81
Views
0
CrossRef citations to date
0
Altmetric
Research Articles

Lasioglossin-1 peptide inhibits binding of spike protein of SARS-CoV-2 to ACE2 receptor: an in silico approach of some bee venom peptides

, &
Pages 214-223 | Received 28 Aug 2023, Accepted 15 Nov 2023, Published online: 30 Nov 2023

References

  • Ebrahimi KS, Ansari M, Hosseyni Moghaddam MS, et al. In silico investigation on the inhibitory effect of fungal secondary metabolites on RNA dependent RNA polymerase of SARS-CoV-II: a docking and molecular dynamic simulation study. Comput Biol Med. 2021;135:104613.
  • Falade VA, Adelusi TI, Adedotun IO, et al. In silico investigation of saponins and tannins as potential inhibitors of SARS-CoV-2 main protease (M pro). In Silico Pharmacol. 2021;9:1–15.
  • Khalifa I, Zhu W, Mohammed HHH, et al. Tannins inhibit SARS-CoV-2 through binding with catalytic dyad residues of 3CLpro: An in silico approach with 19 structural different hydrolysable tannins. J Food Biochem. 2020;44(10):e13432.
  • Chaudhry SN, Hazafa A, Mumtaz M, et al. New insights on possible vaccine development against SARS-CoV-2. Life Sci. 2020;260:118421.
  • Kumar V, Liu H, Wu C. Drug repurposing against SARS-CoV-2 receptor binding domain using ensemble-based virtual screening and molecular dynamics simulations. Comput Biol Med. 2021;135:104634.
  • Mahnam K, Lotfi M, Shapoorabadi FA. Examining the interactions scorpion venom peptides (HP1090, Meucin-13, and Meucin-18) with the receptor binding domain of the coronavirus spike protein to design a mutated therapeutic peptide. J Mol Graphics Modell. 2021;107:107952.
  • Aljindan RY, Al-Subaie AM, Al-Ohali AI, et al. Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach. Comput Biol Med. 2021;135:104654.
  • Abd El-Wahed AA, Khalifa SAM, Sheikh BY., et al.(2019) Bee venom composition: From chemistry to biological activity. Stud Nat Prod Chem. 2019;60:459–484.
  • Čujová S, Slaninová J, Monincová L, et al. Panurgines, novel antimicrobial peptides from the venom of communal bee Panurgus calcaratus (Hymenoptera: Andrenidae). Amino Acids. 2013;45(1):143–157.
  • Čeřovský V, Buděšínský M, Hovorka O, et al. Lasioglossins: three novel antimicrobial peptides from the venom of the eusocial bee Lasioglossum laticeps (Hymenoptera: Halictidae). ChemBioChem. 2009;10(12):2089–2099.
  • Kazuma K, Ando K, Nihei KI, et al. Peptidomic analysis of the venom of the solitary bee Xylocopa appendiculata circumvolans. J Venomous Anim Toxins Incl Trop Dis. 2017;23.
  • Freitas FC, Ferreira PHB, Favaro DC, et al. J. Chem. Inf. Model. 2021;61(3):3615–3624.
  • Thévenet P, Shen Y, Maupetit J, et al. PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides. Nucleic Acids Res. 2012;40.
  • Wiederstein & Sippl. ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res. 2007;35:W407–W410.
  • Abraham MJ, Murtola T, Schulz R, et al. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX. 2015;1–2:19–25.
  • Mahnam K, Rajaee SM. A theoretical survey to find potential natural compound for inhibition of binding the RBD domain to ACE2 receptor based on plant antivirals. J Biomol Struct Dyn. 2023. doi:10.1080/07391102.2023.2183033
  • Hess B, Bekker H, Berendsen HJC, et al. LINCS: a linear constraint solver for molecular simulations. J Comput Chem. 1997;18(12):1463–1472.
  • Dominguez C, Boelens R, Bonvin AMJJ. Haddock:  A protein−protein docking approach based on biochemical or biophysical information. J Am Chem Soc. 2003;125:1731–1737.
  • Prajapat M, Shekhar N, Sarma P, et al. Virtual screening and molecular dynamics study of approved drugs as inhibitors of spike protein S1 domain and ACE2 interaction in SARS-CoV-2. J Mol Graphics Modell. 2020;101:107716.
  • Laskowski RA, Swindells MB. (2011). LigPlot+: multiple ligand–protein interaction diagrams for drug discovery ACS Publications.
  • Kumari R, Kumar R, Lynn A. g_mmpbsa-A GROMACS tool for high-throughput MM-PBSA calculations. J Chem Inf Model. 2014;54(7):1951–1962.
  • Dehouck Y, Kwasigroch JM, Rooman M, et al. BeAtMuSiC: prediction of changes in protein–protein binding affinity on mutations. Nucleic Acids Res. 2013;41(W1):W333–W339.
  • Zhang L, Skolnick J. How do potentials derived from structural databases relate to “true” potentials? Protein Sci. 1998;7(1):112–122.
  • Khan AT, Chowdhury GM, Hafsah J, et al. A student led computational screening of peptide inhibitors against main protease of SARS-CoV-2. Biochem Mol Biol Educ. 2022;50(1):7–20.
  • Schreiner W, Karch R, Knapp B, et al. Relaxation estimation of RMSD in molecular dynamics immunosimulations. Comput Math Methods Med. 2012;2012:173521.
  • Badaczewska-Dawid AE, Nithin C, Wroblewski K, et al. MAPIYA contact map server for identification and visualization of molecular interactions in proteins and biological complexes. Nucleic Acids Res. 2022;50(W1):W474–W482.
  • Parra RG, Schafer NP, Radusky LG, et al. Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics. Nucleic Acids Res. 2016;44(W1):W356–W360.
  • Ramírez-Sarmiento CA, Noel JK, Valenzuela SL, et al. Interdomain contacts control native state switching of RfaH on a dual-funneled landscape. PLoS Comput Biol. 2015;11(7):e1004379.
  • Nguyen MN, Krutz NL, Limviphuvadh V, et al. AllerCatPro 2.0: a web server for predicting protein allergenicity potential. Nucleic Acids Res. 2022;50(W1):W36–W43.
  • Chaudhary K, Kumar R, Singh S, et al. A web server and mobile app for computing hemolytic potency of peptides. Sci Rep. 2016;6:22843.

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.