SARS-CoV-2-induced phosphorylation and its pharmacotherapy backed by artificial intelligence and machine learning

References

• Tao K, Tzou PL, Nouhin J et al. The biological and clinical significance of emerging SARS-CoV-2 variants. Nat. Rev. Genet. 22, 757–773 (2021).
   PubMed Web of Science ®Google Scholar
• Ruiz-Sternberg AM, Chaparro-Solano HM, Albornóz LL et al. Genomic characterization of SARS-CoV-2 and its association with clinical outcomes: a 1-year longitudinal study of the pandemic in Colombia. Int. J. Infect. Dis. 116, 91–100 (2022).
   PubMed Web of Science ®Google Scholar
• Chatterjee B, Thakur SS. SARS-CoV-2 infection triggers phosphorylation: potential target for anti-COVID-19 therapeutics. Front. Immunol. 13, 1–14 (2022).
   Web of Science ®Google Scholar
• Bouhaddou M, Memon D, Meyer B et al. The global phosphorylation landscape of SARS-CoV-2 infection. Cell 180, 685–712 (2020).
   Google Scholar
• Szklarczyk D, Gable AL, Lyon D et al. STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 47, D607–D613 (2019).
   PubMed Web of Science ®Google Scholar
• Davidson AD, Williamson MK, Lewis S et al. Characterisation of the transcriptome and proteome of SARS-CoV-2 reveals a cell passage induced in-frame deletion of the furin-like cleavage site from the spike glycoprotein. Genome Med. 12, 1–15 (2020).
   Web of Science ®Google Scholar
• Klann K, Bojkova D, Tascher G. Growth factor receptor signaling inhibition prevents SARS-CoV-2 replication. Mol. Cell. 80, 164–174 (2020).
   PubMed Web of Science ®Google Scholar
• Hekman RM, Hume AJ, Goel RK et al. Actionable cytopathogenic host responses of human alveolar type 2 cells to SARS-CoV-2. Mol. Cell. 80, 1104–1122 (2020).
   PubMed Web of Science ®Google Scholar
• Alavizadeh SH, Doagooyan M, Zahedipour F et al. Antisense technology as a potential strategy for the treatment of coronaviruses infection: With focus on COVID-19. IET Nanobiotechnol. 16(3), 67–77 (2022).
   PubMed Web of Science ®Google Scholar
• Luttens A, Gullberg H, Abdurakhmanov E et al. Ultralarge virtual screening identifies SARS-CoV-2 main protease inhibitors with broad-spectrum activity against coronaviruses. J. Am. Chem. Soc. 144, 2905–2920 (2022).
   PubMed Web of Science ®Google Scholar
• Clyde A, Galanie S, Kneller DW et al. High-throughput virtual screening and validation of a SARS-CoV-2 main protease noncovalent inhibitor. J. Chem. Inf. Model. 62, 116–128 (2022).
   PubMed Web of Science ®Google Scholar
• Chiu W, Verschueren L, Van den Eynde C et al. Development and optimization of a high-throughput screening assay for in vitro anti-SARS-CoV-2 activity: Evaluation of 5676 Phase 1 Passed Structures. J. Med. Virol. 94, 3101–3111 (2022).
   PubMed Web of Science ®Google Scholar
• C Gorgulla C, Das KMP, Leigh KE et al. A multi-pronged approach targeting SARS-CoV-2 proteins using ultra-large virtual screening. iScience. 24(2), 102021 (2021).
   PubMed Web of Science ®Google Scholar
• Yamamoto KZ, Yasuo N, Sekijima M. Screening for inhibitors of main protease in SARS-CoV-2: in silico and in vitro approach avoiding peptidyl secondary amides. J. Chem. Inf. Model. 62, 350–358 (2022).
   PubMed Web of Science ®Google Scholar
• Pohler A, Abdelfatah S, Riedl M et al. Potential coronaviral inhibitors of the nucleocapsid protein identified in silico and in vitro from a large natural product library. Pharmaceuticals. 15(9), 1046 (2022).
   Web of Science ®Google Scholar
• Yadav R, Imran M, Dhamija P, Suchal K, Handu S. Virtual screening and dynamics of potential inhibitors targeting RNA binding domain of nucleocapsid phosphoprotein from SARS-CoV-2, J. Biomol. Struct. Dyn. 39, 4433–4448 (2021).
