SARS-CoV-2 PLpro whole human proteome cleavage prediction and enrichment/depletion analysis

Abstract

A novel coronavirus (SARS-CoV-2) has caused a pandemic that has killed millions of people, worldwide vaccination and herd immunity are still far away, and few therapeutics are approved by regulatory agencies for widespread use. The coronavirus 3-chymotrypsin-like protease (3CLpro) is a commonly investigated target in COVID-19, however less work has been directed toward the equally important papain-like protease (PLpro). PLpro is less characterized due to its fewer and more diverse cleavages in coronavirus proteomes and the assumption that it mainly modulates host pathways with its deubiquitinating activity. Here, I extend my previous work on 3CLpro human cleavage prediction and enrichment/depletion analysis to PLpro. Using three sets of neural networks trained on different taxonomic ranks of dataset with a maximum of 463 different putative PLpro cleavages, Matthews correlation coefficients of 0.900, 0.948, and 0.966 were achieved for Coronaviridae, Betacoronavirus, and Sarbecovirus, respectively. I predict that more than 1,000 human proteins may be cleaved by PLpro depending on diversity of the training dataset and that many of these proteins are distinct from those previously predicted to be cleaved by 3CLpro. PLpro cleavages are similarly nonrandomly distributed and result in many annotations shared with 3CLpro cleavages including ubiquitination, poly(A) tail and 5' cap RNA binding proteins, helicases, and endogenous viral proteins. Combining PLpro with 3CLpro cleavage predictions, additional novel enrichment analysis was performed on known substrates of cleaved E3 ubiquitin ligases with results indicating that many pathways including viral RNA sensing are affected indirectly by E3 ligase cleavage independent of traditional PLpro deubiquitinating activity. As with 3CLpro, PLpro whole proteome cleavage prediction revealed many novel potential therapeutic targets against coronaviruses, although experimental verification is similarly required.

Alphavirus nsP2 protease structure and cleavage prediction: Possible relevance to the pathogenesis of viral arthritis

“…Similar biases and caveats exist for nsP2pro predictions as with previous viral protease predictions,[14, 15] yet many host pathways likely perturbed by nsP2pro are discoverable. Experimental validation is, however, required for all of the following hypotheses.…”

“…As in my previous work on 3CLpro and PLpro,[14, 15] sequence logo-based logistic regression and naïve Bayes classification and physiochemical and one-hot encoded neural networks (NNs) were used for cleavage prediction. [28] To reduce any potential false positives, only proteins expressed in relevant cell types with cleavages with agreement between all five NN replicates and with total solvent-accessible surface areas (SASAs) of more than 100 Å 2 between positions P5 and P5’ were reported.…”

“…[26] Molecular graphics and analyses were performed using UCSF ChimeraX, developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco, with support from National Institutes of Health R01-GM129325 and the Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases. [27] Cleavage Prediction and Analysis As in my previous work on 3CLpro and PLpro, [14,15] sequence logo-based logistic regression and naïve Bayes classification and physiochemical and one-hot encoded neural networks (NNs) were used for cleavage prediction. [28] To reduce any potential false positives, only proteins expressed in relevant cell types with cleavages with agreement between all five NN replicates and with total solventaccessible surface areas (SASAs) of more than 100 Å 2 between positions P5 and P5' were reported.…”