PNPLA3 and TLL-1 Polymorphisms as Potential Predictors of Disease Severity in Patients With COVID-19

Albeit the pathogenesis of COVID-19 remains unclear, host’s genetic polymorphisms in genes involved in infection and reinfection, inflammation, or immune stimulation could play a role in determining the course and outcome. We studied in the early phase of pandemic consecutive patients (N = 383) with SARS-CoV-2 infection, whose subsequent clinical course was classified as mild or severe, the latter being characterized by admission to intensive therapy unit or death. Five host gene polymorphisms (MERTK rs4374383, PNPLA3 rs738409, TLL-1 rs17047200, IFNL3 rs1297860, and INFL4 rs368234815) were assessed by using whole nucleic acids extracted from nasopharyngeal swabs. Specific protease cleavage sites of TLL-1 on the SARS-CoV-2 Spike protein were predicted in silico. Male subjects and older patients were significantly at higher risk for a severe outcome (p = 0.02 and p < 0.001, respectively). By considering patients ≤65 years, after adjusting for potential confounding due to sex, an increased risk of severe outcome was found in subjects with the GG genotype of PNPLA3 (adj-OR: 4.69; 95% CI = 1.01–22.04) or TT genotype of TLL-1 (adj-OR=9.1; 95% CI = 1.45–57.3). In silico evaluation showed that TLL-1 is potentially involved in the Spike protein cleavage which is essential for viral binding and entry into the host cells using the host receptor angiotensin-converting enzyme 2 (ACE2). Subjects carrying a GG genotype in PNPLA3 gene might have a constitutive upregulation of the NLRP3 inflammasome and be more prone to tissue damage when infected by SARS-CoV-2. The TT genotype in TLL-1 gene might affect its protease activity on the SARS-CoV-2 Spike protein, enhancing the ability to infect or re-infect host’s cells. The untoward effect of these variants on disease course is evident in younger patients due to the relative absence of comorbidities as determinants of prognosis. In the unresolved pathogenetic scenery of COVID-19, the identification of genetic variants associates with more prolonged course or with a severe outcome of infection would support the development of predictive tools useful to stratify subjects by risk class at presentation. Moreover, the individuation of key genes could contribute to a better understanding of the pathways involved in the pathogenesis, giving the basis for rational therapeutic approaches.

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PNPLA3 and TLL-1 polymorphisms affect disease severity in patients with COVID-19

10.21203/rs.3.rs-40510/v1 ◽

2020 ◽

Author(s):

Stefania Grimaudo ◽

Emanuele Amodio ◽

Rosaria Maria Pipitone ◽

Carmelo Massimo Maida ◽

Stefano Pizzo ◽

...

Keyword(s):

In Silico ◽

Intensive Therapy ◽

Cleavage Sites ◽

Protein Cleavage ◽

Protease Cleavage ◽

Increased Risk ◽

Specific Protease ◽

Protease Cleavage Sites ◽

Male Subjects ◽

Affect Disease Severity

Abstract Introduction Albeit the pathogenesis of COVID-19 remains unclear, host’s genetic polymorphisms in genes infection and reinfection, inflammation, or immune stimulation could play a role in determining the course and outcome. Methods We studied in the early phase of pandemic consecutive patients (N=383) with SARS-CoV-2 infection, whose subsequent clinical course was classified as mild or severe, the latter being characterised by admission to intensive therapy unit or death. Five host gene polymorphisms (MERTK rs4374383, PNPLA3 rs738409, TLL-1 rs17047200, IFNL3 rs1297860, and INFL4 rs368234815) were assessed by using whole nucleic acids extracted from nasopharyngeal swabs. Specific protease cleavage sites of TLL-1 on the SARS-CoV-2 Spyke protein were predicted in silico. Results Male subjects and older patients were significantly at higher risk for a severe outcome (p=0.02 and p<0.001, respectively). By considering patients ≤ 65 years, after adjusting for potential confounding due to sex, an increased risk of severe outcome was found in subjects with the GG genotype of PNPLA3 (adj-OR: 4.69; 95% CI= 1.01-22.04) or TT genotype of TLL-1 (adj-OR=9.1; 95% CI= 1.45-57.3). In silico evaluation showed that TLL-1 is potentially involved in the Spike protein cleavage.Discussion Subjects carrying a GG genotype in PNPLA3 gene might have a constitutive upregulation of the NLRP3 inflammosome and be more prone to tissue damage when infected by SARS-CoV-2. The TT genotype in TLL-1 gene might affect its protease activity on the SARS-CoV-2 Spyke protein, enhancing the ability to infect or re-infect host’s cells. The untoward effect of these variants on disease course is evident in younger patients due to the relative absence of comorbidities as determinants of prognosis.

