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Zhao R, Yang CR, Wang YX, Xu ZM, Li SQ, Li JC, Sun XQ, Wang HW, Wang Q, Zhang Y, Li JT. Fads2b Plays a Dominant Role in ∆6/∆5 Desaturation Activities Compared with Fads2a in Common Carp ( Cyprinus carpio). Int J Mol Sci 2023; 24:10638. [PMID: 37445816 DOI: 10.3390/ijms241310638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
Highly unsaturated fatty acids (HUFAs) are essential for mammalian health, development and growth. However, most mammals, including humans, are incapable of synthesizing n-6 and n-3 HUFAs. Fish can convert C18 unsaturated fatty acids into n-6 and n-3 HUFAs via fatty acid desaturase (Fads), in which Fads2 is a key enzyme in HUFA biosynthesis. The allo-tetraploid common carp theoretically encode two duplicated fads2 genes. The expression patterns and desaturase functions of these two homologous genes are still unknown. In this study, the full length of the fads2a and fads2b were identified in common carp (Cyprinus carpio). Expression analyses indicate that both genes were mainly expressed in the liver and the expression of fads2b is higher than fads2a at different developmental stages in carp embryos. Heterogenous expression and 3D docking analyses suggested that Fads2b demonstrated stronger ∆6 and ∆5 desaturase activities than Fads2a. The core promotor regions of fads2a and fads2b were characterized and found to have different potential transcriptional binding sites. These results revealed the same desaturase functions, but different activities of two homologues of fasd2 genes in common carp. The data showed that fads2b played a more important role in HUFA synthesis through both expression and functional analyses.
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Affiliation(s)
- Ran Zhao
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China
| | - Chen-Ru Yang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China
| | - Ya-Xin Wang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China
| | - Zi-Ming Xu
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China
| | - Shang-Qi Li
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China
| | - Jin-Cheng Li
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China
| | - Xiao-Qing Sun
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China
| | - Hong-Wei Wang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China
| | - Qi Wang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China
| | - Yan Zhang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China
| | - Jiong-Tang Li
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing 100141, China
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Prasanna P, Joshi T, Pant M, Pundir H, Chandra S. Evaluation of the inhibitory potential of Valproic acid against histone deacetylase of Leishmania donovani and computational studies of Valproic acid derivatives. J Biomol Struct Dyn 2022:1-18. [PMID: 35706132 DOI: 10.1080/07391102.2022.2087103] [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: 10/18/2022]
Abstract
Valproic acid (VA) is a proven inhibitor of human histone deacetylases (HDACs). The homogenous HDAC has been associated with all major human parasitic pathogens and hence, it has been considered an attractive drug target for anti-leishmanial therapy. To assist in drug design endeavors for HDACs, an in-vitro study has been presented to investigate the VA inhibition on Leishmania donovani HDAC (LdHDAC). The regression analysis of VA by 24 hrs viability assay confirmed its activity against LdHDAC. Moreover, the toxicity of VA is also well documented. Thus, the in-silico experiments were also conducted to screen the non-toxic VA derivatives as anti-leishmanial drug candidates having potential as inhibitors of LdHDAC. For in-silico study, the 3D structure of target LdHDAC was developed by homology modeling. Based on their in-silico activity, we shortlisted 13 VA derivatives having maximum affinity for LdHDAC and identified four potential derivatives that can specifically bind to this protein. After that, these ligands were subjected to molecular dynamics simulation. These derivatives may be effective against L. donovani promastigotes since they followed Lipinski's RO5 and were non-toxic. Thus, screened derivatives can be considered as lead ligands for targeting LdHDAC and may be used as possible drug candidates to treat leishmaniasis and overcome the limitation of anti-leishmanial drugs. This is the first report of antileishmanial potential of VA and its derivatives targeting LdHDAC. Hence, the current investigation presents a search for novel target specific drugs to aid the anti-leishmanial drug development. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Pragya Prasanna
