Integrating multiscale and machine learning approaches towards the SAMPL9 log P challenge

MR Draper, A Waterman, JE Dannatt… - Physical Chemistry …, 2024 - pubs.rsc.org
… enhance the description of the electronic energy beyond a … One of the causes is the large
rotational flexibility exhibited … sampled from the umbrella sampling capture the wide range of …

Can small drugs predict the intrinsic aqueous solubility of 'beyond Rule of 5'big drugs?

A Avdeef, M Kansy - ADMET and DMPK, 2020 - hrcak.srce.hr
… number of rotatable bonds, which suggests that flexibility may … acceptor count increases,
but not so much the donor count. … search for 3D-based descriptors arising from ‘conformational

Solution conformations shed light on PROTAC cell permeability

Y Atilaw, V Poongavanam… - ACS Medicinal …, 2020 - ACS Publications
descriptorsrotatable bonds place 1 into chemical space far beyond the rule of 5. As the
calculated properties of 1 are representative for reported VHL based PROTACs that have flexible

Design principles for balancing lipophilicity and permeability in beyond rule of 5 space

H Möbitz - ChemMedChem, 2024 - Wiley Online Library
… , and high number of rotatable bonds typical for bRo5 drugs. … and 24 replicates of highly
flexible molecules also showed a strong … compartment to reduce lysosomal and cellular trapping. …

Shape-based methods for Structure-based Fragment Growing

P Penner - 2022 - ediss.sub.uni-hamburg.de
One of the hierarchy classes is a catch-all class that accepts … to match all rotatable bonds
in the conformations used as a … , would have gone significantly beyond the scope of this work. …

PackDock: a Diffusion Based Side Chain Packing Model for Flexible Protein-Ligand Docking

R Zhang, X Jiang, D Cao, J Yu, M Chen, Z Fan, X Kong… - bioRxiv, 2024 - biorxiv.org
… for the community to push beyond the limitations of existing … ability to capture accurate pocket
conformations while ensuring … resides in the torsional angles of rotatable bonds. Hence, the …

The hapten rigidity improves antibody performances in immunoassay for rifamycins: Immunovalidation and molecular mechanism

Y Zhang, W Wu, Q Li, P Zhou, K Wen, J Shen… - Journal of Hazardous …, 2024 - Elsevier
… ) flexibility index that counts the number of conformers with an … molecular descriptors,
which considers rotatable bonds, 2D … of rotatable bonds, 2D topology, and 3D conformation, …

Beyond Rule of Five and PROTACs in Modern Drug Discovery: Polarity Reducers, Chameleonicity, and the Evolving Physicochemical Landscape

E Price, M Weinheimer, A Rivkin… - Journal of Medicinal …, 2024 - ACS Publications
… This parameter captures the ability of a compound to achieve … flexible but tended to have
poor absorption due to extreme AB-MPS scores (driven by their high rotatable bond counts as …

Chemical space and molecular descriptors for QSAR studies

V Consonni, D Ballabio, R Todeschini - Cheminformatics, QSAR and …, 2023 - Elsevier
Flexible molecules can have several different conformations … that represent global
information captured from the whole … number of bonds and rings, the number of rotatable bonds, …

Steering new drug discovery campaigns: permeability, solubility, and physicochemical properties in the bRo5 chemical space

G Caron, J Kihlberg, G Goetz, E Ratkova… - ACS Medicinal …, 2021 - ACS Publications
… programs concern compounds in the beyond rule of 5 (bRo5… yet limited flexibility and populate
conformational ensembles … comprehensive descriptors that would be able to capture the …