Mechanism of Action of Small-Molecule Agents in Ongoing Clinical Trials for SARS-CoV-2: A Review

ML241 Antagonizes ERK 1/2 Activation and Inhibits Rotavirus Proliferation

Rotavirus (RV) is the main pathogen that causes severe diarrhea in infants and children under 5 years of age. No specific antiviral therapies or licensed anti-rotavirus drugs are available. It is crucial to develop effective and low-toxicity anti-rotavirus small-molecule drugs that act on novel host targets. In this study, a new anti-rotavirus compound was selected by ELISA, and cell activity was detected from 453 small-molecule compounds. The anti-RV effects and underlying mechanisms of the screened compounds were explored. In vitro experimental results showed that the small-molecule compound ML241 has a good effect on inhibiting rotavirus proliferation and has low cytotoxicity during the virus adsorption, cell entry, and replication stages. In addition to its in vitro effects, ML241 also exerted anti-RV effects in a suckling mouse model. Transcriptome sequencing was performed after adding ML241 to cells infected with RV. The results showed that ML241 inhibited the phosphorylation of ERK1/2 in the MAPK signaling pathway, thereby inhibiting IκBα, activating the NF-κB signaling pathway, and playing an anti-RV role. These results provide an experimental basis for specific anti-RV small-molecule compounds or compound combinations, which is beneficial for the development of anti-RV drugs.

Cell-specific genome-scale metabolic modeling of SARS-CoV-2-infected lung to identify antiviral enzymes

Computational systems biology plays a key role in the discovery of suitable antiviral targets. We designed a cell-specific, constraint-based modeling technique for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected lungs. We used the gene sequence of the alpha variant of SARS-CoV-2 to build a viral biomass reaction (VBR). We also used the mass proportion of lipids between the viral biomass and its host cell to estimate the stoichiometric coefficients of viral lipids in the reaction. We then integrated the VBR, the gene expression of the alpha variant of SARS-CoV-2, and the generic human metabolic network Recon3D to reconstruct a cell-specific genome-scale metabolic model. An antiviral target discovery (AVTD) platform was introduced using this model to identify therapeutic drug targets for combating COVID-19. The AVTD platform not only identified antiviral genes for eliminating viral replication but also predicted side effects of treatments. Our computational results revealed that knocking out dihydroorotate dehydrogenase (DHODH) might reduce the synthesis rate of cytidine-5'-triphosphate and uridine-5'-triphosphate, which terminate the viral building blocks of DNA and RNA for SARS-CoV-2 replication. Our results also indicated that DHODH is a promising antiviral target that causes minor side effects, which is consistent with the results of recent reports. Moreover, we discovered that the genes that participate in the de novo biosynthesis of glycerophospholipids and ceramides become unidentifiable if the VBR does not involve the stoichiometry of lipids.

[Respiratory viral infections : Under special consideration of severe acute respiratory syndrome coronavirus 2 and influenza viruses]

Respiratory viruses cause the highest number of morbidities and deaths annually among all infectious pathogens. This article discusses the current epidemiology, pathogenesis, risk factors, and drug treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza viruses, respiratory syncytial virus (RSV), and other respiratory viruses. The SARS-CoV‑2 and influenza are preventable with vaccines and a first vaccine against RSV is available since 08/2023. For infections with SARS-CoV‑2 and influenza, a stage-specific (antiviral) drug treatment is also recommended. Due to the high and commonly underestimated disease burden caused by RSV, it must be hoped that antiviral substances will be found in the future. In patients at risk, particular attention should be paid to an adequate vaccination status against respiratory pathogens and if there is clinical suspicion of a viral airway infection, the pathogen should be promptly identified and, if necessary, specific treatment should be carried out. Now that effective vaccinations and antiviral drugs are available, the challenge is to use them for all patients at risk and thus really prevent avoidable infections, severe courses and long-term sequelae.

TMPRSS2 and SARS-CoV-2 SPIKE interaction assay for uHTS

SARS-CoV-2, the coronavirus that causes the disease COVID-19, has claimed millions of lives over the past 2 years. This demands rapid development of effective therapeutic agents that target various phases of the viral replication cycle. The interaction between host transmembrane serine protease 2 (TMPRSS2) and viral SPIKE protein is an important initial step in SARS-CoV-2 infection, offering an opportunity for therapeutic development of viral entry inhibitors. Here, we report the development of a time-resolved fluorescence/Förster resonance energy transfer (TR-FRET) assay for monitoring the TMPRSS2-SPIKE interaction in lysate from cells co-expressing these proteins. The assay was configured in a 384-well-plate format for high-throughput screening with robust assay performance. To enable large-scale compound screening, we further miniaturized the assay into 1536-well ultrahigh-throughput screening (uHTS) format. A pilot screen demonstrated the utilization of the assay for uHTS. Our optimized TR-FRET uHTS assay provides an enabling platform for expanded screening campaigns to discover new classes of small-molecule inhibitors that target the SPIKE and TMPRSS2 protein-protein interaction.

