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Hu Y, Yu M, You G, Fan J, Zheng H. Evaluation of MeltPro Assay in Identification of Second-Line Injectable Drug Resistance in Multidrug-Resistant Tuberculosis Isolates. Infect Drug Resist 2024; 17:2069-2076. [PMID: 38807773 PMCID: PMC11131950 DOI: 10.2147/idr.s459142] [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: 02/22/2024] [Accepted: 05/15/2024] [Indexed: 05/30/2024] Open
Abstract
Objective We compared the MeltPro assay to whole-genome sequencing (WGS) to investigate the molecular characterization of second-line injectable drug (SLID) resistance in multidrug-resistant tuberculosis (MDR-TB) isolates in Chongqing, China. Methods A total of 122 MDR-TB patient isolates were collected between March 2019 and June 2020 from Chongqing Municipality, China. Conventional drug-susceptibility testing was performed using the proportion method, followed to generate minimum inhibitory concentrations (MICs) of SLIDs determined by microplate alamarblue assay. All strains were subjected to both MeltPro and WGS assays. Results Among 122 MDR-TB isolates, 30 (24.6%), 22 (18.0%), and 14 (11.5%) were resistant to kanamycin (KM), amikacin (AM), and capreomycin (CM), respectively. Of the 31 SLID-resistant isolates, 24 (77.4%, 24/31) isolates harbored mutations in the rrs gene, with the most prevalent mutations in rrs A1401G (22/24, 91.7%). Mutation in rrs A1401G was associated with high levels of resistance to KM (MIC, ≥40 μg/mL) and AM (MIC, ≥64 μg/mL), but disparities in CM-resistance levels. Using phenotypic drug-susceptibility testing as gold standard, we found that the overall sensitivity of MeltPro and WGS was 87.1% and 90.32% and specificity 100% and 97.8%, respectively. Seven isolates had discordant results between phenotypic and genotypic resistance of SLIDs. Conclusion MeltPro is a promising diagnostic tool for accurate identification of SLID-resistant MTB isolates with mutations in the rrs and eis genes. There was a disparity between MeltPro with WGS results in the proportion of heterogeneous drug-resistant bacteria with rrs mutation and limited probes. Resistance mechanisms other than genetic mutations will affect the consistency of MeltPro and WGS with phenotypic drug-susceptibility results.
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Affiliation(s)
- Yan Hu
- Tuberculosis Reference Laboratory, Chongqing Tuberculosis Control Institute, Chongqing, People’s Republic of China
| | - Min Yu
- Tuberculosis Reference Laboratory, Chongqing Tuberculosis Control Institute, Chongqing, People’s Republic of China
| | - Guoqing You
- Tuberculosis Reference Laboratory, Chongqing Tuberculosis Control Institute, Chongqing, People’s Republic of China
| | - Jun Fan
- Tuberculosis Reference Laboratory, Chongqing Tuberculosis Control Institute, Chongqing, People’s Republic of China
| | - Huiwen Zheng
- Laboratory of Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children’s Health, Beijing, People’s Republic of China
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Shahab M, Danial M, Duan X, Khan T, Liang C, Gao H, Chen M, Wang D, Zheng G. Machine learning-based drug design for identification of thymidylate kinase inhibitors as a potential anti-Mycobacterium tuberculosis. J Biomol Struct Dyn 2024; 42:3874-3886. [PMID: 37232453 DOI: 10.1080/07391102.2023.2216278] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/15/2023] [Indexed: 05/27/2023]
Abstract
The rise of antibiotic-resistant Mycobacterium tuberculosis (Mtb) has reduced the availability of medications for tuberculosis therapy, resulting in increased morbidity and mortality globally. Tuberculosis spreads from the lungs to other parts of the body, including the brain and spine. Developing a single drug can take several decades, making drug discovery costly and time-consuming. Machine learning algorithms like support vector machines (SVM), k-nearest neighbor (k-NN), random forest (RF) and Gaussian naive base (GNB) are fast and effective and are commonly used in drug discovery. These algorithms are ideal for the virtual screening of large compound libraries to classify molecules as active or inactive. For the training of the models, a dataset of 307 was downloaded from BindingDB. Among 307 compounds, 85 compounds were labeled as active, having an IC50 below 58 mM, while 222 compounds were labeled inactive against thymidylate kinase, with 87.2% accuracy. The developed models were subjected to an external ZINC dataset of 136,564 compounds. Furthermore, we performed the 100-ns dynamic simulation and post trajectories analysis of compounds having good interaction and score in molecular docking. As compared to the standard reference compound, the top three hits revealed greater stability and compactness. In conclusion, our predicted hits can inhibit thymidylate kinase overexpression to combat Mycobacterium tuberculosis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Muhammad Shahab
