Imidazolone as an Amide Bioisostere in the Development of β-1,3--Acetylglucosaminyltransferase 2 (B3GNT2) Inhibitors.

B3GNT2 is responsible for elongation of cell surface long-chain polylactosamine, which influences the regulation of the immune response, making it an attractive target for immunomodulation. In the development of amide containing B3GNT2 inhibitors guided by structure-based drug design, imidazolones were found to successfully serve as amide bioisosteres. This novel imidazolone isosteric strategy alleviated torsional strain of the amide bond on binding to B3GNT2 and improved potency, isoform selectivity, as well as certain physicochemical and pharmacokinetic properties.

Systematic Study of the Glutathione Reactivity of -Phenylacrylamides: 2. Effects of Acrylamide Substitution.

A comprehensive understanding of structure-reactivity relationships is critical to the design and optimization of cysteine-targeted covalent inhibitors. Herein, we report glutathione (GSH) reaction rates for -phenyl acrylamides with varied substitutions at the α- and β-positions of the acrylamide moiety. We find that the GSH reaction rates can generally be understood in terms of the electron donating or withdrawing ability of the substituent.

Mechanistic Insights into the Racemization of Fused Cyclopropyl Isoxazolines.

Experimental and computational studies of the unexpected racemization of enantiopure fused cyclopropyl isoxazolines are reported. These studies offer insights into the mechanism of racemization, quantify the position of the transition state on the dipolar-diradical continuum, and establish a relationship between the structure and stability of this class of compounds. Experimental and computed energy barriers for racemization are also presented.

Path optimization by a variational reaction coordinate method. II. Improved computational efficiency through internal coordinates and surface interpolation.

Reaction path optimization is being used more frequently as an alternative to the standard practice of locating a transition state and following the path downhill. The Variational Reaction Coordinate (VRC) method was proposed as an alternative to chain-of-states methods like nudged elastic band and string method. The VRC method represents the path using a linear expansion of continuous basis functions, allowing the path to be optimized variationally by updating the expansion coefficients to minimize the line integral of the potential energy gradient norm, referred to as the Variational Reaction Energy (VRE) of the path.

Path optimization by a variational reaction coordinate method. I. Development of formalism and algorithms.

The development of algorithms to optimize reaction pathways between reactants and products is an active area of study. Existing algorithms typically describe the path as a discrete series of images (chain of states) which are moved downhill toward the path, using various reparameterization schemes, constraints, or fictitious forces to maintain a uniform description of the reaction path. The Variational Reaction Coordinate (VRC) method is a novel approach that finds the reaction path by minimizing the variational reaction energy (VRE) of Quapp and Bofill.

Using bonding to guide transition state optimization.

Optimization of a transition state typically requires both a good initial guess of the molecular structure and one or more computationally demanding Hessian calculations to converge reliably. Often, the transition state being optimized corresponds to the barrier in a chemical reaction where bonds are being broken and formed. Utilizing the geometries and bonding information for reactants and products, an algorithm is outlined to reliably interpolate an initial guess for the transition state geometry.