4.6 Article

Docking and Molecular Dynamics Simulations Clarify Binding Sites for Interactions of Novel Marine Sulfated Glycans with SARS-CoV-2 Spike Glycoprotein

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemistry & Molecular Biology

Structure, anti-SARS-CoV-2, and anticoagulant effects of two sulfated galactans from the red alga Botryocladia occidentalis

Antim K. Maurya et al.

Summary: The structure of sulfated galactan from red alga Botryocladia occidentalis was originally believed to consist of a simple repeating disaccharide with variable sulfation pattern. However, further analysis revealed a more complex sulfation pattern and the presence of an AnGalp unit. The more sulfated fraction showed reduced anti-SARS-CoV-2 and anticoagulant activities, which can be attributed to the AnGalp unit.

INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES (2023)

Article Chemistry, Multidisciplinary

SARS-CoV-2 evolved variants optimize binding to cellular glycocalyx

Sang Hoon Kim et al.

Summary: We investigated the impact of an evolving spike positive charge in SARS-CoV-2 variants on interactions with heparan sulfate and ACE2. The Omicron variant showed enhanced binding to the glycocalyx and stronger interactions with heparan sulfate compared to the Delta variant. This discovery enables the development of a second-generation lateral flow test strip that can detect all variants, including Omicron, by utilizing heparin and ACE2.

CELL REPORTS PHYSICAL SCIENCE (2023)

Article Chemistry, Multidisciplinary

Well-Defined Heparin Mimetics Can Inhibit Binding of the Trimeric Spike of SARS-CoV-2 in a Length-Dependent Manner

Lifeng Sun et al.

Summary: The emergence of new SARS-CoV-2 variants and the dangers of long-covid necessitate the development of broadacting therapeutics that can reduce viral burden. SARS-CoV-2 employs heparan sulfate (HS) as an initial cellular attachment factor, and therefore, there is interest in developing heparin as a therapeutic for SARS-CoV-2. Its use is, however, complicated by structural heterogeneity and the risk of causing bleeding and thrombocytopenia.

JACS AU (2023)

Article Biochemistry & Molecular Biology

Structural remodeling of SARS-CoV-2 spike protein glycans reveals the regulatory roles in receptor-binding affinity

Yen-Pang Hsu et al.

Summary: The glycans of SARS-CoV-2 spike protein play functional roles in the infection process and are highly conserved. Glycosylation of the receptor-binding domain (RBD) of the spike protein can be controlled and simplified through glycoengineering, affecting its behavior and interaction with host receptors. The antibody S309 can neutralize the impact of different RBD glycoforms on receptor binding affinity.

GLYCOBIOLOGY (2023)

Article Biochemistry & Molecular Biology

The binding of heparin to spike glycoprotein inhibits SARS-CoV-2 infection by three mechanisms

Giulia Paiardi et al.

Summary: Heparin has been found to have antiviral activity against SARS-CoV-2 by inhibiting viral binding to host cells, competing with binding to host heparan sulfate proteoglycan coreceptors, and preventing spike cleavage. These findings provide insights into potential strategies for SARS-CoV-2 antiviral therapy.

JOURNAL OF BIOLOGICAL CHEMISTRY (2022)

Article Biochemistry & Molecular Biology

Sialic acid-containing glycolipids mediate binding and viral entry of SARS-CoV-2

Linh Nguyen et al.

Summary: Evidence suggests that host glycans, specifically glycolipids containing sialic acid, play a role in facilitating the entry of SARS-CoV-2 virus into host cells by binding to the receptor-binding domain (RBD) of the spike protein. Depletion of cell surface sialic acid levels through various methods decreases RBD binding and infection of the virus, indicating the importance of sialylated glycans in viral entry.

NATURE CHEMICAL BIOLOGY (2022)

Article Chemistry, Multidisciplinary

GlycoGrip: Cell Surface-Inspired Universal Sensor for Betacoronaviruses

Sang Hoon Kim et al.

Summary: GlycoGrip is a lateral flow assay developed based on the role of cell-surface glycoproteins as coreceptors for pathogens, allowing for the detection of SARS-CoV-2 and its variants. By utilizing glycopolymers and antibody-gold nanoparticle conjugates, it achieves sensitive and rapid virus detection. Through computational optimization, the test strips have been fine-tuned to selectively detect the virus in biofluids.

ACS CENTRAL SCIENCE (2022)

Article Biochemistry & Molecular Biology

Fractionation of sulfated galactan from the red alga Botryocladia occidentalis separates its anticoagulant and anti-SARS-CoV-2 properties

Seon Beom Kim et al.