- State Key Laboratories of Chemical Resources Engineering Beijing University of Chemical Technology, Beijing, China
| | - Muhammad Danial
- University of Chinese Academy of Sciences, Shenzhen Institute of Advanced Technology, Shenzhen, China
| | - Xiuyuan Duan
- State Key Laboratories of Chemical Resources Engineering Beijing University of Chemical Technology, Beijing, China
| | - Taimur Khan
- State Key Laboratories of Chemical Resources Engineering Beijing University of Chemical Technology, Beijing, China
| | - Chaoqun Liang
- State Key Laboratories of Chemical Resources Engineering Beijing University of Chemical Technology, Beijing, China
| | - Hanzi Gao
- State Key Laboratories of Chemical Resources Engineering Beijing University of Chemical Technology, Beijing, China
| | - Meiyu Chen
- State Key Laboratories of Chemical Resources Engineering Beijing University of Chemical Technology, Beijing, China
| | - Daixi Wang
- State Key Laboratories of Chemical Resources Engineering Beijing University of Chemical Technology, Beijing, China
| | - Guojun Zheng
- State Key Laboratories of Chemical Resources Engineering Beijing University of Chemical Technology, Beijing, China
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Hu Y, Chi Y, Feng X, Yu F, Li H, Shang Y, Pan J, Pang Y. Comparison of the Diagnostic Performance of MeltPro and Next-Generation Sequencing in Determining Fluoroquinolone Resistance in Multidrug-Resistant Tuberculosis Isolates. J Mol Diagn 2023; 25:342-351. [PMID: 37208048 DOI: 10.1016/j.jmoldx.2023.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 12/20/2022] [Accepted: 02/09/2023] [Indexed: 05/21/2023] Open
Abstract
This study systematically investigated the performance of MeltPro and next-generation sequencing in the diagnosis of fluoroquinolone (FQ) resistance among multidrug-resistant tuberculosis patients and explored the relationship between nucleotide alteration and the level of phenotypic susceptibility to FQs. From March 2019 to June 2020, a feasibility and validation study with both MeltPro and next-generation sequencing was performed in 126 patients with multidrug-resistant tuberculosis. Using phenotypic drug susceptibility testing as the gold standard, 95.3% (82 of 86) of ofloxacin-resistant isolates were identified correctly by MeltPro. In addition, whole-genome sequencing was able to detect 83 phenotypically ofloxacin-resistant isolates. The isolates with an individual gyrB mutation outside the quinolone resistance-determining region (QRDR) had minimum inhibitory concentrations (MICs) of ≤2 μg/mL. Despite showing low MICs close to the breakpoint for isolates carrying only gyrA_Ala90Val, the combined mutation gyrB_Asp461Asn caused the ofloxacin MIC to be eight higher than that obtained in Mycobacterium tuberculosis (MTB) isolates with the Ala90Val mutation alone (median, 32 μg/mL; P = 0.038). Heteroresistance was observed in 12 of 88 isolates harboring mutations in the QRDRs. In conclusion, our data show that MeltPro and the whole-genome sequencing assay correctly can identify FQ resistance caused by mutations in the gyrA QRDR. The combined gyrB_Asp461Asn mutation may significantly decrease in vitro FQ susceptibility of MTB isolates with low-level-resistance-associated gyrA mutations.
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Affiliation(s)
- Yan Hu
- Tuberculosis Reference Laboratory, Chongqing Municipal Institute of Tuberculosis, Chongqing, China
| | - Yuqing Chi
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Xin Feng
- Tuberculosis Reference Laboratory, Chongqing Municipal Institute of Tuberculosis, Chongqing, China
| | - Fengping Yu
- Tuberculosis Reference Laboratory, Chongqing Municipal Institute of Tuberculosis, Chongqing, China
| | - Haoran Li
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Yuanyuan Shang
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Junhua Pan
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China.
| | - Yu Pang
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China.
