Biology subjects

Pascarella, S.

Publications and source records attributed to Pascarella, S..

4 recordsLinked to original sources

bioRxiv2022

The evolution of Monkeypox virus: a genetic and structural analysis reveals mutations in proteins involved in host-pathogen interaction

BackgroundOver the past few months, we have witnessed a new outbreak of a MPXV that has been detected without a clear link to Africa and has quickly spread globally. MethodsIn this article we investigate the mutational pattern of the MPXV and provide evidence for the presence of 6 new mutations that appear to characterize the current MPX-2022 outbreak. With the use of a number of chemical and physical parameters, we predict the stability of the mutated proteins, and propose an interpretation of the impact of these mutations on viral fitness). FindingsMost mutations, particularly the Immunomodulator A46, TNFr and Large transcript constituent, affect proteins playing an important role in host response to MPVX infection and could also be relevant to the clinical features of the 2022 MPXV outbreak. InterpretationAlthough further, experimental work is necessary for a full understanding of the impact of the mutations here reported on virus replication pathways and host immunomodulation, our in-silico data suggest the importance of monitoring the emergence of new MPXV mutations for the prevention of future outbreaks potentially dangerous for public health. FundingNo funding to declare

bioinformatics↗

bioRxiv2021

Cutting epitopes to survive: the case of lambda variant

This manuscript concisely reports an in-silico study on the potential impact of the Spike protein mutations on immuno-escape ability of SARS-CoV-2 lambda variant. Biophysical and bioinformatics data suggest that a combination of shortening immunogenic epitope loops and generation of potential N-glycosylation sites may be a viable adaptation strategy potentially allowing this emerging viral variant escaping host immunity.

bioinformatics↗

bioRxiv2021

SARS-CoV-2 B.1.617 Indian variants: are electrostatic potential changes responsible for a higher transmission rate?

Lineage B.1.617+, also known as G/452R.V3, is a recently described SARS-CoV-2 variant under investigation (VUI) firstly identified in October 2020 in India. As of May 2021, three sublineages labelled as B.1.617.1, B.1.617.2 and B.1.617.3 have been already identified, and their potential impact on the current pandemic is being studied. This variant has 13 amino acid changes, three in its spike protein, which are currently of particular concern: E484Q, L452R and P681R. Here we report a major effect of the mutations characterizing this lineage, represented by a marked alteration of the surface electrostatic potential (EP) of the Receptor Binding Domain (RBD) of the spike protein. Enhanced RBD-EP is particularly noticeable in the B.1.617.2 sublineage, which shows multiple replacements of neutral or negatively-charged amino acids with positively-charged amino acids. We here hypothesize that this EP change can favor the interaction between the B.1.617+RBD and the negatively-charged ACE2 thus conferring a potential increase in the virus transmission.

bioinformatics↗

bioRxiv2020

Long-chain polyphosphates impair SARS-CoV-2 infection and replication: a route for therapy in man

Anti-viral activities of long-chain inorganic polyphosphates (PolyPs) against severe acute respiratory syndrome coronavirus (SARS-CoV)-2 infection were investigated. In molecular docking analyses, PolyPs interacted with several conserved angiotensin-converting enzyme (ACE)2 and RNA-dependent RNA polymerase (RdRp) amino acids. We thus tested PolyPs for functional interactions in vitro in SARS-CoV-2-infected Vero E6, Caco2 and human primary nasal epithelial cells. Immunofluorescence, qPCR, direct RNA sequencing, FISH and Immunoblotting were used to determine virus loads and transcription levels of genomic(g)RNAs and sub-genomic(sg)RNAs. We show that PolyP120 binds to ACE2 and enhances its proteasomal degradation. PolyP120 shows steric hindrance of the genomic Sars-CoV-2-RNA/RdRP complex, to impair synthesis of positive-sense gRNAs, viral subgenomic transcripts and structural proteins needed for viral replication. Thus, PolyP120 impairs infection and replication of Korean and European (containing non-synonymous variants) SARS-CoV-2 strains. As PolyPs have no toxic activities, we envision their use as a nebulised formula for oropharyngeal delivery to prevent infections of SARS-CoV-2 and during early phases of antiviral therapy.

genetics↗