A memo about New approach of Drug discovery from ACS medchem letters #memo #journal #RIBOTAC

Recently there are lots of publications and patents about PROTACs (Proteolysis targeting chimeric). As name indicates that the target of PROTACs is the specific protein of degradation (POI) so it’s called chemical knockdown. Compared to inhibitor, sometime PROTACs shows a strong biological activity. It’s an interesting approach. And I found another interesting approach in ACSContinue reading “A memo about New approach of Drug discovery from ACS medchem letters #memo #journal #RIBOTAC”

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Data analysis of MMP “from OR to Fluorine” #memo #journal

Control lipophilicity is key strategy for drug design. Medicinal chemist often struggle to ADMET issue due to their compound lipophilicity. Sometime ADMET issue can be improved by reducing LogD but it cause loss of potency. Matched molecular pair approach is used to find bioisosteric replacements that mean the substructure replacement with keeping potency but changeContinue reading “Data analysis of MMP “from OR to Fluorine” #memo #journal”

Control targeted gene transcription with small molecule #journal #memo

As people well know PROTAC(PROteolysis TArgeting Chimeras) is one of the interesting approach for targeted protein degradation. It has warhead, ligand of targeted protein and ligand of E3 ligase. This bi-functional molecule motif ‘A-Linker-B’ is widely used in drug design. And I read a very interesting article found in my twitter TL. The URL isContinue reading “Control targeted gene transcription with small molecule #journal #memo”

Which is better Graph based or descriptor based model for QSAR prediction? #journal #memo #chemoinformatics

There are lots of Graph convolutional network(GCN) models are applied for QSAR tasks instead of traditional descriptor based model. The interesting point of GCN is that we don’t need feature engineering I think. It means that during the learning process, GCN learns molecular feature from given molecular graph. On the other side, descriptor based modelContinue reading “Which is better Graph based or descriptor based model for QSAR prediction? #journal #memo #chemoinformatics”

Build accurate model with small training data and quantum chemistry #memo #from_ChemRxiv

Recently I read the nice article from ChemRxiv.Here is the link ;) The title is ‘Machine Learning Meets Mechanistic Modelling for Accurate Prediction of Experimental Activation Energies’. I don’t have experience there area but I found and read publications which use Mechanistic DFT. The author mentioned that DFT based approach has difficulties to calculate reactionContinue reading “Build accurate model with small training data and quantum chemistry #memo #from_ChemRxiv”

What is scaffold / Medicinal chemist feeling #memo

Recently I’m interested in the following article. https://pubs.acs.org/doi/abs/10.1021/acs.jcim.0c00204 The author tried to detect chemical series (scaffold) like medicinal chemist. In the drug discovery project chemical series / scaffold is very important concept to analyze compounds SAR but it is fuzzy. As chemoinformatitian know Bemis-Murcko scaffold is one of the solution for systemic detection of chemical seriesContinue reading “What is scaffold / Medicinal chemist feeling #memo”