CIGB-300 synthetic peptide, an antagonist of CK2 kinase activity, as a treatment for Covid-19. A computational biology approach

Drug repositioning became the first choice for treating Covid-19 patients due to the urgent need to deal with the pandemic. Similarities in the hijacking mechanisms used by SARS-CoV-2 and several type of cancer, suggest the repurposing of cancer drugs to treat Covid-19. CK2 kinase antagonists have been proposed for the treatment of cancer. A recent study in cells infected with SARS-CoV-2 virus found a significant CK2 kinase activity, and the use of a CK2 inhibitor showed antiviral responses. CIGB-300, originally designed as an anticancer peptide, is an antagonist of CK2 kinase activity that binds to CK2 phospho-acceptor sites. Recent preliminary results show an antiviral activity of CIGB-300 versus a surrogate model of coronavirus. Here we present a computational biology study that provides evidences at the molecular level of how CIGB-300 might interfere with SARS-CoV-2 life cycle inside infected human cells. First, from SARS-CoV studies, we infer the potential incidence of CIGB-300 in SARS-CoV-2 interference on immune response. Next, from the analysis of multiple Omics data, we propose the action of CIGB-300 since early stage of viral infections perturbing the virus hijacking of RNA splicing machinery. It was also predicted the interference of CIGB-300 in virus-host interactions responsible for the high infectivity and the particular immune response to SARS-CoV-2 infection. Further, we provide evidences of CIGB-300 attenuation of phenotypes related to muscle, bleeding, coagulation and respiratory disorders.


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SARS-CoV-2 currently spread world-wide showing high infectivity and transmissibility. 45 Due to the urgency of finding effective therapeutics treatments in the shortest possible 46 time, drug repurposing emerged as the first option [1,2]. The huge amount of data so far 47 generated permit the re-consideration of drugs already evaluated for other diseases, 48 which might have advanced toxicological, preclinical and/or clinical studies. 49 Since the genomic sequence of SARS-CoV-2 was made available in January 2020 [3], 50 diversity of technique and laboratory models has been profusely applied to the study of 51 SARS-CoV-2 replication and infectivity. with CIGB-300 showed a significant reduction of virus production suggesting B23 as an 103 attractive target for antiviral drugs. Lobaina and Perera [12] also proposed B23 as a 104 potential target in antiviral therapies. 105 With this background, CIGB-300 was tested for its safety and clinical benefits in Covid- interaction of CIGB-300 with BCoV nucleocapsid protein(N) was also revealed.

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Functional enrichment found cytoskeleton reorganization and protein folding as the 112 major disturbed biological processes.

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Here we present an in silico analysis of SARS-CoV and SARS-CoV-2 viral infection. We have been also implicated in the inhibition of type I interferon signaling pathway [19].

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A sequence alignment of N protein from SARS-CoV and SARS-CoV-2 viruses show a 132 high similarity (Fig 1). N Protein consists of two structural domains (Fig 1): the N-   and Ser251 were noted as putative phospho-acceptors for CK2 (see Fig 1), though 147 neither has been corroborated experimentally. We collected a total of 33 148 phosphorylation sites for SARS-CoV-2 N protein (see Fig 1 and       binds KPNA2. In this way, the chaperon function of KPNB1 through the nuclear pore is 189 interfered, and STAT1 signaling is interrupted (Fig 2B). respectively. The last two mutants, Orf6 54-58Ala and Orf6 59-63Ala , comprising the ten C-terminal amino acids, did not retain KPNA2 and as consequence, STAT1 function was 196 unaffected. The first mutant Orf6 49-53Ala was still able to retain KPNA2. So, the last ten 197 aminoacids were responsible for KPNA2 binding and, as consequence, for KPNB1 198 recruitment.   Mutant M2 of Lei et al. [28] include Asp53 residue at position +3 relative to Ser50, and this position is known to be important for the recognition of CK2. Therefore, we strongly 218 suggest that the possible binding of CIGB-300 to this phospho-acceptor motif would 219 interfere the interaction of Orf6 C-terminus with KPNA2; avoiding its retention in the 220 ER/Golgi membrane, without interfering KPNA2 chaperon activity of carrying STAT1 221 complex to the nucleus ( Fig 2C). In this regard, CIGB-300 could exhibit an effect that 222 other CK2 antagonists that target CK2 won't.       Taking all these together, we suggest that CIGB-300 intervene SRSF1 role in SARS-

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CoV-2 protein synthesis interfering its phosphorylation by SRPK1 kinase.  shown those sites whose phosphorylation was increased by SARS-CoV-2 infection.
Evaluating how CIGB-300 may interfere host-host protein interactions implicated in 409 virus-induced mechanisms, we found that 68 proteins (SC2_300 set from now on) have 410 activated phospho-acceptor sites in at least two of the four phosphoproteomic studies, 411 which were inhibited by CIGB-300 (see S2 Table). The protein-protein interactions (PPI) 412 network built with these proteins is shown in Fig 8. A majority of the nodes in the  S3 Table). The five proteins with higher degree are also highlighted. In this network HSPB1 heat shock protein (alias HSP27) is one of the highest degree   CoV-2. First, we saw it as the host protein with a higher correlation of expression to viral proteins, in particular to Orf6. Second, we identified B23 as a highly connected 473 node in a network of proteins consistently upregulated by SARS-CoV-2 infection and 474 inhibited by CIGB-300, which is related to Cell Cycle pathway (Fig 8). Third, it was part 475 of a phenotype network related to respiratory, bleeding and coagulation disorders,

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• Interference of IFN signaling, which is responsible for a weak immune response.
• Early stages of virus kidnapping of RNA processing, which plays an essential 517 role in virus genome replication and translation.

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• Aggresome accumulation and its role in Inflammation and fibrosis commonly 519 observed in severe Covid-19 patients.

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• Phenotypes related to muscle, bleeding, coagulation and respiratory disorders.    Additional statistical analysis and graphs were generated and plotted using GraphPad        607 608