1
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Saha P, Sau S, Kalia NP, Sharma DK. Antitubercular activity of 2-mercaptobenzothiazole derivatives targeting Mycobacterium tuberculosis type II NADH dehydrogenase. RSC Med Chem 2024; 15:1664-1674. [PMID: 38784457 PMCID: PMC11110738 DOI: 10.1039/d4md00118d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 03/31/2024] [Indexed: 05/25/2024] Open
Abstract
Mycobacterium tuberculosis (Mtb) type II NADH dehydrogenase (NDH-2) transports electrons into the mycobacterial respiratory pathway at the cost of reduction of NADH to NAD+ and is an attractive drug target. Herein, we have synthesised a series of 2-mercaptobenzothiazoles (C1-C14) and evaluated their anti-tubercular potential as Mtb NDH-2 inhibitors. The synthesised compounds C1-C14 were evaluated for MIC90 and ATP depletion against Mtb H37Ra, M. bovis, and Mtb H37Rv mc2 6230. Compounds C3, C4, and C11 were found to be the active molecules in the series and were further evaluated for their MIC90 against Mtb-resistant strains and for their bactericidal potential against Mtb H37Rv mc26230. The Peredox-mCherry-expressing Mtb strain was used to examine whether C3, C4, and C11 possess NDH-2 inhibitory potential. Furthermore, cytotoxicity analysis against HepG2 displayed a safety index (SI) of >10 for C3 and C4. To get an insight into the mode of interaction at NDH-2, we have performed computational analysis of our active compounds.
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Affiliation(s)
- Pallavi Saha
- Department of Pharmaceutical Engg. and Tech, IIT-Banaras Hindu University Varanasi UP 221005 India
| | - Shashikanta Sau
- Department of Pharmacology and Toxicology, NIPER-Hyderabad Hyderabad 500037 India
| | - Nitin Pal Kalia
- Department of Pharmacology and Toxicology, NIPER-Hyderabad Hyderabad 500037 India
| | - Deepak K Sharma
- Department of Pharmaceutical Engg. and Tech, IIT-Banaras Hindu University Varanasi UP 221005 India
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2
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Adolph C, Cheung CY, McNeil MB, Jowsey WJ, Williams ZC, Hards K, Harold LK, Aboelela A, Bujaroski RS, Buckley BJ, Tyndall JDA, Li Z, Langer JD, Preiss L, Meier T, Steyn AJC, Rhee KY, Berney M, Kelso MJ, Cook GM. A dual-targeting succinate dehydrogenase and F 1F o-ATP synthase inhibitor rapidly sterilizes replicating and non-replicating Mycobacterium tuberculosis. Cell Chem Biol 2024; 31:683-698.e7. [PMID: 38151019 DOI: 10.1016/j.chembiol.2023.12.002] [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: 05/08/2023] [Revised: 09/13/2023] [Accepted: 12/04/2023] [Indexed: 12/29/2023]
Abstract
Mycobacterial bioenergetics is a validated target space for antitubercular drug development. Here, we identify BB2-50F, a 6-substituted 5-(N,N-hexamethylene)amiloride derivative as a potent, multi-targeting bioenergetic inhibitor of Mycobacterium tuberculosis. We show that BB2-50F rapidly sterilizes both replicating and non-replicating cultures of M. tuberculosis and synergizes with several tuberculosis drugs. Target identification experiments, supported by docking studies, showed that BB2-50F targets the membrane-embedded c-ring of the F1Fo-ATP synthase and the catalytic subunit (substrate-binding site) of succinate dehydrogenase. Biochemical assays and metabolomic profiling showed that BB2-50F inhibits succinate oxidation, decreases the activity of the tricarboxylic acid (TCA) cycle, and results in succinate secretion from M. tuberculosis. Moreover, we show that the lethality of BB2-50F under aerobic conditions involves the accumulation of reactive oxygen species. Overall, this study identifies BB2-50F as an effective inhibitor of M. tuberculosis and highlights that targeting multiple components of the mycobacterial respiratory chain can produce fast-acting antimicrobials.
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Affiliation(s)
- Cara Adolph
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland 1042, New Zealand
| | - Chen-Yi Cheung
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Matthew B McNeil
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland 1042, New Zealand
| | - William J Jowsey
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland 1042, New Zealand
| | - Zoe C Williams
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Kiel Hards
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Liam K Harold
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Ashraf Aboelela
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia; Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Richard S Bujaroski
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia; Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Benjamin J Buckley
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia; Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Joel D A Tyndall
- School of Pharmacy, University of Otago, Dunedin 9054, New Zealand
| | - Zhengqiu Li
- School of Pharmacy, Jinan University, Guangzhou, China
| | - Julian D Langer
- Proteomics, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
| | - Laura Preiss
- Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
| | - Thomas Meier
- Department of Life Sciences, Imperial College London, Exhibition Road, London SW7 2AZ, UK; Private University in the Principality of Liechtenstein, Triesen, Liechtenstein
| | - Adrie J C Steyn
- Africa Health Research Institute, University of KwaZulu Natal, Durban, KwaZulu, Natal, South Africa; Department of Microbiology, Centers for AIDs Research and Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Kyu Y Rhee
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, Ithaca, NY 14853, USA; Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Michael Berney
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | - Michael J Kelso
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia; Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Gregory M Cook
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland 1042, New Zealand.
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3
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Saha P, Das S, Indurthi HK, Kumar R, Roy A, Kalia NP, Sharma DK. Cytochrome bd oxidase: an emerging anti-tubercular drug target. RSC Med Chem 2024; 15:769-787. [PMID: 38516593 PMCID: PMC10953478 DOI: 10.1039/d3md00587a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 01/25/2024] [Indexed: 03/23/2024] Open
Abstract
Cytochrome bd (cyt-bd) oxidase, one of the two terminal oxidases in the Mycobacterium tuberculosis (Mtb) oxidative phosphorylation pathway, plays an indispensable role in maintaining the functionality of the metabolic pathway under stressful conditions. However, the absence of this oxidase in eukaryotic cells allows researchers to select it as a potential drug target for the synthesis of anti-tubercular (anti-TB) molecules. Cyt-bd inhibitors have often been combined with cytochrome bcc/aa3 super-complex inhibitors in anti-TB drug regimens to achieve a desired bactericidal response. The functional redundancy between both the terminal oxidases is responsible for this. The cryo-EM structure of cyt-bd oxidase from Mtb (PDB ID: 7NKZ) further accelerated the research to identify its inhibitor. Herein, we have summarized the reported anti-TB cyt-bd inhibitors, insight into the rationale behind targeting cyt-bd oxidase, and an outline of the architecture of Mtb cyt-bd oxidase.
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Affiliation(s)
- Pallavi Saha
- Department of Pharmaceutical Engg. and Tech, IIT-Banaras Hindu University Varanasi UP 221005 India
| | - Samarpita Das
- Department of Pharmaceutical Engg. and Tech, IIT-Banaras Hindu University Varanasi UP 221005 India
| | - Harish K Indurthi
- Department of Pharmaceutical Engg. and Tech, IIT-Banaras Hindu University Varanasi UP 221005 India
| | - Rohit Kumar
- Department of Pharmaceutical Engg. and Tech, IIT-Banaras Hindu University Varanasi UP 221005 India
| | - Arnab Roy
- Department of Pharmacology and Toxicology, NIPER-Hyderabad Hyderabad 500037 India
| | - Nitin Pal Kalia
- Department of Pharmacology and Toxicology, NIPER-Hyderabad Hyderabad 500037 India
| | - Deepak K Sharma
- Department of Pharmaceutical Engg. and Tech, IIT-Banaras Hindu University Varanasi UP 221005 India
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4
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Stanley S, Wang X, Liu Q, Kwon YY, Frey AM, Hicks ND, Vickers AJ, Hui S, Fortune SM. Ongoing evolution of the Mycobacterium tuberculosis lactate dehydrogenase reveals the pleiotropic effects of bacterial adaption to host pressure. PLoS Pathog 2024; 20:e1012050. [PMID: 38422159 DOI: 10.1371/journal.ppat.1012050] [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: 10/20/2023] [Revised: 03/12/2024] [Accepted: 02/13/2024] [Indexed: 03/02/2024] Open
Abstract
The bacterial determinants that facilitate Mycobacterium tuberculosis (Mtb) adaptation to the human host environment are poorly characterized. We have sought to decipher the pressures facing the bacterium in vivo by assessing Mtb genes that are under positive selection in clinical isolates. One of the strongest targets of selection in the Mtb genome is lldD2, which encodes a quinone-dependent L-lactate dehydrogenase (LldD2) that catalyzes the oxidation of lactate to pyruvate. Lactate accumulation is a salient feature of the intracellular environment during infection and lldD2 is essential for Mtb growth in macrophages. We determined the extent of lldD2 variation across a set of global clinical isolates and defined how prevalent mutations modulate Mtb fitness. We show the stepwise nature of lldD2 evolution that occurs as a result of ongoing lldD2 selection in the background of ancestral lineage-defining mutations and demonstrate that the genetic evolution of lldD2 additively augments Mtb growth in lactate. Using quinone-dependent antibiotic susceptibility as a functional reporter, we also find that the evolved lldD2 mutations functionally increase the quinone-dependent activity of LldD2. Using 13C-lactate metabolic flux tracing, we find that lldD2 is necessary for robust incorporation of lactate into central carbon metabolism. In the absence of lldD2, label preferentially accumulates in dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate (G3P) and is associated with a discernible growth defect, providing experimental evidence for accrued lactate toxicity via the deleterious buildup of sugar phosphates. The evolved lldD2 variants increase lactate incorporation to pyruvate while altering triose phosphate flux, suggesting both an anaplerotic and detoxification benefit to lldD2 evolution. We further show that the mycobacterial cell is transcriptionally sensitive to the changes associated with altered lldD2 activity which affect the expression of genes involved in cell wall lipid metabolism and the ESX- 1 virulence system. Together, these data illustrate a multifunctional role of LldD2 that provides context for the selective advantage of lldD2 mutations in adapting to host stress.
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Affiliation(s)
- Sydney Stanley
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Xin Wang
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Qingyun Liu
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Young Yon Kwon
- Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Abigail M Frey
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Nathan D Hicks
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Andrew J Vickers
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Sheng Hui
- Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Sarah M Fortune
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
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5
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Shinde AD, Nandurkar YM, Bhalekar S, Walunj YS, Ugale S, Ahmad I, Patel H, Chavan AP, Mhaske PC. Investigation of new 1,2,3-triazolyl-quinolinyl-propan-2-ol derivatives as potential antimicrobial agents: in vitro and in silico approach. J Biomol Struct Dyn 2024; 42:1191-1207. [PMID: 37254438 DOI: 10.1080/07391102.2023.2217922] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 03/28/2023] [Indexed: 06/01/2023]
Abstract
A new series of 1-((1-(4-substituted benzyl)-1H-1,2,3-triazol-4-yl)methoxy)-2-(2-substituted quinolin-4-yl)propan-2-ol (9a-x) have been synthesized. The newly synthesized 1,2,3-triazolyl-quinolinyl-propan-2-ol (9a-x) derivatives were screened for in vitro antimicrobial activity against M. tuberculosis H37Rv, E. coli, P. mirabilis, B. subtilis, and S. albus. Most of the compounds showed good to moderate antibacterial activity and all derivatives have shown excellent to good antitubercular activity with MIC 0.8-12.5 μg/mL. To know the plausible mode of action for antibacterial activity the docking study against DNA gyrase from M. tuberculosis and S. aureus was investigated. The compounds have shown significant docking scores in the range of -9.532 to -7.087 and -9.543 to -6.621 Kcal/mol with the DNA gyrase enzyme of S. aureus (PDB ID: 2XCT) and M. tuberculosis (PDB ID: 5BS8), respectively. Against the S. aureus and M. tuberculosis H37Rv strains, the compound 9 l showed good activity with MIC values of 62.5 and 3.33 μM. It also showed significant docking scores in both targets with -8.291 and -8.885 Kcal/mol, respectively. Molecular dynamics was studied to investigate the structural and dynamics transitions at the atomistic level in S. aureus DNA gyrase (2XCT) and M. tuberculosis DNA gyrase (5BS8). The results revealed that the residues in the active binding pockets of the S. aureus and M. tuberculosis DNA gyrase proteins that interacted with compound 9 l remained relatively consistent throughout the MD simulations and thus, reflected the conformation stability of the respective complexes. Thus, the significant antimicrobial activity of derivatives 9a-x recommended that these compounds could assist in the development of lead compounds to treat for bacterial infections.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abhijit D Shinde
- Post-Graduate Department of Chemistry, S. P. Mandali's Sir Parashurambhau College (Affiliated to Savitribai Phule Pune University), Pune, India
| | - Yogesh M Nandurkar
- Post-Graduate Department of Chemistry, S. P. Mandali's Sir Parashurambhau College (Affiliated to Savitribai Phule Pune University), Pune, India
- Department of Chemistry, Nowrosjee Wadia College (Affiliated to Savitribai Phule Pune University), Pune, India
| | - Swapnil Bhalekar
- Post-Graduate Department of Chemistry, S. P. Mandali's Sir Parashurambhau College (Affiliated to Savitribai Phule Pune University), Pune, India
| | - Yogesh S Walunj
- Post-Graduate Department of Chemistry, S. P. Mandali's Sir Parashurambhau College (Affiliated to Savitribai Phule Pune University), Pune, India
- Department of Chemistry, Hutatma Rajguru Mahavidyalaya, Rajgurunagar, India (Affiliated to Savitribai Phule Pune University)
| | - Sandip Ugale
- Post-Graduate Department of Chemistry, S. P. Mandali's Sir Parashurambhau College (Affiliated to Savitribai Phule Pune University), Pune, India
| | - Iqrar Ahmad
- Department of Pharmaceutical Chemistry, Prof. Ravindra Nikam College of Pharmacy, Gondur, Dhule, Maharashtra, India
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India
| | - Harun Patel
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India
| | - Abhijit P Chavan
- Post-Graduate Department of Chemistry, S. P. Mandali's Sir Parashurambhau College (Affiliated to Savitribai Phule Pune University), Pune, India
| | - Pravin C Mhaske
- Post-Graduate Department of Chemistry, S. P. Mandali's Sir Parashurambhau College (Affiliated to Savitribai Phule Pune University), Pune, India
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6
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Verma A, Naik B, Kumar V, Mishra S, Choudhary M, Khan JM, Gupta AK, Pandey P, Rustagi S, Kakati B, Gupta S. Revolutionizing Tuberculosis Treatment: Uncovering New Drugs and Breakthrough Inhibitors to Combat Drug-Resistant Mycobacterium tuberculosis. ACS Infect Dis 2023; 9:2369-2385. [PMID: 37944023 DOI: 10.1021/acsinfecdis.3c00436] [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] [Indexed: 11/12/2023]
Abstract
Tuberculosis (TB) is a global health threat that causes significant mortality. This review explores chemotherapeutics that target essential processes in Mycobacterium tuberculosis, such as DNA replication, protein synthesis, cell wall formation, energy metabolism, and proteolysis. We emphasize the need for new drugs to treat drug-resistant strains and shorten the treatment duration. Emerging targets and promising inhibitors were identified by examining the intricate biology of TB. This review provides an overview of recent developments in the search for anti-TB drugs with a focus on newly validated targets and inhibitors. We aimed to contribute to efforts to combat TB and improve therapeutic outcomes.
