Computational analysis on the ACE2-derived peptides for neutralizing the ACE2 binding to the spike protein of SARS-CoV-2
lupala, c. s.; Kumar, V.; li, x.; su, x.; liu, h.
Show abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the COVID-19, is spreading globally and has infected more than 3 million people. It has been discovered that SARS-CoV-2 initiates the entry into cells by binding to human angiotensin-converting enzyme 2 (hACE2) through the receptor binding domain (RBD) of its spike glycoprotein. Hence, drugs that can interfere the SARS-CoV-2-RBD binding to hACE2 potentially can inhibit SARS-CoV-2 from entering human cells. Here, based on the N-terminal helix 1 of human ACE2, we designed nine short peptides that have potential to inhibit SARS-CoV-2 binding. Molecular dynamics simulations of peptides in the their free and SARS-CoV-2 RBD-bound forms allow us to identify fragments that are stable in water and have strong binding affinity to the SARS-CoV-2 spike proteins. The important interactions between peptides and RBD are highlighted to provide guidance for the design of peptidomimetics against the SARS-CoV-2.
Matching journals
The top 9 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- A strategy to optimize the peptide-based inhibitors against different mutants of the spike protein of SARS-CoV-2 98%
- Dynamic conformational states of apo and cabozantinib bound TAM kinases to differentiate active-inactive kinetic models 97%
- An insight into SARS-CoV-2 Membrane protein interaction with Spike, Envelope, and Nucleocapsid proteins 97%
Similar papers in this journal
- Mechanistic insights into the deleterious role of nasu-hakola disease associated TREM2 variants 98%
- S494 O-glycosylation site on the SARS-COV-2 RBD Affects the Virus Affinity to ACE2 and its Infectivity; A Molecular Dynamics Study 97%
- The Hidden Potential of PDE4 Inhibitor Rolipram: A Multifaceted Examination of its Inhibition of MMP2/9 Reveals Therapeutic Implications 97%
Similar papers in this journal
- Molecular Insights into the Differential Dynamics of SARS-CoV-2 Variants of Concern (VOCs) 97%
- In Silico Identification Of Novel PRFA Inhibitors To Fight Listeriosis: A Virtual Screening And Molecular Dynamics Studies 96%
- Impact of non-proteinogenic amino acid norvaline and proteinogenic valine misincorporation on a secondary structure of a model peptide 96%
Similar papers in this journal
- Molecular dynamics simulations reveal the selectivity mechanism of structurally similar agonists to TLR7 and TLR8 97%
- Deep learning based predictive modeling to screen natural compounds against TNF-alpha for the potential management of Rheumatoid Arthritis: Virtual screening to comprehensive in silico investigation 96%
- iBRAB: in silico based-designed Broad-spectrum Fab against H1N1 Influenza A Virus 96%
Similar papers in this journal
- Exploring the effect of Hydrocarbon Cross-linkers on the Structure and Binding of Stapled p53 Peptides 96%
- Interfacial residues in protein-protein complexes are in the eyes of the beholder 96%
- Remarked Suppression of Aβ42 Protomer-protomer Dissociation Reaction via Pentamer Dimerization Elucidated by Molecular Dynamics Simulation 94%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.