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Choudhary DK, Chaturvedi N, Singh A, Mishra A. Catechin isolated from faba beans ( Vicia faba L.): insights from oxidative stress and hypoglycemic effect in yeast cells through confocal microscopy, flow cytometry, and in silico strategy. J Biomol Struct Dyn 2022; 40:10470-10480. [PMID: 34192480 DOI: 10.1080/07391102.2021.1945953] [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: 12/16/2022]
Abstract
The present aim of this investigation was to evaluate the effect of catechin from faba beans on oxidative stress and glucose uptake in yeast cells. Flow cytometry approach indicated that 2-NBDG (1.98 ± 0.37) seed extract had a lower relative fluorescence signal than methanol (5.98 ± 0.67) and acetone seed extract (4.43 ± 0.55). In comparison to the control and seed extract, H2O2 exposure increased the apoptosis rate of yeast cells from 8.20% to 64.80%. Yeast cells incubated with H2O2 produced significantly more ROS intensity (162 ± 4.32, p < 0.05) than control cells (118 ± 2.52, p < 0.05) and less than seed extract-treated cells. Molecular dynamics simulation studies were performed for cat:α-amylase (catechin-α-amylase complex) which revealed the stable and mixed mode of inhibition during a simulation. The synergistic action of polyphenols or catechin present in seed extract may be responsible for the anti-oxidative stress and hypoglycaemic effects. The findings of this study may provide insight into the further development of a novel antidiabetic drug for T2DM. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dhiraj Kumar Choudhary
- Biomolecular Engineering Laboratory, School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Navaneet Chaturvedi
- Biomolecular Engineering Laboratory, School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Amit Singh
- Department of Pharmacology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Abha Mishra
- Biomolecular Engineering Laboratory, School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
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2
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Carvalho-Kelly LF, Dick CF, Rocco-Machado N, Gomes-Vieira AL, Paes-Vieira L, Meyer-Fernandes JR. Anaerobic ATP synthesis pathways and inorganic phosphate transport and their possible roles in encystment in Acanthamoeba castellanii. Cell Biol Int 2022; 46:1288-1298. [PMID: 35673988 DOI: 10.1002/cbin.11830] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 04/07/2022] [Accepted: 04/11/2022] [Indexed: 12/12/2022]
Abstract
Acanthamoeba castellanii is the etiological agent of amoebic keratitis and is present in the environment in trophozoite or cyst forms. Both forms can infect the vertebrate host and colonize different tissues. The high resistance of cysts to standard drugs used in clinics contributes to the lack of effective treatments. Therefore, in this context, studies have emerged to understand cyst physiology and metabolism. Phosphate transporters are proteins responsible for the uptake of extracellular inorganic phosphate and transport to the cytosol. This work aims to verify the relationship between Pi transport and energetic metabolism in cysts of A. castellanii. The phosphate uptake ratio was higher in cysts compared with trophozoites. Recently, three sequences related to phosphate transporters have been identified in the A. castellanii genome (AcPHS1, AcPHS2, and AcPHS3); the messenger RNA expression levels of which differ depending on the amoeba life form. Pi uptake in cysts displayed peak activity at alkaline pH, whereas Pi transport in trophozoites was not affected in the same pH ranges. Cysts harbor a low-affinity Pi transport system (K0,5 and Vmax values of 1.76 ± 0.26 mM and 104.6 ± 6.3 nmol Pi × h-1 × 106 cells) compared to the trophozoite phosphate transport system. Pi transport seems important for anaerobic adenosine triphosphate synthesis in cysts, which initially occurs through the glycolytic pathway and subsequently through the pyruvate ferredoxin oxidoreductase pathway. Altogether, these results suggest that contrary to that previously postulated, cysts are active metabolic forms, and, as noted in trophozoites, phosphate uptake is important for energetic metabolism.
