Virtual screening of natural products inspired in-house library to discover potential lead molecules against the SARS-CoV-2 main protease

SARS-CoV-2, a new coronavirus emerged in 2019, causing a global healthcare epidemic. Although a variety of drug targets have been identified as potential antiviral therapies, and effective candidate against SARS-CoV-2 remains elusive. One of the most promising targets for combating COVID-19 is SARS-CoV-2 Main protease (M^pro, a protein responsible for viral replication. In this work, an in-house curated library was thoroughly evaluated for druggability against M^pro. We identified four ligands (FG, Q5, P5, and PJ4) as potential inhibitors based on docking scores, predicted binding energies (MMGBSA), in silico ADME, and RMSD trajectory analysis. Among the selected ligands, FG, a natural product from Andrographis nallamalayana, exhibited the highest binding energy of -10.31 kcal/mol close to the docking score of clinical candidates Boceprevir and GC376. Other ligands (P5, natural product from cardiospermum halicacabum and two synthetic molecules Q5 and PJ4) have shown comparable docking scores ranging -7.65 kcal/mol to -7.18 kcal/mol. Interestingly, we found all four top ligands had Pi bond interaction with the main amino acid residues HIS41 and CYS145 (catalytic dyad), H-bonding interactions with GLU166, ARG188, and GLN189, and hydrophobic interactions with MET49 and MET165 in the binding site of M^pro. According to the ADME analysis, Q5 and P5 are within the acceptable range of drug likeliness, compared to FG and PJ4. The interaction stability of the lead molecules with viral protease was verified using replicated MD simulations. Thus, the present study opens up the opportunity of developing drug candidates targeting SARS-CoV-2 main protease (M^pro) to mitigate the disease.Communicated by Ramaswamy H. Sarma.

Discovery of Aryl Benzoyl Hydrazide Derivatives as Novel Potent Broad-Spectrum Inhibitors of Influenza A Virus RNA-Dependent RNA Polymerase (RdRp)

Influenza A viruses possess a high antigenic shift, and the approved anti-influenza drugs are extremely limited, which makes the development of novel anti-influenza drugs for the clinical treatment and prevention of influenza outbreaks imperative. Herein, we report a series of novel aryl benzoyl hydrazide analogs as potent anti-influenza agents. Particularly, analogs 10b, 10c, 10g, 11p, and 11q exhibited potent inhibitory activity against the avian H5N1 flu strain with EC₅₀ values ranging from 0.009 to 0.034 μM. Moreover, compound 11q exhibited nanomolar antiviral effects against both the H1N1 virus and Flu B virus and possessed good oral bioavailability and inhibitory activity against influenza A virus in a mouse model. Preliminary mechanistic studies suggested that these compounds exert anti-influenza virus effects mainly by interacting with the PB1 subunit of RNA-dependent RNA polymerase (RdRp). These results revealed that 11q has the potential to become a potent clinical candidate to combat seasonal influenza and influenza pandemics.

Synthesis of 3-Carbonyl Trisubstituted Furans via Pd-Catalyzed Aerobic Cycloisomerization Reaction: Development and Mechanistic Studies

Herein, we report the synthesis of 3-carbonyl-trisubstituted furans via Pd-catalyzed oxidative cycloisomerization reactions of 2-alkenyl-1,3-dicarbonyl scaffolds, using molecular oxygen as the sole oxidant to regenerate active palladium catalytic species, featuring good functional tolerance and mild reaction conditions. Deep investigation of intermediates and transition states of the reaction mechanism were conducted via experimental and DFT studies, providing a detailed mechanistical profile. The new developed methodology presents a greener alternative to Wacker-type cycloisomerizations and avoids the use of stoichiometric amounts of oxidants and strong acid additives.

Furan-2-carboxamide derivative, a novel microtubule stabilizing agent induces mitotic arrest and potentiates apoptosis in cancer cells

The vital role played by microtubules in the cell division process, marks them as a potential druggable target to decimate cancer. A novel furan-2-carboxamide based small molecule, is a selective microtubule stabilizing agent (MSA) with IC₅₀ ranging from 4 µM to 8 µM in different cancer cell lines. Inhibition of tubulin polymerization or stabilization of tubulin polymers abrogates chromosomal segregation during cell division, results in cell cycle arrest and leads to cell death due to the delayed repair mechanism. A novel furan-2-carboxamide based small molecule exhibited potent anti-proliferative and anti-metastatic property In-Vitro against the panel of cancer cells. Annexin V-FITC/PI, double staining reveals potent cytotoxic effect of SH09 against HeLa cells. FACS analysis displays induction of G2/M arrest and accumulation of subG1 population of cells upon treatment with SH09. Molecular docking study unveils SH09 binding affinity to the Taxol binding pocket of tubulin proteins and MM-GBSA also confirms strong binding energies of SH09 with tubulin proteins.

