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Abbas M, Alanzi AR, Sahibzada KI, Nawaz M, Fatima G, Wei DQ. Identification of novel inhibitors targeting Mycobacterium abscessus InhA through virtual screening, docking, and molecular dynamic simulations. Sci Rep 2025; 15:12795. [PMID: 40229331 PMCID: PMC11997171 DOI: 10.1038/s41598-025-97513-2] [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: 10/03/2024] [Accepted: 04/04/2025] [Indexed: 04/16/2025] Open
Abstract
Effective treatment options for Mycobacterium abscessus (MAB) pulmonary diseases (PD) are limited due to inadequate drug efficacy, rising drug resistance, and genetic mutations. New compounds are urgently needed to treat MAB-PD. The MAB Enoyl Acyl Carrier Protein (ACP) Reductase InhA (MAB-InhA) plays a crucial role in mycobacterial cell death and mycolic acid (MA) biosynthesis, making it a potential drug target for new lead identification. The purpose of this study was to identify new potential inhibitors of MAB-InhA in MAB-PD by using structure-based virtual screening, docking, molecular mechanics-based generalized born surface area (MM/GBSA), Absorption, Distribution, Metabolism, and Excretion (ADME), and molecular dynamics (MD) simulations. The Enamine antibacterial library containing 32,000 compounds was prepared using phase to create the database. The identified hits were analysed using the phase score, which combines vector alignments, volume score, and root-mean-square deviation (RMSD) site matching. Based on the docking results and obtained scores of the Glide docking tool, we identified Z2378320480 (Z1), Z1188959831 (Z2), Z5292493137 (Z3), Z2437620504 (Z4), Z2440336150 (Z5), and Z3390516726 (Z6) ligand molecules as potential hits. MD simulations (200 ns) were conducted on the best-docked poses of potential hits Z4, Z5, and Z6 to analyse stability and interaction at the MAB-InhA active site. The MD simulation trajectories, including RMSD, root mean square fluctuation (RMSF), ligand-protein interaction, 2D principal component analysis (PCA), and molecular dynamics secondary structure analysis (SSE), were analysed to interpret the stability.
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Affiliation(s)
- Munawar Abbas
- College of Food Science and Technology, Henan University of Technology, Zhengzhou, 450001, Henan, China
| | - Abdullah R Alanzi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia, Saudi Arabia
| | - Kashif Iqbal Sahibzada
- College of Biological Engineering, Henan University of Technology, Zhengzhou, 454001, P.R. China
- Department of Health Professional Technologies, Faculty of Allied Health Sciences, The University of Lahore, Lahore, 54570, Pakistan
| | - Mariyam Nawaz
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Ghulam Fatima
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Dong-Qing Wei
- College of Food Science and Technology, Henan University of Technology, Zhengzhou, 450001, Henan, China.
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, P.R. China.
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Meixi, Nanyang, 473006, Henan, P.R. China.
- Qihe Laboratory, Qishui Guang East, Qibin District, Hebi, 458030, Henan, China.
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2
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Mujeeb S, Singh K, Al-Zrkani MK, Al-Fahad D, Hasan SM, Shouber MA, Ahmad F, Hameed HN, Iqbal D, Kamal M. Chroman-Schiff base derivatives as potential Anti-Tubercular Agents: In silico studies, Synthesis, and Biological evaluation. Bioorg Chem 2025; 157:108249. [PMID: 39965447 DOI: 10.1016/j.bioorg.2025.108249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2024] [Revised: 01/13/2025] [Accepted: 02/05/2025] [Indexed: 02/20/2025]
Abstract
Tuberculosis (TB) continues to pose a significant public health challenge worldwide. Hydrazide-containing compounds have demonstrated considerable potential as anti- tubercular agents. In this study, we designed, synthesized, and evaluated a series of chroman- Schiff base derivatives, integrating a chroman scaffold with substituted phenyl moieties, as potential therapeutic candidates against TB. In silico studies were conducted to assess the binding interactions of the synthesized derivatives, specifically their R- and S-isomers, with the tuberculosis target protein InhA (PDB ID: 1ZID). Molecular docking revealed that two R-isomer derivatives, SM-5A and SM-6A, exhibited superior binding affinities (-10.6 kcal/mol) compared to the reference ligand INH-NADH (-10.3 kcal/mol) and the natural substrate NADH (-7.5 kcal/mol). Molecular dynamics simulations confirmed the long-term stability of these compound-protein complexes over a 100 ns trajectory, further substantiating their potential as stable inhibitors. The structures of the synthesized derivatives were validated using spectroscopic techniques, including FTIR, 13C NMR, 1H NMR, and HR-MS. Biological evaluation via in vitro anti-tubercular assays against Mycobacterium tuberculosis H37Rv (using the Microplate Alamar Blue Assay) demonstrated that several RRR-isomers displayed notable activity. Among them, SM-2 and SM-5 showed the most potent effects, with minimum inhibitory concentrations (MIC) of 32 µg/mL, comparable to standard anti-tubercular drugs such as isoniazid, ethambutol, and rifampicin. These findings highlight the chroman-schiff base scaffold as a promising foundation for the development of novel anti-tubercular agents. The integration of computational and experimental approaches in this study underscores the potential of these derivatives for further optimization and development into effective anti-tubercular therapeutics.
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Affiliation(s)
- Samar Mujeeb
- Department of Pharmaceutical Chemistry, Hygia Institute of Pharmaceutical Education &Research, Lucknow, Uttar Pradesh 226020, India.
| | - Kuldeep Singh
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Integral University, Lucknow, Uttar Pradesh 226026, India
| | - Martha K Al-Zrkani
- Department of Animal Production, College of Agriculture, Wasit University, Wasit 52001, Iraq
| | - Dhurgham Al-Fahad
- Department of Pathological analysis, college of Science, University of Thi-Qar, Thi-Qar 64001, Iraq
| | - Syed Misbahul Hasan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Integral University, Lucknow, Uttar Pradesh 226026, India
| | - Marwah Al Shouber
- Department of Pharmacy, Kut University College, Kut, Wasit, 52001, Iraq
| | - Fuzail Ahmad
- Respiratory Care Department, College of Applied Sciences, Almaarefa University, Diriya, Riyadh 13713 Saudi Arabia
| | - Husian Njem Hameed
- Department of Animal Production, College of Agriculture, Wasit University, Wasit 52001, Iraq
| | - Danish Iqbal
- Department of Health Information Management, College of Applied Medical Sciences, Buraydah Private Colleges, Buraydah 51418, Saudi Arabia
| | - Mehnaz Kamal
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
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3
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Kızılyıldırım S, Sucu B, Muhammed MT, Akkoç S, Esatbeyoglu T, Ozogul F. Experimental and theoretical studies on antituberculosis activity of different benzimidazole derivatives. Heliyon 2025; 11:e42674. [PMID: 40051852 PMCID: PMC11883371 DOI: 10.1016/j.heliyon.2025.e42674] [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: 09/08/2024] [Revised: 02/11/2025] [Accepted: 02/12/2025] [Indexed: 03/09/2025] Open
Abstract
Tuberculosis (TB) continues to be one of the deadliest infectious diseases with a rapid increase in multidrug-resistant cases. The discovery of new agents against tuberculosis is urgently needed. Thus, the research article focuses on the antituberculosis activity of a series of benzimidazolium compounds. The antituberculosis activities of compounds including benzimidazole core (7a-h) against Mycobacterium tuberculosis H37Rv strain were tested in vitro using the BACTEC MGIT 960 system. The concentrations of benzimidazole compounds were adjusted to range from 0.25 to 4 μg/ml. The antituberculosis interactions of the compounds were investigated by molecular docking and molecular dynamics simulation. The results revealed that only benzimidazolium salt 7h showed antituberculosis activity at MIC value of 2 μg/ml although the other compounds showed no antituberculosis activity. The docking data revealed that 7h could bind to InhA thus indicating its inhibition potential on the enzyme. Molecular dynamics simulation exhibited that 7h formed a stable complex with the enzyme and was able to remain inside the binding region of the enzyme. Besides, the pharmacokinetic and drug-likeness properties of the compounds were assessed through computational approaches. The compounds exhibited drug-like properties. Consequently, 7h could be a good candidate for the development of new TB drugs.
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Affiliation(s)
- Suna Kızılyıldırım
- Cukurova University, Faculty of Pharmacy, Department of Pharmaceutical Microbiology, Adana, Türkiye
| | - Berfin Sucu
- Cukurova University, Institute of Science and Technology, Department of Biotechnology, Adana, Türkiye
| | - Muhammed Tilahun Muhammed
- Süleyman Demirel University, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, 32260, Isparta, Türkiye
| | - Senem Akkoç
- Süleyman Demirel University, Faculty of Pharmacy, Department of Basic Pharmaceutical Sciences, 32260, Isparta, Türkiye
- Bahçeşehir University, Faculty of Engineering and Natural Sciences, Istanbul, 34353, Türkiye
| | - Tuba Esatbeyoglu
- Gottfried Wilhelm Leibniz University Hannover, Institute of Food and One Health, Department of Molecular Food Chemistry and Food Development, Am Kleinen Felde 30, 30167, Hannover, Germany
| | - Fatih Ozogul
- Cukurova University, Faculty of Fisheries, Department of Seafood Processing Technology, Adana, Türkiye
- Cukurova University, Biotechnology Research and Application Center, Adana, Türkiye
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4
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Chikhale RV, Choudhary R, Eldesoky GE, Kolpe MS, Shinde O, Hossain D. Generative AI, molecular docking and molecular dynamics simulations assisted identification of novel transcriptional repressor EthR inhibitors to target Mycobacterium tuberculosis. Heliyon 2025; 11:e42593. [PMID: 40034280 PMCID: PMC11874554 DOI: 10.1016/j.heliyon.2025.e42593] [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] [Received: 07/24/2024] [Revised: 02/08/2025] [Accepted: 02/09/2025] [Indexed: 03/05/2025] Open
Abstract
Tuberculosis (TB) remains a persistent global health threat, with Mycobacterium tuberculosis (Mtb) continuing to be a leading cause of mortality worldwide. Despite efforts to control the disease, the emergence of multi-drug-resistant (MDR) and extensively drug-resistant (XDR) TB strains presents a significant challenge to conventional treatment approaches. Addressing this challenge requires the development of novel anti-TB drug molecules. This study employed de novo drug design approaches to explore new EthR ligands and ethionamide boosters targeting the crucial enzyme InhA involved in mycolic acid synthesis in Mtb. Leveraging REINVENT4, a modern open-source generative AI framework, the study utilized various optimization algorithms such as transfer learning, reinforcement learning, and curriculum learning to design small molecules with desired properties. Specifically, focus was placed on molecule optimization using the Mol2Mol option, which offers multinomial sampling with beam search. The study's findings highlight the identification of six promising compounds exhibiting enhanced activity and improved physicochemical properties through structure-based drug design and optimization efforts. These compounds offer potential candidates for further preclinical and clinical development as novel therapeutics for TB treatment, providing new avenues for combating drug-resistant TB strains and improving patient outcomes.
