1
|
Junghare V, Alex R, Baidya A, Paul M, Alyethodi RR, Sengar GS, Kumar S, Singh U, Deb R, Hazra S. In silico modeling revealed new insights into the mechanism of action of enzyme 2'-5'-oligoadenylate synthetase in cattle. J Biomol Struct Dyn 2022; 40:14013-14026. [PMID: 34873989 DOI: 10.1080/07391102.2021.2001373] [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: 12/29/2022]
Abstract
The innate immune system has an important role in developing the initial resistance to virus infection, and the ability of oligoadenylate synthetase to overcome viral evasion and enhance innate immunity is already established in humans. In the present study, we have tried to explore the molecular and structural variations present in Sahiwal (indigenous) and crossbred (Frieswal) cattle to identify the molecular mechanism of action of OAS1 gene in activation of innate immune response. The significant changes in structural alignment in terms of orientation of loops, shortening of β-sheets and formation of 3-10 α-helix was noticed in Sahiwal and Frieswal cattle. Further, it has been observed that OAS1 from Sahiwal had better binding with APC and DTP ligand than Frieswal OAS1. A remarkable change was seen in orientation at the nucleoside base region of both the ligands, which are bound with OAS1 protein from Frieswal and Sahiwal cattle. The Molecular Dynamic study of apo and ligand complex structures was provided more insight towards the stability of OAS1 from both cattle. This analysis displayed that the Sahiwal cattle protein has more steady nature throughout the simulation and has better binding towards Frieswal in terms of APC and DTP binding. Thus, OAS1 protein is the potential target for explaining the innate immune response in Sahiwal than Frieswal.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Vivek Junghare
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Rani Alex
- ICAR-Central Institute for Research on Cattle, Meerut Cantt, India
| | - Apoorva Baidya
- Department of Chemistry, Indian Intitute of Technology Bombay, Mumbai, India
| | - Manish Paul
- Department of Biotechnology, Maharaja Sriram Chandra Bhanja Deo University, Baripada, India
| | | | | | - Sushil Kumar
- ICAR-National Research Center on Pig, Guwahati, India
| | - Umesh Singh
- ICAR-National Research Center on Pig, Guwahati, India
| | - Rajib Deb
- ICAR-National Research Center on Pig, Guwahati, India
| | - Saugata Hazra
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India.,Center of Nanotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| |
Collapse
|
2
|
Zhang XL, Na HY, Li PS, Chen YX, Li ZL, Liang GD, Hua HM. Hipponorterpenes A and B, two new 14-noreudesmane-type sesquiterpenoids from the juice of Hippophae rhamnoides. PHYTOCHEMISTRY LETTERS 2022; 52:82-86. [DOI: 10.1016/j.phytol.2022.09.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/07/2024]
|
3
|
Savateev KV, Fedotov VV, Slepukhin PA, Ulomsky E, Rusinov VL. Regiospecific way to N9-alkylated thioxanthines. NEW J CHEM 2022. [DOI: 10.1039/d2nj03002k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A regiospecific way to N9-alkylated thioxanthines as novel acyclic nucleoside analogues has been developed. This approach is based on a cleavage methodology involving the construction of a target heterocyclic scaffold...
Collapse
|
4
|
Fedotov VV, Ulomsky EN, Savateev KV, Mukhin EM, Gazizov DA, Gorbunov EB, Rusinov VL. A PASE Approach to the Synthesis of Benzimidazopurines as Polycondensed Purine Derivatives. SYNTHESIS-STUTTGART 2020. [DOI: 10.1055/s-0040-1707228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
A highly efficient PASE approach to a new class of polycyclic purine derivatives has been proposed. The strategy includes a consecutive reduction, auto-aromatization, and heterocyclization of the initial nitrobenzimidazopyrimidines obtained by a three-component condensation. It was shown that reduction of nitrobenzimidazopyrimidines by metals in acidic media was more efficient than heterogeneous hydrogenation. Novel derivatives of benz[4,5]imidazo[1,2-a]purines were obtained in good yields and the proposed structure was confirmed by X-ray crystal structure analysis. The obtained convergent benzimidazopurines combine two relevant medicinal chemistry scaffolds – benzimidazole and purine.
