Biomolecular dynamics in the 21st century

Brooks, Charles L.; MacKerell, Alexander D.; Post, Carol B.; Nilsson, Lennart

doi:10.1016/j.bbagen.2023.130534

Cited by 7 publications

(2 citation statements)

References 94 publications

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“…They found that SARS-CoV-2 shows a higher binding force and binding energy to ACE2 than SARS-CoV-1 [19,20]. We studied the effects of SARS-CoV-2 mutations and found that the N501Y mutation enhances RBD binding to ACE2, while K417N and E484K do not [21]. In addition to measuring protein-protein interaction, AFM-SMFS has been most widely used to measure the mechanical stability of the protein by protein (un)folding experiments, such as the giant muscle protein titin and many other mechanically stable proteins [41,42].…”

Section: Resultsmentioning

confidence: 99%

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Molecular Mechanism of Interaction between DNA Aptamer and Receptor-Binding Domain of Severe Acute Respiratory Syndrome Coronavirus 2 Variants Revealed by Steered Molecular Dynamics Simulations

Ding,

Xu,

Zheng

et al. 2024

Molecules

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The ongoing SARS-CoV-2 pandemic has underscored the urgent need for versatile and rapidly deployable antiviral strategies. While vaccines have been pivotal in controlling the spread of the virus, the emergence of new variants continues to pose significant challenges to global health. Here, our study focuses on a novel approach to antiviral therapy using DNA aptamers, short oligonucleotides with high specificity and affinity for their targets, as potential inhibitors against the spike protein of SARS-CoV-2 variants Omicron and JN.1. Our research utilizes steered molecular dynamics (SMD) simulations to elucidate the binding mechanisms of a specifically designed DNA aptamer, AM032-4, to the receptor-binding domain (RBD) of the aforementioned variants. The simulations reveal detailed molecular insights into the aptamer–RBD interaction, demonstrating the aptamer’s potential to maintain effective binding in the face of rapid viral evolution. Our work not only demonstrates the dynamic interaction between aptamer–RBD for possible antiviral therapy but also introduces a computational method to study aptamer–protein interactions.

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Section: Resultsmentioning

confidence: 99%

“…Molecular dynamics (MD) simulations provide a powerful method approach for studying molecular behavior and understanding their properties [20][21][22][23][24]. These simulations enable researchers to gain insights into various phenomena [19,25,26].…”

Section: Resultsmentioning

confidence: 99%

Molecular Mechanism of Interaction between DNA Aptamer and Receptor-Binding Domain of Severe Acute Respiratory Syndrome Coronavirus 2 Variants Revealed by Steered Molecular Dynamics Simulations

Ding,

Xu,

Zheng

et al. 2024

Molecules

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Benchmarking a dual-scale hybrid simulation framework for small globular proteins combining the CHARMM36 and Martini2 models

Yadav,

Kharche,

Prakash

et al. 2025

Journal of Molecular Graphics and Modelling

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Discovery of a Heparan Sulfate Binding Domain in Monkeypox Virus H3 as an Anti-poxviral Drug Target Combining AI and MD Simulations

Zheng,

Duan,

Huang

et al. 2024

Preprint

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The 2022 global outbreak of mpox virus (MPXV), recognized as a public health emergency by the World Health Organization (WHO), underscored the urgent need for specific antiviral agents. H3, a key antiviral target, mediates the adhesion of MPXV to host cells through its interaction with heparan sulfate (HS). Understanding the details of the H3-HS interaction has been challenging due to the highly flexible and complex nature of HS, which hinders its structural characterization. Utilizing state-of-the-art computational biology techniques, including molecular dynamics (MD) simulations, dynamic molecular docking, and AlphaFold2, we identified a novel α-helical domain in H3 critical for HS binding. This domain, conserved acrossorthopoxviruses, was validated experimentally, confirming its crucial role in viral adhesion at both molecular and cellular levels. Targeting this newly discovered HS-binding domain, wede novodesigned a protein inhibitor, AI-PoxBlock723, which effectively disrupt the H3-HS interaction, and inhibit viral infection. Our work not only introduces a promising anti-poxviral drug candidate, but also provides a comprehensive framework for elucidating complex protein-glycan interactions.

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Biomolecular dynamics in the 21st century

Cited by 7 publications

References 94 publications

Molecular Mechanism of Interaction between DNA Aptamer and Receptor-Binding Domain of Severe Acute Respiratory Syndrome Coronavirus 2 Variants Revealed by Steered Molecular Dynamics Simulations

Molecular Mechanism of Interaction between DNA Aptamer and Receptor-Binding Domain of Severe Acute Respiratory Syndrome Coronavirus 2 Variants Revealed by Steered Molecular Dynamics Simulations

Benchmarking a dual-scale hybrid simulation framework for small globular proteins combining the CHARMM36 and Martini2 models

Discovery of a Heparan Sulfate Binding Domain in Monkeypox Virus H3 as an Anti-poxviral Drug Target Combining AI and MD Simulations

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