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Singh D, Sharma R, Jamal S, Agarwal M, Grover S, Batra JK. Identification and characterization of repurposed small molecule inhibitors of Mycobacterium tuberculosis caseinolytic protease B (ClpB) as anti-mycobacterials. Int J Biol Macromol 2024; 264:130614. [PMID: 38447849 DOI: 10.1016/j.ijbiomac.2024.130614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/29/2024] [Accepted: 03/02/2024] [Indexed: 03/08/2024]
Abstract
Mycobacterium tuberculosis (Mtb) caseinolytic protease B (ClpB) is a chaperone possessing a unique ability to resolubilize the aggregated proteins in vivo. ClpB has been shown to be important for the survival of Mtb within the host. Thus, it appears to be a promising target to develop new therapeutic molecules against tuberculosis. In this study, we have screened FDA approved compounds in silico to identify inhibitors against Mtb ClpB. In our screen, several compounds interacted with ClpB. The top four compounds, namely framycetin, gentamicin, ribostamycin and tobramycin showing the highest binding energy were selected for further investigation. MD simulations and tryptophan-based quenching of ClpB-drug complexes established that the selected inhibitors stably interacted with the target protein. The inhibitor and protein complexes were found to be stabilized by hydrogen bonding, and hydrophobic interactions. Although, the compounds did not affect the ATPase activity of ClpB significantly, the protein resolubilization activity of ClpB was remarkably reduced in their presence. All four compounds potently inhibited the growth of Mtb H37Ra. The antimycobacterial activity of the compounds appears to be due the inhibition of functional ClpB oligomer formation, in turn affecting its chaperonic activity.
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Affiliation(s)
- Digvijay Singh
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India
| | - Rahul Sharma
- Department of Molecular Medicine, School of Interdisciplinary Sciences and Technology, Jamia Hamdard, New Delhi 110062, India
| | - Salma Jamal
- Department of Molecular Medicine, School of Interdisciplinary Sciences and Technology, Jamia Hamdard, New Delhi 110062, India
| | - Meetu Agarwal
- Department of Molecular Medicine, School of Interdisciplinary Sciences and Technology, Jamia Hamdard, New Delhi 110062, India
| | - Sonam Grover
- Department of Molecular Medicine, School of Interdisciplinary Sciences and Technology, Jamia Hamdard, New Delhi 110062, India
| | - Janendra K Batra
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India; ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi 110029, India.
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Hans S, Purkait D, Nandan S, Bansal M, Hameed S, Fatima Z. Rec A disruption unveils cross talk between DNA repair and membrane damage, efflux pump activity, biofilm formation in Mycobacterium smegmatis. Microb Pathog 2020; 149:104262. [PMID: 32439563 DOI: 10.1016/j.micpath.2020.104262] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 05/06/2020] [Accepted: 05/12/2020] [Indexed: 10/24/2022]
Abstract
Tuberculosis (TB) caused by Mycobacterium tuberculosis (MTB) has emerged in recent decades as one of the leading causes of mortality worldwide. The burden of TB is alarmingly high, with one third affected global population as reported by WHO. Short-course treatment with an antibiotic is a powerful weapon to treat infection of susceptible MTB strain, however; MTB has developed resistance to anti-TB drugs, which is an escalating global health crisis. Thus there is urgent need to identify new drug targets. RecA is a 38 kilodalton protein required for the repair and maintenance of DNA and regulation of the SOS response. The objective of this study is to understand the effect of disruption of RecA gene (deletion mutant ΔdisA from previous study) in a surrogate model for MTB, Mycobacterium smegmatis. This study demonstrated that disruption of RecA causes enhanced susceptibility towards rifampicin and generation of ROS leading to lipid peroxidation and impaired membrane homeostasis as depicted by altered cell membrane permeability and efflux pump activity. Mass spectrometry based lipidomic analysis revealed decreased mycolic acid moieties, phosphatidylinositol mannosides (PIM), Phthiocerol dimycocerosate (DIM). Furthermore, biofilm formation was considerably reduced. Additionally, we have validated all the disrupted phenotypes by RT-PCR which showed a good correlation with the biochemical assays. Lastly, RecA mutant displayed reduced infectivity in Caenorhabditis elegans illustrating its vulnerability as antimycobacterial target. Together, present study establishes a link between DNA repair, drug efflux and biofilm formation and validates RecA as an effective drug target. Intricate studies are needed to further understand and exploit this therapeutic opportunity.
