An oral SARS-CoV-2 Mpro inhibitor clinical candidate for the treatment of COVID-19

Exploring covalent inhibitors of SARS-CoV-2 main protease: from peptidomimetics to novel scaffolds

Peptidomimetic inhibitors mimic natural peptide substrates, employing electrophilic warheads to covalently interact with the catalytic Cys145 of Mpro. Examples include aldehydes, α-ketoamides, and aza-peptides, with discussions on their mechanisms of action, potency, and structural insights. Non-peptidomimetic inhibitors utilise diverse scaffolds and mechanisms, achieving covalent modification of Mpro.

Silaproline-bearing nirmatrelvir derivatives are potent inhibitors of the SARS-CoV-2 main protease highlighting the value of silicon-derivatives in structure-activity-relationship studies

Nirmatrelvir is a substrate-related inhibitor of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) main protease (Mpro) that is clinically used in combination with ritonavir to treat COVID-19. Derivatives of nirmatrelvir, modified at the substrate P2-equivalent position, have been developed to fine-tune inhibitor properties and are now in clinical use. We report the synthesis of nirmatrelvir derivatives with a (R)-4,4-dimethyl-4-silaproline (silaproline) group at the P2-equivalent position. Mass spectrometry (MS)-based assays demonstrate that silaproline-bearing nirmatrelvir derivatives efficiently inhibit isolated recombinant Mpro, albeit with reduced potency compared to nirmatrelvir. Investigations with SARS-CoV-2 infected VeroE6 cells reveal that the silaproline-bearing inhibitors with a CF3 group at the P4-equivalent position inhibit viral progression, implying that incorporating silicon atoms into Mpro inhibitors can yield in vivo active inhibitors with appropriate optimization. MS and crystallographic studies show that the nucleophilic active site cysteine residue of Mpro (Cys145) reacts with the nitrile group of the silaproline-bearing inhibitors. Substituting the electrophilic nitrile group for a non-activated terminal alkyne shifts the inhibition mode from reversible covalent inhibition to irreversible covalent inhibition. One of the two prochiral silaproline methyl groups occupies space in the S2 pocket that is unoccupied in Mpro:nirmatrelvir complex structures, highlighting the value of sila-derivatives in structure-activity-relationship (SAR) studies. The combined results highlight the potential of silicon-containing molecules for inhibition of Mpro and, by implication, other nucleophilic cysteine enzymes.

A deep learning model for structure-based bioactivity optimization and its application in the bioactivity optimization of a SARS-CoV-2 main protease inhibitor

Bioactivity optimization is a crucial and technical task in the early stages of drug discovery, traditionally carried out through iterative substituent optimization, a process that is often both time-consuming and expensive. To address this challenge, we present Pocket-StrMod, a deep-learning model tailored for structure-based bioactivity optimization. Pocket-StrMod employs an autoregressive flow-based architecture, optimizing molecules within a specific protein binding pocket while explicitly incorporating chemical expertise. It synchronously optimizes all substituents by generating atoms and covalent bonds at designated sites within a molecular scaffold nestled inside a protein pocket. We applied this model to optimize the bioactivity of Hit1, an inhibitor of the SARS-CoV-2 main protease (Mpro) with initially poor bioactivity (IC50 : 34.56 μM). Following two rounds of optimization, six compounds were selected for synthesis and bioactivity testing. This led to the discovery of C5, a potent compound with an IC50 value of 33.6 nM, marking a remarkable 1028-fold improvement over Hit1. Furthermore, C5 demonstrated promising in vitro antiviral activity against SARS-CoV-2. Collectively, these findings underscore the great potential of deep learning in facilitating rapid and cost-effective bioactivity optimization in the early phases of drug development.

Research progress on critical viral protease inhibitors for coronaviruses and enteroviruses

Viral infectious diseases have been seriously affecting human life and health. SARS-CoV-2 was the pathogen that caused Coronavirus Disease 2019 (COVID-19), and the impact of COVID-19 is still existing. Enterovirus 71 (EV71) is the primary pathogen of hand, foot, and mouth disease (HFMD), and no effective direct-acting antiviral drugs targeting EV71 has been approved yet. Innate antiviral strategies play an important role in preventing virus infections depending on the powerful immune regulatory system of body, while viruses have evolved to exploit diverse methods to overcome immune response. Viral proteases, which are known in cleaving viral polyproteins, have also been found to modulate the innate immunity of host cells, thereby promoting viral proliferation. Herein, we reviewed the current development of SARS-CoV-2 3CLpro, PLpro, and EV71 3Cpro and 2Apro, mainly including structure, function, modulation of immune response, and inhibitors of these four proteases, to further deepen the understanding of viral pathogenesis and provide a new perspective for subsequent corresponding drug development.

Development of acylhydrazone linked thiazoles as non-covalent dual inhibitors of SARS-CoV-2 proteases

SARS-CoV-2's papain-like protease (PLPro) and main protease (MPro) are essential for viral maturation and replication. Currently, Paxlovid is recommended to treat viral infections, but the emergence of Nirmatrelvir resistance new variants poses serious global risks. Dual targeting agents restrict viral replication, act on other crucial viral pathways, or exert simultaneous protease inhibition, increasing the complexity for the virus to develop resistance, and the design of dual inhibitors is an attractive strategy. Herein, we present research on new thiazole-aryl and thiazole-ester compounds that function as cysteine specific non-covalent competitive dual inhibitors of SARS-CoV-2's papain-like protease (PLPro) and main protease (MPro). Twelve of the 36 compounds demonstrated dual inhibition in the range of nanomolar to low micromolar concentrations while five others exhibit selective PLPro inhibition. Minimal cytotoxicity against two mammalian cell lines and no oral toxicity in rats (LD50 > 2000 mg/kg) were observed. SARS-CoV-2 viral load was successfully reduced by several compounds tested. N-acyl hydrazone (NAH)-thiazole core while forms π-π interactions with the catalytic histidine side chain (H41) in MPro active site, it exhibits a series of hydrophobic and hydrophilic interaction in the interface of BL2 loop and the active site of PLPro. Non-covalent dual inhibition demonstrated by novel NAH-thiazole derivatives in this study provides a path for the development of efficient antiviral agents against coronaviruses.

Mutagenesis-Guided Target Identification Reveals the Protein-Binding Domain of Nsp14 in Coronaviruses as the Target of a Labdane-Oxindole Compound

The non-structural protein (nsp) 14 of coronaviruses plays an important role in maintaining the genomic stability of the virus during viral replication. This had garnered significant interest towards the identification and development of inhibitors against nsp14, specifically its exoribonuclease (ExoN) domain. However, no inhibitors have been successfully developed to date. The bioactivity of the nsp14-ExoN is governed through a complex formation with its co-factor nsp10. This provides opportunities to target the protein assembly as an antiviral modality. In this study, a labdane-oxindole compound (OX18) was identified as a promising new antiviral agent against coronaviruses. Through a combination of FRET- and BRET-based approaches, OX18 was found to target the nsp10-binding domain of nsp14. A key escape mutation to OX18 in nsp14 was also identified in our study, albeit compromising its exoribonuclease activity. To our knowledge, OX18 is the first small molecule to target the nsp14/10 protein assembly. As such, our work paves the way for the development of future inhibitors of the nsp14-ExoN with increased potency and complexity.

