Prediction of coronavirus 3C-like protease cleavage sites using machine-learning algorithms

The coronavirus 3C-like (3CL) protease is a Cysteine protease. It plays an important role in viral infection and immune escape by not only cleaving the viral polyprotein ORF1ab at 11 sites, but also cleaving the host proteins. However, there is still a lack of effective tools for determining the cleavage sites of the 3CL protease. This study systematically investigated the diversity of the cleavage sites of the coronavirus 3CL protease on the viral polyprotein, and found that the cleavage motif were highly conserved for viruses in the genera of Alphacoronavirus, Betacoronavirus and Gammacoronavirus. Strong residue preferences were observed at the neighboring positions of the cleavage sites. A random forest (RF) model was built to predict the cleavage sites of the coronavirus 3CL protease based on the representation of residues at cleavage site and neighboring positions by amino acid indexes, and the model achieved an AUC of 0.96 in cross-validations. The RF model was further tested on an independent test dataset composed of cleavage sites on host proteins, and achieved an AUC of 0.88 and a prediction precision of 0.80 when considering the accessibility of the cleavage site. Then, 1,079 human proteins were predicted to be cleaved by the 3CL protease by the RF model. These proteins were enriched in pathways related to neurodegenerative diseases and pathogen infection. Finally, a user-friendly online server named 3CLP was built to predict the cleavage sites of the coronavirus 3CL protease based on the RF model. Overall, the study not only provides an effective tool for identifying the cleavage sites of the 3CL protease, but also provides insights into the molecular mechanism underlying the pathogenicity of coronaviruses.

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Predicted Coronavirus Nsp5 Protease Cleavage Sites in the Human Proteome: A Resource for SARS-CoV-2 Research

10.1101/2021.06.08.447224 ◽

2021 ◽

Author(s):

Benjamin M Scott ◽

Vincent Lacasse ◽

Ditte G Blom ◽

Peter D Tonner ◽

Nikolaj S Blom

Keyword(s):

Protein Interactions ◽

Cleavage Site ◽

Nonstructural Protein ◽

Data Bank ◽

Molecular Pathways ◽

Cleavage Sites ◽

Host Proteins ◽

Structure Information ◽

Human Proteins

Background: The coronavirus nonstructural protein 5 (Nsp5) is a cysteine protease required for processing the viral polyprotein and is therefore crucial for viral replication. Nsp5 from several coronaviruses have also been found to cleave host proteins, disrupting molecular pathways involved in innate immunity. Nsp5 from the recently emerged SARS-CoV-2 virus interacts with and can cleave human proteins, which may be relevant to the pathogenesis of COVID-19. Based on the continuing global pandemic, and emerging understanding of coronavirus Nsp5-human protein interactions, we set out to predict what human proteins are cleaved by the coronavirus Nsp5 protease using a bioinformatics approach. Results: Using a previously developed neural network trained on coronavirus Nsp5 cleavage sites (NetCorona), we made predictions of Nsp5 cleavage sites in all human proteins. Structures of human proteins in the Protein Data Bank containing a predicted Nsp5 cleavage site were then examined, generating a list of 92 human proteins with a highly predicted and accessible cleavage site. Of those, 48 are expected to be found in the same cellular compartment as Nsp5. Analysis of this targeted list of proteins revealed molecular pathways susceptible to Nsp5 cleavage and therefore relevant to coronavirus infection, including pathways involved in mRNA processing, cytokine response, cytoskeleton organization, and apoptosis. Conclusions: This study combines predictions of Nsp5 cleavage sites in human proteins with protein structure information and protein network analysis. We predicted cleavage sites in proteins recently shown to be cleaved in vitro by SARS-CoV-2 Nsp5, and we discuss how other potentially cleaved proteins may be relevant to coronavirus mediated immune dysregulation. The data presented here will assist in the design of more targeted experiments, to determine the role of coronavirus Nsp5 cleavage of host proteins, which is relevant to understanding the molecular pathology of SARS-CoV-2 infection.

