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Gallego RA, Edwards MP, Montgomery TP. An update on lipophilic efficiency as an important metric in drug design. Expert Opin Drug Discov 2024; 19:917-931. [PMID: 38919130 DOI: 10.1080/17460441.2024.2368744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 06/12/2024] [Indexed: 06/27/2024]
Abstract
INTRODUCTION Lipophilic efficiency (LipE) and lipophilic metabolic efficiency (LipMetE) are valuable tools that can be utilized as part of a multiparameter optimization process to advance a hit to a clinical quality compound. AREAS COVERED This review covers recent, effective use cases of LipE and LipMetE that have been published in the literature over the past 5 years. These use cases resulted in the delivery of high-quality molecules that were brought forward to in vivo work and/or to clinical studies. The authors discuss best-practices for using LipE and LipMetE analysis, combined with lipophilicity-focused compound design strategies, to increase the speed and effectiveness of the hit to clinical quality compound optimization process. EXPERT OPINION It has become well established that increasing LipE and LipMetE within a series of analogs facilitates the improvement of broad selectivity, clearance, solubility, and permeability and, through this optimization, also facilitates the achievement of desired pharmacokinetic properties, efficacy, and tolerability. Within this article, we discuss lipophilic efficiency-focused optimization as a tool to yield high-quality potential clinical candidates. It is suggested that LipE/LipMetE-focused optimization can facilitate and accelerate the drug-discovery process.
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Nyambo K, Tapfuma KI, Adu-Amankwaah F, Julius L, Baatjies L, Niang IS, Smith L, Govender KK, Ngxande M, Watson DJ, Wiesner L, Mavumengwana V. Molecular docking, molecular dynamics simulations and binding free energy studies of interactions between Mycobacterium tuberculosis Pks13, PknG and bioactive constituents of extremophilic bacteria. Sci Rep 2024; 14:6794. [PMID: 38514663 PMCID: PMC10957976 DOI: 10.1038/s41598-024-57124-9] [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: 12/16/2023] [Accepted: 03/14/2024] [Indexed: 03/23/2024] Open
Abstract
Mycobacterial pathogens present a significant challenge to disease control efforts globally due to their inherent resistance to multiple antibiotics. The rise of drug-resistant strains of Mycobacterium tuberculosis has prompted an urgent need for innovative therapeutic solutions. One promising way to discover new tuberculosis drugs is by utilizing natural products from the vast biochemical space. Multidisciplinary methods can used to harness the bioactivity of these natural products. This study aimed to evaluate the antimycobacterial efficacy of functional crude extracts from bacteria isolated from gold mine tailings in South Africa. Bacterial strains were identified using 16S rRNA sequencing. The crude extracts obtained from the bacteria were tested against Mycobacterium tuberculosis H37Rv, Mycobacterium smegmatis mc2155, and Mycobacterium aurum A+. Untargeted HPLC-qTOF and molecular networking were used to identify the functional constituents present in extracts that exhibited inhibitory activity. A virtual screening workflow (VSW) was used to filter compounds that were strong binders to Mycobacterium tuberculosis Pks13 and PknG. The ligands returned from the VSW were subjected to optimization using density functional theory (DFT) at M06-2X/6-311++ (d,p) level of theory and basis set implemented in Gaussian16 Rev.C01. The optimized ligands were re-docked against Mycobacterium tuberculosis Pks13 and PknG. Molecular dynamics simulation and molecular mechanics generalized born surface area were used to evaluate the stability of the protein-ligand complexes formed by the identified hits. The hit that showed promising binding characteristics was virtually modified through multiple synthetic routes using reaction-driven enumeration. Three bacterial isolates showed significant activity against the two strains of Mycobacterium, while only two, Bacillus subtilis and Bacillus licheniformis, exhibited activity against both Mycobacterium tuberculosis H37Rv, Mycobacterium smegmatis mc2155, and Mycobacterium aurum A+. The tentatively identified compounds from the bacterial crude extracts belonged to various classes of natural compounds associated with antimicrobial activity. Two compounds, cyclo-(L-Pro-4-OH-L-Leu) and vazabitide A, showed strong binding against PknG and Pks13, with pre-MD MM-GBSA values of - 42.8 kcal/mol and - 47.6 kcal/mol, respectively. The DFT-optimized compounds exhibited the same docking scores as the ligands optimized using the OPSL-4 force field. After modifying vazabitide A, its affinity to the Pks13 binding site increased to - 85.8 kcal/mol, as revealed by the post-MD MM-GBSA analysis. This study highlights the potential of bacteria isolates from gold mine tailings as a source of new scaffolds for designing and optimizing anti-Mycobacterium agents. These agents synthesized in-silico can be further tested in-vitro to evaluate their efficacy.