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Hajipur, Vaishali, India
| | - Tanuja Joshi
- Computational Biology & Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, Uttarakhand, India
| | - Manish Pant
- Department of Post-Harvest Process and Food Engineering, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | - Hemlata Pundir
- Computational Biology & Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, Uttarakhand, India
| | - Subhash Chandra
- Computational Biology & Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, Uttarakhand, India
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Amarnath Jonniya N, Sk MF, Kar P. Elucidating specificity of an allosteric inhibitor WNK476 among With‐No‐Lysine kinase isoforms using molecular dynamic simulations. Chem Biol Drug Des 2021; 98:405-420. [DOI: 10.1111/cbdd.13863] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/19/2021] [Accepted: 05/01/2021] [Indexed: 02/06/2023]
Affiliation(s)
- Nisha Amarnath Jonniya
- Department of Biosciences and Biomedical Engineering Indian Institute of Technology Indore Indore India
| | - Md Fulbabu Sk
- Department of Biosciences and Biomedical Engineering Indian Institute of Technology Indore Indore India
| | - Parimal Kar
- Department of Biosciences and Biomedical Engineering Indian Institute of Technology Indore Indore India
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Joshi T, Joshi T, Sharma P, Pundir H, Chandra S. In silico identification of natural fungicide from Melia azedarach against isocitrate lyase of Fusarium graminearum. J Biomol Struct Dyn 2020; 39:4816-4834. [PMID: 32568603 DOI: 10.1080/07391102.2020.1780941] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Isocitrate Lyase (ICL) is a crucial enzyme involved in the Glyoxylate pathway, essential for the virulence of several fungal pathogens including Fusarium graminearum. ICL is a novel target for the discovery of antifungal compounds and F. graminearum ICL inhibitors can be used to control the growth of this fungus. Although, several inhibitors of ICL have been identified, however, most of these inhibitors are not environment-friendly. Hence there is still a need to discover natural inhibitors of ICL that can be more effective. To identify a potential antifungal compound, we performed a structure-based screening of phytochemicals of Melia azedarach against the FgICL structure by molecular docking and 104 ligands were found to have a better docking score as compared to the reference molecule. These compounds were assessed for drug-likeness and ADMET prediction. After molecular docking, drug-likeness and toxicity analysis, six potential compounds (Melianoninol (-6.6 kcal/mol), Nimbinene (-7.7 kcal/mol), Vilasinin (-8.1 kcal/mol), Fraxinellone (-6.7 kcal/mol), Gedunin (-7.8 kcal/mol), and Meldenin (-7.8 kcal/mol)) were subjected for rescoring by X-Score. The structural stability and dynamics of screened compounds at the active site of FgICL were examined using MD simulation and MM-PBSA analysis. The result of MM-PBSA revealed that four phytochemicals viz. Melianoninol, Nimbinene, Vilasinin, and Fraxinellone had binding free energy of -17.25 kcal/mol, -59.35 kcal/mol, -64.79 kcal/mol, and -29.86 kcal/mol, respectively. Molecular dynamics simulation and MM-PBSA demonstrated that these four phytochemicals displayed considerable significant structural and pharmacological properties and could be probable antifungal drug candidates against F. graminearum. These phyotchemicals of M. azedarach may be suitable candidates for further experimental analysis. [Formula: see text]Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Tanuja Joshi
- Department of Botany, Kumaun University, Almora, Uttarakhand, India
| | - Tushar Joshi
- Department of Botany, Kumaun University, Almora, Uttarakhand, India.,Department of Biotechnology, Bhimtal Campus, Kumaun University, Nainital, Uttarakhand, India
| | - Priyanka Sharma
- Department of Botany, Kumaun University, Nainital, Uttarakhand, India
| | - Hemlata Pundir
- Department of Botany, Kumaun University, Nainital, Uttarakhand, India
| | - Subhash Chandra
- Department of Botany, Kumaun University, Almora, Uttarakhand, India
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Nirmala C, Banerjee S, Imthiyaz M, Sridevi M. Study of fatty acid profiles in fish wastes and in silico evaluation of unsaturated fatty acids for mutant B‐Raf kinase inhibition. J FOOD PROCESS ENG 2020. [DOI: 10.1111/jfpe.13272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Chockalingam Nirmala
