Engineering topics

Wright, David W.

Publications and source records attributed to Wright, David W..

3 records

DOE OSTI2022

The performance of ensemble-based free energy protocols in computing binding affinities to ROS1 kinase

Optimization of binding affinities for compounds to their target protein is a primary objective in drug discovery. Herein we report on a collaborative study that evaluates a set of compounds binding to ROS1 kinase. We use ESMACS (enhanced sampling of molecular dynamics with approximation of continuum solvent) and TIES (thermodynamic integration with enhanced sampling) protocols to rank the binding free energies. The predicted binding free energies from ESMACS simulations show good correlations with experimental data for subsets of the compounds. Consistent binding free energy differences are generated for TIES and ESMACS. Although an unexplained overestimation exists, we obtain excellent statistical rankings across the set of compounds from the TIES protocol, with a Pearson correlation coefficient of 0.90 between calculated and experimental activities.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Ensemble Simulations and Experimental Free Energy Distributions: Evaluation and Characterization of Isoxazole Amides as SMYD3 Inhibitors

Optimization of binding affinities for ligands to their target protein is a primary objective in rational drug discovery. Herein, we report on a collaborative study that evaluates various compounds designed to bind to the SET and MYND domain-containing protein 3 (SMYD3). SMYD3 is a histone methyltransferase and plays an important role in transcriptional regulation in cell proliferation, cell cycle, and human carcinogenesis. Experimental measurements using the scintillation proximity assay show that the distributions of binding free energies from a large number of independent measurements exhibit non-normal properties. We use ESMACS (enhanced sampling of molecular dynamics with approximation of continuum solvent) and TIES (thermodynamic integration with enhanced sampling) protocols to predict the binding free energies and to provide a detailed chemical insight into the nature of ligand-protein binding. Our results show that the 1-trajectory ESMACS protocol works well for the set of ligands studied here. Although one unexplained outlier exists, we obtain excellent statistical ranking across the set of compounds from the ESMACS protocol and good agreement between calculations and experiments for the relative binding free energies from the TIES protocol. ESMACS and TIES are again found to be powerful protocols for the accurate comparison of the binding free energies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Intubation Containment System for Improved Protection From Aerosolized Particles During Airway Management

Worldwide efforts to protect front line providers performing endotracheal intubation during the COVID-19 pandemic have led to innovative devices. Authors evaluated the aerosol containment effectiveness of a novel intubation aerosol containment system (IACS) compared with a recently promoted intubation box and no protective barrier. In a simulation center at the authors’ university, the IACS was compared to no protective barrier and an intubation box. Aerosolization was simulated using a commercial fog machine and leakage of aerosolize mist was visually assessed. The IACS appeared to contain the aerosolized mist, while the intubation box allowed for mist to contact the laryngoscopist and contaminate the clinical space through arm port holes and the open caudal end. Both devices protected the laryngoscopist better than no protective barrier. The IACS with integrated sleeves and plastic drape appears to offer superior protection for the laryngoscopist and assistant providers from aerosolized particles.

aerosols↗