3CLpro Research Articles

Repurposing of Rutan showed effective treatment for COVID-19 disease

Previously, from the tannic sumac plant (Rhus coriaria), we developed the Rutan 25 mg oral drug tablets with antiviral activity against influenza A and B viruses, adenoviruses, paramyxoviruses, herpes virus, and cytomegalovirus. Here, our re-purposing study demonstrated that Rutan at 25, 50, and 100 mg/kg provided a very effective and safe treatment for COVID-19 infection, simultaneously inhibiting two vital enzyme systems of the SARS-CoV-2 virus: 3C-like proteinase (3CLpro) and RNA-dependent RNA polymerase (RdRp). There was no drug accumulation in experimental animals’ organs and tissues. A clinical study demonstrated a statistically significant decrease in the C-reactive protein and a reduction of the viremia period. In patients receiving Rutan 25 mg (children) and 100 mg (adults), the frequency of post-COVID-19 manifestations was significantly less than in the control groups not treated with Rutan tablets. Rutan, having antiviral activity, can provide safe treatment and prevention of COVID-19 in adults and children.Clinical Trial RegistrationClinicalTrials.gov, ID NCT05862883.

AlphaFold modeling of nepovirus 3C-like proteinases provides new insights into their diverse substrate specificities

The majority of picornaviral 3C proteinases (3Cpro) cleavage sites possess glutamine at the P1 position. Plant nepovirus 3C-like proteinases (3CLpro) show however much broader specificity, cleaving not only after glutamine, but also after several basic and hydrophobic residues. To investigate this difference, we employed AlphaFold to generate structural models of twelve selected 3CLpro, representing six substrate specificities. Generally, we observed favorable correlations between the architecture and charge of nepovirus proteinase S1 subsites and their ability to accept or restrict larger residues. The models identified a conserved aspartate residue close to the P1 residue in the S1 subsites of all nepovirus proteinases examined, consistent with the observed strong bias against negatively-charged residues at the P1 position of nepovirus cleavage sites. Finally, a cramped S4 subsite along with the presence of two unique histidine and serine residues explains the strict requirement of the grapevine fanleaf virus proteinase for serine at the P4 position.

Erythromycin, retapamulin, pyridoxine, folic acid, and ivermectin inhibit cytopathic effect, papain-like protease, and MPRO enzymes of SARS-CoV-2.

Although tremendous success has been achieved in the development and deployment of effective COVID-19 vaccines, developing effective therapeutics for the treatment of those who do come down with the disease has been with limited success. To repurpose existing drugs for COVID-19, we previously showed, qualitatively, that erythromycin, retapamulin, pyridoxine, folic acid, and ivermectin inhibit SARS-COV-2-induced cytopathic effect (CPE) in Vero cells. This study aimed to quantitatively explore the inhibition of SARS-CoV-2-induced CPE by erythromycin, retapamulin, pyridoxine, folic acid, and ivermectin and to determine the effect of these drugs on SARS-CoV-2 papain-like protease and 3CL protease (MPRO) enzymes. Neutral red (3-amino-7-dimethylamino-2-methyl-phenazine hydrochloride) cell viability assay was used to quantify CPE after infecting pre-treated Vero cells with clinical SARS-Cov-2 isolates. Furthermore, SensoLyte® 520 SARS-CoV-2 papain-like protease and SensoLyte® 520 SARS-CoV-2 MPRO activity assay kits were used to evaluate the inhibitory activity of the drugs on the respective enzymes. Erythromycin, retapamulin, pyridoxine, folic acid, and ivermectin dose-dependently inhibit SARS-CoV-2-induced CPE in Vero cells, with inhibitory concentration-50 (IC50) values of 3.27 µM, 4.23 µM, 9.29 µM, 3.19 µM, and 84.31 µM, respectively. Furthermore, erythromycin, retapamulin, pyridoxine, folic acid, and ivermectin dose-dependently inhibited SARS-CoV-2 papain-like protease with IC50 values of 0.94 µM, 0.88 µM, 1.14 µM, 1.07 µM, and 1.51 µM, respectively, and inhibited the main protease (MPRO) with IC50 values of 1.35 µM, 1.25 µM, 7.36 µM, 1.15 µM, and 2.44 µM, respectively. The IC50 for all the drugs, except ivermectin, was at the clinically achievable plasma concentration in humans, which supports a possible role for the drugs in the management of COVID-19. The lack of inhibition of CPE by ivermectin at clinical concentrations could be part of the explanation for its lack of effectiveness in clinical trials.

