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Martini BA, Grigorov AS, Skvortsova YV, Bychenko OS, Salina EG, Azhikina TL. Small RNA MTS1338 Configures a Stress Resistance Signature in Mycobacterium tuberculosis. Int J Mol Sci 2023; 24:ijms24097928. [PMID: 37175635 PMCID: PMC10178195 DOI: 10.3390/ijms24097928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
In the course of evolution, Mycobacterium tuberculosis (Mtb), the etiological agent of tuberculosis, has developed sophisticated strategies to evade host immune response, including the synthesis of small non-coding RNAs (sRNAs), which regulate post-transcriptional pathways involved in the stress adaptation of mycobacteria. sRNA MTS1338 is upregulated in Mtb during its infection of cultured macrophages and in the model of chronic tuberculosis, suggesting involvement in host-pathogen interactions. Here, we analyzed the role of MTS1338 in the Mtb response to macrophage-like stresses in vitro. The Mtb strain overexpressing MTS1338 demonstrated enhanced survival ability under low pH, nitrosative, and oxidative stress conditions simulating the antimicrobial environment inside macrophages. Transcriptomic analysis revealed that in MTS1338-overexpressing Mtb, the stress factors led to the activation of a number of transcriptional regulators, toxin-antitoxin modules, and stress chaperones, about half of which coincided with the genes induced in Mtb phagocytosed by macrophages. We determined the MTS1338 "core regulon", consisting of 11 genes that were activated in all conditions under MTS1338 overexpression. Our findings indicate that MTS1338 is a stress-induced sRNA that promotes Mtb survival in macrophages by triggering adaptive transcriptional mechanisms in response to host antimicrobial defense reactions.
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Affiliation(s)
- Billy A Martini
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Artem S Grigorov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Yulia V Skvortsova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Oksana S Bychenko
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Elena G Salina
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Tatyana L Azhikina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
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2
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A New Benzothiazolthiazolidine Derivative, 11726172, Is Active In Vitro, In Vivo, and against Nonreplicating Cells of Mycobacterium tuberculosis. mSphere 2022; 7:e0036922. [PMID: 36377880 PMCID: PMC9769805 DOI: 10.1128/msphere.00369-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Tuberculosis (TB) still poses a global menace as one of the deadliest infectious diseases. A quarter of the human population is indeed latently infected with Mycobacterium tuberculosis. People with latent infection have a 5 to 10% lifetime risk of becoming ill with TB, representing a reservoir for TB active infection. This is a worrisome problem to overcome in the case of relapse; unfortunately, few drugs are effective against nonreplicating M. tuberculosis cells. Novel strategies to combat TB, including its latent form, are urgently needed. In response to the lack of new effective drugs and after screening about 500 original chemical molecules, we selected a compound, 11726172, that is endowed with potent antitubercular activity against M. tuberculosis both in vitro and in vivo and importantly also against dormant nonculturable bacilli. We also investigated the mechanism of action of 11726172 by applying a multidisciplinary approach, including transcriptomic, labeled metabolomic, biochemical, and microbiological procedures. Our results represent an important step forward in the development of a new antitubercular compound with a novel mechanism of action active against latent bacilli. IMPORTANCE The discontinuation of TB services due to COVID-19 causes concern about a future resurgence of TB, also considering that latent infection affects a high number of people worldwide. To combat this situation, the identification of antitubercular compounds targeting Mycobacterium tuberculosis through novel mechanisms of action is necessary. These compounds should be active against not only replicating bacteria cells but also nonreplicating cells to limit the reservoir of latently infected people on which the bacterium can rely to spread after reactivation.
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3
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Lane TR, Urbina F, Rank L, Gerlach J, Riabova O, Lepioshkin A, Kazakova E, Vocat A, Tkachenko V, Cole S, Makarov V, Ekins S. Machine Learning Models for Mycobacterium tuberculosisIn Vitro Activity: Prediction and Target Visualization. Mol Pharm 2022; 19:674-689. [PMID: 34964633 PMCID: PMC9121329 DOI: 10.1021/acs.molpharmaceut.1c00791] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tuberculosis (TB) is a major global health challenge, with approximately 1.4 million deaths per year. There is still a need to develop novel treatments for patients infected with Mycobacterium tuberculosis (Mtb). There have been many large-scale phenotypic screens that have led to the identification of thousands of new compounds. Yet, there is very limited investment in TB drug discovery which points to the need for new methods to increase the efficiency of drug discovery against Mtb. We have used machine learning approaches to learn from the public Mtb data, resulting in many data sets and models with robust enrichment and hit rates leading to the discovery of new active compounds. Recently, we have curated predominantly small-molecule Mtb data and developed new machine learning classification models with 18 886 molecules at different activity cutoffs. We now describe the further validation of these Bayesian models using a library of over 1000 molecules synthesized as part of EU-funded New Medicines for TB and More Medicines for TB programs. We highlight molecular features which are enriched in these active compounds. In addition, we provide new regression and classification models that can be used for scoring compound libraries or used to design new molecules. We have also visualized these molecules in the context of known molecular targets and identified clusters in chemical property space, which may aid in future target identification efforts. Finally, we are also making these data sets publicly available, representing a significant increase to the available Mtb inhibition data in the public domain.
