Characterization of mutations modulating enhanced transmissibility of SARS-CoV-2 B.1.617+ (Delta) variant using In Silico tools.

Since the beginning of the of SARS-CoV-2 (Covid-19) pandemic, variants of concern (VOC) have emerged taxing health systems worldwide. In October 2020, a new variant of SARS-CoV-2 (B.1.617+/Delta variant) emerged in India, triggering a deadly wave of Covid-19. Epidemiological data strongly suggests that B.1.617+ is more transmissible and previous reports have revealed that B.1.617+ has numerous mutations compared to wild type (WT), including several changes in the spike protein (SP). The main goal of this study was to use In Silico (computer simulation) techniques to examine mutations in the SP, specifically L452R and E484Q (part of the receptor binding domain (RBD) for human angiotensin-converting enzyme 2 (hACE2)) and P681R (upstream of the Furin cleavage motif), for effects in modulating the transmissibility of the B.1.617+ variant. Using computational models, the binding free energy (BFE) and H-bond lengths were calculated for SP-hACE2 and SP-Furin complexes. Comparison of the SP-hACE2 complex in the WT and B.1.617+ revealed both complexes have identical receptor-binding modes but the total BFE of B.1.617+ binding was more favorable for complex formation than WT, suggesting L452R and E484Q have a moderate impact on binding affinity. In contrast, the SP-Furin complex of B.1.617+ substantially lowered the BFE and revealed changes in molecular interactions compared to the WT complex, implying stronger complex formation between the variant and Furin. This study provides an insight into mutations that modulate transmissibility of the B.1.617+ variant, specifically the P681R mutation which appears to enhance transmissibility of the B.1.617+ variant by rendering it more receptive to Furin.

FRET-based hACE2 receptor mimic peptide conjugated nanoprobe for simple detection of SARS-CoV-2.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has led to a pandemic of acute respiratory disease, namely coronavirus disease (COVID-19). This disease threatens human health and public safety. Early diagnosis, isolation, and prevention are important to suppress the outbreak of COVID 19 given the lack of specific antiviral drugs to treat this disease and the emergence of various variants of the virus that cause breakthrough infections even after vaccine administration. Simple and prompt testing is paramount to preventing further spread of the virus. However, current testing methods, namely RT-PCR, is time-consuming. Binding of the SARS-CoV-2 spike (S) glycoprotein to human angiotensin-converting enzyme 2 (hACE2) receptor plays a pivotal role in host cell entry. In the present study, we developed a hACE2 mimic peptide beacon (COVID19-PEB) for simple detection of SARS-CoV-2 using a fluorescence resonance energy transfer system. COVID19-PEB exhibits minimal fluorescence in its ''closed'' hairpin structure; however, in the presence of SARS-CoV-2, the specific recognition of the S protein receptor-binding domain by COVID19-PEB causes the beacon to assume an ''open'' structure that emits strong fluorescence. COVID19-PEB can detect SARS-CoV-2 within 3 h or even 50 min and exhibits strong fluorescence even at low viral concentrations, with a detection limit of 4 × 103 plaque-forming unit/test. Furthermore, in SARS-CoV-2-infected patient samples confirmed using polymerase chain reaction, COVID19-PEB accurately detected the virus. COVID19-PEB could be developed as a rapid and accurate diagnostic tool for COVID-19.

Antiviral activity of aframomum melegueta against severe acute respiratory syndrome coronaviruses type 1 and 2.

Plant-based compounds with antiviral properties against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been identified in Aframomum melegueta through computational models. The seed extract have been traditionally used to treat different illnesses. In this study, ethanolic extracts were prepared for six commercial samples of A. melegueta seeds. Antiviral activity was tested using the XTT cytotoxicity assay and cell-based SARS-CoV-1 and 2 pseudoviral models. The presence of gingerols and other non-volatile components in the seed extracts was determined using an Agilent 1290 UPLC/DAD in tandem with an Agilent 6546 QTOF-MS. Our results showed selective antiviral activity with TI values as high as 13.1. Fifteen gingerols were identified by chromatographic analysis, with 6-gingerol being the dominant component in each seed extract. A combination of 6-gingerol with techtochrysin, previously identified in computational models as a potential active ingredient against SARS-CoV-2, demonstrated additive antiviral activity with CI values between 0.8715 and 0.9426. We confirmed the antiviral activity of A. melegueta predicted through computational models and identified a different compound, 6-gingerol, as a potential active ingredient.