Collapse
Affiliation(s)
- Victor V. Fedotov
- Department of Organic and Biomolecular Chemistry, Ural Federal University
| | - Evgeny N. Ulomsky
- Department of Organic and Biomolecular Chemistry, Ural Federal University
| | | | - Evgeny M. Mukhin
- Department of Organic and Biomolecular Chemistry, Ural Federal University
| | - Denis A. Gazizov
- Postovsky Institute of Organic Synthesis, Ural Branch of the Russian Academy of Sciences
| | - Evgeny B. Gorbunov
- Postovsky Institute of Organic Synthesis, Ural Branch of the Russian Academy of Sciences
| | - Vladimir L. Rusinov
- Department of Organic and Biomolecular Chemistry, Ural Federal University
- Postovsky Institute of Organic Synthesis, Ural Branch of the Russian Academy of Sciences
| |
Collapse
|
5
|
Paul M, Kumar Panda M, Thatoi H. Developing Hispolon-based novel anticancer therapeutics against human (NF-κβ) using in silico approach of modelling, docking and protein dynamics. J Biomol Struct Dyn 2018; 37:3947-3967. [PMID: 30295165 DOI: 10.1080/07391102.2018.1532321] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Hispolon is a polyphenolic compound derived from black hoof mushroom (Phellinus linteus) or shaggy bracket mushroom (Inonotus hispidus) which induces the inhibition of cancer-promoting nuclear factor-kappa beta (NF-κβ) complex. To develop more potent lead molecules with enhanced anticancer efficiency, the mechanism of hispolon-mediated nuclear factor-κβ inhibition has been investigated by molecular modelling and docking. Ten derivatives of hispolon (DRG1-10) have been developed by pharmacophore-based design with a view to enhance the anticancer efficacy. Hispolon and its derivatives were further screened for different pharmacological parameters like binding free energy, drug likeliness, absorption-digestion-metabolism-excretion (ADME), permeability, mutagenicity, toxicity and inhibitory concentration 50 (IC50) to find a potent lead molecule. Based on pharmacological validation, comparative molecular dynamics (MD) simulations have been performed for three lead molecules: Hispolon, DRG2 and DRG7 complexed with human NF-κβ up to 50 ns. By analysing different factors like root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent-accessible surface area (SASA) and principal component analysis (PCA), Gibb's free energy plots DRG2 have more binding efficiency compared to hispolon and DRG7. In RMSD plot, hispolon-bound NF-κβ has the most deviation within a range between 0.125 and 0.45 nm, and DRG2-bound complex showed the range between 0.125 and 0.25 nm. The residues of NF-κβ responsible for hydrophobic interactions with ligand, e.g. Met469, Leu522 and Cys533, have the lowest fluctuation values in DRG2-bound complex. The average Rg fluctuation for DRG2-bound NF-κβ has been recorded under 2.025 nm for most of the simulation time which is much less compared to hispolon and DRG7. Gibb's free energy plots also define the highest stability of DRG2-bound NF-κβ. Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Manish Paul
- a Department of Biotechnology, North Orissa University , Baripada , Odisha , India
| | | | - Hrudayanath Thatoi
- a Department of Biotechnology, North Orissa University , Baripada , Odisha , India
| |
Collapse
|
6
|
Slot Christiansen L, Munch-Petersen B, Knecht W. Non-Viral Deoxyribonucleoside Kinases--Diversity and Practical Use. J Genet Genomics 2015; 42:235-48. [PMID: 26059771 DOI: 10.1016/j.jgg.2015.01.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 01/04/2015] [Accepted: 01/05/2015] [Indexed: 12/30/2022]
Abstract
Deoxyribonucleoside kinases (dNKs) phosphorylate deoxyribonucleosides to their corresponding monophosphate compounds. dNks also phosphorylate deoxyribonucleoside analogues that are used in the treatment of cancer or viral infections. The study of the mammalian dNKs has therefore always been of great medical interest. However, during the last 20 years, research on dNKs has gone into non-mammalian organisms. In this review, we focus on non-viral dNKs, in particular their diversity and their practical applications. The diversity of this enzyme family in different organisms has proven to be valuable in studying the evolution of enzymes. Some of these newly discovered enzymes have been useful in numerous practical applications in medicine and biotechnology, and have contributed to our understanding of the structural basis of nucleoside and nucleoside analogue activation.
Collapse
Affiliation(s)
| | - Birgitte Munch-Petersen
- Department of Biology, Lund University, Lund 22362, Sweden; Department of Science, Systems and Models, Roskilde University, Roskilde 4000, Denmark
| | - Wolfgang Knecht
- Department of Biology, Lund University, Lund 22362, Sweden; Lund Protein Production Platform, Lund University, Lund 22362, Sweden.
| |
Collapse
|
7
|
Tyynismaa H, Sun R, Ahola-Erkkilä S, Almusa H, Pöyhönen R, Korpela M, Honkaniemi J, Isohanni P, Paetau A, Wang L, Suomalainen A. Thymidine kinase 2 mutations in autosomal recessive progressive external ophthalmoplegia with multiple mitochondrial DNA deletions. Hum Mol Genet 2011; 21:66-75. [PMID: 21937588 DOI: 10.1093/hmg/ddr438] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Autosomal-inherited progressive external ophthalmoplegia (PEO) is an adult-onset disease characterized by the accumulation of multiple mitochondrial DNA (mtDNA) deletions in post-mitotic tissues. Mutations in six different genes have been described to cause the autosomal dominant form of the disease, but only mutations in the DNA polymerase gamma gene are known to cause autosomal recessive PEO (arPEO), leaving the genetic background of arPEO mostly unknown. Here we used whole-exome sequencing and identified compound heterozygous mutations, leading to two amino acid alterations R225W and a novel T230A in thymidine kinase 2 (TK2) in arPEO patients. TK2 is an enzyme of the mitochondrial nucleotide salvage pathway and its loss-of-function mutations have previously been shown to underlie the early-infantile myopathic form of mtDNA depletion syndrome (MDS). Our TK2 activity measurements of patient fibroblasts and mutant recombinant proteins show that the combination of the identified arPEO variants, R225W and T230A, leads to a significant reduction in TK2 activity, consistent with the late-onset phenotype, whereas homozygosity for R225W, previously associated with MDS, leads to near-total loss of activity. Our finding identifies a new genetic cause of arPEO with multiple mtDNA deletions. Furthermore, MDS and multiple mtDNA deletion disorders are manifestations of the same pathogenic pathways affecting mtDNA replication and repair, indicating that MDS-associated genes should be studied when searching for genetic background of PEO disorders.
Collapse
Affiliation(s)
- Henna Tyynismaa
- Research Programs Unit, Molecular Neurology, Biomedicum Helsinki, Haartmaninkatu 8, Helsinki 00290, Finland.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|