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Affiliation(s)
- Rupesh V. Chikhale
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College London, London, UK
| | - Rinku Choudhary
- SilicoScientia Private Limited, Nagananda Commercial Complex, No. 07/3, 15/1, 18th Main Road, Jayanagar 9th Block, Bengaluru, 560041, India
| | - Gaber E. Eldesoky
- Chemistry Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Mahima Sudhir Kolpe
- SilicoScientia Private Limited, Nagananda Commercial Complex, No. 07/3, 15/1, 18th Main Road, Jayanagar 9th Block, Bengaluru, 560041, India
| | - Omkar Shinde
- SilicoScientia Private Limited, Nagananda Commercial Complex, No. 07/3, 15/1, 18th Main Road, Jayanagar 9th Block, Bengaluru, 560041, India
| | - Dilnawaz Hossain
- SilicoScientia Private Limited, Nagananda Commercial Complex, No. 07/3, 15/1, 18th Main Road, Jayanagar 9th Block, Bengaluru, 560041, India
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5
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Bhaskar V, Kumar S, Sujathan Nair A, Gokul S, Rajappan Krishnendu P, Benny S, Amrutha CT, Manisha DS, Bhaskar V, Mary Zachariah S, Aneesh TP, Abdelgawad MA, Ghoneim MM, Pappachen LK, Nicolotti O, Mathew B. In silico development of potential InhA inhibitors through 3D-QSAR analysis, virtual screening and molecular dynamics. J Biomol Struct Dyn 2025; 43:1329-1351. [PMID: 38064315 DOI: 10.1080/07391102.2023.2291549] [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: 04/05/2023] [Accepted: 11/15/2023] [Indexed: 01/03/2025]
Abstract
Tuberculosis is one of the most ancient infectious diseases known to mankind predating upper Paleolithic era. In the current scenario, treatment of drug resistance tuberculosis is the major challenge as the treatment options are limited, less efficient and more toxic. In our study we have developed an atom based 3D QSAR model, statistically validated sound with R2 > 0.90 and Q2 > 0.72 using reported direct inhibitors of InhA (2018-2022), validated by enzyme inhibition assay. The model was used to screen a library of 3958 molecules taken from Binding DB and candidates molecules with promising predicted activity value (pIC50) > 5) were selected for further analyzed screening by using molecular docking, ADME profiling and molecular dynamic simulations. The lead molecule, ZINC11536150 exhibited good docking score (glideXP = -11.634 kcal/mol) compared to standard triclosan (glideXP = -7.129 kcal/mol kcal/mol) and through molecular dynamics study it was observed that the 2nv6-complex of ZINC11536150 with Mycobacterium tuberculosis InhA (PDB entry: 2NV6) complex remained stable throughout the entire simulation time of 100 ns.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vaishnav Bhaskar
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, Kochi, Kerala, India
| | - Sunil Kumar
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, Kochi, Kerala, India
| | | | - S Gokul
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, Kochi, Kerala, India
| | - Prayaga Rajappan Krishnendu
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, Kochi, Kerala, India
| | - Sonu Benny
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, Kochi, Kerala, India
| | - C T Amrutha
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, Kochi, Kerala, India
| | - Deepthi S Manisha
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, Kochi, Kerala, India
| | - Vaishnavi Bhaskar
- Department of Electronics and Computer Engineering, Amrita Vishwa Vidyapeetham, Kollam, Kerala, India
| | - Subin Mary Zachariah
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, Kochi, Kerala, India
| | - T P Aneesh
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, Kochi, Kerala, India
| | - Mohamed A Abdelgawad
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf university, Sakaka, Saudi Arabia
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - Mohammed M Ghoneim
- Department of Pharmacy Practice, College of Pharmacy, AlMaarefa University, Ad Diriyah, Saudi Arabia
| | - Leena K Pappachen
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, Kochi, Kerala, India
| | - Orazio Nicolotti
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", Bari, Italy
| | - Bijo Mathew
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, Kochi, Kerala, India
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6
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Tailor NK, Deswal G, Guarve K, Grewal AS. Development of Mycobacterium tuberculosis Enoyl Acyl Reductase (InhA) Inhibitors: A Mini-Review. Mini Rev Med Chem 2025; 25:219-233. [PMID: 39301902 DOI: 10.2174/0113895575309785240902102421] [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: 03/12/2024] [Revised: 07/04/2024] [Accepted: 07/27/2024] [Indexed: 09/22/2024]
Abstract
This review article delves into the critical role of Enoyl acyl carrier protein reductase (InhA; ENR), a vital enzyme in the NADH-dependent acyl carrier protein reductase family, emphasizing its significance in fatty acid synthesis and, more specifically, the biosynthesis of mycolic acid. The primary objective of this literature review is to elucidate diverse scaffolds and their developmental progression targeting InhA inhibition, thereby disrupting mycolic acid biosynthesis. Various scaffolds, including thiourea, piperazine, thiadiazole, triazole, quinazoline, benzamide, rhodanine, benzoxazole, and pyridine, have been systematically explored for their potential as InhA inhibitors. Noteworthy findings highlight thiadiazole and triazole derivatives, demonstrating promising IC50 values within the nanomolar concentration range. The review offers comprehensive insights into InhA's structure, structure-activity relationships, and a detailed overview of distinct scaffolds as effective inhibitors of InhA.
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Affiliation(s)
- Navin Kumar Tailor
- University Institute of Pharma Sciences, Chandigarh University, Gharuan, Mohali, Punjab, India
| | - Geeta Deswal
- Department of Pharmacy, Guru Gobind Singh College of Pharmacy, Yamuna Nagar, 135001, Haryana, India
| | - Kumar Guarve
- Department of Pharmacy, Guru Gobind Singh College of Pharmacy, Yamuna Nagar, 135001, Haryana, India
| | - Ajmer Singh Grewal
- Department of Pharmacy, Guru Gobind Singh College of Pharmacy, Yamuna Nagar, 135001, Haryana, India
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Zhang X, Zhao R, Qi Y, Yan X, Qi G, Peng Q. The progress of Mycobacterium tuberculosis drug targets. Front Med (Lausanne) 2024; 11:1455715. [PMID: 39497852 PMCID: PMC11533868 DOI: 10.3389/fmed.2024.1455715] [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: 06/27/2024] [Accepted: 10/02/2024] [Indexed: 11/07/2024] Open
Abstract
Tuberculosis (TB) has been troubling humans for hundreds of years, is a highly infectious disease caused by Mycobacterium tuberculosis (Mtb) infection, Mtb can infect almost all organs of the body and is one of the deadly infectious diseases in the world. At present, the first-line treatment regimen has a long treatment cycle and is prone to multiple drug resistance. Anti-tuberculosis drugs and latent tuberculosis infection (LTBI) resistance are increasing year by year, and new targets and new bioactive compounds are urgently needed to treat this disease. This review focuses on the latest reported anti-TB drug targets and related compounds in recent years, reviews the current TB drug regimen and major defects, outlines the key drug targets developed to date in Mtb, and the current situation of newly discovered anti-TB resistant forms of drugs. To provide a reference for the research and development of new anti-TB drugs and bring new treatment strategies for TB patients.
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Affiliation(s)
- Xin Zhang
- Qingdao Central Hospital, University of Health and Rehabilitation Sciences, Qingdao Central Medical Group, Qingdao, Shandong, China
| | - Ruixia Zhao
- Qingdao Central Hospital, University of Health and Rehabilitation Sciences, Qingdao Central Medical Group, Qingdao, Shandong, China
| | - Yao Qi
- Qingdao Central Hospital, University of Health and Rehabilitation Sciences, Qingdao Central Medical Group, Qingdao, Shandong, China
| | - Xiong Yan
- Qingdao Central Hospital, University of Health and Rehabilitation Sciences, Qingdao Central Medical Group, Qingdao, Shandong, China
| | - Gaoxiu Qi
- Qingdao Central Hospital, University of Health and Rehabilitation Sciences, Qingdao Central Medical Group, Qingdao, Shandong, China
| | - Qiuju Peng
- Qingdao Chest Hospital, Qingdao, Shandong, China
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Al-Warhi T, Sabt A, Korycka-Machala M, Kassem AF, Shaldam MA, Ibrahim HAA, Kawka M, Dziadek B, Kuzioła M, Eldehna WM, Dziadek J. Benzenesulfonohydrazide-tethered non-fused and fused heterocycles as potential anti-mycobacterial agents targeting enoyl acyl carrier protein reductase (InhA) with antibiofilm activity. RSC Adv 2024; 14:30165-30179. [PMID: 39315015 PMCID: PMC11418391 DOI: 10.1039/d4ra05616g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Accepted: 09/09/2024] [Indexed: 09/25/2024] Open
Abstract
Because resistant variants of the disease are always emerging, tuberculosis is a global issue that affects economies. New antitubercular medications should be developed, and this can be done by inhibiting druggable targets. Enoyl acyl carrier protein (ACP) reductase (InhA) is a crucial enzyme for the survival of Mycobacterium tuberculosis (MTB). In this study, a series of small molecules based on non-fused and fused heterocycles (pyridine, coumarin, quinoline, and indole) tethered with benzenesulfonohydrazide were prepared via an aza-Michael reaction exploiting a one-pot synthesis approach. The synthesized molecules (2-7) were evaluated for their activity against tubercle bacilli. Three analogues showed efficacy against tuberculosis, with compound 7 demonstrating a MIC value as low as 8 μg mL-1. Consequently, compounds 3 and 7 successfully hindered the growth of mycobacteria in human monocyte-derived macrophages (MDMs), demonstrating their ability to penetrate human professional phagocytes. Furthermore, they restricted the ability of mycobacteria to produce biofilms. In addition, the inhibitory effects of compounds 3 and 7 against InhA were assessed. Compound 7 exhibited the best efficacy, with an IC50 value of 0.91 μM. The findings showed that the sulfonamide and methyl ester's carbonyl functionalities were engaged in hydrogen bonding with the essential Ile194 and Tyr158 residues, respectively.
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Affiliation(s)
- Tarfah Al-Warhi
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University Riyadh Saudi Arabia
| | - Ahmed Sabt
- Chemistry of Natural Compounds Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre Dokki Cairo 12622 Egypt
| | - Małgorzata Korycka-Machala
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology of the Polish Academy of Sciences Lodz Poland
| | - Asmaa F Kassem
- Department of Chemistry, College of Science and Humanities in Al-Kharj, Prince Sattam Bin Abdulaziz University Al-Kharj 11942 Saudi Arabia
| | - Moataz A Shaldam
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University Kafrelsheikh 33516 Egypt
| | | | - Malwina Kawka
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Lodz Lodz Poland
| | - Bożena Dziadek
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Lodz Lodz Poland
| | - Magdalena Kuzioła
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology of the Polish Academy of Sciences Lodz Poland
- Bio-Med-Chem Doctoral School of the University of Lodz and Lodz Institutes of the Polish Academy of Sciences Lodz Poland
| | - Wagdy M Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University Kafrelsheikh 33516 Egypt
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Pharos University in Alexandria Canal El Mahmoudia St. Alexandria 21648 Egypt
| | - Jarosław Dziadek
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology of the Polish Academy of Sciences Lodz Poland
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Chauhan M, Barot R, Yadav R, Joshi K, Mirza S, Chikhale R, Srivastava VK, Yadav MR, Murumkar PR. The Mycobacterium tuberculosis Cell Wall: An Alluring Drug Target for Developing Newer Anti-TB Drugs-A Perspective. Chem Biol Drug Des 2024; 104:e14612. [PMID: 39237482 DOI: 10.1111/cbdd.14612] [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: 11/16/2023] [Revised: 06/26/2024] [Accepted: 08/05/2024] [Indexed: 09/07/2024]
Abstract
The Mycobacterium cell wall is a capsule-like structure comprising of various layers of biomolecules such as mycolic acid, peptidoglycans, and arabinogalactans, which provide the Mycobacteria a sort of cellular shield. Drugs like isoniazid, ethambutol, cycloserine, delamanid, and pretomanid inhibit cell wall synthesis by inhibiting one or the other enzymes involved in cell wall synthesis. Many enzymes present across these layers serve as potential targets for the design and development of newer anti-TB drugs. Some of these targets are currently being exploited as the most druggable targets like DprE1, InhA, and MmpL3. Many of the anti-TB agents present in clinical trials inhibit cell wall synthesis. The present article covers a systematic perspective of developing cell wall inhibitors targeting various enzymes involved in cell wall biosynthesis as potential drug candidates for treating Mtb infection.
