Small Molecule Antiviral Drugs Research Articles

The Design, Synthesis and Mechanism of Action of Paxlovid, a Protease Inhibitor Drug Combination for the Treatment of COVID-19.

The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has presented an enormous challenge to health care systems and medicine. As a result of global research efforts aimed at preventing and effectively treating SARS-CoV-2 infection, vaccines with fundamentally new mechanisms of action and some small-molecule antiviral drugs targeting key proteins in the viral cycle have been developed. The most effective small-molecule drug approved to date for the treatment of COVID-19 is PaxlovidTM, which is a combination of two protease inhibitors, nirmatrelvir and ritonavir. Nirmatrelvir is a reversible covalent peptidomimetic inhibitor of the main protease (Mpro) of SARS-CoV-2, which enzyme plays a crucial role in viral reproduction. In this combination, ritonavir serves as a pharmacokinetic enhancer, it irreversibly inhibits the cytochrome CYP3A4 enzyme responsible for the rapid metabolism of nirmatrelvir, thereby increasing the half-life and bioavailability of nirmatrelvir. In this tutorial review, we summarize the development and pharmaceutical chemistry aspects of Paxlovid, covering the evolution of protease inhibitors, the warhead design, synthesis and the mechanism of action of nirmatrelvir, as well as the synthesis of ritonavir and its CYP3A4 inhibition mechanism. The efficacy of Paxlovid to novel virus mutants is also overviewed.

Small-molecule anti-COVID-19 drugs and a focus on China's homegrown mindeudesivir (VV116).

The coronavirus disease 2019 (COVID-19) pandemic has stimulated tremendous efforts to develop therapeutic agents that target severe acute respiratory syndrome coronavirus 2 to control viral infection. So far, a few small-molecule antiviral drugs, including nirmatrelvir-ritonavir (Paxlovid), remdesivir, and molnupiravir have been marketed for the treatment of COVID-19. Nirmatrelvir-ritonavir has been recommended by the World Health Organization as an early treatment for outpatients with mild-to-moderate COVID-19. However, the existing treatment options have limitations, and effective treatment strategies that are cost-effective and convenient for tackling COVID-19 are still needed. To date, four domestically developed oral anti-COVID-19 drugs have been granted conditional market approval in China. These drugs include azvudine, simnotrelvir-ritonavir (Xiannuoxin), leritrelvir, and mindeudesivir (VV116). Preclinical and clinical studies have explored the efficacy and tolerability of mindeudesivir and supported its early use in mild-to-moderate COVID-19 cases at high risk for progression. In this review, we discuss the most recent findings regarding the pharmacological mechanism and therapeutic effects focusing on mindeudesivir and other small-molecule antiviral agents for COVID-19. These findings will expand our understanding and highlight the potential widespread application of China's homegrown anti-COVID-19 drugs.

Omicron related COVID-19 prevention and treatment measures for patients with hematological malignancy and strategies for modifying hematologic treatment regimes

The Omicron variant of SARS-CoV-2 has rapidly become the dominant strain worldwide due to its high transmissibility, although it appears to be less pathogenic than previous strains. However, individuals with hematological malignancy (HM) and COVID-19 remain susceptible to severe infection and mortality, especially those with chronic lymphocytic leukemia (CLL) and those undergoing chimeric antigen receptor T-cell (CAR-T) treatment. Hematologists should thoroughly assess the severity of the patient’s hematological disease and the potential risk of SARS-CoV-2 infection before initiating chemotherapy or immunosuppressive treatment. Vaccination and booster doses are strongly recommended and patients with a poor vaccine response may benefit from long-acting COVID-19 neutralizing monoclonal antibodies (such as Evusheld). Early use of small molecule antiviral drugs is recommended for managing mild COVID-19 in HM patients and those with severe immunodeficiency may benefit from SARS-CoV-2 neutralizing monoclonal antibody therapy and high-titer COVID-19 convalescent plasma (CCP). For moderate to severe cases, low-dose glucocorticoids in combination with early antiviral treatment can be administered, with cytokine receptor antagonists or JAK inhibitors added if the condition persists or worsens. In the treatment of hematological malignancies, delaying chemotherapy is preferable for CLL, acute leukemia (AL), and low-risk myelodysplastic syndrome (MDS), but if the disease progresses, appropriate adjustments in dosage and frequency of treatment are required, with the avoidance of anti-CD20 monoclonal antibody, CAR-T and hematopoietic stem cell transplantation (HSCT). Patients with chronic myelocytic leukemia (CML) and myeloproliferative neoplasms (MPNs) can continue current treatment. What’s more, non-drug protective measures, the development of new vaccines and antiviral drugs, and monitoring of mutations in immunocompromised populations are particularly important.