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Affiliation(s)
- Thomas R. Lane
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510 Raleigh, NC 27606, USA
| | - Fabio Urbina
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510 Raleigh, NC 27606, USA
| | - Laura Rank
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510 Raleigh, NC 27606, USA
| | - Jacob Gerlach
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510 Raleigh, NC 27606, USA
| | - Olga Riabova
- Research Center of Biotechnology RAS, 119071 Moscow, Russia
| | | | - Elena Kazakova
- Research Center of Biotechnology RAS, 119071 Moscow, Russia
| | - Anthony Vocat
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - Valery Tkachenko
- Science Data Experts, 14909 Forest Landing Cir, Rockville, MD 20850
| | | | - Vadim Makarov
- Research Center of Biotechnology RAS, 119071 Moscow, Russia
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510 Raleigh, NC 27606, USA
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4
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Egorova A, Salina EG, Makarov V. Targeting Non-Replicating Mycobacterium tuberculosis and Latent Infection: Alternatives and Perspectives (Mini-Review). Int J Mol Sci 2021; 22:ijms222413317. [PMID: 34948114 PMCID: PMC8707483 DOI: 10.3390/ijms222413317] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 01/02/2023] Open
Abstract
Latent tuberculosis infection (LTBI) represents a major challenge to curing TB disease. Current guidelines for LTBI management include only three older drugs and their combinations-isoniazid and rifamycins (rifampicin and rifapentine). These available control strategies have little impact on latent TB elimination, and new specific therapeutics are urgently needed. In the present mini-review, we highlight some of the alternatives that may potentially be included in LTBI treatment recommendations and a list of early-stage prospective small molecules that act on drug targets specific for Mycobacterium tuberculosis latency.
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Affiliation(s)
- Anna Egorova
- The Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences (Research Center of Biotechnology RAS), 119071 Moscow, Russia; (A.E.); (E.G.S.)
| | - Elena G. Salina
- The Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences (Research Center of Biotechnology RAS), 119071 Moscow, Russia; (A.E.); (E.G.S.)
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Vadim Makarov
- The Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences (Research Center of Biotechnology RAS), 119071 Moscow, Russia; (A.E.); (E.G.S.)
- Correspondence:
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5
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Li X, Ru S, Tian H, Zhang S, Lin Z, Gao M, Wang J. Combined exposure to environmentally relevant copper and 2,2'-dithiobis-pyridine induces significant reproductive toxicity in male guppy (Poecilia reticulata). THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 797:149131. [PMID: 34346372 DOI: 10.1016/j.scitotenv.2021.149131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/13/2021] [Accepted: 07/14/2021] [Indexed: 06/13/2023]
Abstract
Metal pyrithiones (MePTs), the most widely used biocides in antifouling paints (AFs) coated on the hulls, are usually used in combination with Cu-containing substances. In the aquatic environment, 2,2'-dithiobis-pyridine ((PS)2), the main degradation product of MePTs, and Cu usually coexist. However, their combined impacts on aquatic organisms are unclear. This study exposed male guppy (Poecilia reticulata) to an environmentally realistic concentration of Cu (10 μg/L) alone or Cu (10 μg/L) combined with 20, 200, and 2000 ng/L (PS)2 to explore their combined reproductive toxicity. The results showed that co-exposure to Cu and (PS)2 increased Cu accumulation in the fish body in a dose-dependent manner and induced obvious spermatozoon apoptosis and necrosis, which was mediated by the peroxidation and caspase activation. Compared to Cu alone, co-exposure to Cu and 200, 2000 ng/L (PS)2 significantly decreased the testosterone level and collapsed spermatogenesis, and depressed male's sexual interest and mating behavior were observed in three co-exposure groups. Moreover, co-exposure to Cu and (PS)2 increased the disturbance on cyp19a and cyp19b transcription and suppressed the "display" reproductive behavior. Eventually, co-exposure to Cu and (PS)2 caused male reproductive failure. Therefore, the concurrence of Cu and (PS)2 induced significant reproductive toxicity in male guppies and would threaten the sustainability of fish populations. Considering the extensive usage of MePTs products in the AFs, their ecological risk warrants more evaluation.
