ArticleJournal of medicinal chemistry2022
Refinement of Computational Access to Molecular Physicochemical Properties: From Ro5 to bRo5.
Article in Journal of medicinal chemistry, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Dual PROTACs Versus Dual Inhibitors in Oncology: A Medicinal Chemistry and Linker Design Perspective.Pharmaceuticals (Basel, Switzerland) · 2026Review
- Toward the Engineering of Chameleonicity: Quantum Mechanical Prediction for the Octanol/Water Distributions of Large Flexible Triazine Macrocycles.Journal of chemical information and modeling · 2026Article
- MK4 Repositioning for IAHSP: OvercomingACS chemical neuroscience · 2026Article
- Targeting Oxalate Production by Combining Enzyme Inhibition and Proteolysis Activation: A Novel Therapeutic Approach for Primary Hyperoxaluria Type 1.Journal of medicinal chemistry · 2026Article
- Diastereomeric Branched-Ester dBET1 Analogs Exhibit Conformation-Dependent Differences in Passive Membrane Permeability.Journal of medicinal chemistry · 2026Article
- Conformational Dynamics in the Cell Membrane Interactions of Bispecific Targeted Degrader Therapeutics.Journal of medicinal chemistry · 2025Article
- Challenges of Aufheben to Promote Druglikeness: Chemical Modification Strategies to Improve Aqueous Solubility and Permeability.Journal of medicinal chemistry · 2025Review
- Linker Methylation as a Strategy to Enhance PROTAC Oral Bioavailability: Insights from Molecular Properties and Conformational Analysis.Journal of medicinal chemistry · 2025Article
- Macrocyclization: Enhancing Drug-like Properties of Discoidin Domain Receptor Kinase Inhibitors.ACS medicinal chemistry letters · 2025Article
- Incorporating Synthetic Accessibility in Drug Design: Predicting Reaction Yields of Suzuki Cross-Couplings by Leveraging AbbVie's 15-Year Parallel Library Data Set.Journal of the American Chemical Society · 2024Article
- Molecular properties, including chameleonicity, as essential tools for designing the next generation of oral beyond rule of five drugs.ADMET & DMPK · 2024Article
- Chamelogk: A Chromatographic Chameleonicity Quantifier to Design Orally Bioavailable Beyond-Rule-of-5 Drugs.Journal of medicinal chemistry · 2023Article
- In Silico Tools to Extract the Drug Design Information Content of Degradation Data: The Case of PROTACs Targeting the Androgen Receptor.Molecules (Basel, Switzerland) · 2023Article
- Conformational Sampling Deciphers the Chameleonic Properties of a VHL-Based Degrader.Pharmaceutics · 2023Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
There is a need of computational tools to rank bRo5 drug candidates in the very early phases of drug discovery when chemical matter is unavailable. In this study, we selected three compounds: (a) a Ro5 drug (Pomalidomide), (b) a bRo5 orally available drug (Saquinavir), and (c) a polar PROTAC (CMP 98) to focus on computational access to physicochemical properties. To provide a benchmark, the three compounds were first experimentally characterized for their lipophilicity, polarity, IMHBs, and chameleonicity. To reproduce the experimental information content, we generated conformer ensembles with conformational sampling and molecular dynamics in both water and nonpolar solvents. Then we calculated Rgyr, 3D PSA, and IMHB number. An innovative pool of strategies for data analysis was then provided. Overall, we report a contribution to close the gap between experimental and computational methods for characterizing bRo5 physicochemical properties.
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