548. Combined Results of the Phase 2a/2b/3 Randomized Controlled Trials of Ensitrelvir for the Treatment of COVID-19 Infection

Abstract Background Ensitrelvir is a selective SARS-CoV-2 3CL protease inhibitor developed as an oral therapy for the treatment of COVID-19 infection. We report the combined results for ensitrelvir 125 mg and 250 mg treatment from the Phase 2a, 2b, 3 parts of the Phase 2/3 study conducted in patients with COVID-19 with or without SARS-CoV-2 vaccination and risk factors for severe disease. Methods The multicenter, randomized, double-blind, placebo-controlled studies were conducted between September 2021 and August 2022 in Japan, South Korea and Vietnam. SARS-CoV-2-positive patients, aged 12–70 years old, were treated with ensitrelvir 125 mg PO (after a loading dose of 375 mg PO on Day 1 only), 250 mg PO (after a loading dose of 750 mg on Day 1only) or placebo, once daily for 5 days, and followed up for 28 days from the start of treatment. Time to resolution of 5 symptoms of COVID-19 (runny or stuffy nose, sore throat, cough, feeling hot or fever, low energy or tiredness) primarily among patients who were randomized within less than 72 hours of symptom onset and safety were assessed. Results In this post-hoc analysis, among patients who were randomized within less than 72 hours of symptom onset, 56.0% of patients were male in the ensitrelvir 125 mg group (N=407), 54.3% in the 250 mg group (N=398) and 52.5% in the placebo group (N=402). The mean (standard deviation) age was 35.8 (12.7) years in the 125 mg group, 35.1 (12.3) in the 250 mg group and 34.9 (12.3) years in the placebo group. The time to resolution of the 5 symptoms was significantly shorter in the 125 mg group (P=0.0120) compared with the placebo group (median: 167.9 hours in the 125 mg group [N=391], 167.8 hours in the 250 mg group [N=385], and 204.4 hours in the placebo group [N=377]). For patients who were randomized from onset within 120 hours, the median time to resolution was 183.2 hours in the 125 mg group (N=702), 168.9 in the 250 mg group (N=697) and 206.3 hours in the placebo group (N=692) (P=0.1235). One (0.1%) patient in the 125 mg group and 3 (0.4%) patients in the placebo group had serious adverse events; none resulted in death. No serious adverse events were observed in the 250 mg group. Conclusion Treatment of patients with COVID-19 with ensitrelvir significantly shortened the time to symptom recovery. Ensitrelvir was well tolerated. Disclosures Yuko Tsuge, MSc, SHIONOGI & CO., LTD.: Stocks/Bonds Hiroshi Yotsuyanagi, MD PhD, Shionogi: Advisor/Consultant|Shionogi: Advisor/Consultant Yohei Doi, MD, PhD, bioMerieux: Advisor/Consultant|FujiFilm: Advisor/Consultant|Gilead: Advisor/Consultant|Gilead: Honoraria|GSK: Advisor/Consultant|Meiji Seika Pharma: Advisor/Consultant|Moderna: Advisor/Consultant|Moderna: Honoraria|MSD: Advisor/Consultant|MSD: Honoraria|Shionogi: Advisor/Consultant|Shionogi: Grant/Research Support|Shionogi: Honoraria Masaya Yamato, MD, PhD, Shionogi: Advisor/Consultant Takuhiro Sonoyama, MD, SHIONOGI & CO., LTD.: I am an employee of SHIONOGI & CO., LTD.|SHIONOGI & CO., LTD.: Stocks/Bonds

549. Ensitrelvir for the Treatment of COVID-19 Infection: Evaluation of Taste Disorder and Smell Disorder in the Phase 3 Part of the Phase 2/3 SCORPIO-SR Randomized Controlled Trial

