We present a net-shaped DNA nanostructure (called “DNA Net” herein) design strategy for selective recognition and high-affinity capture of the intact SARS-CoV-2 virions through spatial pattern-matching and multivalent interactions between the aptamers (targeting wild type spike-RBD) positioned on the DNA Net and the trimeric spike glycoproteins displayed on the viral outer surface. Carrying a designer nanoswitch, the DNA Net-aptamers releases fluorescent signal upon virus binding that is easily read by a hand-held fluorimeter for a rapid (in 10 mins), simple (mix- and-read), sensitive (PCR equivalent), room temperature compatible, and inexpensive (∼ $1.26/test) COVID-19 test assay. The DNA Net-aptamers also impede authentic wild-type SARS-CoV-2 infection in cell culture with a near 1×103-fold enhancement of the monomeric aptamer. Furthermore, our DNA Net design principle and strategy can be customized to tackle other life-threatening and economically influential viruses like influenza and HIV, whose surfaces carry class-I viral envelope glycoproteins like the SARS-CoV-2 spikes in trimeric forms.

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Net-Shaped DNA Nanostructures Designed for Rapid/Sensitive Detection and Potential Inhibition of the SARS-CoV-2 Virus

/pdf/oral-antiviral-treatments-for-covid-19-opportunities-and-1h5knpbr.pdf

Oral antiviral treatments for COVID-19: opportunities and challenges

COVID‐19, caused by SARS‐CoV‐2 infection, continues to be a major public health crisis around the globe. Development of vaccines and the first cluster of antiviral drugs has brought promise and hope for prevention and treatment of severe coronavirus disease. However, continued development of newer, safer, and more effective antiviral drugs are critically important to combat COVID‐19 and counter the looming pathogenic variants. Studies of the coronavirus life cycle revealed several important biochemical targets for drug development. In the present review, we focus on recent drug design and medicinal chemistry efforts in small molecule drug discovery, including the development of nirmatrelvir that targets viral protein synthesis and remdesivir and molnupiravir that target viral RdRp. These are recent FDA approved drugs for the treatment of COVID‐19.

Recent Drug Development and Medicinal Chemistry Approaches for the Treatment of SARS‐CoV‐2 and Covid‐19

We present a net-shaped DNA nanostructure (called “DNA Net” herein) design strategy for selective recognition and high-affinity capture of intact SARS-CoV-2 virions through spatial pattern-matching and multivalent interactions between the aptamers (targeting wild-type spike-RBD) positioned on the DNA Net and the trimeric spike glycoproteins displayed on the viral outer surface. Carrying a designer nanoswitch, the DNA Net-aptamers release fluorescence signals upon virus binding that are easily read with a handheld fluorimeter for a rapid (in 10 min), simple (mix-and-read), sensitive (PCR equivalent), room temperature compatible, and inexpensive (∼$1.26/test) COVID-19 test assay. The DNA Net-aptamers also impede authentic wild-type SARS-CoV-2 infection in cell culture with a near 1 × 103-fold enhancement of the monomeric aptamer. Furthermore, our DNA Net design principle and strategy can be customized to tackle other life-threatening and economically influential viruses like influenza and HIV, whose surfaces carry class-I viral envelope glycoproteins like the SARS-CoV-2 spikes in trimeric forms. 

Abstract The outbreak of COVID-19 has become a global crisis, and brought severe disruptions to societies and economies. Until now, effective therapeutics against COVID-19 are in high demand. Along with our improved understanding of the structure, function, and pathogenic process of SARS-CoV-2, many small molecules with potential anti-COVID-19 effects have been developed. So far, several antiviral strategies were explored. Besides directly inhibition of viral proteins such as RdRp and M pro , interference of host enzymes including ACE2 and proteases, and blocking relevant immunoregulatory pathways represented by JAK/STAT, BTK, NF-κB, and NLRP3 pathways, are regarded feasible in drug development. The development of small molecules to treat COVID-19 has been achieved by several strategies, including computer-aided lead compound design and screening, natural product discovery, drug repurposing, and combination therapy. Several small molecules representative by remdesivir and paxlovid have been proved or authorized emergency use in many countries. And many candidates have entered clinical-trial stage. Nevertheless, due to the epidemiological features and variability issues of SARS-CoV-2, it is necessary to continue exploring novel strategies against COVID-19. This review discusses the current findings in the development of small molecules for COVID-19 treatment. Moreover, their detailed mechanism of action, chemical structures, and preclinical and clinical efficacies are discussed. 