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Affiliation(s)
- Kudakwashe Nyambo
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa
| | - Kudzanai Ian Tapfuma
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa
| | - Francis Adu-Amankwaah
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa
| | - Lauren Julius
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa
| | - Lucinda Baatjies
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa
| | - Idah Sithole Niang
- Department of Biotechnology and Biochemistry, University of Zimbabwe, B064, Mount Pleasant, Harare, Zimbabwe
| | - Liezel Smith
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa
| | - Krishna Kuben Govender
- Department of Chemical Sciences, University of Johannesburg, Doornfontein Campus, P.O. Box 17011, Johannesburg, 2028, South Africa
- National Institute for Theoretical and Computational Sciences (NITheCS), Cape Town, South Africa
| | - Mkhuseli Ngxande
- Computer Science Division, Department of Mathematical Sciences, Faculty of Science, University of Stellenbosch, Matieland, South Africa
| | - Daniel J Watson
- Division of Clinical Pharmacology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Lubbe Wiesner
- Division of Clinical Pharmacology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Vuyo Mavumengwana
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa.
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Goel KK, Thapliyal S, Kharb R, Joshi G, Negi A, Kumar B. Imidazoles as Serotonin Receptor Modulators for Treatment of Depression: Structural Insights and Structure-Activity Relationship Studies. Pharmaceutics 2023; 15:2208. [PMID: 37765177 PMCID: PMC10535231 DOI: 10.3390/pharmaceutics15092208] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/13/2023] [Accepted: 08/19/2023] [Indexed: 09/29/2023] Open
Abstract
Serotoninergic signaling is identified as a crucial player in psychiatric disorders (notably depression), presenting it as a significant therapeutic target for treating such conditions. Inhibitors of serotoninergic signaling (especially selective serotonin reuptake inhibitors (SSRI) or serotonin and norepinephrine reuptake inhibitors (SNRI)) are prominently selected as first-line therapy for the treatment of depression, which benefits via increasing low serotonin levels and norepinephrine by blocking serotonin/norepinephrine reuptake and thereby increasing activity. While developing newer heterocyclic scaffolds to target/modulate the serotonergic systems, imidazole-bearing pharmacophores have emerged. The imidazole-derived pharmacophore already demonstrated unique structural characteristics and an electron-rich environment, ultimately resulting in a diverse range of bioactivities. Therefore, the current manuscript discloses such a specific modification and structural activity relationship (SAR) of attempted derivatization in terms of the serotonergic efficacy of the resultant inhibitor. We also featured a landscape of imidazole-based development, focusing on SAR studies against the serotoninergic system to target depression. This study covers the recent advancements in synthetic methodologies for imidazole derivatives and the development of new molecules having antidepressant activity via modulating serotonergic systems, along with their SAR studies. The focus of the study is to provide structural insights into imidazole-based derivatives as serotonergic system modulators for the treatment of depression.
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Affiliation(s)
- Kapil Kumar Goel
- Department of Pharmaceutical Sciences, Gurukul Kangri (Deemed to Be University), Haridwar 249404, Uttarakhand, India
| | - Somesh Thapliyal
- Department of Pharmaceutical Sciences, HNB Garhwal University, Chauras Campus, Srinagar Garhwal 246174, Uttarakhand, India (G.J.)
| | - Rajeev Kharb
- Amity Institute of Pharmacy, Amity University, Noida 201313, Uttar Pradesh, India
| | - Gaurav Joshi
- Department of Pharmaceutical Sciences, HNB Garhwal University, Chauras Campus, Srinagar Garhwal 246174, Uttarakhand, India (G.J.)
| | - Arvind Negi
- Department of Bioproduct and Biosystems, Aalto University, 02150 Espoo, Finland
| | - Bhupinder Kumar
- Department of Pharmaceutical Sciences, HNB Garhwal University, Chauras Campus, Srinagar Garhwal 246174, Uttarakhand, India (G.J.)