Enantioselective synthesis of novel pyrano[3,2-c]chromene derivatives as AChE inhibitors via an organocatalytic domino reaction

A series of optically active pyrano[3,2-c]chromenes have been synthesized through an asymmetric domino reaction of 4-hydroxy-2H-chromen-2-ones with malononitriles. The targeted molecules were obtained in excellent yields and enantioselectivities (up to 94% yield, 99% ee). The AChE inhibitory activity studies revealed that compounds 4n (IC₅₀ = 21.3 μM) and 4p (IC₅₀ = 19.2 μM) displayed potent acetylcholinesterase inhibition. In most cases, the S-enantiomers were superior to the corresponding R-enantiomers. Moreover, molecular modelling provides a practical method for understanding the enantioselective discrimination of AChE with these kinds of compounds.

Design and synthesis of heteroaromatic-based benzenesulfonamide derivatives as potent inhibitors of H5N1 influenza A virus

Influenza A virus is an enveloped negative single-stranded RNA virus that causes febrile respiratory infection and represents a clinically challenging threat to human health and even lives worldwide. Even more alarming is the emergence of highly pathogenic avian influenza (HPAI) strains such as H5N1, which possess much higher mortality rate (60%) than seasonal influenza strains in human infection. In this study, a novel series of heteroaromatic-based benzenesulfonamide derivatives were identified as M2 proton channel inhibitors. A systematic investigation of the structure-activity relationships and a molecular docking study demonstrated that the sulfonamide moiety and 2,5-dimethyl-substituted thiophene as the core structure played significant roles in the anti-influenza activity. Among the derivatives, compound 11k exhibited excellent antiviral activity against H5N1 virus with an EC50 value of 0.47 μM and selectivity index of 119.9, which are comparable to those of the reference drug amantadine.

Tunable Synthesis of 2-Ene-1,4-diones, 4-Hydroxycyclopent-2-en-1-ones, and 2-(Furan-3-yl)acetamides via Palladium-Catalyzed Cascade Reactions of Allenols

An efficient and regioselective synthesis of 2-ene-1,4-diones, 4-hydroxycyclopent-2-en-1-ones, or 2-(furan-3-yl)acetamides is successfully realized through palladium-catalyzed one-pot multicomponent reactions of allenols with aryl iodides and carbon monoxide in the presence of tertiary amines. Interestingly, the selectivity depends on the substitution patterns of the allenol substrates. To be specific, from the reaction of allenols with no substituent attached on the internal position of the allenic moiety, 2-ene-1,4-diones or 4-hydroxycyclopent-2-en-1-ones were formed selectively through carbonylation of aryl iodide followed by acylation of allenol with the in situ formed acyl palladium species, β-hydride elimination of the in situ formed allyl palladium complex, and further tautomerization or intramolecular aldol reaction. From the reaction of allenols bearing a substituent at the internal position of the allenic unit, on the other hand, diversely substituted 2-(furan-3-yl)acetamides were formed through a cascade process combining carbonylation of aryl iodide, acylation, and carbonylation of allenol followed by intramolecular condensation and amination by tertiary amine featuring an oxidant-free C-N bond cleavage.

Synthesis and structure-activity relationship study of arylsulfonamides as novel potent H5N1 inhibitors

H5N1 virus, one subtype of highly pathogenic influenza A virus in human infection, has recently received attention due to its unpredictable and high mortality. In this study, a series of arylsulfonamide derivatives were identified as improved H5N1 inhibitors for the influenza treatment by systematic structure-activity relationship investigation. Among them, the most potent H5N1 inhibitor 3h exhibited excellent antiviral activity against H5N1 virus with EC₅₀ value of 0.006 μM and selectivity index 33543.3. Moreover, the molecular docking of 3h with M2 proton channel protein provides practical way for understanding the inhibition of H5N1 with this kind of compounds.