Abstract Background Ensitrelvir, a selective SARS-CoV-2 3CL protease inhibitor, is developed as an oral antiviral agent for the treatment of COVID-19 infection. In the Phase 3 part of the randomized SCORPIO-SR trial, the effects of oral ensitrelvir 125 mg and 250 mg on the resolution of taste and smell disorder in patients with COVID-19 with or without SARS-CoV-2 vaccination and risk factors for severe disease were evaluated. Methods This study is a multicenter, randomized, double-blind, placebo-controlled study conducted in Japan, South Korea and Vietnam. SARS-CoV-2-positive patients, aged 12–70 years old, received ensitrelvir 125 mg PO (after 375 mg PO loading dose on Day 1 only), 250 mg PO (after 750 mg PO loading dose on Day 1 only) or placebo, once daily for 5 days, and were followed by Day 21 from start of treatment to analyze the proportion of patients presenting with taste or smell disorder. Results 55.6% of patients were male in the ensitrelvir 125 mg group (N=347), 54.4% in the 250 mg group (N=340), and 50.7% in the placebo group (N=343). The mean (standard deviation) age was 35.7 (12.5) years in the ensitrelvir 125 mg group, 35.3 (12.2) years in the 250 mg group, and 34.7 (12.2) years in the placebo group among patients for whom the time from onset to randomization was less than 72 hours. The proportions of patients with taste disorder or smell disorder were smaller in both the 125 mg and 250 mg groups compared with the placebo group on Day 5 to Day 9 (Figure1). Significantly smaller proportions of patients had taste disorder or smell disorder on Day 7 and Day 8 in the 125 mg ensitrelvir group, and on Day 8 and Day 9 in the 250 mg ensitrelvir group compared with the placebo group, respectively. In the group of patients who did not have taste disorder or smell disorder at the start of treatment, the proportions of patients who developed taste or smell disorder were smaller in both the 125 mg and the 250 mg groups compared with the placebo group after 4 days from the start of treatment (Figure2). Conclusion Early administration of oral ensitrelvir was associated with early improvement or prevention of taste disorder and smell disorder. Disclosures Yuko Tsuge, MSc, SHIONOGI & CO., LTD.: Stocks/Bonds Takuhiro Sonoyama, MD, SHIONOGI & CO., LTD.: I am an employee of SHIONOGI & CO., LTD.|SHIONOGI & CO., LTD.: Stocks/Bonds Hiroshi Yotsuyanagi, MD PhD, Shionogi: Advisor/Consultant|Shionogi: Advisor/Consultant Yohei Doi, MD, PhD, bioMerieux: Advisor/Consultant|FujiFilm: Advisor/Consultant|Gilead: Advisor/Consultant|Gilead: Honoraria|GSK: Advisor/Consultant|Meiji Seika Pharma: Advisor/Consultant|Moderna: Advisor/Consultant|Moderna: Honoraria|MSD: Advisor/Consultant|MSD: Honoraria|Shionogi: Advisor/Consultant|Shionogi: Grant/Research Support|Shionogi: Honoraria Masaya Yamato, MD, PhD, Shionogi: Advisor/Consultant

Inhibition of SARS-CoV-2 3CL protease by the anti-viral chimeric protein RetroMAD1

COVID-19 results from SARS-CoV-2, which mutates frequently, challenging current treatments. Therefore, it is critical to develop new therapeutic drugs against this disease. This study explores the interaction between SARS-CoV-2 3CLpro and RetroMAD1, a well-characterized coronavirus protein and potential drug target, using in-silico methods. The analysis through the HDOCK server showed stable complex formation with a binding energy of -12.3, the lowest among reference drugs. The RetroMAD1-3CLpro complex underwent a 100 ns molecular dynamics simulation (MDS) in an explicit solvation system, generating various trajectories, including RMSD, RMSF, hydrogen bonding, radius of gyration, and ligand binding energy. MDS results confirmed intact interactions within the RetroMAD1-3CLpro complex during simulations. In vitro experiments validated RetroMAD1's ability to inhibit 3CLpro enzyme activity and prevent SARS-CoV-2 infection in human bronchial cells. RetroMAD1 exhibited antiviral efficacy comparable to Remdesivir without cytotoxicity at effective concentrations. These results suggest RetroMAD1 as a potential drug candidate against SARS-CoV-2, warranting further in vivo and clinical studies to assess its efficiency.