Expanding the utilization of binding pockets proves to be effective for noncovalent small molecule inhibitors against SARS-CoV-2 Mpro

The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in millions of deaths and continues to pose serious threats to global public health. The main protease (Mpro) of SARS-CoV-2 is crucial for viral replication and its conservation, making it an attractive drug target. Here, we employed a structure-based drug design strategy to develop and optimize novel inhibitors targeting SARS-CoV-2 Mpro. By fully exploring occupation of the S1, S2, and S3/S4 binding pockets, we identified eight promising inhibitors with half-maximal inhibitory concentration (IC50) values below 20 nM. The cocrystal structure of Mpro with compound 10 highlighted the crucial roles of the interactions within the S3/S4 pockets in inhibitor potency enhancement. These findings demonstrated that expanding the utilization of these binding pockets was an effective strategy for developing noncovalent small molecule inhibitors that target SARS-CoV-2 Mpro. Compound 4 demonstrated outstanding in vitro antiviral activity against wild-type SARS-CoV-2 with an EC50 of 9.4 nM. Moreover, oral treatment with compounds 1 and 9 exhibited excellent antiviral potency and substantially ameliorated virus-induced tissue damage in the lungs of Omicron BA.5-infected K18-human ACE2 (K18-hACE2) transgenic mice, indicating that these novel noncovalent inhibitors could be potential oral agents for the treatment of COVID-19.

The efficiency of high-throughput screening (HTS) and in-silico data analysis during medical emergencies: Identification of effective antiviral 3CLpro inhibitors

The COVID-19 pandemic highlighted the importance of accelerating the drug discovery process. The 3-chymotrypsin-like protease (3CLpro) is a critical enzyme in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral replication process and was quickly identified as a prime target for drug development. This study leverages High-Throughput Screening (HTS) to identify novel 3CLpro inhibitors. We screened a different library of 325,000 compounds, leading to the discovery of two new chemical scaffolds with selective inhibitory activity against 3CLpro. In-silico analysis and further experimental validation, elucidated the binding modes and mechanisms of action, revealing a covalent inhibitor targeting the catalytic pocket and two allosteric inhibitors affecting the monomer/dimer equilibrium of 3CLpro. The identified compounds demonstrated significant antiviral activity in vitro, reducing SARS-CoV-2 replication in VeroE6 and Calu-3 cell lines. This study highlights the potential of combining HTS and computational approaches to accelerate the discovery of effective antiviral agents, suggesting a workflow to support the research and the design of effective therapeutic strategies.

MIDD in Japan- Implementations, challenges and opportunities

In Japan, there has been a growing adoption of Model Informed Drug Development (MIDD) approaches as the rationale for optimal dose decision and modeling outputs have supported better characterizing the risk-benefit profile of a drug by accelerating development period and regulatory-approval pathways. Three primary guidelines on pharmacometric analysis tools issued in Japan between 2019 and 2020 function as a shared communication medium between pharmaceutical companies and the regulatory agency in Japan and have contributed to increasing number of MIDD applications embedded into new drug application documents. This review article describes how the Pharmaceuticals and Medical Devices Agency have been promoting the adoption of modeling and simulation and how MIDD applications have been implemented in Japan by introducing multiple case studies. The intent is to share the knowledge and to promote the harmonization of regulations globally for accelerating the appropriate utilization of MIDD tools and implementation of various new technologies. (149 words).

Safety of Nirmatrelvir-Ritonavir Administration in Children With Immunodeficiency and/or Comorbidities With SARS-CoV-2 Infection: A Retrospective Clinical Report

INTRODUCTION

Despite the generally mild course of COVID-19 in children, immunocompromised patients may experience complications or severe infection. This study reports the clinical outcomes of pediatric patients treated with nirmatrelvir and ritonavir (N/R) for SARS-CoV-2 infection.

METHODS

We retrospectively reported the data of children with any immunodeficiency with COVID-19 who received N/R treatment between March 2022 and June 2023 at the Bambino Gesù Children's Hospital. Patients were treated with N/R for 5 days. We compared liver and kidney function before and after treatment with N/R and looked for a relationship between the duration of COVID-19 infection and the time from positivity to administration of N/R administration.

RESULTS

A total of 85 pediatric immunocompromised patients with COVID-19 were included in the study, with a mean age of 10.7 years (SD 4.8), mostly males (60%). We found a significant difference in the viral load before and after N/R administration. Four patients (4.7%) experienced adverse events related to N/R therapy. One of these had to discontinue N/R administration. Three patients (3.5%) experienced negative effects of drug interactions during N/R therapy, namely an increase of sirolimus and ciclosporin serum levels. A significant positive correlation was found between the time from SARS-CoV-2 positivity to N/R administration and the duration of SARS-CoV-2 swab positivity (R = 0.78, P < 0.001), suggesting that the earlier N/R is administered, the shorter the duration of COVID-19 in the study sample.

CONCLUSION

Our experience shows that N/R is reasonably safe in the pediatric population and could favor viral clearance, thus reducing the duration of infection.

Targeted protein degraders of SARS-CoV-2 Mpro are more active than enzymatic inhibition alone with activity against nirmatrelvir resistant virus

BACKGROUND

Effective antiviral therapy is lacking for most viral infections, and when available, is frequently compromised by the selection of resistance. Targeted protein degraders could provide an avenue to more effective antivirals, able to overcome the selection of resistance. The aim of this study was to determine whether adaptation of SARS-CoV-2 main protease (Mpro, also described as chymotrypsin-like protease (3CLpro) or non-structural protein 5 (Nsp5)) inhibitors into degraders leads to increased antiviral activity, including activity against resistant virus.

METHODS

We adapted the clinically approved Mpro inhibitor nirmatrelvir into a panel of degraders. Size-matched non-degrading controls were also synthesised to discriminate degradation activity from inhibition activity. Degrader activity was confirmed using an inducible Mpro-HiBiT tag expressing cell line. Antiviral activity against both wildtype and nirmatrelvir-resistant virus was performed using infection of susceptible cell lines.

RESULTS

Here we show three compounds, derived from nirmatrelvir and utilising VHL or IAP ubiquitin ligase recruiters, capable of degrading Mpro protein in a concentration, time and proteasome dependent fashion. These compounds also degrade nirmatrelvir-resistant mutant Mpro. The most potent of these compounds possesses enhanced antiviral activity against multiple wildtype SARS-CoV-2 strains and nirmatrelvir-resistant strains compared to non-degrading controls.

CONCLUSIONS

This work demonstrates the feasibility of generating degraders from viral protein inhibitors, and confirms that degraders possess higher antiviral potency and activity against resistant virus, compared to size matched non-degrading enzymatic inhibitors. These findings further support the development of targeted viral protein degraders as antiviral drugs, which may lead to more effective antiviral therapies for the future.

Structure-based discovery of highly bioavailable, covalent, broad-spectrum coronavirus MPro inhibitors with potent in vivo efficacy

The main protease (MPro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a validated drug target. Starting with a lead-like dihydrouracil chemotype identified in a large-library docking campaign, we improved MPro inhibition >1000-fold by engaging additional MPro subsites and using a latent electrophile to engage Cys145. Advanced leads from this series show pan-coronavirus antiviral activity, low clearance in mice, and for AVI-4773, a rapid reduction in viral titers >1,000,000 after just three doses. Both compounds are well distributed in mouse tissues, including brain, where concentrations >1000× the 90% effective concentration are observed 8 hours after oral dosing for AVI-4773. AVI-4516 shows minimal inhibition of major cytochrome P450s and human proteases. AVI-4516 also exhibits synergy with the RNA-dependent RNA polymerase inhibitor, molnupiravir, in cellular infection models. Related analogs strongly inhibit nirmatrelvir-resistant MPro mutant virus. The properties of this chemotype are differentiated from existing clinical and preclinical MPro inhibitors and will advance therapeutic development against emerging SARS-CoV-2 variants and other coronaviruses.

