ArticleBioinformatics (Oxford, England)2018
The size matters? A computational tool to design bivalent ligands.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Targeted Protein Degradation: Advances, Challenges, and Prospects for Computational Methods.Journal of chemical information and modeling · 2023Review
- pyGOMoDo: GPCRs modeling and docking with python.Bioinformatics (Oxford, England) · 2023Article
- Chemical biology-based approaches to study adenosine APurinergic signalling · 2022Article
- A Single Point Mutation Blocks the Entrance of Ligands to the Cannabinoid CBJournal of chemical information and modeling · 2022Article
- Heterobivalent Ligand for the Adenosine AJournal of medicinal chemistry · 2022Article
- Polygodial and Ophiobolin A Analogues for Covalent Crosslinking of Anticancer Targets.International journal of molecular sciences · 2021Article
- Unifying Catalysis Framework to Dissect Proteasomal Degradation Paradigms.ACS central science · 2021Review
- Unraveling the Role of Linker Design in Proteolysis Targeting Chimeras.Journal of medicinal chemistry · 2021Review
- Orally Active Peptide Vector Allows Using Cannabis to Fight Pain While Avoiding Side Effects.Journal of medicinal chemistry · 2021Article
- Discovery of Homobivalent Bitopic Ligands of the Cannabinoid CBChemistry (Weinheim an der Bergstrasse, Germany) · 2020Article
- PRosettaC: Rosetta Based Modeling of PROTAC Mediated Ternary Complexes.Journal of chemical information and modeling · 2020Article
- Design of a True Bivalent Ligand with Picomolar Binding Affinity for a G Protein-Coupled Receptor Homodimer.Journal of medicinal chemistry · 2018Article
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Motivation: Bivalent ligands are increasingly important such as for targeting G protein-coupled receptor (GPCR) dimers or proteolysis targeting chimeras (PROTACs). They contain two pharmacophoric units that simultaneously bind in their corresponding binding sites, connected with a spacer chain. Here, we report a molecular modelling tool that links the pharmacophore units via the shortest pathway along the receptors van der Waals surface and then scores the solutions providing prioritization for the design of new bivalent ligands. Results: Bivalent ligands of known dimers of GPCRs, PROTACs and a model bivalent antibody/antigen system were analysed. The tool could rapidly assess the preferred linker length for the different systems and recapitulated the best reported results. In the case of GPCR dimers the results suggest that in some cases these ligands might bind to a secondary binding site at the extracellular entrance (vestibule or allosteric site) instead of the orthosteric binding site. Availability and implementation: Freely accessible from the Molecular Operating Environment svl exchange server (https://svl.chemcomp.com/). Supplementary information: Supplementary data are available at Bioinformatics online.
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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.