36
Views
0
CrossRef citations to date
0
Altmetric
Short Communication

Triple in Silico Targeting of IMPDH Enzyme and RNA-Dependent RNA Polymerase of Both SARS-CoV-2 and Rhizopus Oryzae

, ORCID Icon &
Pages 9-19 | Received 03 May 2023, Accepted 23 Aug 2023, Published online: 31 Jan 2024

References

  • Werthman-Ehrenreich A . Mucormycosis with orbital compartment syndrome in a patient with COVID-19. Am. J. Emerg. Med. 42, 264.e265–264.e268 (2021).
  • Vaidyanathan G . Coronavirus variants are spreading in India – what scientists know so far. Nature 332 (2021).
  • Elgohary AM , Elfiky AA , Barakat K . GRP78: a possible relationship of COVID-19 and the mucormycosis; in silico perspective. Comp. Biol. Med. 139, 104956 (2021).
  • Elfiky AA . Dual targeting of RdRps of SARS-CoV-2 and the mucormycosis-causing fungus: an in silico perspective. Future Microbiol. 17(10), 755–762 (2022).
  • Abduljalil JM , Elfiky AA , Elgohary AM . Exploration of natural compounds against the human mpox virus DNA-dependent RNA polymerase in silico . J. Infect. Public Health 16(7), 996–1003 (2023).
  • Sonousi A , Mahran HA , Ibrahim IM , Ibrahim MN , Elfiky AA , Elshemey WM . Novel adenosine derivatives against SARS-CoV-2 RNA-dependent RNA polymerase: an in silico perspective. Pharmacol. Rep. 73(6), 1754–1764 (2021).
  • Beigel JH , Tomashek KM , Dodd LE et al.> Remdesivir for the treatment of Covid-19. N. Engl. J. Med. 383(19), 1813–1826 (2020).
  • Elfiky AA , Elshemey WM . Molecular dynamics simulation revealed binding of nucleotide inhibitors to ZIKV polymerase over 444 nanoseconds. J. Med. Virol. 90(1), 13–18 (2018).
  • Elfiky AA . Novel guanosine derivatives against Zika virus polymerase in silico . J. Med. Virol. 92(1), 11–16 (2020).
  • Elfiky AA . The antiviral sofosbuvir against mucormycosis: an in silico perspective. Future Virol. 14(11), 739–744 (2019).
  • Burrell AL , Kollman JM . IMPDH dysregulation in disease: a mini review. Biochem. Soc. Transact. 50(1), 71–82 (2022).
  • Valvezan AJ , Mcnamara MC , Miller SK et al. IMPDH inhibitors for antitumor therapy in tuberous sclerosis complex. JCI Insight 5(7), (2020).
  • Shu Q , Nair V . Inosine monophosphate dehydrogenase (IMPDH) as a target in drug discovery. Med. Res. Rev. 28(2), 219–232 (2008).
  • Burrell AL , Kollman JM . IMPDH dysregulation in disease: a mini review. Biochem. Soc. Trans. 50(1), 71–82 (2022).
  • Hedstrom L . IMP dehydrogenase: structure, mechanism, and inhibition. Chem. Rev. 109(7), 2903–2928 (2009).
  • Loustaud-Ratti V , Debette-Gratien M , Jacques J et al. Ribavirin: past, present and future. World J. Hepatol 8(2), 123–130 (2016).
  • Chen L , Wilson DJ , Xu Y et al. Triazole-linked inhibitors of inosine monophosphate dehydrogenase from human and Mycobacterium tuberculosis. J. Med. Chem. 53(12), 4768–4778 (2010).
  • Jouzani GS , Valijanian E , Sharafi R . Bacillus thuringiensis: a successful insecticide with new environmental features and tidings. Appl. Microbiol. Biotechnol. 101(7), 2691–2711 (2017).
  • Abbas MST . Genetically engineered (modified) crops (Bacillus thuringiensis crops) and the world controversy on their safety. Egypt. J. Biol. Pest Control 28(1), 52 (2018).
  • Kim S , Thiessen PA , Bolton EE et al. PubChem substance and compound databases. Nucleic Acids Res. 44(D1), D1202–D1213 (2016).
  • O’boyle NM , Banck M , James CA , Morley C , Vandermeersch T , Hutchison GR . Open Babel: an open chemical toolbox. J. Cheminform. 3(1), 33 (2011).
  • Morris GM , Huey R , Lindstrom W et al. AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J. Comput. Chem. 30(16), 2785–2791 (2009).
  • Gao Y , Yan L , Huang Y et al. Structure of the RNA-dependent RNA polymerase from COVID-19 virus. Science 368(6492), 779–782 (2020).
