soria
- Universidad de Buenos Aires, Facultad de Agronomía, Cátedra de Microbiología Agrícola, INBA-CONICET, Buenos Aires, Argentina.
| | | | - Matias Cabruja
- Laboratory of Physiology and Genetics of Actinomycetes, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina.
| | - Gabriela Gago
- Laboratory of Physiology and Genetics of Actinomycetes, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina.
| | | | - Christiane Nishibe
- Faculdade de Computação, Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil.
| | - Nalvo F Almeida
- Faculdade de Computação, Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil.
| | | | - Fabiana Bigi
- Instituto de Biotecnología, IABIMO, CICVyA/INTA, Argentina.
| |
Collapse
|
7
|
Zhang Z, Wu T, Li Y, Bai X, Yan X, Gao Y, Shi Q, Zhu G. Contribution of the serine protease HtrA in Escherichia coli to infection in foxes. Microb Pathog 2019; 135:103570. [PMID: 31158492 DOI: 10.1016/j.micpath.2019.103570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 05/27/2019] [Accepted: 05/31/2019] [Indexed: 11/25/2022]
Abstract
Escherichia coli can cause severe, acute hemorrhagic pneumonia and systemic infection in farmed foxes, raccoon dogs and minks, leading to considerable economic losses to the farmers. It is well established that the htrA-encoded serine protease HtrA is critical for bacterial growth and survival under stress, and HtrA has been determined to be a potential vaccine target. However, the roles of HtrA in E. coli pathogenesis remain unknown. In this study, we generated an htrA-deletion mutant of the E. coli protype strain HBCLE-12 that causes pneumonia in silver foxes and then evaluated the changes in bacterial physiological characteristics in the absence of HtrA. The data show that knockout of the htrA gene did not affect growth and biochemical characteristics but led to impaired virulence of the strain. Increased susceptibility to environmental stresses, impaired survival in serum, and reduced biofilm formation may contribute to the virulence attenuation of the mutant. Furthermore, the HtrA-deficient mutant was subjected to RNA-seq analysis, and 16 differentially expressed genes were determined. This study provided insight that HtrA plays a definitive role in E. coli-induced infection.
Collapse
Affiliation(s)
- Zhiqiang Zhang
- Hebei Key Laboratory of Preventive Veterinary Medicine, Hebei Normal University of Science &Technology, Changli, Hebei, 066600, China
| | - Tonglei Wu
- Hebei Key Laboratory of Preventive Veterinary Medicine, Hebei Normal University of Science &Technology, Changli, Hebei, 066600, China
| | - Yonghui Li
- The Second Hospital of Qinhuangdao, Changli, Hebei, 066600, China
| | - Xue Bai
- Institute of Special Animal and Plant Sciences, The Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Xijun Yan
- Institute of Special Animal and Plant Sciences, The Chinese Academy of Agricultural Sciences, Changchun, 130112, China
| | - Yunhang Gao
- College of Animal Science and Technology, Jilin Agriculture University, China
| | - Qiumei Shi
- Hebei Key Laboratory of Preventive Veterinary Medicine, Hebei Normal University of Science &Technology, Changli, Hebei, 066600, China.
| | - Guoqiang Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China.
| |
Collapse
|
8
|
Xu X, Ran J, Jiao L, Liang X, Zhao R. Label free quantitative analysis of Alicyclobacillus acidoterrestris spore germination subjected to low ambient pH. Food Res Int 2019; 115:580-588. [DOI: 10.1016/j.foodres.2018.09.033] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 09/05/2018] [Accepted: 09/10/2018] [Indexed: 11/28/2022]
|
9
|
Kumar S, Sahu P, Jena L. An In silico approach to identify potential inhibitors against multiple drug targets of Mycobacterium tuberculosis. Int J Mycobacteriol 2019; 8:252-261. [DOI: 10.4103/ijmy.ijmy_109_19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
|
10
|
Liu P, Yang Y, Ju Y, Tang Y, Sang Z, Chen L, Yang T, An Q, Zhang T, Luo Y. Design, synthesis and biological evaluation of novel pyrrole derivatives as potential ClpP1P2 inhibitor against Mycobacterium tuberculosis. Bioorg Chem 2018; 80:422-432. [PMID: 30005200 DOI: 10.1016/j.bioorg.2018.06.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 05/21/2018] [Accepted: 06/03/2018] [Indexed: 02/05/2023]
Abstract
In an effort to discover novel inhibitors of M. tuberculosis Caseinolytic proteases (ClpP1P2), a combination strategy of virtual high-throughput screening and in vitro assay was employed and a new pyrrole compound, 1-(2-chloro-6-fluorobenzyl)-2, 5-dimethyl-4-((phenethylamino)methyl)-1H-pyrrole-3-carboxylate was found to display inhibitory effects against H37Ra with an MIC value of 77 µM. In order for discovery of more potent anti-tubercular agents that inhibit ClpP1P2 peptidase in M. tuberculosis, a series of pyrrole derivatives were designed and synthesized based on this hit compound. The synthesized compounds were evaluated forin vitrostudies against ClpP1P2 peptidase and anti-tubercular activities were also evaluated. The most promising compounds 2-(4-bromophenyl)-N-((1-(2-chloro-6-fluorophenyl)-2, 5-dimethyl-1H- pyrrolyl)methyl)ethan-1-aminehydrochloride 7d, ethyl 4-(((4-bromophenethyl) amino) methyl)-2,5-dimethyl-1-phenyl-1H-pyrrole-3-carboxylate hydrochloride 13i, ethyl 1-(4-chlorophenyl)-4-(((2-fluorophenethyl)amino)methyl)-2-methyl-5-phenyl-1H-pyrrole-3-carboxylate hydrochloride 13n exhibited favorable anti-mycobacterial activity with MIC value at 5 µM against Mtb H37Ra, respectively.