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Mundhe P, Kidwai S, Saini SM, Singh HR, Singh R, Chandrashekharappa S. Design, Synthesis, Characterization, and Anti-tubercular activity of Novel Ethyl-3-benzoyl-6, 8-difluoroindolizine-1-carboxylate Analogues: Molecular Target Identification and Molecular Docking Studies. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
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Characteristics and Trend of Drug-Resistant Tuberculosis at a Major Specialized Hospital in Chongqing, China: 2016 Versus 2019. Disaster Med Public Health Prep 2022; 17:e169. [PMID: 35575296 DOI: 10.1017/dmp.2022.88] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
OBJECTIVE The epidemic of drug-resistant tuberculosis (DR-TB) has become a major concern in global TB control. This study aimed to investigate the patterns and trend of DR-TB epidemic between different time periods in Chongqing. METHODS A total of 985 and 835 culture positive TB patients with drug susceptibility testing (DST) results admitted to the hospital in 2016 and 2019, respectively, were included. Chi-square testing was used to compare the prevalence and trends of DR-TB in 2016 and 2019. RESULTS The proportion of previously treated TB cases with culture positivity was 45.7% in 2019, significantly higher than that in 2016 (39.1%, P = 0.004). The overall rate of drug resistance in 2019 was 43.1%, higher than that in 2016 (40.2%). The rates of multi-drug resistant TB (MDR-TB) and pre-extensively drug resistant TB (pre-XDR-TB) increased significantly from 2016 to 2019 among all TB cases (MDR: 25% vs 33.4%, P < 0.001 and pre-XDR: 7.1% vs 12.8%, P < 0.001, respectively) and previously treated TB cases (MDR: 46.5% vs 56%, P = 0.008 and pre-XDR: 13.2% vs 21.5%, P = 0.003, respectively). CONCLUSIONS Our findings indicated that the prevalence of DR-TB remains high in Chongqing. The trend of resistance to anti-TB drugs beccame worse between 2016 and 2019. Moreover, acquired MDR may play a major role in MDR-TB epidemic in Chongqing. Therefore, rapid diagnosis and effective treatment of TB patients will be important to reduce the burden of DR-TB in Chongqing.
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Madukaji L, Okohu I, Usman S, Oyedum U, Enagi A, Usman A, Adedeji AS, Owolagba F, Ofuche E, Samuels JO, Jolayemi T, Okonkwo P. Early detection of Pre-XDR TB with line probe assay in a high TB burden country. Afr Health Sci 2021; 21:968-974. [PMID: 35222556 PMCID: PMC8843309 DOI: 10.4314/ahs.v21i3.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background Worldwide, tuberculosis (TB) is one of the top 10 causes of death. Drug resistant tuberculosis has lately become a major public health problem that threatens progress made in Tuberculosis (TB) care and control worldwide. The aim of this study was to determine the prevalence of Pre-extensive drug resistant TB among MDR TB in North Central of Nigeria. Methods This study was conducted from October, 2018 to August, 2019 with 150 samples. In Nigeria, guidelines for DR-TB as recommended by WHO is followed. All the samples from the patients who gave their consent were transported to a zonal reference TB laboratory (ZRL). Results Mean age was 38.6 ± 13.4 years with peak age at 35–44. Out of these 103 samples processed with LPA, 101(98%) were rifampicin resistant and 2 were rifampicin sensitive, 99(96%) were INH resistant and 4 (4%) were INH sensitive, 5(5%) were fluoroquinolone resistant, 98(95%) were fluoroquinolone sensitive, 12 (12%) were Aminoglycoside + Capreomycin resistant, 91(83%) were Aminoglycoside + Capreomycin sensitive. Conclusion Multidrug resistant TB and its severe forms (Pre-extensive & extensively drug resistant TB) can be detected early with rapid tool- Line Probe Assay rapid and prevented timely by early initiation on treatment.
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Affiliation(s)
| | | | | | - Uche Oyedum
- Federal University of Technology Minna, Nigeria
| | | | | | - AS Adedeji
- Federal University of Technology Minna, Nigeria
| | | | - Eke Ofuche
- APIN Public Health Initiatives Abuja, Nigeria
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Hajissa K, Marzan M, Idriss MI, Islam MA. Prevalence of Drug-Resistant Tuberculosis in Sudan: A Systematic Review and Meta-Analysis. Antibiotics (Basel) 2021; 10:antibiotics10080932. [PMID: 34438982 PMCID: PMC8388945 DOI: 10.3390/antibiotics10080932] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 11/16/2022] Open
Abstract
Drug-resistant tuberculosis (DR-TB) is still one of the most critical issues impeding worldwide TB control efforts. The aim of this systematic review and meta-analysis was to give an updated picture of the prevalence of DR-TB in Sudan. A comprehensive systematic search was performed on four electronic databases (PubMed, Scopus, Web of Science and Google Scholar) to identify all published studies reporting prevalence data of DR-TB in Sudan. Sixteen eligible studies published during 2002-2020 were included. Using meta-analysis of proportions, the pooled prevalence of TB cases with resistance to any anti-TB drugs was 47.0% (95% CI: 35.5-58.6%). The overall prevalence of mono, multi, poly and extensive drug resistance were estimated to be 16.2% (95% CI: 9.0-23.4%), 22.8% (95% CI: 16.0-29.7%), 6.8% (95% CI: 0.5-13.0%) and 0.7% (95% CI: 0-2.1%), respectively. Considering any first-line anti-TB drugs, the resistance prevalence was highest for isoniazid (32.3%) and streptomycin (31.7%), followed by rifampicin (29.2%). In contrast, resistance against second-line drugs was reported for only two antibiotics, namely, ofloxacin (2.1%) and kanamycin (0.7%). Of note, the resistance profile of the previously treated patients was found to be remarkably high compared with the newly diagnosed TB patients. The relatively high prevalence estimation of anti-TB drug resistance warrants strengthening TB control and treatment strategies in Sudan.