- Department of Chemistry, Graphic Era (Deemed to Be University), Dehradun 248002, Uttarakhand, India
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Liu T, Yao X, Zhang R, Wu T, Liu Z, Li D, Dong Q. Design, Synthesis and Biological Evaluation of Novel Indole-piperazine Derivatives as Antibacterial Agents. Bioorg Med Chem Lett 2023; 89:129320. [PMID: 37156392 DOI: 10.1016/j.bmcl.2023.129320] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 04/10/2023] [Accepted: 05/03/2023] [Indexed: 05/10/2023]
Abstract
Herein, a series of novel indole-piperazine derivatives were synthesized. Bioassay results showed the title compounds exhibited moderate to good bacteriostatic efficacy against the test Gram-positive bacteria and Gram-negative bacteria, including methicillin-resistant Staphylococcus aureus (MRSA). Among theses compounds, three remarkable compounds 8f, 9a, and 9h exhibited superior in vitro antibacterial profiles for anti- S. aureus and anti-MRSA to that of gentamicin. Hit compound 9a manifested a rapid bactericidal kinetic effect on MRSA,with no resistance observed after 19 days of sequential passaging. And 8 µg/mL of compound 9a displayed considerable post antibacterial effects to that of ciprofloxacin at the concentration of 2 µg/mL. Cytotoxic and ADMET studies indicated, to some extent, compounds 8f, 9a, and 9h were up to the standard for antibacterial drugs. These results suggest that indole/piperazine derivatives based on the title compounds can serve as a new scaffold for antimicrobial development.
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Affiliation(s)
- Ting Liu
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, China
| | - Xiaofang Yao
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, China
| | - Rongrong Zhang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, China
| | - Tianling Wu
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, China
| | - Zhigang Liu
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, China.
| | - Ding Li
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, China.
| | - Qingjian Dong
- Department of Nuclear Medicine and PET, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
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Metwally NH, El-Desoky EA. Novel Thiopyrano[2,3- d]thiazole-pyrazole Hybrids as Potential Nonsulfonamide Human Carbonic Anhydrase IX and XII Inhibitors: Design, Synthesis, and Biochemical Studies. ACS OMEGA 2023; 8:5571-5592. [PMID: 36816682 PMCID: PMC9933482 DOI: 10.1021/acsomega.2c06954] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/10/2023] [Indexed: 06/18/2023]
Abstract
In recent years, molecular hybridization strategies have developed into a potent strategy for drug discovery. A series of novel thiopyrano[2,3-d]thiazoles linked to the pyrazole moiety was designed and developed as anticancer agents by a molecular hybridization. Target compounds were synthesized and characterized by spectroscopic tools as well as X-ray crystallography analysis as in the case of thiopyrano[2,3-d]thiazole derivative 5a. The MTT assay was used to demonstrate the in vitro efficacy of compounds 5a-g and 7a-j on MCF-7 and HePG-2. The results showed that some cycloadducts such as bromophenyl-4-thioxo-2-thiazolidinone 3e, 4-methylphenyl derivative of thiopyrano[2,3-d]thiazole 5d, and 6-substituted-thiopyrano[2,3-d]thiazoles 7e-j displayed good to excellent IC50 in the range of 10.08 ± 1.5 to 25.95 ± 2.8 μg/mL against the MCF-7 cell line and from 7.83 ±2.1 to 13.37 ± 1.2 μg/mL against the HePG-2 cell line. To explore the enzymatic tests for isozymes hCAIX and hCAXII, the most promising eight compounds 3e, 5d, and 7e-j with IC50 ranging from 7.83 ± 2.1 to 25.95 ± 2.8 μM were chosen. Compound 7e exhibited an IC50 (0.067 ± 0.003 μM) similar to that of the standard drug AZA against CAIX (0.059 ± 0.003 μM)). For CAXII, the compound 7i had an IC50 equal to 0.123 ± 0.007 μM compared to that of AZA (0.083 ± 0.005 μM). In addition, using flow cytometry, cell cycle analysis and apoptosis studies in HePG-2 were performed for the two potent anticancer and selective carbonic anhydrase agents (7e and 7i). An enzymatic assay of these two compounds against caspase-9 was also examined. Interestingly, the molecular docking studies revealed that compounds 7e and 7i successfully embedded themselves in the active pockets of the CAIX and CAXII enzymes through different interactions. Overall, the novel thiopyrano[2,3-d]thiazole-pyrazole hybrids (7e and 7i) were suggested to be potent and selective inhibitors of CAIX and CAXII.
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Benzo[ d]thiazole-2-carboxamides as new antituberculosis chemotypes inhibiting mycobacterial ATP phosphoribosyl transferase. Future Med Chem 2022; 14:1847-1864. [PMID: 36444737 DOI: 10.4155/fmc-2022-0226] [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: 11/30/2022] Open
Abstract
Aims: The screening of antimycobacterial benzo[d]thiazole-2-carboxamides against ATP-phosphoribosyl transferase (ATP-PRTase) was conducted. Materials & methods: The antitubercular potential of compounds 1 and 2 against ATP-PRTase was assessed through the determination of half maximal effective concentration (EC50) and binding constant (Kd), as well as competitive inhibitory studies and studies of perturbation of secondary structure, molecular modeling and L-histidine complementation assay. Results & conclusion: Compounds 1n and 2a significantly inhibited ATP-PRTase as evidenced by their EC50 and Kd values and the perturbation of the secondary structure study. Compound 1n exhibited stronger competitive inhibition toward ATP compared with 2a. The inhibition of the growth of Mycobacterium tuberculosis by targeting the L-histidine biosynthesis pathway and molecular modeling studies further supported the inhibition of ATP-PRTase.