Superior anti-pulmonary viral potential of Natrialba sp. M6-producing surfactin and C50 carotenoid pigment with unveiling its action modes

BackgroundRespiratory viruses, particularly adenoviruses (ADV), influenza A virus (e.g., H1N1), and coronaviruses (e.g., HCoV-229E and SARS-CoV-2) pose a global public health problem. Therefore, developing natural wide-spectrum antiviral compounds for disrupting the viral life cycle with antioxidant activity provides an efficient treatment approach. Herein, biosurfactant (Sur) and C50 carotenoid pigment (Pig) of haloalkaliphilic archaeon Natrialba sp. M6 which exhibited potent efficacy against hepatitis and anti-herpes simplex viruses, were investigated against pulmonary viruses.MethodsThe cytotoxicity of the extracted Sur and Pig was examined on susceptible cell lines for ADV, HIN1, HCoV-229E, and SARS-CoV-2. Their potential against the cytopathic activity of these viruses was detected with investigating the action modes (including, virucidal, anti-adsorption, and anti-replication), unveiling the main mechanisms, and using molecular docking analysis. Radical scavenging activity was determined and HPLC analysis for potent extract (Sur) was performed.ResultsAll current investigations stated higher anti-pulmonary viruses of Sur than Pig via mainly virucidal and/or anti-replicative modes. Moreover, Sur had stronger ADV’s capsid protein binding, ADV’s DNA polymerase inhibition, suppressing hemagglutinin and neuraminidase of H1N1, and inhibiting chymotrypsin-like (3CL) protease of SARS-CoV-2, supporting with in-silico analysis, as well as radical scavenging activity than Pig. HPLC analysis of Sur confirmed the predominate presence of surfactin in it.ConclusionThis study declared the promising efficacy of Sur as an efficient pharmacological treatment option for these pulmonary viruses and considered as guide for further in vivo research.

Synthesis, in silico and in vitro studies of novel quinazolinone derivatives as potential SARS-CoV-2 3CLpro inhibitors

A series of new quinazolinone derivatives (5a-l) were designed as 3CL protease inhibitors for SARS-CoV-2 infection. The designed derivatives were efficiently synthesized by S-alkylation/arylation of an intermediate, 6-fluoro-3-(4-fluorophenyl)-2-mercaptoquinazolin-4(3H)-one and their successful synthesis was established by analytical methods, viz. IR, 1H NMR, &13C NMR spectroscopy. The in silico inhibitory potential against 3CLpro of SARS-CoV-2 were studied by means of docking and dynamics simulations, and compared with the co-crystallized ligand (VR4) of SARS-CoV-2 3CLpro. The compounds interacted strongly within the active catalytic dyad (Cys-His) site, thereby anticipated to obstruct the function of 3CLpro of SARS-CoV-2. Compounds 5b, 5c, 5i, 5j and 5l showed efficient binding with protease 3CLpro with XP Gscore of −7.4, −8.3, −7.8, −7.5 and −8.2 respectively. Furthermore, molecular dynamic simulation study of these compounds (5b, 5c, 5i, 5j and 5 l) showed stable interaction over 50 ns production run. Swiss ADME and pkCSM web tools showed favorable physicochemical and pharmacokinetic properties and fulfilled the criteria for drug-likeness of these selected studied compounds. The toxicity determination of these selected compounds predicted that some compounds were hepatotoxic, but were not AMES toxic. Compounds 5b, 5c, 5i, 5j and 5 l revealed their inhibitory potential against the SARS-CoV-2 3CLpro, and their IC50 values were attained at 1.58, 1.25, 1.97, 0.44 and 2.56 µM, respectively. In addition, these compounds were found to have devoid of any significant cytotoxicity even at a higher concentration of 20 µM against VeroE6 cells. These quinazolinone derivatives showed potent binding and inhibitory potential against SARS-CoV-2 3CLpro and may emerge as compounds that might act as prospective inhibitors.

Synthesis, X-Ray, Spectral Characterization, DFT, and Molecular Docking Calculations of 2-(5-Nitro-1-H-Indazol-1-yl) Acetic Acid

In this work, theoretical and experimental studies of a new Indazole derivative named 2-(5-nitro-1-H-indazol-1-yl) acetic acid (3), including the synthesis and characterization by 1H and 13C-NMR, FT-IR, UV spectroscopies are reported together with its X-ray crystal structure. The compound crystallizes in the monoclinic crystal system of P21/c space group and unit cell constants: a = 7.8541(10) Å, b = 7.9274(11) Å, c = 15.877(2) Å, β = 101.149(5)°. In the crystal, O–H···N and C–H···O hydrogen bonds form a 3-D network structure containing small channels running parallel to the b-axis. B3LYP/6-311++G** calculations in the gas phase and ethanol solution suggest the existence of C1 and C2 conformers where the structure of C1 in both media is in agreement with that observed by X-ray diffraction. Probably, the high values observed in the dipole moments of C1 justify its presence in gas and solution phases. The stabilities of both forms were justified by NBO and AIM calculations where C1 is more stable than C2. C1 shows a higher solvation energy, dipole moment, and higher hydration than C2 while the frontier orbitals suggest a higher reactivity of C1 over C2. Force fields and complete vibrational assignments were performed for the C1 conformer because it was detected in the solid phase. Scaled force constants for both forms are also reported. Calculated chemical shifts for (3) are consistent with the experimental 1H and 13C-NMR spectra in the DMSO-d6 solution. The anti-COVID activity of 3 is investigated by its molecular docking into the binding site of SARS CoV-2 3CLpro (3 C-like protease). It shows a moderate binding affinity into the binding site of 3 C-like protease with a maximum binding energy of −5.57 kcal mol−1.