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Affiliation(s)
- Monica Chauhan
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Rahul Barot
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Rasana Yadav
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Karan Joshi
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Sadaf Mirza
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Rupesh Chikhale
- The Cambridge Crystallography Data Center, Cambridge, UK
- School of Pharmacy, University College London, London, UK
| | | | - Mange Ram Yadav
- Centre of Research for Development, Parul University, Vadodara, Gujarat, India
| | - Prashant R Murumkar
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
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Zhang X, Zheng Y, Zhou C, Cao J, Pan D, Cai Z, Wu Z, Xia Q. Comparative physiological and transcriptomic analysis of sono-biochemical control over post-acidification of Lactobacillus delbrueckii subsp. bulgaricus. Food Microbiol 2024; 122:104563. [PMID: 38839237 DOI: 10.1016/j.fm.2024.104563] [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: 01/03/2024] [Revised: 04/27/2024] [Accepted: 05/16/2024] [Indexed: 06/07/2024]
Abstract
Thermosonication (UT) prestress treatments combining with varied fermentation patterns has been revealed as an effective method to regulate post-acidification as exerted by Lactobacillus delbrueckii subsp. bulgaricus (L. delbrueckii), but sono-biochemical controlling mechanisms remain elusive. This study employed physiological and transcriptomic analysis to explore the response mechanism of L. delbrueckii to UT-induced microstress (600 W, 33 kHz, 10 min). UT stress-induced inhibition of acidification of L. delbrueckii during (post)-fermentation was first confirmed, relying on the UT process parameters such as stress exposure duration and UT power. The significantly enhanced membrane permeability in cells treated by 600 W for 10 min than the microbes stressed by 420 W for 20 min suggested the higher dependence of UT-derived stresses on the treatment durations, relative to the ultrasonic powers. In addition, ultrasonication treatment-induced changes in cell membrane integrity enhanced and/or disrupted permeability of L. delbrueckii, resulting in an imbalance in intracellular conditions associated with corresponding alterations in metabolic behaviors and fermentation efficiencies. UT-prestressed inoculum exhibited a 21.46% decrease in the membrane potential during the lag phase compared to untreated samples, with an intracellular pH of 5.68 ± 0.12, attributed to the lower activities of H+-ATPase and lactate dehydrogenase due to UT stress pretreatments. Comparative transcriptomic analysis revealed that UT prestress influenced the genes related to glycolysis, pyruvate metabolism, fatty acid synthesis, and ABC transport. The genes encoding 3-oxoacyl-[acyl-carrier-protein] reductases I, II, and III, CoA carboxylase, lactate dehydrogenase, pyruvate oxidase, glucose-6-phosphate isomerase, and glycerol-3-phosphate dehydrogenase were downregulated, thus identifying the relevance of the UT microstresses-downregulated absorption and utilization of carbohydrates with the attenuated fatty acid production and energy metabolisms. These findings could contribute to provide a better understanding of the inactivated effects on the post-acidification of L. delbrueckii by ultrasonic pretreatments, thus providing theoretical basis for the targeted optimization of acidification inhibition efficiencies for yogurt products during chilled preservation processes.
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Affiliation(s)
- Xiaohui Zhang
- College of Food Science and Engineering, Zhejiang Key Laboratory of Intelligent Food Logistic and Processing, Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, Ningbo University, Ningbo, 315211, China
| | - Yuanrong Zheng
- State Key Laboratory of Dairy Biotechnology, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy & Food Co., Ltd., Shanghai, 200436, China
| | - Changyu Zhou
- College of Food Science and Engineering, Zhejiang Key Laboratory of Intelligent Food Logistic and Processing, Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, Ningbo University, Ningbo, 315211, China
| | - Jinxuan Cao
- School of Food and Health, China Food Flavor and Nutrition Health Innovation Center, Beijing Technology and Business University, 11 Fucheng Road, Beijing, 100048, China
| | - Daodong Pan
- College of Food Science and Engineering, Zhejiang Key Laboratory of Intelligent Food Logistic and Processing, Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, Ningbo University, Ningbo, 315211, China
| | - Zhendong Cai
- College of Food Science and Engineering, Zhejiang Key Laboratory of Intelligent Food Logistic and Processing, Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, Ningbo University, Ningbo, 315211, China
| | - Zhen Wu
- College of Food Science and Engineering, Zhejiang Key Laboratory of Intelligent Food Logistic and Processing, Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, Ningbo University, Ningbo, 315211, China.
| | - Qiang Xia
- College of Food Science and Engineering, Zhejiang Key Laboratory of Intelligent Food Logistic and Processing, Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, Ningbo University, Ningbo, 315211, China.
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11
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Kassem AF, Sabt A, Korycka-Machala M, Shaldam MA, Kawka M, Dziadek B, Kuzioła M, Dziadek J, Batran RZ. New coumarin linked thiazole derivatives as antimycobacterial agents: Design, synthesis, enoyl acyl carrier protein reductase (InhA) inhibition and molecular modeling. Bioorg Chem 2024; 150:107511. [PMID: 38870705 DOI: 10.1016/j.bioorg.2024.107511] [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: 03/28/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/15/2024]
Abstract
Tuberculosis is a global serious problem that imposes major health, economic and social challenges worldwide. The search for new antitubercular drugs is extremely important which could be achieved via inhibition of different druggable targets. Mycobacterium tuberculosis enoyl acyl carrier protein reductase (InhA) enzyme is essential for the survival of M. tuberculosis. In this investigation, a series of coumarin based thiazole derivatives was synthesized relying on a molecular hybridization approach and was assessed against thewild typeMtb H37Rv and its mutant strain (ΔkatG) via inhibiting InhA enzyme. Among the synthesized derivatives, compounds 2b, 3i and 3j were the most potent against wild type M. tuberculosis with MIC values ranging from 6 to 8 μg/ mL and displayed low cytotoxicity towards mouse fibroblasts at concentrations 8-13 times higher than the MIC values. The three hybrids could also inhibit the growth of ΔkatGmutant strain which is resistant to isoniazid (INH). Compounds 2b and 3j were able to inhibit the growth of mycobacteria inside human macrophages, indicating their ability to penetrate human professional phagocytes. The two derivatives significantly suppress mycobacterial biofilm formation by 10-15 %. The promising target compounds were also assessed for their inhibitory effect against InhA and showed potent effectiveness with IC50 values of 0.737 and 1.494 µM, respectively. Molecular docking studies revealed that the tested compounds occupied the active site of InhA in contact with the NAD+ molecule. The 4-phenylcoumarin aromatic system showed binding interactions within the hydrophobic pocket of the active site. Furthermore, H-bond formation and π -π stacking interactions were also recorded for the promising derivatives.
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Affiliation(s)
- Asmaa F Kassem
- Chemistry of Natural and Microbial Products Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Dokki, Cairo 12622, Egypt
| | - Ahmed Sabt
- Chemistry of Natural Compounds Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Dokki, Cairo 12622, Egypt
| | - Małgorzata Korycka-Machala
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology of the Polish Academy of Sciences, Lodz, Poland
| | - Moataz A Shaldam
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
| | - Malwina Kawka
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Bożena Dziadek
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Magdalena Kuzioła
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology of the Polish Academy of Sciences, Lodz, Poland; Bio-Med-Chem Doctoral School of the University of Lodz and Lodz Institutes of the Polish Academy of Sciences, Lodz, Poland
| | - Jarosław Dziadek
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology of the Polish Academy of Sciences, Lodz, Poland.
| | - Rasha Z Batran
- Chemistry of Natural Compounds Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Dokki, Cairo 12622, Egypt.
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12
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Khetmalis YM, Shobha S, Nandikolla A, Chandu A, Murugesan S, Kumar MMK, Chandra Sekhar KVG. Design, synthesis, and anti-mycobacterial evaluation of 1,8-naphthyridine-3-carbonitrile analogues. RSC Adv 2024; 14:22676-22689. [PMID: 39027042 PMCID: PMC11255784 DOI: 10.1039/d4ra04262j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Accepted: 07/11/2024] [Indexed: 07/20/2024] Open
Abstract
Twenty-eight compounds, viz., 1,8-naphthyridine-3-carbonitrile (ANC and ANA) derivatives, were designed and synthesized through a molecular hybridization approach. The structures of these compounds were analyzed and confirmed using 1H NMR, 13C NMR, LCMS, and elemental analyses. The synthesized compounds were evaluated by in vitro testing for their effectiveness against tuberculosis using the MABA assay, targeting the Mycobacterium tuberculosis H37Rv strain. Their minimum inhibitory concentration (MIC) was determined, showing that the tested compounds' MIC values ranged from 6.25 to ≤50 μg mL-1. Among the derivatives studied, ANA-12 demonstrated prominent anti-tuberculosis activity with a MIC of 6.25 μg mL-1. Compounds ANC-2, ANA-1, ANA 6-8, and ANA-10 displayed moderate to good anti-tuberculosis activity with MIC values of 12.5 μg mL-1. Compounds with MIC ≤ 12.5 μg mL-1 were screened against human embryonic kidney cells to assess their potential cytotoxicity. Interestingly, these compounds showed less toxicity towards normal cells, with a selectivity index value ≥ 11. To further evaluate the binding pattern in the active site of enoyl-ACP reductase (InhA) from Mtb (PDB-4TZK), a molecular docking analysis of compound ANA-12 was performed using the glide module of Schrodinger software. The stability, confirmation, and intermolecular interactions of the cocrystal ligand and the highly active compound ANA-12 on the chosen target protein were investigated through molecular dynamics simulations lasting 100 ns. In silico predictions were utilized to assess the ADMET properties of the final compounds. A suitable single crystal was developed and analyzed for compound ANA-5 to gain a deeper understanding of the compounds' structures.
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Affiliation(s)
- Yogesh Mahadu Khetmalis
- Department of Chemistry, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Jawahar Nagar Hyderabad 500 078 Telangana India +91 40 66303527
| | - Singarapalle Shobha
- College of Pharmaceutical Sciences, Andhra University Visakhapatnam Andhra Pradesh - 530 003 India
| | - Adinarayana Nandikolla
- Department of Chemistry, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Jawahar Nagar Hyderabad 500 078 Telangana India +91 40 66303527
| | - Ala Chandu
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science Pilani 333031 India
| | - Sankaranarayanan Murugesan
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science Pilani 333031 India
| | | | - Kondapalli Venkata Gowri Chandra Sekhar
- Department of Chemistry, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Jawahar Nagar Hyderabad 500 078 Telangana India +91 40 66303527
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13
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Batran RZ, Sabt A, Dziadek J, Kassem AF. Design, synthesis and computational studies of new azaheterocyclic coumarin derivatives as anti- Mycobacterium tuberculosis agents targeting enoyl acyl carrier protein reductase (InhA). RSC Adv 2024; 14:21763-21777. [PMID: 38984262 PMCID: PMC11232110 DOI: 10.1039/d4ra02746a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 06/17/2024] [Indexed: 07/11/2024] Open
Abstract
In this study, we designed and synthesized a series of coumarin derivatives as antitubercular agents targeting the enoyl acyl carrier protein reductase (InhA) enzyme. Among the synthesized compounds, the tetrazole derivative 4c showed the most potent antitubercular effect with a minimum inhibitory concentration value (MIC) of 15 μg mL-1 against Mtb H37Rv and could also inhibit the growth of the mutant strain (ΔkatG). Compound 4c was able to penetrate Mtb-infected human macrophages and suppress the intracellular growth of tubercle bacilli. Moreover, the target derivative 4c showed a potent inhibitory effect against InhA enzyme with an IC50 value of 0.565 μM, which was superior to the reference InhA inhibitor triclosan. Molecular docking of compound 4c within the InhA active site revealed the importance of the 4-phenylcoumarin ring system and tetrazole moiety for activity. Finally, the physicochemical properties and pharmacokinetic parameters of 4c were investigated.