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Proteolytic Cleavage of Bovine Adenovirus 3-Encoded pVIII

Journal of Virology ◽

10.1128/jvi.00211-17 ◽

2017 ◽

Vol 91 (10) ◽

Cited By ~ 5

Author(s):

Amit Gaba ◽

Lisanework Ayalew ◽

Niraj Makadiya ◽

Suresh Tikoo

Keyword(s):

Cleavage Site ◽

Virus Assembly ◽

Proteolytic Cleavage ◽

Efficient Production ◽

Cleavage Sites ◽

Bovine Adenovirus ◽

Protease Cleavage Site ◽

Protease Cleavage ◽

Protease Cleavage Sites ◽

Single Protease

ABSTRACT Proteolytic maturation involving cleavage of one nonstructural and six structural precursor proteins including pVIII by adenovirus protease is an important aspect of the adenovirus life cycle. The pVIII encoded by bovine adenovirus 3 (BAdV-3) is a protein of 216 amino acids and contains two potential protease cleavage sites. Here, we report that BAdV-3 pVIII is cleaved by adenovirus protease at both potential consensus protease cleavage sites. Usage of at least one cleavage site appears essential for the production of progeny BAdV-3 virions as glycine-to-alanine mutation of both protease cleavage sites appears lethal for the production of progeny virions. However, mutation of a single protease cleavage site of BAdV-3 pVIII significantly affects the efficient production of infectious progeny virions. Further analysis revealed no significant defect in endosome escape, genome replication, capsid formation, and virus assembly. Interestingly, cleavage of pVIII at both potential cleavage sites appears essential for the production of stable BAdV-3 virions as BAdV-3 expressing pVIII containing a glycine-to-alanine mutation of either of the potential cleavage sites is thermolabile, and this mutation leads to the production of noninfectious virions. IMPORTANCE Here, we demonstrated that the BAdV-3 adenovirus protease cleaves BAdV-3 pVIII at both potential protease cleavage sites. Although cleavage of pVIII at one of the two adenoviral protease cleavage sites is required for the production of progeny virions, the mutation of a single cleavage site of pVIII affects the efficient production of infectious progeny virions. Further analysis indicated that the mutation of a single protease cleavage site (glycine to alanine) of pVIII produces thermolabile virions, which leads to the production of noninfectious virions with disrupted capsids. We thus provide evidence about the requirement of proteolytic cleavage of pVIII for production of infectious progeny virions. We feel that our study has significantly advanced the understanding of the requirement of adenovirus protease cleavage of pVIII.

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Identification and analysis of the cleavage site in a signal peptide using SMOTE, dagging, and feature selection methods

Molecular Omics ◽

10.1039/c7mo00030h ◽

2018 ◽

Vol 14 (1) ◽

pp. 64-73 ◽

Cited By ~ 16

Author(s):

ShaoPeng Wang ◽

Deling Wang ◽

JiaRui Li ◽

Tao Huang ◽

Yu-Dong Cai

Keyword(s):

Machine Learning ◽

Feature Selection ◽

Signal Peptide ◽

Cleavage Site ◽

Learning Algorithms ◽

Machine Learning Algorithms ◽

Cleavage Sites ◽

Selection Methods

Several machine learning algorithms were adopted to investigate cleavage sites in a signal peptide. An optimal dagging based classifier was constructed and 870 important features were deemed to be important for this classifier.

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Human Immunodeficiency Virus Type 1 Protease Cleavage Site Mutations Associated with Protease Inhibitor Cross-Resistance Selected by Indinavir, Ritonavir, and/or Saquinavir

Journal of Virology ◽

10.1128/jvi.75.2.589-594.2001 ◽

2001 ◽

Vol 75 (2) ◽

pp. 589-594 ◽

Cited By ~ 92

Author(s):

Hélène C. F. Côté ◽

Zabrina L. Brumme ◽

P. Richard Harrigan

Keyword(s):

Human Immunodeficiency Virus ◽

Protease Inhibitor ◽

Cleavage Site ◽

Cross Resistance ◽

Cleavage Sites ◽

Protease Cleavage ◽

Immunodeficiency Virus ◽

Before And After ◽

Protease Cleavage Sites

ABSTRACT We examined the prevalence of cleavage site mutations, both within and outside the gag region, in 28 protease inhibitor (PI) cross-resistant patients treated with indinavir, ritonavir, and/or saquinavir compared to control patients treated with reverse transcriptase inhibitors. Three human immunodeficiency virus protease cleavage sites within gag (p2/NC, NC/p1, and NC/TFP) showed considerable in vivo evolution before and after therapy with indinavir, ritonavir, and/or saquinavir. Another gag cleavage site (p1/p6 gag ) showed a trend compared to matched controls. The other eight recognized cleavage sites showed relatively little difference between PI-resistant cases and controls. An A→V substitution at the P2 position of the NC/p1 and NC/TFP cleavage sites was the most common (29%) change selected by the PIs used in this study.