Nitrogen-Based Organofluorine Functional Molecules: Synthesis and Applications

Fluorine and nitrogen form a successful partnership in organic synthesis, medicinal chemistry, and material sciences. Although fluorine-nitrogen chemistry has a long and rich history, this field has received increasing interest and made remarkable progress over the past two decades, driven by recent advancements in transition metal and organocatalysis and photochemistry. This review, emphasizing contributions from 2015 to 2023, aims to update the state of the art of the synthesis and applications of nitrogen-based organofluorine functional molecules in organic synthesis and medicinal chemistry. In dedicated sections, we first focus on fluorine-containing reagents organized according to the type of fluorine-containing groups attached to nitrogen, including N-F, N-RF, N-SRF, and N-ORF. This review also covers nitrogen-linked fluorine-containing building blocks, catalysts, pharmaceuticals, and agrochemicals, underlining these components' broad applicability and growing importance in modern chemistry.

Synthesis of 3'-modified xylofuranosyl nucleosides bearing 5'-silyl or -butyryl groups and their antiviral effect against RNA viruses

D-xylofuranosyl nucleoside analogues bearing alkylthio and glucosylthio substituents at the C3'-position were prepared by photoinitiated radical-mediated hydrothiolation reactions from the corresponding 2',5'-di-O-silyl-3'-exomethylene uridine. Sequential desilylation and 5'-O-butyrylation of the 3'-thiosubstituted molecules produced a 24-membered nucleoside series with diverse substitution patterns, and the compounds were evaluated for their in vitro antiviral activity against three dangerous human RNA viruses, SARS-CoV-2, SINV and CHIKV. Eight compounds exhibited SARS-CoV-2 activity with low micromolar EC50 values in Vero E6 cells, and two of them also inhibited virus growth in human Calu cells. The best anti-SARS-CoV-2 activity was exhibited by 2',5'-di-O-silylated 3'-C-alkylthio nucleosides. Twelve compounds showed in vitro antiviral activity against CHIKV and fourteen against SINV with low micromolar EC50 values, with the 5'-butyryl-2'-silyl-3'-alkylthio substitution pattern being the most favorable against both viruses. In the case of the tested nucleosides, removal of the 2'-O-silyl group completely abolished the antiviral activity of the compounds against all three viruses. Overall, the most potent antiviral agent was the disilylated 3'-glucosylthio xylonucleoside, which showed excellent and specific antiviral activity against SINV with an EC50 value of 3 μM and no toxic effect at the highest tested concentration of 120 μM.

3-Deazaguanosine inhibits SARS-CoV-2 viral replication and reduces the risk of COVID-19 pneumonia in hamster

The COVID-19 pandemic highlighted the serious threat that coronaviruses have on public health. Because coronavirus continuously undergoes cross-species transmission, additional therapeutic agents and targets are urgently needed. Here, we show that a 3-deazapurine ribonucleoside, 3-Deazaguanosine (C3Guo, 2), has potent antiviral activity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Unexpectedly, C3Guo (2) does not act as an inhibitor of RNA-dependent RNA polymerase (RdRp), which is the therapeutic target of two key nucleoside/nucleotide inhibitors approved for the treatment of COVID-19 (Remdesivir and Molnupiravir); instead, it seems to function by targeting the capping machinery of viral RNA. In hamsters infected with SARS-CoV-2, administration of 2 markedly reduced infectious viral titers, and prevented the development of COVID-19 pneumonia better than Molnupiravir. The potency of 2 against SARS-CoV-2 underscores its potential as an effective therapeutic agent for COVID-19 and future zoonotic coronavirus infections and raises the possibility of antiviral nucleoside analogs with alternative therapeutic targets to RdRp.

Genetic Predictors of Paxlovid Treatment Response: The Role of IFNAR2, OAS1, OAS3, and ACE2 in COVID-19 Clinical Course

Background: This study investigated the role of genetic polymorphisms in IFNAR2, OAS1, OAS3, and ACE2 as predictors of Paxlovid treatment response, specifically examining their influence on the clinical course and laboratory parameters of COVID-19 patients. Methods: We analyzed the impact of polymorphisms in genes associated with the interferon pathway (IFNAR2 rs2236757), antiviral response (OAS1 rs10774671, OAS3 rs10735079), and viral entry (ACE2 rs2074192) in individuals treated with Paxlovid. Results: Our findings suggest that genetic variations in these genes may modulate the immune response and coagulation pathways in the context of Paxlovid treatment during COVID-19 infection. Specifically, the IFNAR2 rs2236757 G allele was associated with alterations in inflammatory and coagulation markers, while polymorphisms in OAS1 and OAS3 influenced coagulation parameters. Furthermore, specific genotypes were linked to changes in clinical parameters such as oxygen saturation, leukocyte count, and liver function markers in Paxlovid-treated patients. Conclusions: These results highlight the potential of considering genetic factors in understanding individual responses to COVID-19 treatment with Paxlovid and informing future personalized approaches.

Empowering Diastereoselective Cyclopropanation of Unactivated Alkenes with Sulfur Ylides through Nucleopalladation

Regio- and stereoselective cyclopropanation of unactivated alkenes under mild conditions remains a challenging yet fundamental transformation. We present a versatile palladium(II)-catalyzed method for the diastereoselective cyclopropanation of alkenyl amines and alkenyl acids, which leverages the nucleopalladation mechanism and the unique ambiphilic reactivity of sulfur ylides. This Pd(II)/Pd(IV) catalytic protocol selectively delivers anti-cyclopropanes for allylamines with a removable isoquinoline-1-carboxamide auxiliary, while enabling excellent syn-selectivity for alkenyl acid derivatives containing a 2-(aminomethyl)pyridine derivative as a directing group. The protocol is operationally simple and scalable, features a wide substrate generality, and also remains effective in the presence of various medicinally relevant scaffolds. The cyclopropane products were further transformed into 1,2,3-trifunctionalized cyclopropanes and engaged in an aza-Piancatelli reaction, introducing additional molecular complexity. DFT studies were performed to shed light on the reaction mechanism and the origins of the observed stereoselectivity.

Go for Gold: Development of a Scalable Synthesis of [1-(Ethoxycarbonyl)cyclopropyl] Triphenylphosphonium Tetrafluoroborate, a Key Reagent to Explore Covalent Monopolar Spindle 1 Inhibitors

Covalent approaches have resurged in drug discovery and chemical biology during the last decade. So-called targeted covalent inhibitors typically show a strong and persistent drug-target interaction as well as a high degree of selectivity. In our research group, RMS-07 (8), a First-in-Class covalent inhibitor of the protein kinase threonine tyrosine kinase (TTK)/monopolar spindle 1, which shows promising results in a variety of different solid cancer cell types and will be further optimized in terms of covalent binding kinetics, has recently been developed. However, synthetic accessibility is restricted by a high price and limited availability of [1-(ethoxycarbonyl)cyclopropyl] triphenylphosphonium tetrafluoroborate (10), a key reagent required to assemble the tricyclic core scaffold in a Wittig-type cyclization reaction. This reagent is also described as a valuable synthon for the synthesis of a range of ring systems with interesting applications in medicinal chemistry. However, reliable procedures for its large-scale synthesis are scarce. Only one prior report describes the synthesis of reagent 10, and it contains limited experimental details, making it challenging to reproduce and scale up. Herein, a concise and reproducible decigram-scale synthetic protocol for accessing key reagent 10 is described.

Mini review: SHEN26, a novel oral antiviral drug for COVID-19 treatment

Over two years into the pandemic, global collaboration led to effective antiviral drugs targeting SARS-CoV-2's RdRp and 3CL protease. However, the virus continues to evolve, and certain low-virulence variants still circulate. Despite reduced virulence, ongoing transmission raises the risk of new mutations, underscoring the need for continued vigilance, research, and expansion of our antiviral and vaccine strategies. Our research team has developed SHEN26, a promising small-molecule antiviral drug for the treatment of COVID-19. This mini-review explores its development, including history, synthesis, preclinical evaluations, and findings from Phase I and II clinical trials. Data from each research phase further underscores SHEN26's potential as a safe and effective oral antiviral treatment for COVID-19, while also emphasizing its broader relevance in combating emerging RNA viral infections.

