Inhibiting Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants: Targeting the Spike and Envelope Proteins Using Nanomaterial Like Peptides

Applications of peptide-functionalized or unfunctionalized selenium nanoparticles for the passivation of SARS-CoV-2 variants and the respiratory syncytial virus (RSV)

The SARS-CoV-2 Omicron subvariants BA.4, BA. 5 and XBB are currently causing a COVID resurgence due to their increased spreading and infectivity. These latest subvariants have been shown to be somewhat resistant to the most common vaccines even with the third dose. Moreover, it has been well documented that when patients stop taking some commercial therapies (such as Paxlovid), COVID from these variants may return and may even be more contagious. Herein, we tested unfunctionalized and functionalized selenium (Se) nanoparticles with three novel peptides (NapFFTLUFLTUTEKKKK, NapFFMLUFLMUMEKKKK, and NapFFSAVLQSGFKKKK) previously shown by themselves to passivate the Omicron SARS-CoV-2 BA.4, BA.5 and XBB variants. Se is a natural element in our diet and is well known to boost the immune system, thus, providing a complementary approach to viral infections. NapFFMLUFLMUMEKKKK showed a stronger inhibition ability at 98 % for Omicron BA.4 % and 96 % for Omicron BA.5 after just 15 min in vitro. Two types of Se nanoparticles (those made chemically or biogenically by cells) were tested to passivate the new SARS-CoV-2 XBB variant. Results showed that the combination of any peptide and using either type of Se NP, the Omicron subvariant XBB was inhibited by 100 % after just 15 min in vitro. Interestingly, the use of Se NPs alone outperformed the peptides in terms of XBB passivation. Also, in order to determine a mechanism of action, functionalizing Se nanoparticles with the NapFFSAVLQSGFKKKK peptide showed a high binding ability toward the chemotrypsin-like cysteine protease (SARS CoV-2 3CLpro). Further, as a demonstration of their versatility, these functionalized peptides also passivated the Respiratory Syncytial Virus (RSV). NapFFTLUFLTUTEKKKK and NapFFMLUFLMUMEKKKK showed in silico interactions with the fusion glycoprotein of RSV prompting in vitro RSV pseudo virus testing. Compared to the conventionally precipitated synthetic Se nanoparticles, in vitro results showed that biogenic Se functionalized with the peptides enhanced the inhibition RSV to 100 % after just 15 min of incubation. NapFFTLUFLTUTEKKKK and NapFFMLUFLMUMEKKKK also showed no potential genotoxicity or carcinogenic effects. The peptides showed good gastro-intestinal (GI) tract absorption and bioavailability as predicted using the partition coefficient (QP logPo/w), and high-water solubility as detected by QPlogS. According to these promising results, functionalizing biogenic Se nanoparticles with these novel peptides should be further studied in vivo for the improved diagnosis, prevention, and treatment of SARS-CoV-2, RSV, and other respiratory virus infections.

Passivating the Omicron SARS-CoV-2 variant with self-assembled nano peptides: Specificity, stability, and no cytotoxicity

The SARS-CoV-2 Omicron variant is called a “variant of concern” (VOC) which has spread all over the world at a faster rate than even the first SARS-CoV-2 outbreak despite travel restrictions. In order to combat the health consequences from a SARS-CoV-2 Omicron variant infection, the objective of the present in vitro study was to develop self-assembled nano peptides to attach to the virus and inhibit its attachment and entry into mammalian cells for replication. For this purpose, two amphipathic peptides containing hydrophobic and hydrophilic peptides and an unnatural amino acid (such as 2-aminoisobutyric acid (U)) were designed to attach to the less mutated virus envelope rather than more frequently mutated S-protein region: NapFFTLUFLTUTEKKKK and NapFFMLUFLMUMEKKKK. These peptides were synthesized using the solid phase peptide synthesis method and were characterized for mammalian cell infection using well-established pseudo virus assays. In vitro results showed that the two self-assembled nano peptides significantly inhibited the ability of the SARS-CoV-2 Omicron variant virus to infect mammalian cells and replicate with IC50 values of 0.5 and 360 mg/ml for NapFFTLUFLTUTEKKKK and NapFFMLUFLMUMEKKKK, respectively. Most impressively, 1 mg/ml of NapFFTLUFLTUTEKKKK resulted in a 2 log reduction in pseudovirus replication after just 15 min at a viral load of 10⁶ copies/ml. Results further confirmed that the peptides continued to passivate the SARS-CoV-2 Omicron variant for up to one week and were stable in cell culture media before being added to the virus. Mechanistically, in vitro results showed selective binding of the peptides to the SARS-CoV-2 Omicron variant envelop protein over the more frequently mutated spike protein up to one week demonstrating the stability of the peptides. Cytotoxicity studies with fibroblasts also showed no toxicity when exposed to the peptides for 72 h. In summary, the present results strongly suggest that the two peptides developed in this study should be further researched for a wide range of anti-SARS-CoV-2 virus applications, including the present Omicron and future mutations.