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Family-wide characterization of matrix metalloproteinases from Arabidopsis thaliana reveals their distinct proteolytic activity and cleavage site specificity

Biochemical Journal ◽

10.1042/bj20130196 ◽

2013 ◽

Vol 457 (2) ◽

pp. 335-346 ◽

Cited By ~ 23

Author(s):

Giada Marino ◽

Pitter F. Huesgen ◽

Ulrich Eckhard ◽

Christopher M. Overall ◽

Wolfgang P. Schröder ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Cleavage Site ◽

Biochemical Properties ◽

Site Specificity ◽

Sequence Specificity ◽

Cleavage Sites ◽

Protease Cleavage ◽

Protease Cleavage Sites ◽

Proteomic Identification

The five recombinant MMP-like proteins of Arabidopsis thaliana have specific biochemical properties. Detailed analysis of their sequence specificity using proteomic identification of protease cleavage sites revealed cleavage profiles similar to human MMPs.

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A Comparison of Machine Learning Algorithms for the Prediction of Hepatitis C NS3 Protease Cleavage Sites

10.35248/0974-276x.19.12.501 ◽

2019 ◽

Vol 12 (5) ◽

Author(s):

Harry Chown

Keyword(s):

Machine Learning ◽

Hepatitis C ◽

Learning Algorithms ◽

Machine Learning Algorithms ◽

Cleavage Sites ◽

Protease Cleavage ◽

Protease Cleavage Sites ◽

Ns3 Protease

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Variability at Human Immunodeficiency Virus Type 1 Subtype C Protease Cleavage Sites: an Indication of Viral Fitness?

Journal of Virology ◽

10.1128/jvi.77.17.9422-9430.2003 ◽

2003 ◽

Vol 77 (17) ◽

pp. 9422-9430 ◽

Cited By ~ 45

Author(s):

Tulio de Oliveira ◽

Susan Engelbrecht ◽

Estrelita Janse van Rensburg ◽

Michelle Gordon ◽

Karen Bishop ◽

...

Keyword(s):

Human Immunodeficiency Virus ◽

Human Immunodeficiency Virus Type ◽

Cleavage Site ◽

Cleavage Sites ◽

Subtype C ◽

Protease Cleavage ◽

Immunodeficiency Virus ◽

Protease Cleavage Sites ◽

Hiv 1

ABSTRACT Naturally occurring polymorphisms in the protease of human immunodeficiency virus type 1 (HIV-1) subtype C would be expected to lead to adaptive (compensatory) changes in protease cleavage sites. To test this hypothesis, we examined the prevalences and patterns of cleavage site polymorphisms in the Gag, Gag-Pol, and Nef cleavage sites of C compared to those in non-C subtypes. Codon-based maximum-likelihood methods were used to assess the natural selection and evolutionary history of individual cleavage sites. Seven cleavage sites (p17/p24, p24/p2, NC/p1, NC/TFP, PR/RT, RT/p66, and p66/IN) were well conserved over time and in all HIV-1 subtypes. One site (p1/p6 gag ) exhibited moderate variation, and four sites (p2/NC, TFP/p6 pol , p6 pol /PR, and Nef) were highly variable, both within and between subtypes. Three of the variable sites are known to be major determinants of polyprotein processing and virion production. P2/NC controls the rate and order of cleavage, p6 gag is an important phosphoprotein required for virion release, and TFP/p6 pol , a novel cleavage site in the transframe domain, influences the specificity of Gag-Pol processing and the activation of protease. Overall, 58.3% of the 12 HIV-1 cleavage sites were significantly more diverse in C than in B viruses. When analyzed as a single concatenated fragment of 360 bp, 96.0% of group M cleavage site sequences fell into subtype-specific phylogenetic clusters, suggesting that they coevolved with the virus. Natural variation at C cleavage sites may play an important role, not only in regulation of the viral cycle but also in disease progression and response to therapy.

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