SARS-CoV-2 spillover transmission due to recombination event.

In late 2019, a novel Coronavirus emerged in China. Perceiving the modulating factors of cross-species virus transmission is critical to elucidate the nature of virus emergence. Using bioinformatics tools, we analyzed the mapping of the SARS-CoV-2 genome, modeling of protein structure, and analyze the evolutionary origin of SARS-CoV-2, as well as potential recombination events. Phylogenetic tree analysis shows that SARS-CoV-2 has the closest evolutionary relationship with Bat-SL-CoV-2 (RaTG13) at the scale of the complete virus genome, and less similarity to Pangolin-CoV. However, the Receptor Binding Domain (RBD) of SARS-CoV-2 is almost identical to Pangolin-CoV at the aa level, suggesting that spillover transmission probably occurred directly from pangolins, but not bats. Further recombination analysis revealed the pathway for spillover transmission from Bat-SL-CoV-2 and Pangolin-CoV. Here, we provide evidence for recombination event between Bat-SL-CoV-2 and Pangolin-CoV that resulted in the emergence of SARS-CoV-2. Nevertheless, the role of mutations should be noted as another influencing factor in the continuing evolution and resurgence of novel SARS-CoV-2 variants.

Development of a SARS-CoV-2-derived receptor-binding domain-based ACE2 biosensor.

The global outbreak of coronavirus disease and rapid spread of the causative severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) represent a significant threat to human health. A key mechanism of human SARS-CoV-2 infection is initiated by the combination of human angiotensin-converting enzyme 2 (hACE2) and the receptor-binding domain (RBD) of the SARS-CoV-2-derived spike glycoprotein. Despite the importance of these protein interactions, there are still insufficient detection methods to observe their activity at the cellular level. Herein, we developed a novel fluorescence resonance energy transfer (FRET)-based hACE2 biosensor to monitor the interaction between hACE2 and SARS-CoV-2 RBD. This biosensor facilitated the visualization of hACE2-RBD activity with high spatiotemporal resolutions at the single-cell level. Further studies revealed that the FRET-based hACE2 biosensors were sensitive to both exogenous and endogenous hACE2 expression, suggesting that they might be safely applied to the early stage of SARS-CoV-2 infection without direct virus use. Therefore, our novel biosensor could potentially help develop drugs that target SARS-CoV-2 by inhibiting hACE2-RBD interaction.

Unraveling the molecular basis of host cell receptor usage in SARS-CoV-2 and other human pathogenic ß-CoVs.

The recent emergence of the novel SARS-CoV-2 in China and its rapid spread in the human population has led to a public health crisis worldwide. Like in SARS-CoV, horseshoe bats currently represent the most likely candidate animal source for SARS-CoV-2. Yet, the specific mechanisms of cross-species transmission and adaptation to the human host remain unknown. Here we show that the unsupervised analysis of conservation patterns across the ß-CoV spike protein family, using sequence information alone, can provide valuable insights on the molecular basis of the specificity of ß-CoVs to different host cell receptors. More precisely, our results indicate that host cell receptor usage is encoded in the amino acid sequences of different CoV spike proteins in the form of a set of specificity determining positions (SDPs). Furthermore, by integrating structural data, in silico mutagenesis and coevolution analysis we could elucidate the role of SDPs in mediating ACE2 binding across the Sarbecovirus lineage, either by engaging the receptor through direct intermolecular interactions or by affecting the local environment of the receptor binding motif. Finally, by the analysis of coevolving mutations across a paired MSA we were able to identify key intermolecular contacts occurring at the spike-ACE2 interface. These results show that effective mining of the evolutionary records held in the sequence of the spike protein family can help tracing the molecular mechanisms behind the evolution and host-receptor adaptation of circulating and future novel ß-CoVs.

The Integrin Binding Peptide, ATN-161, as a Novel Therapy for SARS-CoV-2 Infection.

Many efforts to design and screen therapeutics for the current severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) pandemic have focused on inhibiting viral host cell entry by disrupting angiotensin-converting enzyme-2 (ACE2) binding with the SARS-CoV-2 spike protein. This work focuses on the potential to inhibit SARS-CoV-2 entry through a hypothesized α5ß1 integrin-based mechanism and indicates that inhibiting the spike protein interaction with α5ß1 integrin (+/- ACE2) and the interaction between α5ß1 integrin and ACE2 using a novel molecule (ATN-161) represents a promising approach to treat coronavirus disease-19.