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Affiliation(s)
- Rasha Z Batran
- Chemistry of Natural Compounds Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre Dokki Cairo 12622 Egypt
| | - Ahmed Sabt
- Chemistry of Natural Compounds Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre Dokki Cairo 12622 Egypt
| | - Jarosław Dziadek
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology of the Polish Academy of Sciences Lodz Poland
| | - Asmaa F Kassem
- Chemistry of Natural and Microbial Products Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre Dokki Cairo 12622 Egypt
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14
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Xiao B, Feng X, Li P, Sui Z. Analysis of Hyperosmotic Tolerance Mechanisms in Gracilariopsis lemaneiformis Based on Weighted Co-Expression Network Analysis. Genes (Basel) 2024; 15:781. [PMID: 38927717 PMCID: PMC11203144 DOI: 10.3390/genes15060781] [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: 05/10/2024] [Revised: 06/07/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
We conducted transcriptome sequencing on salt-tolerant mutants X5 and X3, and a control (Ctr) strain of Gracilariopsis lemaneiformis after treatment with artificial seawater at varying salinities (30‱, 45‱, and 60‱) for 3 weeks. Differentially expressed genes were identified and a weighted co-expression network analysis was conducted. The blue, red, and tan modules were most closely associated with salinity, while the black, cyan, light cyan, and yellow modules showed a close correlation with strain attributes. KEGG enrichment of genes from the aforementioned modules revealed that the key enrichment pathways for salinity attributes included the proteasome and carbon fixation in photosynthesis, whereas the key pathways for strain attributes consisted of lipid metabolism, oxidative phosphorylation, soluble N-ethylmaleimide-sensitive factor-activating protein receptor (SNARE) interactions in vesicular transport, and porphyrin and chlorophyll metabolism. Gene expression for the proteasome and carbon fixation in photosynthesis was higher in all strains at 60‱. In addition, gene expression in the proteasome pathway was higher in the X5-60 than Ctr-60 and X3-60. Based on the above data and relevant literature, we speculated that mutant X5 likely copes with high salt stress by upregulating genes related to lysosome and carbon fixation in photosynthesis. The proteasome may be reset to adjust the organism's proteome composition to adapt to high-salt environments, while carbon fixation may aid in maintaining material and energy metabolism for normal life activities by enhancing carbon dioxide uptake via photosynthesis. The differences between the X5-30 and Ctr-30 expression of genes involved in the synthesis of secondary metabolites, oxidative phosphorylation, and SNARE interactions in vesicular transport suggested that the X5-30 may differ from Ctr-30 in lipid metabolism, energy metabolism, and vesicular transport. Finally, among the key pathways with good correlation with salinity and strain traits, the key genes with significant correlation with salinity and strain traits were identified by correlation analysis.
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Affiliation(s)
| | | | | | - Zhenghong Sui
- Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Ministry of Education, Qingdao 266003, China; (B.X.); (X.F.); (P.L.)
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15
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Chikhale RV, Abdelghani HTM, Deka H, Pawar AD, Patil PC, Bhowmick S. Machine learning assisted methods for the identification of low toxicity inhibitors of Enoyl-Acyl Carrier Protein Reductase (InhA). Comput Biol Chem 2024; 110:108034. [PMID: 38430612 DOI: 10.1016/j.compbiolchem.2024.108034] [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: 11/30/2023] [Revised: 01/20/2024] [Accepted: 02/18/2024] [Indexed: 03/05/2024]
Abstract
Tuberculosis (TB) is one of the life-threatening infectious diseases with prehistoric origins and occurs in almost all habitable parts of the world. TB mainly affects the lungs, and its etiological agent is Mycobacterium tuberculosis (Mtb). In 2022, more than 10 million people were infected worldwide, and 1.3 million were children. The current study considered the in-silico and machine learning (ML) approaches to explore the potential anti-TB molecules from the SelleckChem database against Enoyl-Acyl Carrier Protein Reductase (InhA). Initially, the entire database of ∼ 119000 molecules was sorted out through drug-likeness. Further, the molecular docking study was conducted to reduce the chemical space. The standard TB drug molecule's binding energy was considered a threshold, and molecules found with lower affinity were removed for further analyses. Finally, the molecules were checked for the pharmacokinetic and toxicity studies, and compounds found to have acceptable pharmacokinetic parameters and were non-toxic were considered as final promising molecules for InhA. The above approach further evaluated five molecules for ML-based toxicity and synthetic accessibility assessment. Not a single molecule was found toxic and each of them was revealed as easy to synthesise. The complex between InhA and proposed and standard molecules was considered for molecular dynamics simulation. Several statistical parameters showed the stability between InhA and the proposed molecule. The high binding affinity was also found for each of the molecules towards InhA using the MM-GBSA approach. Hence, the above approaches and findings exposed the potentiality of the proposed molecules against InhA.
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Affiliation(s)
- Rupesh V Chikhale
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College London, London, UK
| | - Heba Taha M Abdelghani
- Department of Exercise Physiology, College of Sport Sciences and Physical Activity, King Saud University, Riyadh 11451, Saudi Arabia
| | - Hemchandra Deka
- SilicoScientia Private Limited, Nagananda Commercial Complex, No. 07/3, 15/1, 18th Main Road, Jayanagar 9th Block, Bengaluru 560041, India
| | - Atul Darasing Pawar
- SilicoScientia Private Limited, Nagananda Commercial Complex, No. 07/3, 15/1, 18th Main Road, Jayanagar 9th Block, Bengaluru 560041, India
| | - Pritee Chunarkar Patil
- Department of Bioinformatics, Rajiv Gandhi Institute of IT and Biotechnology, Bharati Vidyapeeth (Deemed to be University), Pune-Satara Road, Pune, India
| | - Shovonlal Bhowmick
- SilicoScientia Private Limited, Nagananda Commercial Complex, No. 07/3, 15/1, 18th Main Road, Jayanagar 9th Block, Bengaluru 560041, India.
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16
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Wahan SK, Bhargava G, Chawla V, Chawla PA. Unlocking InhA: Novel approaches to inhibit Mycobacterium tuberculosis. Bioorg Chem 2024; 146:107250. [PMID: 38460337 DOI: 10.1016/j.bioorg.2024.107250] [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: 12/21/2023] [Revised: 01/29/2024] [Accepted: 02/28/2024] [Indexed: 03/11/2024]
Abstract
Multidrug-resistant tuberculosis continues to pose a health security risk and remains a public health emergency. Antimicrobial resistance result from treatment regimens that are both insufficient and incomplete leading to the emergence of multidrug-resistant tuberculosis, extensively drug-resistant tuberculosis and totally drug-resistant tuberculosis. The impact of tuberculosis on the people suffering from HIV (Human immunodeficiency virus infection) have resulted in the increased research efforts in designing and discovery of novel antitubercular drugs that may result in decreasing treatment duration, minimising the need for multiple drug intake, minimising cytotoxicity and enhancing the mechanism of action of drug. While many drugs are available to treat tuberculosis, a precise and timely cure is still absent. Consequently, further investigation is needed to identify more recent molecular equivalents that have the potential to swiftly remove this disease. Isoniazid (INH), a treatment for tuberculosis (TB), targets the enzyme InhA (mycobacterium enoyl acyl carrier protein reductase), the Mycobacterium tuberculosis enoyl-acyl carrier protein (ACP) reductase, most common INH resistance is circumvented by InhA inhibitors that do not require KatG (catalase-peroxidase) activation, as a result, researchers are trying to work in the area of development of InhA inhibitors which could help in eradicating the era of tuberculosis from the world.
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Affiliation(s)
- Simranpreet K Wahan
- Department of Chemical Sciences, I.K. Gujral Punjab Technical University, Kapurthala, India
| | - Gaurav Bhargava
- Department of Chemical Sciences, I.K. Gujral Punjab Technical University, Kapurthala, India
| | - Viney Chawla
- University Institute of Pharmaceutical Sciences and Research, Baba Farid University of Health Sciences, Faridkot, Punjab 151203, India
| | - Pooja A Chawla
- University Institute of Pharmaceutical Sciences and Research, Baba Farid University of Health Sciences, Faridkot, Punjab 151203, India.
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17
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Xiong XS, Zhang XD, Yan JW, Huang TT, Liu ZZ, Li ZK, Wang L, Li F. Identification of Mycobacterium tuberculosis Resistance to Common Antibiotics: An Overview of Current Methods and Techniques. Infect Drug Resist 2024; 17:1491-1506. [PMID: 38628245 PMCID: PMC11020249 DOI: 10.2147/idr.s457308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 03/26/2024] [Indexed: 04/19/2024] Open
Abstract
Multidrug-resistant tuberculosis (MDR-TB) is an essential cause of tuberculosis treatment failure and death of tuberculosis patients. The rapid and reliable profiling of Mycobacterium tuberculosis (MTB) drug resistance in the early stage is a critical research area for public health. Then, most traditional approaches for detecting MTB are time-consuming and costly, leading to the inappropriate therapeutic schedule resting on the ambiguous information of MTB drug resistance, increasing patient economic burden, morbidity, and mortality. Therefore, novel diagnosis methods are frequently required to meet the emerging challenges of MTB drug resistance distinguish. Considering the difficulty in treating MDR-TB, it is urgently required for the development of rapid and accurate methods in the identification of drug resistance profiles of MTB in clinical diagnosis. This review discussed recent advances in MTB drug resistance detection, focusing on developing emerging approaches and their applications in tangled clinical situations. In particular, a brief overview of antibiotic resistance to MTB was present, referred to as intrinsic bacterial resistance, consisting of cell wall barriers and efflux pumping action and acquired resistance caused by genetic mutations. Then, different drug susceptibility test (DST) methods were described, including phenotype DST, genotype DST and novel DST methods. The phenotype DST includes nitrate reductase assay, RocheTM solid ratio method, and liquid culture method and genotype DST includes fluorescent PCR, GeneXpert, PCR reverse dot hybridization, ddPCR, next-generation sequencing and gene chips. Then, novel DST methods were described, including metabolism testing, cell-free DNA probe, CRISPR assay, and spectral analysis technique. The limitations, challenges, and perspectives of different techniques for drug resistance are also discussed. These methods significantly improve the detection sensitivity and accuracy of multidrug-resistant tuberculosis (MRT) and can effectively curb the incidence of drug-resistant tuberculosis and accelerate the process of tuberculosis eradication.
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Affiliation(s)
- Xue-Song Xiong
- Department of Laboratory Medicine, The Affiliated Huai’an Hospital of Yangzhou University, Huai’an, Jiangsu Province, People’s Republic of China
- Department of Laboratory Medicine, The Fifth People’s Hospital of Huai’an, Huai’an, Jiangsu Province, People’s Republic of China
| | - Xue-Di Zhang
- Department of Laboratory Medicine, Xuzhou Infectious Diseases Hospital, Xuzhou, Jiangsu Province, People’s Republic of China
| | - Jia-Wei Yan
- Department of Laboratory Medicine, Xuzhou Infectious Diseases Hospital, Xuzhou, Jiangsu Province, People’s Republic of China
| | - Ting-Ting Huang
- Department of Laboratory Medicine, The Affiliated Huai’an Hospital of Yangzhou University, Huai’an, Jiangsu Province, People’s Republic of China
- Department of Laboratory Medicine, The Fifth People’s Hospital of Huai’an, Huai’an, Jiangsu Province, People’s Republic of China
| | - Zhan-Zhong Liu
- Department of Pharmacy, Xuzhou Infectious Diseases Hospital, Xuzhou, Jiangsu Province, People’s Republic of China
| | - Zheng-Kang Li
- Department of Laboratory Medicine, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong Province, People’s Republic of China
| | - Liang Wang
- Department of Laboratory Medicine, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong Province, People’s Republic of China
| | - Fen Li
- Department of Laboratory Medicine, The Affiliated Huai’an Hospital of Yangzhou University, Huai’an, Jiangsu Province, People’s Republic of China
- Department of Laboratory Medicine, The Fifth People’s Hospital of Huai’an, Huai’an, Jiangsu Province, People’s Republic of China
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18
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Canales CSC, Pavan AR, Dos Santos JL, Pavan FR. In silico drug design strategies for discovering novel tuberculosis therapeutics. Expert Opin Drug Discov 2024; 19:471-491. [PMID: 38374606 DOI: 10.1080/17460441.2024.2319042] [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: 11/08/2023] [Accepted: 02/12/2024] [Indexed: 02/21/2024]
Abstract
INTRODUCTION Tuberculosis remains a significant concern in global public health due to its intricate biology and propensity for developing antibiotic resistance. Discovering new drugs is a protracted and expensive endeavor, often spanning over a decade and incurring costs in the billions. However, computer-aided drug design (CADD) has surfaced as a nimbler and more cost-effective alternative. CADD tools enable us to decipher the interactions between therapeutic targets and novel drugs, making them invaluable in the quest for new tuberculosis treatments. AREAS COVERED In this review, the authors explore recent advancements in tuberculosis drug discovery enabled by in silico tools. The main objectives of this review article are to highlight emerging drug candidates identified through in silico methods and to provide an update on the therapeutic targets associated with Mycobacterium tuberculosis. EXPERT OPINION These in silico methods have not only streamlined the drug discovery process but also opened up new horizons for finding novel drug candidates and repositioning existing ones. The continued advancements in these fields hold great promise for more efficient, ethical, and successful drug development in the future.