Design, synthesis and activity evaluation of 4-(quinoline-2-yl)aniline derivatives as SARS-CoV‑2 main protease inhibitors

Since 2020, numerous compounds have been investigated for their potential use in treating SARS-CoV-2 infections. By identifying the molecular targets during the virus replication process, rationally designed anti-SARS-CoV-2 agents are developed. Among these targets, the main protease (Mpro) is a crucial enzyme required for virus replication, and its highly conserved characteristic make it an important drug target for the development of anti-SARS-CoV-2 drugs. Herein, we utilized warhead-based design strategy to conduct the structural optimization of M-1 developed through virtual screening, leading to a series of novel Mpro inhibitors with 4-(quinolin-2-yl)aniline scaffold. Among them, M-32 exhibited good SARS-CoV-2 Mpro inhibitory activity (IC50 = 5.2 μM) with a nearly 25-fold increase. Isothermal titration calorimetry (ITC) directly proved that M-32 binds directly to SARS-CoV-2 Mpro in an entropy-driven manner. Mass spectrometry (MS) further confirmed the covalent binding ability of M-32 to Mpro. Meanwhile, M-32 effectively inhibited the replication of SARS-CoV-2 in Vero E6 cells (EC50 = 5.29 μM).

Design and synthesis of novel thioether analogs as promising antiviral agents: In vitro activity against enteroviruses of interest

The Enterovirus genus contains two major subgroups: rhinovirus (RV) species A-C and enterovirus (EV) ones A-D. While RV only infects the respiratory system, the EV can cause a wide variety of diseases, ranging from non-specific febrile illness to severe neurologic complications. To date, no curative treatments are commercially available. Our research team had recently developed EV-A71 inhibitors. To improve their activity and broaden their spectrum, we performed optimization of the structure following an iterative cycle of chemical modulations. As a result, we obtained two broad-spectrum inhibitors with micromolar activity against these 3 types of viruses (OM1260: EC50 (MRC-5, EV-A71) = 1.15 μM; EC50 (RD, EV-A71) = 4.38 μM; EC50 (MRC-5, E30) = 0.41 μM; EC50 (MRC-5, CVA24) = 1.15 μM; HR-568: EC50 (MRC-5, EV-A71) = 3.25 μM; EC50 (RD, EV-A71) = 1.53 μM; EC50 (MRC-5, E30) = 0.40 μM; EC50 (MRC-5, CVA24) = 1.22 μM). Docking studies shed light on structure-activity relationships, while time-of-drug addition assays confirmed their intervention during the early step of viral replication. Eventually, some pharmacokinetic modelling has been carried out to evaluate their druggability. All these results showed that OM1260 and HR-568 are promising candidates for further development.

A phycobiliprotein-based reporter assay for the evaluation of SARS-CoV-2 main protease activity

SARS-CoV-2 Mpro is crucial for viral replication and transcription and is highly conserved. Therefore, it is an ideal target for developing broad-spectrum antiviral drugs. To address resistance to existing drugs caused by mutations, a simple and sensitive method for detecting the activity of Mpro is needed. Considering the excellent fluorescence properties of phycobiliproteins, this study developed a phycobiliprotein-based reporter assay to evaluate Mpro activity. An engineered lyase was generated by inserting the Mpro recognition sequence between the phycobiliprotein lyases CpcF and CpcE. To ensure that the binding of CpcE and CpcF depended on the linker, a series of truncated forms were constructed. Among them, the activity of CpcE/F-10 was significantly reduced in the presence of Mpro; however, both genetic and chemical inhibition of Mpro activity reversed these results. These data indicated that the fluorescence of phycobiliproteins was negatively correlated with Mpro activity. The reporter assay developed here will contribute to determining the impact of Mpro mutations and screening for new inhibitors.

The Sprint to Develop Coronavirus Antivirals

The preclinical work leading to the discovery of PF-07321332 (nirmatrelvir) is described in the Featured Article summarized in this Viewpoint. This work resulted in an Emergency Use Authorization (EUA) for Paxlovid within two years of the project's start. In addition to the medicinal chemistry approach taken, the authors describe how they achieved this remarkable speed.

Decoding the selective chemical modulation of CYP3A4

Drug-drug interactions associate with concurrent uses of multiple medications. Cytochrome P450 (CYP) 3A4 metabolizes a large portion of marketed drugs. To maintain the efficacy of drugs metabolized by CYP3A4, pan-CYP3A inhibitors such as ritonavir are often co-administered. Although selective CYP3A4 inhibitors have greater therapeutic benefits as they avoid inhibiting unintended CYPs and undesirable clinical consequences, the high homology between CYP3A4 and CYP3A5 has hampered the development of such selective inhibitors. Here, we report a series of selective CYP3A4 inhibitors with scaffolds identified by high-throughput screening. Structural, functional, and computational analyses reveal that the differential C-terminal loop conformations and two distinct ligand binding surfaces disfavor the binding of selective CYP3A4 inhibitors to CYP3A5. Structure-guided design of compounds validates the model and yields analogs that are selective for CYP3A4 versus other major CYPs. These findings demonstrate the feasibility to selectively inhibit CYP3A4 and provide guidance for designing better CYP3A4 selective inhibitors.

Discovery of Nirmatrelvir (PF-07321332): A Potent, Orally Active Inhibitor of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS CoV-2) Main Protease

In early 2020, severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) infections leading to COVID-19 disease reached a global level leading to the World Health Organization (WHO) declaration of a pandemic. Scientists around the globe rapidly responded to try and discover novel therapeutics and repurpose extant drugs to treat the disease. This work describes the preclinical discovery efforts that led to the invention of PF-07321332 (nirmatrelvir, 14), a potent and orally active inhibitor of the SARS CoV-2 main protease (Mpro) enzyme. At the outset we focused on modifying PF-00835231 (1) discovered in 2004 as a potent inhibitor of the SARS CoV-1 Mpro with poor systemic exposure. Our effort was focused on modifying 1 with the goal of engineering in oral bioavailability by design, while maintaining cellular potency and low metabolic clearance. Modifications of 1 ultimately led to the invention of nirmatrelvir 14, the Mpro inhibitor component in PAXLOVID.

Lessons from the PROTECT-CH COVID-19 platform trial in care homes

Background

Coronavirus disease-2019 was associated with significant mortality and morbidity in care homes in 2020-1. Repurposed antiviral drugs might reduce morbidity and mortality through reducing viral transmission, infection, replication and inflammation. We aimed to compare the safety and efficacy of potential antiviral drugs in care home residents.

Methods

We designed a cluster-randomised, open-label, blinded end-point platform trial to test drugs in a postexposure prophylaxis paradigm. Participants aged 65+ years from United Kingdom care homes, with or without nursing, were eligible for participation. Care homes were to be allocated at random by computer to administer 42 days of antiviral agent (ciclesonide or niclosamide) plus standard care versus standard care alone to residents. The primary outcome at 60 days after randomisation comprised the most serious outcome, which was defined as all-cause mortality, all-cause hospitalisation, severe acute respiratory syndrome coronavirus 2 infection or no infection. Analysis would be by intention to treat using ordinal logistic regression. Other outcomes included individual components of the primary outcome, transmission, plus health economic and process evaluation outcomes. The planned sample size was 300 care homes corresponding to 9600 residents. With ~40% of care homes predicted to develop an outbreak during the trial, we needed to recruit 750 homes/24,000 residents.

