Macrocycles in drug discovery─ learning from the past for the future
D Garcia Jimenez, V Poongavanam… - Journal of Medicinal …, 2023 - ACS Publications
We have analyzed FDA-approved macrocyclic drugs, clinical candidates, and the recent
literature to understand how macrocycles are used in drug discovery. Current drugs are …
literature to understand how macrocycles are used in drug discovery. Current drugs are …
[HTML][HTML] Bayer's in silico ADMET platform: a journey of machine learning over the past two decades
AH Göller, L Kuhnke, F Montanari, A Bonin… - Drug Discovery …, 2020 - Elsevier
Highlights•Evolution of Bayer's in silico ADMET platform, modelling pharmacokinetic and
physicochemical endpoints.•Application of machine learning, deep learning and artificial …
physicochemical endpoints.•Application of machine learning, deep learning and artificial …
Linker-dependent folding rationalizes PROTAC cell permeability
V Poongavanam, Y Atilaw, S Siegel… - Journal of Medicinal …, 2022 - ACS Publications
Proteolysis-targeting chimeras (PROTACs) must be cell permeable to reach their target
proteins. This is challenging as the bivalent structure of PROTACs puts them in chemical …
proteins. This is challenging as the bivalent structure of PROTACs puts them in chemical …
Improving conformer generation for small rings and macrocycles based on distance geometry and experimental torsional-angle preferences
S Wang, J Witek, GA Landrum… - Journal of chemical …, 2020 - ACS Publications
The conformer generator ETKDG is a stochastic search method that utilizes distance
geometry together with knowledge derived from experimental crystal structures. It has been …
geometry together with knowledge derived from experimental crystal structures. It has been …
Cheminformatics in natural product‐based drug discovery
Y Chen, J Kirchmair - Molecular Informatics, 2020 - Wiley Online Library
This review seeks to provide a timely survey of the scope and limitations of cheminformatics
methods in natural product‐based drug discovery. Following an overview of data resources …
methods in natural product‐based drug discovery. Following an overview of data resources …
Lipophilic permeability efficiency reconciles the opposing roles of lipophilicity in membrane permeability and aqueous solubility
MR Naylor, AM Ly, MJ Handford… - Journal of medicinal …, 2018 - ACS Publications
As drug discovery moves increasingly toward previously “undruggable” targets such as
protein–protein interactions, lead compounds are becoming larger and more lipophilic …
protein–protein interactions, lead compounds are becoming larger and more lipophilic …
Elucidating solution structures of cyclic peptides using molecular dynamics simulations
Protein–protein interactions are vital to biological processes, but the shape and size of their
interfaces make them hard to target using small molecules. Cyclic peptides have shown …
interfaces make them hard to target using small molecules. Cyclic peptides have shown …
Solution conformations explain the chameleonic behaviour of macrocyclic drugs
E Danelius, V Poongavanam, S Peintner… - … A European Journal, 2020 - Wiley Online Library
It has been hypothesised that drugs in the chemical space “beyond the rule of 5”(bRo5) must
behave as molecular chameleons to combine otherwise conflicting properties, including …
behave as molecular chameleons to combine otherwise conflicting properties, including …
Molecular chameleons in drug discovery
V Poongavanam, LHE Wieske, S Peintner… - Nature Reviews …, 2024 - nature.com
Molecular chameleons possess a flexibility that allows them to dynamically shield or expose
polar functionalities in response to the properties of the environment. Although the concept …
polar functionalities in response to the properties of the environment. Although the concept …
Intramolecular hydrogen bonding: An opportunity for improved design in medicinal chemistry
Recent literature shows that intramolecular hydrogen bond (IMHB) formation can positively
impact upon the triad of permeability, solubility, and potency of drugs and candidates. IMHB …
impact upon the triad of permeability, solubility, and potency of drugs and candidates. IMHB …