Design and selection of peptides to block the SARS-CoV-2 receptor binding domain by molecular docking

Kendra Ramirez-Acosta, Ivan A. Rosales-Fuerte, J. Eduardo Perez-Sanchez, Alfredo Nuñez-Rivera, Josue Juarez and Ruben D. Cadena-Nava
Beilstein J. Nanotechnol. 2022, 13, 699–711. https://doi.org/10.3762/bjnano.13.62

Supporting Information

Supporting Information features previously reported antiviral activities of APD peptides (Table S1); molecular docking scores of the 104 peptides (Table S2); Ligplot+ diagrams of the hydrogen bonds and hydrophobic interactions between ACE2 and the SARS-CoV-2 RBD (Figure S1); distribution of electrostatic potential on the surface of APD peptide candidates docked to the SARS-CoV-2 RBD (Figure S2); secondary structure, docking, and distribution of electrostatic charges of aligned peptides (Figure S3); physicochemical properties, hydrogen bonds, and hydrophobic interactions of the peptide candidates against SARS-CoV-2 (Table S3); principal docking regions of screened APD and lysozyme peptides against the SARS-CoV-2 RBD (Figure S4); immunogenicity analysis of peptides against human MHC I to determine the number of alleles with IC50 < 50 nM and IC50 < 500 nM (Table S4); and the contact areas of peptides docked to SARS-CoV-2.

Supporting Information File 1: Additional experimental data.
Format: PDF Size: 1.5 MB Download

Cite the Following Article

Design and selection of peptides to block the SARS-CoV-2 receptor binding domain by molecular docking
Kendra Ramirez-Acosta, Ivan A. Rosales-Fuerte, J. Eduardo Perez-Sanchez, Alfredo Nuñez-Rivera, Josue Juarez and Ruben D. Cadena-Nava
Beilstein J. Nanotechnol. 2022, 13, 699–711. https://doi.org/10.3762/bjnano.13.62

How to Cite

Ramirez-Acosta, K.; Rosales-Fuerte, I. A.; Perez-Sanchez, J. E.; Nuñez-Rivera, A.; Juarez, J.; Cadena-Nava, R. D. Beilstein J. Nanotechnol. 2022, 13, 699–711. doi:10.3762/bjnano.13.62

Download Citation

Citation data can be downloaded as file using the "Download" button or used for copy/paste from the text window below.
Citation data in RIS format can be imported by all major citation management software, including EndNote, ProCite, RefWorks, and Zotero.

Presentation Graphic

Picture with graphical abstract, title and authors for social media postings and presentations.
Format: PNG Size: 9.8 MB Download

Citations to This Article

Up to 20 of the most recent references are displayed here.

Scholarly Works

  • Vincenzi, M.; Mercurio, F. A.; Leone, M. Virtual Screening of Peptide Libraries: The Search for Peptide-Based Therapeutics Using Computational Tools. International journal of molecular sciences 2024, 25, 1798. doi:10.3390/ijms25031798
  • Yaghoobizadeh, F.; Roayaei Ardakani, M.; Ranjbar, M. M.; Khosravi, M.; Galehdari, H. Development of a potent recombinant scFv antibody against the SARS-CoV-2 by in-depth bioinformatics study: Paving the way for vaccine/diagnostics development. Computers in biology and medicine 2024, 170, 108091. doi:10.1016/j.compbiomed.2024.108091
  • Luz, A. B. S.; de Medeiros, A. F.; Bezerra, L. L.; Lima, M. S. R.; Pereira, A. S.; E Silva, E. G. O.; Passos, T. S.; Monteiro, N. d. K. V.; Morais, A. H. d. A. Prospecting native and analogous peptides with anti-SARS-CoV-2 potential derived from the trypsin inhibitor purified from tamarind seeds. Arabian journal of chemistry 2023, 16, 104886. doi:10.1016/j.arabjc.2023.104886
  • Show, P.-L.; Chew, K. W.; Ong, W.-J.; Varjani, S.; Juan, J. C. New trends in nanobiotechnology. Beilstein journal of nanotechnology 2023, 14, 377–379. doi:10.3762/bjnano.14.32
Other Beilstein-Institut Open Science Activities