Modelling the solubility of compounds in the "beyond Rule of 5" (bRo5) chemical space is in its infancy and to date only a few studies have been reported in the literature. Based on our own results, and those already published, we conclude that consideration of conformational flexibility and chameleon like behaviour is important, but quantitative models that account for these properties remain to be developed. Inclusion of 3D information appears to be somewhat less important than for cell permeability and extremely challenging due to the difficulties of accurate conformational sampling in the bRo5 space. Currently, methods for modelling of solubility will have to be tailored to the set of investigated compounds.
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http://dx.doi.org/10.5599/admet.834 | DOI Listing |
J Pharm Sci
December 2024
Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, IL 60064, United States.
Biopharmaceutical companies generate a wealth of data, ranging from in silico physicochemical properties and machine learning models to both low and high-throughput in vitro assays and in vivo studies. To effectively harnesses this extensive data, we introduce a statistical methodology facilitated by Accuracy, Utility, and Rank Order Assessment (AURA), which combines basic statistical analyses with dynamic data visualizations to evaluate endpoint effectiveness in predicting intestinal absorption. We demonstrated that various physicochemical properties uniquely influence intestinal absorption on a project-specific basis, considering factors like intestinal efflux, passive permeability, and clearance.
View Article and Find Full Text PDFJ Chem Inf Model
December 2024
Preclinical Modeling and Simulation, Preclinical Development, Bayer AG, Muellerstr. 178, 13353 Berlin, Germany.
Machine learning (ML) techniques are being widely implemented to fill the gap in simple molecular design guidelines for newer therapeutic modalities in the extended and beyond rule of five chemical space (eRo5, bRo5). These ML techniques predict molecular properties directly from the structure, allowing for the prioritization of promising compounds. However, the performance of models varies greatly among ML use cases.
View Article and Find Full Text PDFADMET DMPK
August 2024
CASSMedChem, Molecular Biotechnology and Health Sciences Dept., University of Torino, Piazza Nizza 44, 10126 Torino, Italy.
Background And Purpose: The classical drug discovery toolbox continually expands beyond traditional rule of five (Ro5)-compliant small molecules to include new chemical modalities for difficult-to-drug targets. The paper focuses on the molecular properties essential to drive oral bioavailability within the bRo5 framework.
Experimental Approach: The first part outlines the concept and methodologies for characterizing bRo5 physicochemical properties, including considerations on chameleonicity; in particular, the paper summarizes the content of the last author's talk presented during the IAPC-10 Meeting held in Belgrade in September 2023 (https://iapchem.
Pharmaceutics
June 2024
Quantitative, Translational and ADME Sciences, AbbVie Deutschland GmbH & Co. KG, Knollstrasse, 67061 Ludwigshafen, Germany.
Current drug development tends towards complex chemical molecules, referred to as "beyond rule of five" (bRo5) compounds, which often exhibit challenging physicochemical properties. Measuring Caco-2 permeability of those compounds is difficult due to technical limitations, including poor recovery and detection sensitivity. We implemented a novel assay, with optimized incubation and analytics, to measure permeability close to equilibrium.
View Article and Find Full Text PDFJ Org Chem
April 2024
Department of Discovery Chemistry, Merck & Co., Inc., 33 Ave. Louis Pasteur, Boston, Massachusetts 02215, United States.
Recent years have seen novel modalities emerge for the treatment of human diseases resulting in an increase in beyond rule of 5 (bRo5) chemical matter. As a result, synthetic innovations aiming to enable rapid access to complex bRo5 molecular entities have become increasingly valuable for medicinal chemists' toolkits. Herein, we report the general synthesis of a new class of noncanonical amino acids (ncAA) with a cyclopropyl backbone to achieve conformational constraint and bearing C()-rich benzene bioisosteres.
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