Results

We initiated the trial including protocol, approvals, insurance, website, database, data algorithms, intervention selection and training materials. We built a network of principal investigators and staff (91) and care homes (299) to support the trial. However, we never contracted care homes or general practitioners since the trial was stopped in September 2021, as vaccination in care homes had significantly reduced infections. Multiple delays significantly delayed the start date, such as: (1) reduced prioritisation of pandemic trials in 2021; (2) cumbersome mechanisms for choosing the investigational medicinal products; (3) contracting between National Institute for Health and Care Research and the investigational medicinal product manufacturers; (4) publicising the investigational medicinal products; (5) identification of sufficient numbers of care homes; (6) identification and contracting with several thousand general practitioners; (7) limited research nurse availability and (8) identification of adequate insurance to cover care homes for research. Generic challenges included working across the four home nations with their different structures and regulations.

Limitations

The feasibility of contracting between the sponsor and the principal investigators, general practitioners and care homes; screening, consent and treatment of care home residents; data acquisition and the potential benefit of postexposure prophylaxis were never tested.

Conclusions

The success of vaccination meant that the role of postexposure prophylaxis of coronavirus disease-2019 in care home residents was not tested. Significant progress was made in developing the infrastructure and expertise necessary for a large-scale clinical trial of investigational medicinal products in United Kingdom care homes.

Future work

The role of postexposure prophylaxis of coronavirus disease-2019 in care home residents remains undefined. Significant logistical barriers to conducting research in care homes need to be removed urgently before future studies are possible. Further work is required to develop the infrastructure for clinical trials of investigational medicinal products in care homes. Serious consideration should be given to building and then hibernating a pandemic-ready platform trial suitable for care home research.

Funding

This article presents independent research funded by the National Institute for Health and Care Research (NIHR) Health Technology Assessment programme as award number NIHR133443.

Dynamic Cap-Mediated Substrate Access and Potent Inhibitor Design of Monkeypox Virus I7L Protease

Monkeypox virus (MPXV), an orthopoxvirus that has long been endemic in Africa, has posed a significant global health threat since 2022. The I7L protease, a highly conserved cysteine proteinase essential for orthopoxvirus replication, represents a promising target for broad-spectrum antiviral drug development. Here, the first crystal structure of MPXV I7L protease is reported, revealing its unique dimeric form and different conformations of a cap region nearby the active site. Molecular dynamics simulations and AlphaFold3 prediction of protease-substrate structures both suggest that this highly flexible cap acts as a conformational switch, regulating the substrate access to the active site. Additionally, the structural basis of substrate recognition and the catalytic mechanism of the protease are elucidated, mapping determinants of substrate specificity. These insights enable us to design covalent inhibitors to mimic the natural substrates and develop a fluorescence resonance energy transfer (FRET)-based protease assay to effectively assess the inhibitory activity, leading to the discovery of first-in-class inhibitors of MPXV I7L protease with nanomolar potency. Therefore, this work provides a comprehensive understanding of the MPXV I7L protease's structure, dynamics, and function, and presents an example of successful rational design of covalent peptidomimetic inhibitors, serving as a good starting point for drug development against MPXV.

Targeting the liquid-liquid phase separation of nucleocapsid broadly inhibits the replication of SARS-CoV-2 strains

The COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to a global public health crisis. The nucleocapsid (N) protein plays a pivotal role in a variety of biological processes in the life cycle of SARS-CoV-2, such as viral assembly. In this study, we investigated the liquid-liquid phase separation (LLPS) capacity of the N protein of seven SARS-CoV-2 strains, including the variants of concern (VOC) and interest (VOI), and its impact on viral replication. Using bioinformatic tools, we analyzed 11,433,558 complete genomes of SARS-CoV-2 and revealed a high degree of sequence conservation of N gene. While all the seven N proteins could undergo LLPS with RNA, the mutations in N impair its capacity of LLPS. With a SARS-CoV-2 trans-complementation system, we showed that SARS-CoV-2 variants carrying mutated N proteins exhibit impaired replication, highlighting the importance of LLPS of N in viral replication. We further demonstrated that (-)-gallocatechin gallate (GCG) efficiently inhibits the LLPS of N proteins and significantly suppresses the replication of different SARS-CoV-2 strains. Thus, our findings indicate that targeting the N-LLPS could be a viable strategy for the development of antiviral treatments against various SARS-CoV-2 strains, including those yet to emerge.

A novel PLpro inhibitor improves outcomes in a pre-clinical model of long COVID

The COVID-19 pandemic caused by the coronavirus SARS-CoV-2 has highlighted the vulnerability of a globally connected population to zoonotic viruses. The FDA-approved coronavirus antiviral Paxlovid targets the essential SARS-CoV-2 main protease, Mpro. Whilst effective in the acute phase of a COVID infection, Paxlovid cannot be used by all patients, can lead to viral recurrence, and does not protect against post-acute sequelae of COVID-19 (PASC), commonly known as long COVID, an emerging significant health burden that remains poorly understood and untreated. Alternative antivirals that are addressing broader patient needs are urgently required. We here report our drug discovery efforts to target PLpro, a further essential coronaviral protease, for which we report a novel chemical scaffold that targets SARS-CoV-2 PLpro with low nanomolar activity, and which exhibits activity against PLpro of other pathogenic coronaviruses. Our lead compound shows excellent in vivo efficacy in a mouse model of severe acute disease. Importantly, our mouse model recapitulates long-term pathologies matching closely those seen in PASC patients. Our lead compound offers protection against a range of PASC symptoms in this model, prevents lung pathology and reduces brain dysfunction. This provides proof-of-principle that PLpro inhibition may have clinical relevance for PASC prevention and treatment going forward.

A Reflection on the Use of Molecular Simulation to Respond to SARS-CoV-2 Pandemic Threats

Molecular simulations play important roles in understanding the lifecycle of the SARS-CoV-2 virus and contribute to the design and development of antiviral agents and diagnostic tests for COVID. Here, we discuss the insights that such simulations have provided and the challenges involved, focusing on the SARS-CoV-2 main protease (Mpro) and the spike glycoprotein. Mpro is the leading target for antivirals, while the spike glycoprotein is the target for vaccine design. Finally, we reflect on lessons from this pandemic for the simulation community. Data sharing initiatives and collaborations across the international research community contributed to advancing knowledge and should be built on to help in future pandemics and other global challenges such as antimicrobial resistance.

Development of a highly sensitive luciferase assay for intracellular evaluation of coronavirus Mpro activity

COVID-19, caused by SARS-CoV-2 virus, has emerged as a global threat to human health. The main protease (Mpro) of SARS-CoV-2 is an excellent target for the development of antiviral drugs against COVID-19, and various protease biosensors have been developed to evaluate anti-coronavirus drugs. However, the application of these protease biosensors was limited due to high background fluorescence, poor signal-to-noise ratios, and constraints in enzyme activity thresholds for accessing live viruses. In this study, we rationally designed a highly conserved Mpro cleavage site sequence among different coronaviruses (CoVs) with high proteolytic activity, and described an intracellular coronavirus Mpro proteolytic (ICMP) reporter system that takes advantage of virus-encoded Mpro expressed in infected cells to reform the NanoBiT fluorescent protein. The system can be used to visualize and identify cells infected with coronavirus, and demonstrated high compatibility with various Mpro proteins from 13 different mammalian coronaviruses (covering α, β, γ, and δ CoVs), exhibiting at least a 1,030-fold increase in luminescence. Stronger Nluc signals were detectable with CoV 229E virus infection at a MOI of 0.001. Additionally, the system proved suitable for evaluating and screening of antiviral compounds, including lufotrelvir, GC376, Nirmatrelvir, X77, MG-101, and the potential inhibitor Cynaroside. The ICMP system is not only an invaluable tool for the detection of live coronaviruses, but also for the discovery of antivirals against current and future pandemic coronaviruses.

