Probing the Dynamic Structure-Function and Structure-Free Energy Relationships of the Coronavirus Main Protease with Biodynamics Theory.

The SARS-CoV-2 main protease (M) is of major interest as an antiviral drug target. Structure-based virtual screening efforts, fueled by a growing list of apo and inhibitor-bound SARS-CoV/CoV-2 M crystal structures, are underway in many laboratories. However, little is known about the dynamic enzyme mechanism, which is needed to inform both assay development and structure-based inhibitor design.

Toward in vivo-relevant hERG safety assessment and mitigation strategies based on relationships between non-equilibrium blocker binding, three-dimensional channel-blocker interactions, dynamic occupancy, dynamic exposure, and cellular arrhythmia.

The human ether-a-go-go-related voltage-gated cardiac ion channel (commonly known as hERG) conducts the rapid outward repolarizing potassium current in cardiomyocytes (IKr). Inadvertent blockade of this channel by drug-like molecules represents a key challenge in pharmaceutical R&D due to frequent overlap between the structure-activity relationships of hERG and many primary targets. Building on our previous work, together with recent cryo-EM structures of hERG, we set about to better understand the energetic and structural basis of promiscuous blocker-hERG binding in the context of Biodynamics theory.

Toward in vivo relevant drug design.

Current early and preclinical drug discovery are rooted in decades-old empirical principles describing structure-free energy and structure-function relationships under equilibrium conditions that frequently break down under in vivo conditions. Improved prediction of efficacy and toxicity depends on a paradigm shift to in vivo-relevant principles describing the true nonequilibrium/nonlinear dynamic (NLD) nature of cellular systems. Here, we outline a holistic, in vivo-relevant first principles theory ('Biodynamics'), in which cellular function/dysfunction, and pharmaco-/toxicodynamic effects are considered as emergent behaviors of multimolecular systems powered by covalent and noncovalent free energy sources.

Biodynamics: A novel quasi-first principles theory on the fundamental mechanisms of cellular function/dysfunction and the pharmacological modulation thereof.

Cellular function depends on heterogeneous dynamic intra-, inter-, and supramolecular structure-function relationships. However, the specific mechanisms by which cellular function is transduced from molecular systems, and by which cellular dysfunction arises from molecular dysfunction are poorly understood. We proposed previously that cellular function manifests as a molecular form of analog computing, in which specific time-dependent state transition fluxes within sets of molecular species ("molecular differential equations" (MDEs)) are sped and slowed in response to specific perturbations (inputs).

In Situ Infrared Absorption Study of Plasma-Enhanced Atomic Layer Deposition of Silicon Nitride.

Despite the success of plasma-enhanced atomic layer deposition (PEALD) in depositing quality silicon nitride films, a fundamental understanding of the growth mechanism has been difficult to obtain because of lack of in situ characterization to probe the surface reactions noninvasively and the complexity of reactions induced/enhanced by the plasma. These challenges have hindered the direct observation of intermediate species formed during the reactions. We address this challenge by examining the interaction of Ar plasma using atomically flat, monohydride-terminated Si(111) as a well-defined model surface and focusing on the initial PEALD with aminosilanes.