Structure-based development and preclinical evaluation of the SARS-CoV-2 3C-like protease inhibitor simnotrelvir

The persistent pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants accentuates the great demand for developing effective therapeutic agents. Here, we report the development of an orally bioavailable SARS-CoV-2 3C-like protease (3CLpro) inhibitor, namely simnotrelvir, and its preclinical evaluation, which lay the foundation for clinical trials studies as well as the conditional approval of simnotrelvir in combination with ritonavir for the treatment of COVID-19. The structure-based optimization of boceprevir, an approved HCV protease inhibitor, leads to identification of simnotrelvir that covalently inhibits SARS-CoV-2 3CLpro with an enthalpy-driven thermodynamic binding signature. Multiple enzymatic assays reveal that simnotrelvir is a potent pan-CoV 3CLpro inhibitor but has high selectivity. It effectively blocks replications of SARS-CoV-2 variants in cell-based assays and exhibits good pharmacokinetic and safety profiles in male and female rats and monkeys, leading to robust oral efficacy in a male mouse model of SARS-CoV-2 Delta infection in which it not only significantly reduces lung viral loads but also eliminates the virus from brains. The discovery of simnotrelvir thereby highlights the utility of structure-based development of marked protease inhibitors for providing a small molecule therapeutic effectively combatting human coronaviruses.

Reversible and irreversible inhibitors of coronavirus Nsp15 endoribonuclease

The emergence of severe acute respiratory syndrome coronavirus 2, the causative agent of coronavirus disease 2019, has resulted in the largest pandemic in recent history. Current therapeutic strategies to mitigate this disease have focused on the development of vaccines and on drugs that inhibit the viral 3CL protease or RNA-dependent RNA polymerase enzymes. A less-explored and potentially complementary drug target is Nsp15, a uracil-specific RNA endonuclease that shields coronaviruses and other nidoviruses from mammalian innate immune defenses. Here, we perform a high-throughput screen of over 100,000 small molecules to identify Nsp15 inhibitors. We characterize the potency, mechanism, selectivity, and predicted binding mode of five lead compounds. We show that one of these, IPA-3, is an irreversible inhibitor that might act via covalent modification of Cys residues within Nsp15. Moreover, we demonstrate that three of these inhibitors (hexachlorophene, IPA-3, and CID5675221) block severe acute respiratory syndrome coronavirus 2 replication in cells at subtoxic doses. This study provides a pipeline for the identification of Nsp15 inhibitors and pinpoints lead compounds for further development against coronavirus disease 2019 and related coronavirus infections.

Broad antagonism of coronaviruses nsp5 to evade the host antiviral responses by cleaving POLDIP3.