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Affiliation(s)
- Xuefu Li
- Colleges of Marine Life Sciences, Ocean University of China, Qingdao 266003, Shandong Province, China
| | - Shaoguo Ru
- Colleges of Marine Life Sciences, Ocean University of China, Qingdao 266003, Shandong Province, China
| | - Hua Tian
- Colleges of Marine Life Sciences, Ocean University of China, Qingdao 266003, Shandong Province, China
| | - Suqiu Zhang
- Colleges of Marine Life Sciences, Ocean University of China, Qingdao 266003, Shandong Province, China
| | - Zhenxian Lin
- School of Biology and Brewing Engineering, Taishan University, 525 Dongyue Street, Tai'an 271000, Shandong Province, China
| | - Ming Gao
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, Jiangsu Province, China
| | - Jun Wang
- Colleges of Marine Life Sciences, Ocean University of China, Qingdao 266003, Shandong Province, China.
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6
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Lopes LGF, Carvalho EM, Sousa EHS. A bioinorganic chemistry perspective on the roles of metals as drugs and targets against Mycobacterium tuberculosis - a journey of opportunities. Dalton Trans 2021; 49:15988-16003. [PMID: 32583835 DOI: 10.1039/d0dt01365j] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Medicinal inorganic chemists have provided many strategies to tackle a myriad of diseases, pushing forward the frontiers of pharmacology. As an example, the fight against tuberculosis (TB), an infectious bacterial disease, has led to the development of metal-based compounds as potential drugs. This disease remains a current health issue causing over 1.4 million of deaths per year. The emergence of multi- (MDR) and extensively-drug resistant (XDR) Mycobacterium tuberculosis (Mtb) strains along with a long dormancy process, place major challenges in developing new therapeutic compounds. Isoniazid is a front-line prodrug used against TB with appealing features for coordination chemists, which have been explored in a series of cases reported here. An isoniazid iron-based compound, called IQG-607, has caught our attention, whose in vitro and in vivo studies are advanced and thoroughly discussed, along with other metal complexes. Isoniazid is inactive against dormant Mtb, a hard to eliminate state of this bacillus, found in one-fourth of the world's population and directly implicated in the lengthy treatment of TB (ca. 6 months). Thus, our understanding of this phenomenon may lead to a rational design of new drugs. Along these lines, we describe how metals as targets can cross paths with metals used as selective therapeutics, where we mainly review heme-based sensors, DevS and DosT, as a key system in the Mtb dormancy process and a current drug target. Overall, we report new opportunities for bioinorganic chemists to tackle this longstanding and current threat.
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Affiliation(s)
- Luiz G F Lopes
- Group of Bioinorganic, Department of Organic and Inorganic Chemistry, Federal University of Ceará, Fortaleza, Brazil.
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7
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Saha P, Kumari Agarwala P, Dadhich R, Adhyapak P, Kapoor S, Madhavan N. Ligand Induced Cu II Transport Restricts Cancer and Mycobacterial Growth: Towards a Plug-and-Select Ion Channel Scaffold. Chembiochem 2021; 22:1424-1429. [PMID: 33347676 DOI: 10.1002/cbic.202000731] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/01/2020] [Indexed: 11/09/2022]
Abstract
Synthetic channels with high ion selectivity are attractive drug targets for diseases involving ion dysregulation. Achieving selective transport of divalent ions is highly challenging due their high hydration energies. A small tripeptide amphiphilic scaffold installed with a pybox ligand selectively transports CuII ions across membranes. The peptide forms stable dimeric pores in the membrane and transports ions by a Cu2+ /H+ antiport mechanism. The ligand-induced excellent CuII selectivity as well as high membrane permeability of the peptide is exploited to promote cancer cell death. The peptide's ability to restrict mycobacterial growth serves as seeds to evolve antibacterial strategies centred on selectively modulating ion homeostasis in pathogens. This simple peptide can potentially function as a universal, yet versatile, scaffold wherein the ion selectivity can be precisely controlled by modifying the ligand at the C terminus.