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Affiliation(s)
- Khalid Hajissa
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia;
- Department of Zoology, Faculty of Science and Technology, Omdurman Islamic University, P.O. Box 382, Omdurman 14415, Sudan
| | - Mahfuza Marzan
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh;
| | | | - Md Asiful Islam
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
- Correspondence: or
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Hu Y, Liu J, Shen J, Feng X, Liu W, Zhu D, Zheng H, Hu D. Genotyping and Molecular Characterization of Fluoroquinolone's Resistance Among Multidrug-Resistant Mycobacterium tuberculosis in Southwest of China. Microb Drug Resist 2020; 27:865-870. [PMID: 33305990 DOI: 10.1089/mdr.2019.0339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Although fluoroquinolones (FQs) are the backbone drugs for the treatment of multidrug-resistant tuberculosis (MDR-TB), the knowledge about the resistance pattern and molecular characterization of new-generation FQs in Chongqing is limited. This study aimed to investigate the resistance rate and mutation types of later-generation FQs against MDR-TB in Chongqing, and further to explore the relationship between different genotypes and phenotypes. A total of 967 clinical strains were characterized using multilocus sequence typing and drug susceptibility testing, followed by analysis of genotype/phenotype association. The 229 (23.7%, 229/967) isolates were identified as MDR-TB. The most effective agent against MDR-TB was gatifloxacin (GFX) (20.1%, 46/229), and the highest resistant rate was observed in ofloxacin (OFX) (41.0%, 94/229). Of the 190 strains (83.0%) identified as Beijing genotype, 111 isolates were modern Beijing genotype (58.4%) and 79 isolates were ancient Beijing genotype (41.6%). By analyzing 94 OFX-resistant isolates, 13 isolates were clustered with the cumulative clustering rate of 13.8% (13/94). Of the 91 isolates (39.7%, 91/229) with a mutation in gyrA gene, mutation in codon 94 was the most prevalent. Only 15 isolates (6.6%, 15/229) harbored a mutation in gyrB gene. There was no significant difference in the mutation rate of gyrA gene between Beijing and non-Beijing genotype, clustered isolates, and nonclustered isolates (p > 0.05).
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Affiliation(s)
- Yan Hu
- Tuberculosis Reference Laboratory, Chongqing Tuberculosis Control Institute, Chongqing, China
| | - Jie Liu
- Tuberculosis Reference Laboratory, Chongqing Tuberculosis Control Institute, Chongqing, China
| | - Jing Shen
- Tuberculosis Reference Laboratory, Chongqing Tuberculosis Control Institute, Chongqing, China
| | - Xin Feng
- Tuberculosis Reference Laboratory, Chongqing Tuberculosis Control Institute, Chongqing, China
| | - Wenguo Liu
- Tuberculosis Reference Laboratory, Chongqing Tuberculosis Control Institute, Chongqing, China
| | - Damian Zhu
- Tuberculosis Reference Laboratory, Chongqing Tuberculosis Control Institute, Chongqing, China
| | - Huiwen Zheng
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Daiyu Hu
- Tuberculosis Reference Laboratory, Chongqing Tuberculosis Control Institute, Chongqing, China
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Ngilirabanga JB, Aucamp M, Pires Rosa P, Samsodien H. Mechanochemical Synthesis and Physicochemical Characterization of Isoniazid and Pyrazinamide Co-crystals With Glutaric Acid. Front Chem 2020; 8:595908. [PMID: 33282840 PMCID: PMC7706006 DOI: 10.3389/fchem.2020.595908] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 10/12/2020] [Indexed: 11/15/2022] Open
Abstract
The present work reports two novel pharmaceutical co-crystals; 2:1 isoniazid-glutaric acid (INHGA) and 2:1 pyrazinamide-glutaric acid (PGA). Isoniazid and pyrazinamide are key first-line drugs used for the treatment of tuberculosis. The co-crystals were produced via solid-state and solvent assisted grinding methods. Thermal characteristics of the samples were obtained using the differential scanning calorimetry, hot stage microscopy, and thermogravimetric analyses. The morphology of the powder samples by scanning electron microscopy, structural analysis by Fourier transform infrared spectroscopy and powder X-rays diffraction ensured co-crystal formation. Thermal analyses confirmed the co-crystals with new melting transitions ranging between their respective starting materials. Unique morphologies of the co-crystal particles were clear in SEM micrographs. The formation of intermolecular interactions with the co-crystal former was confirmed by the FT-IR spectral band shifting and was supported by distinct PXRD patterns of co-crystals thereby authenticating the successful co-crystal formation. In vitro solubility evaluation of the synthesized co-crystals by HPLC suggested a remarkable increase in solubility of both INH and PZA in their respective co-crystals.