Coronaviruses (CoVs) are a family of the largest RNA viruses that typically cause respiratory, enteric, and hepatic diseases in animals and humans, imposing great threats to the public safety and animal health. Porcine deltacoronavirus (PDCoV), a newly emerging enteropathogenic coronavirus, causes severe diarrhea in suckling piglets all over the world and poses potential risks of cross-species transmission. Here, we use PDCoV as a model of CoVs to illustrate the reciprocal regulation between CoVs infection and host antiviral responses. In this study, downregulation of DNA polymerase delta interacting protein 3 (POLDIP3) was confirmed in PDCoV infected IPEC-J2 cells by isobaric tags for relative and absolute quantification (iTRAQ) and Western blotting analysis. Overexpression of POLDIP3 inhibits PDCoV infection, whereas POLDIP3 knockout (POLDIP3-/-) by CRISPR-Cas9 editing significantly promotes PDCoV infection, indicating POLDIP3 as a novel antiviral regulator against PDCoV infection. Surprisingly, an antagonistic strategy was revealed that PDCoV encoded nonstructural protein 5 (nsp5) was responsible for POLDIP3 reduction via its 3C-like protease cleavage of POLDIP3 at the glutamine acid 176 (Q176), facilitating PDCoV infection due to the loss of antiviral effects of the cleaved fragments. Consistent with the obtained data in IPEC-J2 cell model in vitro, POLDIP3 reduction by cleavage was also corroborated in PDCoV infected-SPF piglets in vivo. Collectively, we unveiled a new antagonistic strategy evolved by PDCoV to counteract antiviral innate immunity by nsp5-mediated POLDIP3 cleavage, eventually ensuring productive virus replication. Importantly, we further demonstrated that nsp5s from PEDV and TGEV harbor the conserved function to cleave porcine POLDIP3 at the Q176 to despair POLDIP3-mediated antiviral effects. In addition, nsp5 from SARS-CoV-2 also cleaves human POLDIP3. Therefore, we speculate that coronaviruses employ similar POLDIP3 cleavage mechanisms mediated by nsp5 to antagonize the host antiviral responses to sustain efficient virus infection.

PBPK Modeling of PAXLOVIDTM: Incorporating Rotamer Conversion Kinetics to Advanced Dissolution and Absorption Model

PAXLOVID™ is a combination medicine of nirmatrelvir tablets co-packaged with ritonavir tablets. Nirmatrelvir is a peptidomimetic inhibitor of SARS-CoV2 main protease (Mpro), developed for the treatment of COVID-19. Ritonavir is co-administered as a pharmacokinetics (PK) enhancer to inhibit CYP3A mediated metabolism increasing exposures of nirmatrelvir. In the solid form, nirmatrelvir exists in a stable single conformational state (ANTI form). However, nirmatrelvir exhibits atropisomerism in solution whereby upon dissolution the ANTI rotational isomer reversibly converts to another conformation state (SYN form). Nirmatrelvir rotamer conversion follows pseudo first order kinetics with a conversion half-life of approximately 15 min in aqueous solutions, which is on a similar time scale of diffusion mediated dissolution from the solid form. In vitro dissolution studies further indicated that rotamer conversion is one of the processes controlling nirmatrelvir dissolution. It was hypothesized that rotamer conversion kinetics would affect oral absorption of nirmatrelvir in vivo. Consequently, a physiologically based pharmacokinetic (PBPK) model for Paxlovid was developed in Simcyp™ using the advanced dissolution, absorption, and metabolism model (ADAM) by incorporating rotamer conversion kinetics to achieve a more mechanistic description of nirmatrelvir oral absorption. The results demonstrate that the established absorption model with rotamer kinetics adequately described observed clinical data from various nirmatrelvir doses, dosage forms, and dosing regimens. The predicted vs. observed AUCinf and Cmax ratios were within 2-fold. The model has been internally used to inform clinical studies and dose recommendations for pediatrics.

Pharmacokinetic and Pharmacodynamic Analysis of the 3CL Protease Inhibitor Ensitrelvir in a SARS-CoV-2 Infection Mouse Model.

The small-molecule antiviral drug ensitrelvir targets the 3C-like protease of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This study evaluated its inhibitory effect on viral replication in a delayed-treatment mouse model and investigated the relationship between pharmacokinetic (PK) parameters and pharmacodynamic (PD) effects. SARS-CoV-2 gamma-strain-infected BALB/c mice were orally treated with various doses of ensitrelvir starting 24 h post-infection. Effectiveness was determined 48 h after first administration based on lung viral titers. Ensitrelvir PK parameters were estimated from previously reported plasma concentration data and PK/PD analyses were performed. Ensitrelvir doses ≥ 16 mg/kg once daily, ≥8 mg/kg twice daily, or ≥8 mg/kg thrice daily for two days significantly reduced lung viral titers compared to that of the vehicle. PK/PD analyses revealed that mean AUC0-48h post-first administration, plasma concentration 48 h post-first administration (C48h), and total time above the target plasma concentration (TimeHigh) were PK parameters predictive of viral titer reduction. In conclusion, ensitrelvir dose-dependently reduced lung SARS-CoV-2 titers in mice, suggesting it inhibited viral replication. PK parameters C48h and TimeHigh were associated with sustained ensitrelvir plasma concentrations and correlated with the reduced viral titers. The findings suggest that maintaining ensitrelvir plasma concentration is effective for exerting antiviral activity against SARS-CoV-2.