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Affiliation(s)
- Parichita Saha
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Prema Kumari Agarwala
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Ruchika Dadhich
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Pranav Adhyapak
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Shobhna Kapoor
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Nandita Madhavan
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
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8
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Steuer P, Tejeda C, Martinez O, Ramirez-Reveco A, González N, Grant IR, Foddai ACG, Collins MT, Salgado M. Effectiveness of copper ions against Mycobacterium avium subsp. paratuberculosis and bacterial communities in naturally contaminated raw cow's milk. J Appl Microbiol 2020; 131:146-154. [PMID: 33151641 DOI: 10.1111/jam.14923] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 11/02/2020] [Indexed: 01/14/2023]
Abstract
AIM The focus of the present study was to evaluate the copper ions treatment on the viability of Mycobacterium avium subsp. paratuberculosis (MAP) and other bacterial communities in cow's milk. METHODS AND RESULTS A copper ions treatment was evaluated in naturally contaminated cow's milk to assay MAP load and/or viability, and relative abundance of other bacterial communities. In addition, physical-chemical analyses of the milk were also performed. All analyses were carried out before and after a copper ions treatment. After copper ions treatment, pH and copper concentration markedly increased in milk; the numbers of viable MAP significantly decreased. The relative abundance of the four target phyla decreased, with the phyla Bacteroidetes and Firmicutes surviving treatment in higher proportions (4 and 2·1% of original populations, respectively). A progressively higher percentage of dead bacterial cells after 5 and 20 min copper ions treatments was found (12 and 35%, respectively). CONCLUSION With the exception of some MAP-tolerant strains, we have once again demonstrated that copper ions have a significant inactivating effect on MAP as well as certain other bacterial communities found in naturally contaminated cow's milk. SIGNIFICANCE AND IMPACT OF THE STUDY This study showed a significant inactivation of both MAP and other bacteria by copper ions in raw cow's milk, information that could be useful as a tool for MAP control.
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Affiliation(s)
- P Steuer
- Instituto de Medicina Preventiva Veterinaria, Valdivia, Chile.,Facultad de Ciencias Veterinarias, Escuela de Graduados, Valdivia, Chile
| | - C Tejeda
- Instituto de Medicina Preventiva Veterinaria, Valdivia, Chile
| | - O Martinez
- Instituto de Bioquímica y Microbiología, Universidad Austral de Chile, Valdivia, Chile
| | | | - N González
- Instituto de Medicina Preventiva Veterinaria, Valdivia, Chile
| | - I R Grant
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - A C G Foddai
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - M T Collins
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - M Salgado
- Instituto de Medicina Preventiva Veterinaria, Valdivia, Chile
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Banerjee U, Sankar S, Singh A, Chandra N. A Multi-Pronged Computational Pipeline for Prioritizing Drug Target Strategies for Latent Tuberculosis. Front Chem 2020; 8:593497. [PMID: 33381491 PMCID: PMC7767875 DOI: 10.3389/fchem.2020.593497] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/24/2020] [Indexed: 12/02/2022] Open
Abstract
Tuberculosis is one of the deadliest infectious diseases worldwide and the prevalence of latent tuberculosis acts as a huge roadblock in the global effort to eradicate tuberculosis. Most of the currently available anti-tubercular drugs act against the actively replicating form of Mycobacterium tuberculosis (Mtb), and are not effective against the non-replicating dormant form present in latent tuberculosis. With about 30% of the global population harboring latent tuberculosis and the requirement for prolonged treatment duration with the available drugs in such cases, the rate of adherence and successful completion of therapy is low. This necessitates the discovery of new drugs effective against latent tuberculosis. In this work, we have employed a combination of bioinformatics and chemoinformatics approaches to identify potential targets and lead candidates against latent tuberculosis. Our pipeline adopts transcriptome-integrated metabolic flux analysis combined with an analysis of a transcriptome-integrated protein-protein interaction network to identify perturbations in dormant Mtb which leads to a shortlist of 6 potential drug targets. We perform a further selection of the candidate targets and identify potential leads for 3 targets using a range of bioinformatics methods including structural modeling, binding site association and ligand fingerprint similarities. Put together, we identify potential new strategies for targeting latent tuberculosis, new candidate drug targets as well as important lead clues for drug design.