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Affiliation(s)
| | - Marique Aucamp
- School of Pharmacy, University of the Western Cape, Cape Town, South Africa
| | - Paulo Pires Rosa
- Faculty of Pharmaceutical Sciences, State University of Campinas, Saö Paulo, Brazil
| | - Halima Samsodien
- School of Pharmacy, University of the Western Cape, Cape Town, South Africa
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Anti-Tubercular Properties of 4-Amino-5-(4-Fluoro-3- Phenoxyphenyl)-4 H-1,2,4-Triazole-3-Thiol and Its Schiff Bases: Computational Input and Molecular Dynamics. Antibiotics (Basel) 2020; 9:antibiotics9090559. [PMID: 32878018 PMCID: PMC7560126 DOI: 10.3390/antibiotics9090559] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/26/2020] [Accepted: 08/29/2020] [Indexed: 12/26/2022] Open
Abstract
In the present investigation, the parent compound 4-amino-5-(4-fluoro-3-phenoxyphenyl)-4H-1,2,4-triazole-3-thiol (1) and its Schiff bases 2, 3, and 4 were subjected to whole-cell anti-TB against H37Rv and multi-drug-resistant (MDR) strains of Mycobacterium tuberculosis (MTB) by resazurin microtiter assay (REMA) plate method. Test compound 1 exhibited promising anti-TB activity against H37Rv and MDR strains of MTB at 5.5 µg/mL and 11 µg/mL, respectively. An attempt to identify the suitable molecular target for compound 1 was performed using a set of triazole thiol cellular targets, including β-ketoacyl carrier protein synthase III (FABH), β-ketoacyl ACP synthase I (KasA), CYP121, dihydrofolate reductase, enoyl-acyl carrier protein reductase, and N-acetylglucosamine-1-phosphate uridyltransferase. MTB β-ketoacyl ACP synthase I (KasA) was identified as the cellular target for the promising anti-TB parent compound 1 via docking and molecular dynamics simulation. MM(GB/PB)SA binding free energy calculation revealed stronger binding of compound 1 compared with KasA standard inhibitor thiolactomycin (TLM). The inhibitory mechanism of test compound 1 involves the formation of hydrogen bonding with the catalytic histidine residues, and it also impedes access of fatty-acid substrates to the active site through interference with α5–α6 helix movement. Test compound 1-specific structural changes at the ALA274–ALA281 loop might be the contributing factor underlying the stronger anti-TB effect of compound 1 when compared with TLM, as it tends to adopt a closed conformation for the access of malonyl substrate to its binding site.