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Affiliation(s)
- Ankit Verma
- Himalayan School of Biosciences, Swami Rama Himalayan University, Jolly Grant, Dehradun 248016, Uttarakhand, India
| | - Bindu Naik
- Department of Food Science and Technology, Graphic Era Deemed to be University, Bell Road, Clement Town, Dehradun 248002, Uttarakhand, India
| | - Vijay Kumar
- Himalayan School of Biosciences, Swami Rama Himalayan University, Jolly Grant, Dehradun 248016, Uttarakhand, India
| | - Sadhna Mishra
- Faculty of Agricultural Sciences, GLA University, Mathura 281406, UP, India
| | - Megha Choudhary
- Himalayan School of Biosciences, Swami Rama Himalayan University, Jolly Grant, Dehradun 248016, Uttarakhand, India
| | - Javed Masood Khan
- Department of Food Science and Nutrition, Faculty of Food and Agricultural Sciences, King Saud University, 2460, Riyadh 11451, Saudi Arabia
| | - Arun Kumar Gupta
- Department of Food Science and Technology, Graphic Era Deemed to be University, Bell Road, Clement Town, Dehradun 248002, Uttarakhand, India
| | - Piyush Pandey
- Department of Microbiology, Assam University, Silchur 788011, Assam, India
| | - Sarvesh Rustagi
- Department of Food Technology, UCALS, Uttaranchal University, Dehradun 248007, Uttarakhand, India
| | - Barnali Kakati
- Department of Microbiology, Himalayan Institute of Medical Sciences, Swami Rama Himalayan University, Jolly Grant, Dehradun 248016, U.K., India
| | - Sanjay Gupta
- Himalayan School of Biosciences, Swami Rama Himalayan University, Jolly Grant, Dehradun 248016, Uttarakhand, India
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7
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Subramaniyan S, Nagarajan H, Vetrivel U, Jeyaraman J. Multilayer precision-based screening of potential inhibitors targeting Mycobacterium tuberculosis acetate kinase using in silico approaches. Comput Biol Chem 2023; 107:107942. [PMID: 37673012 DOI: 10.1016/j.compbiolchem.2023.107942] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/20/2023] [Accepted: 08/22/2023] [Indexed: 09/08/2023]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (MTB), remains a major threat to global health, with the emergence of multi-drug and extensively drug-resistant strains posing a serious challenge. Thereby, understanding the molecular basis of MTB virulence and disease pathogenesis is critical for developing effective therapeutic strategies. Targeting proteins involved in central metabolism has been recognized as a promising therapeutic approach to combat MTB. In this regard, the enzyme AckA of the acetate metabolic pathway which produces acetate from acetyl phosphate, is an important drug target for various pathogenic organisms. Therefore, this study aimed to identify potential AckA inhibitors through in silico methods, including molecular modeling, molecular dynamics simulation (MDS), and high-throughput virtual screening (HTVS) followed by ADMETox, MMGBSA, Density Functional Theory (DFT) calculations. HTVS of one million compounds from the ZINC database against AckA resulted in the top five hits (ZINC82048449, ZINC1219737510, ZINC1771921358, ZINC119699567, and ZINC1427100376) with better binding affinity and optimal binding free energy. MDS studies on complexes revealed that key residues, Asn195, Asp266, Phe267, Gly314, and Asn318 played a significant role in stable interactions of the top-ranked compounds to AckA. These outcomes provide insights into the optimal binding of the leads to inhibit the acetate pathway and aid in the rational design of novel therapeutic agents. Thus, the identified leads may act as promising compounds for targeting AckA and may serve as a potential therapeutic modality for treating TB. Our findings offer valuable insights into the inhibition of the acetate pathway, while also serving as a blueprint for rational drug design. The identified leads hold promise as compelling compounds for targeting AckA, thereby offering a potential therapeutic avenue for tackling TB. Thus, our study uncovers a pathway toward promising TB therapeutics by elucidating AckA inhibitors. By leveraging in silico methodologies, potent compounds that hold the potential to thwart AckA's role in MTB's acetate pathway have been unveiled. This breakthrough fosters optimism in the quest for novel and effective TB treatments, addressing a global health challenge with renewed vigor.
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Affiliation(s)
- Sneha Subramaniyan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi 630 003, Tamil Nadu, India
| | - Hemavathy Nagarajan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi 630 003, Tamil Nadu, India
| | - Umashankar Vetrivel
- Virology & Biotechnology/Bioinformatics Division, ICMR-National Institute for Research in Tuberculosis, Chennai, Tamil Nadu 600 031, India
| | - Jeyakanthan Jeyaraman
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi 630 003, Tamil Nadu, India.
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8
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Chasák J, Oorts L, Dak M, Šlachtová V, Bazgier V, Berka K, De Vooght L, Smiejkowska N, Calster KV, Van Moll L, Cappoen D, Cos P, Brulíková L. Expanding the squaramide library as mycobacterial ATP synthase inhibitors: Innovative synthetic pathway and biological evaluation. Bioorg Med Chem 2023; 95:117504. [PMID: 37871508 DOI: 10.1016/j.bmc.2023.117504] [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: 07/28/2023] [Revised: 10/11/2023] [Accepted: 10/16/2023] [Indexed: 10/25/2023]
Abstract
Mycobacterial ATP synthase is a validated therapeutic target for combating drug-resistant tuberculosis. Inhibition of this enzyme has been featured as an efficient strategy for the development of new antimycobacterial agents against drug-resistant pathogens. In this study, we synthesised and explored two distinct series of squaric acid analogues designed to inhibit mycobacterial ATP synthase. Among the extensive array of compounds investigated, members of the phenyl-substituted sub-library emerged as primary hits. To gain deeper insights into their mechanisms of action, we conducted advanced biological studies, focusing on the compounds displaying a direct binding of a nitrogen heteroatom to the phenyl ring, resulting in the highest potency. Our investigations into spontaneous mutants led to the validation of a single point mutation within the atpB gene (Rv1304), responsible for encoding the ATP synthase subunit a. This genetic alteration sheds light on the molecular basis of resistance to squaramides. Furthermore, we explored the possibility of synergy between squaramides and the reference drug clofazimine using a checkerboard assay, highlighting the promising avenue for enhancing the effectiveness of existing treatments through combined therapeutic approaches. This study contributes to the expansion of investigating squaramides as promising drug candidates in the ongoing battle against drug-resistant tuberculosis.
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Affiliation(s)
- Jan Chasák
- Department of Organic Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 77146, Olomouc, Czech Republic
| | - Lauren Oorts
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), S7, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
| | - Milan Dak
- Department of Organic Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 77146, Olomouc, Czech Republic
| | - Veronika Šlachtová
- Department of Organic Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 77146, Olomouc, Czech Republic
| | - Václav Bazgier
- Department of Physical Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 771 46, Olomouc, Czech Republic
| | - Karel Berka
- Department of Physical Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 771 46, Olomouc, Czech Republic
| | - Linda De Vooght
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), S7, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
| | - Natalia Smiejkowska
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), S7, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
| | - Kevin Van Calster
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), S7, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
| | - Laurence Van Moll
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), S7, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
| | - Davie Cappoen
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), S7, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
| | - Paul Cos
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), S7, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
| | - Lucie Brulíková
- Department of Organic Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 77146, Olomouc, Czech Republic.
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9
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Smajdor J, Jedlińska K, Porada R, Górska-Ratusznik A, Policht A, Śróttek M, Więcek G, Baś B, Strus M. The impact of gut bacteria producing long chain homologs of vitamin K 2 on colorectal carcinogenesis. Cancer Cell Int 2023; 23:268. [PMID: 37950262 PMCID: PMC10638769 DOI: 10.1186/s12935-023-03114-2] [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: 02/15/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023] Open
Abstract
Colorectal cancer (CRC) is one of the foremost causes of cancer-related deaths. Lately, a close connection between the course of CRC and the intestinal microbiota has been revealed. Vitamin K2 (VK2) is a bacterially derived compound that plays a crucial role in the human body. Its significant anti-cancer properties may result, inter alia, from a quinone ring possessing a specific chemical structure found in many chemotherapeutics. VK2 can be supplied to our body exogenously, i.e., through dietary supplements or fermented food (e.g., yellow cheese, fermented soybeans -Natto), and endogenously, i.e., through the production of bacteria that constantly colonize the human microbiome of the large intestine.This paper focuses on endogenous K2 synthesized by the most active members of the human gut microbiome. This analysis tested 86 intestinally derived bacterial strains, among which the largest VK2 producers (Lactobacillus, Bifidobacterium, Bacillus) were selected. Moreover, based on the chosen VK2-MK4 homolog, the potential of VK2 penetration into Caco-2 cells in an aqueous environment without the coexistence of fats, pancreatic enzymes, or bile salts has been displayed. The influence of three VK2 homologs: VK2-MK4, VK2-MK7 and VK2-MK9 on apoptosis and necrosis of Caco-2 cells was tested proving the lack of their harmful effects on the tested cells. Moreover, the unique role of long-chain homologs (VK2-MK9 and VK2-MK7) in inhibiting the secretion of pro-inflammatory cytokines such as IL-8 (for Caco-2 tissue) and IL-6 and TNFα (for RAW 264.7) has been documented.
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Affiliation(s)
- Joanna Smajdor
- Department of Analytical Chemistry and Biochemistry, Faculty of Materials Science and Ceramics, AGH University of Science and Technology, Al. Mickiewicza, Kraków, 30-059, Poland
| | - Katarzyna Jedlińska
- Department of Analytical Chemistry and Biochemistry, Faculty of Materials Science and Ceramics, AGH University of Science and Technology, Al. Mickiewicza, Kraków, 30-059, Poland
| | - Radosław Porada
- Department of Analytical Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, Kraków, 30- 387, Poland
| | - Anna Górska-Ratusznik
- Sieć Badawcza Łukasiewicz-Krakowski Instytut Technologiczny, ul. Zakopiańska 73, Cracow, 30-418, Poland
| | - Aleksandra Policht
- Chair of Microbiology, Jagiellonian University Medical College, Czysta 18, Krakow, 31-121, Poland
| | - Małgorzata Śróttek
- Chair of Microbiology, Jagiellonian University Medical College, Czysta 18, Krakow, 31-121, Poland
| | - Grażyna Więcek
- Chair of Microbiology, Jagiellonian University Medical College, Czysta 18, Krakow, 31-121, Poland
| | - Bogusław Baś
- Department of Analytical Chemistry and Biochemistry, Faculty of Materials Science and Ceramics, AGH University of Science and Technology, Al. Mickiewicza, Kraków, 30-059, Poland
| | - Magdalena Strus
- Chair of Microbiology, Jagiellonian University Medical College, Czysta 18, Krakow, 31-121, Poland.
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10
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Ofori-Anyinam N, Hamblin M, Coldren ML, Li B, Mereddy G, Shaikh M, Shah A, Ranu N, Lu S, Blainey PC, Ma S, Collins JJ, Yang JH. KatG catalase deficiency confers bedaquiline hyper-susceptibility to isoniazid resistant Mycobacterium tuberculosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.17.562707. [PMID: 37905073 PMCID: PMC10614911 DOI: 10.1101/2023.10.17.562707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Multidrug-resistant tuberculosis (MDR-TB) is a growing source of global mortality and threatens global control of tuberculosis (TB) disease. The diarylquinoline bedaquiline (BDQ) recently emerged as a highly efficacious drug against MDR-TB, defined as resistance to the first-line drugs isoniazid (INH) and rifampin. INH resistance is primarily caused by loss-of-function mutations in the catalase KatG, but mechanisms underlying BDQ's efficacy against MDR-TB remain unknown. Here we employ a systems biology approach to investigate BDQ hyper-susceptibility in INH-resistant Mycobacterium tuberculosis . We found hyper-susceptibility to BDQ in INH-resistant cells is due to several physiological changes induced by KatG deficiency, including increased susceptibility to reactive oxygen species and DNA damage, remodeling of transcriptional programs, and metabolic repression of folate biosynthesis. We demonstrate BDQ hyper-susceptibility is common in INH-resistant clinical isolates. Collectively, these results highlight how altered bacterial physiology can impact drug efficacy in drug-resistant bacteria.
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11
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Yang J, Zhang L, Qiao W, Luo Y. Mycobacterium tuberculosis: Pathogenesis and therapeutic targets. MedComm (Beijing) 2023; 4:e353. [PMID: 37674971 PMCID: PMC10477518 DOI: 10.1002/mco2.353] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 09/08/2023] Open
Abstract
Tuberculosis (TB) remains a significant public health concern in the 21st century, especially due to drug resistance, coinfection with diseases like immunodeficiency syndrome (AIDS) and coronavirus disease 2019, and the lengthy and costly treatment protocols. In this review, we summarize the pathogenesis of TB infection, therapeutic targets, and corresponding modulators, including first-line medications, current clinical trial drugs and molecules in preclinical assessment. Understanding the mechanisms of Mycobacterium tuberculosis (Mtb) infection and important biological targets can lead to innovative treatments. While most antitubercular agents target pathogen-related processes, host-directed therapy (HDT) modalities addressing immune defense, survival mechanisms, and immunopathology also hold promise. Mtb's adaptation to the human host involves manipulating host cellular mechanisms, and HDT aims to disrupt this manipulation to enhance treatment effectiveness. Our review provides valuable insights for future anti-TB drug development efforts.