Grp94 Inhibitor HCP1 Suppressed the Replication of SVA in BHK-21 Cells and PK-15 Cells.

Glucoregulatory protein 94 (Grp94) is necessary for the post-viral life cycle and plays a quality control role in viral proteins, but the role of Grp94 in regulating viral replication in host cells is not well known. Therefore, finding a compound that can regulate Grp94 will help us to study the mechanism of viral replication. Previously, we synthesized a coumarin pyrazoline derivative HCP1 that is an effective inhibitor of Grp94. We suppose that HCP1 may inhibit viral replication. This study aimed to investigate the effect of HCP1 on the replication ability of Senecavirus A (SVA), so as to provide a target and a leading compound for revealing the pathogenic mechanism of the virus and developing antiviral drugs. Rat cell lines BHK-21 and porcine cell lines PK-15 were infected with SVA, and the infected cells were treated with different concentrations of HCP1. The cell viability (CCK-8), virus titer (TCID50), autophagy level, and Grp94 expression were measured. The results showed that a low concentration of HCP1 decreased viral titer and viral load in BHK-21 and PK-15 cells, and 5μM HCP1 significantly decreased the expression of SVA VP2 protein. In addition, SVA infection can lead to an increased level of autophagy, and HCP1 can inhibit host cell autophagy caused by SVA infection, thereby inhibiting viral replication and infection. These findings reveal that Grp94 is a key factor in controlling SVA replication, and its inhibitor HCP1 suppresses SVA replication by inhibiting the increase of Grp94 protein level and autophagy induced by SVA. This study will contribute to the development of a new class of small-molecule antiviral drugs.

Therapeutic strategies for COVID-19: progress and lessons learned.

The coronavirus disease 2019 (COVID-19) pandemic has stimulated tremendous efforts to develop therapeutic strategies that target severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and/or human proteins to control viral infection, encompassing hundreds of potential drugs and thousands of patients in clinical trials. So far, a few small-molecule antiviral drugs (nirmatrelvir-ritonavir, remdesivir and molnupiravir) and 11 monoclonal antibodies have been marketed for the treatment of COVID-19, mostly requiring administration within 10 days of symptom onset. In addition, hospitalized patients with severe or critical COVID-19 may benefit from treatment with previously approved immunomodulatory drugs, including glucocorticoids such as dexamethasone, cytokine antagonists such as tocilizumab and Janus kinase inhibitors such as baricitinib. Here, we summarize progress with COVID-19 drug discovery, based on accumulated findings since the pandemic began and a comprehensive list of clinical and preclinical inhibitors with anti-coronavirus activities. We also discuss the lessons learned from COVID-19 and other infectious diseases with regard to drug repurposing strategies, pan-coronavirus drug targets, in vitro assays and animal models, and platform trial design for the development of therapeutics to tackle COVID-19, long COVID and pathogenic coronaviruses in future outbreaks.

Tucaresol: A Unique Oral Candidate Drug Ideally Accessible For Treatment Of Covid-19 Disease

The SARS-CoV-2 pandemic has significantly impacted world health and economic status. In response, much work has been undertaken to provide effective, safe vaccines, antibodies and antiviral drugs with which to address this pandemic. Treatment of a pandemic population presents multiple challenges in addition to the primary issue of drug efficacy and safety, such as large scale drug manufacture and distribution, drug stability, oral dosing and pharmacoeconomic considerations. Ideally, these factors must be addressed if new candidate drugs are to be advanced for treatment of large (pandemic) populations. Subsequently, new antivirals have reached the market but choices are few. According to the NIH Covid Treatment Guidelines, only three small molecule antiviral drugs are available to treat COVID-19 disease. As such, a significant part of the research towards discovery of new antiviral drugs has focused on screening and evaluation of ‘repurposed drugs’ or previously approved or clinical stage drugs. Yet, in spite of this increased research activity, one promising clinical stage candidate drug has received little attention regarding its potential as a monotherapy or component of combination therapy for treatment of COVID-19 disease. Tucaresol, with documented human safety and pharmacokinetic data, is an orally active, stable, small molecule amenable to large scale manufacture by a proprietary two-step synthesis developed by us. Tucaresol functions as a host-targeted antiviral by selective protection/reconstitution of CD4+ T helper cells as demonstrated in HIV patients and SIV macaques. In view of similarities between HIV and SARS-CoV-2, especially with respect to host CD4+ T helper cells, and the suitability of Tucaresol for facile treatment of pandemic populations, Tucaresol is presented herein for treatment of mild-to-moderate COVID-19 patients but may also be useful for treatment of advanced disease accompanied by lymphopenia.

Expert Consensus on Prevention and Treatment of COVID-19 Infection in Patients with Lung Cancer.