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Affiliation(s)
| | - Claudia Fernanda Dick
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Nathalia Rocco-Machado
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - André Luiz Gomes-Vieira
- Departamento de Bioquímica, Instituto de Química, Universidade Federal Rural do Rio de Janeiro, Seropédica, Brazil
| | - Lisvane Paes-Vieira
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - José Roberto Meyer-Fernandes
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
- Institute of National Science and Technology of Structural Biology and Bioimage (INCTBEB), CCS, Bloco H, Cidade Universitária, Ilha do Fundão, Rio de Janeiro, Brazil
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3
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Identification of novel paralytic shellfish toxin binding protein via homology modeling and molecular docking. Toxicon 2022; 211:61-69. [DOI: 10.1016/j.toxicon.2022.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 02/21/2022] [Accepted: 03/14/2022] [Indexed: 11/21/2022]
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Chandra A, Chaudhary M, Qamar I, Singh N, Nain V. In silico identification and validation of natural antiviral compounds as potential inhibitors of SARS-CoV-2 methyltransferase. J Biomol Struct Dyn 2021; 40:6534-6544. [PMID: 33583328 PMCID: PMC7885726 DOI: 10.1080/07391102.2021.1886174] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The novel Coronavirus disease 2019 (COVID-19) is potentially fatal and caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Due to the unavailability of any proven treatment or vaccination, the outbreak of COVID-19 is wreaking havoc worldwide. Hence, there is an urgent need for therapeutics targeting SARS-CoV-2. Since, botanicals are an important resource for several efficacious antiviral agents, natural compounds gaining significant attention for COVID-19 treatment. In the present study, methyltranferase (MTase) of the SARS-CoV-2 is targeted using computational approach. The compounds were identified using molecular docking, virtual screening and molecular dynamics simulation studies. The binding mechanism of each compound was analyzed considering the stability and energetic parameter using in silico methods. We have found four natural antiviral compounds Amentoflavone, Baicalin, Daidzin and Luteoloside as strong inhibitors of methyltranferase of SARS-CoV-2. ADMET prediction and target analysis of the selected compounds showed favorable results. MD simulation was performed for four top-scored molecules to analyze the stability, binding mechanism and energy requirements. MD simulation studies indicated energetically favorable complex formation between MTase and the selected antiviral compounds. Furthermore, the structural effects on these substitutions were analyzed using the principles of each trajectories, which validated the interaction studies. Our analysis suggests that there is a very high probability that these compounds may have a good potential to inhibit Methyltransferase (MTase) of SARS-CoV-2 and to be used in the treatment of COVID-19. Further studies on these natural compounds may offer a quick therapeutic choice to treat COVID-19. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- Anshuman Chandra
- School of Biotechnology, Gautam Buddha University, Greater Noida, India
| | - Meenakshi Chaudhary
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida, India
| | - Imteyaz Qamar
- School of Biotechnology, Gautam Buddha University, Greater Noida, India
| | - Nagendra Singh
- School of Biotechnology, Gautam Buddha University, Greater Noida, India
| | - Vikrant Nain
- School of Biotechnology, Gautam Buddha University, Greater Noida, India
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Chandra A, Gurjar V, Qamar I, Singh N. Identification of potential inhibitors of SARS-COV-2 endoribonuclease (EndoU) from FDA approved drugs: a drug repurposing approach to find therapeutics for COVID-19. J Biomol Struct Dyn 2020; 39:4201-4211. [PMID: 32462970 PMCID: PMC7298882 DOI: 10.1080/07391102.2020.1775127] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
SARS-CoV-2 is causative agent of COVID-19, which is responsible for severe social and economic disruption globally. Lack of vaccine or antiviral drug with clinical efficacy suggested that drug repurposing approach may provide a quick therapeutic solution to COVID-19. Nonstructural protein-15 (NSP15) encodes for an uridylate-specific endoribonuclease (EndoU) enzyme, essential for virus life cycle and an attractive target for drug development. We have performed in silico based virtual screening of FDA approved compounds targeting EndoU in search of COVID-19 drugs from commercially available approved molecules. Two drugs Glisoxepide and Idarubicin used for treatment for diabetes and leukemia, respectively, were selected as stronger binder of EndoU. Both the drugs bound to the active site of the viral endonuclease by forming