Structure–Kinetic Relationships of Passive Membrane Permeation from Multiscale Modeling

Passive membrane permeation of small molecules is essential to achieve the required absorption, distribution, metabolism, and excretion (ADME) profiles of drug candidates, in particular intestinal absorption and transport across the blood–brain barrier. Computational investigations of this process typically involve either building QSAR models or performing free energy calculations of the permeation event. Although insightful, these methods rarely bridge the gap between computation and experiment in a quantitative manner, and identifying structural insights to apply toward the design of compounds with improved permeability can be difficult. In this work, we combine molecular dynamics simulations capturing the kinetic steps of permeation at the atomistic level with a dynamic mechanistic model describing permeation at the in vitro level, finding a high level of agreement with experimental permeation measurements. Calculation of the kinetic rate constants determining each step in the permeation event allows derivation of structure–kinetic relationships of permeation. We use these relationships to probe the structural determinants of membrane permeation, finding that the desolvation/loss of hydrogen bonding required to leave the membrane partitioned position controls the membrane flip-flop rate, whereas membrane partitioning determines the rate of leaving the membrane

Antifungal Spectrum, In Vivo Efficacy, and Structure–Activity Relationship of Ilicicolin H

Ilicicolin H is a polyketidenonribosomal peptide synthase (NRPS)natural product isolated from <i>Gliocadium roseum</i>, which exhibits potent and broad spectrum antifungal activity, with sub-μg/mL MICs against <i>Candida</i> spp., <i>Aspergillus fumigatus</i>, and <i>Cryptococcus</i> spp. It showed a novel mode of action, potent inhibition (IC₅₀ = 2–3 ng/mL) of the mitochondrial cytochrome bc1 reductase, and over 1000-fold selectivity relative to rat liver cytochrome bc1 reductase. Ilicicolin H exhibited in vivo efficacy in murine models of <i>Candida albicans</i> and <i>Cryptococcus neoformans</i> infections, but efficacy may have been limited by high plasma protein binding. Systematic structural modification of ilicicolin H was undertaken to understand the structural requirement for the antifungal activity. The details of the biological activity of ilicicolin H and structural modification of some of the key parts of the molecule and resulting activity of the derivatives are discussed. These data suggest that the β-keto group is critical for the antifungal activity

Design of Potent and Orally Active GPR119 Agonists for the Treatment of Type II Diabetes

We report herein the design and synthesis of a series of potent and selective GPR119 agonists. Our objective was to develop a GPR119 agonist with properties that were suitable for fixed-dose combination with a DPP4 inhibitor. Starting from a phenoxy analogue (<b>1</b>), medicinal chemistry efforts directed toward reducing half-life and increasing solubility led to the synthesis of a series of benzyloxy analogues. Compound <b>28</b> was chosen for further profiling because of its favorable physicochemical properties and excellent GPR119 potency across species. This compound exhibited a clean off-target profile in counterscreens and good <i>in vivo</i> efficacy in mouse oGTT

Discovery of 8‑Amino-imidazo[1,5‑<i>a</i>]pyrazines as Reversible BTK Inhibitors for the Treatment of Rheumatoid Arthritis

Bruton’s tyrosine kinase (BTK) is a Tec family kinase with a well-defined role in the B cell receptor (BCR) pathway. It has become an attractive kinase target for selective B cell inhibition and for the treatment of B cell related diseases. We report a series of compounds based on 8-amino-imidazo­[1,5-<i>a</i>]­pyrazine that are potent reversible BTK inhibitors with excellent kinase selectivity. Selectivity is achieved through specific interactions of the ligand with the kinase hinge and driven by aminopyridine hydrogen bondings with Ser538 and Asp539, and by hydrophobic interaction of trifluoropyridine in the back pocket. These interactions are evident in the X-ray crystal structure of the lead compounds <b>1</b> and <b>3</b> in the complex with the BTK enzyme. Our lead compounds show desirable PK profiles and efficacy in the preclinical rat collagen induced arthritis model