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Affiliation(s)
- Sandeep Hans
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram, Manesar, 122413, India
| | - Dyuti Purkait
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram, Manesar, 122413, India
| | - Shiv Nandan
- Amity Lipidomics Research Facility, Amity University Haryana, Gurugram, Manesar, 122413, India
| | - Maghav Bansal
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram, Manesar, 122413, India
| | - Saif Hameed
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram, Manesar, 122413, India.
| | - Zeeshan Fatima
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram, Manesar, 122413, India.
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Ghio AJ, Soukup JM, Dailey LA, Madden MC. Air pollutants disrupt iron homeostasis to impact oxidant generation, biological effects, and tissue injury. Free Radic Biol Med 2020; 151:38-55. [PMID: 32092410 PMCID: PMC8274387 DOI: 10.1016/j.freeradbiomed.2020.02.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 01/27/2020] [Accepted: 02/10/2020] [Indexed: 02/07/2023]
Abstract
Air pollutants cause changes in iron homeostasis through: 1) a capacity of the pollutant, or a metabolite(s), to complex/chelate iron from pivotal sites in the cell or 2) an ability of the pollutant to displace iron from pivotal sites in the cell. Through either pathway of disruption in iron homeostasis, metal previously employed in essential cell processes is sequestered after air pollutant exposure. An absolute or functional cell iron deficiency results. If enough iron is lost or is otherwise not available within the cell, cell death ensues. However, prior to death, exposed cells will attempt to reverse the loss of requisite metal. This response of the cell includes increased expression of metal importers (e.g. divalent metal transporter 1). Oxidant generation after exposure to air pollutants includes superoxide production which functions in ferrireduction necessary for cell iron import. Activation of kinases and phosphatases and transcription factors and increased release of pro-inflammatory mediators also result from a cell iron deficiency, absolute or functional, after exposure to air pollutants. Finally, air pollutant exposure culminates in the development of inflammation and fibrosis which is a tissue response to the iron deficiency challenging cell survival. Following the response of increased expression of importers and ferrireduction, activation of kinases and phosphatases and transcription factors, release of pro-inflammatory mediators, and inflammation and fibrosis, cell iron is altered, and a new metal homeostasis is established. This new metal homeostasis includes increased total iron concentrations in cells with metal now at levels sufficient to meet requirements for continued function.
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Affiliation(s)
- Andrew J Ghio
- From the National Health and Environmental Effects Research Laboratory, Environmental Protection Agency, Chapel Hill, NC, USA.
| | - Joleen M Soukup
- From the National Health and Environmental Effects Research Laboratory, Environmental Protection Agency, Chapel Hill, NC, USA
| | - Lisa A Dailey
- From the National Health and Environmental Effects Research Laboratory, Environmental Protection Agency, Chapel Hill, NC, USA
| | - Michael C Madden
- From the National Health and Environmental Effects Research Laboratory, Environmental Protection Agency, Chapel Hill, NC, USA
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Forging New Antibiotic Combinations under Iron-Limiting Conditions. Antimicrob Agents Chemother 2020; 64:AAC.01909-19. [PMID: 31907180 DOI: 10.1128/aac.01909-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 12/23/2019] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas aeruginosa is a multidrug-resistant nosocomial pathogen. We showed previously that thiostrepton (TS), a Gram-positive thiopeptide antibiotic, is imported via pyoverdine receptors and synergizes with iron chelator deferasirox (DSX) to inhibit the growth of P. aeruginosa and Acinetobacter baumannii clinical isolates. A small number of P. aeruginosa and A. baumannii isolates were resistant to the combination, prompting us to search for other compounds that could synergize with TS against those strains. From literature surveys, we selected 14 compounds reported to have iron-chelating activity, plus one iron analogue, and tested them for synergy with TS. Doxycycline (DOXY), ciclopirox olamine (CO), tropolone (TRO), clioquinol (CLI), and gallium nitrate (GN) synergized with TS. Individual compounds were bacteriostatic, but the combinations were bactericidal. Our spectrophotometric data and chrome azurol S agar assay confirmed that the chelators potentiate TS activity through iron sequestration rather than through their innate antimicrobial activities. A triple combination of TS plus DSX plus DOXY had the most potent activity against P. aeruginosa and A. baumannii isolates. One P. aeruginosa clinical isolate was resistant to the triple combination but susceptible to a triple combination containing higher concentrations of CLI, CO, or DOXY. All A. baumannii isolates were susceptible to the triple combinations. Our data reveal a diverse set of compounds with dual activity as antibacterial agents and TS adjuvants, allowing combinations to be tailored for resistant clinical isolates.