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7
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Bacterial FtsZ inhibition by benzo[ d]imidazole-2-carboxamide derivative with anti-TB activity. Future Med Chem 2022; 14:1361-1373. [DOI: 10.4155/fmc-2022-0120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Aims: The present study aimed to assess the mode of action of previously reported anti- Mycobacterium tuberculosis benzo[ d]imidazole-2-carboxamides against FtsZ along with their antibacterial potential. Materials & methods: The anti-mycobacterial action of benzo[ d]imidazole-2-carboxamides against FtsZ was evaluated using inhibition of Bacillus subtilis 168, light scattering assay, circular dichroism spectroscopy, in silico molecular docking and molecular dynamics simulations. Results & conclusion: Three compounds (1k, 1o and 1e) were active against isoniazid-resistant strains. Four compounds (1h, 1i, 1o and 4h) showed >70% inhibition against B. subtilis 168. Compound 1o was the most potent inhibitor (91 ± 5% inhibition) of B. subtilis 168 FtsZ and perturbed its secondary structure. Molecular docking and molecular dynamics simulation of complexed 1o suggested M. tuberculosis FtsZ as a possible target for antitubercular activity.
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Chudasama SJ, Shah BJ, Patel KM, Dhameliya TM. The spotlight review on ionic liquids catalyzed synthesis of aza- and oxa-heterocycles reported in 2021. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119664] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Shah R, Shah M, Kumar V, Verma PK. Synthesis and antimycobacterial evaluation of pyrazinamide, benzimidazole and carboxamide derivatives. J Heterocycl Chem 2022. [DOI: 10.1002/jhet.4557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Rashmi Shah
- Department of Pharmaceutical Sciences Maharshi Dayanand University Rohtak Haryana India
| | | | - Vipan Kumar
- Department of Pharmaceutical Chemistry JCDV College of Pharmacy Sirsa India
| | - Prabhakar Kumar Verma
- Department of Pharmaceutical Sciences Maharshi Dayanand University Rohtak Haryana India
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Ullah S, Pelletier J, Sévigny J, Iqbal J. Synthesis and Biological Evaluation of Arylamide Sulphonate Derivatives as Ectonucleotide Pyrophosphatase/Phosphodiesterase-1 and -3 Inhibitors. ACS OMEGA 2022; 7:26905-26918. [PMID: 35936461 PMCID: PMC9352230 DOI: 10.1021/acsomega.2c03473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
Aberrant level of ectonucleotide pyrophosphatase/phosphodiesterase-1 and -3 is linked with numerous disorders, for instance, diabetes, cancer, osteoarthritis, chondrocalcinosis, and allergic reactions. These disorders may be cured or minimized by blocking the activity of ENPP1 and ENPP3 isozymes. In this study, arylamide sulphonates were synthesized, characterized, and evaluated for their capability to affect the activity of isozymes ENPP1 and ENPP3. Among the selective inhibitors of ENPP1, compounds 4f and 4q exhibited sub-micromolar IC50 values of 0.28 ± 0.08 and 0.37 ± 0.03 μM, respectively, followed by 7a, with IC50 equal to 0.81 ± 0.05 μM, whereas out of the selective inhibitors of isozyme ENPP3, 4t and 7d preferably lessened the activity to half of the maximal inhibitory concentration of 0.15 ± 0.04 and 0.16 ± 0.01 μM alternatively. In addition, many structures including 4c, 4g, 4k, 4l, 4n, 4o, 4r, 4s, 7b, 7c, and 7e inhibited the activity of both isozymes to a significant level. Enzyme kinetic study of compound 4j revealed an uncompetitive mode of inhibition of ENPP1 isozyme, while 7e competitively blocked the activity of ENPP3. Cell viability analysis revealed the compound 4o as a cytotoxic agent against MCF7 (human breast cancer cell line) with a percentage inhibition of 63.2 ± 2.51%, whereas compounds 4c, 4d, 4n, and 7d decreased the HeLa cell viability (human cervical cancer cell line) to more than 50%. The tested compounds were non-cytotoxic against HEK293 (a human embryonic kidney cell line). Molecular docking analysis of selected inhibitors of both isozymes produced optimistic interactions with the influential amino acids, such as Leu290, Lys295, Tyr340, Asp376, His380, and Pro323 of ENPP1, whereas residues Asn226, His329, Leu239, Tyr289, Pro272, Tyr320, and Ala205 of ENPP3 crystallographic structure formed interactions with the potent inhibitors.