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Venugopala KN, Tratrat C, Pillay M, Chandrashekharappa S, Al-Attraqchi OHA, Aldhubiab BE, Attimarad M, Alwassil OI, Nair AB, Sreeharsha N, Venugopala R, Morsy MA, Haroun M, Kumalo HM, Odhav B, Mlisana K. In silico Design and Synthesis of Tetrahydropyrimidinones and Tetrahydropyrimidinethiones as Potential Thymidylate Kinase Inhibitors Exerting Anti-TB Activity Against Mycobacterium tuberculosis. DRUG DESIGN DEVELOPMENT AND THERAPY 2020; 14:1027-1039. [PMID: 32214795 PMCID: PMC7082623 DOI: 10.2147/dddt.s228381] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 02/20/2020] [Indexed: 01/03/2023]
Abstract
Background and Purpose Tuberculosis has been reported to be the worldwide leading cause of death resulting from a sole infectious agent. The emergence of multidrug-resistant tuberculosis and extensively drug-resistant tuberculosis has made the battle against the infection more difficult since most currently available therapeutic options are ineffective against these resistant strains. Therefore, novel molecules need to be developed to effectively treat tuberculosis disease. Preliminary docking studies revealed that tetrahydropyrimidinone derivatives have favorable interactions with the thymidylate kinase receptor. In the present investigation, we report the synthesis and the mycobacterial activity of several pyrimidinones and pyrimidinethiones as potential thymidylate kinase inhibitors. Methods The title compounds (1a-d) and (2a-b) were synthesized by a one-pot three-component Biginelli reaction. They were subsequently characterized and used for whole-cell anti-TB screening against H37Rv and multidrug-resistant (MDR) strains of Mycobacterium tuberculosis (MTB) by the resazurin microplate assay (REMA) plate method. Molecular modeling was conducted using the Accelry's Discovery Studio 4.0 client program to explain the observed bioactivity of the compounds. The pharmacokinetic properties of the synthesized compounds were predicted and analyzed. Results Of the compounds tested for anti-TB activity, pyrimidinone 1a and pyrimidinethione 2a displayed moderate activity against susceptible MTB H37Rv strains at 16 and 32 µg/mL, respectively. Only compound 2a was observed to exert modest activity at 128 µg/mL against MTB strains with cross-resistance to rifampicin and isoniazid. The presence of the trifluoromethyl group was essential to retain the inhibitory activity of compounds 1a and 2a. Molecular modeling studies of these compounds against thymidylate kinase targets demonstrated a positive correlation between the bioactivity and structure of the compounds. The in-silico ADME (absorption, distribution, metabolism, and excretion) prediction indicated favorable pharmacokinetic and drug-like properties for most compounds. Conclusion Pyrimidinone 1a and pyrimidinethione 2a were identified as the leading compounds and can serve as a starting point to develop novel anti-TB therapeutic agents.
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Affiliation(s)
- Katharigatta N Venugopala
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Kingdom of Saudi Arabia.,Department of Biotechnology and Food Technology, Durban University of Technology, Durban 4001, South Africa
| | - Christophe Tratrat
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Kingdom of Saudi Arabia
| | - Melendhran Pillay
- Department of Microbiology, National Health Laboratory Services, KZN Academic Complex, Inkosi Albert Luthuli Central Hospital, Durban 4001, South Africa
| | | | | | - Bandar E Aldhubiab
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Kingdom of Saudi Arabia
| | - Mahesh Attimarad
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Kingdom of Saudi Arabia
| | - Osama I Alwassil
- Department of Pharmaceutical Sciences, College of Pharmacy, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Anroop B Nair
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Kingdom of Saudi Arabia
| | - Nagaraja Sreeharsha
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Kingdom of Saudi Arabia
| | - Rashmi Venugopala
- Department of Public Health Medicine, University of KwaZulu-Natal, Howard College Campus, Durban 4001, South Africa
| | - Mohamed A Morsy
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Kingdom of Saudi Arabia.,Department of Pharmacology, Faculty of Medicine, Minia University, El-Minia 61511, Egypt
| | - Michelyne Haroun
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Kingdom of Saudi Arabia
| | - Hezekiel M Kumalo
- Department of Medical Biochemistry, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Medical School, Durban 4001, South Africa
| | - Bharti Odhav
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban 4001, South Africa
| | - Koleka Mlisana
- Department of Microbiology, National Health Laboratory Services, KZN Academic Complex, Inkosi Albert Luthuli Central Hospital, Durban 4001, South Africa
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Anti-Tubercular Activity of Substituted 7-Methyl and 7-Formylindolizines and In Silico Study for Prospective Molecular Target Identification. Antibiotics (Basel) 2019; 8:antibiotics8040247. [PMID: 31816928 PMCID: PMC6963442 DOI: 10.3390/antibiotics8040247] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/27/2019] [Accepted: 11/29/2019] [Indexed: 11/17/2022] Open
Abstract
Novel series of diversely substituted indolizines were designed, synthesized, and evaluated for their in vitro anti-mycobacterial activity against H37Rv and multi-drug-resistant (MDR) strains of Mycobacterium tuberculosis (MTB). Many compounds exhibited significant inhibitory activity against MTB H37Rv strains. Indolizines 2d, 2e, and 4 were also found to be active against MTB clinical isolates with multi-resistance to rifampicin and isoniazid. Indolizine 4 was identified as the most promising anti-mycobacterial agent, displaying minimum inhibitory concentration (MIC) values of 4 and 32 μg/mL against H37Rv and MDR strains, respectively. Furthermore, an in silico study was carried out for prospective molecular target identification and revealed favorable interactions with the target enzymes CYP 121, malate synthase, and DNA GyrB ATPase. None of the potent molecules presented toxicity against peripheral blood mononuclear (PBM) cell lines, demonstrating their potentiality to be used for drug-sensitive and drug-resistant tuberculosis therapy.
