An inexpensive virus detection scheme with high sensitivity and specificity is desirable for broad applications such as the COVID-19 virus. In this article, we introduce the localized surface plasmon resonance (LSPR) principle on the aggregation of antigen-coated gold nanoparticles (GNPs) to detect SARS-CoV-2 Nucleocapsid (N) proteins. Experiments show this technique can produce results observable by the naked eye in 5 min with a LOD (Limits of Detection) of 150 ng/ml for the N proteins. A comprehensive numerical model of the LSPR effect on the aggregation of GNPs has been developed to identify the key parameters in the reaction processes. The color-changing behaviors can be readily utilized to detect the existence of the virus while the quantitative concentration value is characterized with the assistance of an optical spectrometer. A parameter defined as the ratio of the light absorption intensity at the upper visible band region of 700 nm to the light absorption intensity at the peak optical absorption spectrum of the GNPs at 530 nm is found to have a linear relationship with respect to the N protein concentrations. As such, this scheme could be utilized as an inexpensive testing methodology for applications in POC (Point-of-Care) diagnostics to combat current and future virus-induced pandemics.

We present a novel systematic MEMS structure design approach based on a 'deep conditional generative model'. Utilizing the conditional generative adversarial network (CGAN) on a case study of circular-shaped MEMS resonators, three major advancements have been demonstrated: 1) a high-throughput vectorized MEMS design generation scheme that satisfies the geometric constraints; 2) MEMS structural customization toward tunable, desired physical properties with excellent generation accuracy; and 3) experience-free design space explorations to achieve extreme physical properties, such as low anchor loss of micro resonators. Excellent agreements with experimental data, numerical ulations, and a previously reported machine learning-based analyzer are achieved for validation of our methodology. As such, the proposed scheme could open up a new class of data-driven, intelligent design systems for a wide range of MEMS applications.

We demonstrate a design scheme for weakly coupled resonators (WCRs) by integrating the supervised learning (SL) with the genetic algorithm (GA). In this work, three distinctive achievements have been accomplished: 1) the precise prediction of coupling characteristics of WCRs with an accuracy of 98.7% via SL; 2) the stepwise evolutionary optimization of WCR geometries while maintaining their geometric connectivity via GA; and 3) the highly efficient generation of WCR designs with a mean coupling factor down to 0.0056, which outperforms 98% of random designs. The coupling behavior analysis and prediction are validated with experimental data of coupled microcantilevers from a published work. As such, this newly proposed scheme could shed light upon the structural optimization methods for high-performance MEMS devices with high degree of design freedom.

The papain-like protease (PLpro) plays a critical role in SARS-CoV-2 (SCoV-2) pathogenesis and is essential for viral replication and for allowing the virus to evade the host immune response. Inhibitors of PLpro have great therapeutic potential, however, developing them has been challenging due to PLpro's restricted substrate binding pocket. In this report, we screened a 115 000-compound library for PLpro inhibitors and identified a new pharmacophore, based on a mercapto-pyrimidine fragment that is a reversible covalent inhibitor (RCI) of PLpro and inhibits viral replication in cells. Compound 5 had an IC₅₀ of 5.1 μM for PLpro inhibition and hit optimization yielded a derivative with increased potency (IC₅₀ 0.85 μM, 6-fold higher). Activity based profiling of compound 5 demonstrated that it reacts with PLpro cysteines. We show here that compound 5 represents a new class of RCIs, which undergo an addition elimination reaction with cysteines in their target proteins. We further show that their reversibility is catalyzed by exogenous thiols and is dependent on the size of the incoming thiol. In contrast, traditional RCIs are all based upon the Michael addition reaction mechanism and their reversibility is base-catalyzed. We identify a new class of RCIs that introduces a more reactive warhead with a pronounced selectivity profile based on thiol ligand size. This could allow the expansion of RCI modality use towards a larger group of proteins important for human disease.

Covalent inhibitors of the papain-like protease (PLpro) from SARS-CoV-2 have great potential as antivirals, but their non-specific reactivity with thiols has limited their development. In this report, we performed an 8000 molecule electrophile screen against PLpro and identified an α-chloro amide fragment, termed compound 1, which inhibited SARS-CoV-2 replication in cells, and also had low non-specific reactivity with thiols. Compound 1 covalently reacts with the active site cysteine of PLpro, and had an IC50 of 18 μM for PLpro inhibition. Compound 1 also had low non-specific reactivity with thiols and reacted with glutathione 1-2 orders of magnitude slower than other commonly used electrophilic warheads. Finally, compound 1 had low toxicity in cells and mice and has a molecular weight of only 247 daltons and consequently has great potential for further optimization. Collectively, these results demonstrate that compound 1 is a promising lead fragment for future PLpro drug discovery campaigns.