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Affiliation(s)
- Ushashi Banerjee
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Santhosh Sankar
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Amit Singh
- Center for Infectious Disease Research, Indian Institute of Science, Bangalore, India
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science, Bangalore, India.,Center for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, India
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10
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11
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Potential therapeutic approaches for a sleeping pathogen: tuberculosis a case for bioinorganic chemistry. J Biol Inorg Chem 2020; 25:685-704. [PMID: 32676771 DOI: 10.1007/s00775-020-01803-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 06/30/2020] [Indexed: 12/18/2022]
Abstract
Mycobacterium tuberculosis (Mtb) has an old history as a human pathogen and still kills over one million people every year. One key feature of this bacterium is its dormancy: a phenomenon responsible for major changes in its metabolism and replication that have been associated with the need for a lengthy therapy for Mtb. This process is regulated by key heme-based sensors, particularly DosT and DevS (DosS), among other co-regulators, and also linked to nitrogen utilization (nitrate/nitrite) and stringent responses. In face of the current threat of tuberculosis, there is an urgent need to develop new therapeutic agents capable of targeting the dormant state, associated with the need for a lengthy therapy. Interestingly, many of those key proteins are indeed metallo-containing or metallo-dependent biomolecules, opening exciting bioinorganic opportunities. Here, we critically reviewed a series of small molecules targeting key proteins involved in these processes, including DosT/DevS/DevR, RegX3, MprA, MtrA, NarL, PknB, Rel, PPK, nitrate and nitrite reductases, GlnA1, aiming for new opportunities and alternative therapies. In the battle against Mycobacterium tuberculosis, new drug targets must be searched, in particular those involved in dormancy. A series of exciting cases for drug development involving metallo-containing or metallo-dependent biomolecules are reviewed, opening great opportunities for the bioinorganic chemistry community.
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12
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Crawford CL, Dalecki AG, Perez MD, Schaaf K, Wolschendorf F, Kutsch O. A copper-dependent compound restores ampicillin sensitivity in multidrug-resistant Staphylococcus aureus. Sci Rep 2020; 10:8955. [PMID: 32488067 PMCID: PMC7265353 DOI: 10.1038/s41598-020-65978-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 03/09/2020] [Indexed: 12/11/2022] Open
Abstract
Multi-drug resistant Staphylococcus aureus, including methicillin-resistant S. aureus (MRSA), has become a worldwide, major health care problem. While initially restricted to clinical settings, drug resistant S. aureus is now one of the key causative agents of community-acquired infections. We have previously demonstrated that copper dependent inhibitors (CDIs), a class of antibiotics that are only active in the presence of copper ions, are effective bactericidal agents against MRSA. A second-generation CDI, APT-6K, exerted bactericidal activity at nanomolar concentrations. At sub-bactericidal concentrations, it effectively synergized with ampicillin to reverse drug resistance in multiple MRSA strains. APT-6K had a favorable therapeutic index when tested on eukaryotic cells (TI: > 30) and, unlike some previously reported CDIs, did not affect mitochondrial activity. These results further establish inhibitors that are activated by the binding of transition metal ions as a promising class of antibiotics, and for the first time, describe their ability to reverse existing drug resistance against clinically relevant antibiotics.
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Affiliation(s)
- Cameron L Crawford
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Alex G Dalecki
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Mildred D Perez
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Kaitlyn Schaaf
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Frank Wolschendorf
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Olaf Kutsch
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.
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13
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Shleeva MO, Savitsky AP, Nikitushkin VD, Soloviev ID, Trutneva KA, Keruchenko YS, Kaprelyants AS. Effect of Photodynamic Inactivation against Dormant Forms and Active Growing Cells of Mycobacterium smegmatis. APPL BIOCHEM MICRO+ 2020. [DOI: 10.1134/s000368382003014x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Dalecki AG, Zorn KM, Clark AM, Ekins S, Narmore WT, Tower N, Rasmussen L, Bostwick R, Kutsch O, Wolschendorf F. High-throughput screening and Bayesian machine learning for copper-dependent inhibitors of Staphylococcus aureus. Metallomics 2020; 11:696-706. [PMID: 30839007 DOI: 10.1039/c8mt00342d] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
One potential source of new antibacterials is through probing existing chemical libraries for copper-dependent inhibitors (CDIs), i.e., molecules with antibiotic activity only in the presence of copper. Recently, our group demonstrated that previously unknown staphylococcal CDIs were frequently present in a small pilot screen. Here, we report the outcome of a larger industrial anti-staphylococcal screen consisting of 40 771 compounds assayed in parallel, both in standard and in copper-supplemented media. Ultimately, 483 had confirmed copper-dependent IC50 values under 50 μM. Sphere-exclusion clustering revealed that these hits were largely dominated by sulfur-containing motifs, including benzimidazole-2-thiones, thiadiazines, thiazoline formamides, triazino-benzimidazoles, and pyridinyl thieno-pyrimidines. Structure-activity relationship analysis of the pyridinyl thieno-pyrimidines generated multiple improved CDIs, with activity likely dependent on ligand/ion coordination. Molecular fingerprint-based Bayesian classification models were built using Discovery Studio and Assay Central, a new platform for sharing and distributing cheminformatic models in a portable format, based on open-source tools. Finally, we used the latter model to evaluate a library of FDA-approved drugs for copper-dependent activity in silico. Two anti-helminths, albendazole and thiabendazole, scored highly and are known to coordinate copper ions, further validating the model's applicability.
