4.8 Article

Rapid Assessment of Binding Affinity of SARS-COV-2 Spike Protein to the Human Angiotensin-Converting Enzyme 2 Receptor and to Neutralizing Biomolecules Based on Computer Simulations

Related references

Note: Only part of the references are listed.
News Item Medicine, General & Internal

Covid-19: What new variants are emerging and how are they being investigated?

Elisabeth Mahase

BMJ-BRITISH MEDICAL JOURNAL (2021)

Article Biochemistry & Molecular Biology

Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity

Wilfredo F. Garcia-Beltran et al.

Summary: New variants of SARS-CoV-2 show high resistance to vaccine neutralization, with some able to escape vaccine responses with just a few mutations, highlighting the importance of developing broadly protective measures against variants.
Article Biochemistry & Molecular Biology

In Silico Investigation of the New UK (B.1.1.7) and South African (501Y.V2) SARS-CoV-2 Variants with a Focus at the ACE2-Spike RBD Interface

Bruno O. Villoutreix et al.

Summary: The SARS-CoV-2 virus exploits ACE2 as a receptor for cell invasion, with certain mutations potentially enhancing its transmission capabilities and pathogenicity through effects on ACE2 binding. The UK strain may exhibit higher affinity for ACE2, while the transmission level of the South African strain could be influenced by the N501Y substitution.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

Article Multidisciplinary Sciences

Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies

Dami A. Collier et al.

Summary: The B.1.1.7 variant of SARS-CoV-2 exhibited reduced neutralization by vaccines and antibodies from recovered COVID-19 patients, with a more substantial loss seen when introducing the E484K mutation. This mutation poses a threat to the efficacy of the BNT162b2 vaccine.

NATURE (2021)

Article Multidisciplinary Sciences

Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7

Pengfei Wang et al.

Summary: The COVID-19 pandemic has had global repercussions, with promising vaccines and monoclonal antibody therapies. However, newly detected variants of SARS-CoV-2 present challenges to these treatment options.

NATURE (2021)

Article Multidisciplinary Sciences

mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants

Zijun Wang et al.

Summary: Volunteers who received the Moderna or Pfizer-BioNTech vaccine showed high levels of antibodies and memory B cell responses against SARS-CoV-2, with activity similar to individuals who had recovered from natural infection. However, their efficacy against specific SARS-CoV-2 variants was reduced, indicating a potential need for periodic updates to mRNA vaccines to maintain clinical efficacy.

NATURE (2021)

Article Multidisciplinary Sciences

Potent neutralization of clinical isolates of SARS-CoV-2 D614 and G614 variants by a monomeric, sub-nanomolar affinity nanobody

Guillermo Valenzuela Nieto et al.

Summary: Despite global efforts to develop SARS-CoV-2 treatments, the urgent need for effective diagnosis, treatment, and prophylactic measures remains critical. The development of alpaca Nanobody W25 shows promise as a potential antiviral agent, efficiently neutralizing SARS-CoV-2 strains with high affinity.

SCIENTIFIC REPORTS (2021)

Article Cell Biology

The effect of spike mutations on SARS-CoV-2 neutralization

Chloe Rees-Spear et al.

Summary: The study found that emerging variants of the coronavirus may lead to reduced neutralization by antibodies induced by vaccines or previous infection, but some samples still retain effectiveness. This highlights the importance of real-time monitoring of emerging mutations and their impact on vaccine efficacy.

CELL REPORTS (2021)

Review Immunology

SARS-CoV-2 vaccines strategies: a comprehensive review of phase 3 candidates

Nikolaos C. Kyriakidis et al.

Summary: The new SARS-CoV-2 virus is rapidly spreading worldwide, causing the COVID-19 pandemic with more than 1.866 million deaths. Over 64 vaccine candidates are being developed globally, aiming to induce antibodies to prevent viral entry. Thirteen vaccine candidates are currently in Phase 3 clinical trials, showing promising progress towards approval for large-scale immunizations.

NPJ VACCINES (2021)

Article Virology

Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics

Jorge Gonzalez-Puelma et al.

Summary: The emergence of a SARS-CoV-2 haplotype in the subantarctic Magallanes Region of southern Chile with nine mutations, including the D614G/T307I double-mutation of the spike protein, resulted in rapid spread and complete replacement of previous lineages. The T307I mutation showed a synergistic effect with the D614G mutation, leading to a significant increase in cases and one of the highest incidence rates worldwide. Continued surveillance and molecular analysis of new mutations are essential for understanding the infectivity and virulence of current and future SARS-CoV-2 strains.

VIRUSES-BASEL (2021)

Article Infectious Diseases

Neutralization of SARS-CoV-2 by highly potent, hyperthermostable, and mutation-tolerant nanobodies

Thomas Guettler et al.

Summary: This study introduces the use of single-domain (VHH) antibodies as an alternative for combating SARS-CoV-2, showing their ability to neutralize the virus, inhibit its infectivity, and tolerate immune-escape mutations. The research also suggests that this approach may simplify vaccine production and adapt to viral escape mutations.