Collapse
Affiliation(s)
- Pingxian Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Yang Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Yuan Ju
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Yunxiang Tang
- State Key Laboratory of Respiratory Disease, Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China; Institute of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Zitai Sang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Lijuan Chen
- Guangdong Zhongsheng Pharmaceutical Co., Ltd, Dongguan, Guangdong 523325, China
| | - Tao Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China.
| | - Qi An
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China.
| | - Youfu Luo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China.
| |
Collapse
|
11
|
Lupoli TJ, Vaubourgeix J, Burns-Huang K, Gold B. Targeting the Proteostasis Network for Mycobacterial Drug Discovery. ACS Infect Dis 2018; 4:478-498. [PMID: 29465983 PMCID: PMC5902792 DOI: 10.1021/acsinfecdis.7b00231] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains one of the world's deadliest infectious diseases and urgently requires new antibiotics to treat drug-resistant strains and to decrease the duration of therapy. During infection, Mtb encounters numerous stresses associated with host immunity, including hypoxia, reactive oxygen and nitrogen species, mild acidity, nutrient starvation, and metal sequestration and intoxication. The Mtb proteostasis network, composed of chaperones, proteases, and a eukaryotic-like proteasome, provides protection from stresses and chemistries of host immunity by maintaining the integrity of the mycobacterial proteome. In this Review, we explore the proteostasis network as a noncanonical target for antibacterial drug discovery.
Collapse
Affiliation(s)
- Tania J. Lupoli
- Department of Microbiology and Immunology, Weill Cornell Medicine, 413 East 69th Street, New York, New York 10021, United States
| | - Julien Vaubourgeix
- Department of Microbiology and Immunology, Weill Cornell Medicine, 413 East 69th Street, New York, New York 10021, United States
| | - Kristin Burns-Huang
- Department of Microbiology and Immunology, Weill Cornell Medicine, 413 East 69th Street, New York, New York 10021, United States
| | - Ben Gold
- Department of Microbiology and Immunology, Weill Cornell Medicine, 413 East 69th Street, New York, New York 10021, United States
| |
Collapse
|
12
|
Correa AF, Bastos IMD, Neves D, Kipnis A, Junqueira-Kipnis AP, de Santana JM. The Activity of a Hexameric M17 Metallo-Aminopeptidase Is Associated With Survival of Mycobacterium tuberculosis. Front Microbiol 2017; 8:504. [PMID: 28396657 PMCID: PMC5366330 DOI: 10.3389/fmicb.2017.00504] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 03/10/2017] [Indexed: 01/06/2023] Open
Abstract
Mycobacterium tuberculosis is one of the most prevalent human pathogens causing millions of deaths in the last years. Moreover, tuberculosis (TB) treatment has become increasingly challenging owing to the emergence of multidrug resistant M. tuberculosis strains. Thus, there is an immediate need for the development of new anti-TB drugs. Proteases appear to be a promising approach and may lead to shortened and effective treatments for drug-resistant TB. Although the M. tuberculosis genome predicts more than 100 genes encoding proteases, only a few of them have been studied. Aminopeptidases constitute a set of proteases that selectively remove amino acids from the N-terminus of proteins and peptides and may act as virulence factors, essential for survival and maintenance of many microbial pathogens. Here, we characterized a leucine aminopeptidase of M. tuberculosis (MtLAP) as a cytosolic oligomeric metallo-aminopeptidase. Molecular and enzymatic properties lead us to classify MtLAP as a typical member of the peptidase family M17. Furthermore, the aminopeptidase inhibitor bestatin strongly inhibited MtLAP activity, in vitro M. tuberculosis growth and macrophage infection. In murine model of TB, bestatin treatment reduced bacterial burden and lesion in the lungs of infected mice. Thus, our data suggest that MtLAP participates in important metabolic pathways of M. tuberculosis necessary for its survival and virulence and consequently may be a promising target for new anti-TB drugs.