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Small molecules in the treatment of COVID-19

Emerging SARS-CoV-2 variants continue to cause waves of new infections globally. Developing effective antivirals against SARS-CoV-2 and its variants is an urgent task. The main protease (Mpro) of SARS-CoV-2 is an attractive drug target because of its central role in viral replication and its conservation among variants. We herein report a series of potent α-ketoamide-containing Mpro inhibitors obtained using the Ugi four-component reaction. The prioritized compound, Y180, showed an IC50 of 8.1 nM against SARS-CoV-2 Mpro and had oral bioavailability of 92.9%, 31.9% and 85.7% in mice, rats and dogs, respectively. Y180 protected against wild-type SARS-CoV-2, B.1.1.7 (Alpha), B.1.617.1 (Kappa) and P.3 (Theta), with EC50 of 11.4, 20.3, 34.4 and 23.7 nM, respectively. Oral treatment with Y180 displayed a remarkable antiviral potency and substantially ameliorated the virus-induced tissue damage in both nasal turbinate and lung of B.1.1.7-infected K18-human ACE2 (K18-hACE2) transgenic mice. Therapeutic treatment with Y180 improved the survival of mice from 0 to 44.4% (P = 0.0086) upon B.1.617.1 infection in the lethal infection model. Importantly, Y180 was also highly effective against the B.1.1.529 (Omicron) variant both in vitro and in vivo. Overall, our study provides a promising lead compound for oral drug development against SARS-CoV-2. An inhibitor of the SARS-CoV-2 main protease (Mpro), Y180, showed therapeutic efficacy against wild-type SARS-CoV-2 and its variants including Omicron after oral administration and improved survival in a humanized mouse model. 

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An orally available Mpro inhibitor is effective against wild-type SARS-CoV-2 and variants including Omicron

Rapid testing, generally refers to the paper-based diagnostic platform known as “lateral flow assay” (LFA), has emerged as a critical asset to the containment of coronavirus disease 2019 (COVID-19) around the world. LFA technology stands out amongst peer platforms due to its cost-effective design, user-friendly interface, and low sample-to-readout times. This article aims to introduce its design, use, and practicality for the purpose of diagnosing SARS-CoV-2 infection. A connection is made from the normal COVID-19 immune response to the design and efficacy of rapid testing. Interference in test results is a challenge shared by most diagnostic platforms and can be rooted in various underlying issues. The current knowledge and situation about interference in rapid COVID-19 tests due to variant strains as well as vaccination are discussed. The cost and societal impact are reviewed as they play important roles in determining how to properly implement public testing practices. Perspectives on improving the performance, especially detection sensitivity, of LFA for COVID-19 are provided. Graphical abstract

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Rapid testing for coronavirus disease 2019 (COVID-19)

HIV-1 subtype B gag genes were cloned from the infected paid blood donors in Henan, and the consensus sequence based on these prevalent strains was obtained by aligning. The codons of the consensus gag sequence were modified according to mammalian codon usage. Western blot analysis was used to compare the expression level of wild type and codon-modified gag gene. It was found that the expression level of Gag protein was improved largely by codon-modification. Then the mod. gag gene was inserted into the adenovirus vector and the recombinant adenovirus rAdV-mod. gag was constructed. 10(8) PFU or 10(9) PFU rAdV-mod, gag vaccinated mice twicely could elicit high level Gag-specific CTL responses in immunized mice. In conclusion,the codon modification of gag gene is successful. The recombinant adenovirus vaccine harbouring mod. gag can induce robust Gag-specific CTL immune response in mice.

[Codon modification of HIV-1 subtype B gag gene and its immunogenicity in mice].

OBJECTIVE To study the immune effect of a chimeric adenovirus type 5 vector with type 35 fiber (rAd5/F35) vaccine in BALB/c mice. METHODS The expression of HIV Gag protein was determined using indirect immunofluorescent staining. The rAd5/F35-mod.gag vector was injected intramuscularly to mice. The IgG antibody was detected by ELISA and CTL response was detected by intracellular cytokine stain assay. RESULTS The rAd5/F35-mod.gag vector could express HIV Gag protein in vitro and generate strong HIV-specific immune responses in vivo. But anti-Ad5 immunity could limit its immunogenicity in vivo. CONCLUSION The rAd5/F35-mod.gag vector can elicit specific CTL response and IgG antibody in animal model. In mice with high Ad5 vector-specific immunity, Ad5/F35-mod.gag showed lower level of Gag specific CTL and antibody response than in mice without pre-existing adenovirus type 5 immunity. The results indicated that fiber exchange alone does not evade pre-existing Ad5 immunity.

Xin-lei Liu

Papers

An orally available Mpro inhibitor is effective against wild-type SARS-CoV-2 and variants including Omicron

Rapid testing for coronavirus disease 2019 (COVID-19)

[Codon modification of HIV-1 subtype B gag gene and its immunogenicity in mice].

[Immunogenicity of a chimeric adenovirus type 5 vector with type 35 fiber containing HIV-1 gag in mice].