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Affiliation(s)
- Jiaxing Yang
- Center of Infectious Diseases and State Key Laboratory of Biotherapy, West China HospitalSichuan UniversityChengduChina
| | - Laiying Zhang
- Center of Infectious Diseases and State Key Laboratory of Biotherapy, West China HospitalSichuan UniversityChengduChina
| | - Wenliang Qiao
- Department of Thoracic Surgery, West China HospitalSichuan UniversityChengduSichuanChina
- Lung Cancer Center, West China HospitalSichuan UniversityChengduSichuanChina
| | - Youfu Luo
- Center of Infectious Diseases and State Key Laboratory of Biotherapy, West China HospitalSichuan UniversityChengduChina
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12
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Jiang M, Li X, Xie CL, Chen P, Luo W, Lin CX, Wang Q, Shu DM, Luo CL, Qu H, Ji J. Fructose-enabled killing of antibiotic-resistant Salmonella enteritidis by gentamicin: Insight from reprogramming metabolomics. Int J Antimicrob Agents 2023; 62:106907. [PMID: 37385564 DOI: 10.1016/j.ijantimicag.2023.106907] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/29/2023] [Accepted: 06/25/2023] [Indexed: 07/01/2023]
Abstract
Salmonella enterica is a food-borne pathogen that poses a severe threat to both poultry production and human health. Antibiotics are critical for the initial treatment of bacterial infections. However, the overuse and misuse of antibiotics results in the rapid evolution of antibiotic-resistant bacteria, and the discovery and development of new antibiotics are declining. Therefore, understanding antibiotic resistance mechanisms and developing novel control measures are essential. In the present study, GC-MS-based metabolomics analysis was performed to determine the metabolic profile of gentamicin sensitive (SE-S) and resistant (SE-R) S. enterica. Fructose was identified as a crucial biomarker. Further analysis demonstrated a global depressed central carbon metabolism and energy metabolism in SE-R. The decrease in the pyruvate cycle reduces the production of NADH and ATP, causing a decrease in membrane potential, which contributes to gentamicin resistance. Exogenous fructose potentiated the effectiveness of gentamicin in killing SE-R by promoting the pyruvate cycle, NADH, ATP and membrane potential, thereby increasing gentamicin intake. Further, fructose plus gentamicin improved the survival rate of chicken infected with gentamicin-resistant Salmonella in vivo. Given that metabolite structures are conserved across species, fructose identified from bacteria could be used as a biomarker for breeding disease-resistant phenotypes in chicken. Therefore, a novel strategy is proposed for fighting against antibiotic-resistant S. enterica, including exploring molecules suppressed by antibiotics and providing a new approach to find pathogen targets for disease resistance in chicken breeding.
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Affiliation(s)
- Ming Jiang
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China; The Third Affiliated Hospital, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xia Li
- The Third Affiliated Hospital, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Chun-Lin Xie
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Peng Chen
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Wei Luo
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Chu-Xiao Lin
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Qiao Wang
- Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ding-Ming Shu
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Cheng-Long Luo
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Hao Qu
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China.
| | - Jian Ji
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China.
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13
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Costa SK, Antosca K, Beekman CN, Peterson RL, Penumutchu S, Belenky P. Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis. Microbiol Spectr 2023; 11:e0237623. [PMID: 37439681 PMCID: PMC10434222 DOI: 10.1128/spectrum.02376-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 06/22/2023] [Indexed: 07/14/2023] Open
Abstract
Antibiotic-induced gut microbiome dysbiosis (AID) is known to be influenced by host dietary composition. However, how and when diet modulates gut dysbiosis remains poorly characterized. Thus, here, we utilize a multi-omics approach to characterize how a diet supplemented with oats, a rich source of microbiota-accessible carbohydrates, or dextrose impacts amoxicillin-induced changes to gut microbiome structure and transcriptional activity. We demonstrate that oat administration during amoxicillin challenge provides greater protection from AID than the always oats or recovery oats diet groups. In particular, the group in which oats were provided at the time of antibiotic exposure induced the greatest protection against AID while the other oat diets saw greater effects after amoxicillin challenge. The oat diets likewise reduced amoxicillin-driven elimination of Firmicutes compared to the dextrose diet. Functionally, gut communities fed dextrose were carbohydrate starved and favored respiratory metabolism and consequent metabolic stress management while oat-fed communities shifted their transcriptomic profile and emphasized antibiotic stress management. The metabolic trends were exemplified when assessing transcriptional activity of the following two common gut commensal bacteria: Akkermansia muciniphila and Bacteroides thetaiotaomicron. These findings demonstrate that while host diet is important in shaping how antibiotics effect the gut microbiome composition and function, diet timing may play an even greater role in dietary intervention-based therapeutics. IMPORTANCE We utilize a multi-omics approach to demonstrate that diets supplemented with oats, a rich source of microbiota-accessible carbohydrates, are able to confer protection against antibiotic-induced dysbiosis (AID). Our findings affirm that not only is host diet important in shaping antibiotics effects on gut microbiome composition and function but also that the timing of these diets may play an even greater role in managing AID. This work provides a nuanced perspective on dietary intervention against AID and may be informative on preventing AID during routine antibiotic treatment.
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Affiliation(s)
- Stephen K. Costa
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Katherine Antosca
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Chapman N. Beekman
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Rachel L. Peterson
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Swathi Penumutchu
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
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14
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Kägi J, Sloan W, Schimpf J, Nasiri HR, Lashley D, Friedrich T. Exploring ND-011992, a quinazoline-type inhibitor targeting quinone reductases and quinol oxidases. Sci Rep 2023; 13:12226. [PMID: 37507428 PMCID: PMC10382516 DOI: 10.1038/s41598-023-39430-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 07/25/2023] [Indexed: 07/30/2023] Open
Abstract
Bacterial energy metabolism has become a promising target for next-generation tuberculosis chemotherapy. One strategy to hamper ATP production is to inhibit the respiratory oxidases. The respiratory chain of Mycobacterium tuberculosis comprises a cytochrome bcc:aa3 and a cytochrome bd ubiquinol oxidase that require a combined approach to block their activity. A quinazoline-type compound called ND-011992 has previously been reported to ineffectively inhibit bd oxidases, but to act bactericidal in combination with inhibitors of cytochrome bcc:aa3 oxidase. Due to the structural similarity of ND-011992 to quinazoline-type inhibitors of respiratory complex I, we suspected that this compound is also capable of blocking other respiratory chain complexes. Here, we synthesized ND-011992 and a bromine derivative to study their effect on the respiratory chain complexes of Escherichia coli. And indeed, ND-011992 was found to inhibit respiratory complex I and bo3 oxidase in addition to bd-I and bd-II oxidases. The IC50 values are all in the low micromolar range, with inhibition of complex I providing the lowest value with an IC50 of 0.12 µM. Thus, ND-011992 acts on both, quinone reductases and quinol oxidases and could be very well suited to regulate the activity of the entire respiratory chain.
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Affiliation(s)
- Jan Kägi
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Willough Sloan
- Department of Chemistry, William & Mary, Williamsburg, VA, USA
| | - Johannes Schimpf
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Hamid R Nasiri
- Department of Cellular Microbiology, University Hohenheim, Stuttgart, Germany
| | - Dana Lashley
- Department of Chemistry, William & Mary, Williamsburg, VA, USA.
| | - Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.
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15
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Heithoff DM, Barnes V L, Mahan SP, Fried JC, Fitzgibbons LN, House JK, Mahan MJ. Re-evaluation of FDA-approved antibiotics with increased diagnostic accuracy for assessment of antimicrobial resistance. Cell Rep Med 2023; 4:101023. [PMID: 37116500 PMCID: PMC10213814 DOI: 10.1016/j.xcrm.2023.101023] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/16/2023] [Accepted: 04/05/2023] [Indexed: 04/30/2023]
Abstract
Accurate assessment of antibiotic susceptibility is critical for treatment of antimicrobial resistant (AMR) infections. Here, we examine whether antimicrobial susceptibility testing in media more physiologically representative of in vivo conditions improves prediction of clinical outcome relative to standard bacteriologic medium. This analysis reveals that ∼15% of minimum inhibitory concentration (MIC) values obtained in physiologic media predicted a change in susceptibility that crossed a clinical breakpoint used to categorize patient isolates as susceptible or resistant. The activities of antibiotics having discrepant results in different media were evaluated in murine sepsis models. Testing in cell culture medium improves the accuracy by which MIC assays predict in vivo efficacy. This analysis identifies several antibiotics for treatment of AMR infections that standard testing failed to identify and those that are ineffective despite indicated use by standard testing. Methods with increased diagnostic accuracy mitigate the AMR crisis via utilizing existing agents and optimizing drug discovery.
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Affiliation(s)
- Douglas M Heithoff
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA; Institute for Collaborative Biotechnologies, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Lucien Barnes V
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA; Institute for Collaborative Biotechnologies, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Scott P Mahan
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA; Institute for Collaborative Biotechnologies, University of California, Santa Barbara, Santa Barbara, CA 93106, USA; Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, CA 95616, USA
| | - Jeffrey C Fried
- Department of Medical Education, Santa Barbara Cottage Hospital, Santa Barbara, CA 93105, USA; Department of Pulmonary and Critical Care Medicine, Santa Barbara Cottage Hospital, Santa Barbara, CA 93105, USA
| | - Lynn N Fitzgibbons
- Department of Medical Education, Santa Barbara Cottage Hospital, Santa Barbara, CA 93105, USA; Division of Infectious Diseases, Santa Barbara Cottage Hospital, Santa Barbara, CA 93105, USA
| | - John K House
- Faculty of Science, School of Veterinary Science, The University of Sydney, Camden, NSW 2570, Australia.
| | - Michael J Mahan
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA; Institute for Collaborative Biotechnologies, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
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16
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Samanta S, Kumar S, Aratikatla EK, Ghorpade SR, Singh V. Recent developments of imidazo[1,2- a]pyridine analogues as antituberculosis agents. RSC Med Chem 2023; 14:644-657. [PMID: 37122538 PMCID: PMC10131611 DOI: 10.1039/d3md00019b] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
Over the past 2000 years, tuberculosis (TB) has killed more people than any other infectious disease. In 2021, TB claimed 1.6 million lives worldwide, making it the second leading cause of death from an infectious disease after COVID-19. Unfortunately, TB drug discovery research was neglected in the last few decades of the twentieth century. Recently, the World Health Organization has taken the initiative to develop new TB drugs. Imidazopyridine, an important fused bicyclic 5,6 heterocycle has been recognized as a "drug prejudice" scaffold for its wide range of applications in medicinal chemistry. A few examples of imidazo[1,2-a]pyridine exhibit significant activity against multidrug-resistant TB (MDR-TB) and extensively drug-resistant TB (XDR-TB). Here, we critically review anti-TB compounds of the imidazo[1,2-a]pyridine class by discussing their development based on the structure-activity relationship, mode-of-action, and various scaffold hopping strategies over the last decade, which is identified as a renaissance era of TB drug discovery research.
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Affiliation(s)
- Sauvik Samanta
- Holistic Drug Discovery and Development (H3D) Centre, University of Cape Town Rondebosch 7701 South Africa
| | - Sumit Kumar
- Holistic Drug Discovery and Development (H3D) Centre, University of Cape Town Rondebosch 7701 South Africa
| | - Eswar K Aratikatla
- Holistic Drug Discovery and Development (H3D) Centre, University of Cape Town Rondebosch 7701 South Africa
| | - Sandeep R Ghorpade
- Holistic Drug Discovery and Development (H3D) Centre, University of Cape Town Rondebosch 7701 South Africa
| | - Vinayak Singh
- Holistic Drug Discovery and Development (H3D) Centre, University of Cape Town Rondebosch 7701 South Africa
- South African Medical Research Council Drug Discovery and Development Research Unit, Institute of Infectious Disease and Molecular Medicine, University of Cape Town Rondebosch 7701 South Africa
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17
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Kelam LM, Wani MA, Dhaked DK. An update on ATP synthase inhibitors: A unique target for drug development in M. tuberculosis. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023; 180-181:87-104. [PMID: 37105260 DOI: 10.1016/j.pbiomolbio.2023.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 04/29/2023]
Abstract
ATP synthase is a key protein in the oxidative phosphorylation process, as it aids in the effective production of ATP (Adenosine triphosphate) in all life's of kingdoms. ATP synthases have distinctive properties that contribute to efficient ATP synthesis. The ATP synthase of mycobacterium is of special relevance since it has been identified as a target for potential anti-TB molecules, especially Bedaquiline (BDQ). Better knowledge of how mycobacterial ATP synthase functions and its peculiar characteristics will aid in our understanding of bacterial energy metabolism adaptations. Furthermore, identifying and understanding the important distinctions between human ATP synthase and bacterial ATP synthase may provide insight into the design and development of inhibitors that target specific ATP synthase. In recent years, many potential candidates targeting the ATP synthase of mycobacterium have been developed. In this review, we discuss the druggable targets of the Electron transport chain (ETC) and recently identified potent inhibitors (including clinical molecules) from 2015 to 2022 of diverse classes that target ATP synthase of M. tuberculosis.
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Affiliation(s)
- Lakshmi Mounika Kelam
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER)-Kolkata, Chunilal Bhawan, 168 Maniktala Main Road, Kolkata, 700054, West Bengal, India
| | - Mushtaq Ahmad Wani
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER)-Kolkata, Chunilal Bhawan, 168 Maniktala Main Road, Kolkata, 700054, West Bengal, India
| | - Devendra K Dhaked
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER)-Kolkata, Chunilal Bhawan, 168 Maniktala Main Road, Kolkata, 700054, West Bengal, India.
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18
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Wu D, Mehdipour AR, Finke F, Goojani HG, Groh RR, Grund TN, Reichhart TMB, Zimmermann R, Welsch S, Bald D, Shepherd M, Hummer G, Safarian S. Dissecting the conformational complexity and mechanism of a bacterial heme transporter. Nat Chem Biol 2023:10.1038/s41589-023-01314-5. [PMID: 37095238 PMCID: PMC10374445 DOI: 10.1038/s41589-023-01314-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 03/14/2023] [Indexed: 04/26/2023]
Abstract
Iron-bound cyclic tetrapyrroles (hemes) are redox-active cofactors in bioenergetic enzymes. However, the mechanisms of heme transport and insertion into respiratory chain complexes remain unclear. Here, we used cellular, biochemical, structural and computational methods to characterize the structure and function of the heterodimeric bacterial ABC transporter CydDC. We provide multi-level evidence that CydDC is a heme transporter required for functional maturation of cytochrome bd, a pharmaceutically relevant drug target. Our systematic single-particle cryogenic-electron microscopy approach combined with atomistic molecular dynamics simulations provides detailed insight into the conformational landscape of CydDC during substrate binding and occlusion. Our simulations reveal that heme binds laterally from the membrane space to the transmembrane region of CydDC, enabled by a highly asymmetrical inward-facing CydDC conformation. During the binding process, heme propionates interact with positively charged residues on the surface and later in the substrate-binding pocket of the transporter, causing the heme orientation to rotate 180°.