Potent antiviral activity of simnotrelvir against key epidemic SARS-CoV-2 variants with a high resistance barrier

Simnotrelvir is an oral small-molecule antiviral agent targeting the 3C-like protease (3CLpro) of SARS-CoV-2, proven effective against the Delta variant with favorable pharmacokinetics and safety in preclinical study. In this study, we further evaluated the antiviral efficacy of simnotrelvir against a range of emerging Omicron variants, including BA.1, BA.4, BA.5, CH.1.1, XBB.1.5, XBB.1.16, EG.5, and JN.1. In vitro assays with Vero E6 cells confirmed that simnotrelvir exhibited robust antiviral activity across these variants, comparable to the Food and Drug Administration (FDA)-approved drug nirmatrelvir. Additionally, simnotrelvir demonstrated effective inhibition against several nirmatrelvir-resistant SARS-CoV-2 3CLpro mutants, including A260V, Y54A, (T21I + S144A), F140A, H172Y, and E166V. Importantly, simnotrelvir showed better potency against the E166V mutation compared to nirmatrelvir. Resistance selection studies revealed that BA.5 developed reduced sensitivity after 5 and 10 passages, increasing the IC50 values by 3.2 and 4.5-fold, respectively, while HCoV-OC43 showed an 8.3-fold increase after 12 passages. Despite this, simnotrelvir's overall efficacy remains strong. Furthermore, clinical trials demonstrated that combining simnotrelvir with ritonavir significantly shortened symptom resolution in COVID-19 patients. Genomic analysis of treated patients found random nucleotide substitutions but no significant mutations linked to 3CLpro resistance. In conclusion, simnotrelvir shows strong antiviral activity against SARS-CoV-2 variants and maintains a high barrier to resistance, reinforcing its potential as an effective therapeutic option for current and future SARS-CoV-2 variants.

Effectiveness of nirmatrelvir/ritonavir in hospitalized haematological malignancy patients with mild-to-moderate COVID-19: A retrospective study

Patients with haematological malignancies (HMs) are highly vulnerable to COVID-19 due to their immunocompromised status, which leads to prolonged viral clearance and severe outcomes. Nirmatrelvir/ritonavir has shown efficacy in reducing severity and mortality in high-risk COVID-19 outpatients, but its effectiveness in hospitalized HM patients remains unclear. We conducted a retrospective study to assess the effectiveness of nirmatrelvir/ritonavir on mortality and viral clearance in hospitalized HM patients with mild-to-moderate COVID-19 during China's first COVID-19 surge. Mortality rate and viral clearance time were the primary end-points. Cox proportional hazards models were used to detect factors associated with mortality and viral clearance. A total of 116 HM patients, with a median age of 47.2 years, hospitalized for a minimum of 5 days with mild-to-moderate COVID-19, were included in this study. There was no difference in the 90-day mortality rate between HM patients treated with nirmatrelvir/ritonavir within 5 days and those not treated (4.9% vs. 5.3%, p = 1.000). Nirmatrelvir/ritonavir use within 5 days reduced the time to viral clearance (hazard ratio [HR] = 1.59, 95% confidence interval [CI] 1.04-2.42). Nirmatrelvir/ritonavir use within 5 days in hospitalized HM patients with mild-to-moderate COVID-19 does not reduce mortality but accelerates viral clearance.

A small-molecule SARS-CoV-2 inhibitor targeting the membrane protein

The membrane (M) protein of betacoronaviruses is well conserved and has a key role in viral assembly1,2. Here we describe the identification of JNJ-9676, a small-molecule inhibitor targeting the coronavirus M protein. JNJ-9676 demonstrates in vitro nanomolar antiviral activity against SARS-CoV-2, SARS-CoV and sarbecovirus strains from bat and pangolin zoonotic origin. Using cryogenic electron microscopy (cryo-EM), we determined a binding pocket of JNJ-9676 formed by the transmembrane domains of the M protein dimer. Compound binding stabilized the M protein dimer in an altered conformational state between its long and short forms, preventing the release of infectious virus. In a pre-exposure Syrian golden hamster model, JNJ-9676 (25 mg per kg twice per day) showed excellent efficacy, illustrated by a significant reduction in viral load and infectious virus in the lung by 3.5 and 4 log10-transformed RNA copies and 50% tissue culture infective dose (TCID50) per mg lung, respectively. Histopathology scores at this dose were reduced to the baseline. In a post-exposure hamster model, JNJ-9676 was efficacious at 75 mg per kg twice per day even when added at 48 h after infection, when peak viral loads were observed. The M protein is an attractive antiviral target to block coronavirus replication, and JNJ-9676 represents an interesting chemical series towards identifying clinical candidates addressing the current and future coronavirus pandemics.

Therapeutic Drug Monitoring of Nirmatrelvir/Ritonavir (Paxlovid) in Patients Treated for COVID-19: Results From a Prospective Multicenter Observational Study

BACKGROUND

Paxlovid is a combination of the antiviral agents nirmatrelvir and ritonavir indicated for the oral treatment of high-risk, symptomatic patients with coronavirus disease 2019 (COVID-19). As real-world data on the plasma concentrations of nirmatrelvir/ritonavir (Paxlovid) are limited, the aim of this study was to investigate nirmatrelvir/ritonavir plasma trough levels in a clinical setting using therapeutic drug monitoring.

METHODS

A prospective, noninterventional, multicenter, observational clinical study was conducted in which the plasma trough levels of nirmatrelvir/ritonavir were simultaneously determined by using liquid chromatography tandem mass spectrometry in patients with symptomatic COVID-19. The blood samples were collected on days 1, 3, and 5 after the first full-dose day (day 0), and patient data such as sex, height, weight, renal function, liver enzymes, and concomitant (co-) medications were obtained to describe the plasma levels with respect to potential influencing factors.

RESULTS

A total of 46 blood samples from 21 patients were analyzed. The geometric mean C min was 4997 ng/mL for nirmatrelvir and 529.4 ng/mL for ritonavir. The plasma concentrations covered a wide range, the highest being observed in patients with advanced age and renally excreted comedications. Patients older than 65 years had a significantly higher risk of achieving excessive plasma trough concentrations above 8840 ng/mL for nirmatrelvir and 1440 ng/mL for ritonavir compared with younger patients (odds ratio 11.2, 95% confidence interval 1.04-120.4).

CONCLUSIONS

The plasma trough concentrations of nirmatrelvir and ritonavir in patients treated for symptomatic COVID-19 were higher than the reference values of 2210 ng/mL for nirmatrelvir and 360 ng/mL for ritonavir stated in the product characteristics. Advanced age and renally eliminated comedication were identified as possible influencing factors that warrant further investigation.

Endolysosome-targeted nanoparticle delivery of antiviral therapy for coronavirus infections

SARS-CoV-2 can infect cells through endocytic uptake, a process that is targeted by inhibition of lysosomal proteases. However, clinically this approach to treat viral infections has afforded mixed results, with some studies detailing an oral regimen of hydroxychloroquine accompanied by significant off-target toxicities. We rationalized that an organelle-targeted approach will avoid toxicity while increasing the concentration of the drug at the target. Here, we describe a lysosome-targeted, mefloquine-loaded poly(glycerol monostearate-co-ε-caprolactone) nanoparticle (MFQ-NP) for pulmonary delivery via inhalation. Mefloquine is a more effective inhibitor of viral endocytosis than hydroxychloroquine in cellular models of COVID-19. MFQ-NPs are less toxic than molecular mefloquine, are 100-150 nm in diameter, and possess a negative surface charge, which facilitates uptake via endocytosis allowing inhibition of lysosomal proteases. MFQ-NPs inhibit coronavirus infection in mouse MHV-A59 and human OC43 coronavirus model systems and inhibit SARS-CoV-2 WA1 and its Omicron variant in a human lung epithelium model. Organelle-targeted delivery is an effective means to inhibit viral infection.