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Li Q, Wang Y, Li Y, Gao H, Zhang Z, Feng F, Dai E. Characterisation of drug resistance-associated mutations among clinical multidrug-resistant Mycobacterium tuberculosis isolates from Hebei Province, China. J Glob Antimicrob Resist 2019; 18:168-176. [DOI: 10.1016/j.jgar.2019.03.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 03/09/2019] [Accepted: 03/14/2019] [Indexed: 10/27/2022] Open
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Li Q, Gao H, Zhang Z, Tian Y, Liu T, Wang Y, Lu J, Liu Y, Dai E. Mutation and Transmission Profiles of Second-Line Drug Resistance in Clinical Isolates of Drug-Resistant Mycobacterium tuberculosis From Hebei Province, China. Front Microbiol 2019; 10:1838. [PMID: 31447823 PMCID: PMC6692474 DOI: 10.3389/fmicb.2019.01838] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 07/25/2019] [Indexed: 11/30/2022] Open
Abstract
The emergence of drug-resistant tuberculosis (TB) is involved in ineffective treatment of TB, especially multidrug resistant/extensively resistant TB (MDR/XDR-TB), leading to acquired resistance and transmission of drug-resistant strains. Second-line drugs (SLD), including both fluoroquinolones and injectable drugs, were commonly proved to be the effective drugs for treatment of drug-resistant TB. The purpose of this study was to investigate the prevalence of SLD-resistant strains and its specific mutations in drug-resistant Mycobacterium tuberculosis clinical isolates, and to acknowledge the transmission pattern of SLD resistance strains in Hebei. The genes gyrA, gyrB, rrs, eis promoter and tlyA of 257 drug-resistant clinical isolates were sequenced to identify mutations that could be responsible for resistance against fluoroquinolones and second-line injectable drugs. Each isolate was genotyped by Spoligotyping and 15-loci MIRU-VNTR. Our results indicated that 48.2% isolates were resistant to at least one of five SLD. Of them, 37.7% isolates were resistant to fluoroquinolones and 24.5% isolates were resistant to second-line injectable drugs. Mutations in genes gyrA, gyrB, rrs, eis promoter and tlyA were detected in 73 (75.3%), 7 (7.2%), 24 (38.1%), 5 (7.9%), and 3 (4.8%) isolates, respectively. The most prevalent mutations were the D94G (23.7%) in gyrA gene and the A1401G (33.3%) in rrs gene. A combination of gyrA, rrs and eis promoter can act as a valuable predicator for predicting XDR phenotype. These results highlight the development of rapid diagnosis are the effective manners for the control of SLD-TB or XDR-TB.
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Affiliation(s)
- Qianlin Li
- Department of Epidemiology and Statistics, North China University of Science and Technology, Tangshan, China
| | - Huixia Gao
- Department of Laboratory Medicine, The Fifth Affiliated Hospital of Shijiazhuang, North China University of Science and Technology, Shijiazhuang, China
| | - Zhi Zhang
- Department of Laboratory Medicine, The Fifth Affiliated Hospital of Shijiazhuang, North China University of Science and Technology, Shijiazhuang, China
| | - Yueyang Tian
- Department of Laboratory Medicine, The Fifth Affiliated Hospital of Shijiazhuang, North China University of Science and Technology, Shijiazhuang, China
| | - Tengfei Liu
- Department of Laboratory Medicine, The Fifth Affiliated Hospital of Shijiazhuang, North China University of Science and Technology, Shijiazhuang, China
| | - Yuling Wang
- Department of Laboratory Medicine, The Fifth Affiliated Hospital of Shijiazhuang, North China University of Science and Technology, Shijiazhuang, China
| | - Jianhua Lu
- Department of Laboratory Medicine, The Fifth Affiliated Hospital of Shijiazhuang, North China University of Science and Technology, Shijiazhuang, China
| | - Yuzhen Liu
- Department of Laboratory Medicine, The Fifth Affiliated Hospital of Shijiazhuang, North China University of Science and Technology, Shijiazhuang, China
| | - Erhei Dai
- Department of Laboratory Medicine, The Fifth Affiliated Hospital of Shijiazhuang, North China University of Science and Technology, Shijiazhuang, China
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Venugopala KN, Chandrashekharappa S, Pillay M, Abdallah HH, Mahomoodally FM, Bhandary S, Chopra D, Attimarad M, Aldhubiab BE, Nair AB, Sreeharsha N, Morsy MA, Pottathil S, Venugopala R, Odhav B, Mlisana K. Computational, crystallographic studies, cytotoxicity and anti-tubercular activity of substituted 7-methoxy-indolizine analogues. PLoS One 2019; 14:e0217270. [PMID: 31163040 PMCID: PMC6548424 DOI: 10.1371/journal.pone.0217270] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 05/08/2019] [Indexed: 11/18/2022] Open