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Affiliation(s)
- Di Wu
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt/Main, Germany
| | - Ahmad R Mehdipour
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt/Main, Germany
- Center for Molecular Modeling (CMM), Ghent University, Zwijnaarde, Belgium
| | - Franziska Finke
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt/Main, Germany
| | - Hojjat G Goojani
- Amsterdam Institute for Life and Environment (A-LIFE), AIMMS, Faculty of Science, Vrije University of Amsterdam, Amsterdam, the Netherlands
| | - Roan R Groh
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt/Main, Germany
| | - Tamara N Grund
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt/Main, Germany
| | - Thomas M B Reichhart
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt/Main, Germany
| | - Rita Zimmermann
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt/Main, Germany
| | - Sonja Welsch
- Central Electron Microscopy Facility, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Dirk Bald
- Amsterdam Institute for Life and Environment (A-LIFE), AIMMS, Faculty of Science, Vrije University of Amsterdam, Amsterdam, the Netherlands
| | - Mark Shepherd
- School of Biosciences, RAPID Group, University of Kent, Canterbury, UK
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt/Main, Germany
- Institute of Biophysics, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Schara Safarian
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt/Main, Germany.
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand.
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Frankfurt/Main, Germany.
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19
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Imran M, Alotaibi NM, Thabet HK, Alruwaili JA, Asdaq SMB, Eltaib L, Alshehri A, Alsaiari AA, Almehmadi M, Alshammari ABH, Alshammari AM. QcrB inhibition as a potential approach for the treatment of tuberculosis: A review of recent developments, patents, and future directions. J Infect Public Health 2023; 16:928-937. [PMID: 37086552 DOI: 10.1016/j.jiph.2023.04.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/28/2023] [Accepted: 04/11/2023] [Indexed: 04/24/2023] Open
Abstract
The unmet medical need for drug-resistant tuberculosis (DRTB) is a significant concern. Accordingly, identifying new drug targets for tuberculosis (TB) treatment and developing new therapies based on these drug targets is one of the strategies to tackle DRTB. QcrB is an innovative drug target to create treatments for DRTB. This article highlights QcrB inhibitors and their therapeutic compositions for treating TB. The literature for this article was gathered from PubMed and free patent databases utilizing different keywords related to QcrB inhibitor-based inventions. The data was collected from the conceptualization of telacebec (2010) QcrB to December 2022. A little interesting and encouraging research has been performed on QcrB inhibitors. Telacebec and TB47 are established QcrB inhibitors in the clinical trial. The inventive QcrB inhibitor-based drug combinations can potentially handle DRTB and reduce the TB therapy duration. The authors anticipate great opportunities in fostering QcrB inhibitor-based patentable pharmaceutical inventions against TB. Drug repurposing can be a promising strategy to get safe and effective QcrB inhibitors. However, developing drug resistance, drug tolerance, and selectivity of QcrB inhibitors for Mtb will be the main challenges in developing effective QcrB inhibitors. In conclusion, QcrB is a promising drug target for developing effective treatments for active, latent, and drug-resistant TB. Many inventive and patentable combinations and compositions of QcrB inhibitors with other anti-TB drugs are anticipated as future treatments for TB.
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Affiliation(s)
- Mohd Imran
- Department of Pharmaceutical Chemistry, College of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia.
| | - Nawaf M Alotaibi
- Department of Clinical Pharmacy, College of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia; Chemistry Department, College of Sciences and Arts, Northern Border University, Rafha 91911, Saudi Arabia
| | - Hamdy K Thabet
- Chemistry Department, College of Sciences and Arts, Northern Border University, Rafha 91911, Saudi Arabia
| | - Jamal A Alruwaili
- College of Applied Medical Sciences, Medical Lab Technology Department, Northern Border University, Arar 91431, Saudi Arabia
| | - Syed M B Asdaq
- Department of Pharmacy Practice, College of Pharmacy, AlMaarefa University, Dariyah, Riyadh 13713, Saudi Arabia
| | - Lina Eltaib
- Department of Pharmaceutics, College of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia
| | - Ahmed Alshehri
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Northern Border University, Rafha, Saudi Arabia; Department of Pharmacology, College of Clinical Pharmacy, Imam Abdulrahman Bin Faisal University, King Faisal Road, Dammam 31441, Saudi Arabia
| | - Ahad A Alsaiari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Mazen Almehmadi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
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20
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Makarchuk I, Kägi J, Gerasimova T, Wohlwend D, Friedrich T, Melin F, Hellwig P. pH-dependent kinetics of NO release from E. coli bd-I and bd-II oxidase reveals involvement of Asp/Glu58 B. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148952. [PMID: 36535430 DOI: 10.1016/j.bbabio.2022.148952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 12/06/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022]
Abstract
Escherichia coli contains two cytochrome bd oxidases, bd-I and bd-II. The structure of both enzymes is highly similar, but they exhibit subtle differences such as the accessibility of the active site through a putative proton channel. Here, we demonstrate that the duroquinol:dioxygen oxidoreductase activity of bd-I increased with alkaline pH, whereas bd-II showed a broad activity maximum around pH 7. Likewise, the pH dependence of NO release from the reduced active site, an essential property of bd oxidases, differed between the two oxidases as detected by UV/vis spectroscopy. Both findings may be attributed to differences in the proton channel leading to the active site heme d. The channel comprises a titratable residue (Asp58B in bd-I and Glu58B in bd-II). Conservative mutations at this position drastically altered NO release demonstrating its contribution to the process.
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Affiliation(s)
- Iryna Makarchuk
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, 67000 Strasbourg, France
| | - Jan Kägi
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr 21, 79104 Freiburg, Germany
| | - Tatjana Gerasimova
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, 67000 Strasbourg, France; Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr 21, 79104 Freiburg, Germany
| | - Daniel Wohlwend
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr 21, 79104 Freiburg, Germany
| | - Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr 21, 79104 Freiburg, Germany
| | - Frédéric Melin
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, 67000 Strasbourg, France
| | - Petra Hellwig
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, 67000 Strasbourg, France.
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21
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Liang Y, Plourde A, Bueler SA, Liu J, Brzezinski P, Vahidi S, Rubinstein JL. Structure of mycobacterial respiratory complex I. Proc Natl Acad Sci U S A 2023; 120:e2214949120. [PMID: 36952383 PMCID: PMC10068793 DOI: 10.1073/pnas.2214949120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 02/10/2023] [Indexed: 03/24/2023] Open
Abstract
Oxidative phosphorylation, the combined activity of the electron transport chain (ETC) and adenosine triphosphate synthase, has emerged as a valuable target for the treatment of infection by Mycobacterium tuberculosis and other mycobacteria. The mycobacterial ETC is highly branched with multiple dehydrogenases transferring electrons to a membrane-bound pool of menaquinone and multiple oxidases transferring electrons from the pool. The proton-pumping type I nicotinamide adenine dinucleotide (NADH) dehydrogenase (Complex I) is found in low abundance in the plasma membranes of mycobacteria in typical in vitro culture conditions and is often considered dispensable. We found that growth of Mycobacterium smegmatis in carbon-limited conditions greatly increased the abundance of Complex I and allowed isolation of a rotenone-sensitive preparation of the enzyme. Determination of the structure of the complex by cryoEM revealed the "orphan" two-component response regulator protein MSMEG_2064 as a subunit of the assembly. MSMEG_2064 in the complex occupies a site similar to the proposed redox-sensing subunit NDUFA9 in eukaryotic Complex I. An apparent purine nucleoside triphosphate within the NuoG subunit resembles the GTP-derived molybdenum cofactor in homologous formate dehydrogenase enzymes. The membrane region of the complex binds acyl phosphatidylinositol dimannoside, a characteristic three-tailed lipid from the mycobacterial membrane. The structure also shows menaquinone, which is preferentially used over ubiquinone by gram-positive bacteria, in two different positions along the quinone channel, comparable to ubiquinone in other structures and suggesting a conserved quinone binding mechanism.
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Affiliation(s)
- Yingke Liang
- Molecular Medicine Program, The Hospital for Sick Children, TorontoM5G 0A4, Canada
- Department of Biochemistry, University of Toronto, TorontoM5S 1A8, Canada
| | - Alicia Plourde
- Department of Molecular and Cellular Biology, University of Guelph, TorontoN1G 2W1, Canada
| | - Stephanie A. Bueler
- Molecular Medicine Program, The Hospital for Sick Children, TorontoM5G 0A4, Canada
| | - Jun Liu
- Department of Molecular Genetics, University of Toronto, TorontoM5S 1A8, Canada
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91Stockholm, Sweden
| | - Siavash Vahidi
- Department of Molecular and Cellular Biology, University of Guelph, TorontoN1G 2W1, Canada
| | - John L. Rubinstein
- Molecular Medicine Program, The Hospital for Sick Children, TorontoM5G 0A4, Canada
- Department of Biochemistry, University of Toronto, TorontoM5S 1A8, Canada
- Department of Medical Biophysics, University of Toronto, TorontoM5G 1L7, Canada
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22
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Morita R, Shigeta Y, Harada R. Efficient screening of protein-ligand complexes in lipid bilayers using LoCoMock score. J Comput Aided Mol Des 2023; 37:217-225. [PMID: 36943644 DOI: 10.1007/s10822-023-00502-8] [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: 01/17/2023] [Accepted: 03/05/2023] [Indexed: 03/23/2023]
Abstract
Membrane proteins are attractive targets for drug discovery due to their crucial roles in various biological processes. Studying the binding poses of amphipathic molecules to membrane proteins is essential for understanding the functions of membrane proteins and docking simulations can facilitate the screening of protein-ligand complexes at low computational costs. However, identifying docking poses for a ligand in non-aqueous environments such as lipid bilayers can be challenging. To address this issue, we propose a new docking score called logP-corrected membrane docking (LoCoMock) score. To screen putative protein-ligand complexes embedded in a membrane, the LoCoMock score considers the affinity between a target ligand and the membrane. It combines the docking score of the protein-ligand complex with the logP of the target ligand. In demonstrations using several model ligands, the LoCoMock score screened more putative complexes than the conventional docking score. As extended docking, the LoCoMock score makes it possible to screen membrane proteins more effectively as drug targets than the conventional docking.
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Affiliation(s)
- Rikuri Morita
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, 305-8577, Tsukuba, Ibaraki, Japan.
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, 305-8577, Tsukuba, Ibaraki, Japan
| | - Ryuhei Harada
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, 305-8577, Tsukuba, Ibaraki, Japan.
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23
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Berg K, Hegde P, Pujari V, Brinkmann M, Wilkins DZ, Parish T, Crick DC, Aldrich CC. SAR study of piperidine derivatives as inhibitors of 1,4-dihydroxy-2-naphthoate isoprenyltransferase (MenA) from Mycobacterium tuberculosis. Eur J Med Chem 2023; 249:115125. [PMID: 36682292 PMCID: PMC9975056 DOI: 10.1016/j.ejmech.2023.115125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/11/2023] [Accepted: 01/14/2023] [Indexed: 01/19/2023]
Abstract
The electron transport chain (ETC) in the cell membrane consists of a series of redox complexes that transfer electrons from electron donors to acceptors and couples this electron transfer with the transfer of protons (H+) across a membrane. This process generates proton motive force which is used to produce ATP and a myriad of other functions and is essential for the long-term survival of Mycobacterium tuberculosis (Mtb), the causative organism of tuberculosis (TB), under the hypoxic conditions present within infected granulomas. Menaquinone (MK), an important carrier molecule within the mycobacterial ETC, is synthesized de novo by a cluster of enzymes known as the classic/canonical MK biosynthetic pathway. MenA (1,4-dihydroxy-2-naphthoate prenyltransferase), the antepenultimate enzyme in this pathway, is a verified target for TB therapy. In this study, we explored structure-activity relationships of a previously discovered MenA inhibitor scaffold, seeking to improve potency and drug disposition properties. Focusing our campaign upon three molecular regions, we identified two novel inhibitors with potent activity against MenA and Mtb (IC50 = 13-22 μM, GIC50 = 8-10 μM). These analogs also displayed substantially improved pharmacokinetic parameters and potent synergy with other ETC-targeting agents, achieving nearly complete sterilization of Mtb in combination therapy within two weeks in vivo. These new inhibitors of MK biosynthesis present a promising new strategy to curb the continued spread of TB.
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Affiliation(s)
- Kaja Berg
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street Southeast, Minneapolis, MN, 55455, USA
| | - Pooja Hegde
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street Southeast, Minneapolis, MN, 55455, USA
| | - Venugopal Pujari
- Mycobacteria Research Laboratories, Microbiology, Immunology, and Pathology Department, Colorado State University, Fort Collins, CO, 80523, USA
| | - Marzena Brinkmann
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street Southeast, Minneapolis, MN, 55455, USA
| | - David Z Wilkins
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, 98109, USA
| | - Tanya Parish
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, 98109, USA
| | - Dean C Crick
- Mycobacteria Research Laboratories, Microbiology, Immunology, and Pathology Department, Colorado State University, Fort Collins, CO, 80523, USA.
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street Southeast, Minneapolis, MN, 55455, USA.
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24
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Shinde A, Thakare PP, Nandurkar Y, Chavan A, Shaikh ALN, Mhaske PC. Synthesis of 2-(6-substituted quinolin-4-yl)-1-alkoxypropan-2-ol as potential antimycobacterial agents. CHEMICKE ZVESTI 2023; 77:3791-3802. [PMID: 37252671 PMCID: PMC9961301 DOI: 10.1007/s11696-023-02741-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 02/17/2023] [Indexed: 02/27/2023]
Abstract
Resistance to antibiotic drugs has directed global health security to a life-threatening situation due to mycobacterial infections. In search of a new potent antimycobacterial, a series of (±) 2-(6-substituted quinolin-4-yl)-1-alkoxypropan-2-ol (8a-p) have been synthesized. The structures of the newly synthesized derivatives were characterized by spectrometric analysis. Derivatives 8a-p were evaluated for antitubercular activity against Mycobacterium tuberculosis H37Rv (ATCC 25177), antibacterial activity against Proteus mirabilis (NCIM2388), Escherichia coli (NCIM 2065), Bacillus subtilis (NCIM2063) Staphylococcus albus (NCIM 2178) and antifungal activity against Candida albicans (NCIM 3100), Aspergillus niger (ATCC 504). Thirteen 2-(6-substituted quinolin-4-yl)-1-alkoxypropan-2-ol (8a-m) derivatives reported moderate to good antitubercular activity against M. tuberculosis H37Rv with MIC 9.2-106.4 μM. Compounds 8a and 8h showed comparable activity with respect to the standard drug pyrazinamide. The active compounds screened for cytotoxicity activity against L929 mouse fibroblast cells showed no significant cytotoxic activity. Compounds 8c, 8d, 8e, 8g, 8k, and 8o displayed good activity against S. albus. Compounds 8c and 8n showed good activity against P. mirabilis and E. coli, respectively. The potential antimycobacterial activities imposed that the 2-(6-substituted quinolin-4-yl)-1-alkoxypropan-2-ol derivatives could lead to compounds that could treat tuberculosis. Graphical abstract Supplementary Information The online version contains supplementary material available at 10.1007/s11696-023-02741-3.