   PubMed Web of Science ®Google Scholar
• Li Z, Li X, Huang Y-Y et al. Identify potent SARS-CoV-2 main protease inhibitors via accelerated free energy perturbation-based virtual screening of existing drugs. Proc. Natl Acad. Sci. 117, 27381–27387 (2020).
   PubMed Web of Science ®Google Scholar
• MorselliGysi D, Valle ÍD, Zitnik M et al. Network medicine framework for identifying drug-repurposing opportunities for COVID-19. Proc. Natl Acad. Sci. USA 118, e2025581118 (2021).
   PubMed Web of Science ®Google Scholar
• Ahmed F, Soomro AM, Chethikkattuveli Salih AR et al. A comprehensive review of artificial intelligence and network based approaches to drug repurposing in Covid-19. Biomed. Pharmacother. 153, 113350 (2022).
   PubMed Web of Science ®Google Scholar
• Hofmarcher M, Mayr A, Rumetshofer E et al. Large-scale ligand-based virtual screening for SARS-CoV-2 inhibitors using deep neural networks. SSRN Electron. J. 1–7 (2020).
   Google Scholar
• Pillaiyar T, Laufer S. Kinases as potential therapeutic targets for anti-coronaviral therapy. J. Med. Chem. 65, 955–982 (2022).
   PubMed Web of Science ®Google Scholar
• Liu X, Verma A, Garcia G et al. Targeting the coronavirus nucleocapsid protein through GSK-3 inhibition. Proc. Natl Acad. Sci. USA 118, e2113401118 (2021).
   PubMed Web of Science ®Google Scholar
• Gordon DE, Jang GM, Bouhaddou M et al. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature 583, 459–468 (2020).
   PubMed Web of Science ®Google Scholar
• Licheva M, Raman B, Kraft C, Reggiori F. Phosphoregulation of the autophagy machinery by kinases and phosphatases. Autophagy 18(1), 104–123 (2022).
   PubMed Web of Science ®Google Scholar
• Cheng C, Qi RZ, Paudel H, Zhu J. Regulation and function of protein kinases and phosphatases. Enzyme Res. 79408.9 (2011).
   Google Scholar
• Deng K, Liu L, Tan X et al. WIP1 promotes cancer stem cell properties by inhibiting p38 MAPK in NSCLC. Signal. Transduct. Target Ther. 5, 36 (2020).
   PubMed Web of Science ®Google Scholar
• Theivendren P, Kunjiappan S, Yashoda MY et al. Importance of protein kinase and its inhibitor: A Review. In: Protein kinases. Singh RK ( Ed.). (2021).
   Google Scholar
• Paunovska K, Loughrey D, Dahlman JE. Drug delivery systems for RNA therapeutics. Nat. Rev. Genet. 23, 265–280 (2022).
   PubMed Web of Science ®Google Scholar
• Zhu N, Zhang D, Wang W et al. A novel coronavirus from patients with pneumonia in China, 2019. NEJM. 382(8), 727–733 (2020).
   PubMed Web of Science ®Google Scholar
• Bouhaddou M, Memon D, Meyer B et al. The global phosphorylation landscape of SARS-CoV-2 infection. Cell 182(3), 685–712.e19 (2020).
   PubMed Web of Science ®Google Scholar
• Bojkova D, Klann K, Koch B et al. Proteomics of SARS-CoV-2-infected host cells reveals therapy targets. Nature 583(7816), 469–472 (2020).
   PubMed Web of Science ®Google Scholar
• Daniloski Z, Jordan TX, Wessels HH et al. Identification of required host factors for SARS-CoV-2 infection in human cells. Cell 184(1), 92–105.e16 (2021).
   PubMed Web of Science ®Google Scholar
• Xia H, Cao Z, Xie X et al. Evasion of Type I Interferon by SARS-CoV-2. Cell Rep. 33(1), 108234 (2020).
   PubMed Web of Science ®Google Scholar
• Swayamsiddha S, Rath S. Antisense oligonucleotide therapy: the road less traveled in SARS-CoV-2 treatment. Front. Mol. Biosci. 8, 675583 (2021).
   Google Scholar
• Calabrese R, Capriotti E, Fariselli P, Martelli PL, Casadio R. Functional annotations improve the predictive score of human disease-related mutations in proteins. Hum. Mutat. 30(8), 1237–1244 (2009).
   PubMed Web of Science ®Google Scholar
• Choi Y. A fast computation of pairwise sequence alignment scores between a protein and a set of single-locus variants of another protein. In: Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine. 414–417 (2012).
