ArticlePloS one2017
A molecular dynamics-based algorithm for evaluating the glycosaminoglycan mimicking potential of synthetic, homogenous, sulfated small molecules.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 26 citations in OpenAlex.
- Benchmark of Available Explicit Solvent Models in CHARMM36m to Characterize Glycosaminoglycans.The journal of physical chemistry. B · 2025Article
- A Robust Proteomics-Based Method for Identifying Preferred Protein Targets of Synthetic Glycosaminoglycan Mimetics.bioRxiv : the preprint server for biology · 2025Article
- Benchmarking Water Models in Molecular Dynamics of Protein-Glycosaminoglycan Complexes.Journal of chemical information and modeling · 2024Article
- Solvent Model Benchmark for Molecular Dynamics of Glycosaminoglycans.Journal of chemical information and modeling · 2023Article
- Designing Synthetic, Sulfated Glycosaminoglycan Mimetics That Are Orally Bioavailable and ExhibitingJournal of medicinal chemistry · 2023Article
- Molecular dynamics simulations to understand glycosaminoglycan interactions in the free- and protein-bound states.Current opinion in structural biology · 2022Review
- Aqueous Molecular Dynamics for Understanding Glycosaminoglycan Recognition by Proteins.Methods in molecular biology (Clifton, N.J.) · 2022Article
- 3-Computational and structural biotechnology journal · 2022Article
- On the Selectivity of Heparan Sulfate Recognition by SARS-CoV-2 Spike Glycoprotein.ACS medicinal chemistry letters · 2021Article
- Glycosaminoglycan-Protein Interactions and Their Roles in Human Disease.Frontiers in molecular biosciences · 2021Review
- Article
- Rigorous analysis of free solution glycosaminoglycan dynamics using simple, new tools.Glycobiology · 2020Article
- Sulfated Non-Saccharide Glycosaminoglycan Mimetics as Novel Drug Discovery Platform for Various Pathologies.Current medicinal chemistry · 2020Review
- On the Process of Discovering Leads That Target the Heparin-Binding Site of Neutrophil Elastase in the Sputum of Cystic Fibrosis Patients.Journal of medicinal chemistry · 2019Article
- A Unique Nonsaccharide Mimetic of Heparin Hexasaccharide Inhibits Colon Cancer Stem Cells via p38 MAP Kinase Activation.Molecular cancer therapeutics · 2019Article
- Inhibition of Herpes Simplex Virus-1 Entry into Human Cells by Nonsaccharide Glycosaminoglycan Mimetics.ACS medicinal chemistry letters · 2018Article
- So you think computational approaches to understanding glycosaminoglycan-protein interactions are too dry and too rigid? Think again!Current opinion in structural biology · 2018Review
- Perspective on computational simulations of glycosaminoglycans.Wiley interdisciplinary reviews. Computational molecular scienceArticle
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Glycosaminoglycans (GAGs) are key natural biopolymers that exhibit a range of biological functions including growth and differentiation. Despite this multiplicity of function, natural GAG sequences have not yielded drugs because of problems of heterogeneity and synthesis. Recently, several homogenous non-saccharide glycosaminoglycan mimetics (NSGMs) have been reported as agents displaying major therapeutic promise. Yet, it remains unclear whether sulfated NSGMs structurally mimic sulfated GAGs. To address this, we developed a three-step molecular dynamics (MD)-based algorithm to compare sulfated NSGMs with GAGs. In the first step of this algorithm, parameters related to the range of conformations sampled by the two highly sulfated molecules as free entities in water were compared. The second step compared identity of binding site geometries and the final step evaluated comparable dynamics and interactions in the protein-bound state. Using a test case of interactions with fibroblast growth factor-related proteins, we show that this three-step algorithm effectively predicts the GAG structure mimicking property of NSGMs. Specifically, we show that two unique dimeric NSGMs mimic hexameric GAG sequences in the protein-bound state. In contrast, closely related monomeric and trimeric NSGMs do not mimic GAG in either the free or bound states. These results correspond well with the functional properties of NSGMs. The results show for the first time that appropriately designed sulfated NSGMs can be good structural mimetics of GAGs and the incorporation of a MD-based strategy at the NSGM library screening stage can identify promising mimetics of targeted GAG sequences.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.