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Affiliation(s)
- Alex G Dalecki
- Department of Medicine, Division of Infectious Diseases, University of Alabama at Birmingham, BBRB 562, 845 19th St S, Birmingham, AL 35294, USA.
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15
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Nunvar J, Hogan AM, Buroni S, Savina S, Makarov V, Cardona ST, Drevinek P. The Effect of 2-Thiocyanatopyridine Derivative 11026103 on Burkholderia Cenocepacia: Resistance Mechanisms and Systemic Impact. Antibiotics (Basel) 2019; 8:antibiotics8040159. [PMID: 31546596 PMCID: PMC6963507 DOI: 10.3390/antibiotics8040159] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/09/2019] [Accepted: 09/17/2019] [Indexed: 02/07/2023] Open
Abstract
Bacteria of the Burkholderia cepacia complex (Bcc) are associated with significant decline of lung functions in cystic fibrosis patients. Bcc infections are virtually impossible to eradicate due to their irresponsiveness to antibiotics. The 2-thiocyanatopyridine derivative 11026103 is a novel, synthetic compound active against Burkholderia cenocepacia. To characterize mechanisms of resistance to 11026103, B. cenocepacia was subjected to chemical mutagenesis, followed by whole genome sequencing. Parallel mutations in resistant isolates were localized in a regulatory protein of the efflux system Resistance-Nodulation-Division (RND)-9 (BCAM1948), RNA polymerase sigma factor (BCAL2462) and its cognate putative anti-sigma factor (BCAL2461). Transcriptomic analysis identified positive regulation of a major facilitator superfamily (MFS) efflux system BCAL1510-1512 by BCAL2462. Artificial overexpression of both efflux systems increased resistance to the compound. The effect of 11026103 on B. cenocepacia was analyzed by RNA-Seq and a competitive fitness assay utilizing an essential gene knockdown mutant library. 11026103 exerted a pleiotropic effect on transcription including profound downregulation of cluster of orthologous groups (COG) category “Translation, ribosomal structure, and biogenesis”. The competitive fitness assay identified many genes which modulated susceptibility to 11026103. In summary, 11026103 exerts a pleiotropic cellular response in B. cenocepacia which can be prevented by efflux system-mediated export.
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Affiliation(s)
- Jaroslav Nunvar
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, V Uvalu 84, 15400 Prague, Czech Republic.
| | - Andrew M Hogan
- Department of Microbiology, Faculty of Science, University of Manitoba, 213 Buller Building, Winnipeg, MB R3T 2N2, Canada.
| | - Silvia Buroni
- Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy.
| | - Svetlana Savina
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, Moscow 119071, Russia.
| | - Vadim Makarov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, Moscow 119071, Russia.
| | - Silvia T Cardona
- Department of Microbiology, Faculty of Science, University of Manitoba, 213 Buller Building, Winnipeg, MB R3T 2N2, Canada.
- Department of Medical Microbiology and Infectious Diseases, Rady Faculty of Health Sciences, University of Manitoba, 727 McDermot Avenue, Winnipeg, MB R3E 3P5, Canada.
| | - Pavel Drevinek
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, V Uvalu 84, 15400 Prague, Czech Republic.