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Affiliation(s)
- Abhijit Shinde
- Department of Chemistry, S. P. Mandali’s Sir Parashurambhau College (Affiliated to, Savitribai Phule Pune University), Tilak Road, Pune, 411030 India
| | - Prashant P. Thakare
- Department of Chemistry, S. P. Mandali’s Sir Parashurambhau College (Affiliated to, Savitribai Phule Pune University), Tilak Road, Pune, 411030 India
| | - Yogesh Nandurkar
- Department of Chemistry, S. P. Mandali’s Sir Parashurambhau College (Affiliated to, Savitribai Phule Pune University), Tilak Road, Pune, 411030 India
- Department of Chemistry, N. Wadia College (Affiliated to Savitribai Phule Pune University), Pune, India
| | - Abhijit Chavan
- Department of Chemistry, S. P. Mandali’s Sir Parashurambhau College (Affiliated to, Savitribai Phule Pune University), Tilak Road, Pune, 411030 India
| | - Abdul Latif N. Shaikh
- Department of Chemistry, S. P. Mandali’s Sir Parashurambhau College (Affiliated to, Savitribai Phule Pune University), Tilak Road, Pune, 411030 India
- Department of Chemistry, Jijamata College of Science and Arts (Affiliated to Savitribai Phule Pune University), Bhende, Ahmednagar, India
| | - Pravin C. Mhaske
- Department of Chemistry, S. P. Mandali’s Sir Parashurambhau College (Affiliated to, Savitribai Phule Pune University), Tilak Road, Pune, 411030 India
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25
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Gupta S, Kumawat S, Fatima Z, Priya, Chatterjee S. Quantitative analysis of the bioenergetics of Mycobacterium tuberculosis along with Glyoxylate cycle as a drug target under inhibition of enzymes using Petri net. Comput Biol Chem 2023; 104:107828. [PMID: 36893566 DOI: 10.1016/j.compbiolchem.2023.107828] [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: 10/26/2022] [Revised: 02/02/2023] [Accepted: 02/10/2023] [Indexed: 03/09/2023]
Abstract
The bacteria Mycobacterium tuberculosis is responsible for the infectious disease Tuberculosis. Targeting the tubercule bacteria is an important challenge in developing the antimycobacterials. The glyoxylate cycle is considered as a potential target for the development of anti-tuberculosis agents, due to its absence in the humans. Humans only possess tricarboxylic acid cycle, while this cycle gets connected to glyoxylate cycle in microbes. Glyoxylate cycle is essential to the Mycobacterium for its growth and survival. Due to this reason, it is considered as a potential therapeutic target for the development of anti-tuberculosis agents. Here, we explore the effect on the behavior of the tricarboxylic acid cycle, glyoxylate cycle and their integrated pathway with the bioenergetics of the Mycobacterium, under the inhibition of key glyoxylate cycle enzymes using Continuous Petri net. Continuous Petri net is a special Petri net used to perform the quantitative analysis of the networks. We first study the tricarboxylic acid cycle and glyoxylate cycle of the tubercule bacteria by simulating its Continuous Petri net model under different scenarios. Both the cycles are then integrated with the bioenergetics of the bacteria and the integrated pathway is again simulated under different conditions. The simulation graphs show the metabolic consequences of inhibiting the key glyoxylate cycle enzymes and adding the uncouplers on the individual as well as integrated pathway. The uncouplers that inhibit the synthesis of adenosine triphosphate, play an important role as anti-mycobacterials. The simulation study done here validates the proposed Continuous Petri net model as compared with the experimental outcomes and also explains the consequences of the enzyme inhibition on the biochemical reactions involved in the metabolic pathways of the mycobacterium.
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Affiliation(s)
- Sakshi Gupta
- Department of Mathematics, Faculty of Science, Shree Guru Gobind Singh Tricentenary University, Gurugram, India; Department of Mathematics, Amity School of Applied Sciences, Amity University Haryana, Gurugram, India.
| | - Sunita Kumawat
- Department of Mathematics, Amity School of Applied Sciences, Amity University Haryana, Gurugram, India.
| | - Zeeshan Fatima
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, University of Bisha, Bisha, Saudi Arabia; Amity Institute of Biotechnology, Amity University Haryana, Gurugram, India.
| | - Priya
- Department of Mathematics, Amity School of Applied Sciences, Amity University Haryana, Gurugram, India.
| | - Samrat Chatterjee
- Complex Analysis Group, Translational Health science and Technology Institute, Faridabad, India.
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26
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Li P, Wang B, Chen X, Lin Z, Li G, Lu Y, Huang H. Design, synthesis and biological evaluation of alkynyl-containing maleimide derivatives for the treatment of drug-resistant tuberculosis. Bioorg Chem 2023; 131:106250. [PMID: 36423487 DOI: 10.1016/j.bioorg.2022.106250] [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: 09/21/2022] [Revised: 10/26/2022] [Accepted: 11/01/2022] [Indexed: 11/17/2022]
Abstract
A series of alkynyl-containing maleimides with potent anti-tuberculosis (TB) activity was developed through a rigid group substitution strategy based on our previous study. Systematic optimization of the two side chains flanking the maleimide core led to new compounds with potent activity against Mycobacterium tuberculosis (MIC < 1 μg/mL) and low cytotoxicity (IC50 > 64 μg/mL). Among them, compound 29 not only possessed good activity against extensively drug-resistant TB and favorable hepatocyte stability, but also displayed good intracellular antimycobacterial activity in macrophages. This study lays a good foundation for identifying new alkynyl-containing maleimides as promising leads for treating drug-resistant TB.
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Affiliation(s)
- Peng Li
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Chinese Academy of Medical Sciences Key Laboratory of Anti-DR TB Innovative Drug Research, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, PR China
| | - Bin Wang
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Department of Pharmacology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, 97 Ma Chang Street, Beijing 101149, PR China
| | - Xi Chen
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Department of Pharmacology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, 97 Ma Chang Street, Beijing 101149, PR China
| | - Ziyun Lin
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Chinese Academy of Medical Sciences Key Laboratory of Anti-DR TB Innovative Drug Research, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, PR China
| | - Gang Li
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Chinese Academy of Medical Sciences Key Laboratory of Anti-DR TB Innovative Drug Research, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, PR China.
| | - Yu Lu
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Department of Pharmacology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, 97 Ma Chang Street, Beijing 101149, PR China.
| | - Haihong Huang
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Chinese Academy of Medical Sciences Key Laboratory of Anti-DR TB Innovative Drug Research, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, PR China.
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27
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Safety, Tolerability, Pharmacokinetics, and Metabolism of Telacebec (Q203) for the Treatment of Tuberculosis: a Randomized, Placebo-Controlled, Multiple Ascending Dose Phase 1B Trial. Antimicrob Agents Chemother 2023; 67:e0112322. [PMID: 36507677 PMCID: PMC9872581 DOI: 10.1128/aac.01123-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
A phase 1b, randomized, placebo-controlled, double-blind, multiple ascending dose study (NCT02858973) was conducted to assess the safety, tolerability, and pharmacokinetics of the new antituberculosis agent telacebec (Q203). A total of 47 healthy adult subjects entered the study; 36 received telacebec, and 11 received placebo. Telacebec at doses of 20, 50, 100, 160, 250, and 320 mg was orally administered once daily with a standard meal for 14 days. Multiple oral doses of telacebec up to 320 mg daily for 14 days appeared to be safe and well tolerated by healthy adult subjects in this study. There were no deaths, serious adverse events, or subject discontinuations due to adverse events. Following oral doses of telacebec, the overall extent (AUCτ) and peak (Cmax) exposures of telacebec increased from 538.94 to 10,098.47 ng·h/mL and from 76.43 to 1502.33 ng/mL, respectively, with increasing telacebec doses from 20 mg to 320 mg. A steady state was achieved for plasma telacebec by day 12, and there was 1.9- to 3.1-fold accumulation in the extent of telacebec exposure after daily doses for 14 days. Analysis of plasma samples from the participants indicated that telacebec was the primary circulating entity with no significant metabolites. Three potential metabolites of telacebec have been identified, which may be relatively minimal compared to the parent drug. Consistent with findings from preclinical and previous single-dose clinical studies, these results also support the potential of telacebec for further development as a safe and effective agent for the treatment of tuberculosis.
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28
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Singh P, Rawat S, Agrahari AK, Singh M, Chugh S, Gurcha S, Singh A, Abrahams K, Besra GS, Asthana S, Rawat DS, Singh R. NSC19723, a Thiacetazone-Like Benzaldehyde Thiosemicarbazone Improves the Efficacy of TB Drugs In Vitro and In Vivo. Microbiol Spectr 2022; 10:e0259222. [PMID: 36314972 PMCID: PMC9769743 DOI: 10.1128/spectrum.02592-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 08/31/2022] [Indexed: 12/24/2022] Open
Abstract
The complexity and duration of tuberculosis (TB) treatment contributes to the emergence of drug resistant tuberculosis (DR-TB) and drug-associated side effects. Alternate chemotherapeutic agents are needed to shorten the time and improve efficacy of current treatment. In this study, we have assessed the antitubercular activity of NSC19723, a benzaldehyde thiosemicarbazone molecule. NSC19723 is structurally similar to thiacetazone (TAC), a second-line anti-TB drug used to treat individuals with DR-TB. NSC19723 displayed better MIC values than TAC against Mycobacterium tuberculosis and Mycobacterium bovis BCG. In our checkerboard experiments, NSC19723 displayed better profiles than TAC in combination with known first-line and recently approved drugs. Mechanistic studies revealed that NSC19723 inhibits mycolic acid biosynthesis by targeting the HadABC complex. Computational studies revealed that the binding pocket of HadAB is similarly occupied by NSC19723 and TAC. NSC19723 also improved the efficacy of isoniazid in macrophages and mouse models of infection. Cumulatively, we have identified a benzaldehyde thiosemicarbazone scaffold that improved the activity of TB drugs in liquid cultures, macrophages, and mice. IMPORTANCE Mycobacterium tuberculosis, the causative agent of TB is among the leading causes of death among infectious diseases in humans. This situation has worsened due to the failure of BCG vaccines and the increased number of cases with HIV-TB coinfections and drug-resistant strains. Another challenge in the field is the lengthy duration of therapy for drug-sensitive and -resistant TB. Here, we have deciphered the mechanism of action of NSC19723, benzaldehyde thiosemicarbazone. We show that NSC19723 targets HadABC complex and inhibits mycolic acid biosynthesis. We also show that NSC19723 enhances the activity of known drugs in liquid cultures, macrophages, and mice. We have also performed molecular docking studies to identify the interacting residues of HadAB with NSC19723. Taken together, we demonstrate that NSC19723, a benzaldehyde thiosemicarbazone, has better antitubercular activity than thiacetazone.
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Affiliation(s)
- Padam Singh
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Srishti Rawat
- Department of Chemistry, University of Delhi, Delhi, India
| | - Ashish Kumar Agrahari
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Manisha Singh
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Saurabh Chugh
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Sudagar Gurcha
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Albel Singh
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Katherine Abrahams
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Gurdyal S. Besra
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Shailendra Asthana
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Diwan S. Rawat
- Department of Chemistry, University of Delhi, Delhi, India
| | - Ramandeep Singh
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
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29
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Shinde A, Ugale SR, Nandurkar Y, Modak M, Chavan AP, Mhaske PC. Synthesis, Characterization, and Antimicrobial Activity Screening of Some Novel 3-(2-(3-(Substituted benzyloxy)oxetan-3-yl)-3-fluorophenoxy)-8-fluoro-2-methylquinoline Derivatives as Potential Antimycobacterial Agents. ACS OMEGA 2022; 7:47096-47107. [PMID: 36570236 PMCID: PMC9773968 DOI: 10.1021/acsomega.2c06245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Microbial infections remain a grave threat to global health security due to increasing antibiotic resistance. The coronavirus pandemic has increased the risk of microbial infection. To combat these infections, the search for new therapeutic agents is in high demand. A series of new 3-(2-(3-(substituted benzyloxy)oxetan-3-yl)-3-fluorophenoxy)-8-fluoro-2-methylquinoline (9a-i) derivatives have been synthesized. The structure of synthesized compounds was analyzed by spectroscopic methods. The newly synthesized oxetanyl-quinoline derivatives were evaluated for in vitro antibacterial activity against Escherichia coli (NCIM 2574), Proteus mirabilis (NCIM 2388), Bacillus subtilis (NCIM 2063), Staphylococcus albus (NCIM 2178), and in vitro antifungal activity against Aspergillus niger (ATCC 504) and Candida albicans (NCIM 3100). Six oxetanyl-quinoline derivatives 9a, 9b, 9c, 9d, 9e, and 9h have shown good antibacterial activity against P. mirabilis with MIC 31.25-62.5 μM, 3-(((3-(2-fluoro-6-((8-fluoro-2-methylquinolin-3-yl)oxy)phenyl)oxetan-3-yl)oxy)methyl)benzonitrile (9f) reporting comparable activity against P. mirabilis with respect to the standard drug streptomycin. Compound 9a also showed good activity against B. subtilis with MIC 31.25 μM. The eight compounds 9a, 9b, 9d, 9e, 9f, 9g, 9h, and 9i have shown good antifungal activity against A. niger. The synthesized compounds were also screened for antimycobacterial activity against Mycobacterium tuberculosis H37Rv by MTT assay. Among the nine derivatives, compounds 9b, 9c, 9d, 9f, 9g, 9h, and 9i showed excellent antimycobacterial activity with MIC 3.41-12.23 μM, and two derivatives showed good activity with MIC 27.29-57.73 μM. All the derivatives were further evaluated for cytotoxicity against the Vero cell line and were found to be nontoxic. The in silico study of compounds 9a-i was performed against ATP synthase (PDB ID: 4V1F) and most of the compounds showed the stable and significant binding to ATP synthase, confirming their plausible mode of action as ATP synthase inhibitors. Thus, the significant antimycobacterial activity of 3-(2-(3-(substituted benzyloxy)oxetan-3-yl)-3-fluorophenoxy)-8-fluoro-2-methylquinoline derivatives has suggested that the oxatenyl-quinoline compounds could assist in the development of lead compounds to treat mycobacterial infections.