Corona virus disease 2019 (COVID-19) infection has become a major public health issue affecting human health. The main goal of epidemic prevention and control at the current stage in China is to "protect people's health and prevent severe cases". Patients with lung cancer who receive antitumor therapy have low immunity, and the risk of severe illness and death once infected is much higher than healthy people, so they are vulnerable to COVID-19 infection. At present, less attention has been paid to the prevention and treatment of COVID-19 infection in patients with lung cancer in domestic guidelines and consensus. Based on the published data in China and abroad, we proposed recommendations and formed expert consensus on the vaccination of COVID-19, the use of neutralizing antibodies and small molecule antiviral drugs for patients with lung cancer, for physician's reference.

Dietary phytochemicals against COVID‐19: A focus on thymoquinone

It has been three years since the outbreak of the Coronavirus disease 2019 (COVID-19) at the end of 2019 in Wuhan, China, which is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). So far, over six million people around the world have died of COVID-19 (Murakami et al., 2023). With huge efforts from both academic and industrial organizations worldwide, the development of various types of vaccines and several new drugs has been made and the situation has been significantly improved to fight against the virus (Murakami et al., 2023). Regarding new medicines or treatments approved by Food and Drug Administration, USA, so far, they include anti-inflammatory agents (e.g., dexamethasone and Baricitinib), anti-SARS-CoV-2 (neutralizing) monoclonal antibody (mAbs), antivirals (Remdesivir, Paxlovid, and Molnupiravir), and antithrombotics. The mAbs can bind to the viral spike proteins, and block the virus attachment to host cell surface proteins, therefore reducing the viral load. Remdesivir is an inhibitor of RNA-dependent RNA-polymerase (RdRp), which is essential to virus genome replication. Paxlovid is a combination of Nirmatrelvir and Ritonavir, which acts as an oral SARS-CoV-2 Mpro (or 3CL) protease inhibitor to stop viral replication and a strong cytochrome P450 3A4 inhibitor as a booster of the pharmacokinetics of Nirmatrelvir, respectively (Murakami et al., 2023). However, new mutant variants of coronaviruses are emerging, which could cause the loss of the efficacy of the approved vaccines, mAbs, and small molecule antiviral drugs, exposing the elderly and those with chronic conditions, such as diabetes and cancers. Moreover, many drugs such as mAbs and Paxlovid are expensive and not easily available in developing countries. Therefore, novel vaccines, effective therapies, and affordable management, such as phytochemicals, are highly desirable. Plants, including food and traditional herbs, have benefited human beings over thousands of years. To fight coronavirus, herbal medicines have been explored to treat COVID patients across the world. Many nutrients in food play important roles by boosting the immune system and/or reducing viral respiratory tract infections (Omer et al., 2022). For example, Zinc as an antioxidant mineral (Dhawan et al., 2022), and vitamin D in food (Wimalawansa, 2022) can exhibit immunomodulatory and anti-inflammatory properties. Honey, rich in nutrients and bioactive compounds, is recommended by National Health Service, England to ease a cough in COVID-19 patients (www.nhs.uk). Numerous phytochemicals such as flavonoids including quercetin (e.g., apples, onions, parsley, and sage), kaempferol (spinach and kale), isoliquiritigenin (soybean and shallots), tangeretin (tangerine), and baicalein (Scutellaria baicalensis, Huang-qin) (Song et al., 2021) (Figure 1) are shown to be inhibitors of SARS-CoV-2 Mpro with a similar mechanism as Nirmatrelvir in Paxlovid (Mandal et al., 2021). Other phenolics such as epigallocatechin gallate (green tea) and hesperidin (citrus fruits) (Figure 1) could inhibit RdRp activity in a similar way as Remdesivir (Bahun et al., 2022; Omer et al., 2022). Thymoquinone (TQ, Figure 1) is the major bioactive compound in N. sativa, black cumin seed (Johnson-Ajinwo & Li, 2014). It shows antiviral, antimalarial, anticancer (Johnson-Ajinwo et al., 2018), anti-inflammatory, and immunomodulatory (Ahmad et al., 2020; Khazdair et al., 2021) activities. Various reviews relating to the roles of TQ and N. sativa in COVID-19 have been published (Abdelrahim et al., 2022; Ahmad et al., 2020; He et al., 2022; Islam et al., 2021; Khazdair et al., 2021; Kulyar et al., 2021; Taysi et al., 2022). Here, this update is focused on its direct applications in targeting the SARS-CoV-2 virus in silico, in vitro, in vivo, and in clinical trials. Docking studies suggested TQ can bind human angiotensin-converting enzyme 2 (ACE2) as the receptor of SARS-CoV-2 spike proteins (Jakhmola Mani et al., 2022; Srivastava et al., 2021; Xu et al., 2021) and a sheddase ADAM7 (a membrane-bound metalloprotease) associated with the modulation of ACE2 (He et al., 2022), thus blocking the virus entry to human cells. Further studies show that TQ binds to SARS-CoV-2 Mpro via interaction with the active site (His41 and Cys145) and the Glu166 (Abdallah et al., 2022; Khan et al., 2024; Ullah et al., 2022). TQ as an unsubstituted quinone has inherent reactivity to free cysteine via thiol addition reaction (Li et al., 2005; Lu et al., 2010). TQ can covalently bind to the free cysteines of human hemoglobin (unpublished). Thus, it is highly likely that TQ can also covalently bind to the free catalytic cysteine (Cys145) residue of the protease as Nirmatrelvir does. TQ was found to inhibit the replication of SARS-CoV-2 and SARS-CoV after infecting HEK293-ACE2 cells, with IC50 of 5.0 and 7.6 μM, respectively (Xu et al., 2021). TQ shows relatively high cytotoxicity in in vitro assessment of SARS-CoV-2 (hCoV-19/Egypt/NRC-03/2020) (Abdallah et al., 2022). TQ inhibits four further SARS-CoV-2 variants (Omicron, 614D, Delta, UK, Brazil) in infection of HEK293-ACE2 cells with an IC50 value range between 1 and 3 µM (Bencheqroun et al., 2022). Compared with IC50 of Nirmatrelvir at the nanomolar range (Rosales et al., 2022), these values seem to be much greater. Future structure modification of TQ (Johnson-Ajinwo et al., 2018) or its use in combination with other approved antiviral drugs could enhance