ArticleChemical science2021
Molecular recognition of SARS-CoV-2 spike glycoprotein: quantum chemical hot spot and epitope analyses.
Article in Chemical science, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 51 citations in OpenAlex.
- Guiding point-of-care therapeutic drug monitoring through structure-toxicity principles.Chemical science · 2026Article
- Advancing Medicinal Chemistry Through FMO: Sygnature's Platform.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Fragment Molecular Orbital Drug Design Consortium (FMODD): Bridging Academia and Industry Through Prospective FMO-Driven Drug Design.Methods in molecular biology (Clifton, N.J.) · 2026Article
- In Silico and in vitro evaluation of Cucurbitaceae seed lectins as promising prophylactic and therapeutic agents against SARS-CoV-2.Glycoconjugate journal · 2025Article
- Quantum chemical calculation dataset for representative protein folds by the fragment molecular orbital method.Scientific data · 2024Article
- FMOe: Preprocessing and Visualizing Package of the Fragment Molecular Orbital Method for Molecular Operating Environment and Its Applications in Covalent Ligand and Metalloprotein Analyses.Journal of chemical information and modeling · 2024Article
- Brain Pathology in COVID-19: Clinical Manifestations and Potential Mechanisms.Neuroscience bulletin · 2024Review
- Binding Free Energy Calculation Based on the Fragment Molecular Orbital Method and Its Application in Designing Novel SHP-2 Allosteric Inhibitors.International journal of molecular sciences · 2024Article
- SARS-CoV-2 spike proteins react with Au and Si, are electrically conductive and denature at 3 × 10Chemical science · 2023Article
- Towards Quantum-Chemical Level Calculations of SARS-CoV-2 Spike Protein Variants of Concern by First Principles Density Functional Theory.Biomedicines · 2023Review
- 2-Deoxy-D-Glucose: A Novel Pharmacological Agent for Killing Hypoxic Tumor Cells, Oxygen Dependence-Lowering in Covid-19, and Other Pharmacological Activities.Advances in pharmacological and pharmaceutical sciences · 2023Review
- Article
- Effect of Delta and Omicron Mutations on the RBD-SD1 Domain of the Spike Protein in SARS-CoV-2 and the Omicron Mutations on RBD-ACE2 Interface Complex.International journal of molecular sciences · 2022Article
- The Role of Spike Protein Mutations in the Infectious Power of SARS-COV-2 Variants: A Molecular Interaction Perspective.Chembiochem : a European journal of chemical biology · 2022Article
- Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding.Cell reports · 2021Article
- SARS-CoV-2 S glycoprotein binding to multiple host receptors enables cell entry and infection.Glycoconjugate journal · 2021Review
- Attractive and repulsive residue fragments at the interface of SARS-CoV-2 and hACE2.Scientific reports · 2021Article
- Non-conventional interactions of N3 inhibitor with the main protease of SARS-CoV and SARS-CoV-2.Computational and structural biotechnology journal · 2021Article
Corrections and comments
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Authors and funding
5 authors at 5 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Due to the COVID-19 pandemic, researchers have attempted to identify complex structures of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoprotein (S-protein) with angiotensin-converting enzyme 2 (ACE2) or a blocking antibody. However, the molecular recognition mechanism-critical information for drug and antibody design-has not been fully clarified at the amino acid residue level. Elucidating such a microscopic mechanism in detail requires a more accurate molecular interpretation that includes quantum mechanics to quantitatively evaluate hydrogen bonds, XH/π interactions (X = N, O, and C), and salt bridges. In this study, we applied the fragment molecular orbital (FMO) method to characterize the SARS-CoV-2 S-protein binding interactions with not only ACE2 but also the B38 Fab antibody involved in ACE2-inhibitory binding. By analyzing FMO-based interaction energies along a wide range of binding interfaces carefully, we identified amino acid residues critical for molecular recognition between S-protein and ACE2 or B38 Fab antibody. Importantly, hydrophobic residues that are involved in weak interactions such as CH-O hydrogen bond and XH/π interactions, as well as polar residues that construct conspicuous hydrogen bonds, play important roles in molecular recognition and binding ability. Moreover, through these FMO-based analyses, we also clarified novel hot spots and epitopes that had been overlooked in previous studies by structural and molecular mechanical approaches. Altogether, these hot spots/epitopes identified between S-protein and ACE2/B38 Fab antibody may provide useful information for future antibody design, evaluation of the binding property of the SARS-CoV-2 variants including its N501Y, and small or medium drug design against the SARS-CoV-2.
Identifiers
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.