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Affiliation(s)
- Saif Ullah
- Centre
for Advanced Drug Research, COMSATS University
Islamabad, Abbottabad
Campus, Abbottabad22060, Pakistan
- Department
of Pharmacy, COMSATS University Islamabad, Abbottabad Campus, Abbottabad22060, Pakistan
| | - Julie Pelletier
- Centre
de Recherche Du CHU de Québec−Université Laval, QuébecG1V 4G2, QC, Canada
| | - Jean Sévigny
- Centre
de Recherche Du CHU de Québec−Université Laval, QuébecG1V 4G2, QC, Canada
- Département
de Microbiologie-infectiologie et D’immunologie, Faculté
de Médecine, Université Laval, QuébecG1V 0A6, QC, Canada
| | - Jamshed Iqbal
- Centre
for Advanced Drug Research, COMSATS University
Islamabad, Abbottabad
Campus, Abbottabad22060, Pakistan
- Department
of Pharmacy, COMSATS University Islamabad, Abbottabad Campus, Abbottabad22060, Pakistan
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Sureja DK, Shah AP, Gajjar ND, Jadeja SB, Bodiwala KB, Dhameliya TM. In-silico Computational Investigations of AntiViral Lignan Derivatives as Potent Inhibitors of SARS CoV-2. ChemistrySelect 2022; 7:e202202069. [PMID: 35942360 PMCID: PMC9349937 DOI: 10.1002/slct.202202069] [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: 05/28/2022] [Accepted: 07/05/2022] [Indexed: 11/11/2022]
Abstract
Due to alarming outbreak of pandemic COVID-19 in recent times, there is a strong need to discover and identify new antiviral agents acting against SARS CoV-2. Among natural products, lignan derivatives have been found effective against several viral strains including SARS CoV-2. Total of twenty-seven reported antiviral lignan derivatives of plant origin have been selected for computational studies to identify the potent inhibitors of SARS CoV-2. Molecular docking study has been carried out in order to predict and describe molecular interaction between active site of enzyme and lignan derivatives. Out of identified hits, clemastatin B and erythro-strebluslignanol G demonstrated stronger binding and high affinity with all selected proteins. Molecular dynamics simulation studies of clemastin B and savinin against promising targets of SARS CoV-2 have revealed their inhibitory potential against SARS CoV-2. In fine, in-silico computational studies have provided initial breakthrough in design and discovery of potential SARS CoV-2 inhibitors.
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Affiliation(s)
- Dipen K. Sureja
- Department of Pharmaceutical Chemistry and Quality AssuranceL. M. College of Pharmacy, NavrangpuraAhmedabad380009, GujaratIndia
| | - Ashish P. Shah
- Department of Pharmacy, Sumandeep VidyapeethVadodara391760, GujaratIndia
| | - Normi D. Gajjar
- Department of Pharmaceutical Chemistry and Quality AssuranceL. M. College of Pharmacy, NavrangpuraAhmedabad380009, GujaratIndia
| | - Shwetaba B. Jadeja
- Department of Pharmaceutical Chemistry and Quality AssuranceL. M. College of Pharmacy, NavrangpuraAhmedabad380009, GujaratIndia
| | - Kunjan B. Bodiwala
- Department of Pharmaceutical Chemistry and Quality AssuranceL. M. College of Pharmacy, NavrangpuraAhmedabad380009, GujaratIndia
| | - Tejas M. Dhameliya
- Department of Pharmaceutical Chemistry and Quality AssuranceL. M. College of Pharmacy, NavrangpuraAhmedabad380009, GujaratIndia
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An Overview of the Biological Evaluation of Selected Nitrogen-Containing Heterocycle Medicinal Chemistry Compounds. Int J Mol Sci 2022; 23:ijms23158117. [PMID: 35897691 PMCID: PMC9368212 DOI: 10.3390/ijms23158117] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/16/2022] [Accepted: 07/21/2022] [Indexed: 11/26/2022] Open
Abstract
Heterocyclic compounds are a class of compounds of natural origin with favorable properties and hence have major pharmaceutical significance. They have an exceptional adroitness favoring their use as diverse smart biomimetics, in addition to possessing an active pharmacophore in a complex structure. This has made them an indispensable motif in the drug discovery field. Heterocyclic compounds are usually classified according to the ring size, type, and the number of heteroatoms present in the ring. Among different heterocyclic ring systems, nitrogen heterocyclic compounds are more abundant in nature. They also have considerable pharmacological significance. This review highlights recent pioneering studies in the biological assessment of nitrogen-containing compounds, namely: triazoles, tetrazoles, imidazole/benzimidazoles, pyrimidines, and quinolines. It explores publications between April 2020 and February 2022 and will benefit researchers in medicinal chemistry and pharmacology. The present work is organized based on the size of the heterocyclic ring.