Phase III randomized clinical trial of BV ‐4051, an Ayurvedic polyherbal formulation in moderate SARS‐CoV ‐2 infections and its impact on inflammatory biomarkers

SARS-CoV-2 virus and its variants continue to be a challenge inspite of widespread vaccination and preventive measures. We hypothesized an oral, safe polyherbal formulation with antiinflammatory properties may improve the clinical outcome of this disease. BV-4051, a formulation from four Ayurvedic plants namely Ashwagandha, Boswellia, Ginger and Turmeric was used for the treatment of hospitalized moderate COVID-19 patients along with standard of care (SOC). Patients were randomly assigned to receive BV-4051 or placebo tablets for 14 days, at four sites in India during late 2020 to early 2021. Among 208 randomized subjects, 175 completed the study. In BV-4051 group the mean reduction in duration of illness (p = 0.036), alleviation and severity scores of several symptoms like fever, cough, smell, and taste disorders were statistically significant (p ≤ 0.05). A sub-set analysis of subjects treated with or without Remdesivir as SOC showed mean reduction in duration of illness in BV-4051 (p = 0.030), and severity scores (p ≤ 0.05). Mean difference in Interleukin-6 was statistically significant (p = 0.042) on BV-4051 without Remdesivir. BV-4051 may reduce duration of illness, symptoms severity, Interleukin-6, and prevent the incidence of COVID-19 complications. It may have an adjunctive effect with other SOC. Larger extensive clinical testing may give a better understanding of its effect.

Magnetic triazine-based dendrimer as a versatile nanocarrier for efficient antiviral drugs delivery

Nanoscale engineering is an efficient method for the treatment of multiple infectious diseases. Due to the controllable functionalities, surface properties, and internal cavities, dendrimer-based nanoparticles represent high performance in drug delivery, making their application attractive in pharmaceutical and medicinal chemistry. In this study, a dendritic nanostructure (Fe₃O₄@SiO₂@TAD-G3) was designed and fabricated by grafting a triazine-based dendrimer on a magnetic nanomaterial. The structure of synthesized hybrid nanostructure was characterized by Fourier transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), energy-dispersive X-ray (EDX) spectroscopy, elemental mapping, scanning electron microscopy (SEM), transmission electron microscopy (TEM), thermogravimetric analysis (TGA), and vibrating sample magnetometry (VSM). The prepared nanostructure (Fe₃O₄@SiO₂@TAD-G3) combines the unique properties of magnetic nanoparticles and a hyperbranched dendrimer for biomedical applications. Its dual nature and highly exposed active sites, could make the transportation of drugs to targeted sites of interest through the magnetic field. A study was conducted on model drugs loading (Favipiravir and Zidovudine) and in vitro release behaviour of Fe₃O₄@SiO₂@TAD-G3, which was monitored by ultraviolet spectroscopy. The dendritic nanostructure exhibited high drug-loading capacity for Favipiravir (63.2%) and Zidovudine (76.5%). About (90.8% and 80.2%) and (95.5% and 83.4%) of loaded Favipiravir and Zidovudine were released from Fe₃O₄@SiO₂@TAD-G3 at pH 1.5 and 6.8 respectively, within 600 min and at 37 °C. The initial fast release attributed to the drug molecules on the surface of nanostructure while the drugs incorporated deeply into the pores of the Fe₃O₄@SiO₂@TAD-G3 released with a delay. We proposed that Fe₃O₄@SiO₂@TAD-G3 could be tested as an effective carrier in the targeted (cellular or tissue) delivery of drugs. We think that the prepared nanostructure will not deposit in the liver and lungs due to the small size of the nanoparticles.

Nirmatrelvir/Ritonavir and Molnupiravir in the Treatment of Mild/Moderate COVID-19: Results of a Real-Life Study

Molnupiravir and nirmatrelvir were the first available oral antivirals (OAs) active against SARS-CoV-2. Trials evaluating the efficacy of OAs involved patients unvaccinated and infected with variants different from those currently circulating. We conducted a retrospective study on patients with confirmed SARS-CoV-2 infection treated with OAs during the omicron surge in Italy in order to provide real-life data on the efficacy and safety of OAs during the omicron surge of the COVID-19 pandemic. Among 257 patients, 56.8% received molnupiravir, while 43.2% received nirmatrelvir/ritonavir. Patients in the molnupiravir group were older, had a lower body mass index, and had a higher rate of chronic heart disease than those treated with nirmatrelvir/ritonavir. Three hospitalizations were recorded in the molnupiravir (2.1%) group and one in the nirmatrelvir/ritonavir (0.9%) group. One patient treated with molnupiravir died. The median time to negativity was 8 days in the nirmatrelvir/ritonavir group vs. 10 days in the molnupiravir group, p < 0.01. We recorded 37 ADRs (mainly dysgeusia, diarrhea, and nausea) in 31 individuals (12.1%). Only two patients (0.8%) treated with molnupiravir terminated treatment due to ADRs. In conclusion, in a population of mostly vaccinated patients treated with OAs, we observed a low rate of hospitalization, death, and adverse drug reactions. These rates were lower than those reported in pivotal trials.