its activity. TQ showed protective effects against acute kidney damage (AKI) in septic BALB/c mice caused by cecal ligation and puncture (Guo et al., 2020). However, there are no reported studies of the effect of TQ or N. sativa oils/extracts on the SARS-CoV-2 -infected animal models. A phase I clinical trial study showed that TQ-rich black cumin oil (containing 5% of TQ) was safe at 200 mg/adult/day (Thomas et al., 2022). A phase II clinical trial of oral N. sativa oil in adult patients with mild COVID-19 was carried out in Saudi Arabia (clinicaltrials.gov, Identifier: NCT04401202 on) (Koshak et al., 2021). A total of 173 patients, with an average age of 36 ± 11 years, were randomly divided into a treatment group (86) and a control group (87). The treatment group was treated with two N. sativa oil (NSO, 500 mg) capsules per day for 10 days, whilst the control group received standard treatment (Koshak et al., 2020). The percentages of recovered patients in the treatment and control groups were 62% (mean duration of recovery, 10.7 ± 3.2 days) and 36% (12.3 ± 2.8 days), respectively. These results indicated that NSO treatment could cause faster recovery of symptoms than usual care alone. A clinical trial was carried out using honey and N. sativa seeds (HNS) for the treatment of COVID-19 patients with moderate or severe conditions, from April to July 2020 in Pakistan (ClinicalTrials.gov; Identifier: NCT04347382). Among the moderate cases, 210 patients were randomly assigned to either receive a combination of honey (1 g/kg/day), N. sativa seeds (80 mg/kg/day), and standard care, or a placebo along with standard care. Among the severe cases, 50 were given HNS and 53 the placebo. HNS caused ~50% decrease in time taken to improve symptoms as compared with the placebo (moderate cases, 4 vs. 7 days; Hazard Ratio [HR], 6.1; p < 0.0001 and for severe cases, 6 vs. 13 days; HR, 4.0; p < 0.0001). HNS also cleared the virus earlier than the placebo in both moderate cases (6 vs. 10 days; HR, 5.5; p < 0.0001) and severe cases (8.5 vs. 12 days; HR, 4.3; p < 0.0001). In severe cases, the mortality rate was less than 25% in the HNS group than in the placebo group (4% vs. 18.9%; odds ratio (OR), 0.18; p = 0.03). HNS significantly improved symptoms, sped up viral load clearance, and reduced mortality in COVID-19 patients. A clinical trial was carried out to evaluate the efficacy and safety of a Persian herbal medicine formula (extract of the Glycyrrhiza glabra, Punica granatum, and Rheum palmatum) along with N. sativa powder among patients with COVID-19 from June to September 2020 in Iran (Registration: Iranian Registry of Clinical Trials [www.irct.ir]: IRCT20200330046899N1). In total, 79 cases (mean age, 59.1 ± 17.1 years) completed the trial. The combined treatment significantly improved the symptoms and decreased the mean hospitalization days by 3 ± 0.4 days (Setayesh et al., 2022). A clinical trial was carried out to study the effects of N. sativa and/or vitamin D3 on COVID-19 and the alleviation of symptoms (ClinicalTrials.gov, Identifier: NCT04981743). In total, 120 COVID-19 patients with mild to moderate symptoms were recruited and randomly assigned to four groups with 30 patients each. Groups 1–4 received an oral dose of 900 mg N. sativa twice daily for 14 days, 2000 IU of vitamin D3, 900 mg of N. sativa and 2000 IU of vitamin D3, and none of these two agents, respectively. All groups received standard therapy at the same time. The combination of N. sativa–vitamin D3 besides the standard therapy significantly alleviated most COVID-19 symptoms. Virus clearing test by quantitative polymerase chain reaction on the 7th and 14th day of treatment indicated that the N. sativa and vitamin D3 combination is the best among the four treatments, where the values of the OR on the 7th and 14th day were 0.13 and 0.09, respectively (Said et al., 2022). A randomized, double-blind, placebo-controlled phase II trial from May to September of 2021 in the USA (ClinicalTrials.gov, Identifier: NCT04914377) was conducted to assess the safety and efficacy of a patent thymoquinone formula (TQF) derived from N. sativa oil containing 1.7% of TQ. A total of 55 symptomatic SARS-CoV-2 adult patients (>18 years) were randomly assigned to receive oral TQF (29) or a placebo (26). The results showed that the median time-to-sustained-clinical-response (SCR) was 6 days in the TQF treatment versus 8 days in the placebo group (p = 0.77). However, while the SCR difference is not significant, the trend towards the benefit of using TQF is encouraging. There was no significant difference in the rate of adverse events (p = 0.16), indicating its safety, which is consistent with a previous Phase 1 study (Thomas et al., 2022). TQF significantly improved the total symptom burden faster (p < 0.001), and increased cytotoxic CD4+ (p = 0.04) and helper CD8+ (p = 0.04) central memory T lymphocytes (Bencheqroun et al., 2022). Four phase II clinical studies across the world using N. sativa alone or in combination with other herbs or honey or vitamin D3 have been conducted. All these studies indicated some benefits of treating COVID-19 patients with N. sativa. However, the quality of these studies varied and the numbers of patients recruited were generally small. The content of the bioactive compound-TQ might vary a lot across these studies, so the clinical performance of the N. sativa could be different as observed. Also, only single doses of these products were used. It would be good to carry out future clinical trials using standardized products by quantifying TQ content in the N. sativa extract or oils (Bencheqroun et al., 2022; Johnson-Ajinwo & Li, 2014) or even use the pure TQ formulation at different doses with a larger number of patients in a randomized, double-blind, and placebo-controlled manner (Bencheqroun et al., 2022). Considering the benefits of honey in managing COVID-19, the preparation of a combination of honey with N. sativa oil with a determined quantity of TQ is also recommended for future clinical investigation against COVID-19 or other diseases. Phytochemical constituents in foods, fruits, herbs, and spices may provide preventive and even adjunct therapeutic effects on COVID-19 patients via multiple mechanisms. The widely available and cheap N. sativa and its bioactive compound-TQ could be further explored for their application in fighting COVID-19.

