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Current Neuropharmacology

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ISSN (Print): 1570-159X
ISSN (Online): 1875-6190

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Review Article

Viruses Broaden the Definition of Life by Genomic Incorporation of Artificial Intelligence and Machine Learning Processes

Author(s): George B. Stefano* and Richard M. Kream

Volume 20, Issue 10, 2022

Published on: 04 July, 2022

Page: [1888 - 1893] Pages: 6

DOI: 10.2174/1570159X20666220420121746

open access plus

Abstract

Viruses have been classified as non-living because they require a cellular host to support their replicative processes. Empirical investigations have significantly advanced our understanding of the many strategies employed by viruses to usurp and divert host regulatory and metabolic processes to drive the synthesis and release of infectious particles. The recent emergence of SARS-CoV-2 has permitted us to evaluate and discuss a potentially novel classification of viruses as living entities. The ability of SARS CoV-2 to engender comprehensive regulatory control of integrative cellular processes is strongly suggestive of an inherently dynamic informational registry that is programmatically encoded by linear ssRNA sequences responding to distinct evolutionary constraints. Responses to positive evolutionary constraints have resulted in a single-stranded RNA viral genome that occupies a threedimensional space defined by conserved base-paring resulting from a complex pattern of both secondary and tertiary structures. Additionally, regulatory control of virus-mediated infectious processes relies on extensive protein-protein interactions that drive conformational matching and shape recognition events to provide a functional link between complementary viral and host nucleic acid and protein domains. We also recognize that the seamless integration of complex replicative processes is highly dependent on the precise temporal matching of complementary nucleotide sequences and their corresponding structural and non-structural viral proteins. Interestingly, the deployment of concerted transcriptional and translational activities within targeted cellular domains may be modeled by artificial intelligence (AI) strategies that are inherently fluid, self-correcting, and adaptive at accommodating temporal changes in host defense mechanisms. An in-depth understanding of multiple self-correcting AIassociated viral processes will most certainly lead to novel therapeutic development platforms, notably the design of efficacious neuropharmacological agents to treat chronic CNS syndromes associated with long-COVID. In summary, it appears that viruses, notably SARS-CoV-2, are very much alive due to acquired genetic advantages that are intimately entrained to existential host processes via evolutionarily constrained AI-associated learning paradigms.

Keywords: Virus, artificial intelligence, long-COVID, mitochondrial genome, eukaryotic genome, SARS-CoV-2, RNAdependent RNA polymerase.