Summary: Sulfation pattern and molecular weight are crucial for the biological actions of sulfated glycans. This study investigated the differences in anti-SARS-CoV-2 and anticoagulant activities of low molecular weight derivatives of the red alga Botryocladia occidentalis sulfated galactan (BoSG). The results showed that lower molecular weight BoSG derivatives retained anti-SARS-CoV-2 activity while exhibiting weak anticoagulant activity. Additionally, the study observed distinct affinities of BoSG derivatives for different SARS-CoV-2 strains, with stronger affinity for the N501Y-containing variants.

JOURNAL OF BIOLOGICAL CHEMISTRY (2022)

Article Biochemistry & Molecular Biology

Application of per-Residue Energy Decomposition to Design Peptide Inhibitors of PSD95 GK Domain

Miao Tian et al.

Summary: This study describes the design of new peptide inhibitors with higher binding affinity for postsynaptic density protein 95 (PSD95) using molecular dynamics simulations. The results show that enhancing hydrophobic interactions is an important strategy for the design of inhibitory peptides targeting PSD95. The synthesized peptides exhibited higher binding affinity compared to the original peptide, and F10W was identified as the most potent inhibitor.

FRONTIERS IN MOLECULAR BIOSCIENCES (2022)

Review Biochemistry & Molecular Biology

Molecular simulations of complex carbohydrates and glycoconjugates

Elisa Fadda

Summary: Complex carbohydrates are abundant and versatile biopolymers in nature, with a wide range of biochemical functions. Molecular simulations can address the challenges of experimental characterization and provide important insights into the study of complex carbohydrates. This short review discusses the state-of-the-art in molecular simulations of complex carbohydrates, highlighting methodological strengths and weaknesses, and suggesting future perspectives.

CURRENT OPINION IN CHEMICAL BIOLOGY (2022)

Article Biochemistry & Molecular Biology

Spike-heparan sulfate interactions in SARS-CoV-2 infection

Fiona L. Kearns et al.

Summary: Heparan sulfate, a major component of the cellular glycocalyx, plays a crucial role in the infection cycle of SARS-CoV-2. It facilitates the open conformation of the spike protein, enabling its binding to ACE2. The coordination between viral and host glycans on the spike protein is essential for the binding and subsequent infection.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2022)

Article Biochemical Research Methods

Site-specific N-glycosylation Characterization of Recombinant SARS-CoV-2 Spike Proteins

Yong Zhang et al.

Summary: This study characterized the N-glycosylation of the S protein of SARS-CoV-2, revealing differences in glycan type and abundance between human and insect cell-expressed proteins. These findings shed light on the infection mechanism and offer new perspectives for the development of vaccines and targeted drugs.

MOLECULAR & CELLULAR PROTEOMICS (2021)

Article Chemistry, Analytical

N- and O-Glycosylation of the SARS-CoV-2 Spike Protein

Miloslav Sanda et al.

Summary: The outbreak of the Covid-19 pandemic has caused the current global health crisis, prompting the need for detailed studies on SARS-CoV-2 proteins to develop effective antiviral compounds and vaccines. The glycosylation of the spike (S) protein plays a significant role in its proteolytic activation, expanding the current knowledge in this area.

ANALYTICAL CHEMISTRY (2021)

Letter Infectious Diseases

First detection of SARS-CoV-2 spike protein N501 mutation in Italy in August, 2020

Simona Fiorentini et al.

LANCET INFECTIOUS DISEASES (2021)

Article Pharmacology & Pharmacy

Antiviral activities of four marine sulfated glycans against adenovirus and human cytomegalovirus

Mary Zoepfl et al.

Summary: The need for broad-spectrum antivirals is increasing, especially for novel emerging viruses and those with limited treatment options or resistance. Research has shown that specific marine sulfated glycans can inhibit viral attachment and entry, potentially through interactions with virions, suggesting unique opportunities for exploring relationships between glycan structure and antiviral activities.

ANTIVIRAL RESEARCH (2021)

Article Biochemistry & Molecular Biology

Enhanced binding of the N501Y-mutated SARS-CoV-2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations

Binquan Luan et al.

Summary: Recently emerged SARS-CoV-2 variants with mutations, such as N501Y, may enhance binding to hACE2. Molecular dynamics simulations show that Y501 in the mutated RBD can interact with Y41 and K353 in hACE2, potentially increasing the overall binding affinity by approximately 0.81 kcal center dot mol(-1). This binding dynamics may aid in designing more effective antibodies.

FEBS LETTERS (2021)

Review Biochemical Research Methods

Glycosylation of SARS-CoV-2: structural and functional insights

Asif Shajahan et al.