Collapse
Affiliation(s)
- Andre F Correa
- Laboratório de Interação Patógeno-Hospedeiro, Instituto de Biologia Universidade de BrasíliaBrasília, Brazil; Instituto de Patologia Tropical e Saúde Pública Universidade Federal de GoiásGoiânia, Brazil
| | - Izabela M D Bastos
- Laboratório de Interação Patógeno-Hospedeiro, Instituto de Biologia Universidade de Brasília Brasília, Brazil
| | - David Neves
- Laboratório de Interação Patógeno-Hospedeiro, Instituto de Biologia Universidade de Brasília Brasília, Brazil
| | - Andre Kipnis
- Instituto de Patologia Tropical e Saúde Pública Universidade Federal de Goiás Goiânia, Brazil
| | - Ana P Junqueira-Kipnis
- Instituto de Patologia Tropical e Saúde Pública Universidade Federal de Goiás Goiânia, Brazil
| | - Jaime M de Santana
- Laboratório de Interação Patógeno-Hospedeiro, Instituto de Biologia Universidade de Brasília Brasília, Brazil
| |
Collapse
|
13
|
Verma R, Pinto SM, Patil AH, Advani J, Subba P, Kumar M, Sharma J, Dey G, Ravikumar R, Buggi S, Satishchandra P, Sharma K, Suar M, Tripathy SP, Chauhan DS, Gowda H, Pandey A, Gandotra S, Prasad TSK. Quantitative Proteomic and Phosphoproteomic Analysis of H37Ra and H37Rv Strains of Mycobacterium tuberculosis. J Proteome Res 2017; 16:1632-1645. [DOI: 10.1021/acs.jproteome.6b00983] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Renu Verma
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- School
of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Sneha Maria Pinto
- YU-IOB
Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore 575020, India
| | - Arun Hanumana Patil
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- School
of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Jayshree Advani
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Manipal University, Madhav Nagar, Manipal 576104, India
| | - Pratigya Subba
- YU-IOB
Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore 575020, India
| | - Manish Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Manipal University, Madhav Nagar, Manipal 576104, India
| | - Jyoti Sharma
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Gourav Dey
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- Manipal University, Madhav Nagar, Manipal 576104, India
| | | | - Shashidhar Buggi
- Intermediate
Reference Laboratory, State Tuberculosis Training and Demonstration Centre, Someshwaranagar, SDSTRC and RGICD Campus, Bangalore 560029, India
- Department
of Cardio Thoracic Surgery, Super Specialty State Referral Hospital for Chest Diseases, Someshwaranagar First Main Road, Dharmaram College
Post, Bangalore 560029, India
| | | | - Kusum Sharma
- Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research (PGIMER), Chandigarh 160012, India
| | - Mrutyunjay Suar
- School
of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Srikanth Prasad Tripathy
- National Institute
for Research in Tuberculosis (Indian Council of Medical Research), Chennai 600031, India
| | - Devendra Singh Chauhan
- Department of Microbiology, National JALMA Institute for Leprosy & Other Mycobacterial Diseases (Indian Council of Medical Research), Agra 282004, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- YU-IOB
Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore 575020, India
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Sheetal Gandotra
- CSIR-Institute of Genomics & Integrative Biology, SukhdevVihar, New Delhi 110020, India
| | - Thottethodi Subrahmanya Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
- YU-IOB
Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore 575020, India
| |
Collapse
|
14
|
Portugal B, Motta FN, Correa AF, Nolasco DO, de Almeida H, Magalhães KG, Atta ALV, Vieira FD, Bastos IMD, Santana JM. Mycobacterium tuberculosis Prolyl Oligopeptidase Induces In vitro Secretion of Proinflammatory Cytokines by Peritoneal Macrophages. Front Microbiol 2017; 8:155. [PMID: 28223969 PMCID: PMC5293833 DOI: 10.3389/fmicb.2017.00155] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 01/20/2017] [Indexed: 11/13/2022] Open
Abstract
Tuberculosis (TB) is a disease that leads to death over 1 million people per year worldwide and the biological mediators of this pathology are poorly established, preventing the implementation of effective therapies to improve outcomes in TB. Host-bacterium interaction is a key step to TB establishment and the proteases produced by these microorganisms seem to facilitate bacteria invasion, migration and host immune response evasion. We presented, for the first time, the identification, biochemical characterization, molecular dynamics (MDs) and immunomodulatory properties of a prolyl oligopeptidase (POP) from Mycobacterium tuberculosis (POPMt). POP is a serine protease that hydrolyzes substrates with high specificity for proline residues and has already been characterized as virulence factor in infectious diseases. POPMt reveals catalytic activity upon N-Suc-Gly-Pro-Leu-Gly-Pro-AMC, a recognized POP substrate, with optimal activity at pH 7.5 and 37°C. The enzyme presents KM and Kcat/KM values of 108 μM and 21.838 mM-1 s-1, respectively. MDs showed that POPMt structure is similar to that of others POPs, which consists of a cylindrical architecture divided into an α/β hydrolase catalytic domain and a β-propeller domain. Finally, POPMt was capable of triggering in vitro secretion of proinflammatory cytokines by peritoneal macrophages, an event dependent on POPMt intact structure. Our data suggests that POPMt may contribute to an inflammatory response during M. tuberculosis infection.