   Google Scholar
• Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat. Protoc. 4(7), 1073–1081 (2009).
   PubMed Web of Science ®Google Scholar
• Capriotti E, Calabrese R, Casadio R. Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information. Bioinform. 21(10), 2518–2525 (2005).
   Google Scholar
• Pejaver V, Hsu WL, Xin F et al. The structural and functional signatures of proteins that undergo multiple events of post-translational modification. Protein Sci. 26(2), 262–274 (2017).
   Google Scholar
• Bromberg Y, Rost B. SNAP: predict effect of non-synonymous polymorphisms on function. Nucleic Acids Res. 35(11), 3823–3835 (2007).
   PubMed Web of Science ®Google Scholar
• Kozakov D, Hall DR, Xia B et al. The ClusPro web server for protein–protein docking. Nat. Protoc. 12(2), 255–278 (2017).
   PubMed Web of Science ®Google Scholar
• Lavecchia A, Di Giovanni C. Virtual screening strategies in drug discovery: a critical review. Curr. Med. Chem. 20(23), 2839–2860 (2013).
   PubMed Web of Science ®Google Scholar
• Xu L, Sun J, Lu Z, Yao J, Wang Y. A large-scale screening of host-directed compounds for theinhibition of SARS-CoV-2 infection. Signal transduction and targeted therapy. 5(1), 1–3 (2020).
   PubMed Web of Science ®Google Scholar
• Shannon A, Selisko B, Le NT et al. Rapid incorporation of favipiravir by the fast and permissive viral RNA polymerase complex results in SARS-CoV-2 lethal mutagenesis. Nat. Commun. 11(1), 1–9 (2020).
   PubMed Web of Science ®Google Scholar
• Cho A, Saunders OL, Butler T et al. Synthesis and antiviral activity of a series of 1′-substituted 4-aza-7, 9-dideazaadenosine C-nucleosides. Bioorg. Med. Chem. Lett. 22(5), 2207–2209 (2012).
   Google Scholar
• Cameron CE, Castro C, Arnold JJ. The mechanism of action of ribavirin: lethal mutagenesis of RNA virus genomes mediated by the viral RNA-dependent RNA polymerase. Curr. Opin. Infect. Dis. 23(3), 231–236 (2010).
   PubMedGoogle Scholar
• Peters HL, Jochmans D, de Wilde AH et al. Design, synthesis and evaluation of a series of acyclic fleximer nucleoside analogues with anti-coronavirus activity. Bioorg. Med. Chem. Lett. 25(13), 2923–2926 (2015).
   PubMedGoogle Scholar
• Matsuyama S, Nao N, Shirato K et al. Enhanced isolation of SARS-CoV-2 by TMPRSS2-expressing cells. Proc. Natl Acad. Sci. USA 117(13), 7001–7003 (2020).
   PubMed Web of Science ®Google Scholar
• Li Q, Kang C, Zhang Y, Chen R. Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites. Acta Pharm. Sin. B. 10(7), 1228–1238 (2020).
   PubMed Web of Science ®Google Scholar
• Yin W, Mao C, Luan X et al. Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir. Science 368(6498), 1499–1504 (2020).
   PubMed Web of Science ®Google Scholar
• Feldmann H, Sprecher A, Geisbert T, Zaki S. Filoviridae: Marburg and Ebola Viruses. In: Advances in Virus Research. Academic Press, 100, 307–337 (2020).
   Google Scholar
• Gautret P, Lagier JC, Parola P et al. Hydroxychloroquine and azithromycin as a treatment of COVID-19: results of an open-label non-randomized clinical trial. Int. J. Antimicrob. Agents 56(1), 105949 (2020).
   PubMed Web of Science ®Google Scholar
• Cao B, Wang Y, Wen D et al. A trial of lopinavir–ritonavir in adults hospitalized with severe Covid-19. N. Engl. J. Med. 382(19), 1787–1799 (2020).
   PubMed Web of Science ®Google Scholar
• Bojkova D, Klann K, Koch B et al. Proteomics of SARS-CoV-2-infected host cells reveals therapy targets. Nature 583(7816), 469–472 (2020).
   PubMed Web of Science ®Google Scholar
• Xia H, Cao Z, Xie X et al. Evasion of type I interferon by SARS-CoV-2. Cell Rep. 33(1), 108234 (2020).
   PubMed Web of Science ®Google Scholar