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Techniques to Understand Mycobacterial Lipids and Use of Lipid-Based Nanoformulations for Tuberculosis Management. Nanobiomedicine (Rij) 2020. [DOI: 10.1007/978-981-32-9898-9_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Huang W, Yang Y, Wen W, Luo Y, Wu J, Xiang L, Hu Y, Xu S, Chen S, Wang P. Vanillin enhances the passive transport rate and absorption of drugs with moderate oral bioavailability in vitro and in vivo by affecting the membrane structure. Food Funct 2020; 11:700-710. [DOI: 10.1039/c9fo02846c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Vanillin is a popular flavoring agent in the food, tobacco, and perfume industries.
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Affiliation(s)
- Wen'ge Huang
- Institute of Material Medical Integration and Transformation for Brain Disorders
- Chengdu University of Traditional Chinese Medicine
- Chengdu
- China
| | - Yingzhuo Yang
- Department of Nuclear Medicine
- Sichuan Cancer Hospital
- Chengdu
- China
| | - Wen Wen
- Institute of Material Medical Integration and Transformation for Brain Disorders
- Chengdu University of Traditional Chinese Medicine
- Chengdu
- China
| | - Yu Luo
- College of Pharmacy
- Chengdu University of Traditional Chinese Medicine
- Chengdu
- China
| | - Jiasi Wu
- College of Pharmacy
- Chengdu University of Traditional Chinese Medicine
- Chengdu
- China
| | - Li Xiang
- College of Pharmacy
- Chengdu University of Traditional Chinese Medicine
- Chengdu
- China
| | - Yinfan Hu
- College of Pharmacy
- Chengdu University of Traditional Chinese Medicine
- Chengdu
- China
| | - Shijun Xu
- Institute of Material Medical Integration and Transformation for Brain Disorders
- Chengdu University of Traditional Chinese Medicine
- Chengdu
- China
| | - Simin Chen
- College of Pharmacy
- Chengdu University of Traditional Chinese Medicine
- Chengdu
- China
| | - Ping Wang
- Institute of Material Medical Integration and Transformation for Brain Disorders
- Chengdu University of Traditional Chinese Medicine
- Chengdu
- China
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Lipidomic insights to understand membrane dynamics in response to vanillin in Mycobacterium smegmatis. Int Microbiol 2019; 23:263-276. [DOI: 10.1007/s10123-019-00099-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/13/2019] [Accepted: 08/26/2019] [Indexed: 11/24/2022]
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Sharma S, Hameed S, Fatima Z. Monoterpenoid Geraniol Improves Anti-mycobacterial Drug Efficiency by Interfering with Lipidome and Virulence of Mycobacteria. Infect Disord Drug Targets 2019; 20:467-485. [PMID: 31241021 DOI: 10.2174/1871526519666190625113203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 05/27/2019] [Accepted: 05/29/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Tuberculosis (TB) remains a global infectious disorder for which efficient therapeutics are elusive. Nature is a source of novel pharmacologically active compounds with many potential drugs being derived directly or indirectly from plants, microorganisms and marine organisms. OBJECTIVE The present study aimed to elucidate the antimycobacterial potential of Geraniol (Ger), monoterpene alcohol, against Mycobacterium smegmatis. METHODS Disrupted membrane integrity was studied by membrane permeability assay and PI uptake. Cell surface phenotypes were studied by colony morphology, sliding motility and cell sedimentation rate. Lipidome profile was demonstrated by thin-layer chromatography and liquid chromatography-electrospray ionization mass spectrometry. Amendment in iron homeostasis was assessed by using iron chelator ferrozine and ferroxidase assay while genotoxicity was estimated with EtBr and DAPI staining. Biofilm formation was measured by staining, dry mass and metabolic activity using crystal violet. Cell adherence was examined microscopically and spectrophotometrically. RESULTS We found the antimycobacterial activity of Ger to be 500 