Collapse
Affiliation(s)
- Brina Portugal
- Pathogen-Host Interface Laboratory, Department of Cell Biology, The University of Brasília, Brasília Brazil
| | - Flávia N Motta
- Pathogen-Host Interface Laboratory, Department of Cell Biology, The University of Brasília, BrasíliaBrazil; Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de GoiásGoiânia, Brazil
| | - Andre F Correa
- Pathogen-Host Interface Laboratory, Department of Cell Biology, The University of Brasília, BrasíliaBrazil; Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de GoiásGoiânia, Brazil
| | - Diego O Nolasco
- Physics Course and Postgraduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília Brasília, Brazil
| | - Hugo de Almeida
- Pathogen-Host Interface Laboratory, Department of Cell Biology, The University of Brasília, Brasília Brazil
| | - Kelly G Magalhães
- Laboratory of Immunology and Inflammation, Department of Cell Biology, The University of Brasília Brasília, Brazil
| | - Ana L V Atta
- Laboratório Central de Saúde Pública do Distrito Federal Brasília, Brazil
| | - Francisco D Vieira
- Laboratório Central de Saúde Pública do Distrito Federal Brasília, Brazil
| | - Izabela M D Bastos
- Pathogen-Host Interface Laboratory, Department of Cell Biology, The University of Brasília, Brasília Brazil
| | - Jaime M Santana
- Pathogen-Host Interface Laboratory, Department of Cell Biology, The University of Brasília, Brasília Brazil
| |
Collapse
|
15
|
Wessler S, Schneider G, Backert S. Bacterial serine protease HtrA as a promising new target for antimicrobial therapy? Cell Commun Signal 2017; 15:4. [PMID: 28069057 PMCID: PMC5223389 DOI: 10.1186/s12964-017-0162-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 01/04/2017] [Indexed: 12/19/2022] Open
Abstract
Recent studies have demonstrated that the bacterial chaperone and serine protease high temperature requirement A (HtrA) is closely associated with the establishment and progression of several infectious diseases. HtrA activity enhances bacterial survival under stress conditions, but also has direct effects on functions of the cell adhesion protein E-cadherin and extracellular matrix proteins, including fibronectin and proteoglycans. Although HtrA cannot be considered as a pathogenic factor per se, it exhibits favorable characteristics making HtrA a potentially attractive drug target to combat various bacterial infections.
Collapse
Affiliation(s)
- Silja Wessler
- Department of Molecular Biology, Division of Microbiology, Paris-Lodron University of Salzburg, Billroth Str. 11, A-5020, Salzburg, Austria.
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Vladimir-Prelog-Weg 4, CH-8093, Zürich, Switzerland
| | - Steffen Backert
- Division of Microbiology, University of Erlangen-Nuremberg, Staudtstr. 5, D-91058, Erlangen, Germany
| |
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|
17
|
Gil F, Paredes-Sabja D. Acyldepsipeptide antibiotics as a potential therapeutic agent against Clostridium difficile recurrent infections. Future Microbiol 2016; 11:1179-89. [DOI: 10.2217/fmb-2016-0064] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Alternative antimicrobial therapies based on acyldepsipeptides may hold promising results, based on the fact that they have shown to efficiently eradicate persister cells, stationary cells and cell in biofilm structures of several pathogenic bacteria from the infected host. Clostridium difficile infection is considered the result of extensive hospital use of expanded-spectrum antibiotics, which cause dysbiosis of the intestinal microbiota, enhancing susceptibility to infection and persistence. Considering the urgent need for the development of novel and efficient antimicrobial strategies against C. difficile, we review the potential application to treat C. difficile infections of acyldepsipeptides family of antibiotics, its mechanism of action and current developmental stages.