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16
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Lopez Quezada L, Li K, McDonald SL, Nguyen Q, Perkowski AJ, Pharr CW, Gold B, Roberts J, McAulay K, Saito K, Somersan Karakaya S, Javidnia PE, Porras de Francisco E, Amieva MM, Dı́az SP, Mendoza Losana A, Zimmerman M, Liang HPH, Zhang J, Dartois V, Sans S, Lagrange S, Goullieux L, Roubert C, Nathan C, Aubé J. Dual-Pharmacophore Pyrithione-Containing Cephalosporins Kill Both Replicating and Nonreplicating Mycobacterium tuberculosis. ACS Infect Dis 2019; 5:1433-1445. [PMID: 31184461 DOI: 10.1021/acsinfecdis.9b00112] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The historical view of β-lactams as ineffective antimycobacterials has given way to growing interest in the activity of this class against Mycobacterium tuberculosis (Mtb) in the presence of a β-lactamase inhibitor. However, most antimycobacterial β-lactams kill Mtb only or best when the bacilli are replicating. Here, a screen of 1904 β-lactams led to the identification of cephalosporins substituted with a pyrithione moiety at C3' that are active against Mtb under both replicating and nonreplicating conditions, neither activity requiring a β-lactamase inhibitor. Studies showed that activity against nonreplicating Mtb required the in situ release of the pyrithione, independent of the known class A β-lactamase, BlaC. In contrast, replicating Mtb could be killed both by released pyrithione and by the parent β-lactam. Thus, the antimycobacterial activity of pyrithione-containing cephalosporins arises from two mechanisms that kill mycobacteria in different metabolic states.
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Affiliation(s)
- Landys Lopez Quezada
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Kelin Li
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, 125 Mason Farm Road, Chapel Hill, North Carolina 27599, United States
| | - Stacey L. McDonald
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, 125 Mason Farm Road, Chapel Hill, North Carolina 27599, United States
| | - Quyen Nguyen
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, 125 Mason Farm Road, Chapel Hill, North Carolina 27599, United States
| | - Andrew J. Perkowski
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, 125 Mason Farm Road, Chapel Hill, North Carolina 27599, United States
| | - Cameron W. Pharr
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, 125 Mason Farm Road, Chapel Hill, North Carolina 27599, United States
| | - Ben Gold
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Julia Roberts
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Kathrine McAulay
- Center for Global Health, Weill Cornell Medicine, 402 East 67th Street, New York, New York 10065, United States
- Les Centres GHESKIO, 33, Boulevard Harry Truman, Port-au-Prince, Haiti
| | - Kohta Saito
- Department of Medicine, Weill Cornell Medical College, New York, New York 10065, United States
| | - Selin Somersan Karakaya
- Department of Medicine, Weill Cornell Medical College, New York, New York 10065, United States
| | - Prisca Elis Javidnia
- Department of Medicine, Weill Cornell Medical College, New York, New York 10065, United States
| | - Esther Porras de Francisco
- Diseases of the Developing World (DDW), Tres Cantos Medicine Development Campus, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Manuel Marin Amieva
- Diseases of the Developing World (DDW), Tres Cantos Medicine Development Campus, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Sara Palomo Dı́az
- Diseases of the Developing World (DDW), Tres Cantos Medicine Development Campus, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Alfonso Mendoza Losana
- Diseases of the Developing World (DDW), Tres Cantos Medicine Development Campus, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Matthew Zimmerman
- Public Health Research Institute, New Jersey Medical School, Rutgers, the State University of New Jersey, 225 Warren Street, Newark, New Jersey 07013, United States
| | - Hsin-Pin Ho Liang
- Public Health Research Institute, New Jersey Medical School, Rutgers, the State University of New Jersey, 225 Warren Street, Newark, New Jersey 07013, United States
| | - Jun Zhang
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Veronique Dartois
- Public Health Research Institute, New Jersey Medical School, Rutgers, the State University of New Jersey, 225 Warren Street, Newark, New Jersey 07013, United States
| | - Stéphanie Sans
- Evotec ID (Lyon), SAS, 1541, Avenue Marcel Merieux, Marcy l’Etoile 69280, France
| | - Sophie Lagrange
- Evotec ID (Lyon), SAS, 1541, Avenue Marcel Merieux, Marcy l’Etoile 69280, France
| | - Laurent Goullieux
- Evotec ID (Lyon), SAS, 1541, Avenue Marcel Merieux, Marcy l’Etoile 69280, France
| | - Christine Roubert
- Evotec ID (Lyon), SAS, 1541, Avenue Marcel Merieux, Marcy l’Etoile 69280, France
