Prolonged and tunable residence time using reversible covalent kinase inhibitors.

Drugs with prolonged on-target residence times often show superior efficacy, yet general strategies for optimizing drug-target residence time are lacking. Here we made progress toward this elusive goal by targeting a noncatalytic cysteine in Bruton's tyrosine kinase (BTK) with reversible covalent inhibitors. Using an inverted orientation of the cysteine-reactive cyanoacrylamide electrophile, we identified potent and selective BTK inhibitors that demonstrated biochemical residence times spanning from minutes to 7 d. An inverted cyanoacrylamide with prolonged residence time in vivo remained bound to BTK for more than 18 h after clearance from the circulation. The inverted cyanoacrylamide strategy was further used to discover fibroblast growth factor receptor (FGFR) kinase inhibitors with residence times of several days, demonstrating the generalizability of the approach. Targeting of noncatalytic cysteines with inverted cyanoacrylamides may serve as a broadly applicable platform that facilitates 'residence time by design', the ability to modulate and improve the duration of target engagement in vivo

Substrate Distortion to a Boat Conformation at Subsite −1 Is Critical in the Mechanism of Family 18 Chitinases

Using molecular dynamics simulations, we examined the plausible conformations for a hexaNAG substrate bound to the active site of Chitinase A. We find that (i) the hydrolysis mechanism of Chitinase A (a family 18 chitinase from Serratia marcescens) involves substrate distortion, (ii) the first step of acid-catalyzed hydrolysis (protonation of the linking anomeric oxygen between GlcNAc residues −1 and +1) requires a boat conformation for the GlcNAc residue at binding subsite −1; (iii) ab initio quantum mechanical calculations (HF/6-31G**) predict that protonation of a GlcNAc in a boat conformation leads to spontaneous anomeric bond cleavage to yield an oxazoline ion intermediate. We also studied several conformations of two possible hydrolysis intermediates:  the oxocarbenium ion and the oxazoline ion. Only the oxazoline ion orients in the enzyme active site so as to allow stereoselective attack by water. This leads to retention of configuration in the anomeric product as observed experimentally. It is possible that all family 18 chitinases share a common mechanism. Hence, we suspect that distortion of the substrate into a boat form at subsite −1 is required for any glycosyl hydrolase which has only one acidic residue in the active site. The design of an inhibitor for these systems based on the boat distorted sugar conformation is discussed

The pK(BHX) Database: Toward a Better Understanding of Hydrogen-Bond Basicity for Medicinal Chemists

International audienc

Discovery of the Irreversible Covalent FGFR Inhibitor 8‑(3-(4-Acryloyl­piperazin-1-yl)propyl)-6-(2,6-dichloro-3,5-dimethoxyphenyl)-2-(methylamino)­pyrido[2,3‑<i>d</i>]­pyrimidin-7(8<i>H</i>)‑one (PRN1371) for the Treatment of Solid Tumors

Aberrant signaling of the FGF/FGFR pathway occurs frequently in cancers and is an oncogenic driver in many solid tumors. Clinical validation of FGFR as a therapeutic target has been demonstrated in bladder, liver, lung, breast, and gastric cancers. Our goal was to develop an irreversible covalent inhibitor of FGFR1–4 for use in oncology indications. An irreversible covalent binding mechanism imparts many desirable pharmacological benefits including high potency, selectivity, and prolonged target inhibition. Herein we report the structure-based design, medicinal chemistry optimization, and unique ADME assays of our irreversible covalent drug discovery program which culminated in the discovery of compound <b>34</b> (PRN1371), a highly selective and potent FGFR1–4 inhibitor