attractive intermolecular interactions with catalytically essential amino acid residues, His235, His250, and Lys290. Molecular dynamics simulation studies showed stable conformation dynamics upon drugs binding to endoU. The binding free energies for Glisoxepide and Idarubicin were calculated to be –141 ± 11 and –136 ± 16 kJ/mol, respectively. The IC50 were predicted to be 9.2 µM and 30 µM for Glisoxepide and Idarubicin, respectively. Comparative structural analysis showed the stronger binding of EndoU to Glisoxepide and Idarubicin than to uridine monophosphate (UMP). Surface area calculations showed buried are of 361.8Å2 by Glisoxepide which is almost double of the area occupied by UMP suggesting stronger binding of the drug than the ribonucleotide. However, further studies on these drugs for evaluation of their clinical efficacy and dose formulations may be required, which may provide a quick therapeutic option to treat COVID-19. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- Anshuman Chandra
- School of Biotechnology, Gautam Buddha University, Greater Noida, Uttar Pradesh, India
| | - Vaishali Gurjar
- Savitri Bai Phule Balika Inter College, Greater Noida, Uttar Pradesh, India
| | - Imteyaz Qamar
- School of Biotechnology, Gautam Buddha University, Greater Noida, Uttar Pradesh, India
| | - Nagendra Singh
- School of Biotechnology, Gautam Buddha University, Greater Noida, Uttar Pradesh, India
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Pandey T, Ghosh A, Todur VN, Rajendran V, Kalita P, Kalita J, Shukla R, Chetri PB, Shukla H, Sonkar A, Lyngdoh DL, Singh R, Khan H, Nongkhlaw J, Das KC, Tripathi T. Draft Genome of the Liver Fluke Fasciola gigantica. ACS OMEGA 2020; 5:11084-11091. [PMID: 32455229 PMCID: PMC7241025 DOI: 10.1021/acsomega.0c00980] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/23/2020] [Indexed: 05/22/2023]
Abstract
Fascioliasis, a neglected foodborne disease caused by liver flukes (genus Fasciola), affects more than 200 million people worldwide. Despite technological advances, little is known about the molecular biology and biochemistry of these flukes. We present the draft genome of Fasciola gigantica for the first time. The assembled draft genome has a size of ∼1.04 Gb with an N50 and N90 of 129 and 149 kb, respectively. A total of 20 858 genes were predicted. The de novo repeats identified in the draft genome were 46.85%. The pathway included all of the genes of glycolysis, Krebs cycle, and fatty acid metabolism but lacked the key genes of the fatty acid biosynthesis pathway. This indicates that the fatty acid required for survival of the fluke may be acquired from the host bile. It may be hypothesized that the relatively larger F. gigantica genome did not evolve through genome duplications but rather is interspersed with many repetitive elements. The genomic information will provide a comprehensive resource to facilitate the development of novel interventions for fascioliasis control.
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Affiliation(s)
- Tripti Pandey
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Arpita Ghosh
- Eurofins
Genomics India Pvt. Ltd., Doddanekkundi, Bengaluru 560048, India
| | - Vivek N. Todur
- Eurofins
Genomics India Pvt. Ltd., Doddanekkundi, Bengaluru 560048, India
| | - Vijayakumar Rajendran
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Parismita Kalita
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Jupitara Kalita
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Rohit Shukla
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Purna B. Chetri
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Harish Shukla
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Amit Sonkar
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Denzelle Lee Lyngdoh
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Radhika Singh
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Heena Khan
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Joplin Nongkhlaw
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Kanhu Charan Das
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Timir Tripathi
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
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Chandra A, Goyal N, Qamar I, Singh N. Identification of hot spot residues on serine-arginine protein kinase-1 by molecular dynamics simulation studies. J Biomol Struct Dyn 2020; 39:1579-1587. [DOI: 10.1080/07391102.2020.1734487] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Anshuman Chandra
- School of Biotechnology, Gautam Buddha University, Greater Noida, Uttar Pradesh, India
| | - Nainee Goyal
- School of Biotechnology, Gautam Buddha University, Greater Noida, Uttar Pradesh, India
| | - Imteyaz Qamar
- School of Biotechnology, Gautam Buddha University, Greater Noida, Uttar Pradesh, India
| | - Nagendra Singh
- School of Biotechnology, Gautam Buddha University, Greater Noida, Uttar Pradesh, India
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