NFκB and Cyclic AMP Response Element Sites Mediate the Valproic Acid and UL138 Responsiveness of the Human Cytomegalovirus Major Immediate Early Enhancer and Promoter.

The major immediate early enhancer and promoter (MIEP) of human cytomegalovirus (HCMV) drives the transcription of the immediate early one (IE1) and IE2 genes, whose encoded proteins stimulate productive, lytic replication. The MIEP is activated by the virally encoded and tegument-delivered pp71 protein at the start of de novo lytic infections of fully differentiated cells. Conversely, the MIEP is silenced at the start of de novo latent infections within incompletely differentiated myeloid cells in part because tegument-delivered pp71 is sequestered in the cytoplasm in these cells, but also by viral factors that repress transcription from this locus, including the UL138 protein. During both modes of infection, MIEP activity can be increased by the histone deacetylase inhibitor valproic acid (VPA); however, UL138 inhibits the VPA-responsiveness of the MIEP. Here, we show that two families of cellular transcription factors, NF-κB and cAMP response element-binding protein (CREB), together control the VPA-mediated activation and UL138-mediated repression of the HCMV MIEP. IMPORTANCE Artificial regulation of the HCMV MIEP, either activation or repression, is an attractive potential means to target the latent reservoirs of virus for which there is currently no available intervention. The MIEP could be repressed to prevent latency reactivation or induced to drive the virus into the lytic stage that is visible to the immune system and inhibited by multiple small-molecule antiviral drugs. Understanding how the MIEP is regulated is a critical part of designing and implementing either strategy. Our revelation here that NF-κB and CREB control the responsiveness of the MIEP to the viral UL138 protein and the FDA-approved drug VPA could help in the formulation and execution of promoter regulatory strategies against latent HCMV.

