☆ 4.6 Article

Different In Silico Approaches Using Heterocyclic Derivatives against the Binding between Different Lineages of SARS-CoV-2 and ACE2

MOLECULES (2023)

Related references

Note: Only part of the references are listed.

Article Chemistry, Multidisciplinary

In Silico Discovery of Small Molecule Modulators Targeting the Achilles' Heel of SARS-CoV-2 Spike Protein

Qing Wang et al.

Summary: Structure-based virtual screening of the conserved free fatty acid (FFA)-binding pocket of SARS-CoV-2 spike protein identified six small molecule modulators with micromolar binding affinities. Further evaluation of commercially available and synthesized analogs led to the discovery of compounds with improved binding affinities and solubilities. The identified compounds exhibited similar binding affinities against both the spike protein of prototypic SARS-CoV-2 and the currently circulating Omicron BA.4 variant. The compound SPC-14 was found to shift the conformational equilibrium of the spike protein towards the closed conformation, rendering it inaccessible to human ACE2. These small molecule modulators targeting the conserved FFA-binding pocket could serve as a starting point for the future development of broad-spectrum COVID-19 intervention treatments.

ACS CENTRAL SCIENCE (2023)

Add to Collection

Article Biochemistry & Molecular Biology

Scanning the RBD-ACE2 molecular interactions in Omicron variant

Soumya Lipsa Rath et al.

Summary: The emergence of new SARS-CoV-2 variants poses a threat to the human population, and assessing their severity is challenging. This study compares the interaction of the wild-type and the latest Omicron variant using molecular dynamics simulations, revealing diverse changes in the properties of the mutated protein complex. These findings enhance our understanding of the binding mechanism between the Omicron variant and the wild-type SARS-CoV-2.

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2022)

Add to Collection

News Item Microbiology

UNDER THE LENS Simulations of the spike: molecular dynamics and SARS-CoV-2

Conrado Pedebos et al.

Summary: This article discusses a few recent molecular simulation studies that have made substantial contributions to our understanding of the spike protein of SARS-CoV-2.

NATURE REVIEWS MICROBIOLOGY (2022)

Add to Collection

Article Chemistry, Multidisciplinary

Discovery of potential small molecular SARS-CoV-2 entry blockers targeting the spike protein

Lin Wang et al.

Summary: This study identified five potential small molecular anti-virus blockers targeting the SARS-CoV-2 spike protein through a combination of in silico technologies and in vitro experimental methods. The optimal molecule, H69C2, exhibited strong binding affinity and anti-viral activity, making it a promising candidate for virus prevention and treatment.

ACTA PHARMACOLOGICA SINICA (2022)

Add to Collection

Article Immunology

Missense mutations in spike protein of SARS-CoV-2 delta variant contribute to the alteration in viral structure and interaction with hACE2 receptor

Tousif Bin Mahmood et al.

Summary: This study investigates the conformational and functional significance of missense mutations in the spike glycoprotein of SARS-CoV-2 Delta variant through computational analysis. The findings suggest that these mutations have a significant impact on the morphology and attributes of the virus.

IMMUNITY INFLAMMATION AND DISEASE (2022)

Add to Collection

Review Microbiology

Determinants of Virus Variation, Evolution, and Host Adaptation

Katherine LaTourrette et al.

Summary: Virus evolution refers to the changes in the genetic structure of a viral population over time, leading to the emergence of new viral variants, strains, and species. Viruses generate genetic diversity through mutation, reassortment, and recombination, allowing them to adapt to different hosts, vectors, and environments. Selection effects and mutations play important roles in virus host adaptation and the emergence of new species.

PATHOGENS (2022)

Add to Collection

Article Biochemistry & Molecular Biology

Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm

Yuri Yepez et al.

Summary: This study aimed to provide a detailed description of the evolutionary history of Gamma and its derived lineages (P.1.1 and P.1.2). Positive selection sites were detected in P.1.1 and P.1.2, with an exclusive haplotype in P.1.2 originating from a non-synonymous mutational step. Phenomena such as epistasis and antagonistic pleiotropy may limit the emergence of new alleles in SARS-COV-2 lineages.

GENETICS AND MOLECULAR BIOLOGY (2022)

Add to Collection

Article Biochemistry & Molecular Biology

Protein structure analysis of the interactions between SARS-CoV-2 spike protein and the human ACE2 receptor: from conformational changes to novel neutralizing antibodies

Ivan Mercurio et al.

Summary: The recent COVID-19 pandemic has led to a global health emergency and calls for the scientific community to identify new tools for diagnosis and treatment. In silico analysis has provided insights into conformational changes of the SARS-CoV-2 spike protein and potential antibodies that could target it to prevent virus invasion into human cells. This analysis also offers guidance for developing new vaccines and treatments based on targeting the spike protein.

