Discovery and optimization of phthalazinone derivatives as a new class of potent dengue virus inhibitors

THE REPLICATION EFFICIENCY OF DENGUE VIRUS SEROTYPE 1 ISOLATED FROM PATIENTS WITH DENGUE FEVER IN HUMAN HEPATOCYTE CELL LINES

Background

The Efficiency of viral replication in cells depends on the capability of supporting virus replication by the cells. We characterized the effectiveness of Dengue Virus Serotype 1 (DENV-1) replication in various cell lines and various multiplicity of infection (MOI) starting from 2 FFU/cell up to 0,3125 FFU/cell.

Materials and Method

We used HepG2 and Huh-7 human hepatocyte cell lines and in addition, we also used non-human kidney cells (Vero cells). DENV-1 strain IDS 11/2010 was isolated from DF patients and previously propagated in Huh7 and Vero cells as DENV-1-adapted Huh-7 and DENV-1-adapted Vero cells, respectively. Huh7 cells, Hep G2 cells, and Vero cells were infected with DENV-1 at various MOI and incubated for 48 hours at 370C with 5% CO2. DENV-infected cells were determined by indirect immuno-peroxidase staining using 3,3'-Diaminobenzidine (DAB). DENV-1 infected cells as foci were counted under inverted light microscopy and were used to determine the virus titer.

Results

The virus was adapted to Huh-7 and Vero cells, with results showing that Vero cells exhibited the highest replication efficiency, evidenced by significant viral titers. Among human hepatocyte cell lines, DENV-1 demonstrated greater replication in Huh-7 cells than in HepG2 cells. Notably, no foci formation was observed in HepG2 cells after 48 hours of infection.

Conclusion

These findings underscore the suitability of Vero and Huh-7 cells as optimal environments for DENV-1 replication, offering valuable insights for enhancing laboratory diagnostics and advancing antiviral strategies and vaccine development against DENV-1.

Mechanism of action of phthalazinone derivatives against rabies virus

Rabies, a viral zoonosis, is responsible for almost 59,000 deaths each year, despite the existence of an effective post-exposure prophylaxis. Indeed, rabies causes acute encephalomyelitis, with a case-fatality rate of 100 % after the onset of neurological clinical signs. Therefore, the development of therapies to inhibit the rabies virus (RABV) is crucial. Here, we identified, from a 30,000 compound library screening, phthalazinone derivative compounds as potent inhibitors of RABV infection and more broadly of Lyssavirus and even Mononegavirales infections. Combining in vitro experiments, structural modelling, in silico docking and in vivo assays, we demonstrated that phthalazinone derivatives display a strong inhibition of lyssaviruses infection by acting directly on the replication complex of the virus, and with noticeable effects in delaying the onset of the clinical signs in our mouse model.

Identification of an Arylnaphthalene Lignan Derivative as an Inhibitor against Dengue Virus Serotypes 1 to 4 (DENV-1 to -4) Using a Newly Developed DENV-3 Infectious Clone and Replicon

Dengue virus (DENV) is the most widespread arbovirus, causing symptoms ranging from dengue fever to severe dengue, including hemorrhagic fever and shock syndrome. Four serotypes of DENV (DENV-1 to -4) can infect humans; however, no anti-DENV drug is available. To facilitate the study of antivirals and viral pathogenesis, here we developed an infectious clone and a subgenomic replicon of DENV-3 strains for anti-DENV drug discovery by screening a synthetic compound library. The viral cDNA was amplified from a serum sample from a DENV-3-infected individual during the 2019 epidemic; however, fragments containing the prM-E-partial NS1 region could not be cloned until a DENV-3 consensus sequence with 19 synonymous substitutions was introduced to reduce putative Escherichia coli promoter activity. Transfection of the resulting cDNA clone, plasmid DV3syn, released an infectious virus titer of 2.2 × 102 focus-forming units (FFU)/mL. Through serial passages, four adaptive mutations (4M) were identified, and addition of 4M generated recombinant DV3syn_4M, which produced viral titers ranging from 1.5 × 104 to 6.7 × 104 FFU/mL and remained genetically stable in transformant bacteria. Additionally, we constructed a DENV-3 subgenomic replicon and screened an arylnaphthalene lignan library, from which C169-P1 was identified as exhibiting inhibitory effects on viral replicon. A time-of-drug addition assay revealed that C169-P1 also impeded the internalization process of cell entry. Furthermore, we demonstrated that C169-P1 inhibited the infectivity of DV3syn_4M, as well as DENV-1, DENV-2, and DENV-4, in a dose-dependent manner. This study provides an infectious clone and a replicon for the study of DENV-3 and a candidate compound for future development against DENV-1 to -4 infections. IMPORTANCE Dengue virus (DENV) is the most prevalent mosquito-transmitted virus, and there is no an anti-dengue drug. Reverse genetic systems representative of different serotype viruses are invaluable tools for the study of viral pathogenesis and antiviral drugs. Here, we developed an efficient infectious clone of a clinical DENV-3 genotype III isolate. We successfully overcame the instability of flavivirus genome-length cDNA in transformant bacteria, an unsolved issue for construction of cDNA clones of flaviviruses, and adapted this clone to efficiently produce infectious viruses following plasmid transfection of cell culture. Moreover, we constructed a DENV-3 subgenomic replicon and screened a compound library. An arylnaphthalene lignan, C169-P1, was identified as an inhibitor of virus replication and cell entry. Finally, we demonstrated that C169-P1 exhibited a broad-spectrum antiviral effect against the infections with DENV-1 to -4. The reverse genetic systems and the compound candidate described here facilitate the study of DENV and related RNA viruses.