Phellinus linteus mycelia extract in COVID-19 prevention and identification of its key metabolic compounds profiling using UPLC-QTOF-MS/MS spectrometry

For centuries, food, herbal medicines, and natural products have been valuable resources for discovering novel antiviral drugs, uncovering new structure-activity relationships, and developing effective strategies to prevent/treat viral infections. One such resource is Phellinus linteus, a mushroom used in folk medicine in Taiwan, Japan, Korea, and China. In this rich historical context, the key metabolites of Phellinus linteus mycelia ethanolic extract (GKPL) impacting the entry of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at multiple stages have yet to be explored. Thus, this study systematically identifies and assesses the inhibitory effect of GKPL on the SARS-CoV-2 virus. Initially, the concentrations and contact times of GKPL against SARS-CoV-2 pseudovirus were assessed in HepG2 cells. Subsequently, utilizing the Ultra Performance Liquid Chromatography-Quadrupole Time-of-Flight Mass Spectrometry method, potential biomarkers in the fungal extract were discerned. Metabolomic analysis identified 18 compounds in GKPL, with hispidin and hypholomine B present in the highest amounts. These compounds were isolated using chromatographic techniques and further identified through 1D NMR spectroscopic and mass spectrometry analysis. Hispidin and hypholomine B were found to inhibit the infection of SARS-CoV-2 pseudovirus by reducing angiotensin-converting enzyme 2 gene expression in HepG2, thereby decreasing viral entry. Moreover, hispidin and hypholomine B effectively block the spike receptor-binding domain, while hypholomine B, for the first time, showed significant inhibition of 3CL protease. This suggests that GKPL, enriched with hispidin and hypholomine B, has the potential to be used as an active ingredient against SARS-CoV-2.

An insight into the structure and functions of flabelliferins and borassosides; nutraceuticals in Asian palm (Borassus flabellifer)

Palmyraculture is a sustainable livelihood, in which people structure their lifestyle utilizing the values of Palmyra palm. The Asian Palmyra palm, Borassus flabellifer, gives a lot of nutritional and nutraceutical products, as it is rich in vital biomolecules, especially flabelliferins and borassosides. Flabelliferins are found in the fruit, tuber, and inflorescence of Palmyra palm, and the borassosides are found in the inflorescence. There are 14 types of flabelliferins (only nine of their structures are known) and six types of borassosides have been extracted so far. Flabelliferin F-II reduces intestinal glucose uptake and is anti-diabetic, and antiobesitic. Flabelliferin FB is antimicrobial, an inhibitor for SARS-CoV main proteinase, SARS-CoV main protease, and human cellular transmembrane serine proteinase, and Borassoside E is antifungal. Further studies have to be conducted to determine the structures and functions of the other flabelliferins and borassosides.

A first-in-human phase 1 study of simnotrelvir, a 3CL-like protease inhibitor for treatment of COVID-19, in healthy adult subjects

Safe and efficacious antiviral therapeutics are in urgent need for the treatment of coronavirus disease 2019. Simnotrelvir is a selective 3C-like protease inhibitor that can effectively inhibit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We evaluated the safety, tolerability, and pharmacokinetics of dose escalations of simnotrelvir alone or with ritonavir (simnotrelvir or simnotrelvir/ritonavir) in healthy subjects, as well as the food effect (ClinicalTrials.gov Identifier: NCT05339646). The overall incidence of adverse events (AEs) was 22.2% (17/72) and 6.3% (1/16) in intervention and placebo groups, respectively. The simnotrelvir apparent clearance was 135–369 L/h with simnotrelvir alone, and decreased significantly to 19.5–29.8 L/h with simnotrelvir/ritonavir. The simnotrelvir exposure increased in an approximately dose-proportional manner between 250 and 750 mg when co-administered with ritonavir. After consecutive twice daily dosing of simnotrelvir/ritonavir, simnotrelvir had a low accumulation index ranging from 1.39 to 1.51. The area under the curve of simnotrelvir increased 44.0 % and 47.3 % respectively, after high fat and normal diet compared with fasted status. In conclusion, simnotrelvir has adequate safety and tolerability. Its pharmacokinetics indicated a trough concentration above the level required for 90 % inhibition of SARS-CoV-2 in vitro at 750 mg/100 mg simnotrelvir/ritonavir twice daily under fasted condition, supporting further development using this dosage as the clinically recommended dose regimen.