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The insert sequence in SARS-CoV-2 enhances spike protein cleavage by TMPRSS

10.1101/2020.02.08.926006 ◽

2020 ◽

Cited By ~ 29

Author(s):

Tong Meng ◽

Hao Cao ◽

Hao Zhang ◽

Zijian Kang ◽

Da Xu ◽

...

Keyword(s):

Insertion Sequence ◽

Cell Receptor ◽

Host Cells ◽

Spike Protein ◽

Target Cells ◽

Cleavage Sites ◽

Protein Cleavage ◽

Protease Cleavage ◽

Cleavage Efficiency ◽

Protease Cleavage Sites

AbstractAt the end of 2019, the SARS-CoV-2 induces an ongoing outbreak of pneumonia in China1, even more spread than SARS-CoV infection2. The entry of SARS-CoV into host cells mainly depends on the cell receptor (ACE2) recognition and spike protein cleavage-induced cell membrane fusion3,4. The spike protein of SARS-CoV-2 also binds to ACE2 with a similar affinity, whereas its spike protein cleavage remains unclear5,6. Here we show that an insertion sequence in the spike protein of SARS-CoV-2 enhances the cleavage efficiency, and besides pulmonary alveoli, intestinal and esophagus epithelium were also the target tissues of SARS-CoV-2. Compared with SARS-CoV, we found a SPRR insertion in the S1/S2 protease cleavage sites of SARS-CoV-2 spike protein increasing the cleavage efficiency by the protein sequence aligment and furin score calculation. Additionally, the insertion sequence facilitates the formation of an extended loop which was more suitable for protease recognition by the homology modeling and molicular docking. Furthermore, the single-cell transcriptomes identified that ACE2 and TMPRSSs are highly coexpressed in AT2 cells of lung, along with esophageal upper epithelial cells and absorptive enterocytes. Our results provide the bioinformatics evidence for the increased spike protein cleavage of SARS-CoV-2 and indicate its potential target cells.

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In Silico Study of Polyunsaturated Fatty Acids as Potential SARS-CoV-2 Spike Protein Closed Conformation Stabilizers: Epidemiological and Computational Approaches

Molecules ◽

10.3390/molecules26030711 ◽

2021 ◽

Vol 26 (3) ◽

pp. 711

Author(s):

Alonso Vivar-Sierra ◽

María José Araiza-Macías ◽

José Patricio Hernández-Contreras ◽

Arely Vergara-Castañeda ◽

Gabriela Ramírez-Vélez ◽

...

Keyword(s):

Linoleic Acid ◽

In Silico ◽

Cell Types ◽

Host Cells ◽

Spike Protein ◽

Omega 3 ◽

Angiotensin Converting Enzyme 2 ◽

Closed Conformation ◽

In Silico Study ◽

Omega 6

SARS-CoV-2 infects host cells by interacting its spike protein with surface angiotensin-converting enzyme 2 (ACE2) receptors, expressed in lung and other cell types. Although several risk factors could explain why some countries have lower incidence and fatality rates than others, environmental factors such as diet should be considered. It has been described that countries with high polyunsaturated fatty acid (PUFA) intake have a lower number of COVID-19 victims and a higher rate of recovery from the disease. Moreover, it was found that linoleic acid, an omega-6 PUFA, could stabilize the spike protein in a closed conformation, blocking its interaction with ACE2. These facts prompted us to perform in silico simulations to determine if other PUFA could also stabilize the closed conformation of spike protein and potentially lead to a reduction in SARS-CoV-2 infection. We found that: (a) countries whose source of omega-3 is from marine origin have lower fatality rates; and (b) like linoleic acid, omega-3 PUFA could also bind to the closed conformation of spike protein and therefore, could help reduce COVID-19 complications by reducing viral entrance to cells, in addition to their known anti-inflammatory effects.