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Affiliation(s)
- Abhijit Shinde
- Post-Graduate
Department of Chemistry, S. P. Mandali’s
Sir Parashurambhau College (Affiliated to Savitribai
Phule Pune University), Tilak Road, Pune 411 030, India
| | - Sandip R. Ugale
- Post-Graduate
Department of Chemistry, S. P. Mandali’s
Sir Parashurambhau College (Affiliated to Savitribai
Phule Pune University), Tilak Road, Pune 411 030, India
| | - Yogesh Nandurkar
- Post-Graduate
Department of Chemistry, S. P. Mandali’s
Sir Parashurambhau College (Affiliated to Savitribai
Phule Pune University), Tilak Road, Pune 411 030, India
- Department
of Chemistry, Nowrosjee Wadia College (Affiliated to Savitribai Phule Pune University), Pune 411 001, India
| | - Manisha Modak
- Department
of Zoology, S. P. Mandali’s Sir Parashurambhau
College (Affiliated to Savitribai Phule Pune University), Tilak Road, Pune 411 030, India
| | - Abhijit P. Chavan
- Post-Graduate
Department of Chemistry, S. P. Mandali’s
Sir Parashurambhau College (Affiliated to Savitribai
Phule Pune University), Tilak Road, Pune 411 030, India
| | - Pravin C. Mhaske
- Post-Graduate
Department of Chemistry, S. P. Mandali’s
Sir Parashurambhau College (Affiliated to Savitribai
Phule Pune University), Tilak Road, Pune 411 030, India
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30
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Fridianto KT, Gunawan GA, Hards K, Sarathy JP, Cook GM, Dick T, Go ML, Lam Y. Alkyltriphenylphosphonium turns naphthoquinoneimidazoles into potent membrane depolarizers against mycobacteria. RSC Med Chem 2022; 13:1605-1613. [PMID: 36545436 PMCID: PMC9749938 DOI: 10.1039/d2md00251e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/10/2022] [Indexed: 11/05/2022] Open
Abstract
Due to its central role in energy generation and bacterial viability, mycobacterial bioenergetics is an attractive therapeutic target for anti-tuberculosis drug discovery. Building upon our work on antimycobacterial dioxonaphthoimidazoliums that were activated by a proximal positive charge and generated reactive oxygen species upon reduction by Type II NADH dehydrogenase, we herein studied the effect of a distal positive charge on the antimycobacterial activity of naphthoquinoneimidazoles by incorporating a trialkylphosphonium cation. The potency-enhancing properties of the linker length were affirmed by structure-activity relationship studies. The most active compound against M. tb H37Rv displayed good selectivity index (SI = 34) and strong bactericidal activity in the low micromolar range, which occurred through rapid bacterial membrane depolarization that resulted in depletion of intracellular ATP. Through this work, we demonstrated a switch of the scaffold's mode-of-action via relocation of positive charge while retaining its excellent antibacterial activity and selectivity.
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Affiliation(s)
| | | | - Kiel Hards
- Department of Microbiology and Immunology, University of OtagoDunedin 9054New Zealand
| | - Jickky Palmae Sarathy
- Center for Discovery and Innovation, Hackensack Meridian Health & Department of Medical Sciences, Hackensack Meridian School of Medicine Nutley NJ 071110 USA
| | - Gregory M. Cook
- Department of Microbiology and Immunology, University of OtagoDunedin 9054New Zealand
| | - Thomas Dick
- Center for Discovery and Innovation, Hackensack Meridian Health & Department of Medical Sciences, Hackensack Meridian School of Medicine Nutley NJ 071110 USA .,Department of Microbiology and Immunology, Georgetown University Washington DC USA
| | - Mei-Lin Go
- Department of Pharmacy, National University of Singapore 117543 Singapore
| | - Yulin Lam
- Department of Chemistry, National University of Singapore 117543 Singapore
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31
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Nishida Y, Yanagisawa S, Morita R, Shigematsu H, Shinzawa-Itoh K, Yuki H, Ogasawara S, Shimuta K, Iwamoto T, Nakabayashi C, Matsumura W, Kato H, Gopalasingam C, Nagao T, Qaqorh T, Takahashi Y, Yamazaki S, Kamiya K, Harada R, Mizuno N, Takahashi H, Akeda Y, Ohnishi M, Ishii Y, Kumasaka T, Murata T, Muramoto K, Tosha T, Shiro Y, Honma T, Shigeta Y, Kubo M, Takashima S, Shintani Y. Identifying antibiotics based on structural differences in the conserved allostery from mitochondrial heme-copper oxidases. Nat Commun 2022; 13:7591. [PMID: 36481732 PMCID: PMC9731990 DOI: 10.1038/s41467-022-34771-y] [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] [Received: 05/15/2022] [Accepted: 11/07/2022] [Indexed: 12/13/2022] Open
Abstract
Antimicrobial resistance (AMR) is a global health problem. Despite the enormous efforts made in the last decade, threats from some species, including drug-resistant Neisseria gonorrhoeae, continue to rise and would become untreatable. The development of antibiotics with a different mechanism of action is seriously required. Here, we identified an allosteric inhibitory site buried inside eukaryotic mitochondrial heme-copper oxidases (HCOs), the essential respiratory enzymes for life. The steric conformation around the binding pocket of HCOs is highly conserved among bacteria and eukaryotes, yet the latter has an extra helix. This structural difference in the conserved allostery enabled us to rationally identify bacterial HCO-specific inhibitors: an antibiotic compound against ceftriaxone-resistant Neisseria gonorrhoeae. Molecular dynamics combined with resonance Raman spectroscopy and stopped-flow spectroscopy revealed an allosteric obstruction in the substrate accessing channel as a mechanism of inhibition. Our approach opens fresh avenues in modulating protein functions and broadens our options to overcome AMR.
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Affiliation(s)
- Yuya Nishida
- grid.410796.d0000 0004 0378 8307Department of Molecular Pharmacology, National Cerebral and Cardiovascular Center, Suita, Osaka Japan ,grid.136593.b0000 0004 0373 3971Department of Medical Biochemistry, Osaka University Graduate School of Frontier Biological Science, Suita, Osaka Japan
| | - Sachiko Yanagisawa
- grid.266453.00000 0001 0724 9317Graduate School of Science, University of Hyogo, Hyogo, Japan
| | - Rikuri Morita
- grid.20515.330000 0001 2369 4728Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki Japan
| | - Hideki Shigematsu
- grid.472717.0RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo Japan ,grid.410592.b0000 0001 2170 091XPresent Address: Structural Biology Division, Japan Synchrotron Radiation Research Institute, SPring-8; Sayo, Hyogo, Japan
| | - Kyoko Shinzawa-Itoh
- grid.266453.00000 0001 0724 9317Graduate School of Science, University of Hyogo, Hyogo, Japan
| | - Hitomi Yuki
- grid.508743.dRIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa Japan
| | - Satoshi Ogasawara
- grid.136304.30000 0004 0370 1101Department of Chemistry, Graduate School of Science, Chiba University, Inage, Chiba Japan
| | - Ken Shimuta
- grid.410795.e0000 0001 2220 1880Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan ,grid.410795.e0000 0001 2220 1880Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takashi Iwamoto
- grid.136593.b0000 0004 0373 3971Department of Medical Biochemistry, Osaka University Graduate School of Frontier Biological Science, Suita, Osaka Japan
| | - Chisa Nakabayashi
- grid.410796.d0000 0004 0378 8307Department of Molecular Pharmacology, National Cerebral and Cardiovascular Center, Suita, Osaka Japan ,grid.136593.b0000 0004 0373 3971Department of Medical Biochemistry, Osaka University Graduate School of Frontier Biological Science, Suita, Osaka Japan
| | - Waka Matsumura
- grid.266453.00000 0001 0724 9317Graduate School of Science, University of Hyogo, Hyogo, Japan
| | - Hisakazu Kato
- grid.136593.b0000 0004 0373 3971Department of Medical Biochemistry, Osaka University Graduate School of Frontier Biological Science, Suita, Osaka Japan
| | | | - Takemasa Nagao
- grid.410796.d0000 0004 0378 8307Department of Molecular Pharmacology, National Cerebral and Cardiovascular Center, Suita, Osaka Japan
| | - Tasneem Qaqorh
- grid.410796.d0000 0004 0378 8307Department of Molecular Pharmacology, National Cerebral and Cardiovascular Center, Suita, Osaka Japan ,grid.136593.b0000 0004 0373 3971Department of Medical Biochemistry, Osaka University Graduate School of Frontier Biological Science, Suita, Osaka Japan
| | - Yusuke Takahashi
- grid.410796.d0000 0004 0378 8307Department of Molecular Pharmacology, National Cerebral and Cardiovascular Center, Suita, Osaka Japan
| | - Satoru Yamazaki
- grid.410796.d0000 0004 0378 8307Department of Molecular Pharmacology, National Cerebral and Cardiovascular Center, Suita, Osaka Japan
| | - Katsumasa Kamiya
- grid.419709.20000 0004 0371 3508Center for Basic Education Integrated Learning, Kanagawa Institute of Technology, Atsugi, Kanagawa Japan
| | - Ryuhei Harada
- grid.20515.330000 0001 2369 4728Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki Japan
| | - Nobuhiro Mizuno
- grid.410592.b0000 0001 2170 091XProtein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, SPring-8, Sayo, Hyogo Japan
| | - Hideyuki Takahashi
- grid.410795.e0000 0001 2220 1880Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yukihiro Akeda
- grid.410795.e0000 0001 2220 1880Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Ohnishi
- grid.410795.e0000 0001 2220 1880Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoshikazu Ishii
- grid.265050.40000 0000 9290 9879Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan
| | - Takashi Kumasaka
- grid.410592.b0000 0001 2170 091XProtein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, SPring-8, Sayo, Hyogo Japan
| | - Takeshi Murata
- grid.136304.30000 0004 0370 1101Department of Chemistry, Graduate School of Science, Chiba University, Inage, Chiba Japan
| | - Kazumasa Muramoto
- grid.266453.00000 0001 0724 9317Graduate School of Science, University of Hyogo, Hyogo, Japan
| | - Takehiko Tosha
- grid.472717.0RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo Japan
| | - Yoshitsugu Shiro
- grid.266453.00000 0001 0724 9317Graduate School of Science, University of Hyogo, Hyogo, Japan
| | - Teruki Honma
- grid.508743.dRIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa Japan
| | - Yasuteru Shigeta
- grid.20515.330000 0001 2369 4728Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki Japan
| | - Minoru Kubo
- grid.266453.00000 0001 0724 9317Graduate School of Science, University of Hyogo, Hyogo, Japan
| | - Seiji Takashima
- grid.136593.b0000 0004 0373 3971Department of Medical Biochemistry, Osaka University Graduate School of Frontier Biological Science, Suita, Osaka Japan
| | - Yasunori Shintani
- grid.410796.d0000 0004 0378 8307Department of Molecular Pharmacology, National Cerebral and Cardiovascular Center, Suita, Osaka Japan ,grid.136593.b0000 0004 0373 3971Department of Medical Biochemistry, Osaka University Graduate School of Frontier Biological Science, Suita, Osaka Japan
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32
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Zhou Y, Yong Y, Zhu C, Yang H, Fang B. Exogenous D-ribose promotes gentamicin treatment of several drug-resistant Salmonella. Front Microbiol 2022; 13:1053330. [PMID: 36419438 PMCID: PMC9676500 DOI: 10.3389/fmicb.2022.1053330] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 10/21/2022] [Indexed: 07/28/2023] Open
Abstract
The metabolic microenvironment of bacteria impacts drug efficacy. However, the metabolic mechanisms of drug-resistant Salmonella spp. remain largely unknown. This study characterized the metabolic mechanism of gentamicin-resistant Salmonella Choleraesuis and found that D-ribose increased the gentamicin-mediated killing of this bacteria. Non-targeted metabolomics of homologous gentamicin-susceptible Salmonella Choleraesuis (SCH-S) and gentamicin-resistant S. Choleraesuis (SCH-R) was performed using UHPLC-Q-TOF MS. The metabolic signature of SCH-R included disrupted central carbon metabolism and energy metabolism, along with dysregulated amino acid and nucleotide metabolism, vitamin and cofactor metabolism, and fatty acid synthesis. D-ribose, the most suppressed metabolite in SCH-R, was shown to strengthen gentamicin efficacy against SCH-R and a clinically isolated multidrug-resistant strain. This metabolite had a similar impact on Salmonella. Derby and Salmonella. Typhimurium. D-ribose activates central carbon metabolism including glycolysis, the pentose phosphate pathway (PPP), and the tricarboxylic acid cycle (TCA cycle), increases the abundance of NADH, polarizes the electron transport chain (ETC), and elevates the proton motive force (PMF) of cells, and induces drug uptake and cell death. These findings suggest that central carbon metabolism plays a critical role in the acquisition of gentamicin resistance by Salmonella, and that D-ribose may serve as an antibiotic adjuvant for gentamicin treatment of resistant bacterial infections.
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Affiliation(s)
- Yanhong Zhou
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
| | - Yan Yong
- Guangdong Wens Dahuanong Biotechnology Limited Company, Yun Fu, China
| | - Chunyang Zhu
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
| | - Heng Yang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
| | - Binghu Fang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
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33
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Response of Mycobacterium smegmatis to the Cytochrome bcc Inhibitor Q203. Int J Mol Sci 2022; 23:ijms231810331. [PMID: 36142240 PMCID: PMC9498996 DOI: 10.3390/ijms231810331] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022] Open
Abstract
For the design of next-generation tuberculosis chemotherapy, insight into bacterial defence against drugs is required. Currently, targeting respiration has attracted strong attention for combatting drug-resistant mycobacteria. Q203 (telacebec), an inhibitor of the cytochrome bcc complex in the mycobacterial respiratory chain, is currently evaluated in phase-2 clinical trials. Q203 has bacteriostatic activity against M. tuberculosis, which can be converted to bactericidal activity by concurrently inhibiting an alternative branch of the mycobacterial respiratory chain, cytochrome bd. In contrast, non-tuberculous mycobacteria, such as Mycobacterium smegmatis, show only very little sensitivity to Q203. In this report, we investigated factors that M. smegmatis employs to adapt to Q203 in the presence or absence of a functional cytochrome bd, especially regarding its terminal oxidases. In the presence of a functional cytochrome bd, M. smegmatis responds to Q203 by increasing the expression of cytochrome bcc as well as of cytochrome bd, whereas a M. smegmatisbd-KO strain adapted to Q203 by increasing the expression of cytochrome bcc. Interestingly, single-cell studies revealed cell-to-cell variability in drug adaptation. We also investigated the role of a putative second cytochrome bd isoform postulated for M. smegmatis. Although this putative isoform showed differential expression in response to Q203 in the M. smegmatisbd-KO strain, it did not display functional features similar to the characterised cytochrome bd variant.