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[1]
Koshland, D.E. Jr Special essay. The seven pillars of life. Science, 2002, 295(5563), 2215-2216.
[http://dx.doi.org/10.1126/science.1068489] [PMID: 11910092]
[2]
Huston, N.C.; Wan, H.; Strine, M.S.; de Cesaris Araujo Tavares, R.; Wilen, C.B.; Pyle, A.M. Comprehensive in vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms. Mol. Cell, 2021, 81(3), 584-598.e5.
[http://dx.doi.org/10.1016/j.molcel.2020.12.041] [PMID: 33444546]
[3]
de Haan, C.A.; Rottier, P.J. Molecular interactions in the assembly of coronaviruses. Adv. Virus Res., 2005, 64, 165-230.
[http://dx.doi.org/10.1016/S0065-3527(05)64006-7] [PMID: 16139595]
[4]
Kim, D.; Lee, J.Y.; Yang, J.S.; Kim, J.W.; Kim, V.N.; Chang, H. The Architecture of SARS-CoV-2 transcriptome. Cell, 2020, 181(4), 914-921.e10.
[http://dx.doi.org/10.1016/j.cell.2020.04.011] [PMID: 32330414]
[5]
Wong, N.A.; Saier, M.H., Jr The SARS-coronavirus infection cycle: A survey of viral membrane proteins, their functional interactions and pathogenesis. Int. J. Mol. Sci., 2021, 22(3), 1308.
[http://dx.doi.org/10.3390/ijms22031308] [PMID: 33525632]
[6]
Stefano, G.B. Conformational matching: A possible evolutionary force in the evolvement of signal systems.CRC Handbook of comparative opioid and related neuropeptide mechanisms; Stefano, G.B., Ed.; CRC Press Inc.: Boca Raton, 1986, Vol. 2, pp. 271-277.
[7]
Stefano, G.B. The evolvement of signal systems: Conformational matching a determining force stabilizing families of signal molecules. Comp. Biochem. Physiol. C. Comp. Pharmacol. Toxicol., 1988, 90(2), 287-294.
[http://dx.doi.org/10.1016/0742-8413(88)90001-1] [PMID: 2902990]
[8]
Nasir, A.; Romero-Severson, E.; Claverie, J.M. Investigating the concept and origin of viruses. Trends Microbiol., 2020, 28(12), 959-967.
[http://dx.doi.org/10.1016/j.tim.2020.08.003] [PMID: 33158732]
[9]
Stefano, G.B.; Kream, R.M. Mitochondrial DNA heteroplasmy as an informational reservoir dynamically linked to metabolic and immunological processes associated with COVID-19 neurological disorders. Cell. Mol. Neurobiol., 2021, 42(1), 99-107.
[http://dx.doi.org/10.1007/s10571-021-01117-z]
[10]
Gordon, D.E.; Jang, G.M.; Bouhaddou, M.; Xu, J.; Obernier, K.; White, K.M.; O’Meara, M.J.; Rezelj, V.V.; Guo, J.Z.; Swaney, D.L.; Tummino, T.A.; Hüttenhain, R.; Kaake, R.M.; Richards, A.L.; Tutuncuoglu, B.; Foussard, H.; Batra, J.; Haas, K.; Modak, M.; Kim, M.; Haas, P.; Polacco, B.J.; Braberg, H.; Fabius, J.M.; Eckhardt, M.; Soucheray, M.; Bennett, M.J.; Cakir, M.; McGregor, M.J.; Li, Q.; Meyer, B.; Roesch, F.; Vallet, T.; Mac Kain, A.; Miorin, L.; Moreno, E.; Naing, Z.Z.C.; Zhou, Y.; Peng, S.; Shi, Y.; Zhang, Z.; Shen, W.; Kirby, I.T.; Melnyk, J.E.; Chorba, J.S.; Lou, K.; Dai, S.A.; Barrio-Hernandez, I.; Memon, D.; Hernandez-Armenta, C.; Lyu, J.; Mathy, C.J.P.; Perica, T.; Pilla, K.B.; Ganesan, S.J.; Saltzberg, D.J.; Rakesh, R.; Liu, X.; Rosenthal, S.B.; Calviello, L.; Venkataramanan, S.; Liboy-Lugo, J.; Lin, Y.; Huang, X.P.; Liu, Y.; Wankowicz, S.A.; Bohn, M.; Safari, M.; Ugur, F.S.; Koh, C.; Savar, N.S.; Tran, Q.D.; Shengjuler, D.; Fletcher, S.J.; O’Neal, M.C.; Cai, Y.; Chang, J.C.J.; Broadhurst, D.J.; Klippsten, S.; Sharp, P.P.; Wenzell, N.A.; Kuzuoglu-Ozturk, D.; Wang, H.Y.; Trenker, R.; Young, J.M.; Cavero, D.A.; Hiatt, J.; Roth, T.L.; Rathore, U.; Subramanian, A.; Noack, J.; Hubert, M.; Stroud, R.M.; Frankel, A.D.; Rosenberg, O.S.; Verba, K.A.; Agard, D.A.; Ott, M.; Emerman, M.; Jura, N.; von Zastrow, M.; Verdin, E.; Ashworth, A.; Schwartz, O.; d’Enfert, C.; Mukherjee, S.; Jacobson, M.; Malik, H.S.; Fujimori, D.G.; Ideker, T.; Craik, C.S.; Floor, S.N.; Fraser, J.S.; Gross, J.D.; Sali, A.; Roth, B.L.; Ruggero, D.; Taunton, J.; Kortemme, T.; Beltrao, P.; Vignuzzi, M.; García-Sastre, A.; Shokat, K.M.; Shoichet, B.K.; Krogan, N.J.A.A. SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature, 2020, 583(7816), 459-468.
[http://dx.doi.org/10.1038/s41586-020-2286-9] [PMID: 32353859]
[11]
Malone, B.; Urakova, N.; Snijder, E.J.; Campbell, E.A. Structures and functions of coronavirus replication-transcription complexes and their relevance for SARS-CoV-2 drug design. Nat. Rev. Mol. Cell Biol., 2021.
[PMID: 34824452]
[12]
Kelly, J.A.; Olson, A.N.; Neupane, K.; Munshi, S.; San Emeterio, J.; Pollack, L.; Woodside, M.T.; Dinman, J.D. Structural and functional conservation of the programmed -1 ribosomal frameshift signal of SARS coronavirus 2 (SARS-CoV-2). J. Biol. Chem., 2020, 295(31), 10741-10748.
[http://dx.doi.org/10.1074/jbc.AC120.013449] [PMID: 32571880]
[13]
Fehr, A.R.; Perlman, S. Coronaviruses: An overview of their replication and pathogenesis. Methods Mol. Biol., 2015, 1282, 1-23.
[http://dx.doi.org/10.1007/978-1-4939-2438-7_1] [PMID: 25720466]
[14]
Faheem; Kumar, B.K.; Sekhar, K.V.G.C.; Kunjiappan, S.; Jamalis, J.; Balaña-Fouce, R.; Tekwani, B.L.; Sankaranarayanan, M. Druggable targets of SARS-CoV-2 and treatment opportunities for COVID-19. Bioorg. Chem., 2020, 104, 104269.
[http://dx.doi.org/10.1016/j.bioorg.2020.104269]
[15]
Emmert-Streib, F.; Yli-Harja, O.; Dehmer, M. Artificial intelligence: A clarification of misconceptions, myths and desired status. Front Artif Intell, 2020, 3, 524339.
[http://dx.doi.org/10.3389/frai.2020.524339] [PMID: 33733197]
[16]
Krupovic, M.; Dolja, V.V.; Koonin, E.V. Origin of viruses: Primordial replicators recruiting capsids from hosts. Nat. Rev. Microbiol., 2019, 17(7), 449-458.
[http://dx.doi.org/10.1038/s41579-019-0205-6] [PMID: 31142823]
[17]
Int. International Committee on Taxonomy of Viruses Executive Committee. 2020 The new scope of virus taxonomy: Partitioning the virosphere into 15 hierarchical ranks. Nat. Microbiol., 2020.
[18]
Ho, J.S.Y.; Zhu, Z.; Marazzi, I. Unconventional viral gene expression mechanisms as therapeutic targets. Nature, 2021, 593(7859), 362-371.
[http://dx.doi.org/10.1038/s41586-021-03511-5] [PMID: 34012080]

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