Novel designed analogues of quercetin against SARS-CoV2:an in-silico pharmacokinetic evaluation, molecular modeling, MD simulations based study

Here we present the design of the series of quercetin analogues and their molecular docking study involving the binding of quercetin and its analogues with SARS-CoV2 3CLpro. The scientific literature shows that quercetin compound has been successfully used against SARS-CoV by inhibiting the replication of virus in respiratory epithelial cell through the inhibition of the SARS-CoV main protease (3CLpro.) It was suggested that the modification at position 3 in quercetin structure may produce potent compounds against SARS-CoV2. A series of quercetin analogues were designed and screened for physicochemical and pharmacokinetics parameters. The activities of selected compounds against SARS-CoV2 were screened by molecular modelling and evaluated that analogues, Q5, Q6 and Q13 have the best docking scores (-8.01 to −8.17 kcal/mol) and also better than quercetin, α-ketoamide and current available inhibitors of the same target. The structure-activity relationship (SAR) study revealed that the introduction of the amino group in a designed molecule was highly promising for increasing the inhibitory activity against SARS-CoV2 3CL pro. Moreover, to check the stability and orientation of selected compounds inside the binding pocket, the molecular dynamic simulations were performed for 100 ns. Results revealed that the designed analogues Q1, Q6 and Q13 having lowest binding energies (-8.0, −8.17 and −8.06 kcal/mol respectively) as well as better physicochemical properties, pharmacokinetics, and toxicity profile show their potential to synthesize and develop as the therapeutic agents against corona virus. Communicated by Ramaswamy H. Sarma

Design, Synthesis, and Biological Activity Evaluation of Novel AZT and Adenosine-Derived 1,2,3-Triazoles

CuSO4/hydrazine hydrate was used as a catalyst system for copper(I)-catalyzed alkyne-azide cycloaddition (CuAAC) of AZT and 5′-azido adenosine with terminal alkynes to give 30 novel 1,2,3-triazole derivatives. Screening for their anticancer, anti-inflammatory, angiotensin-converting enzyme 2 (ACE2), and 3C-like protease (3CLpro) inhibitory activities showed that several triazoles of AZT containing murayafoline A and indirubin-3′-oxime inhibited the growth of HepG2 and LU-1 with the IC50 values ranging from 11.01 to 19.87 μg/mL. Besides that, some triazole derivatives of adenosine exhibited anti-inflammatory activity against RAW264.7 cells with the IC50 values within an interval of 12.00–59.48.00 μg/mL. Especially, two triazoles of adenosine with indirubin-3′-oxime at O- and N1 positions expressed the ACE2 and 3CLpro inhibitory activities in which the triazole of adenosine with indirubin-3′-oxime at N1 inhibited both ACE2 and 3CLpro inhibitory activities with IC50 values of 135.62 and 142.95 μg/mL, respectively.

Utility of Coproporphyrin-I Determination in First-in-Human Study for Early Evaluation of OATP1B Inhibitory Potential Based on Investigation of Ensitrelvir, an Oral SARS-CoV-2 3C-Like Protease Inhibitor

Coproporphyrin-I (CP-I) has been investigated as an endogenous biomarker of organic anion transporting polypeptide (OATP) 1B. Here, we determined the CP-I concentrations in a cocktail drug-drug interaction (DDI) study of ensitrelvir to evaluate the OATP1B inhibitory potential because ensitrelvir had increased plasma concentrations of rosuvastatin in this study, raising concerns about breast cancer resistance protein and OATP1B inhibition. Furthermore, CP-I concentrations were compared between active and placebo groups in a first-in-human (FIH) study of ensitrelvir to verify whether the OATP1B inhibitory potential could be estimated at an early drug development stage. In the cocktail DDI study, CP-I did not differ between with/without administration of ensitrelvir, indicating that ensitrelvir has no OATP1B inhibitory effect. Although there were some individual variabilities in CP-I concentrations among the treatment groups in the FIH study, the normalization of CP-I concentrations with pre-dose values minimized these variabilities, suggesting that this normalized method would be helpful for comparing the CP-I from different participants. Finally, we concluded that CP-I concentrations were not affected by ensitrelvir in the FIH study. These results suggested that the CP-I determination in an FIH study and its normalized method can be useful for an early evaluation of the OATP1B-mediated DDI potential in humans.