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Si A, Landgraf AD, Geden S, Sucheck SJ, Rohde KH. Synthesis and Evaluation of Marine Natural Product-Inspired Meroterpenoids with Selective Activity toward Dormant Mycobacterium tuberculosis. ACS OMEGA 2022; 7:23487-23496. [PMID: 35847331 PMCID: PMC9281309 DOI: 10.1021/acsomega.2c01887] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Tuberculosis is a disease caused primarily by the organism Mycobacterium tuberculosis (Mtb), which claims about 1.5 million lives every year. A challenge that impedes the elimination of this pathogen is the ability of Mtb to remain dormant after primary infection, thus creating a reservoir for the disease in the population that reactivates under more ideal conditions. A better understanding of the physiology of dormant Mtb and therapeutics able to kill these phenotypically tolerant bacilli will be critical for completely eradicating Mtb. Our groups are focusing on characterizing the activity of derivatives of the marine natural product (+)-puupehenone (1). Recently, the Rohde group reported that puupehedione (2) and 15-α-methoxypuupehenol (3) exhibit enhanced activity in an in vitro multi-stress dormancy model of Mtb. To optimize the antimycobacterial activity of these terpenoids, novel 15-α-methoxy- and 15-α-acetoxy-puupehenol esters were prepared from (+)-puupehenone (1) accessed through a (+)-sclareolide-derived β-hydroxyl aldehyde. For added diversity, various congeners related to (1) were also prepared from a common borono-sclareolide donor, which resulted in the synthesis of epi-puupehenol and the natural products (+)-chromazonarol and (+)-yahazunol. In total, we generated a library of 24 compounds, of which 14 were found to be active against Mtb, and the most active compounds retained the enhanced activity against dormant Mtb seen in the parent compound. Several of the 15-α-methoxy- and 15-α-acetoxy-puupehenol esters possessed potent activity against actively dividing and dormant Mtb. Intriguingly, the closely related triisobutyl derivative 16 showed similar activity to 1 in actively dividing Mtb but lost about 178-fold activity against dormant Mtb. However, the monopivaloyl compound 13 showed a modest 3- to 4-fold loss in activity in both actively dividing and dormant Mtb relative to the activity of 1 revealing the importance of the free OH at C19 supporting the potential role of quinone methide formation as critical for activity in dormant Mtb. Elucidating important structure-activity relationships and the mechanism of action of this natural product-inspired chemical series may yield insights into vulnerable drug targets in dormant bacilli and new therapeutics to more effectively target dormant Mtb.
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Affiliation(s)
- Anshupriya Si
- Department
of Chemistry and Biochemistry, University
of Toledo, 2801 West Bancroft Street, Toledo, Ohio 43606, United
States
| | - Alexander D. Landgraf
- Department
of Chemistry and Biochemistry, University
of Toledo, 2801 West Bancroft Street, Toledo, Ohio 43606, United
States
| | - Sandra Geden
- Division
of Immunity and Pathogenesis, Burnett School of Biomedical Sciences,
College of Medicine, University of Central
Florida, Orlando, Florida 32827, United
States
| | - Steven J. Sucheck
- Department
of Chemistry and Biochemistry, University
of Toledo, 2801 West Bancroft Street, Toledo, Ohio 43606, United
States
| | - Kyle H. Rohde
- Division
of Immunity and Pathogenesis, Burnett School of Biomedical Sciences,
College of Medicine, University of Central
Florida, Orlando, Florida 32827, United
States
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14
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Bhakhar KA, Vaghela PV, Varakala SD, Chudasma SJ, Gajjar ND, Nagar PR, Sriram D, Dhameliya TM. Indole‐2‐carboxamides as New Anti‐Mycobacterial Agents: Design, Synthesis, Biological Evaluation and Molecular Modeling against mmpL3. ChemistrySelect 2022. [DOI: 10.1002/slct.202201813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Kaushikkumar A. Bhakhar
- Department of Pharmaceutical Chemistry and Quality Assurance L. M. College of Pharmacy, Navrangpura Ahmedabad 380009 Gujarat India
| | - Punit V. Vaghela
- Department of Pharmaceutical Chemistry and Quality Assurance L. M. College of Pharmacy, Navrangpura Ahmedabad 380009 Gujarat India
| | - Saiprasad D. Varakala
- Department of Pharmacy Birla Institute of Technology & Science - Pilani Hyderabad Campus, Jawahar Nagar Hyderabad 500 078 India
| | - Shrdhhaba J. Chudasma
- Department of Pharmaceutical Chemistry and Quality Assurance L. M. College of Pharmacy, Navrangpura Ahmedabad 380009 Gujarat India
| | - Normi D. Gajjar
- Department of Pharmaceutical Chemistry and Quality Assurance L. M. College of Pharmacy, Navrangpura Ahmedabad 380009 Gujarat India
| | - Prinsa R. Nagar
- Department of Pharmaceutical Chemistry and Quality Assurance L. M. College of Pharmacy, Navrangpura Ahmedabad 380009 Gujarat India