Pharmacophore-based virtual screening and in-silico study of natural products as potential DENV-2 RdRp inhibitors

Dengue fever is a significant public health concern throughout the world, causing an estimated 500,000 hospitalizations and 20,000 deaths each year, despite the lack of effective therapies. The DENV-2 RdRp has been identified as a potential target for the development of new and effective dengue therapies. This research's primary objective was to discover an anti-DENV inhibitor using in silico ligand- and structure-based approaches. To begin, a ligand-based pharmacophore model was developed, and 130 distinct natural products (NPs) were screened. Docking of the pharmacophore-matched compounds were performed to the active site of DENV-2 RdRp protease . Eleven compounds were identified as potential DENV-2 RdRp inhibitors based on docking energy and binding interactions. ADMET and drug-likeness were done to predict their pharmacologic, pharmacokinetic, and drug-likeproperties . Compounds ranked highest in terms of pharmacokinetics and drug-like appearances were then subjected to additional toxicity testing to determine the leading compound. Additionally, MD simulation of the lead compound was performed to confirm the docked complex's stability and the binding site determined by docking. As a result, the lead compound (compound-108) demonstrated an excellent match to the pharmacophore, a strong binding contact and affinity for the RdRp enzyme, favourable pharmacokinetics, and drug-like characteristics. In summary, the lead compound identified in this study could be a possible DENV-2 RdRp inhibitor that may be further studied on in vitro and in vivo models to develop as a drug candidate.Communicated by Ramaswamy H. Sarma.

Molecular docking and QSAR theoretical model for prediction of phthalazinone derivatives as new class of potent dengue virus inhibitors

Background

Dengue fever is a key public health unease in various tropical and sub-tropical regions. The improvement of existing agents that can inhibit the dengue virus is therefore of utmost importance. In this work, the QSAR study was carried out on 25 molecules of phthalazinone derivatives which have been reported to possess excellent dengue virus inhibitory activity. Density functional computational technique was used in the optimisation of the molecules with the basis set at theory level (B3LYP, 6-31G*) respectively. The multiple linear regression (MLR) model was built using genetic function approximation (GFA) in the material studio software package. Also, in this study, molecular docking simulation was carried between dengue virus serotype 2 protease (PDB CODE: 6mol) and some selected phthalazinone derivatives (compounds 1, 2, 7, 11, and 21).

Results

The model was robust as evidenced by validation and robustness statistical parameter which include predicted R2pred., adjusted R2adj., cross-validated Q2 and R2 regression coefficient, etc (R2pred. = 0.71922, R2adj. = 0.939699, Q2CV = 0.905909, R2 = 0.955567) respectively. The molecular docking studies conducted in this study have outlined the binding affinities of the selected compounds (1, 2, 7 11, and 21) which are all in good correlation with their respective pIC50 values. The free binding affinities of the selected compounds were found to be (− 8.7, − 8.8, − 8.7, − 8.3, and − 8.9 kcal/mol) respectively, compound 21 with the binding affinity of − 8.9 kcal/mol had the best binding free energy with the protease relative to other compounds under consideration.

Conclusion

The MLR-GFA model study alongside with the molecular docking analysis has essentially provided a valuable and in-depth understanding as well as knowledge for the development of novel chemical compounds with enhanced inhibitory potential against the dengue virus serotype 2 (DNV-2). Hence, the developed model can be applicable in predicting the anti-dengue activity of a new set of chemical compounds that fall within its applicability domain.

Viral replicons as valuable tools for drug discovery

RNA viruses can cause severe diseases such as dengue, Lassa, chikungunya and Ebola. Many of these viruses can only be propagated under high containment levels, necessitating the development of low containment surrogate systems such as subgenomic replicons and minigenome systems. Replicons are self-amplifying recombinant RNA molecules expressing proteins sufficient for their own replication but which do not produce infectious virions. Replicons can persist in cells and are passed on during cell division, enabling quick, efficient and high-throughput testing of drug candidates that act on viral transcription, translation and replication. This review will explore the history and potential for drug discovery of hepatitis C virus, dengue virus, respiratory syncytial virus, Ebola virus and norovirus replicon and minigenome systems.

Facile Synthesis of 2,2-Diacyl Spirocyclohexanones via an N-Heterocyclic Carbene-Catalyzed Formal [3C + 3C] Annulation

A novel strategy for the construction of 2,2-diacyl spirocyclohexanones 3 has been demonstrated on the basis of an NHC-catalyzed [3C + 3C] annulation of potassium 2-oxo-3-enoates with 2-ethylidene 1,3-indandiones. Furthermore, enantioenriched 3 was obtained in good to excellent yields with good enantioselectivities when chiral N-heterocyclic carbene (NHC) was employed. Notably, ring opening of the resulting 2,2-diacyl spirocyclohexanones 3 with hydrazine led to the formation of phthalazinones in good to excellent yields.

Dengue drug discovery: Progress, challenges and outlook

In the context of the only available vaccine (DENGVAXIA) that was marketed in several countries, but poses higher risks to unexposed individuals, the development of antivirals for dengue virus (DENV), whilst challenging, would bring significant benefits to public health. Here recent progress in the field of DENV drug discovery made in academic laboratories and industry is reviewed. Characteristics of an ideal DENV antiviral molecule, given the specific immunopathology provoked by this acute viral infection, are described. New chemical classes identified from biochemical, biophysical and phenotypic screens that target viral (especially NS4B) and host proteins, offer promising opportunities for further development. In particular, new methodologies ("omics") can accelerate the discovery of much awaited flavivirus specific inhibitors. Challenges and opportunities in lead identification activities as well as the path to clinical development of dengue drugs are discussed. To galvanize DENV drug discovery, collaborative public-public partnerships and open-access resources will greatly benefit both the DENV research community and DENV patients.