| | - Carl Nathan
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10065, United States
| | - Jeffrey Aubé
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, 125 Mason Farm Road, Chapel Hill, North Carolina 27599, United States
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17
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Pavlin M, Qasem Z, Sameach H, Gevorkyan-Airapetov L, Ritacco I, Ruthstein S, Magistrato A. Unraveling the Impact of Cysteine-to-Serine Mutations on the Structural and Functional Properties of Cu(I)-Binding Proteins. Int J Mol Sci 2019; 20:E3462. [PMID: 31337158 PMCID: PMC6679193 DOI: 10.3390/ijms20143462] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 07/09/2019] [Accepted: 07/11/2019] [Indexed: 02/03/2023] Open
Abstract
Appropriate maintenance of Cu(I) homeostasis is an essential requirement for proper cell function because its misregulation induces the onset of major human diseases and mortality. For this reason, several research efforts have been devoted to dissecting the inner working mechanism of Cu(I)-binding proteins and transporters. A commonly adopted strategy relies on mutations of cysteine residues, for which Cu(I) has an exquisite complementarity, to serines. Nevertheless, in spite of the similarity between these two amino acids, the structural and functional impact of serine mutations on Cu(I)-binding biomolecules remains unclear. Here, we applied various biochemical and biophysical methods, together with all-atom simulations, to investigate the effect of these mutations on the stability, structure, and aggregation propensity of Cu(I)-binding proteins, as well as their interaction with specific partner proteins. Among Cu(I)-binding biomolecules, we focused on the eukaryotic Atox1-ATP7B system, and the prokaryotic CueR metalloregulator. Our results reveal that proteins containing cysteine-to-serine mutations can still bind Cu(I) ions; however, this alters their stability and aggregation propensity. These results contribute to deciphering the critical biological principles underlying the regulatory mechanism of the in-cell Cu(I) concentration, and provide a basis for interpreting future studies that will take advantage of cysteine-to-serine mutations in Cu(I)-binding systems.
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Affiliation(s)
- Matic Pavlin
- CNR-IOM at SISSA, via Bonomea 265, 34135 Trieste, Italy
| | - Zena Qasem
- Department of Chemistry, Faculty of Exact Sciences, Bar Ilan University, Ramat-Gan 5290002, Israel
| | - Hila Sameach
- Department of Chemistry, Faculty of Exact Sciences, Bar Ilan University, Ramat-Gan 5290002, Israel
| | - Lada Gevorkyan-Airapetov
- Department of Chemistry, Faculty of Exact Sciences, Bar Ilan University, Ramat-Gan 5290002, Israel
| | - Ida Ritacco
- CNR-IOM at SISSA, via Bonomea 265, 34135 Trieste, Italy
| | - Sharon Ruthstein
- Department of Chemistry, Faculty of Exact Sciences, Bar Ilan University, Ramat-Gan 5290002, Israel.
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18
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Crawford CL, Dalecki AG, Narmore WT, Hoff J, Hargett AA, Renfrow MB, Zhang M, Kalubowilage M, Bossmann SH, Queern SL, Lapi SE, Hunter RN, Bao D, Augelli-Szafran CE, Kutsch O, Wolschendorf F. Pyrazolopyrimidinones, a novel class of copper-dependent bactericidal antibiotics against multi-drug resistant S. aureus. Metallomics 2019; 11:784-798. [DOI: 10.1039/c8mt00316e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Pyrazolopyrimidinones traffic copper into S. aureus, depleting ATP and altering essential ion concentrations, resulting in the death of the bacteria.
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Affiliation(s)
| | - Alex G. Dalecki
- Department of Medicine
- University of Alabama at Birmingham
- Birmingham
- USA
| | | | - Jessica Hoff
- Department of Medicine
- University of Alabama at Birmingham
- Birmingham
- USA
| | - Audra A. Hargett
- Department of Biochemistry and Molecular Genetics
- University of Alabama at Birmingham
- Birmingham
- USA
| | - Matthew B. Renfrow
- Department of Biochemistry and Molecular Genetics
- University of Alabama at Birmingham
- Birmingham
- USA
| | - Man Zhang
- Department of Chemistry
- Kansas State University
- Manhattan
- USA
| | | | | | - Stacy L. Queern
- Department of Radiology
- University of Alabama at Birmingham
- Birmingham
- USA
- Department of Chemistry
| | - Suzanne E. Lapi
- Department of Radiology
- University of Alabama at Birmingham
- Birmingham
- USA
- Department of Chemistry
| | - Robert N. Hunter
- Department of Chemistry
- Drug Discovery Division
- Southern Research
- Birmingham
- USA
| | - Donghui Bao
- Department of Chemistry
- Drug Discovery Division
- Southern Research
- Birmingham
- USA
| | | | - Olaf Kutsch
- Department of Medicine
- University of Alabama at Birmingham
- Birmingham
- USA
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