μg/ml against M. smegmatis. Underlying mechanisms revealed impaired cell surface phenotypes. Lipidomics analysis exposed profound decrement of mycolic acids, phosphatidylinositol mannosides and triacylglycerides which are crucial for MTB pathogenicity. We further explored that Ger impairs iron homeostasis and leads to genotoxic stress. Moreover, Ger inhibited the potential virulence attributes such as biofilm formation and cell adherence to both polystyrene surface and epithelial cells. Finally, we have validated all the disrupted phenotypes by RT-PCR which showed good correlation with the biochemical assays. CONCLUSION Taken together, the current study demonstrates the antimycobacterial mechanisms of Ger, which may be exploited as an effective candidate of pharmacological interest.
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Affiliation(s)
- Sharda Sharma
- Amity Institute of Biotechnology, Amity University Haryana, Gurgugram (Manesar)-122413, India
| | - Saif Hameed
- Amity Institute of Biotechnology, Amity University Haryana, Gurgugram (Manesar)-122413, India
| | - Zeeshan Fatima
- Amity Institute of Biotechnology, Amity University Haryana, Gurgugram (Manesar)-122413, India
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Bezerra CF, Camilo CJ, do Nascimento Silva MK, de Freitas TS, Ribeiro-Filho J, Coutinho HDM. Vanillin selectively modulates the action of antibiotics against resistant bacteria. Microb Pathog 2017; 113:265-268. [PMID: 29107747 DOI: 10.1016/j.micpath.2017.10.052] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 09/19/2017] [Accepted: 10/26/2017] [Indexed: 10/18/2022]
Abstract
The treatment of infections caused by microorganisms that are resistant to antibiotics represent one of the main challenges of medicine today, especially due to the inefficacy of long-term drug therapy. In the search for new alternatives to treat these infections, many researchers have been looking for new substances derived from natural products to replace, or be used in combination with conventional antibiotics. Vanillin is a phenolic compound whose antimicrobial activity has been used in the elimination of pathogens present in fruits and vegetables. However, its antibacterial and modulating properties remain to be characterized. Therefore, this work aimed to evaluate the antibacterial activity and analyze the modulator activity of vanillin in association with conventional antibiotics. The antimicrobial activity of vanillin was evaluated using the microdilution method to determine the Minimum Inhibitory Concentration (MIC) Standard strains of Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, and multi-resistant strains of Escherichia coli 06, Staphylococcus aureus 10, Pseudomonas aeruginosa 24 were used in this study. The antibiotic modulating effect was analyzed by combining vanillin with Norfloxacin, Imipenem, Gentamicin, Erythromycin and Tetracycline against the following multiresistant bacteria strains: Escherichia coli 06, Staphylococcus aureus 10 and Pseudomonas aeruginosa 24. Data were analyzed using the ANOVA test of two tracks followed by the post hoc Bonferroni test. Vanillin presented CIMs ≥1024μg/mL against all tested strains demonstrating that it did not present significant antibacterial activity. However, modulated the activity of gentamicin and imipenem against S. aureus and E. coli, causing a synergistic effect, but did not affect the activity of norfloxacin, tetracycline and erythromycin against these same microorganisms. A synergistic effect was also obtained from the association of vanillin with norfloxacin against P. aeruginosa. On the other hand, against this strain the association of vanillin with tetracycline and erythromycin caused antagonism, although the activity of gentamicin and imipenem was not affected. In conclusion, vanillin selectively modulated the activity of antibiotics against multiresistant bacteria and as such, might be useful in the development of new therapies against resistant microorganism.