Mechanistic Characterization of Covalent Enzyme Inhibition by Isothermal Titration Calorimetry Kinetic Competition (ITC-KC)

Covalent enzyme inhibitors can offer high potency and specificity and are increasingly sought after in drug discovery. They typically inhibit in two steps: noncovalent binding followed by covalent bond formation. Rational optimization requires quantitative information on both steps. Current methods for measuring these steps are technically demanding, time-consuming, and are not well suited for routine insertion into drug discovery pipelines. We have developed a new approach, using isothermal titration calorimetry kinetic competition (ITC-KC), that overcomes many of these challenges. ITC-KC measures enzyme activity directly, via the heat flow generated during catalysis, making it a sensitive and nearly universal approach. We performed extensive numerical simulations in which ITC-KC outperformed current methods with 3- to 10-fold greater accuracy. We applied ITC-KC to a library of 19 inhibitors of the protease 3CLpro from SARS-CoV-2 and found that the reactive warheads and noncovalent binding portions of these molecules influenced the two-step inhibition mechanism in complex and unpredictable ways. This highlights the need for detailed mechanistic information in the development of covalent inhibitors, information that ITC-KC can provide rapidly, accurately, and essentially universally.

Physiologically-based pharmacokinetic modelling guided dose evaluations of nirmatrelvir/ritonavir in renal impairment for the management of COVID-19

We aimed to address factors contributing to the pharmacokinetic changes of nirmatrelvir/ritonavir in renal impaired (RI) patients and recommend dosing adjustment via a physiologically-based pharmacokinetic (PBPK) modelling approach. A PBPK model of nirmatrelvir/ritonavir was developed via Simcyp® Simulator. Sensitivity analysis of the influence of hepatic CYP3A4 intrinsic clearance and abundance, as well as hepatic non-CYP3A4 metabolism (other human liver microsomes [HLM] CLint) was performed to evaluate the effects of RI on oral clearance of nirmatrelvir. Other HLM CLint, the most sensitive parameter, was adjusted, and the simulated plasma concentration profiles of nirmatrelvir in severe RI subjects were within the therapeutic index of 292-10 000 ng/mL for dosing regimens of loading doses of 300/100 mg followed by 150/100 mg or 75/100 mg twice daily of nirmatrelvir/ritonavir. Considering that nirmatrelvir is available as a 150 mg tablet, we recommend 300/100 mg followed by 150/100 mg twice daily as the dosing regimen to be investigated in severe RI.

The oral bioavailability of a pleuromutilin antibiotic candidate is increased after co-administration with the CYP3A4 inhibitor ritonavir and the P-gp inhibitor zosuquidar formulated as amorphous solid dispersions

The aim of the present work was to investigate if CYP-mediated metabolism or P-gp recognition were the main limitations to developing oral formulations of the pleuromutilin drug candidate CVH-174, 16, and to subsequently increase the bioavailability through a formulation design based on amorphous solid dispersions (ASDs) containing either a CYP3A inhibitor or a P-gp inhibitor or both. ASDs were produced using HPMC-5 with ritonavir and zosuquidar as CYP3A4 and P-gp inhibitors, respectively, through freeze-drying. The ASDs were characterized using XRPD over time to assess the stability of the formulations. The oral bioavailability was investigated in Sprague-Dawley rats following either oral or intravenous (IV) dosing. The results showed that ritonavir could be supersaturated when formulated in an HPMC-5-based ASD, whereas HPMC-5-based ASDs could not increase the solubility of CVH-174 and zosuquidar. The ASD formulations remained stable for the period covering the experiments. In vivo IV dosing showed that CVH-174 was metabolized fast with a half-life of 0.15 h. The oral bioavailability of CVH-174 was low ∼ 1 % and could not be increased by co-dosing with a P-gp inhibitor alone, whereas the CYP3A4 inhibitor ritonavir did increase the bioavailability. The combined co-administration of ritonavir- and zosuquidar-containing ASDs surprisingly increased CVH-174 bioavailability to around 18 %. In conclusion, the oral bioavailability of CVH-174 can be significantly increased through a formulation design encompassing an inhibitor of the CYP3A4 enzyme, and this holds great potential for the future development of an inherent metabolic labile pleuromutilin drug class.

Inhibitory efficacy and structural insights of Bofutrelvir against SARS-CoV-2 Mpro mutants and MERS-CoV Mpro

The COVID-19 pandemic has caused significant global health and economic disruption. Mutations E166N, E166R, E166N, S144A and His163A in the SARS-CoV-2 main protease (Mpro) have been implicated in reducing the efficacy of certain antiviral treatments. Bofutrelvir, a promising inhibitor, has shown effectiveness against SARS-CoV-2 Mpro. This study aims to evaluate the inhibitory effects of Bofutrelvir on the E166N, E166R, His163A, E166V and S144A mutants of SARS-CoV-2 Mpro, as well as on MERS-CoV Mpro. Our findings indicate a substantial reduction in the inhibitory potency of Bofutrelvir against these mutants and MERS-CoV, with IC50 values significantly higher than those for the wild-type SARS-CoV-2 Mpro. Specifically, the E166N, E166R, E166V, S144A, and H163A mutations significantly reduce the binding affinity and inhibitory effectiveness of Bofutrelvir due to disrupted hydrogen bonds, altered binding site stability, and reduced enzyme activity. Structural analysis of the crystal complexes showed that changes in interactions at the S1 subsite in the mutants and the loss of hydrogen bonds at the S4 subsite in MERS-CoV Mpro are critical factors contributing to the diminished inhibitory activity. These insights reveal the necessity of ongoing structural analysis to adapt therapeutic strategies.

Enzymatic Cascades for Stereoselective and Regioselective Amide Bond Assembly

Amide bond formation is fundamental in nature and is widely used in the synthesis of pharmaceuticals and other valuable products. Current methods for amide synthesis are often step and atom inefficient, requiring the use of protecting groups, deleterious reagents and organic solvents that create significant waste. The development of cleaner and more efficient catalytic methods for amide synthesis remains an urgent unmet need. Herein, we present novel biocatalytic cascade reactions for synthesising various amides under mild aqueous conditions from readily available organic nitriles combining nitrile hydrolysing enzymes and amide bond synthetase enzymes. These cooperative biocatalytic cascades enable kinetic resolution of racemic nitriles and provide a highly enantioselective biocatalytic extension of the Strecker reaction. The regioselective non-directed C-H bond amidation of simple arenes was demonstrated through the incorporation of photoredox catalysis to the front end of the cascade. C-H bond amidation of simple aromatic precursors was also achieved via a CO2 fixation cascade combining enzymatic carboxylation and amide bond synthesis in one-pot.

Bat-infecting merbecovirus HKU5-CoV lineage 2 can use human ACE2 as a cell entry receptor

Merbecoviruses comprise four viral species with remarkable genetic diversity: MERS-related coronavirus, Tylonycteris bat coronavirus HKU4, Pipistrellus bat coronavirus HKU5, and Hedgehog coronavirus 1. However, the potential human spillover risk of animal merbecoviruses remains to be investigated. Here, we reported the discovery of HKU5-CoV lineage 2 (HKU5-CoV-2) in bats that efficiently utilize human angiotensin-converting enzyme 2 (ACE2) as a functional receptor and exhibits a broad host tropism. Cryo-EM analysis of HKU5-CoV-2 receptor-binding domain (RBD) and human ACE2 complex revealed an entirely distinct binding mode compared with other ACE2-utilizing merbecoviruses with RBD footprint largely shared with ACE2-using sarbecoviruses and NL63. Structural and functional analyses indicate that HKU5-CoV-2 has a better adaptation to human ACE2 than lineage 1 HKU5-CoV. Authentic HKU5-CoV-2 infected human ACE2-expressing cell lines and human respiratory and enteric organoids. This study reveals a distinct lineage of HKU5-CoVs in bats that efficiently use human ACE2 and underscores their potential zoonotic risk.