LANCET INFECTIOUS DISEASES (2021)

Article Multidisciplinary Sciences

Potent neutralizing nanobodies resist convergent circulating variants of SARS-CoV-2 by targeting diverse and conserved epitopes

Dapeng Sun et al.

Summary: Highly potent neutralizing nanobodies (Nbs) targeting the receptor binding domain (RBD) of the SARS-CoV-2 spike protein show effectiveness against circulating variants of concern. Structural analysis of the Nbs provides insights into their high-affinity and broadly neutralizing activity against the virus.

NATURE COMMUNICATIONS (2021)

Article Biochemistry & Molecular Biology

Neutralization of SARS-CoV-2 by highly potent, hyperthermostable, and mutation-tolerant nanobodies

Thomas Guettler et al.

Summary: Monoclonal anti-SARS-CoV-2 immunoglobulins are effective in treating COVID-19, but their production in mammalian cells is not scalable. This study isolated 45 infection-blocking VHH antibodies from alpaca immune libraries, with one particularly effective VHH antibody capable of neutralizing the virus at low concentrations and showing strong binding to the Spike protein in different conformations. Additionally, the research identified VHH antibodies that can tolerate immune-escape mutations, as well as fold-promoting nanobodies that could simplify vaccine production and adaptation to viral mutations.

EMBO JOURNAL (2021)

Article Multidisciplinary Sciences

A new coronavirus associated with human respiratory disease in China

Fan Wu et al.

NATURE (2020)

Article Multidisciplinary Sciences

A pneumonia outbreak associated with a new coronavirus of probable bat origin

Peng Zhou et al.

NATURE (2020)

Article Multidisciplinary Sciences

Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation

Daniel Wrapp et al.

SCIENCE (2020)

Article Biochemistry & Molecular Biology

Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2

Qihui Wang et al.

Article Biochemistry & Molecular Biology

Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein

Alexandra C. Walls et al.

Article Multidisciplinary Sciences

SARS-CoV-2 infection protects against rechallenge in rhesus macaques

Abishek Chandrashekar et al.

SCIENCE (2020)

Article Multidisciplinary Sciences

Emergence of SARS-CoV-2 through recombination and strong purifying selection

Xiaojun Li et al.

SCIENCE ADVANCES (2020)

Article Biochemistry & Molecular Biology

The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity

Qianqian Li et al.

Article Chemistry, Medicinal

Computational Prediction of Mutational Effects on SARS-CoV-2 Binding by Relative Free Energy Calculations

Junjie Zou et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)

Article Multidisciplinary Sciences

De novo design of picomolar SARS-CoV-2 miniprotein inhibitors

Longxing Cao et al.

SCIENCE (2020)

Article Medicine, Research & Experimental

Convalescent plasma anti SARS-CoV-2 spike protein ectodomain and receptor-binding domain IgG correlate with virus neutralization

Eric Salazar et al.

JOURNAL OF CLINICAL INVESTIGATION (2020)

Article Multidisciplinary Sciences

Versatile and multivalent nanobodies efficiently neutralize SARS-CoV-2

Yufei Xiang et al.

SCIENCE (2020)

Review Microbiology

Origin and evolution of pathogenic coronaviruses

Jie Cui et al.

NATURE REVIEWS MICROBIOLOGY (2019)

Article Chemistry, Medicinal

Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations

Zoe Cournia et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2017)

Article Biochemical Research Methods

PRODIGY: a web server for predicting the binding affinity of protein-protein complexes

Li C. Xue et al.

BIOINFORMATICS (2016)

Review Virology

Structure, Function, and Evolution of Coronavirus Spike Proteins

Fang Li

ANNUAL REVIEW OF VIROLOGY, VOL 3 (2016)

Article Biochemistry & Molecular Biology

The p.Cys169Tyr variant of connexin 26 is not a polymorphism

Francesco Zonta et al.

HUMAN MOLECULAR GENETICS (2015)

Article Chemistry, Physical

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

James A. Maier et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

Article Biochemistry & Molecular Biology

Role of gamma carboxylated Glu47 in connexin 26 hemichannel regulation by extracellular Ca2+: Insight from a local quantum chemistry study

Francesco Zonta et al.

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2014)

Article Biochemical Research Methods

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

Sander Pronk et al.

BIOINFORMATICS (2013)

Article Biochemistry & Molecular Biology

Mechanisms of Host Receptor Adaptation by Severe Acute Respiratory Syndrome Coronavirus

Kailang Wu et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2012)

Article Virology

SARS-CoV and emergent coronaviruses: viral determinants of interspecies transmission

Meagan Bolles et al.

CURRENT OPINION IN VIROLOGY (2011)

Article Chemistry, Multidisciplinary

UCSF chimera - A visualization system for exploratory research and analysis

EF Pettersen et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)

Review Chemistry, Multidisciplinary

Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models

PA Kollman et al.

ACCOUNTS OF CHEMICAL RESEARCH (2000)