Summary: The COVID-19 pandemic is caused by the SARS-CoV-2 virus, which contains glycosylated proteins that interact with host receptors like hACE2 to facilitate infection. Studies show that these glycosylated proteins play important roles in viral infection and immune evasion, understanding which can aid in developing suitable prevention and therapy strategies.

ANALYTICAL AND BIOANALYTICAL CHEMISTRY (2021)

Article Biochemistry & Molecular Biology

Site-Specific Steric Control of SARS-CoV-2 Spike Glycosylation

Joel D. Allen et al.

Summary: This study investigated the glycosylation of recombinant SARS-CoV-2 spike proteins from five different laboratories and compared them against S protein from infectious virus, finding conserved patterns across all samples. The results suggest that recombinant spike-based SARS-CoV-2 immunogen glycosylation reproducibly recapitulates signatures of viral glycosylation.

BIOCHEMISTRY (2021)

Article Biochemistry & Molecular Biology

Heparin: A simplistic repurposing to prevent SARS-CoV-2 transmission in light of its in-vitro nanomolar efficacy

Yash Gupta et al.

Summary: The world is currently facing a pandemic caused by the novel coronavirus (SARS-CoV-2) with drug repurposing, such as heparin, being considered an effective strategy to combat COVID-19. Research has shown that heparin has highly efficacious viral entry blocking properties and could potentially be used as a transmission blocker.

INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES (2021)

Article Biochemistry & Molecular Biology

Structural and kinetic analyses of holothurian sulfated glycans suggest potential treatment for SARS-CoV-2 infection

Rohini Dwivedi et al.

Summary: Certain sulfated glycans from marine sources, such as a new fucosylated chondroitin sulfate from a sea cucumber, show potential effects against SARS-CoV-2. These glycans demonstrated anti-viral activity similar to 12 times more efficient than heparin with no cytotoxic effects. Computational simulations suggest an influence of the sulfation patterns of the glycans on interactions with the virus, highlighting the potential for further investigation against SARS-CoV-2.

JOURNAL OF BIOLOGICAL CHEMISTRY (2021)

Article Chemistry, Physical

OPLS4: Improving Force Field Accuracy on Challenging Regimes of Chemical Space

Chao Lu et al.

Summary: The development and validation of the OPLS4 force field, which builds upon previous work with OPLS3e, improved model accuracy on challenging regimes of drug-like chemical space. A novel parametrization strategy for charged species was introduced, leading to improved accuracy on benchmarks assessing small-molecule solvation and protein-ligand binding.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)

Review Biochemistry & Molecular Biology

The glycosylation in SARS-CoV-2 and its receptor ACE2

Yanqiu Gong et al.

Summary: This article reviews the detection, substrates, biological functions of glycosylation in SARS-CoV-2 proteins, as well as the human receptor ACE2. It also summarizes approved and ongoing SARS-CoV-2 therapeutics associated with glycosylation. This review not only helps broaden the understanding of viral glycobiology, but also provides key clues for the development of new preventive and therapeutic methodologies against SARS-CoV-2 and its variants.

SIGNAL TRANSDUCTION AND TARGETED THERAPY (2021)

Article Biochemistry & Molecular Biology

Evidence of a putative glycosaminoglycan binding site on the glycosylated SARS-CoV-2 spike protein N-terminal domain

Zachariah P. Schuurs et al.

Summary: A new GAG binding site was identified in the spike protein, which may be crucial for understanding recent UK and South African strains. These findings could also aid in future targeted therapy programs.

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2021)

Article Virology

Effective Inhibition of SARS-CoV-2 Entry by Heparin and Enoxaparin Derivatives

Ritesh Tandon et al.

Summary: SARS-CoV-2 virus relies on spike glycoprotein for cell entry, and several sulfated polysaccharides have shown potent neutralizing effects against the virus, demonstrating potential prophylactic and therapeutic applications.

JOURNAL OF VIROLOGY (2021)

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)

Article Multidisciplinary Sciences

Site-specific glycan analysis of the SARS-CoV-2 spike

Yasunori Watanabe et al.

SCIENCE (2020)

Article Chemistry, Physical

Developing a Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein Model in a Viral Membrane

Hyeonuk Woo et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2020)

Article Biochemistry & Molecular Biology

SARS-CoV-2 Infection Depends on Cellular Heparan Sulfate and ACE2

Thomas Mandel Clausen et al.

Article Multidisciplinary Sciences

Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion

Donald J. Benton et al.

NATURE (2020)

Article Multidisciplinary Sciences

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

Longxing Cao et al.

