Heparan sulfate (HS) linear polysaccharide glycosaminoglycan compound is linked to components from the cell surface and the extracellular matrix. HS mediates SARS-CoV-2 infection through spike protein binding to cell surface receptors and is required to bind ACE2, prompting the need for electronic structure and molecular docking evaluation of this core system to exploit this attachment in developing new derivatives. Therefore, we have studied five molecules based on HS using molecular docking and electronic structure analysis. Non-covalent interaction analysis shows hydrogen bonding and van der Waals interactions in the binding to RBD-ACE2 interface and 3CLpro. SDM3 and SDM1 molecules present the lowest gap, including solvent effect under 154.6 kcal/mol, and exhibit the most reactivity behavior in this group, potentially leading to enhanced interaction in docking studies.

Luiz F M A Benício

Érica C M Nascimento

João B L Martins

Journal of Molecular Modeling

JOURNAL OF MOLECULAR MODELING 专注于“硬核”建模，发表高质量的研究和报告。它成立于 1995 年，是一家纯电子期刊，现已调整其格式，包括全彩印刷版，并调整其目标和范围以适应快速变化的分子建模领域，特别关注 3D 建模。今天，该杂志涵盖了包括生命科学建模在内的分子建模的各个方面；材料建模；新方法；和计算化学。主题包括计算机辅助分子设计；合理的药物设计、从头配体设计、受体建模与对接；化学信息学、数据分析、可视化和挖掘；计算药物化学；同源建模；肽、DNA和其他生物聚合物的模拟；定量构效关系 (QSAR) 和 ADME 建模；生物反应机制的建模；并结合实验和计算研究，其中计算起主要作用。

The Journal of Molecular Modeling focuses on high-quality research and reports in the field of molecular modeling. Established in 1995, it is a fully electronic journal that has adapted its format to include full-color print versions and has updated its aims and scope to keep pace with the rapidly evolving field of molecular modeling, with a particular emphasis on 3D modeling. Today, the journal covers various aspects of molecular modeling, including life sciences modeling, materials modeling, new methodologies, and computational chemistry. Key topics include computer-aided molecular design, rational drug design, de novo ligand design, receptor modeling and docking, cheminformatics, data analysis, visualization and mining, computational drug chemistry, homology modeling, simulations of peptides, DNA, and other biopolymers, quantitative structure-activity relationships (QSAR) and ADME modeling, modeling of biological reaction mechanisms, and research that combines experimental and computational approaches, where computation plays a central role.

《Journal of Molecular Modeling》专注于高质量的分子建模研究与报告。该期刊成立于1995年，是一家纯电子期刊，现已调整格式，包括全彩印刷版，并更新了目标和范围，以适应快速发展的分子建模领域，特别关注三维建模。如今，该杂志涵盖了分子建模的各个方面，包括生命科学建模、材料建模、新方法和计算化学等。主要主题包括计算机辅助分子设计、合理药物设计、从头配体设计、受体建模与对接、化学信息学、数据分析、可视化与挖掘、计算药物化学、同源建模、肽、DNA及其他生物聚合物的模拟、定量构效关系（QSAR）和ADME建模、生物反应机制的建模，以及结合实验与计算研究，其中计算起主要作用。

Category	Quartile
化学	4
化学, 生化与分子生物学	4
化学, 生物物理	4
化学, 化学综合	4
化学, 计算机跨学科应用	4

Docking heparan sulfate-based ligands as a promising inhibitor for SARS-CoV-2

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Category	Quartile
COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS	3