| | - Dharmarajan Sriram
- Department of Pharmacy Birla Institute of Technology & Science - Pilani Hyderabad Campus, Jawahar Nagar Hyderabad 500 078 India
| | - Tejas M. Dhameliya
- Department of Pharmaceutical Chemistry and Quality Assurance L. M. College of Pharmacy, Navrangpura Ahmedabad 380009 Gujarat India
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15
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Ray R, Das S, Lobo M, Birangal SR, Shenoy GG. A holistic molecular modelling approach to design novel indole-2-carboxamide derivatives as potential inhibitors of MmpL3. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2022; 33:551-581. [PMID: 35850557 DOI: 10.1080/1062936x.2022.2096691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
Tuberculosis is an infectious air-borne disease and one of the leading causes of death globally among all infectious diseases. There is an urgent need to develop antitubercular drugs that would be highly efficient and less toxic than the presently available marketed drugs. Mycobacterium membrane protein large 3 (MmpL3) is an emerging drug target in tuberculosis with various classes of molecules that have been known to inhibit it. In this study, a dataset of indole-2-carboxamides showing antitubercular activity by inhibiting MmpL3 was utilized. Initially, a chimera-based homology model was developed and docking was performed with the filtered dataset to analyse the interactions. Thereafter, molecular dynamics simulations were run with representative molecules to gain a better insight on the binding patterns. To attain a more quantitative correlation, an atom-based 3D QSAR model was developed which complemented the results from the previous models. A library of novel indole-2-carboxamides was then generated using core hopping-based ligand enumeration and upon screening on our workflow model it predicted three molecules as potent antitubercular compounds. This work not only helps to gain new insights on the interactions at the MmpL3 binding site but also provides novel indole-2-carboxamides having the potential to become antitubercular drugs in future.
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Affiliation(s)
- R Ray
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - S Das
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - M Lobo
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - S R Birangal
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - G G Shenoy
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
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16
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17
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Dhameliya TM, Devani AA, Patel KA, Shah KC. Comprehensive Coverage on Anti‐mycobacterial Endeavour Reported in 2021. ChemistrySelect 2022. [DOI: 10.1002/slct.202200921] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
| | - Aanal A. Devani
- L. M. College of Pharmacy, Navrangpura Ahmedabad 380 009 Gujarat India
| | - Krupa A. Patel
- L. M. College of Pharmacy, Navrangpura Ahmedabad 380 009 Gujarat India
| | - Kashvi C. Shah
- L. M. College of Pharmacy, Navrangpura Ahmedabad 380 009 Gujarat India
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18
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Dhameliya TM, Nagar PR, Bhakhar KA, Jivani HR, Shah BJ, Patel KM, Patel VS, Soni AH, Joshi LP, Gajjar ND. Recent advancements in applications of ionic liquids in synthetic construction of heterocyclic scaffolds: A spotlight. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118329] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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19
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A review on synthetic account of 1,2,4-oxadiazoles as anti-infective agents. Mol Divers 2022; 26:2967-2980. [PMID: 34984590 PMCID: PMC8727175 DOI: 10.1007/s11030-021-10375-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/24/2021] [Indexed: 11/03/2022]
Abstract
Most of the currently marketed drugs consist of heterocyclic scaffolds containing nitrogen and or oxygen as heteroatoms in their structures. Several research groups have synthesized diversely substituted 1,2,4-oxadiazoles as anti-infective agents having anti-bacterial, anti-viral, anti-leishmanial, etc. activities. For the first time, the present review article will provide the coverage of synthetic account of 1,2,4-oxadiazoles as anti-infective agents along with their potential for SAR, activity potential, promising target for mode of action. The efforts have been made to provide the chemical intuitions to the reader to design new chemical entity with potential of anti-infective activity. This review will mark the impact as the valuable, comprehensive and pioneered work along with the library of synthetic strategies for the organic and medicinal chemists for further refinement of 1,2,4-oxadiazole as anti-infective agents.
