Inhibitors of mpox VP39 2'-O methyltransferase efficiently inhibit the monkeypox virus

Elucidating the suppressive mechanism of four inhibitors on VP39 and unique conformational changes with protein in mode 2

Methyltransferase VP39 is an important target for the treatment of monkeypox, and inhibition of VP39 can effectively suppresses the transcription and translation of early viral RNA. However, very few inhibitors have been designed against VP39 and other viral MTases. In this work, four inhibitors (SFG, TO507, TO427 and TO1119) were used to investigate the binding mechanism with VP39. Moreover, VP39 has different modes of existence, but we do not understand the interaction mechanism of the complex system formed by the inhibitors with different modes of VP39, so we performed 1000 ns molecular dynamics simulations of the complexes formed by four inhibitors with VP39 in mode 1 and mode 2, and performed energy calculation and conformational analysis. The results of binding free energy showed that in the inhibitors-VP39 (mode 1) systems, TO507 and TO427 had a strong inhibitory effect on VP39, and residues ASP95, ARG97, PHE115 and VAL139 played important roles in the binding process of all four systems. Surprisingly, in the inhibitors-VP39 (mode 2) systems, four inhibitors underwent a large conformational change, with the amino acid moieties of the inhibitors undergoing a nearly 90° folding. And this change reduced the inhibitory effect of the inhibitors on VP39. In addition, the inhibitor TO507 also had a good inhibition effect on nsp14 of SARS-CoV-2 and NS5 of Zika virus. Therefore, this study suggests new ideas for the design and improvement of pan-MTase inhibitors, which are important for the treatment of pandemic infectious diseases, such as monkeypox and SARS-CoV-2.

Structure-based profiling of putative therapeutics against monkeypox virus VP39 using pharmacophore modelling and molecular dynamics simulation studies

The growing global health threat of the monkeypox virus (MPXV) underscores the critical need for effective antiviral agents, since there are currently no therapeutics. The MPXV VP39, a methyltransferase, is essential for viral replication, hence a potential target for anti-MPXV drug candidates. Herein, a structure-based pharmacophore modelling and molecular docking approach was employed to screen natural compounds (NCs: 581,426) from the COCONUT database for potential inhibitors of MPXV VP39. After ranking of the docking scores, an ensemble-based docking of the top-ranked 20 NCs against multiple conformations obtained from ttcluster analysis of the molecular dynamics simulation trajectory of unbound MPXV VP39 further identified five leads with favourable interaction profiles, drug-likeness, ADMET properties, and synthetic features when compared to the reference standard (sinefungin). Further analysis of the thermodynamic stability of the resulting complexes of the leads over a 100-ns MD simulation period revealed varying degrees of thermodynamic stability while maintaining the structural integrity of MPXV VP39. Furthermore, the thermodynamic binding free energy calculation, while corroborating the docking analysis, identified CNP0297833 (-39.07 kcal/mol), CNP0371756 (-25.76 kcal/mol), and CNP0402319 (-19.26 kcal/mol) as the most promising candidates, with better modulatory effect against MPXV VP39 relative to sinefungin (-3.68 kcal/mol). These leads were stabilised with hydrophobic (Phe115, Val139, and Val116) and electrostatic (Glu46 and Asp138) interactions in different conformational clusters. In addition to the observed consistent interaction patterns, favourable binding energies, pharmacokinetics, ADMET, thermodynamic stability, and molecular orbital energies of these leads, the potential for optimisation for enhanced binding features for the active site of MPXV VP39 was elucidated. Further in vitro investigation to validate these findings is suggested to establish the putative leads as therapeutics targeting the replication phase of MPXV.

Structural basis for broad-spectrum binding of AT-9010 to flaviviral methyltransferases

AT-9010 (2'-methyl-2'-fluoro guanosine triphosphate) is a GTP analog whose prodrug, AT-752 is under consideration in human medicine as a potential antiviral drug against certain flaviviruses. It was previously believed to inhibit viral replication by acting primarily as a chain terminator. However, it was discovered recently that it also binds the GTP binding site of the methyltransferase (MTase) domain of the orthoflavivirus polymerase, thus interfering with RNA capping. Here, we investigated the binding of AT-9010 to Ntaya and Zika virus MTases. Structural analysis using X-ray crystallography revealed similar interactions between the base and sugar moieties of AT-9010 and key residues in both MTases, although differences in hydrogen bonding were observed. Our analysis also suggested that the triphosphate part of AT-9010 is flexible. Despite minor variations, the overall binding mode of AT-9010 was found to be the same for all of the flaviviral MTases examined, suggesting a structural basis for the efficacy of AT-9010 against multiple orthoflavivirus MTases.