Collapse
Affiliation(s)
- Fernando Gil
- Microbiota–Host Interactions & Clostridia Research Group, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile
| | - Daniel Paredes-Sabja
- Microbiota–Host Interactions & Clostridia Research Group, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile
- Center for Bioinformatic & Integrative Biology, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile
| |
Collapse
|
18
|
Transcriptional Profiling of Mycobacterium tuberculosis Exposed to In Vitro Lysosomal Stress. Infect Immun 2016; 84:2505-23. [PMID: 27324481 DOI: 10.1128/iai.00072-16] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Accepted: 06/10/2016] [Indexed: 12/27/2022] Open
Abstract
Increasing experimental evidence supports the idea that Mycobacterium tuberculosis has evolved strategies to survive within lysosomes of activated macrophages. To further our knowledge of M. tuberculosis response to the hostile lysosomal environment, we profiled the global transcriptional activity of M. tuberculosis when exposed to the lysosomal soluble fraction (SF) prepared from activated macrophages. Transcriptome sequencing (RNA-seq) analysis was performed using various incubation conditions, ranging from noninhibitory to cidal based on the mycobacterial replication or killing profile. Under inhibitory conditions that led to the absence of apparent mycobacterial replication, M. tuberculosis expressed a unique transcriptome with modulation of genes involved in general stress response, metabolic reprogramming, respiration, oxidative stress, dormancy response, and virulence. The transcription pattern also indicates characteristic cell wall remodeling with the possible outcomes of increased infectivity, intrinsic resistance to antibiotics, and subversion of the host immune system. Among the lysosome-specific responses, we identified the glgE-mediated 1,4 α-glucan synthesis pathway and a defined group of VapBC toxin/anti-toxin systems, both of which represent toxicity mechanisms that potentially can be exploited for killing intracellular mycobacteria. A meta-analysis including previously reported transcriptomic studies in macrophage infection and in vitro stress models was conducted to identify overlapping and nonoverlapping pathways. Finally, the Tap efflux pump-encoding gene Rv1258c was selected for validation. An M. tuberculosis ΔRv1258c mutant was constructed and displayed increased susceptibility to killing by lysosomal SF and the antimicrobial peptide LL-37, as well as attenuated survival in primary murine macrophages and human macrophage cell line THP-1.
Collapse
|
19
|
HtrA, a Temperature- and Stationary Phase-Activated Protease Involved in Maturation of a Key Microbial Virulence Determinant, Facilitates Borrelia burgdorferi Infection in Mammalian Hosts. Infect Immun 2016; 84:2372-2381. [PMID: 27271745 DOI: 10.1128/iai.00360-16] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 05/31/2016] [Indexed: 01/04/2023] Open
Abstract
High-temperature requirement protease A (HtrA) represents a family of serine proteases that play important roles in microbial biology. Unlike the genomes of most organisms, that of Borrelia burgdorferi notably encodes a single HtrA gene product, termed BbHtrA. Previous studies identified a few substrates of BbHtrA; however, their physiological relevance could not be ascertained, as targeted deletion of the gene has not been successful. Here we show that BbhtrA transcripts are induced during spirochete growth either in the stationary phase or at elevated temperature. Successful generation of a BbhtrA deletion mutant and restoration by genetic complementation suggest a nonessential role for this protease in microbial viability; however, its remarkable growth, morphological, and structural defects during cultivation at 37°C confirm a high-temperature requirement for protease activation and function. The BbhtrA-deficient spirochetes were unable to establish infection of mice, as evidenced by assessment of culture, PCR, and serology. We show that transcript abundance as well as proteolytic processing of a borrelial protein required for cell fission and infectivity, BB0323, is impaired in BbhtrA mutants grown at 37°C, which likely contributed to their inability to survive in a mammalian host. Together, these results demonstrate the physiological relevance of a unique temperature-regulated borrelial protease, BbHtrA, which further enlightens our knowledge of intriguing aspects of spirochete biology and infectivity.