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Affiliation(s)
- Camila Fonseca Bezerra
- Laboratório de Microbiologia e Biologia Molecular- LMBM, Universidade Regional do Cariri- URCA, Crato, Ceará, Brazil.
| | - Cicera Janaine Camilo
- Laboratório de Microbiologia e Biologia Molecular- LMBM, Universidade Regional do Cariri- URCA, Crato, Ceará, Brazil
| | - Maria Karollyna do Nascimento Silva
- Laboratório de Microbiologia e Biologia Molecular- LMBM, Universidade Regional do Cariri- URCA, Crato, Ceará, Brazil; Centro Universitário Dr. Leão Sampaio - Unileão - Juazeiro do Norte, Ceará, Brazil
| | - Thiago Sampaio de Freitas
- Laboratório de Microbiologia e Biologia Molecular- LMBM, Universidade Regional do Cariri- URCA, Crato, Ceará, Brazil
| | - Jaime Ribeiro-Filho
- Centro Universitário Dr. Leão Sampaio - Unileão - Juazeiro do Norte, Ceará, Brazil
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Sesamol exhibits potent antimycobacterial activity: Underlying mechanisms and impact on virulence traits. J Glob Antimicrob Resist 2017; 10:228-237. [DOI: 10.1016/j.jgar.2017.06.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 05/31/2017] [Accepted: 06/12/2017] [Indexed: 12/18/2022] Open
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Pal R, Hameed S, Sharma S, Fatima Z. Influence of iron deprivation on virulence traits of mycobacteria. Braz J Infect Dis 2016; 20:585-591. [PMID: 27755980 PMCID: PMC9427566 DOI: 10.1016/j.bjid.2016.08.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Revised: 08/11/2016] [Accepted: 08/30/2016] [Indexed: 01/17/2023] Open
Abstract
Novel strategies to combat the ever increasing burden of drug resistance in Mycobacterium tuberculosis (MTB) causing tuberculosis (TB) remains a global concern. The ability of MTB to sense and adapt to restricted iron conditions in the hostile environment is essential for their survival and confers the basis of their success as dreadful pathogen. The striking and clinically relevant virulence trait of MTB is its ability to form biofilms and adhere to the host cells. The present study elucidated the effect of iron deprivation on biofilm formation and cell adherence of Mycobacterium smegmatis, a non-pathogenic surrogate of MTB. Firstly, we showed that iron deprivation leads to enhanced cell sedimentation rate and altered colony morphology depicting alterations in cell surface envelope properties. We explored that biofilm formation and cell adherence to polystyrene surface as well as human oral epithelial cells were considerably reduced under iron deprivation both in presence of 2,2 BP (iron chelator) and siderophore mutant Δ011-14 strain. We further investigated that the potency of three first line anti-TB drugs (Isoniazid, Ethambutol, Rifampicin) to inhibit both biofilm formation and cell adhesion were enhanced under iron deprivation in contrast to the drugs when tested alone. Taken together, by virtue of the indispensability of iron for functional virulence traits in mycobacteria, iron deprivation strategies could be further exploited against this notorious human pathogen to explore novel drug targets.
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Affiliation(s)
- Rahul Pal
- Amity University Haryana, Amity Institute of Biotechnology, Gurgaon, India
| | - Saif Hameed
- Amity University Haryana, Amity Institute of Biotechnology, Gurgaon, India
| | - Sharda Sharma
- Amity University Haryana, Amity Institute of Biotechnology, Gurgaon, India
| | - Zeeshan Fatima
- Amity University Haryana, Amity Institute of Biotechnology, Gurgaon, India.
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