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Updated: Nov 4, 2025
Engineering Antiviral Agents via Surface Plasmon Resonance
Published on: June 14, 2022
Molecular dynamics analysis of N-acetyl-D-glucosamine against specific SARS-CoV-2's pathogenicity factors
Ömür Baysal1, Naeem Abdul Ghafoor1, Ragıp Soner Silme2
1Faculty of Science, Department of Molecular Biology and Genetics, Molecular Microbiology Unit, Muğla Sıtkı Koçman University, Menteşe-Muğla, Turkey.
Abstract:
The causative agent of the pandemic identified as SARS-CoV-2 leads to a severe respiratory illness similar to SARS and MERS with fever, cough, and shortness of breath symptoms and severe cases that can often be fatal. In our study, we report our findings based on molecular docking analysis which could be the new effective way for controlling the SARS-CoV-2 virus and additionally, another manipulative possibilities involving the mimicking of immune system as occurred during the bacterial cell recognition system. For this purpose, we performed molecular docking using computational biology techniques on several SARS-CoV-2 proteins that are responsible for its pathogenicity against N-acetyl-D-glucosamine. A similar molecular dynamics analysis has been carried out on both SARS-CoV-2 and anti-Staphylococcus aureus neutralizing antibodies to establish the potential of N-acetyl-D-glucosamine which likely induces the immune response against the virus. The results of molecular dynamic analysis have confirmed that SARS-CoV-2 spike receptor-binding domain (PDB: 6M0J), RNA-binding domain of nucleocapsid phosphoprotein (PDB: 6WKP), refusion SARS-CoV-2 S ectodomain trimer (PDB: 6X79), and main protease 3clpro at room temperature (PDB: 7JVZ) could bind with N-acetyl-D-glucosamine that these proteins play an important role in SARS-CoV-2's infection and evade the immune system. Moreover, our molecular docking analysis has supported a strong protein-ligand interaction of N-acetyl-D-glucosamine with these selected proteins. Furthermore, computational analysis against the D614G mutant of the virus has shown that N-acetyl-D-glucosamine affinity and its binding potential were not affected by the mutations occurring in the virus' receptor binding domain. The analysis on the affinity of N-acetyl-D-glucosamine towards human antibodies has shown that it could potentially bind to both SARS-CoV-2 proteins and antibodies based on our predictive modelling work. Our results confirmed that N-acetyl-D-glucosamine holds the potential to inhibit several SARS-CoV-2 proteins as well as induce an immune response against the virus in the host.
Insights
N-acetyl-D-glucosamine shows potential in controlling SARS-CoV-2 by inhibiting key viral proteins and mimicking immune responses. This compound
Area of Science:
- Computational Biology
- Virology
- Immunology
Background:
- Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) causes a fatal respiratory illness.
- Existing treatments are limited, necessitating novel therapeutic strategies.
Purpose of the Study:
- To investigate N-acetyl-D-glucosamine as a potential antiviral agent against SARS-CoV-2.
- To explore its ability to inhibit viral proteins and modulate the immune system.
Main Methods:
- Molecular docking and molecular dynamics simulations were employed.
- Analysis focused on SARS-CoV-2 proteins like spike receptor-binding domain and main protease.
- Interactions with human antibodies were also assessed.
Main Results:
- N-acetyl-D-glucosamine demonstrated strong binding affinity with critical SARS-CoV-2 proteins.
- The compound's efficacy was unaffected by the D614G mutation.
- Predictive modeling indicated potential for immune response induction.
Conclusions:
- N-acetyl-D-glucosamine is a promising candidate for SARS-CoV-2 inhibition.
- It may serve as a dual-action agent, inhibiting the virus and stimulating host immunity.