Abstract
Indolizines are heteroaromatic compounds, and their synthetic analogues have reportedly showed promising pharmacological properties. In this study, a series of synthetic 7-methoxy-indolizine derivatives were synthesised, characterised and evaluated for in vitro whole-cell anti-tuberculosis (TB) screening against susceptible (H37Rv) and multi-drug-resistant (MDR) strains of Mycobacterium tuberculosis (MTB) using the resazurin microplate assay method. The cytotoxicity was evaluated using the MTT assay. In silico molecular-docking study was conducted for compounds 5a-j against enoyl-[acyl-carrier] protein reductase, a key enzyme of the type II fatty acid synthesis that has attracted much interest for the development of novel anti-TB compounds. Thereafter, molecular dynamic (MD) simulation was undertaken for the most active inhibitors. Compounds 5i and 5j with the methoxy functional group at the meta position of the benzoyl group, which was at the third position of the indolizine nucleus, demonstrated encouraging anti-TB activity against MDR strains of MTB at 16 μg/mL. In silico studies showed binding affinity within the range of 7.07-8.57 kcal/mol, with 5i showing the highest binding affinity. Hydrogen bonding, π-π- interactions, and electrostatic interactions were common with the active site. Most of these interactions occurred with the catalytic amino acids (Pro193, Tyr158, Phe149, and Lys165). MD simulation showed that 5j possessed the highest binding affinity toward the enzyme, according to the two calculation methods (MM/PBSA and MM/GBSA). The single-crystal X-ray studies of compounds 5c and 5d revealed that the molecular arrangements in these two structures were mostly guided by C-H···O hydrogen-bonded dimeric motifs and C-H···N hydrogen bonds, while various secondary interactions (such as π···π and C-H···F) also contributed to crystal formation. Compounds 5a, 5c, 5i, and 5j exhibited no toxicity up to 500 μg/mL. In conclusion, 5i and 5j are promising anti-TB compounds that have shown high affinity based on docking and MD simulation results.
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Affiliation(s)
- Katharigatta Narayanaswamy Venugopala
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Kingdom of Saudi Arabia
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban, South Africa
- * E-mail:
| | | | - Melendhran Pillay
- Department of Microbiology, National Health Laboratory Services, KZN Academic Complex, Inkosi Albert Luthuli Central Hospital, Durban, South Africa
| | - Hassan H. Abdallah
- School of Pharmacy, Universiti Sains Malaysia, Penang, Malaysia
- Chemistry Department, College of Education, Salahaddin University, Erbil, Iraq
| | - Fawzi M. Mahomoodally
- Department of Health Sciences, Faculty of Science, University of Mauritius, Réduit, Mauritius
| | - Subhrajyoti Bhandary
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal, Madhya Pradesh, India
| | - Deepak Chopra
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal, Madhya Pradesh, India
| | - Mahesh Attimarad
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Kingdom of Saudi Arabia
| | - Bandar E. Aldhubiab
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Kingdom of Saudi Arabia
| | - Anroop B. Nair
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Kingdom of Saudi Arabia
| | - Nagaraja Sreeharsha
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Kingdom of Saudi Arabia
| | - Mohamed A. Morsy
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Kingdom of Saudi Arabia
- Department of Pharmacology, Faculty of Medicine, Minia University, El-Minia, Egypt
| | - Shinu Pottathil
- Department of Biomedical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Kingdom of Saudi Arabia
| | - Rashmi Venugopala
- Department of Public Health Medicine, University of KwaZulu-Natal, Howard College Campus, Durban, South Africa
| | - Bharti Odhav
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban, South Africa
| | - Koleka Mlisana
- Department of Microbiology, National Health Laboratory Services, KZN Academic Complex, Inkosi Albert Luthuli Central Hospital, Durban, South Africa
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