Targeting SARS-CoV‑2 Receptor Binding Domain with Stapled Peptides: An In Silico Study
| العنوان: | Targeting SARS-CoV‑2 Receptor Binding Domain with Stapled Peptides: An In Silico Study |
|---|---|
| المؤلفون: | Luana Janaína de Campos (10959927), Nicholas Y. Palermo (2093596), Martin Conda-Sheridan (2069608) |
| سنة النشر: | 2021 |
| المجموعة: | Smithsonian Institution: Digital Repository |
| مصطلحات موضوعية: | Biophysics, Biochemistry, Molecular Biology, Pharmacology, Immunology, Infectious Diseases, Virology, Computational Biology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, docking predictions, refinement process, FIBERDOCK, surface area, structure-based design, syndrome coronavirus 2, α- helical character, binding affinity analysis, stapled peptides, double-stapled peptide, control NYBSP -4, SARS-CoV -2 infection, interaction profile, docking strategies, angiotensin-converting enzyme 2 rec., solubility profile, MD, MM, peptide inhibitor |
| الوصف: | Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved into a pandemic of unprecedented scale. This coronavirus enters cells by the interaction of the receptor binding domain (RBD) with the human angiotensin-converting enzyme 2 receptor (hACE2). In this study, we employed a rational structure-based design to propose 22-mer stapled peptides using the structure of the hACE2 α1 helix as a template. These peptides were designed to retain the α-helical character of the natural structure, to enhance binding affinity, and to display a better solubility profile compared to other designed peptides available in the literature. We employed different docking strategies (PATCHDOCK and ZDOCK) followed by a double-step refinement process (FIBERDOCK) to rank our peptides, followed by stability analysis/evaluation of the interaction profile of the best docking predictions using a 500 ns molecular dynamics (MD) simulation, and a further binding affinity analysis by molecular mechanics with generalized Born and surface area (MM/GBSA) method. Our most promising stapled peptides presented a stable profile and could retain important interactions with the RBD in the presence of the E484K RBD mutation. We predict that these peptides can bind to the viral RBD with similar potency to the control NYBSP-4 (a 30-mer experimentally proven peptide inhibitor). Furthermore, our study provides valuable information for the rational design of double-stapled peptide as inhibitors of SARS-CoV-2 infection. |
| نوع الوثيقة: | dataset |
| اللغة: | unknown |
| العلاقة: | https://figshare.com/articles/media/Targeting_SARS-CoV_2_Receptor_Binding_Domain_with_Stapled_Peptides_An_i_In_Silico_i_Study/14770809Test |
| DOI: | 10.1021/acs.jpcb.1c02398.s002 |
| الإتاحة: | https://doi.org/10.1021/acs.jpcb.1c02398.s002Test |
| حقوق: | CC BY-NC 4.0 |
| رقم الانضمام: | edsbas.80B5A3E1 |
| قاعدة البيانات: | BASE |
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