Cell permeability as a parameter for lead generation in the protein Tyrosine kinase inhibition field

Imidazo[4,5-b]pyridine inhibitors of B-Raf kinase

This Letter details the synthesis and evaluation of imidazo[4,5-b]pyridines as inhibitors of B-Raf kinase. These compounds bind in a DFG-in, αC-helix out conformation of B-Raf, which is a binding mode associated with significant kinase selectivity. Structure-activity relationship studies involved optimization of the ATP-cleft binding region of these molecules, and led to compound 23, an inhibitor with excellent enzyme/cell potency, and kinase selectivity.

What has polar surface area ever done for drug discovery?

Over the last decade, polar surface area (PSA) has become a ubiquitous term in medicinal and computational chemistry circles. This article charts the development of the increasingly efficient methods for the calculation of PSA before illustrating its usefulness through selected examples drawn from the medicinal chemistry literature. Consideration of PSA is shown to assist in the improvement of cellular potency, intestinal absorption and blood-brain barrier permeation or restriction to the peripheral circulation.

Optimization of a pyrazoloquinolinone class of Chk1 kinase inhibitors

The development of 2,5-dihydro-4H-pyrazolo[4,3-c]quinolin-4-ones as inhibitors of Chk1 kinase is described. Introduction of a fused ring at the C7/C8 positions of the pyrazoloquinolinone provided an increase in potency while guidance from overlapping inhibitor bound Chk1 X-ray crystal structures contributed to the discovery of a potent and solubilizing propyl amine moiety in compound 52 (Chk1 IC(50)=3.1 nM).

Development of 6-substituted indolylquinolinones as potent Chek1 kinase inhibitors

Through a comparison of X-ray co-crystallographic data for 1 and 2 in the Chek1 active site, it was hypothesized that the affinity of the indolylquinolinone series (2) for Chek1 kinase would be improved via C6 substitution into the hydrophobic region I (HI) pocket. An efficient route to 6-bromo-3-indolyl-quinolinone (9) was developed, and this series was rapidly optimized for potency by modification at C6. A general trend was observed among these low nanomolar Chek1 inhibitors that compounds with multiple basic amines, or elevated polar surface area (PSA) exhibited poor cell potency. Minimization of these parameters (basic amines, PSA) resulted in Chek1 inhibitors with improved cell potency, and preliminary pharmacokinetic data are presented for several of these compounds.

3-(Indol-2-yl)indazoles as Chek1 kinase inhibitors: Optimization of potency and selectivity via substitution at C6

The development of 3-(indol-2-yl)indazoles as inhibitors of Chek1 kinase is described. Introduction of amides and heteroaryl groups at the C6 position of the indazole ring system provided sufficient Chek1 potency and selectivity over Cdk7 to permit escape from DNA damage-induced arrest in a cellular assay. Enzyme potency against Chek1 was optimized by the incorporation of a hydroxymethyl triazole moiety in compound 21 (Chek1 IC(50)=0.30nM) that was shown by X-ray crystallography to displace one of three highly conserved water molecules in the HI region of the ATP-binding cleft.

New Methodology Toward Chiral, Non-Racemic 2,5-cis-Substituted Piperidines via Suzuki Cross-Coupling

1,2,3,4-Tetrahydropyridines were halogenated upon treatment with iodine to obtain the desired cross-coupling precursors. Diastereoselective hydrogenation of Suzuki cross-coupling adducts allowed the facile asymmetric synthesis of 2,5-cis-substituted piperidines in five steps from readily available pyridine.

A structure-permeability study of small drug-like molecules

A systematic structure-permeability relationship study on a set of small drug-like molecules with log D values in the range -2.5 to 3 and carrying a diverse array of functionality reveals that the compounds with log D>0 and <3 are highly permeable. Surprisingly, several tetrazole derivatives were found to be substrates for efflux pump(s).

Prediction of intestinal permeability

This review focuses on computational methods for the prediction of passive intestinal permeability. Existing computational models are surveyed and assessed in terms of descriptors, model type/complexity, speed of computation, predictive performance, and interpretability. Challenges to the successful computational prediction of intestinal permeability, i.e. data quantity, measurement imprecision, confounding factors such as solubility, metabolism, or active efflux, and the need for robust statistical methods, are also discussed.