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Sea Urchin Pigments as Potential Therapeutic Agents Against the Spike Protein of SARS-CoV-2 Based on in Silico Analysis

10.26434/chemrxiv.12568595.v1 ◽

2020 ◽

Cited By ~ 1

Author(s):

Elena Susana Barbieri ◽

Tamara Rubilar ◽

Ayelén Gázquez ◽

Marisa Avaro ◽

Erina Noé Seiler ◽

...

Keyword(s):

Sea Urchin ◽

In Silico ◽

In Silico Analysis ◽

Protein S ◽

Host Cells ◽

Spike Protein ◽

Therapeutic Drug ◽

The Novel ◽

Novel Coronavirus ◽

Silico Analysis

Several studies have been published regarding the interaction between the spike protein of the novel coronavirus SARS-CoV-2 and ACE2 receptor in the host cells. In the presente work, we evaluated the in silico properties of two sea urchin pigments, Echinochrome A (EchA) and Spinochromes (SpinA) against the Spike protein (S) towards finding a potential therapeutic drug against the disease caused by the novel coronavirus (COVID-19). The best ensemble docking pose of EchaA and SpinA showed a binding affinity of -5.9 and -6.7 kcal mol-1, respectively. The linked aminoacids (T505, G496 and Y449 for EchA and Y449, Q493 and G496 for SpinA) are in positions involved in ACE2 binding in both RBDs frim SARS-CoV and SARS-CoV-2 suggesting that EchA and SpinA may interact with Spike proteins drom both viruses. The results suggest that these pigments could act as inhibitors of S protein, pointing them as antiviral drugs for SARS-CoV-2.<br>

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Effect of mutations in the SARS-CoV-2 spike protein on protein stability, cleavage, and cell-cell fusion function

10.1101/2021.01.24.428007 ◽

2021 ◽

Author(s):

Chelsea T. Barrett ◽

Hadley E. Neal ◽

Kearstin Edmonds ◽

Carole L. Moncman ◽

Rachel Thompson ◽

...

Keyword(s):

Cell Fusion ◽

Viral Entry ◽

Protein S ◽

Proteolytic Processing ◽

Spike Protein ◽

Protein Cleavage ◽

Fusion Event ◽

Viral Binding ◽

Mammalian Cell Lines ◽

Cell Cell

AbstractThe SARS-CoV-2 spike protein (S) is the sole viral protein responsible for both viral binding to a host cell and the membrane fusion event needed for cell entry. In addition to facilitating fusion needed for viral entry, S can also drive cell-cell fusion, a pathogenic effect observed in the lungs of SARS-CoV-2 infected patients. While several studies have investigated S requirements involved in viral particle entry, examination of S stability and factors involved in S cell-cell fusion remain limited. We demonstrate that S must be processed at the S1/S2 border in order to mediate cell-cell fusion, and that mutations at potential cleavage sites within the S2 subunit alter S processing at the S1/S2 border, thus preventing cell-cell fusion. We also identify residues within the internal fusion peptide and the cytoplasmic tail that modulate S cell-cell fusion. Additionally, we examine S stability and protein cleavage kinetics in a variety of mammalian cell lines, including a bat cell line related to the likely reservoir species for SARS-CoV-2, and provide evidence that proteolytic processing alters the stability of the S trimer. This work therefore offers insight into S stability, proteolytic processing, and factors that mediate S cell-cell fusion, all of which help give a more comprehensive understanding of this highly sought-after therapeutic target.

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Sea Urchin Pigments as Potential Therapeutic Agents Against the Spike Protein of SARS-CoV-2 Based on in Silico Analysis

10.26434/chemrxiv.12568595 ◽

2020 ◽

Author(s):

Elena Susana Barbieri ◽

Tamara Rubilar ◽

Ayelén Gázquez ◽

Marisa Avaro ◽

Erina Noé Seiler ◽

...