Collapse
|
20
|
Goodreid JD, Janetzko J, Santa Maria JP, Wong KS, Leung E, Eger BT, Bryson S, Pai EF, Gray-Owen SD, Walker S, Houry WA, Batey RA. Development and Characterization of Potent Cyclic Acyldepsipeptide Analogues with Increased Antimicrobial Activity. J Med Chem 2016; 59:624-46. [PMID: 26818454 DOI: 10.1021/acs.jmedchem.5b01451] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The problem of antibiotic resistance has prompted the search for new antibiotics with novel mechanisms of action. Analogues of the A54556 cyclic acyldepsipeptides (ADEPs) represent an attractive class of antimicrobial agents that act through dysregulation of caseinolytic protease (ClpP). Previous studies have shown that ADEPs are active against Gram-positive bacteria (e.g., MRSA, VRE, PRSP (penicillin-resistant Streptococcus pneumoniae)); however, there are currently few studies examining Gram-negative bacteria. In this study, the synthesis and biological evaluation of 14 novel ADEPs against a variety of pathogenic Gram-negative and Gram-positive organisms is outlined. Optimization of the macrocyclic core residues and N-acyl side chain culminated in the development of 26, which shows potent activity against the Gram-negative species Neisseria meningitidis and Neisseria gonorrheae and improved activity against the Gram-positive organisms Staphylococcus aureus and Enterococcus faecalis in comparison with known analogues. In addition, the co-crystal structure of an ADEP-ClpP complex derived from N. meningitidis was solved.
Collapse
Affiliation(s)
- Jordan D Goodreid
- Davenport Research Laboratories, Department of Chemistry, University of Toronto , 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - John Janetzko
- Department of Microbiology and Immunobiology, Harvard Medical School , Boston, Massachusetts 02115, United States
- Department of Chemistry and Chemical Biology, Harvard University , Cambridge, Massachusetts 02138, United States
| | - John P Santa Maria
- Department of Microbiology and Immunobiology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Keith S Wong
- Department of Biochemistry, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Elisa Leung
- Department of Biochemistry, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Bryan T Eger
- Department of Biochemistry, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Steve Bryson
- Department of Biochemistry, University of Toronto , Toronto, Ontario M5S 1A8, Canada
- The Campbell Family Institute for Cancer Research, University Health Network , Toronto, Ontario M5G 1L7, Canada
| | - Emil F Pai
- Department of Biochemistry, University of Toronto , Toronto, Ontario M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto , Toronto, Ontario M5S 1A8, Canada
- Department of Medical Biophysics, University of Toronto , Toronto, Ontario M5S 1A8, Canada
- The Campbell Family Institute for Cancer Research, University Health Network , Toronto, Ontario M5G 1L7, Canada
| | - Scott D Gray-Owen
- Department of Molecular Genetics, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Suzanne Walker
- Department of Microbiology and Immunobiology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Walid A Houry
- Department of Biochemistry, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Robert A Batey
- Davenport Research Laboratories, Department of Chemistry, University of Toronto , 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| |
Collapse
|
21
|
|
22
|
Frasinyuk MS, Kwiatkowski S, Wagner JM, Evans TJ, Reed RW, Korotkov KV, Watt DS. Pentapeptide boronic acid inhibitors of Mycobacterium tuberculosis MycP1 protease. Bioorg Med Chem Lett 2014; 24:3546-8. [PMID: 24915878 DOI: 10.1016/j.bmcl.2014.05.056] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 05/14/2014] [Accepted: 05/15/2014] [Indexed: 01/16/2023]
Abstract
Mycosin protease-1 (MycP1) cleaves ESX secretion-associated protein B (EspB) that is a virulence factor of Mycobacterium tuberculosis, and accommodates an octapeptide, AVKAASLG, as a short peptide substrate. Because peptidoboronic acids are known inhibitors of serine proteases, the synthesis and binding of a boronic acid analog of the pentapeptide cleavage product, AVKAA, was studied using MycP1 variants from Mycobacterium thermoresistible (MycP1mth), Mycobacterium smegmatis (MycP1msm) and M. tuberculosis (MycP1mtu). We synthesized the boropentapeptide, HAlaValLysAlaAlaB(OH)2 (1) and the analogous pinanediol PD-protected HAlaValLysAlaAlaBO2(PD) (2) using an Fmoc/Boc peptide strategy. The pinanediol boropentapeptide 2 displayed IC50 values 121.6±25.3 μM for MycP1mth, 93.2±37.3 μM for MycP1msm and 37.9±5.2 μM for MycP1mtu. Such relatively strong binding creates a chance for crystalizing the complex with 2 and finding the structure of the unknown MycP1 catalytic site that would potentially facilitate the development of new anti-tuberculosis drugs.