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20
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Bhakhar KA, Sureja DK, Dhameliya TM. Synthetic account of indoles in search of potential anti-mycobacterial agents: A review and future insights. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131522] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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21
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Recent advancements and developments in search of anti-tuberculosis agents: A quinquennial update and future directions. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131473] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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22
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Biswas SK, Das D. One-pot Synthesis of Pyrano[2,3-c]pyrazole Derivatives via Multicomponent Reactions (MCRs) and their Applications in Medicinal Chemistry. MINI-REV ORG CHEM 2021. [DOI: 10.2174/1570193x19666211220141622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Many pyrano[2,3-c]pyrazole derivatives display diverse biological activities and some of them are known as anticancer, analgesic, anticonvulsant, antimicrobial, anti-inflammatory, and anti-malarial agents. In recent years, easy convergent, multicomponent reactions (MCRs) have been adopted to make highly functionalizedpyrano[2,3-c]pyrazole derivatives of biological interest. The synthesis of 1,4-dihydropyrano[2,3-c]pyrazole (1,4-DHPP, 2), 2,4-dihydropyrano[2,3-c]pyrazole (2,4-DHPP, 3), 4-hydroxypyrano[2,3-c]pyrazole (4-HPP, 4) derivatives, 1,4,4-substitied pyranopyrazole (SPP, 5) were reported via two-, three-, four- and five-component reactions (MCRs).
Methods:
This review article compiles the preparation of pyrano[2,3-c]pyrazole derivatives, and it highlights the applications of various pyrano[2,3-c]pyrazole derivatives in medicinal chemistry.
Results:
Varieties of pyrano[2,3-c]pyrazole derivatives were achieved via “One-pot” multicomponent reactions (MCRs). Different reaction conditions in the presence of a catalyst or without catalysts were adapted to prepare the pyrano[2,3-c]pyrazole derivatives.
Conclusion:
Biologically active pyrano[2,3-c]pyrazole derivatives were prepared and used in drug discovery research.
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Affiliation(s)
- Swapan Kumar Biswas
- Department of Chemistry, Sree Chaitanya College, Habra, 24-Pgs(N), West Bengal 743268, India
| | - Debasis Das
- Department Discovery Chemistry Research, Arromax Pharmatech Co. Ltd.Sangtian Island Innovation Park, No. 1 Huayun Road, SIP, Suzhou 215123, China
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23
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Abdullahi M, Das N, Adeniji SE, Usman AK, Sani AM. In-silico design and ADMET predictions of some new imidazo[1,2-a]pyridine-3-carboxamides (IPAs) as anti-tubercular agents. J Clin Tuberc Other Mycobact Dis 2021; 25:100276. [PMID: 34568589 PMCID: PMC8450222 DOI: 10.1016/j.jctube.2021.100276] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Tuberculosis (TB) is one of the leading infectious diseases worldwide even with the ravaging COVID-19 pandemic in recent times. This mandated further search and exploration of more possible anti-TB drug candidates against M. tuberculosis strains. As an extension of our previous work on the homology modeled cytochrome b subunit of the bc1 complex (QcrB) of Mycobacterium tuberculosis, an in-silico design was carried out in order to further explore more newly potential anti-TB compounds. Ligand 26 was selected as the lead template (scaffold A) based on our previous docking results and its less bulky structure. Successively, eight (8) new ligands (A1–A8) were designed with better binding affinities in comparison to the scaffold template (−6.8 kcal/mol) and isoniazid standard drug (−6.00 kcal/mol) respectively. In addition, three (3) designed ligands namely, A6, A2, and A7 with higher binding affinities were validated via ADME and toxicity prediction analysis, and the results showed zero violations of Lipinski rules with similar bioavailability, and high rate in gastrointestinal absorption, while toxicity parameters such as carcinogenicity and cytotoxicity were all predicted as non-toxic (inactiveness). The designed IPA compounds in the present study could serve as a promising gateway that could help the medicinal and synthetic chemist in the exploration of a new set of derivatives as anti-TB agents. Therefore, this research strongly recommends further experimental consideration of the newly designed IPA compounds through synthesis, in-vitro and in-vivo studies to validate the theoretical findings.
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Affiliation(s)
- Mustapha Abdullahi
- Faculty of Sciences, Department of Pure and Applied Chemistry, Kaduna State University, Tafawa Balewa Way, Kaduna State, Nigeria
| | - Niloy Das
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
| | - Shola Elijah Adeniji
- Faculty of Physical Sciences, Department of Chemistry, Ahmadu Bello University, P.M.B. 1044 Zaria, Kaduna State, Nigeria
| | - Alhassan Kabiru Usman
- Faculty of Sciences, Department of Pure and Applied Chemistry, Kaduna State University, Tafawa Balewa Way, Kaduna State, Nigeria
| | - Ahmad Muhammad Sani
- Faculty of Sciences, Department of Pure and Applied Chemistry, Kaduna State University, Tafawa Balewa Way, Kaduna State, Nigeria
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