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34
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Design, synthesis and biological evaluation of (Quinazoline 4-yloxy)acetamide and (4-oxoquinazoline-3(4H)-yl)acetamide derivatives as inhibitors of Mycobacterium tuberculosis bd oxidase. Eur J Med Chem 2022; 242:114639. [DOI: 10.1016/j.ejmech.2022.114639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/25/2022] [Accepted: 07/25/2022] [Indexed: 11/23/2022]
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35
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Impaired Succinate Oxidation Prevents Growth and Influences Drug Susceptibility in Mycobacterium tuberculosis. mBio 2022; 13:e0167222. [PMID: 35856639 PMCID: PMC9426501 DOI: 10.1128/mbio.01672-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Succinate is a major focal point in mycobacterial metabolism and respiration, serving as both an intermediate of the tricarboxylic acid (TCA) cycle and a direct electron donor for the respiratory chain. Mycobacterium tuberculosis encodes multiple enzymes predicted to be capable of catalyzing the oxidation of succinate to fumarate, including two different succinate dehydrogenases (Sdh1 and Sdh2) and a separate fumarate reductase (Frd) with possible bidirectional behavior. Previous attempts to investigate the essentiality of succinate oxidation in M. tuberculosis have relied on the use of single-gene deletion mutants, raising the possibility that the remaining enzymes could catalyze succinate oxidation in the absence of the other. To address this, we report on the use of mycobacterial CRISPR interference (CRISPRi) to construct single, double, and triple transcriptional knockdowns of sdhA1, sdhA2, and frdA in M. tuberculosis. We show that the simultaneous knockdown of sdhA1 and sdhA2 is required to prevent succinate oxidation and overcome the functional redundancy within these enzymes. Succinate oxidation was demonstrated to be essential for the optimal growth of M. tuberculosis, with the combined knockdown of sdhA1 and sdhA2 significantly impairing the activity of the respiratory chain and preventing growth on a range of carbon sources. Moreover, impaired succinate oxidation was shown to influence the activity of cell wall-targeting antibiotics and bioenergetic inhibitors against M. tuberculosis. Together, these data provide fundamental insights into mycobacterial physiology, energy metabolism, and antimicrobial susceptibility. IMPORTANCE New drugs are urgently required to combat the tuberculosis epidemic that claims 1.5 million lives annually. Inhibitors of mycobacterial energy metabolism have shown significant promise clinically; however, further advancing this nascent target space requires a more fundamental understanding of the respiratory enzymes and pathways used by Mycobacterium tuberculosis. Succinate is a major focal point in mycobacterial metabolism and respiration; yet, the essentiality of succinate oxidation and the consequences of inhibiting this process are poorly defined. In this study, we demonstrate that impaired succinate oxidation prevents the optimal growth of M. tuberculosis on a range of carbon sources and significantly reduces the activity of the electron transport chain. Moreover, we show that impaired succinate oxidation both positively and negatively influences the activity of a variety of antituberculosis drugs. Combined, these findings provide fundamental insights into mycobacterial physiology and drug susceptibility that will be useful in the continued development of bioenergetic inhibitors.
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36
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Defining the Genes Required for Survival of Mycobacterium bovis in the Bovine Host Offers Novel Insights into the Genetic Basis of Survival of Pathogenic Mycobacteria. mBio 2022; 13:e0067222. [PMID: 35862770 PMCID: PMC9426507 DOI: 10.1128/mbio.00672-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This is the first report of the genetic requirements of an animal-adapted member of the
Mycobacterium tuberculosis
complex (MTBC) in a natural host.
M. bovis
has devastating impacts on cattle, and bovine tuberculosis is a considerable economic, animal welfare, and public health concern. The data highlight the importance of mycobacterial cholesterol catabolism and identify several new virulence factors.
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37
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Deng W, Zheng Z, Chen Y, Yang M, Yan J, Li W, Zeng J, Xie J, Gong S, Zeng H. Deficiency of GntR Family Regulator MSMEG_5174 Promotes Mycobacterium smegmatis Resistance to Aminoglycosides via Manipulating Purine Metabolism. Front Microbiol 2022; 13:919538. [PMID: 35898907 PMCID: PMC9309504 DOI: 10.3389/fmicb.2022.919538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 06/20/2022] [Indexed: 11/30/2022] Open
Abstract
The increasing incidence of drug-resistant tuberculosis is still an emergency for global public health and a major obstacle to tuberculosis treatment. Therefore, deciphering the novel mechanisms of mycobacterial antibiotic resistance is crucial for combatting the rapid emergence of drug-resistant strains. In this study, we identified an unexpected role of Mycobacterium smegmatis GntR family transcriptional regulator MSMEG_5174 and its homologous gene Mycobacterium tuberculosis Rv1152 in aminoglycoside antibiotic resistance. Deficiency of MSMEG_5174 rendered Mycobacterium smegmatis highly resistant to aminoglycoside antibiotic treatment, and ectopic expression of Rv1152 in MSMEG_5174 mutants restored antibiotic-induced bacterial killing. We further demonstrated that MSMEG_5174 negatively regulates the expression of purine metabolism-related genes and the accumulation of purine metabolites. Moreover, overexpression of xanthine dehydrogenase MSMEG_0871 or xanthine treatment elicited a significant decrease in aminoglycoside antibiotic lethality for Mycobacterium smegmatis. Together, our findings revealed MSMEG_5174 as a metabolic regulator and hint toward unexplored crosstalk between purine metabolism and antibiotic resistance.
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Affiliation(s)
- Wanyan Deng
- The Joint Center for Infection and Immunity, Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou, China
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Department of Infectious Diseases, Institute for Viral Hepatitis, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
- *Correspondence: Wanyan Deng,
| | - Zengzhang Zheng
- The Joint Center for Infection and Immunity, Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou, China
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Yi Chen
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Department of Infectious Diseases, Institute for Viral Hepatitis, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Maoyi Yang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Department of Infectious Diseases, Institute for Viral Hepatitis, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jun Yan
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Department of Infectious Diseases, Institute for Viral Hepatitis, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Wu Li
- The Joint Center for Infection and Immunity, Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou, China
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Jie Zeng
- Department of Respiratory Medicine, The First People’s Hospital of Yunnan Province, Kunming, China
- Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Jianping Xie
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Institute of Modern Biopharmaceuticals, Southwest University, Chongqing, China
| | - Sitang Gong
- The Joint Center for Infection and Immunity, Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou, China
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
- Sitang Gong,
| | - Huasong Zeng
- The Joint Center for Infection and Immunity, Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou, China
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
- Huasong Zeng,
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Evsyutina DV, Semashko TA, Galyamina MA, Kovalchuk SI, Ziganshin RH, Ladygina VG, Fisunov GY, Pobeguts OV. Molecular Basis of the Slow Growth of Mycoplasma hominis on Different Energy Sources. Front Cell Infect Microbiol 2022; 12:918557. [PMID: 35873139 PMCID: PMC9301678 DOI: 10.3389/fcimb.2022.918557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/15/2022] [Indexed: 12/05/2022] Open
Abstract
Mycoplasma hominis is an opportunistic urogenital pathogen in vertebrates. It is a non-glycolytic species that produces energy via arginine degradation. Among genital mycoplasmas, M. hominis is the most commonly reported to play a role in systemic infections and can persist in the host for a long time. However, it is unclear how M. hominis proceeds under arginine limitation. The recent metabolic reconstruction of M. hominis has demonstrated its ability to catabolize deoxyribose phosphate to produce ATP. In this study, we cultivated M. hominis on two different energy sources (arginine and thymidine) and demonstrated the differences in growth rate, antibiotic sensitivity, and biofilm formation. Using label-free quantitative proteomics, we compared the proteome of M. hominis under these conditions. A total of 466 proteins were identified from M. hominis, representing approximately 85% of the predicted proteome, while the levels of 94 proteins changed significantly. As expected, we observed changes in the levels of metabolic enzymes. The energy source strongly affects the synthesis of enzymes related to RNA modifications and ribosome assembly. The translocation of lipoproteins and other membrane-associated proteins was also impaired. Our study, the first global characterization of the proteomic switching of M. hominis in arginine-deficiency media, illustrates energy source-dependent control of pathogenicity factors and can help to determine the mechanisms underlying the interaction between the growth rate and fitness of genome-reduced bacteria.
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Affiliation(s)
- Daria V. Evsyutina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency Malaya Pirogovskaya 1a, Moscow, Russia
- Department of Systems and Synthetic Biology, Scientific Research Institute for Systems Biology and Medicine Nauchniy proezd 18, Moscow, Russia
- *Correspondence: Daria V. Evsyutina,
| | - Tatiana A. Semashko
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency Malaya Pirogovskaya 1a, Moscow, Russia
- Department of Systems and Synthetic Biology, Scientific Research Institute for Systems Biology and Medicine Nauchniy proezd 18, Moscow, Russia
| | - Maria A. Galyamina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency Malaya Pirogovskaya 1a, Moscow, Russia
| | - Sergey I. Kovalchuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10, Moscow, Russia
| | - Rustam H. Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10, Moscow, Russia
| | - Valentina G. Ladygina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency Malaya Pirogovskaya 1a, Moscow, Russia
| | - Gleb Y. Fisunov
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency Malaya Pirogovskaya 1a, Moscow, Russia
- Department of Systems and Synthetic Biology, Scientific Research Institute for Systems Biology and Medicine Nauchniy proezd 18, Moscow, Russia
| | - Olga V. Pobeguts
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency Malaya Pirogovskaya 1a, Moscow, Russia
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Khan A, Poojary SS, Bhave KK, Nandan SR, Iyer KR, Coutinho EC. Prediction of QcrB Inhibition as a Measure of Antitubercular Activity with Machine Learning Protocols. ACS OMEGA 2022; 7:18094-18102. [PMID: 35664614 PMCID: PMC9161412 DOI: 10.1021/acsomega.2c01613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/06/2022] [Indexed: 05/07/2023]
Abstract
It has always been a challenge to develop interventional therapies for Mycobacterium tuberculosis. Over the years, several attempts at developing such therapies have hit a dead-end owing to rapid mutation rates of the tubercular bacilli and their ability to lay dormant for years. Recently, cytochrome bcc complex (QcrB) has shown some promise as a novel target against the tubercular bacilli, with Q203 being the first molecule acting on this target. In this paper, we report the deployment of several ML-based approaches to design molecules against QcrB. Machine learning (ML) models were developed based on a data set of 350 molecules using three different sets of molecular features, i.e., MACCS keys, ECFP6 fingerprints, and Mordred descriptors. Each feature set was trained on eight ML classifier algorithms and optimized to classify molecules accurately. The support vector machine-based classifier using the ECFP6 feature set was found to be the best classifier in this study. Further, screening of the known imidazopyridine amide inhibitors demonstrated that the model correctly classified the most potent molecules as actives, hence validating the model for future applications.
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Affiliation(s)
- Afreen
A. Khan
- Department
of Pharmaceutical Chemistry, Vasvik Research Centre, Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai 400 098, India
| | - Sannidhi S. Poojary
- Department
of Pharmaceutical Chemistry, Vasvik Research Centre, Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai 400 098, India
| | - Ketki K. Bhave
- Department
of Pharmaceutical Chemistry, Vasvik Research Centre, Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai 400 098, India
| | - Santosh R. Nandan
- Ambernath
Organics Pvt. Ltd., 222,
The Summit Business Bay, Andheri (E), Mumbai 400 093, India
| | - Krishna R. Iyer
- Department
of Pharmaceutical Chemistry, Vasvik Research Centre, Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai 400 098, India
| | - Evans C. Coutinho
- Department
of Pharmaceutical Chemistry, Vasvik Research Centre, Bombay College of Pharmacy, Kalina, Santacruz (E), Mumbai 400 098, India
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Single-Fluorescence ATP Sensor Based on Fluorescence Resonance Energy Transfer Reveals Role of Antibiotic-Induced ATP Perturbation in Mycobacterial Killing. mSystems 2022; 7:e0020922. [PMID: 35615956 PMCID: PMC9238375 DOI: 10.1128/msystems.00209-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The rapid emergence of multidrug-resistant/extensively drug-resistant tuberculosis (TB) is responsible for treatment failure in patients with TB and significantly endangers global public health. Recently, bioenergetics has become a new paradigm for anti-TB drug discovery and is based on the link between bacterial ATP levels and drug efficacy. A better understanding of the role of ATP fluctuations during antibiotic treatment may provide insight into antibiotic-mediated killing of mycobacteria. Here, we employed an advanced single-fluorescence FRET (fluorescence resonance energy transfer)-based ATP biosensor, ATPser, for the stable and convenient detection of intracellular ATP fluctuations in mycobacteria. This strategy correlated closely with the results obtained from conventional luminescence ATP assays, indicating the reliability of the system for bioenergetics analysis in mycobacteria. Moreover, the reporter strains expressing ATPser displayed obvious ATP changes when subjected to different stresses, such as starvation and ATP depletion. Interestingly, we observed that different antibiotics induced fluctuations in cellular ATP levels in individual cells of various magnitudes, revealing a strong connection between ATP fluctuations and drug efficacy. Furthermore, drug combinations accelerated ATP perturbation, resulting in increased cell death. We concluded that ATPser enabled real-time measurement of ATP at the single-cell level in mycobacteria, and monitoring ATP dynamics in drug-treated bacteria may shed light on novel treatment strategies. IMPORTANCE Bioenergetics has emerged as a new paradigm for antituberculosis (anti-TB) drug discovery, and the cellular ATP level is the core indicator reflecting bacterial metabolic homeostasis. Although several bulk assays have been designed for the measurement of cellular ATP content, a more convenient strategy is required for real-time ATP measurement of single viable cells. In this study, by combining the ε-subunit of Bacillus subtilis FoF1-ATP synthase with a circularly permuted green fluorescent protein [(cp)GFP], we constructed a FRET-based single-fluorescence ATP sensor, ATPser, for real-time single-cell ATP detection among a mycobacterial population. Using the ATPser, we designed different drug combinations containing components that have similar/opposite effects on ATP alternation. Our results demonstrated that increased cellular ATP fluctuations were associated with depletion of mycobacterial viability, while counteracting ATP fluctuations weakened the killing effect of the drug regime. Thus, potentially efficient drug combinations can be considered based on their similar effects on mycobacterial ATP levels, and ATPser may be a useful tool to study mycobacterial bioenergetics and to guide drug regime design.