Tucaresol: A Unique Oral Candidate Drug Ideally Accessible for Treatment Of COVID-19 Disease

The SARS-CoV-2 pandemic has significantly impacted world health and economic status. In response, much work has been undertaken to provide effective, safe vaccines, antibodies and antiviral drugs with which to address this pandemic. Treatment of a pandemic population presents multiple challenges in addition to the primary issue of drug efficacy and safety, such as large-scale drug manufacture and distribution, drug stability, oral dosing and pharmacoeconomic considerations. Ideally, these factors must be addressed if new candidate drugs are to be advanced for treatment of large (pandemic) populations. Subsequently, new antivirals have reached the market but choices are few. According to the NIH Covid Treatment Guidelines, only three small molecule antiviral drugs are available to treat COVID-19 disease. As such, a significant part of the research towards discovery of new antiviral drugs has focused on screening and evaluation of ‘repurposed drugs’ or previously approved or clinical stage drugs. Yet, in spite of this increased research activity, one promising clinical stage candidate drug has received little attention regarding its potential as a monotherapy or component of combination therapy for treatment of COVID-19 disease. Tucaresol, with documented human safety and pharmacokinetic data, is an orally active, stable, small molecule amenable to large scale manufacture by a proprietary two-step synthesis developed by us. Tucaresol functions as a host- targeted antiviral by selective protection/reconstitution of CD4+ T helper cells as demonstrated in HIV patients and SIV macaques. In view of similarities between HIV and SARSCoV-2, especially with respect to host CD4+ T helper cells, and the suitability of Tucaresol for facile treatment of pandemic populations, Tucaresol is presented herein for treatment of mild-to- moderate COVID-19 patients but may also be useful for treatment of advanced disease accompanied by lymphopenia.

Cryo-EM reveals binding of linoleic acid to SARS-CoV-2 spike glycoprotein, suggesting an antiviral treatment strategy.

The COVID-19 pandemic and concomitant lockdowns presented a global health challenge and triggered unprecedented research efforts to elucidate the molecular mechanisms and pathogenicity of SARS-CoV-2. The spike glycoprotein decorating the surface of SARS-CoV-2 virions is a prime target for vaccine development, antibody therapy and serology as it binds the host cell receptor and is central for viral cell entry. The electron cryo-microscopy structure of the spike protein revealed a hydrophobic pocket in the receptor-binding domain that is occupied by an essential fatty acid, linoleic acid (LA). The LA-bound spike protein adopts a non-infectious locked conformation which is more stable than the infectious form and shields important immunogenic epitopes. Here, the impact of LA binding on viral infectivity and replication, and the evolutionary conservation of the pocket in other highly pathogenic coronaviruses, including SARS-CoV-2 variants of concern (VOCs), are reviewed. The importance of LA metabolic products, the eicosanoids, in regulating the human immune response and inflammation is highlighted. Lipid and fatty-acid binding to a hydrophobic pocket in proteins on the virion surface appears to be a broader strategy employed by viruses, including picornaviruses and Zika virus. Ligand binding stabilizes their protein structure and assembly, and downregulates infectivity. In the case of rhinoviruses, this has been exploited to develop small-molecule antiviral drugs that bind to the hydrophobic pocket. The results suggest a COVID-19 antiviral treatment based on the LA-binding pocket.

Antiviral Disaccharide Lead Compounds against SARS-CoV-2 through Computer-Aided High-Throughput Screen.

SARS-CoV-2 infects human epithelial cells through specific interaction with angiotensin-converting enzyme 2 (ACE2). In addition, heparan sulfate proteoglycans act as the attachment factor to promote the binding of viral spike protein receptor binding domain (RBD) to ACE2 on host cells. Though the rapid development of vaccines has contributed significantly to preventing severe disease, mutated SARS-CoV-2 strains, especially the SARS-CoV-2 Omicron variant, show increased affinity of RBD binding to ACE2, leading to immune escape. Thus, there is still an unmet need for new antiviral drugs. In this study, we constructed pharmacophore models based on the spike RBD of SARS-CoV-2 and SARS-CoV-2 Omicron variant and performed virtual screen for best-hit compounds from our disaccharide library. Screening of 96 disaccharide structures identified two disaccharides that displayed higher binding affinity to RBD in comparison to reported small molecule antiviral drugs. Further, screening PharmMapper demonstrated interactions of the disaccharides with a number of inflammatory cytokines, suggesting a potential for disaccharides with multiple-protein targets.

Pyronaridine Protects against SARS-CoV-2 Infection in Mouse.