Structural insights into the RNA binding inhibitors of the C-terminal domain of the SARS-CoV-2 nucleocapsid

The SARS-CoV-2 nucleocapsid (N) protein is an essential structural element of the virion, playing a crucial role in enclosing the viral genome into a ribonucleoprotein (RNP) assembly, as well as viral replication and transmission. The C-terminal domain of the N-protein (N-CTD) is essential for encapsidation, contributing to the stabilization of the RNP complex. In a previous study, three inhibitors (ceftriaxone, cefuroxime, and ampicillin) were screened for their potential to disrupt the RNA packaging process by targeting the N-protein. However, the binding efficacy, mechanism of RNA binding inhibition, and molecular insights of binding with N-CTD remain unclear. In this study, we evaluated the binding efficacy of these inhibitors using isothermal titration calorimetry (ITC), revealing the affinity of ceftriaxone (18 ± 1.3 μM), cefuroxime (55 ± 4.2 μM), and ampicillin (28 ± 1.2 μM) with the N-CTD. Further inhibition assay and fluorescence polarisation assay demonstrated RNA binding inhibition, with IC50 ranging from ∼ 12 to 18 μM and KD values between 24 μM to 32 μM for the inhibitors, respectively. Additionally, we also determined the inhibitor-bound complex crystal structures of N-CTD-Ceftriaxone (2.0 Å) and N-CTD-Ampicillin (2.2 Å), along with the structure of apo N-CTD (1.4 Å). These crystal structures revealed previously unobserved interaction sites involving residues K261, K266, R293, Q294, and W301 at the oligomerization interface and the predicted RNA-binding region of N-CTD. These findings provide valuable molecular insights into the inhibition of N-CTD, highlighting its potential as an underexplored but promising target for the development of novel antiviral agents against coronaviruses.

Design, synthesis, and antiviral activity of fragmented-lapatinib aminoquinazoline analogs towards SARS-CoV-2 inhibition

The severe impact of COVID-19 on global health and economies highlights the critical need for innovative treatments. Recently, lapatinib, a drug initially used for breast cancer, has been identified as a potential inhibitor of the main protease (Mpro) of SARS-CoV-2, meriting further investigation. Utilizing rational design strategies and guided by MD simulations, we developed novel aminoquinazoline analogs based on fragmented lapatinib's structure. Preliminary computational screenings identified promising candidates, which were synthesized using a concise 3-4 step process. In vitro assays demonstrated notable antiviral efficacy against SARS-CoV-2-infected cells for all analogs, with Bb1 showing an EC50 of 1.10 μM and significantly lower toxicity (13.55 % at 50 μM) compared to lapatinib. Further studies confirmed that these analogs effectively inhibit SARS-CoV-2 Mpro, with Bb7 displaying the highest activity. MD simulations revealed that Bb7 achieves stability within the Mpro binding pocket through interactions with specific residues. These findings indicate that aminoquinazoline analogs hold significant promise as therapeutic candidates for COVID-19.

Development of a Fluorescence Polarization Assay for the SARS-CoV-2 Papain-like Protease

The COVID-19 pandemic has caused significant losses to the global community. Although effective vaccination and antiviral therapeutics provide primary defense, SARS-CoV-2 remains a public health threat, given the emerging resistant variants. The SARS-CoV-2 papain-like protease (PLpro) is essential for viral replication and is a promising drug target. We recently designed a series of biarylphenyl PLpro inhibitors with a representative lead Jun12682 showing potent antiviral efficacy in a SARS-CoV-2 infection mouse model. In this study, we designed a fluorescein-labeled biarylphenyl probe Jun12781 and used it to optimize a fluorescence polarization (FP) assay. The FP assay is suitable for high-throughput screening with a Z' factor of 0.69. In addition, we found a positive correlation between the FP binding affinity and the enzymatic inhibitory potency of PLpro inhibitors, suggesting that the FP assay is valid in characterizing the binding affinity of PLpro inhibitors.

Structural Virology: The Key Determinants in Development of Antiviral Therapeutics

Structural virology has emerged as the foundation for the development of effective antiviral therapeutics. It is pivotal in providing crucial insights into the three-dimensional frame of viruses and viral proteins at atomic-level or near-atomic-level resolution. Structure-based assessment of viral components, including capsids, envelope proteins, replication machinery, and host interaction interfaces, is instrumental in unraveling the multiplex mechanisms of viral infection, replication, and pathogenesis. The structural elucidation of viral enzymes, including proteases, polymerases, and integrases, has been essential in combating viruses like HIV-1 and HIV-2, SARS-CoV-2, and influenza. Techniques including X-ray crystallography, Nuclear Magnetic Resonance spectroscopy, Cryo-electron Microscopy, and Cryo-electron Tomography have revolutionized the field of virology and significantly aided in the discovery of antiviral therapeutics. The ubiquity of chronic viral infections, along with the emergence and reemergence of new viral threats necessitate the development of novel antiviral strategies and agents, while the extensive structural diversity of viruses and their high mutation rates further underscore the critical need for structural analysis of viral proteins to aid antiviral development. This review highlights the significance of structure-based investigations for bridging the gap between structure and function, thus facilitating the development of effective antiviral therapeutics, vaccines, and antibodies for tackling emerging viral threats.

Single- and multiple-dose pharmacokinetics and safety of the SARS-CoV-2 3CL protease inhibitor RAY1216: a phase 1 study in healthy participants

Coronavirus disease 2019, which leads to pneumonia, is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). RAY1216 is a 3C-like protease inhibitor that targets SARS-CoV-2. The aim of our study was to assess the pharmacokinetics (PK) and safety of RAY1216 in healthy volunteers. This was a randomized, placebo-controlled, double-blind study consisting of four components: a single ascending dose study, a drug-drug interaction study, a multiple ascending dose study, and a food-effect study. All participants were randomly assigned to receive either a single dose or multiple doses of RAY1216 or placebo. A total of 88 healthy adult participants (male-to-female ratio of 1:1) aged 18-50 years were enrolled. A total of 37 participants (42%) experienced at least one adverse event (AE). All AEs were mild or moderate and were resolved without additional treatment. The most commonly reported adverse drug reactions were hypertriglyceridemia, hyperuricemia, and elevated serum creatinine levels. RAY1216 was well-absorbed after administration with exposure increasing in a dose-dependent manner. Food appeared to increase exposure and delay the absorption of RAY1216. Ritonavir significantly inhibited drug metabolism, and increased drug exposure increased the associated safety risks. RAY1216 was found to be well tolerated and safe in healthy participants. On the basis of preclinical results, PK characteristics, and the safety profile of RAY1216, a dosage of 400 mg three times daily was selected, thereby establishing a foundation for future research and for the clinical application of RAY1216.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT05829551.

Covalent inhibition of the SARS-CoV-2 NiRAN domain via an active-site cysteine

The kinase-like nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain of nsp12 in SARS-CoV-2 catalyzes the formation of the 5' RNA cap structure. This activity is required for viral replication, offering a new target for the development of antivirals. Here, we develop a high-throughput assay to screen for small molecule inhibitors targeting the SARS-CoV-2 NiRAN domain. We identified NiRAN covalent inhibitor 2 (NCI-2), a compound with a reactive chloromethyl group that covalently binds to an active site cysteine (Cys53) in the NiRAN domain, inhibiting its activity. NCI-2 can enter cells, bind to, and inactivate ectopically expressed nsp12. A cryo-EM reconstruction of the SARS-CoV-2 replication-transcription complex bound to NCI-2 offers a detailed structural blueprint for rational drug design. Although NCI-2 showed limited potency against SARS-CoV-2 replication in cells, our work lays the groundwork for developing more potent and selective inhibitors targeting the NiRAN domain. This approach presents a promising therapeutic strategy for effectively combating COVID-19 and potentially mitigating future coronavirus outbreaks.