A critical overview of current progress for COVID-19: development of vaccines, antiviral drugs, and therapeutic antibodies

The novel coronavirus disease (COVID-19) pandemic remains a global public health crisis, presenting a broad range of challenges. To help address some of the main problems, the scientific community has designed vaccines, diagnostic tools and therapeutics for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. The rapid pace of technology development, especially with regard to vaccines, represents a stunning and historic scientific achievement. Nevertheless, many challenges remain to be overcome, such as improving vaccine and drug treatment efficacies for emergent mutant strains of SARS-CoV-2. Outbreaks of more infectious variants continue to diminish the utility of available vaccines and drugs. Thus, the effectiveness of vaccines and drugs against the most current variants is a primary consideration in the continual analyses of clinical data that supports updated regulatory decisions. The first two vaccines granted Emergency Use Authorizations (EUAs), BNT162b2 and mRNA-1273, still show more than 60% protection efficacy against the most widespread current SARS-CoV-2 variant, Omicron. This variant carries more than 30 mutations in the spike protein, which has largely abrogated the neutralizing effects of therapeutic antibodies. Fortunately, some neutralizing antibodies and antiviral COVID-19 drugs treatments have shown continued clinical benefits. In this review, we provide a framework for understanding the ongoing development efforts for different types of vaccines and therapeutics, including small molecule and antibody drugs. The ripple effects of newly emergent variants, including updates to vaccines and drug repurposing efforts, are summarized. In addition, we summarize the clinical trials supporting the development and distribution of vaccines, small molecule drugs, and therapeutic antibodies with broad-spectrum activity against SARS-CoV-2 strains.

Broad-Spectrum Small-Molecule Inhibitors of the SARS-CoV-2 Spike-ACE2 Protein-Protein Interaction from a Chemical Space of Privileged Protein Binders

Therapeutically useful small-molecule inhibitors (SMIs) of protein−protein interactions (PPIs) initiating the cell attachment and entry of viruses could provide novel alternative antivirals that act via mechanisms similar to that of neutralizing antibodies but retain the advantages of small-molecule drugs such as oral bioavailability and low likelihood of immunogenicity. From screening our library, which is focused around the chemical space of organic dyes to provide good protein binders, we have identified several promising SMIs of the SARS-CoV-2 spike—ACE2 interaction, which is needed for the attachment and cell entry of this coronavirus behind the COVID-19 pandemic. They included organic dyes, such as Congo red, direct violet 1, and Evans blue, which seem to be promiscuous PPI inhibitors, as well as novel drug-like compounds (e.g., DRI-C23041). Here, we show that in addition to the original SARS-CoV-2 strain, these SMIs also inhibit this PPI for variants of concern including delta (B.1.617.2) and omicron (B.1.1.529) as well as HCoV-NL63 with low- or even sub-micromolar activity. They also concentration-dependently inhibited SARS-CoV-2-S expressing pseudovirus entry into hACE2-expressing cells with low micromolar activity (IC50 < 10 μM) both for the original strain and the delta variant. DRI-C23041 showed good therapeutic (selectivity) index, i.e., separation between activity and cytotoxicity (TI > 100). Specificities and activities require further optimization; nevertheless, these results provide a promising starting point toward novel broad-spectrum small-molecule antivirals that act via blocking the interaction between the spike proteins of coronaviruses and their ACE2 receptor initiating cellular entry.

Paxlovid: Mechanism of Action, Synthesis, and In Silico Study

In this work, the discovery and description of PF-07321332, a major bioavailable oral SARS-CoV-2 protease inhibitor with in vitro human coronavirus antiviral activity, and excellent selection of off-target and in vivo immune profiles are reported. Various drugs and novel compound candidates for the treatment of the COVID-19 pandemic have been developed. PF-07321332 (or nirmatrelvir) is a new oral antiviral drug developed by Pfizer. In response to the pandemic, Pfizer has developed the COVID vaccine and in 2022 will launch its new major anti-SARS-Cov-2 protease inhibitor (PI). The combination of ritonavir and nirmatrelvir is under study in phase III of the clinical trial with a brand name Paxlovid. Paxlovid is an active 3Cl protease inhibitor. Paxlovid exerts its antiviral efficacy by inhibiting a necessary protease in the viral replication procedure. Proteases of coronavirus cleave several sites in the viral polyprotein where pyrrolidone was replaced by flexible glutamine. Due to the coronavirus pandemic, there is high demand for synthesis and development of this novel drug. Herein, we report the synthetic route and the mechanism of action was recently published on nirmatrelvir. Also, a comparison of the performance of two new oral antiviruses (molnupiravir and nirmatrelvir) for the treatment of COVID-19 is described. This review will be helpful for different disciplines such as biochemistry, organic chemistry, medicinal chemistry, and pharmacology.