Sinefungin analogs targeting VP39 methyltransferase as potential anti-monkeypox therapeutics: a multi-step computational approach

The increasing spread of the Monkeypox virus (MPXV) presents a significant public health challenge, emphasising the urgent requirement for effective treatments. Our study focuses on the VP39 Methyltransferase enzyme of MPXV as a critical target for therapy. By utilising virtual screening, we investigated natural compounds with structural similarities to sinefungin, a broad-acting MTase inhibitor. From an initial set of 177 compounds, we identified three promising compounds-CNP0346326, CNP0343532, and CNP008361, whose binding scores were notably close to that of sinefungin. These candidates bonded strongly to the VP39 enzyme, hinting at a notable potential to impede the virus. Our rigorous computational assays, including re-docking, extended molecular dynamics simulations, and energetics analyses, validate the robustness of these interactions. The data paint a promising picture of these natural compounds as front-runners in the ongoing race to develop MPXV therapeutics and set the stage for subsequent empirical trials to refine these discoveries into actionable medical interventions.

Structure of SARS-CoV-2 MTase nsp14 with the inhibitor STM957 reveals inhibition mechanism that is shared with a poxviral MTase VP39

Nsp14 is an RNA methyltransferase (MTase) encoded by all coronaviruses. In fact, many viral families, including DNA viruses, encode MTases that catalyze the methylation of the RNA precap structure, resulting in fully capped viral RNA. This capping is crucial for efficient viral RNA translation, stability, and immune evasion. Our previous research identified nsp14 inhibitors based on the chemical scaffold of its methyl donor - the S-adenosyl methionine (SAM) - featuring a modified adenine base and a substituted arylsulfonamide. However, the binding mode of these inhibitors was based only on docking experiments. To uncover atomic details of nsp14 inhibition we solved the crystal structure of nsp14 bound to STM957. The structure revealed the atomic details of nsp14 inhibition such that the 7-deaza-adenine moiety of STM957 forms specific interactions with Tyr368, Ala353, and Phe367, while the arylsulfonamide moiety engages with Asn388 and Phe506. The large aromatic substituent at the 7-deaza position displaces a network of water molecules near the adenine base. Surprisingly, this was recently observed in the case of an unrelated monkeypox MTase VP39, where the 7-deaza modified SAH analogs also displaced water molecules from the vicinity of the active site.

Meeting report of the 37th International Conference on Antiviral Research in Gold Coast, Australia, May 20-24, 2024, organized by the International Society for Antiviral Research

The 37th International Conference on Antiviral Research (ICAR) was held in Gold Coast, Australia, May 20-24, 2024. ICAR 2024 featured over 75 presentations along with two poster sessions and special events, including those specifically tailored for trainees and early-career scientists. The meeting served as a platform for the exchange of cutting-edge research, with presentations and discussions covering novel antiviral compounds, vaccine development, clinical trials, and therapeutic advancements. A comprehensive array of topics in antiviral science was covered, from the latest breakthroughs in antiviral drug development to innovative strategies for combating emerging viral threats. The keynote presentations provided fascinating insight into two diverse areas fundamental to medical countermeasure development and use, including virus emergence at the human-animal interface and practical considerations for bringing antivirals to the clinic. Additional sessions addressed a variety of timely post-pandemic topics, such as the hunt for broad spectrum antivirals, combination therapy, pandemic preparedness, application of in silico tools and AI in drug discovery, the virosphere, and more. Here, we summarize all the presentations and special sessions of ICAR 2024 and introduce the 38th ICAR, which will be held in Las Vegas, USA, March 17-21, 2025.

Evaluating the Binding Potential and Stability of Drug-like Compounds with the Monkeypox Virus VP39 Protein Using Molecular Dynamics Simulations and Free Energy Analysis

Background/Objectives: Monkeypox is a re-emerging viral disease with features of infectiously transmitted zoonoses. It is now considered a public health priority because of its rising incidence and transmission from person to person. Monkeypox virus (MPXV) VP39 protein is identified as an essential protein for replication of the virus, and therefore, it is a potential target for antiviral drugs. Methods: This work analyzes the binding affinities and the differential conformational stability of three target compounds and one control compound with the VP39 protein through multiple computational methods. Results: The re-docking analysis revealed that the compounds had high binding affinities towards the target protein; among these compounds, compounds 1 and 2 showed the highest binding energies in the virtual screening, and thus, these were considered as the most active inhibitor candidates. Intermolecular interaction analysis revealed distinct binding mechanisms. While compound 1 had very strong hydrogen bonds and hydrophobic interactions, compound 2 had numerous water-mediated interactions, and compound 3 had only ionic and hydrophobic contacts. In molecular dynamic simulations, compounds 1 and 2 showed that the protein-ligand complexes had a stable conformation, with protein RMSD values around 2 Å for both compounds. In contrast, compound 3 was slightly flexible, and the control compound was more flexible. MM/GBSA analysis again supported these results, which gave the binding free energies that were also supportive for these compounds. Conclusions: Notably, all the selected compounds, especially compounds 1 and 2, demonstrate high binding affinity. Therefore, these compounds can be further tested as antiviral agents against monkeypox treatment.