CELLULAR AND MOLECULAR LIFE SCIENCES (2021)

Add to Collection

Review Microbiology

SARS-CoV-2, the pandemic coronavirus: Molecular and structural insights

Swapnil B. Kadam et al.

Summary: The outbreak of COVID-19 marked the third spillover of an animal coronavirus to humans in the last 20 years, likely originating from bats and possibly transmitted to humans via unknown intermediate host (potentially a pangolin). The causative pathogen, SARS-CoV-2, shares genetic similarities with bat and pangolin coronaviruses in terms of protein structure and genome, suggesting a zoonotic origin.

JOURNAL OF BASIC MICROBIOLOGY (2021)

Add to Collection

Article Biochemical Research Methods

E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies

Wei Bu Wang et al.

Summary: The COVID-19 pandemic has caused a global outbreak, with hopes pinned on effective vaccines and antibody treatments. However, the virus continues to mutate, with the E484K mutation potentially increasing transmissibility and reducing antibody effectiveness. Research shows that the E484K mutation enhances virus-receptor binding affinity while diminishing antibody binding strength.

JOURNAL OF MOLECULAR GRAPHICS & MODELLING (2021)

Add to Collection

Article Biochemistry & Molecular Biology

Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity

Emma C. Thomson et al.

Summary: SARS-CoV-2 virus can mutate and evade immunity, with mutations like N439K conferring resistance against neutralizing monoclonal antibodies and enhancing binding affinity to hACE2 receptor. Despite similar in vitro replication fitness and clinical outcomes compared to wild type, N439K mutation highlights the importance of ongoing molecular surveillance for guiding vaccine and therapeutic development and usage.

CELL (2021)

Add to Collection

Review Genetics & Heredity

Contributions of human ACE2 and TMPRSS2 in determining host-pathogen interaction of COVID-19

Sabyasachi Senapati et al.

Summary: The ACE2 and TMPRSS2 play crucial roles in the virulence and pathogenesis of SARS-CoV-2, with the interaction between them and the virus's S-protein being key in COVID-19 susceptibility. Identification of specific protein-protein interactions and potential drug targets for inhibiting these interactions could aid in the development of anti-COVID-19 drugs.

JOURNAL OF GENETICS (2021)

Add to Collection

Article Biochemistry & Molecular Biology

A Biochemical Perspective of the Nonstructural Proteins (NSPs) and the Spike Protein of SARS CoV-2

Francis K. Yoshimoto

Summary: The global pandemic in 2020 was caused by the virus SARS CoV-2, with discussions on the chemistry of its various nonstructural proteins and the significance of variant strains. The emerging strains like D614G, 501Y.V1, and 501Y.V2 show structural changes that increase infectivity, emphasizing the need for continued efforts in researching and understanding this rapidly evolving virus.

PROTEIN JOURNAL (2021)

Add to Collection

Article Virology

Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity

Anwar Mohammad et al.

VIRUS RESEARCH (2021)

Add to Collection

Article Chemistry, Medicinal

Small-Molecule Inhibitors of the Coronavirus Spike: ACE2 Protein- Protein Interaction as Blockers of Viral Attachment and Entry for SARS-CoV-2

Damir Bojadzic et al.

Summary: In this study, small-molecule inhibitors targeting the protein-protein interaction between SARS-CoV-2 and hACE2 were identified through screening a compound library focused on organic dyes. These inhibitors showed low micromolar activity and effectively blocked the interaction between the virus and cells in experiments. This provides a new approach for the prevention and treatment of viral infections.

ACS INFECTIOUS DISEASES (2021)

Add to Collection

Review Infectious Diseases

Recent progress on the mutations of SARS-CoV-2 spike protein and suggestions for prevention and controlling of the pandemic

Xue Li et al.

Summary: The mutations and variants of the SARS-CoV-2 virus have impact on its transmissibility and pathogenicity, enhancing its infectivity, transmissibility, and resistance to neutralization. Suggestions for prevention and control of the pandemic are being proposed.

INFECTION GENETICS AND EVOLUTION (2021)

Add to Collection

Review Biochemistry & Molecular Biology

Structural Evaluation of the Spike Glycoprotein Variants on SARS-CoV-2 Transmission and Immune Evasion

Mohd Zulkifli Salleh et al.

Summary: The emergence of SARS-CoV-2 has posed significant challenges worldwide, resulting in millions of deaths. Mutations in the spike (S) glycoprotein may impact vaccine efficacy. Variants such as Alpha, Beta, Gamma have mutations in their spike proteins that enhance viral fitness.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

Add to Collection

Review Microbiology

SARS-CoV-2 variants, spike mutations and immune escape

William T. Harvey et al.

Summary: The evolution of SARS-CoV-2 has been characterized by the emergence of mutations and variants that impact virus characteristics. Manufacturers are preparing for possible updates to vaccines in response to changes in the virus population, and it is crucial to monitor genetic and antigenic changes alongside experiments to understand the impacts of mutations.