  • Biasini M , Bienert S , Waterhouse A et al. SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res. 42(Web Server issue), W252–W258 (2014).
  • Pettersen EF , Goddard TD , Huang CC et al. UCSF Chimera-a visualization system for exploratory research and analysis. J. Computat. Chem. 25(13), 1605–1612 (2004).
  • Elfiky AA , Azzam EB , Shafaa MW . The anti-HCV, sofosbuvir, versus the anti-EBOV remdesivir against SARS-CoV-2 RNA dependent RNA polymerase in silico . Mol. Divers 26(1), 171–181 (2022).
  • Rauf MA , Zubair S , Azhar A . Ligand docking and binding site analysis with pymol and autodock/vina. Int. J. Basic Appl. Sci. 4(2), 168 (2015).
  • Trott O , Olson AJ . AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem. 31(2), 455–461 (2010).
  • Seeliger D , De Groot BL . Ligand docking and binding site analysis with PyMOL and Autodock/Vina. J. Comput. Aided. Mol. Des. 24(5), 417–422 (2010).
  • Schrödinger, LLC . The PyMOL Molecular Graphics System, Version 2.4.1 Schrödinger, LLC. https://pymol.org/2/
  • Jejurikar BL , Rohane SH . Drug designing in discovery studio. Asian J. Res. Chem. 14(2), 135–138 (2021).
  • Elfiky AA . Zika virus: novel guanosine derivatives revealed strong binding and possible inhibition of the polymerase. Future Virol. 12(12), 721–728 (2017).
  • Elfiky AA , Ismail A . Molecular dynamics and docking reveal the potency of novel GTP derivatives against RNA dependent RNA polymerase of genotype 4a HCV. Life Sci. 238, 116958 (2019).
  • Elfiky AA . Novel guanosine derivatives as anti-HCV NS5b polymerase: a QSAR and molecular docking study. Med. Chem. 15(2), 130–137 (2019).
  • Adem S , Eyupoglu V , Sarfraz I et al. Caffeic acid derivatives (CAFDs) as inhibitors of SARS-CoV-2: CAFDs-based functional foods as a potential alternative approach to combat COVID-19. Phytomedicine 85, 153310 (2021).
  • Silver LL . Multi-targeting by monotherapeutic antibacterials. Nat. Rev. Drug Discov. 6(1), 41–55 (2007).
  • Joshi RS , Jagdale SS , Bansode SB et al. Discovery of potential multi-target-directed ligands by targeting host-specific SARS-CoV-2 structurally conserved main protease. J. Biomolec. Struct. Dynam. 39(9), 3099–3114 (2021).
  • Mishra P , Kumar A , Panda G . Anti-cholinesterase hybrids as multi-target-directed ligands against Alzheimer’s disease (1998–2018). Bioorg. Med. Chem. 27(6), 895–930 (2019).
  • Artasensi A , Pedretti A , Vistoli G , Fumagalli L . Type 2 diabetes mellitus: a review of multi-target drugs. Molecules 25(8), 1987 (2020).
  • Trapero A , Pacitto A , Singh V et al. Fragment-based approach to targeting inosine-5′-monophosphate dehydrogenase (IMPDH) from Mycobacterium tuberculosis . J. Med. Chem. 61(7), 2806–2822 (2018).
  • Eweas AF , Alhossary AA , Abdel-Moneim AS . Molecular docking reveals ivermectin and remdesivir as potential repurposed drugs against SARS-CoV-2. Front. Microbiol. 11, 592908 (2020).
  • Patil SM , Maruthi KR , Bajpe SN et al. Comparative molecular docking and simulation analysis of molnupiravir and remdesivir with SARS-CoV-2 RNA dependent RNA polymerase (RdRp). Bioinformation 17(11), 932–939 (2021).
  • Gan CS , Lim SK , Chee CF , Yusof R , Heh CH . Sofosbuvir as treatment against dengue? Chem. Biol. Drug Des. 91(2), 448–455 (2018).
  • Yang H , Huang Y , Wu D , Yan J , He J , Li H . In vitro investigation of the interaction between the hepatitis C virus drug sofosbuvir and human serum albumin through 1H NMR, molecular docking, and spectroscopic analyses. N. J. Chem. 40(3), 2530–2540 (2016).
  • De Freitas CS , Higa LM , Sacramento CQ et al. Yellow fever virus is susceptible to sofosbuvir both in vitro and in vivo . PLOS Negl. Trop. Dis. 13(1), e0007072 (2019).

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.