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Fernandes GFS, Thompson AM, Castagnolo D, Denny WA, Dos Santos JL. Tuberculosis Drug Discovery: Challenges and New Horizons. J Med Chem 2022; 65:7489-7531. [PMID: 35612311 DOI: 10.1021/acs.jmedchem.2c00227] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Over the past 2000 years, tuberculosis (TB) has claimed more lives than any other infectious disease. In 2020 alone, TB was responsible for 1.5 million deaths worldwide, comparable to the 1.8 million deaths caused by COVID-19. The World Health Organization has stated that new TB drugs must be developed to end this pandemic. After decades of neglect in this field, a renaissance era of TB drug discovery has arrived, in which many novel candidates have entered clinical trials. However, while hundreds of molecules are reported annually as promising anti-TB agents, very few successfully progress to clinical development. In this Perspective, we critically review those anti-TB compounds published in the last 6 years that demonstrate good in vivo efficacy against Mycobacterium tuberculosis. Additionally, we highlight the main challenges and strategies for developing new TB drugs and the current global pipeline of drug candidates in clinical studies to foment fresh research perspectives.
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Affiliation(s)
- Guilherme F S Fernandes
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Andrew M Thompson
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Daniele Castagnolo
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - William A Denny
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Jean L Dos Santos
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara 14800903, Brazil
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Anand P, Akhter Y. A review on enzyme complexes of electron transport chain from Mycobacterium tuberculosis as promising drug targets. Int J Biol Macromol 2022; 212:474-494. [PMID: 35613677 DOI: 10.1016/j.ijbiomac.2022.05.124] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/05/2022] [Accepted: 05/17/2022] [Indexed: 12/20/2022]
Abstract
Energy metabolism is a universal process occurring in all life forms. In Mycobacterium tuberculosis (Mtb), energy production is carried out in two possible ways, oxidative phosphorylation (OxPhos) and substrate-level phosphorylation. Mtb is an obligate aerobic bacterium, making it dependent on OxPhos for ATP synthesis and growth. Mtb inhabits varied micro-niches during the infection cycle, outside and within the host cells, which alters its primary metabolic pathways during the pathogenesis. In this review, we discuss cellular respiration in the context of the mechanism and structural importance of the proteins and enzyme complexes involved. These protein-protein complexes have been proven to be essential for Mtb virulence as they aid the bacteria's survival during aerobic and hypoxic conditions. ATP synthase, a crucial component of the electron transport chain, has been in the limelight, as a prominent drug target against tuberculosis. Likewise, in this review, we have explored other protein-protein complexes of the OxPhos pathway, their functional essentiality, and their mechanism in Mtb's diverse lifecycle. The review summarises crucial target proteins and reported inhibitors of the electron transport chain pathway of Mtb.
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Affiliation(s)
- Pragya Anand
- Department of Biotechnology, School of Life Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Lucknow, Uttar Pradesh 226025, India
| | - Yusuf Akhter
- Department of Biotechnology, School of Life Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Lucknow, Uttar Pradesh 226025, India.
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Semenya D, Touitou M, Masci D, Ribeiro CM, Pavan FR, Dos Santos Fernandes GF, Gianibbi B, Manetti F, Castagnolo D. Tapping into the antitubercular potential of 2,5-dimethylpyrroles: A structure-activity relationship interrogation. Eur J Med Chem 2022; 237:114404. [PMID: 35486992 DOI: 10.1016/j.ejmech.2022.114404] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/16/2022] [Accepted: 04/18/2022] [Indexed: 01/29/2023]
Abstract
An exploration of the chemical space around a 2,5-dimethylpyrrole scaffold of antitubercular hit compound 1 has led to the identification of new derivatives active against Mycobacterium tuberculosis and multidrug-resistant clinical isolates. Analogues incorporating a cyclohexanemethyl group on the methyleneamine side chain at C3 of the pyrrole core, including 5n and 5q, exhibited potent inhibitory effects against the M. tuberculosis strains, substantiating the essentiality of the moiety to their antimycobacterial activity. In addition, selected derivatives showed promising cytotoxicity profiles against human pulmonary fibroblasts and/or murine macrophages, proved to be effective in inhibiting the growth of intracellular mycobacteria, and elicited either bactericidal effects, or bacteriostatic activity comparable to 1. Computational studies revealed that the new compounds bind to the putative target, MmpL3, in a manner similar to that of known inhibitors BM212 and SQ109.
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Affiliation(s)
- Dorothy Semenya
- School of Cancer and Pharmaceutical Sciences, King's College London, 150 Stamford Street, SE1 9NH, London, United Kingdom
| | - Meir Touitou
- School of Cancer and Pharmaceutical Sciences, King's College London, 150 Stamford Street, SE1 9NH, London, United Kingdom
| | - Domiziana Masci
- School of Cancer and Pharmaceutical Sciences, King's College London, 150 Stamford Street, SE1 9NH, London, United Kingdom
| | - Camila Maringolo Ribeiro
- Tuberculosis Research Laboratory, School of Pharmaceutical Sciences, Sao Paulo State University (UNESP), Rod. Araraquara-Jau, km1, 14800-903, Araraquara, Brazil
| | - Fernando Rogerio Pavan
- Tuberculosis Research Laboratory, School of Pharmaceutical Sciences, Sao Paulo State University (UNESP), Rod. Araraquara-Jau, km1, 14800-903, Araraquara, Brazil
| | | | - Beatrice Gianibbi
- Dipartimento di Biotecnologie, Chimica e Farmacia, Dipartimento di Eccellenza 2018-2022, University of Siena, via A. Moro 2, I-53100, Siena, Italy
| | - Fabrizio Manetti
- Dipartimento di Biotecnologie, Chimica e Farmacia, Dipartimento di Eccellenza 2018-2022, University of Siena, via A. Moro 2, I-53100, Siena, Italy
| | - Daniele Castagnolo
- School of Cancer and Pharmaceutical Sciences, King's College London, 150 Stamford Street, SE1 9NH, London, United Kingdom.
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44
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Dong Y, Ou X, Liu C, Fan W, Zhao Y, Zhou X. Diversity of glpK Gene and Its Effect on Drug Sensitivity in Mycobacterium bovis. Infect Drug Resist 2022; 15:1467-1475. [PMID: 35401008 PMCID: PMC8986483 DOI: 10.2147/idr.s346724] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 03/01/2022] [Indexed: 11/23/2022] Open
Affiliation(s)
- Yuhui Dong
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, People’s Republic of China
| | - Xichao Ou
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Chunfa Liu
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Weixing Fan
- National Reference Laboratory for Animal Tuberculosis, China Animal Health and Epidemiology Center, Qingdao, 266032, People’s Republic of China
| | - Yanlin Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Xiangmei Zhou
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, People’s Republic of China
- Correspondence: Xiangmei Zhou, Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, People’s Republic of China, Email
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Friedrich T, Wohlwend D, Borisov VB. Recent Advances in Structural Studies of Cytochrome bd and Its Potential Application as a Drug Target. Int J Mol Sci 2022; 23:ijms23063166. [PMID: 35328590 PMCID: PMC8951039 DOI: 10.3390/ijms23063166] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/14/2022] [Accepted: 03/14/2022] [Indexed: 02/06/2023] Open
Abstract
Cytochrome bd is a triheme copper-free terminal oxidase in membrane respiratory chains of prokaryotes. This unique molecular machine couples electron transfer from quinol to O2 with the generation of a proton motive force without proton pumping. Apart from energy conservation, the bd enzyme plays an additional key role in the microbial cell, being involved in the response to different environmental stressors. Cytochrome bd promotes virulence in a number of pathogenic species that makes it a suitable molecular drug target candidate. This review focuses on recent advances in understanding the structure of cytochrome bd and the development of its selective inhibitors.
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Affiliation(s)
- Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, D-79104 Freiburg, Germany; (T.F.); (D.W.)
| | - Daniel Wohlwend
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, D-79104 Freiburg, Germany; (T.F.); (D.W.)
| | - Vitaliy B. Borisov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia
- Correspondence:
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Advances in Key Drug Target Identification and New Drug Development for Tuberculosis. BIOMED RESEARCH INTERNATIONAL 2022; 2022:5099312. [PMID: 35252448 PMCID: PMC8896939 DOI: 10.1155/2022/5099312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 02/14/2022] [Indexed: 12/15/2022]
Abstract
Tuberculosis (TB) is a severe infectious disease worldwide. The increasing emergence of drug-resistant Mycobacterium tuberculosis (Mtb) has markedly hampered TB control. Therefore, there is an urgent need to develop new anti-TB drugs to treat drug-resistant TB and shorten the standard therapy. The discovery of targets of drug action will lay a theoretical foundation for new drug development. With the development of molecular biology and the success of Mtb genome sequencing, great progress has been made in the discovery of new targets and their relevant inhibitors. In this review, we summarized 45 important drug targets and 15 new drugs that are currently being tested in clinical stages and several prospective molecules that are still at the level of preclinical studies. A comprehensive understanding of the drug targets of Mtb can provide extensive insights into the development of safer and more efficient drugs and may contribute new ideas for TB control and treatment.
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47
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Targeting the ATP synthase in bacterial and fungal pathogens – beyond Mycobacterium tuberculosis. J Glob Antimicrob Resist 2022; 29:29-41. [DOI: 10.1016/j.jgar.2022.01.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 01/24/2022] [Accepted: 01/30/2022] [Indexed: 11/23/2022] Open
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Lee BS, Pethe K. Telacebec: an investigational antibiotic for the treatment of tuberculosis (TB). Expert Opin Investig Drugs 2022; 31:139-144. [PMID: 35034512 DOI: 10.1080/13543784.2022.2030309] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Tuberculosis is a leading cause of death by an infectious agent and has affected more than 50 million people and killed 6.7 million patients in the past 5 years alone. Rising incidence of resistance to treatment threatens the global effort to eradicate the disease. With limited options available, additional novel antibiotics are needed to form efficacious combinations for the treatment of multi-drug resistant tuberculosis (MDR-TB). Telacebec is a first-in-class antibiotic that inhibits growth of mycobacterium tuberculosis by targeting its energy metabolism. The compound has undergone three clinical studies, the latest being a phase 2a efficacy trial. AREAS COVERED This paper provides an overview of the recent progress in the development and testing of telacebec. We discuss published clinical data and examine the design and set up of its clinical trials. We also offer insights on the therapeutic potential of telacebec and aspects of which should be evaluated in the future. EXPERT OPINION The first phase 2a trial showed a correlation between dosage and bacterial load in patient sputum which should be confirmed using a direct measurement method such as colony-forming unit counting. Its clinical efficacy, favourable pharmacokinetic properties, low arrhythmogenic risk, and activity against MDR-TB strains make telacebec a suitable candidate for further development. Future clinical testing in combination with approved second-line drugs will reveal its full potential against MDR-TB. Considering recent preclinical studies, we also recommend initiating clinical trials for Buruli ulcer and leprosy.
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Affiliation(s)
- Bei Shi Lee
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Kevin Pethe
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551.,Lee Kong Chian School of Medicine, Nanyang Technological University, Experimental Medicine Building, 59 Nanyang Drive, Singapore 636921
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Perveen S, Sharma R. Screening approaches and therapeutic targets: The two driving wheels of tuberculosis drug discovery. Biochem Pharmacol 2022; 197:114906. [PMID: 34990594 DOI: 10.1016/j.bcp.2021.114906] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/28/2021] [Accepted: 12/28/2021] [Indexed: 12/21/2022]
Abstract
Tuberculosis (TB) is an infectious disease, infecting a quarter of world's population. Drug resistant TB further exacerbates the grim scenario of the drying TB drug discovery pipeline. The limited arsenal to fight TB presses the need for thorough efforts for identifying promising hits to combat the disease. The review highlights the efforts in the field of tuberculosis drug discovery, with an emphasis on massive drug screening campaigns for identifying novel hits against Mtb in both industry and academia. As an intracellular pathogen, mycobacteria reside in a complicated intracellular environment with multiple factors at play. Here, we outline various strategies employed in an effort to mimic the intracellular milieu for bringing the screening models closer to the actual settings. The review also focuses on the novel targets and pathways that could aid in target-based drug discovery in TB. The recent high throughput screening efforts resulting in the identification of potent hits against Mtb has been summarized in this article. There is a pressing need for effective screening strategies and approaches employing innovative tools and recent technologies; including nanotechnology, gene-editing tools such as CRISPR-cas system, host-directed bacterial killing and high content screening to augment the TB drug discovery pipeline with safer and shorter drug regimens.
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Affiliation(s)
- Summaya Perveen
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Rashmi Sharma
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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50
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Thomas SS, Pethe K. Determination of Bioenergetic Parameters in Mycobacterium ulcerans. Methods Mol Biol 2022; 2387:219-230. [PMID: 34643916 DOI: 10.1007/978-1-0716-1779-3_21] [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] [Indexed: 06/13/2023]
Abstract
The oxidative phosphorylation (OxPhos) pathway has emerged as an attractive pathway for the development of anti-mycobacterial drugs. The OxPhos pathway is essential for ATP resynthesis and maintenance of the electrochemical transmembrane gradient. The bioenergetic parameters of the pathway such as oxygen consumption rate and ATP levels are quantifiable using current technology. Measuring these parameters are useful tools to gauge rapidly the impact of drug candidates on their capacity to inhibit the OxPhos pathway in Mycobacterium ulcerans.
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Affiliation(s)
- Sangeeta Susan Thomas
- NTU Institute for Health Technologies (HealthTech NTU), Interdisciplinary Graduate Programme, Nanyang Technological University, Singapore, Singapore
- Lee Kong Chian School of Medicine, Experimental Medicine Building, Nanyang Technological University, Singapore, Singapore
| | - Kevin Pethe
- Lee Kong Chian School of Medicine, Experimental Medicine Building, Nanyang Technological University, Singapore, Singapore.
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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