NATURE REVIEWS MICROBIOLOGY (2021)

Add to Collection

Article Biochemistry & Molecular Biology

Effect of SARS-CoV-2 B.1.1.7 mutations on spike protein structure and function

Tzu-Jing Yang et al.

Summary: The spike protein of the SARS-CoV-2 B.1.1.7 variant exhibits mutations that affect virus binding to the host ACE2 receptor and immune evasion. The A570D and N501Y mutations have been shown to impact the stability of the spike protein structure, and an introduced neutralizing antibody can effectively neutralize different strains of the virus.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2021)

Add to Collection

Review Medicine, General & Internal

Role of Iron Chelation and Protease Inhibition of Natural Products on COVID-19 Infection

Giuseppe Carota et al.

Summary: This review focuses on the analysis of natural products that could act as both iron chelators and protease inhibitors to counteract SARS-CoV-2 infection, addressing the association between higher iron levels in respiratory diseases such as pulmonary fibrosis and viral infection.

JOURNAL OF CLINICAL MEDICINE (2021)

Add to Collection

Article Microbiology

SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India

Sarah Cherian et al.

Summary: Genomic epidemiology and whole genome sequencing were used to investigate the transmission and evolution of the SARS-CoV-2 virus during the global pandemic. The study identified new variants B.1.617.1 and B.1.617.2 in India, responsible for the second wave of COVID-19 in Maharashtra, with B.1.617.2 designated as a VOC delta and B.1.617.1 as a variant of interest kappa. Monitoring of these and emerging variants in India is crucial for public health.

MICROORGANISMS (2021)

Add to Collection

Article Multidisciplinary Sciences

Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2

Renhong Yan et al.

SCIENCE (2020)

Add to Collection

Article Chemistry, Medicinal

Assessment of Binding Affinity via Alchemical Free-Energy Calculations

Maximilian Kuhn et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)

Add to Collection

Article Multidisciplinary Sciences

Cell entry mechanisms of SARS-CoV-2

Jian Shang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Add to Collection

Review Virology

Coronavirus disease 2019: What we know?

Feng He et al.

JOURNAL OF MEDICAL VIROLOGY (2020)

Add to Collection

Article Multidisciplinary Sciences

Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor

Jun Lan et al.

NATURE (2020)

Add to Collection

Review Immunology

SARS-CoV-2: Structure, Biology, and Structure-Based Therapeutics Development

Mei-Yue Wang et al.

FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY (2020)

Add to Collection

Article Infectious Diseases

Characterizations of SARS-CoV-2 mutational profile, spike protein stability and viral transmission

Sayantan Laha et al.

INFECTION GENETICS AND EVOLUTION (2020)

Add to Collection

Review Microbiology

Origin and evolution of pathogenic coronaviruses

Jie Cui et al.

NATURE REVIEWS MICROBIOLOGY (2019)

Add to Collection

Review Virology

Structure, Function, and Evolution of Coronavirus Spike Proteins

Fang Li

ANNUAL REVIEW OF VIROLOGY, VOL 3 (2016)

Add to Collection

Review Chemistry, Multidisciplinary

The ONIOM Method and Its Applications

Lung Wa Chung et al.

CHEMICAL REVIEWS (2015)

Add to Collection

Review Chemistry, Multidisciplinary

Fundamental aspects of property tuning in push-pull molecules

Filip Bures

RSC ADVANCES (2014)

Add to Collection

Article Biochemistry & Molecular Biology

Modeling, design and synthesis of new heteroaryl ethylenes active against the MCF-7 breast cancer cell-line

Vincenza Barresi et al.

MOLECULAR BIOSYSTEMS (2013)

Add to Collection

Article Biochemistry & Molecular Biology

Photochemistry and DNA-affinity of some pyrimidine-substituted styryl-azinium iodides

Alessandra Mazzoli et al.

PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES (2011)

Add to Collection

Article Chemistry, Medicinal

A common reference framework for analyzing/comparing proteins and ligands. Fingerprints for ligands and proteins (FLAP): Theory and application

Massimo Baroni et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2007)

Add to Collection

Article Chemistry, Medicinal

Hydrogen bonding interactions of covalently bonded fluorine atoms: From crystallographic data to a new angular function in the GRID force field

E Carosati et al.

JOURNAL OF MEDICINAL CHEMISTRY (2004)

Add to Collection

Article Medicine, General & Internal

Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection

YJ Ruan et al.

LANCET (2003)

Add to Collection

Article Biochemistry & Molecular Biology

The Protein Data Bank

HM Berman et al.

NUCLEIC ACIDS RESEARCH (2000)

Add to Collection

© Peeref 2019-2024. All rights reserved.