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Affiliation(s)
- Christian S Carnero Canales
- School of Pharmaceutical Science, São Paulo State University (UNESP), Araraquara, Brazil
- School of Pharmacy, biochemistry and biotechnology, Santa Maria Catholic University, Arequipa, Perú
| | - Aline Renata Pavan
- School of Pharmaceutical Science, São Paulo State University (UNESP), Araraquara, Brazil
| | | | - Fernando Rogério Pavan
- School of Pharmaceutical Science, São Paulo State University (UNESP), Araraquara, Brazil
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19
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Chikhale RV, Eldesoky GE, Kolpe MS, Suryawanshi VS, Patil PC, Bhowmick S. Identification of Mycobacterium tuberculosis transcriptional repressor EthR inhibitors: Shape-based search and machine learning studies. Heliyon 2024; 10:e26802. [PMID: 38434349 PMCID: PMC10907797 DOI: 10.1016/j.heliyon.2024.e26802] [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: 11/09/2023] [Revised: 01/16/2024] [Accepted: 02/20/2024] [Indexed: 03/05/2024] Open
Abstract
Tuberculosis has been a challenge to the world since prehistoric times, and with the advent of drug-resistant strains, it has become more challenging to treat this infection. Ethionamide (ETH), a second-line drug, acts as a prodrug and targets mycolic acid synthesis by targeting the enoyl-acyl carrier protein reductase (InhA) enzyme. Mycobacterium tuberculosis (Mtb) EthR is an ethA gene repressor required to activate prodrug ETH. Recent studies suggest targeting the EthR could lead to newer drug molecules that would help better activate the ETH or complement this process. In this report, we have attempted and successfully identified three new molecules from the drug repurposing library that can target EthR protein and function as ETH boosters. These molecules were obtained after rigorous filtering of the database for their physicochemical, toxicological properties and safety. The molecular docking, molecular dynamics simulations and binding energy studies yielded three compounds, Ethyl (2-amino-4-((4-fluorobenzyl)amino)phenyl)carbamate) (L1), 2-((2,2-Difluorobenzo [d] [1,3]dioxol-5-yl)amino)-2-oxoethyl (E)-3-(5-bromofuran-2-yl)acrylate (L2), and N-(2,3-Dihydrobenzo [b] [1,4]dioxin-6-yl)-4-(2-((4-fluorophenyl)amino)-2-oxoethoxy)-3-methoxy benzamide (L3) are potential EthR inhibitors. We applied machine learning methods to evaluate these molecules for toxicity and synthesisability, suggesting safety and ease of synthesis for these molecules. These molecules are known for other pharmacological activities and can be repurposed faster as adjuvant therapy for tuberculosis.
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Affiliation(s)
- Rupesh V. Chikhale
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College London, London, UK
| | - Gaber E. Eldesoky
- Chemistry Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Mahima Sudhir Kolpe
- SilicoScientia Private Limited, Nagananda Commercial Complex, No. 07/3, 15/1, 18th Main Road, Jayanagar 9th Block, Bengaluru, 560041, India
| | - Vikramsinh Sardarsinh Suryawanshi
- SilicoScientia Private Limited, Nagananda Commercial Complex, No. 07/3, 15/1, 18th Main Road, Jayanagar 9th Block, Bengaluru, 560041, India
| | - Pritee Chunarkar Patil
- Department of Bioinformatics, Rajiv Gandhi Institute of IT and Biotechnology, Bharati Vidyapeeth Deemed to be University, Pune-Satara Road, Pune, India
| | - Shovonlal Bhowmick
- SilicoScientia Private Limited, Nagananda Commercial Complex, No. 07/3, 15/1, 18th Main Road, Jayanagar 9th Block, Bengaluru, 560041, India
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Shekhar, Alcaraz M, Seboletswe P, Manhas N, Kremer L, Singh P, Kumar V. Tailoring selective triclosan azo-adducts: Design, synthesis, and anti-mycobacterial evaluation. Heliyon 2023; 9:e22182. [PMID: 38034623 PMCID: PMC10685269 DOI: 10.1016/j.heliyon.2023.e22182] [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] [Received: 05/29/2023] [Revised: 11/04/2023] [Accepted: 11/06/2023] [Indexed: 12/02/2023] Open
Abstract
A series of triclosan azo-adducts were synthesized to investigate their structure-activity relationship against Mycobacterium tuberculosis and non-tuberculous mycobacteria. The series' most potent compound was four and sixteen times more active than triclosan and rifabutin against drug-resistant Mycobacterium abscessus, respectively, while being less cytotoxic to human macrophages than triclosan on day one. Additionally, one of the azo-adducts was twice as efficient against M. tuberculosis as triclosan and twice as effective against Mycobacterium marinum as isoniazid. Furthermore, the synthesized azo-adducts were equally effective against M. abscessus strains overexpressing InhA, suggesting that these compounds work through a distinct mechanism.
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Affiliation(s)
- Shekhar
- Department of Chemistry, Guru Nanak Dev University, Amritsar, India
| | - Matthéo Alcaraz
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, 1919 route de Mende, 34293, Montpellier, France
| | - Pule Seboletswe
- School of Chemistry and Physics, University of KwaZulu-Natal, P/Bag X54001, Westville, Durban, South Africa
| | - Neha Manhas
- School of Chemistry and Physics, University of KwaZulu-Natal, P/Bag X54001, Westville, Durban, South Africa
| | - Laurent Kremer
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, 1919 route de Mende, 34293, Montpellier, France
- INSERM, IRIM, 34293 Montpellier, France
| | - Parvesh Singh
- School of Chemistry and Physics, University of KwaZulu-Natal, P/Bag X54001, Westville, Durban, South Africa
| | - Vipan Kumar
- Department of Chemistry, Guru Nanak Dev University, Amritsar, India
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21
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Özcan E, Vagolu SK, Gündüz MG, Stevanovic M, Kökbudak Z, Tønjum T, Nikodinovic-Runic J, Çetinkaya Y, Doğan ŞD. Novel Quinoline-Based Thiosemicarbazide Derivatives: Synthesis, DFT Calculations, and Investigation of Antitubercular, Antibacterial, and Antifungal Activities. ACS OMEGA 2023; 8:40140-40152. [PMID: 37929089 PMCID: PMC10620885 DOI: 10.1021/acsomega.3c03018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 09/12/2023] [Indexed: 11/07/2023]
Abstract
The discovery of new antimicrobial agents as a means of treating drug-resistant microbial pathogens is of utmost significance to overcome their immense risk to human well-being. The current investigation involves the development, synthesis, and assessment of the antimicrobial efficacy of novel quinoline derivatives incorporating a thiosemicarbazide functionality. To design the target compounds (QST1-QST14), we applied the molecular hybridization approach to link various thiosemicarbazides to the quinoline core with a sulfonyl group. Upon the synthesis and completion of structural characterization via spectroscopic techniques (1H NMR, 13C NMR, 15N NMR, IR, and HRMS), the title molecules were extensively evaluated for their potential antitubercular, antibacterial, and antifungal activities. N-(3-Chlorophenyl)-2-(quinolin-8-ylsulfonyl)hydrazine-1-carbothioamide (QST4), the most effective compound against Mycobacterium tuberculosis H37Rv, was also tested on isoniazid-resistant clinical isolates with katG and inhA promoter mutations. Based on molecular docking studies, QST4 was also likely to demonstrate its antimycobacterial activity through inhibition of the InhA enzyme. Furthermore, three derivatives (QST3, QST4, and QST10) with preferable antimicrobial and drug-like profiles were also shown to be nontoxic against human embryonic kidney (HEK) cells. All compounds were optimized by the density functional theory method using B3LYP with the 6-31+G(d,p) basis set. Structural analysis, natural bond orbital calculations of donor-acceptor interactions, molecular electrostatic potential analysis, and frontier molecular orbital analysis were carried out. Quantum chemical descriptors and charges on the atoms were determined to compare the strengths of the intramolecular hydrogen bonds formed and their stabilities. We determined that the sulfur atom forms a stronger intramolecular hydrogen bond than the nitrogen, oxygen, and fluorine atoms in these sulfonyl thiosemicarbazide derivatives.
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Affiliation(s)
- Esma Özcan
- Department
of Chemistry, Faculty of Science, Erciyes
University, 38039 Kayseri, Turkey
- Department
of Basic Sciences, Faculty of Pharmacy, Erciyes University, 38039 Kayseri, Turkey
| | - Siva Krishna Vagolu
- Unit
for Genome Dynamics, Department of Microbiology, University of Oslo, 0316 Oslo, Norway
| | - Miyase Gözde Gündüz
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, Hacettepe University, Sıhhiye, 06100 Ankara, Turkey
| | - Milena Stevanovic
- Institute
of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000 Belgrade, Serbia
| | - Zülbiye Kökbudak
- Department
of Chemistry, Faculty of Science, Erciyes
University, 38039 Kayseri, Turkey
| | - Tone Tønjum
- Unit
for Genome Dynamics, Department of Microbiology, University of Oslo, 0316 Oslo, Norway
- Unit for
Genome Dynamics, Department of Microbiology, Oslo University Hospital, 0316 Oslo, Norway
| | - Jasmina Nikodinovic-Runic
- Institute
of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000 Belgrade, Serbia
| | - Yasin Çetinkaya
- Department
of Chemistry, Faculty of Science, Atatürk
University, 25240 Erzurum, Turkey
| | - Şengül Dilem Doğan
- Department
of Basic Sciences, Faculty of Pharmacy, Erciyes University, 38039 Kayseri, Turkey
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22
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Alcaraz M, Edwards TE, Kremer L. New therapeutic strategies for Mycobacterium abscessus pulmonary diseases - untapping the mycolic acid pathway. Expert Rev Anti Infect Ther 2023; 21:813-829. [PMID: 37314394 PMCID: PMC10529309 DOI: 10.1080/14787210.2023.2224563] [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: 02/28/2023] [Accepted: 06/08/2023] [Indexed: 06/15/2023]
Abstract
INTRODUCTION Treatment options against Mycobacterium abscessus infections are very limited. New compounds are needed to cure M. abscessus pulmonary diseases. While the mycolic acid biosynthetic pathway has been largely exploited for the treatment of tuberculosis, this metabolic process has been overlooked in M. abscessus, although it offers many potential drug targets for the treatment of this opportunistic pathogen. AREAS COVERED Herein, the authors review the role of the MmpL3 membrane protein and the enoyl-ACP reductase InhA involved in the transport and synthesis of mycolic acids, respectively. They discuss their importance as two major vulnerable drug targets in M. abscessus and report the activity of MmpL3 and InhA inhibitors. In particular, they focus on NITD-916, a direct InhA inhibitor against M. abscessus, particularly warranted in the context of multidrug resistance. EXPERT OPINION There is an increasing body of evidence validating the mycolic acid pathway as an attractive drug target to be further exploited for M. abscessus lung disease treatments. The NITD-916 studies provide a proof-of-concept that direct inhibitors of InhA are efficient in vitro, in macrophages and in zebrafish. Future work is now required to improve the activity and pharmacological properties of these inhibitors and their evaluation in pre-clinical models.