SCIENCE (2020)

Article Chemistry, Multidisciplinary

Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein

Lorenzo Casalino et al.

ACS CENTRAL SCIENCE (2020)

Article Biochemistry & Molecular Biology

Deducing the N- and O-glycosylation profile of the spike protein of novel coronavirus SARS-CoV-2

Asif Shajahan et al.

GLYCOBIOLOGY (2020)

Article Biochemistry & Molecular Biology

Rigorous analysis of free solution glycosaminoglycan dynamics using simple, new tools

Balaji Nagarajan et al.

GLYCOBIOLOGY (2020)

Article Computer Science, Interdisciplinary Applications

Revealing the Mechanism of SARS-CoV-2 Spike Protein Binding With ACE2

Yixin Xie et al.

COMPUTING IN SCIENCE & ENGINEERING (2020)

Article Biochemical Research Methods

Docking software performance in protein-glycosaminoglycan systems

Urszula Uciechowska-Kaczmarzyk et al.

JOURNAL OF MOLECULAR GRAPHICS & MODELLING (2019)

Article Biochemistry & Molecular Biology

CHARMM-GUI Glycan Modeler for modeling and simulation of carbohydrates and glycoconjugates

Sang-Jun Park et al.

GLYCOBIOLOGY (2019)

Review Chemistry, Medicinal

Antimicrobial Sulfated Glycans: Structure and Function

Vitor H. Pomin

CURRENT TOPICS IN MEDICINAL CHEMISTRY (2017)

Review Biochemistry & Molecular Biology

Biological roles of glycans

Ajit Varki

GLYCOBIOLOGY (2017)

Article Chemistry, Multidisciplinary

CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules

Seonghoon Kim et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2017)

Article Chemistry, Multidisciplinary

Extension and validation of the GLYCAM force field parameters for modeling glycosaminoglycans

Arunima Singh et al.

CANADIAN JOURNAL OF CHEMISTRY (2016)

Article Biochemistry & Molecular Biology

Computational analysis of interactions in structurally available protein-glycosaminoglycan complexes

Sergey A. Samsonov et al.

GLYCOBIOLOGY (2016)

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)

Review Chemistry, Medicinal

A Dilemma in the Glycosaminoglycan-Based Therapy: Synthetic or Naturally Unique Molecules?

Vitor H. Pomin

MEDICINAL RESEARCH REVIEWS (2015)

Review Chemistry, Medicinal

Marine Non-Glycosaminoglycan Sulfated Glycans as Potential Pharmaceuticals

Vitor H. Pomin

PHARMACEUTICALS (2015)

Article Chemistry, Medicinal

Docking Server for the Identification of Heparin Binding Sites on Proteins

Scott E. Mottarella et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2014)

Review Chemistry, Medicinal

Holothurian Fucosylated Chondroitin Sulfate

Vitor H. Pomin

MARINE DRUGS (2014)

Article Chemistry, Multidisciplinary

CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data

Jing Huang et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2013)

Article Biochemistry & Molecular Biology

Sequence determination and anticoagulant and antithrombotic activities of a novel sulfated fucan isolated from the sea cucumber Isostichopus badionotus

Shiguo Chen et al.

BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS (2012)

Review Chemistry, Applied

Anticancer polysaccharides from natural resources: A review of recent research

Aizhen Zong et al.

CARBOHYDRATE POLYMERS (2012)

Article Chemistry, Multidisciplinary

AutoDock4 and AutoDockTools4: Automated Docking with Selective Receptor Flexibility

Garrett M. Morris et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2009)

Article Chemistry, Multidisciplinary

Software news and updates - CHARNIM-GUI: A web-based grraphical user interface for CHARMM

Sunhwan Jo et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2008)

Review Chemistry, Multidisciplinary

GLYCAM06: A generalizable Biomolecular force field. Carbohydrates

Karl N. Kirschner et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2008)

Article Chemistry, Medicinal

Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes

Richard A. Friesner et al.

JOURNAL OF MEDICINAL CHEMISTRY (2006)

Article Biochemistry & Molecular Biology

Heparan sulfate targets the HIV-1 envelope glycoprotein gp120 coreceptor binding site

RR Vivès et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2005)

Article Chemistry, Medicinal

Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy

RA Friesner et al.

JOURNAL OF MEDICINAL CHEMISTRY (2004)

Article Chemistry, Medicinal

Glide: A new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening

TA Halgren et al.

JOURNAL OF MEDICINAL CHEMISTRY (2004)

Article Biochemistry & Molecular Biology

Internalization of HIV-1 Tat requires cell surface heparan sulfate proteoglycans

M Tyagi et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2001)