Collapse
Affiliation(s)
- Mykhaylo S Frasinyuk
- Institute of Bioorganic Chemistry and Petrochemistry, Kyiv-94 02660, Ukraine; Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536-0509, USA
| | - Stefan Kwiatkowski
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536-0509, USA; Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596, USA
| | - Jonathan M Wagner
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536-0509, USA
| | - Timothy J Evans
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536-0509, USA
| | - Robert W Reed
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536-0509, USA
| | - Konstantin V Korotkov
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536-0509, USA
| | - David S Watt
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536-0509, USA; Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596, USA; Lucille Parker Markey Cancer Center, University of Kentucky, Lexington, KY 40536-0093, USA.
| |
Collapse
|
23
|
Hamza A, Wagner JM, Evans T, Frasinyuk MS, Kwiatkowski S, Zhan CG, Watt DS, Korotkov KV. Novel mycosin protease MycP₁ inhibitors identified by virtual screening and 4D fingerprints. J Chem Inf Model 2014; 54:1166-73. [PMID: 24628123 PMCID: PMC4010288 DOI: 10.1021/ci500025r] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Indexed: 01/17/2023]
Abstract
The rise of drug-resistant Mycobacterium tuberculosis lends urgency to the need for new drugs for the treatment of tuberculosis (TB). The identification of a serine protease, mycosin protease-1 (MycP₁), as the crucial agent in hydrolyzing the virulence factor, ESX-secretion-associated protein B (EspB), potentially opens the door to new tuberculosis treatment options. Using the crystal structure of mycobacterial MycP₁ in the apo form, we performed an iterative ligand- and structure-based virtual screening (VS) strategy to identify novel, nonpeptide, small-molecule inhibitors against MycP₁ protease. Screening of ∼485,000 ligands from databases at the Genomics Research Institute (GRI) at the University of Cincinnati and the National Cancer Institute (NCI) using our VS approach, which integrated a pharmacophore model and consensus molecular shape patterns of active ligands (4D fingerprints), identified 81 putative inhibitors, and in vitro testing subsequently confirmed two of them as active inhibitors. Thereafter, the lead structures of each VS round were used to generate a new 4D fingerprint that enabled virtual rescreening of the chemical libraries. Finally, the iterative process identified a number of diverse scaffolds as lead compounds that were tested and found to have micromolar IC₅₀ values against the MycP₁ target. This study validated the efficiency of the SABRE 4D fingerprints as a means of identifying novel lead compounds in each screening round of the databases. Together, these results underscored the value of using a combination of in silico iterative ligand- and structure-based virtual screening of chemical libraries with experimental validation for the identification of promising structural scaffolds, such as the MycP₁ inhibitors.
Collapse
Affiliation(s)
- Adel Hamza
- Department
of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536, United States
- Center
for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Jonathan M. Wagner
- Department
of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536, United States
- Center
for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Timothy
J. Evans
- Department
of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536, United States
- Center
for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Mykhaylo S. Frasinyuk
- Department
of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536, United States
- Center
for Pharmaceutical Research and Innovation, University of Kentucky, Lexington, Kentucky 40536, United States
- Institute
of Bioorganic Chemistry and Petrochemistry, Kyiv-94, 02660, Ukraine
| | - Stefan Kwiatkowski
- Department
of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536, United States
- Center
for Pharmaceutical Research and Innovation, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Chang-Guo Zhan
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Center
for Pharmaceutical Research and Innovation, University of Kentucky, Lexington, Kentucky 40536, United States
| | - David S. Watt
- Department
of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536, United States
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Center
for Pharmaceutical Research and Innovation, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Konstantin V. Korotkov
- Department
of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536, United States
- Center
for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, United States
| |
Collapse
|
24
|
Abstract
Bacterial collagenases are metalloproteinases involved in the degradation of the extracellular matrices of animal cells, due to their ability to digest native collagen. These enzymes are important virulence factors in a variety of pathogenic bacteria. Nonetheless, there is a lack of scientific consensus for a proper and well-defined classification of these enzymes and a vast controversy regarding the correct identification of collagenases. Clostridial collagenases were the first ones to be identified and characterized and are the reference enzymes for comparison of newly discovered collagenolytic enzymes. In this review we present the most recent data regarding bacterial collagenases and overview the functional and structural diversity of bacterial collagenases. An overall picture of the molecular diversity and distribution of these proteins in nature will also be given. Particular aspects of the different proteolytic activities will be contextualized within relevant areas of application, mainly biotechnological processes and therapeutic uses. At last, we will present a new classification guide for bacterial collagenases that will allow the correct and straightforward classification of these enzymes.