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Affiliation(s)
- Matthéo Alcaraz
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, 1919 route de Mende, 34293, Montpellier, France
| | - Thomas E. Edwards
- UCB BioSciences, Bainbridge Island, WA 98109 USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109 USA
| | - Laurent Kremer
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, 1919 route de Mende, 34293, Montpellier, France
- INSERM, IRIM, 34293 Montpellier, France
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23
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Roquet-Banères F, Alcaraz M, Hamela C, Abendroth J, Edwards TE, Kremer L. In Vitro and In Vivo Efficacy of NITD-916 against Mycobacterium fortuitum. Antimicrob Agents Chemother 2023; 67:e0160722. [PMID: 36920188 PMCID: PMC10112203 DOI: 10.1128/aac.01607-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/16/2023] [Indexed: 03/16/2023] Open
Abstract
Mycobacterium fortuitum represents one of the most clinically relevant rapid-growing mycobacterial species. Treatments are complex due to antibiotic resistance and to severe side effects of effective drugs, prolonged time of treatment, and co-infection with other pathogens. Herein, we explored the activity of NITD-916, a direct inhibitor of the enoyl-ACP reductase InhA of the type II fatty acid synthase in Mycobacterium tuberculosis. We found that this compound displayed very low MIC values against a panel of M. fortuitum clinical strains and exerted potent antimicrobial activity against M. fortuitum in macrophages. Remarkably, the compound was also highly efficacious in a zebrafish model of infection. Short duration treatments were sufficient to significantly protect the infected larvae from M. fortuitum-induced killing, which correlated with reduced bacterial burdens and abscesses. Biochemical analyses demonstrated an inhibition of de novo synthesis of mycolic acids. Resolving the crystal structure of the InhAMFO in complex with NAD and NITD-916 confirmed that NITD-916 is a direct inhibitor of InhAMFO. Importantly, single nucleotide polymorphism leading to a G96S substitution in InhAMFO conferred high resistance levels to NITD-916, thus resolving its target in M. fortuitum. Overall, these findings indicate that NITD-916 is highly active against M. fortuitum both in vitro and in vivo and should be considered in future preclinical evaluations for the treatment of M. fortuitum pulmonary diseases.
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Affiliation(s)
- Françoise Roquet-Banères
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France
| | - Matthéo Alcaraz
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France
| | - Claire Hamela
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France
| | - Jan Abendroth
- UCB BioSciences, Bainbridge Island, Washington, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | - Thomas E. Edwards
- UCB BioSciences, Bainbridge Island, Washington, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | - Laurent Kremer
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France
- INSERM, IRIM, Montpellier, France
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24
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Teneva Y, Simeonova R, Valcheva V, Angelova VT. Recent Advances in Anti-Tuberculosis Drug Discovery Based on Hydrazide-Hydrazone and Thiadiazole Derivatives Targeting InhA. Pharmaceuticals (Basel) 2023; 16:ph16040484. [PMID: 37111241 PMCID: PMC10140854 DOI: 10.3390/ph16040484] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/15/2023] [Accepted: 03/21/2023] [Indexed: 04/29/2023] Open
Abstract
Tuberculosis is an extremely serious problem of global public health. Its incidence is worsened by the presence of multidrug-resistant (MDR) strains of Mycobacterium tuberculosis. More serious forms of drug resistance have been observed in recent years. Therefore, the discovery and/or synthesis of new potent and less toxic anti-tubercular compounds is very critical, especially having in mind the consequences and the delays in treatment caused by the COVID-19 pandemic. Enoyl-acyl carrier protein reductase (InhA) is an important enzyme involved in the biosynthesis of mycolic acid, a major component of the M. tuberculosis cell wall. At the same time, it is a key enzyme in the development of drug resistance, making it an important target for the discovery of new antimycobacterial agents. Many different chemical scaffolds, including hydrazide hydrazones and thiadiazoles, have been evaluated for their InhA inhibitory activity. The aim of this review is to evaluate recently described hydrazide-hydrazone- and thiadiazole-containing derivatives that inhibit InhA activity, resulting in antimycobacterial effects. In addition, a brief review of the mechanisms of action of currently available anti-tuberculosis drugs is provided, including recently approved agents and molecules in clinical trials.
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Affiliation(s)
- Yoanna Teneva
- Faculty of Pharmacy, Medical University of Sofia, 1000 Sofia, Bulgaria
| | - Rumyana Simeonova
- Faculty of Pharmacy, Medical University of Sofia, 1000 Sofia, Bulgaria
| | - Violeta Valcheva
- The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
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25
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Sulistyowaty MI, Putra GS, Ekowati J, Widiandani T, Matsunami K. <em>In silico</em> study of phytochemicals contained in brucea javanica in inhibiting the InhA enzyme as antituberculosis. J Public Health Afr 2023. [PMID: 37492543 PMCID: PMC10365667 DOI: 10.4081/jphia.2023.2518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
Abstract
Background: Currently Mycobacterium tuberculosis is found to be resistant to the treatment of tuberculosis with rifampin and isoniazid (INH) and often stated as multi-drug resistance (MDR). Knowledge and determination of biological properties of plant extracts is a source of drug candidates in various health fields. Therefore, natural products are important in the discovery of new drugs, especially in disease therapy, particularly for tropical dis- eases, tuberculosis. Brucea javanica, known as Buah Makasar, is found in many Asian countries including Indonesia. This plant fruit has a very bitter taste so it cannot be directly consumed and is often used as a traditional medicine to prevent some diseases, especially malaria. There has been no research on the effectiveness of Buah Makasar in tuberculosis.
Objective: This study aims to identify compounds contained in Brucea javanica, namely bruceines, bruceosides and yadanzio-sides in inhibiting the InhA enzyme found in the wall of Mycobacterium tuberculosis.
Methods: This in-silico study is using Molegro Virtual Docker (MVD) Ver. 5.5. We compared it to the native ligand, namely N-(4- Methylbenzoyl)-4-Benzylpiperidine (code: 4PI) and the reference drug standard, INH.
Results: In-silico results show that yadanziosides found in Brucea javanica have the potential to inhibit the InhA enzyme. Bruceoside F (-190.76 Kcal/mol) has the lowest MolDock score among the 27 other compounds. It is also having lower MolDock score than the native ligand 4PI (-120.61 Kcal/mol) and INH (- 54.44 Kcal/mol).
Conclusions: Brucea javanica can be considered as source of drug development for againts tuberculosis.
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26
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Xu X, Dong B, Peng L, Gao C, He Z, Wang C, Zeng J. Anti-tuberculosis drug development via targeting the cell envelope of Mycobacterium tuberculosis. Front Microbiol 2022; 13:1056608. [PMID: 36620019 PMCID: PMC9810820 DOI: 10.3389/fmicb.2022.1056608] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/25/2022] [Indexed: 12/24/2022] Open
Abstract
Mycobacterium tuberculosis possesses a dynamic cell envelope, which consists of a peptidoglycan layer, a mycolic acid layer, and an arabinogalactan polysaccharide. This envelope possesses a highly complex and unique structure representing a barrier that protects and assists the growth of M. tuberculosis and allows its adaptation to the host. It regulates the immune response of the host cells, causing their damage. Therefore, the cell envelope of M. tuberculosis is an attractive target for vaccine and drug development. The emergence of multidrug-resistant as well as extensively drug resistant tuberculosis and co-infection with HIV prevented an effective control of this disease. Thus, the discovery and development of new drugs is a major keystone for TB treatment and control. This review mainly summarizes the development of drug enzymes involved in the biosynthesis of the cell wall in M. tuberculosis, and other potential drug targets in this pathway, to provide more effective strategies for the development of new drugs.
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Affiliation(s)
- Xinyue Xu
- West China-PUMC CC Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Baoyu Dong
- West China-PUMC CC Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Lijun Peng
- West China-PUMC CC Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Chao Gao
- State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China.,Laboratory of Human Diseases and Immunotherapies, West China Hospital, Sichuan University, Chengdu, China
| | - Zhiqun He
- West China-PUMC CC Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Chuan Wang
- West China-PUMC CC Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Jumei Zeng
- West China-PUMC CC Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
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27
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Li S, Chen W, Feng M, Liu Y, Wang F. Drug Resistance and Molecular Characteristics of Mycobacterium tuberculosis: A Single Center Experience. J Pers Med 2022; 12:jpm12122088. [PMID: 36556308 PMCID: PMC9783070 DOI: 10.3390/jpm12122088] [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: 11/17/2022] [Revised: 12/11/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
In recent years, the incidence of tuberculosis (TB) and mortality caused by the disease have been decreasing. However, the number of drug-resistant tuberculosis patients is increasing rapidly year by year. Here, a total of 380 Mycobacterium tuberculosis (MTB)-positive formalin-fixed and paraffin-embedded tissue (FFPE) specimens diagnosed in the Department of Pathology of the Eighth Medical Center, Chinese PLA General Hospital were collected. Among 380 cases of MTB, 85 (22.37%) were susceptible to four anti-TB drugs and the remaining 295 (77.63%) were resistant to one or more drugs. The rate of MDR-TB was higher in previously treated cases (52.53%) than in new cases [(36.65%), p < 0.05]. Of previously treated cases, the rate of drug resistance was higher in females than in males (p < 0.05). Among specimens obtained from males, the rate of drug resistance was higher in new cases than in previously treated cases (p < 0.05). Of mutation in drug resistance-related genes, the majority (53/380, 13.95%) of rpoB gene carried the D516V mutation, and 13.42% (51/380) featured mutations in both the katG and inhA genes. Among the total specimens, 18.68% (71/380) carried the 88 M mutation in the rpsL gene, and the embB gene focused on the 306 M2 mutation with a mutation rate of 19.74%. Among the resistant INH, the mutation rate of −15 M was higher in resistance to more than one drug than in monodrug-resistant (p < 0.05). In conclusion, the drug resistance of MTB is still very severe and the timely detection of drug resistance is conducive to the precise treatment of TB.