- Department of BiotechnologyVinayaka Mission's Kirupananda Variyar Engineering College, Vinayaka Mission's Research Foundation (Deemed to be University) Salem Tamil Nadu India
| | | | - Mohammed Imthiyaz
- Department of BiotechnologyVinayaka Mission's Kirupananda Variyar Engineering College, Vinayaka Mission's Research Foundation (Deemed to be University) Salem Tamil Nadu India
| | - Muruhan Sridevi
- Department of BiotechnologyVinayaka Mission's Kirupananda Variyar Engineering College, Vinayaka Mission's Research Foundation (Deemed to be University) Salem Tamil Nadu India
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Kumar N, Srivastava R, Prakash A, Lynn AM. Structure-based virtual screening, molecular dynamics simulation and MM-PBSA toward identifying the inhibitors for two-component regulatory system protein NarL of Mycobacterium Tuberculosis. J Biomol Struct Dyn 2019; 38:3396-3410. [PMID: 31422761 DOI: 10.1080/07391102.2019.1657499] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The nitrate/nitrite response regulatory protein NarL belongs to the two-component regulatory system of Mycobacterium tuberculosis (MTB), plays a crucial role in anaerobic survival of mycobacteria in host. The absence of this protein in humans, makes it an attractive drug target for MTB treatment. However, the specific drug molecules targeting NarL are yet to be identified. In this study, we identified the promising drug candidates using structure based virtual screening of compounds from chemical libraries (ChEMBL and ZINC), followed by the extensive physicochemical properties analyses and molecular dynamics (MD) simulation. As the initial results, we obtained 4,754 bioactive compounds from ChEMBL having anti-tuberculosis activity which is finally narrowed down to the best 10 hits. A similar approach was applied to search for structurally similar compounds from ZINC data, corresponding to the top hits obtained from ChEMBL. Our collective results show that two compounds, ChEMBL509609 (Gscore - 5.054 kcal/mol, Xscore - 6.47 kcal/mol) and ZINC01843143 (Gscore - 5.114 kcal/mol, Xscore - 6.46 kcal/mol) having the best docking score and ADMET profile. The structural stability and dynamics of lead molecules at active site of NarL were examined using MD simulation and the binding free energies were estimated with MM-PBSA. Essential dynamics and MM-PBSA demonstrated that NarL-ChEMBL509609 complex remains the most stable during simulation of 100 ns with the higher binding free energy which may be a suitable candidate for further experimental analysis. AbbreviationsADMEAbsorption, Distribution, Metabolism, And ExcretionBCGBacillus Calmette-GuerinCNSCentral nervous systemDOTSDirectly observed treatment, short courseEDEssential dynamicsHIVHuman immunodeficiency virusHKHistidine kinaseHOAHuman oral absorptionHTVSHigh throughput virtual screeningIRRIIrritationMDMolecular dynamicsMDRMultidrug resistantMTBMycobacterium tuberculosisMUTMutagenicityMWMolecular weightPHOAPercentage of human oral absorptionREPReproductive developmentRgRadius of gyrationRMSDRoot mean square deviationRMSFRoot mean square fluctuationRO5Lipinski's rule of fiveRRResponse regulatorSPStandard precisionSPGStandard precision glideTBTuberculosisTCSTwo-component regulatory systemTDRTotally drug-resistantTUMOTumorigenicityWHOWorld health organizationXDRExtensively drug-resistantXPExtra precisionCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Niranjan Kumar
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rakesh Srivastava
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Amresh Prakash
- Amity Institute of Integrative Sciences and Health, Amity University, Haryana, Gurgaon, India
| | - Andrew M Lynn
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
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Xu Y, Zheng Y, Li W, Ding Z. Dietary Polyunsaturated Fatty Acid Supplementations Could Significantly Promote the Δ6 Fatty Acid Desaturase and Fatty Acid Elongase Gene Expression, Long Chain Polyunsaturated Fatty Acids, and Growth of Juvenile Cobia. EUR J LIPID SCI TECH 2018. [DOI: 10.1002/ejlt.201800212] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Youqing Xu
- Institute for Fisheries Sciences; Guangxi University; Nanning 530004 China
| | - Yimin Zheng
- Institute for Fisheries Sciences; Guangxi University; Nanning 530004 China
| | - Weifeng Li
- Institute for Fisheries Sciences; Guangxi University; Nanning 530004 China
- Guangxi Key Laboratory of Beibu Gulf Biodiversity Conservation; Qinzhou University; Qinzhou 535011 China
| | - Zhaokun Ding
- Institute for Fisheries Sciences; Guangxi University; Nanning 530004 China
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