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 …

[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 …

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 …

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 …

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 …

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 …

Elucidating solution structures of cyclic peptides using molecular dynamics simulations

J Damjanovic, J Miao, H Huang, YS Lin - Chemical reviews, 2021 - ACS Publications
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 …

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 …

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 …

Intramolecular hydrogen bonding: An opportunity for improved design in medicinal chemistry

G Caron, J Kihlberg, G Ermondi - Medicinal Research Reviews, 2019 - Wiley Online Library
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 …