Collapse
Affiliation(s)
- Ana Sofia Duarte
- a Department of Biology and Cesam , University of Aveiro, Campus Universitario de Santiago , Aveiro , Portugal
| | - Antonio Correia
- a Department of Biology and Cesam , University of Aveiro, Campus Universitario de Santiago , Aveiro , Portugal
| | - Ana Cristina Esteves
- a Department of Biology and Cesam , University of Aveiro, Campus Universitario de Santiago , Aveiro , Portugal
| |
Collapse
|
25
|
Carney D, Schmitz KR, Truong J, Sauer RT, Sello JK. Restriction of the conformational dynamics of the cyclic acyldepsipeptide antibiotics improves their antibacterial activity. J Am Chem Soc 2014; 136:1922-9. [PMID: 24422534 PMCID: PMC4004210 DOI: 10.1021/ja410385c] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Indexed: 02/07/2023]
Abstract
The cyclic acyldepsipeptide (ADEP) antibiotics are a new class of antibacterial agents that kill bacteria via a mechanism that is distinct from all clinically used drugs. These molecules bind and dysregulate the activity of the ClpP peptidase. The potential of these antibiotics as antibacterial drugs has been enhanced by the elimination of pharmacological liabilities through medicinal chemistry efforts. Here, we demonstrate that the ADEP conformation observed in the ADEP-ClpP crystal structure is fortified by transannular hydrogen bonding and can be further stabilized by judicious replacement of constituent amino acids within the peptidolactone core structure with more conformationally constrained counterparts. Evidence supporting constraint of the molecule into the bioactive conformer was obtained by measurements of deuterium-exchange kinetics of hydrogens that were proposed to be engaged in transannular hydrogen bonds. We show that the rigidified ADEP analogs bind and activate ClpP at lower concentrations in vitro. Remarkably, these compounds have up to 1200-fold enhanced antibacterial activity when compared to those with the peptidolactone core structure common to two ADEP natural products. This study compellingly demonstrates how rational modulation of conformational dynamics may be used to improve the bioactivities of natural products.
Collapse
Affiliation(s)
- Daniel
W. Carney
- Department
of Chemistry, Brown University, 324 Brook Street, Providence, Rhode Island 02912, United States
| | - Karl R. Schmitz
- Department
of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jonathan
V. Truong
- Department
of Chemistry, Brown University, 324 Brook Street, Providence, Rhode Island 02912, United States
| | - Robert T. Sauer
- Department
of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jason K. Sello
- Department
of Chemistry, Brown University, 324 Brook Street, Providence, Rhode Island 02912, United States
| |
Collapse
|
26
|
Compton CL, Schmitz KR, Sauer RT, Sello JK. Antibacterial activity of and resistance to small molecule inhibitors of the ClpP peptidase. ACS Chem Biol 2013; 8:2669-77. [PMID: 24047344 DOI: 10.1021/cb400577b] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
There is rapidly mounting evidence that intracellular proteases in bacteria are compelling targets for antibacterial drugs. Multiple reports suggest that the human pathogen Mycobacterium tuberculosis and other actinobacteria may be particularly sensitive to small molecules that perturb the activities of self-compartmentalized peptidases, which catalyze intracellular protein turnover as components of ATP-dependent proteolytic machines. Here, we report chemical syntheses and evaluations of structurally diverse β-lactones, which have a privileged structure for selective, suicide inhibition of the self-compartmentalized ClpP peptidase. β-Lactones with certain substituents on the α- and β-carbons were found to be toxic to M. tuberculosis. Using an affinity-labeled analogue of a bioactive β-lactone in a series of chemical proteomic experiments, we selectively captured the ClpP1P2 peptidase from live cultures of two different actinobacteria that are related to M. tuberculosis. Importantly, we found that the growth inhibitory β-lactones also inactivate the M. tuberculosis ClpP1P2 peptidase in vitro via formation of a covalent adduct at the ClpP2 catalytic serine. Given the potent antibacterial activity of these compounds and their medicinal potential, we sought to identify innate mechanisms of resistance. Using a genome mining strategy, we identified a genetic determinant of β-lactone resistance in Streptomyces coelicolor, a non-pathogenic relative of M. tuberculosis. Collectively, these findings validate the potential of ClpP inhibition as a strategy in antibacterial drug development and define a mechanism by which bacteria could resist the toxic effects of ClpP inhibitors.
Collapse
Affiliation(s)
- Corey L. Compton
- Department
of Chemistry, Brown University, 324 Brook Street, Providence, Rhode Island 02912, United States
| | - Karl R. Schmitz
- Department
of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Robert T. Sauer
- Department
of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jason K. Sello
- Department
of Chemistry, Brown University, 324 Brook Street, Providence, Rhode Island 02912, United States
| |
Collapse
|
27
|
Gherardini FC. Borrelia burgdorferi HtrA may promote dissemination and irritation. Mol Microbiol 2013; 90:209-13. [PMID: 23998919 PMCID: PMC4260139 DOI: 10.1111/mmi.12390] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2013] [Indexed: 01/08/2023]
Affiliation(s)
- Frank C Gherardini
- Laboratory of Zoonotic Pathogens, Division of Intramural Research, National Institutes of Allergy and Infectious Diseases, Hamilton, MT, 59840, USA; National Institutes of Health, Rocky Mountain Laboratories, Hamilton, MT, 59840, USA
| |
Collapse
|