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28
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Paz JD, Denise de Moura Sperotto N, Ramos AS, Pissinate K, da Silva Rodrigues Junior V, Abbadi BL, Borsoi AF, Rambo RS, Corso Minotto AC, da Silva Dadda A, Galina L, Macchi Hopf FS, Muniz MN, Borges Martinelli LK, Roth CD, Madeira Silva RB, Perelló MA, de Matos Czeczot A, Neves CE, Duarte LS, Leyser M, Dias de Oliveira S, Bizarro CV, Machado P, Basso LA. Novel 4-aminoquinolines: Synthesis, inhibition of the Mycobacterium tuberculosis enoyl-acyl carrier protein reductase, antitubercular activity, SAR, and preclinical evaluation. Eur J Med Chem 2022; 245:114908. [DOI: 10.1016/j.ejmech.2022.114908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/25/2022] [Accepted: 11/03/2022] [Indexed: 11/19/2022]
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29
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Koçak Aslan E, Han Mİ, Krishna VS, Tamhaev R, Dengiz C, Doğan ŞD, Lherbet C, Mourey L, Tønjum T, Gündüz MG. Isoniazid Linked to Sulfonate Esters via Hydrazone Functionality: Design, Synthesis, and Evaluation of Antitubercular Activity. Pharmaceuticals (Basel) 2022; 15:ph15101301. [PMID: 36297413 PMCID: PMC9609273 DOI: 10.3390/ph15101301] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/16/2022] [Accepted: 10/19/2022] [Indexed: 01/24/2023] Open
Abstract
Isoniazid (INH) is one of the key molecules employed in the treatment of tuberculosis (TB), the most deadly infectious disease worldwide. However, the efficacy of this cornerstone drug has seriously decreased due to emerging INH-resistant strains of Mycobacterium tuberculosis (Mtb). In the present study, we aimed to chemically tailor INH to overcome this resistance. We obtained thirteen novel compounds by linking INH to in-house synthesized sulfonate esters via a hydrazone bridge (SIH1-SIH13). Following structural characterization by FTIR, 1H NMR, 13C NMR, and HRMS, all compounds were screened for their antitubercular activity against Mtb H37Rv strain and INH-resistant clinical isolates carrying katG and inhA mutations. Additionally, the cytotoxic effects of SIH1-SIH13 were assessed on three different healthy host cell lines; HEK293, IMR-90, and BEAS-2B. Based on the obtained data, the synthesized compounds appeared as attractive antimycobacterial drug candidates with low cytotoxicity. Moreover, the stability of the hydrazone moiety in the chemical structure of the final compounds was confirmed by using UV/Vis spectroscopy in both aqueous medium and DMSO. Subsequently, the compounds were tested for their inhibitory activities against enoyl acyl carrier protein reductase (InhA), the primary target enzyme of INH. Although most of the synthesized compounds are hosted by the InhA binding pocket, SIH1-SIH13 do not primarily show their antitubercular activities by direct InhA inhibition. Finally, in silico determination of important physicochemical parameters of the molecules showed that SIH1-SIH13 adhered to Lipinski's rule of five. Overall, our study revealed a new strategy for modifying INH to cope with the emerging drug-resistant strains of Mtb.
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Affiliation(s)
- Ebru Koçak Aslan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Hacettepe University, Sıhhiye, Ankara 06100, Turkey
| | - Muhammed İhsan Han
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri 38039, Turkey
| | - Vagolu Siva Krishna
- Unit for Genome Dynamics, Department of Microbiology, University of Oslo, 0316 Oslo, Norway
| | - Rasoul Tamhaev
- LSPCMIB, UMR-CNRS 5068, Université Paul Sabatier-Toulouse III, 118 Route de Narbonne, CEDEX 9, 31062 Toulouse, France
- Institut de Pharmacologie et de Biologie Structurale, Université Toulouse III—Paul Sabatier, Centre National de la Recherche Scientifique, 31077 Toulouse, France
| | - Cagatay Dengiz
- Department of Chemistry, Middle East Technical University, Ankara 06800, Turkey
| | - Şengül Dilem Doğan
- Department of Basic Sciences, Faculty of Pharmacy, Erciyes University, Kayseri 38039, Turkey
| | - Christian Lherbet
- LSPCMIB, UMR-CNRS 5068, Université Paul Sabatier-Toulouse III, 118 Route de Narbonne, CEDEX 9, 31062 Toulouse, France
| | - Lionel Mourey
- Institut de Pharmacologie et de Biologie Structurale, Université Toulouse III—Paul Sabatier, Centre National de la Recherche Scientifique, 31077 Toulouse, France
| | - Tone Tønjum
- Unit for Genome Dynamics, Department of Microbiology, University of Oslo, 0316 Oslo, Norway
- Unit for Genome Dynamics, Department of Microbiology, Oslo University Hospital, 0424 Oslo, Norway
| | - Miyase Gözde Gündüz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Hacettepe University, Sıhhiye, Ankara 06100, Turkey
- Correspondence:
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30
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Sun M, Ge S, Li Z. The Role of Phosphorylation and Acylation in the Regulation of Drug Resistance in Mycobacterium tuberculosis. Biomedicines 2022; 10:biomedicines10102592. [PMID: 36289854 PMCID: PMC9599588 DOI: 10.3390/biomedicines10102592] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/12/2022] [Accepted: 10/14/2022] [Indexed: 11/16/2022] Open
Abstract
Tuberculosis is a chronic and lethal infectious disease caused by Mycobacterium tuberculosis. In previous decades, most studies in this area focused on the pathogenesis and drug targets for disease treatments. However, the emergence of drug-resistant strains has increased the difficulty of clinical trials over time. Now, more post-translational modified proteins in Mycobacterium tuberculosis have been discovered. Evidence suggests that these proteins have the ability to influence tuberculosis drug resistance. Hence, this paper systematically summarizes updated research on the impacts of protein acylation and phosphorylation on the acquisition of drug resistance in Mycobacterium tuberculosis through acylation and phosphorylation protein regulating processes. This provides us with a better understanding of the mechanism of antituberculosis drugs and may contribute to a reduction the harm that tuberculosis brings to society, as well as aiding in the discovery of new drug targets and therapeutic regimen adjustments in the future.
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Affiliation(s)
- Manluan Sun
- School of Medicine, Shanxi Datong University, Datong 037009, China
- Institute of Carbon Materials Science, Shanxi Datong University, Datong 037009, China
- Correspondence:
| | - Sai Ge
- Institute of Carbon Materials Science, Shanxi Datong University, Datong 037009, China
- Center of Academic Journal, Shanxi Datong University, Datong 037009, China
| | - Zhaoyang Li
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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Alcaraz M, Roquet-Banères F, Leon-Icaza SA, Abendroth J, Boudehen YM, Cougoule C, Edwards TE, Kremer L. Efficacy and Mode of Action of a Direct Inhibitor of Mycobacterium abscessus InhA. ACS Infect Dis 2022; 8:2171-2186. [PMID: 36107992 DOI: 10.1021/acsinfecdis.2c00314] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
There is an unmet medical need for effective treatments against Mycobacterium abscessus pulmonary infections, to which cystic fibrosis (CF) patients are particularly vulnerable. Recent studies showed that the antitubercular drug isoniazid is inactive against M. abscessus due to the incapacity of the catalase-peroxidase to convert the pro-drug into a reactive metabolite that inhibits the enoyl-ACP reductase InhA. To validate InhAMAB as a druggable target in M. abscessus, we assayed the activity of NITD-916, a 4-hydroxy-2-pyridone lead candidate initially described as a direct inhibitor of InhA that bypasses KatG bioactivation in Mycobacterium tuberculosis. The compound displayed low MIC values against rough and smooth clinical isolates in vitro and significantly reduced the bacterial burden inside human macrophages. Moreover, treatment with NITD-916 reduced the number and size of intracellular mycobacterial cords, regarded as markers of the severity of the infection. Importantly, NITD-916 significantly lowered the M. abscessus burden in CF-derived lung airway organoids. From a mechanistic perspective, NITD-916 abrogated de novo synthesis of mycolic acids and NITD-916-resistant spontaneous mutants harbored point mutations in InhAMAB at residue 96. That NITD-916 targets InhAMAB directly without activation requirements was confirmed genetically and by resolving the crystal structure of the protein in complex with NADH and NITD-916. These findings collectively indicate that InhAMAB is an attractive target to be exploited for future chemotherapeutic developments against this difficult-to-treat mycobacterium and highlight the potential of NITD-916 derivatives for further evaluation in preclinical settings.
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Affiliation(s)
- Matthéo Alcaraz
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, 1919 route de Mende, 34293 Montpellier, France
| | - Françoise Roquet-Banères
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, 1919 route de Mende, 34293 Montpellier, France
| | - Stephen Adonai Leon-Icaza
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, 31400 Toulouse, France
| | - Jan Abendroth
- UCB BioSciences, Bainbridge Island, Washington 98109, United States.,Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
| | - Yves-Marie Boudehen
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, 1919 route de Mende, 34293 Montpellier, France
| | - Céline Cougoule
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, 31400 Toulouse, France
| | - Thomas E Edwards
- UCB BioSciences, Bainbridge Island, Washington 98109, United States.,Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
| | - Laurent Kremer
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, 1919 route de Mende, 34293 Montpellier, France.,INSERM, IRIM, 34293 Montpellier, France
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32
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Roubert C, Fontaine E, Upton AM. “Upcycling” known molecules and targets for drug-resistant TB. Front Cell Infect Microbiol 2022; 12:1029044. [PMID: 36275029 PMCID: PMC9582839 DOI: 10.3389/fcimb.2022.1029044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 09/21/2022] [Indexed: 11/13/2022] Open
Abstract
Despite reinvigorated efforts in Tuberculosis (TB) drug discovery over the past 20 years, relatively few new drugs and candidates have emerged with clear utility against drug resistant TB. Over the same period, significant technological advances and learnings around target value have taken place. This has offered opportunities to re-assess the potential for optimization of previously discovered chemical matter against Mycobacterium tuberculosis (M.tb) and for reconsideration of clinically validated targets encumbered by drug resistance. A re-assessment of discarded compounds and programs from the “golden age of antibiotics” has yielded new scaffolds and targets against TB and uncovered classes, for example beta-lactams, with previously unappreciated utility for TB. Leveraging validated classes and targets has also met with success: booster technologies and efforts to thwart efflux have improved the potential of ethionamide and spectinomycin classes. Multiple programs to rescue high value targets while avoiding cross-resistance are making progress. These attempts to make the most of known classes, drugs and targets complement efforts to discover new chemical matter against novel targets, enhancing the chances of success of discovering effective novel regimens against drug-resistant TB.
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Keleş Atıcı R, Doğan ŞD, Gündüz MG, Krishna VS, Chebaiki M, Homberset H, Lherbet C, Mourey L, Tønjum T. Urea derivatives carrying a thiophenylthiazole moiety: Design, synthesis, and evaluation of antitubercular and InhA inhibitory activities. Drug Dev Res 2022; 83:1292-1304. [PMID: 35769019 DOI: 10.1002/ddr.21958] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 05/18/2022] [Accepted: 05/24/2022] [Indexed: 11/05/2022]
Abstract
The recent emergence of drug-resistant strains of Mycobacterium tuberculosis (Mtb) has complicated and significantly slowed efforts to eradicate and/or reduce the worldwide incidence of life-threatening acute and chronic cases of tuberculosis. To overcome this setback, researchers have increased the intensity of their work to identify new small-molecule compounds that are expected to remain efficacious antimicrobials against Mtb. Here, we describe our effort to apply the principles of molecular hybridization to synthesize 16 compounds carrying thiophene and thiazole rings beside the core urea functionality (TTU1-TTU16). Following extensive structural characterization, the obtained compounds were initially evaluated for their antimycobacterial activity against Mtb H37Rv. Subsequently, three derivatives standing out with their anti-Mtb activity profiles and low cytotoxicity (TTU5, TTU6, and TTU12) were tested on isoniazid-resistant clinical isolates carrying katG and inhA mutations. Additionally, due to their pharmacophore similarities to the well-known InhA inhibitors, the molecules were screened for their enoyl acyl carrier protein reductase (InhA) inhibitory potentials. Molecular docking studies were performed to support the experimental enzyme inhibition data. Finally, drug-likeness of the selected compounds was established by theoretical calculations of physicochemical descriptors.
