Small Glycols Discover Cryptic Pockets on Proteins for Fragment-Based Approaches
Sign Up to like & getrecommendations! Published in 2021 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.0c01126
Abstract: Cryptic pockets are visible in ligand-bound protein structures but are occluded in unbound structures. Utilizing these pockets in fragment-based drug-design provides an attractive option for proteins not tractable by classical binding sites. However, owing to… read more here.
Keywords: fragment based; small glycols; cryptic pocket; pocket ... See more keywords
A benzene-mapping approach for uncovering cryptic pockets in membrane-bound proteins.
Sign Up to like & getrecommendations! Published in 2020 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.0c00370
Abstract: Molecular dynamics (MD) simulations in combination with small organic probes present in the solvent have previously been used as a method to reveal cryptic pockets that may not have been identified in experimental structures. We… read more here.
Keywords: protein; benzene mapping; membrane embedded; membrane ... See more keywords
Accelerated Ligand-Mapping Molecular Dynamics Simulations for the Detection of Recalcitrant Cryptic Pockets and Occluded Binding Sites.
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.1c01177
Abstract: The identification and characterization of binding sites is a critical component of structure-based drug design (SBDD). Probe-based/cosolvent molecular dynamics (MD) methods that allow for protein flexibility have been developed to predict ligand binding sites. However,… read more here.
Keywords: detection; binding sites; occluded binding; cryptic pockets ... See more keywords
Abstract PL05-03: What if all your favorite proteins are druggable
Sign Up to like & getrecommendations! Published in 2023 at "Cancer Research"
DOI: 10.1158/1538-7445.am2023-pl05-03
Abstract: Many proteins that play key roles in cancer are considered difficult drug targets, if not entirely undruggable, due to an apparent lack of pockets where small molecules can bind with the affinity and specificity required… read more here.
Keywords: abstract pl05; favorite proteins; druggable abstract; proteins druggable ... See more keywords
What Features of Ligands Are Relevant to the Opening of Cryptic Pockets in Drug Targets?
Sign Up to like & getrecommendations! Published in 2022 at "Informatics"
DOI: 10.3390/informatics9010008
Abstract: Small-molecule drug design aims to identify inhibitors that can specifically bind to a functionally important region on the target, i.e., an active site of an enzyme. Identification of potential binding pockets is typically based on… read more here.
Keywords: cryptic pockets; relevant opening; opening cryptic; features ligands ... See more keywords