Keyword(s):

Sea Urchin ◽

In Silico ◽

In Silico Analysis ◽

Protein S ◽

Host Cells ◽

Spike Protein ◽

Therapeutic Drug ◽

The Novel ◽

Novel Coronavirus ◽

Silico Analysis

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Silybin B and Cianidanol Inhibit M pro and Spike Protein of SARS-CoV-2: Evidence from in Silico Molecular Docking Studies

Current Pharmaceutical Design ◽

10.2174/1381612826666201210122726 ◽

2020 ◽

Vol 26 ◽

Author(s):

Rashi Srivastava ◽

Shubham Tripathi ◽

Sreepoorna Unni ◽

Arif Hussain ◽

Shafiul Haque ◽

...

Keyword(s):

Molecular Docking ◽

In Silico ◽

Drug Repositioning ◽

Docking Studies ◽

Host Cells ◽

Spike Protein ◽

Ligand Interactions ◽

Adme Properties ◽

Approved Drugs ◽

In Silico Molecular Docking

Background: The main proteases (Mpro) and Spike Proteins (SP) of Severe Acute Respiratory Syndrome Coronavirus 2 (SARSCoV-2) play a major role in viral infection development by producing several non-structural proteins (nsPs) and penetrating the host cells respectively. In this study, the potential of in silico molecular docking-based drug repositioning approach was exploited for identifying the inhibitors of Mpro and SP of SARS-CoV-2. Methods: A total of 196 compounds including various US-FDA-approved drugs, vitamins and their analogs were docked with Mpro (PDB IDs: 6YB7 and 6Y84), and the top six ligands were further tested for ADME properties followed by docking with SP (PDB IDs: 6LXT and 6W41). Results: Out of 196 compounds, binding energy (DE) of Silybin B (6YB7: DE: -11.20 kcal/mol; 6Y84: DE: -10.18 kcal/mol; 6LXT:DE: -10.47 kcal/mol; 6W41:DE: -10.96 kcal/mol) and Cianidanol (6YB7:DE: -8.85 kcal/mol; 6Y84:DE:-10.02 kcal/mol; 6LXT:DE:-9.36 kcal/mol; 6W41:DE: -9.52 kcal/mol) demonstrated better binding and ADME properties compared with the currently endeavored drugs like Hydroxychloroquine and Lopinavir. Additionally, Elliptinone, Diospyirin, SCHEMBL94263 and Fiboflavin have shown encouraging results. Fiboflavin, an immunity booster, was found to inhibit both the Mpro and spike protein of SARS-CoV-2. It was observed that amino acid residues MET6, ALA7, PHE8, PRO9, ASP295, GLY302, VAL303 and THR304 play significant roles in protein-ligand interactions through hydrogen bonds and Vander Waals forces. Conclusion: Silybin B and Cianidanol showed excellent binding and ADME properties compared with the currently endeavored drugs and can be exploited as therapeutic options against SARS-CoV-2 infection after experimental validation and clinical trials.

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Tinjauan Molekuler dan Epidemiologi Mutasi pada Virus SARS-CoV-2

bionature ◽

10.35580/bionature.v22i1.22379 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Hartono Hartono ◽

Yenni Yusuf

Keyword(s):

Immune System ◽

Literature Review ◽

Viral Entry ◽

Host Cells ◽

Spike Protein ◽

Wild Type ◽

Viral Binding ◽

Viral Mutation ◽

Alpha Beta ◽

The Impact

Abstract. The SARS-CoV-2 virus which is the cause of the COVID-19 pandemic since the end of 2019 has undergone many mutations that gave rise to several variants of concern (VOC) with higher transmission, virulence, and ability to evade the immune system than the initial variant (wild-type). Until now, there are four variants included in the VOC of the virus, namely alpha, beta, gamma and delta variants. The increased transmission and virulence of these VOCs were associated with mutational changes in the spike protein, which is the structure of the virus that plays a role in binding to host cells. In this article, we conduct a literature review on VOCs from the SARS-CoV-2 virus related to mutations that occur and their impact on the viral binding process. To gain an understanding of the impact of mutations in these variants, we also reviewed the structure of the spike protein and the process of viral entry into host cells. Keywords: viral mutation, variants of concern (VOC), COVID-19, SARS-CoV-2.

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