There are currently relatively few small-molecule antiviral drugs that are either approved or emergency-approved for use against severe acute respiratory coronavirus 2 (SARS-CoV-2). One of these is remdesivir, which was originally repurposed from its use against Ebola. We evaluated three molecules we had previously identified computationally with antiviral activity against Ebola and Marburg and identified pyronaridine, which inhibited the SARS-CoV-2 replication in A549-ACE2 cells. The in vivo efficacy of pyronaridine has now been assessed in a K18-hACE transgenic mouse model of COVID-19. Pyronaridine treatment demonstrated a statistically significant reduction of viral load in the lungs of SARS-CoV-2-infected mice, reducing lung pathology, which was also associated with significant reduction in the levels of pro-inflammatory cytokines/chemokine and cell infiltration. Pyronaridine inhibited the viral PLpro activity in vitro (IC50 of 1.8 μM) without any effect on Mpro, indicating a possible molecular mechanism involved in its ability to inhibit SARS-CoV-2 replication. We have also generated several pyronaridine analogs to assist in understanding the structure activity relationship for PLpro inhibition. Our results indicate that pyronaridine is a potential therapeutic candidate for COVID-19.

Current Strategies in Treating Cytokine Release Syndrome Triggered by Coronavirus SARS-CoV-2.

Since the beginning of the SARS-CoV-2 pandemic, the treatments and management of the deadly COVID-19 disease have made great progress. The strategies for developing novel treatments against COVID-19 include antiviral small molecule drugs, cell and gene therapies, immunomodulators, neutralizing antibodies, and combination therapies. Among them, immunomodulators are the most studied treatments. The small molecule antiviral drugs and immunoregulators are expected to be effective against viral variants of SARS-CoV-2 as these drugs target either conservative parts of the virus or common pathways of inflammation. Although the immunoregulators have shown benefits in reducing mortality of cytokine release syndrome (CRS) triggered by SARS-CoV-2 infections, extensive investigations on this class of treatment to launch novel therapies that substantially improve efficacy and reduce side effects are still warranted. Moreover, great challenges have emerged as the SARS-CoV-2 virus quickly, frequently, and continuously evolved. This review provides an update and summarizes the recent advances in the treatment of COVID-19 and in particular emphasized the strategies in managing CRS triggered by SARS-CoV-2. A brief perspective in the battle against the deadly disease was also provided.

Synthesis, Structure-Activity Relationships, and Antiviral Profiling of 1-Heteroaryl-2-Alkoxyphenyl Analogs as Inhibitors of SARS-CoV-2 Replication.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, has led to a pandemic, that continues to be a huge public health burden. Despite the availability of vaccines, there is still a need for small-molecule antiviral drugs. In an effort to identify novel and drug-like hit matter that can be used for subsequent hit-to-lead optimization campaigns, we conducted a high-throughput screening of a 160 K compound library against SARS-CoV-2, yielding a 1-heteroaryl-2-alkoxyphenyl analog as a promising hit. Antiviral profiling revealed this compound was active against various beta-coronaviruses and preliminary mode-of-action experiments demonstrated that it interfered with viral entry. A systematic structure–activity relationship (SAR) study demonstrated that a 3- or 4-pyridyl moiety on the oxadiazole moiety is optimal, whereas the oxadiazole can be replaced by various other heteroaromatic cycles. In addition, the alkoxy group tolerates some structural diversity.

Antiviral Peptides with in vivo Activity: Development and Modes of Action.

The viral pandemic has resulted in a growing demand for antiviral drugs. The existing small-molecule antiviral drugs are limited, due to their incidence of drug resistance and adverse side effects. As potential drugs, antiviral peptides have the benefits of high activity, high stability, and few side effects. Furthermore, the diversity of acquisition methods allows antiviral peptides to be quickly designed and yielded. The drug properties (such as high bioavailability and in vivo stability) of antiviral peptides can be improved by the developed modifications. Currently, two peptide antiviral drugs have been approved for the treatment of acquired immunodeficiency syndrome (AIDS). Many antiviral peptides have entered clinical trials for the treatment of diseases caused by viruses. In addition, new antiviral peptides are continuously being identified and validated against virus infections. Given the benefits of antiviral peptides, they will become major antiviral drugs to combat new outbreaks caused by unknown viruses in the future. This review provides an overview of recent developments in antiviral peptides with in vivo activity.

Repurposed Antiviral Drugs for the Treatment of COVID-19: Syntheses, Mechanism of Infection and Clinical Trials.

COVID-19 is a public health emergency of international concern. Although considerable knowledge has been acquired with time about the viral mechanism of infection and mode of replication, yet no specific drugs or vaccines have been discovered against SARS-CoV-2 to date. There are few small molecule antiviral drugs like Remdesivir and Favipiravir, which have shown promising results in different advanced stages of clinical trials. Chloroquinine, Hydroxychloroquine, and Lopinavir- Ritonavir combination, although initially were hypothesized to be effective against SARSCoV- 2, are now discontinued from the solidarity clinical trials. This review provides a brief description of their chemical syntheses along with their mode of action, and clinical trial results available on Google and in different peer-reviewed journals till 24th October 2020.