Structural and functional insights in flavivirus NS5 proteins gained by the structure of Ntaya virus polymerase and methyltransferase

Flaviviruses are single-stranded positive-sense RNA (+RNA) viruses that are responsible for several (re)emerging diseases such as yellow, dengue, or West Nile fevers. The Zika epidemic highlighted their dangerousness when a relatively benign virus known since the 1950s turned into a deadly pathogen. The central protein for their replication is NS5 (non-structural protein 5), which is composed of the N-terminal methyltransferase (MTase) domain and the C-terminal RNA-dependent RNA-polymerase (RdRp) domain. It is responsible for both RNA replication and installation of the 5' RNA cap. We structurally and biochemically analyzed the Ntaya virus MTase and RdRp domains and we compared their properties to other flaviviral NS5s. The enzymatic centers are well conserved across Flaviviridae, suggesting that the development of drugs targeting all flaviviruses is feasible. However, the enzymatic activities of the isolated proteins were significantly different for the MTase domains.

Targeting Monkeypox Virus Methyltransferase: Virtual Screening of Natural Compounds from Middle-Eastern Medicinal Plants

Monkeypox is an infectious disease resulting from the monkeypox virus, and its fatality rate varies depending on the virus clade and the location of the outbreak. In monkeypox virus, methyltransferase (MTase) plays a crucial role in modifying the cap structure of viral mRNA. This alteration assists the virus in evading the host's immune system, enhances viral protein synthesis, and ultimately enables successful infection and replication within host cells. Given the significance of MTase in viral infection and spread within the host, our study aimed to identify a natural inhibitor for this enzyme using docking and molecular dynamic (MD) simulations. We collected a total of 12,971 natural compounds from 200 medicinal plants in the Middle East. After eliminating duplicate compounds, we had 5,749 unique ligand conformers, which we then subjected to high-throughput virtual screening against MTase. The most promising hits were further evaluated using the extra-precision (XP) tool. The affinity of these hits was also assessed by Prime-Molecular Mechanics/Generalized Born Surface Area (MMGBSA) tool. The analysis revealed that two standard controls (sinefungin and TO1119) and two Middle-Eastern compounds (folic acid and 1,2,4,6-tetragalloylglucose) exhibited the best XP docking scores. According to Prime MMGBSA calculations, the Middle-Eastern compounds showed higher affinities, with values of - 60.61 kcal/mol for 1,2,4,6-tetragalloylglucose and - 51.87 kcal/mol for folic acid, surpassing the controls (TO1119 at - 35.71 kcal/mol and sinefungin at - 31.51 kcal/mol). In the majority of Molecular dynamic (MD) simulations, folic acid exhibited demonstrated greater stability than sinefungin. Further investigation revealed that folic acid occupied a critical position in the active site of MTase, which reduced its interaction with the mRNA substrate. Based on these findings, it can be concluded that folic acid is a highly promising natural compound for potential use in the cost-effective treatment of monkeypox virus. The identification of folic acid as a potential antiviral agent highlights the importance of nature in providing new therapeutic uses that have significant implications for global health, particularly in regions where monkeypox viral outbreaks are prevalent. However, it is essential to note that further wet-lab validations are necessary to confirm its efficacy for treatment in a medical context.

Discovery of highly potent SARS-CoV-2 nsp14 methyltransferase inhibitors based on adenosine 5'-carboxamides

The emergence of SARS-CoV-2, the causative agent of COVID-19, has highlighted the need for advanced antiviral strategies. Targeting the coronaviral methyltransferase nsp14, which is essential for RNA capping, offers a promising approach for the development of small-molecule inhibitors. We designed and synthesized a series of adenosine 5'-carboxamide derivatives as potential nsp14 inhibitors and identified coumarin analogs to be particularly effective. Structural modifications revealed the importance of the 5'-carboxyl moiety for the inhibitory activity, showing superior efficacy compared to other modifications. Notably, compound 18l (HK370) demonstrated high selectivity and favorable in vitro pharmacokinetic properties and exhibited moderate antiviral activity in cell-based assays. These findings provide a robust foundation for developing targeted nsp14 inhibitors as a potential treatment for COVID-19 and related diseases.

N-Arylsulfonamide-based adenosine analogues to target RNA cap N7-methyltransferase nsp14 of SARS-CoV-2

RNA cap methylations have been shown to be crucial for the life cycle, replication, and infection of ssRNA viruses, as well as for evading the host's innate immune system. Viral methyltransferases (MTases) therefore represent an attractive target for the development of compounds as tools and inhibitors. In coronaviruses, N7-methyltransferase function is localized in nsp14, which has become an increasingly important therapeutic target with the COVID-19 pandemic. In recent years, we have been developing SAH-derived bisubstrates with adenosine and an N-arylsulfonamide moiety targeting both SAM and RNA binding sites in nsp14. We report here the synthesis of 31 SAH analogues with the N-arylsulfonamide attached to the 5'-position of adenosine via different linkers such as N-ethylthioether, N-ethylsulfone, N-ethylamino or N-methyltriazole. The compounds were obtained efficiently by amine sulfonylation or click chemistry. Their ability to inhibit SARS-CoV-2 N7-MTase was evaluated and the best inhibitors showed a submicromolar inhibitory activity against N7-MTase nsp14.