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Affiliation(s)
- Rüveyde Keleş Atıcı
- Department of Basic Sciences, Faculty of Pharmacy, Erciyes University, Kayseri, Turkey
| | - Şengül Dilem Doğan
- Department of Basic Sciences, Faculty of Pharmacy, Erciyes University, Kayseri, Turkey
| | - Miyase Gözde Gündüz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Hacettepe University, Sıhhiye, Ankara, Turkey
| | - Vagolu Siva Krishna
- Unit for Genome Dynamics, Department of Microbiology, University of Oslo, Oslo, Norway
| | - Melina Chebaiki
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.,LSPCMIB, UMR-CNRS 5068, Université Paul Sabatier-Toulouse III, Toulouse, France
| | - Håvard Homberset
- Unit for Genome Dynamics, Department of Microbiology, University of Oslo, Oslo, Norway
| | - Christian Lherbet
- LSPCMIB, UMR-CNRS 5068, Université Paul Sabatier-Toulouse III, Toulouse, France
| | - Lionel Mourey
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Tone Tønjum
- Unit for Genome Dynamics, Department of Microbiology, University of Oslo, Oslo, Norway.,Unit for Genome Dynamics, Department of Microbiology, Oslo University Hospital, Oslo, Norway
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34
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Hanwarinroj C, Phusi N, Kamsri B, Kamsri P, Punkvang A, Ketrat S, Saparpakorn P, Hannongbua S, Suttisintong K, Kittakoop P, Spencer J, Mulholland AJ, Pungpo P. Discovery of novel and potent InhA inhibitors by an in silico screening and pharmacokinetic prediction. Future Med Chem 2022; 14:717-729. [PMID: 35485258 DOI: 10.4155/fmc-2021-0348] [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] [Indexed: 11/17/2022] Open
Abstract
Aim: In silico screening approaches were performed to discover novel InhA inhibitors. Methods: Candidate InhA inhibitors were obtained from the combination of virtual screening and pharmacokinetic prediction. In addition, molecular mechanics Poisson-Boltzmann surface area, molecular mechanics Generalized Born surface area and WaterSwap methods were performed to investigate the binding interactions and binding energy of candidate compounds. Results: Four candidate compounds with suitable physicochemical, pharmacokinetic and antibacterial properties are proposed. The crucial interactions of the candidate compounds were H-bond, pi-pi and sigma-pi interactions observed in the InhA binding site. The binding affinity of these compounds was improved by hydrophobic interactions with hydrophobic side chains in the InhA pocket. Conclusion: The four newly identified InhA inhibitors reported in this study could serve as promising hit compounds against Mycobacterium tuberculosis and may be considered for further experimental studies.
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Affiliation(s)
- Chayanin Hanwarinroj
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani, 34190, Thailand
| | - Nareudon Phusi
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani, 34190, Thailand
| | - Bundit Kamsri
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani, 34190, Thailand
| | - Pharit Kamsri
- Division of Chemistry, Faculty of Science, Nakhon Phanom University, Nakhon Phanom, 48000, Thailand
| | - Auradee Punkvang
- Division of Chemistry, Faculty of Science, Nakhon Phanom University, Nakhon Phanom, 48000, Thailand
| | - Sombat Ketrat
- School of Information Science & Technology, Vidyasirimedhi Institute of Science & Technology, Rayong, 21210, Thailand
| | | | - Supa Hannongbua
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | | | - Prasat Kittakoop
- Chulabhorn Research Institute, Bangkok, 10210, Thailand
- Chulabhorn Graduate Institute, Chemical Biology Program, Chulabhorn Royal Academy, Bangkok, 10210, Thailand
- Center of Excellence on Environmental Health & Toxicology (EHT), CHE, Ministry of Education, Bangkok, 10300, Thailand
| | - James Spencer
- School of Cellular & Molecular Medicine, Biomedical Sciences Building, University of Bristol, Bristol, BS8 1TD, United Kingdom
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, United Kingdom
| | - Pornpan Pungpo
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani, 34190, Thailand
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35
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Kuang W, Zhang H, Wang X, Yang P. Overcoming Mycobacterium tuberculosis through small molecule inhibitors to break down cell wall synthesis. Acta Pharm Sin B 2022; 12:3201-3214. [PMID: 35967276 PMCID: PMC9366312 DOI: 10.1016/j.apsb.2022.04.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/08/2022] [Accepted: 04/19/2022] [Indexed: 12/16/2022] Open
Abstract
Mycobacterium tuberculosis (MTB) utilizes multiple mechanisms to obtain antibiotic resistance during the treatment of infections. In addition, the biofilms, secreted by MTB, can further protect the latter from the contact with drug molecules and immune cells. These self-defending mechanisms lay a formidable challenge to develop effective therapeutic agents against chronic and recurring antibiotic-tolerant MTB infections. Although several inexpensive and effective drugs (isoniazid, rifampicin, pyrazinamide and ethambutol) have been discovered for the treatment regimen, MTB continues to cause considerable morbidity and mortality worldwide. Antibiotic resistance and tolerance remain major global issues, and innovative therapeutic strategies are urgently needed to address the challenges associated with pathogenic bacteria. Gratifyingly, the cell wall synthesis of tubercle bacilli requires the participation of many enzymes which exclusively exist in prokaryotic organisms. These enzymes, absent in human hepatocytes, are recognized as promising targets to develop anti-tuberculosis drug. In this paper, we discussed the critical roles of potential drug targets in regulating cell wall synthesis of MTB. And also, we systematically reviewed the advanced development of novel bioactive compounds or drug leads for inhibition of cell wall synthesis, including their discovery, chemical modification, in vitro and in vivo evaluation.
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Affiliation(s)
- Wenbin Kuang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Haolin Zhang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Xiao Wang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Peng Yang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
- Corresponding author.
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36
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Mi J, Gong W, Wu X. 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: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [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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Affiliation(s)
- Jie Mi
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing 100091, China
| | - Wenping Gong
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing 100091, China
| | - Xueqiong Wu
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing 100091, China
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37
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Khan A, Siddique AM, Shaikh M, Khan IA, Shafi S. Microwave-assisted solvent-free tandem cross-metathesis/intramolecular isomerization-cyclization reaction for the synthesis of N-substituted pyrroles: It’s computational analysis. SYNTHETIC COMMUN 2022. [DOI: 10.1080/00397911.2022.2039710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Arif Khan
- Department of Chemistry, School of Chemical and Life Sciences, New Delhi, India
| | - Asher M. Siddique
- Department of Chemistry, School of Chemical and Life Sciences, New Delhi, India
| | - Majeed Shaikh
- Natural product and Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India
| | - Imran A. Khan
- Department of Chemistry, School of Chemical and Life Sciences, New Delhi, India
| | - Syed Shafi
- Department of Chemistry, School of Chemical and Life Sciences, New Delhi, India
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38
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Hernández-Bustamante I, Santander-Plantamura Y, Mata-Espinosa D, Reyes-Chaparro A, Bini EI, Torre-Villalvazo I, Tovar AR, Barrios-Payan J, Marquina-Castillo B, Hernández-Pando R, Carranza A. Structural homology between 11 beta-hydroxysteroid dehydrogenase and Mycobacterium tuberculosis Inh-A enzyme: Dehydroepiandrosterone as a potential co-adjuvant treatment in diabetes-tuberculosis comorbidity. Front Endocrinol (Lausanne) 2022; 13:1055430. [PMID: 36699022 PMCID: PMC9870073 DOI: 10.3389/fendo.2022.1055430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/29/2022] [Indexed: 01/11/2023] Open
Abstract
Metabolic syndrome is considered the precursor of type 2 diabetes mellitus. Tuberculosis is a leading infection that constitutes a global threat remaining a major cause of morbi-mortality in developing countries. People with type 2 diabetes mellitus are more likely to suffer from infection with Mycobacterium tuberculosis. For both type 2 diabetes mellitus and tuberculosis, there is pulmonary production of anti-inflammatory glucocorticoids mediated by the enzyme 11β-hydroxysteroid dehydrogenase type 1 (11β-HSD1). The adrenal hormone dehydroepiandrosterone (DHEA) counteracts the glucocorticoid effects of cytokine production due to the inhibition of 11β-HSD1. Late advanced tuberculosis has been associated with the suppression of the Th1 response, evidenced by a high ratio of cortisol/DHEA. In a murine model of metabolic syndrome, we determined whether DHEA treatment modifies the pro-inflammatory cytokines due to the inhibition of the 11β-HSD1 expression. Since macrophages express 11β-HSD1, our second goal was incubating them with DHEA and Mycobacterium tuberculosis to show that the microbicide effect was increased by DHEA. Enoyl-acyl carrier protein reductase (InhA) is an essential enzyme of Mycobacterium tuberculosis involved in the mycolic acid synthesis. Because 11β-HSD1 and InhA are members of a short-chain dehydrogenase/reductase family of enzymes, we hypothesize that DHEA could be an antagonist of InhA. Our results demonstrate that DHEA has a direct microbicide effect against Mycobacterium tuberculosis; this effect was supported by in silico docking analysis and the molecular dynamic simulation studies between DHEA and InhA. Thus, DHEA increases the production of pro-inflammatory cytokines in the lung, inactivates GC by 11β-HSD1, and inhibits mycobacterial InhA. The multiple functions of DHEA suggest that this hormone or its synthetic analogs could be an efficient co-adjuvant for tuberculosis treatment.
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Affiliation(s)
- Israel Hernández-Bustamante
- Sección de Patología Experimental, Departamento de Patología, Instituto Nacional de Ciencias Médicas y Nutrición “Salvador Zubirán”, Mexico City, Mexico
| | - Yanina Santander-Plantamura
- Departamento de Farmacología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Dulce Mata-Espinosa
- Sección de Patología Experimental, Departamento de Patología, Instituto Nacional de Ciencias Médicas y Nutrición “Salvador Zubirán”, Mexico City, Mexico
| | - Andrés Reyes-Chaparro
- Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Mexico City, Mexico
| | - Estela I. Bini
- Sección de Patología Experimental, Departamento de Patología, Instituto Nacional de Ciencias Médicas y Nutrición “Salvador Zubirán”, Mexico City, Mexico
| | - Iván Torre-Villalvazo
- Departamento de Fisiología de la Nutrición, Instituto Nacional de Ciencias Médicas y Nutrición “Salvador Zubirán”, Mexico City, Mexico
| | - Armando R. Tovar
- Departamento de Fisiología de la Nutrición, Instituto Nacional de Ciencias Médicas y Nutrición “Salvador Zubirán”, Mexico City, Mexico
| | - Jorge Barrios-Payan
- Sección de Patología Experimental, Departamento de Patología, Instituto Nacional de Ciencias Médicas y Nutrición “Salvador Zubirán”, Mexico City, Mexico
| | - Brenda Marquina-Castillo
- Sección de Patología Experimental, Departamento de Patología, Instituto Nacional de Ciencias Médicas y Nutrición “Salvador Zubirán”, Mexico City, Mexico
| | - Rogelio Hernández-Pando
- Sección de Patología Experimental, Departamento de Patología, Instituto Nacional de Ciencias Médicas y Nutrición “Salvador Zubirán”, Mexico City, Mexico
| | - Andrea Carranza
- Departamento de Farmacología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- *Correspondence: Andrea Carranza,
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39
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Singh G, Priyanka, Sushma, Pawan, Diksha, Suman, Mohit, Devi A, Gupta S. Tetrazole conjoined organosilane and organosilatrane via the ‘click approach’: a potent Mycobacterium tuberculosis enoyl ACP reductase inhibitor and a dual sensor for Fe(iii) and Cu(ii) ions. NEW J CHEM 2022. [DOI: 10.1039/d1nj05126a] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
This article includes the synthesis and characterization of tetrazole-allied organosilane and organosilatrane. The tetrazole-allied silatrane was explored for molecular docking and optical aspects.
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Affiliation(s)
- Gurjaspreet Singh
- Department of Chemistry, Panjab University, Chandigarh-160014, India
| | - Priyanka
- Department of Chemistry, Panjab University, Chandigarh-160014, India
| | - Sushma
- Department of Chemistry, Panjab University, Chandigarh-160014, India
| | - Pawan
- Department of Chemistry, Panjab University, Chandigarh-160014, India
| | - Diksha
- Department of Chemistry, Panjab University, Chandigarh-160014, India
| | - Suman
- Department of Chemistry, Panjab University, Chandigarh-160014, India
| | - Mohit
- Department of Chemistry, Panjab University, Chandigarh-160014, India
| | - Anita Devi
- Department of Chemistry, Panjab University, Chandigarh-160014, India
| | - Sofia Gupta
- Department of Chemistry, Panjab University, Chandigarh-160014, India
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