Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method
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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Engineering topics
Stevenson, Garrett A.
Publications and source records attributed to Stevenson, Garrett A..
Discovery of Small-Molecule Inhibitors of SARS-CoV-2 Proteins Using a Computational and Experimental Pipeline
A rapid response is necessary to contain emergent biological outbreaks before they can become pandemics. The novel coronavirus (SARS-CoV-2) that causes COVID-19 was first reported in December of 2019 in Wuhan, China and reached most corners of the globe in less than two months. In just over a year since the initial infections, COVID-19 infected almost 100 million people worldwide. Although similar to SARS-CoV and MERS-CoV, SARS-CoV-2 has resisted treatments that are effective against other coronaviruses. Crystal structures of two SARS-CoV-2 proteins, spike protein and main protease, have been reported and can serve as targets for studies in neutralizing this threat. We have employed molecular docking, molecular dynamics simulations, and machine learning to identify from a library of 26 million molecules possible candidate compounds that may attenuate or neutralize the effects of this virus. The viability of selected candidate compounds against SARS-CoV-2 was determined experimentally by biolayer interferometry and FRET-based activity protein assays along with virus-based assays. In the pseudovirus assay, imatinib and lapatinib had IC 50 values below 10 μM, while candesartan cilexetil had an IC 50 value of approximately 67 µM against M pro in a FRET-based activity assay. Comparatively, candesartan cilexetil had the highest selectivity index of all compounds tested as its half-maximal cytotoxicity concentration 50 (CC 50 ) value was the only one greater than the limit of the assay (>100 μM).
59 BASIC BIOLOGICAL SCIENCES↗
Modeling Buried Object Brightness and Visibility for Ground Penetrating Radar
Comparing the observed brightness of various buried objects is a straightforward way to characterize the performance of a ground penetrating radar (GPR) system. However, a limitation arises. A simple comparison of buried object brightness values does not disentangle the effects of the GPR system itself from the system's operating environment and the objects being observed. Therefore, with brightness values exhibiting an unknown synthesis of systemic, environmental, and object factors, GPR system analysis becomes a convoluted affair. In this work, we use an experimentally collected dataset of over 25,000 object observations from five different multistatic radar arrays to develop models of buried object brightness and control for these various effects. Additionally, our modeling efforts provide a means for quantifying the relative brightness of GPR systems, the objects they detect, and the physical properties of those objects that influence observed brightness. To evaluate the models' performance on new object observations, we repeatedly simulate fitting them to half the dataset and predicting the observed brightness values of the unseen half. In addition, we introduce a method for estimating the probability that individual observations constitute a visible object, which aids in failure analysis, performance characterization, and dataset cleaning.
97 MATHEMATICS AND COMPUTING↗
Clutter Distributions for Tomographic Image Standardization in Ground-Penetrating Radar
Multistatic ground-penetrating radar (GPR) signals can be imaged tomographically to produce 3-D distributions of image intensities. In the absence of objects of interest, these intensities can be considered to be estimates of clutter. These clutter intensities spatially vary over several orders of magnitude and vary across different arrays, which makes a direct comparison of these raw intensities difficult. However, by gathering statistics on these intensities and their spatial variation, a variety of metrics can be determined. In this study, the clutter distribution is found to fit better to a two-parameter Weibull distribution than Gaussian or log-normal distributions. Based on the spatial variation of the two Weibull parameters, scale and shape, more information may be gleaned from these data. How well the GPR array is illuminating various parts of the ground, in depth and cross track, may be determined from the spatial variation of the Weibull scale parameter, which may in turn be used to estimate an effective attenuation coefficient in the soil. The transition in depth from clutter- to noise-limited conditions (which is one possible definition of GPR penetration depth) can be estimated from the spatial variation of the Weibull shape parameter. Lastly, the underlying clutter distributions also provide an opportunity to standardize image intensities to determine when a statistically significant deviation from background (clutter) has occurred, which is convenient for buried threat detection algorithm development that needs to be robust across multiple different arrays.
42 ENGINEERING↗