Recent advances of traditional Chinese medicine on the prevention and treatment of COVID-19.

Coronavirus disease-2019 (COVID-19) is a new highly infectious disease caused by a novel coronavirus. Recently, the number of new cases infected pneumonia in the world continues to increase, which has aroused great concern from the international community. At present, there are no small-molecule specific anti-viral drugs for the treatment. The high mortality rate seriously threatens human health. Traditional Chinese medicine (TCM) is a unique health resource in China. The combination of TCM and Western medicine has played a positive and important role in combating COVID-19 in China. In this review, through literature mining and analysis, it was found that TCM has the potential to prevent and treat the COVID-19. Then, the network pharmacological studies demonstrated that TCM played roles of anti-virus, anti-inflammation and immunoregulation in the management of COVID-19 via multiple components acting on multiple targets and multiple pathways. Finally, clinical researches also confirmed the beneficial effects of TCM on the treatment of patients. This review may provide meaningful and useful information on further drug development of COVID-19 and other viral infectious diseases.

Raltegravir, Indinavir, Tipranavir, Dolutegravir, and Etravirine against main protease and RNA-dependent RNA polymerase of SARS-CoV-2: A molecular docking and drug repurposing approach

BackgroundOutbreak of COVID-19 has been recognized as a global health concern since it causes high rates of morbidity and mortality. No specific antiviral drugs are available for the treatment of COVID-19 till date. Drug repurposing strategy helps to find out the drugs for COVID-19 treatment from existing FDA approved antiviral drugs. In this study, FDA approved small molecule antiviral drugs were repurposed against the major viral proteins of SARS-CoV-2. MethodsThe 3D structures of FDA approved small molecule antiviral drugs were retrieved from PubChem. Virtual screening was performed to find out the lead antiviral drug molecules against main protease (Mpro) and RNA-dependent RNA polymerase (RdRp) using COVID-19 Docking Server. Furthermore, lead molecules were individually docked against protein targets using AutoDock 4.0.1 software and their drug-likeness and ADMET properties were evaluated. ResultsOut of 65 FDA approved small molecule antiviral drugs screened, Raltegravir showed highest interaction energy value of -9 kcal/mol against Mpro of SARS-CoV-2 and Indinavir, Tipranavir, and Pibrentasvir exhibited a binding energy value of ≥−8 kcal/mol. Similarly Indinavir showed the highest binding energy of -11.5 kcal/mol against the target protein RdRp and Dolutegravir, Elbasvir, Tipranavir, Taltegravir, Grazoprevir, Daclatasvir, Glecaprevir, Ledipasvir, Pibrentasvir and Velpatasvir showed a binding energy value in range from -8 to -11.2 kcal/mol. The antiviral drugs Raltegravir, Indinavir, Tipranavir, Dolutegravir, and Etravirine also exhibited good bioavailability and drug-likeness properties. ConclusionThis study suggests that the screened small molecule antiviral drugs Raltegravir, Indinavir, Tipranavir, Dolutegravir, and Etravirine could serve as potential drugs for the treatment of COVID-19 with further validation studies.

Interaction of small molecules with the SARS-CoV-2 main protease in silico and in vitro validation of potential lead compounds using an enzyme-linked immunosorbent assay

Caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the COVID-19 pandemic is ongoing, with no proven safe and effective vaccine to date. Further, effective therapeutic agents for COVID-19 are limited, and as a result, the identification of potential small molecule antiviral drugs is of particular importance. A critical antiviral target is the SARS-CoV-2 main protease (Mpro), and our aim was to identify lead compounds with potential inhibitory effects. We performed an initial molecular docking screen of 300 small molecules, which included phenolic compounds and fatty acids from our OliveNet™ library (224), and an additional group of curated pharmacological and dietary compounds. The prototypical α-ketoamide 13b inhibitor was used as a control to guide selection of the top 30 compounds with respect to binding affinity to the Mpro active site. Further studies and analyses including blind docking were performed to identify hypericin, cyanidin-3-O-glucoside and SRT2104 as potential leads. Molecular dynamics simulations demonstrated that hypericin (ΔG = -18.6 and -19.3 kcal/mol), cyanidin-3-O-glucoside (ΔG = -50.8 and -42.1 kcal/mol), and SRT2104 (ΔG = -8.7 and -20.6 kcal/mol), formed stable interactions with the Mpro active site. An enzyme-linked immunosorbent assay indicated that, albeit, not as potent as the covalent positive control (GC376), our leads inhibited the Mpro with activity in the micromolar range, and an order of effectiveness of hypericin and cyanidin-3-O-glucoside > SRT2104 > SRT1720. Overall, our findings, and those highlighted by others indicate that hypericin and cyanidin-3-O-glucoside are suitable candidates for progress to in vitro and in vivo antiviral studies.