Design, synthesis, assessment, and molecular docking of novel pyrrolopyrimidine (7-deazapurine) derivatives as non-nucleoside hepatitis C virus NS5B polymerase inhibitors

Synthesis and Applications of Nitrogen-Containing Heterocycles as Antiviral Agents

Viruses have been a long-term source of infectious diseases that can lead to large-scale infections and massive deaths. Especially with the recent highly contagious coronavirus (COVID-19), antiviral drugs were developed nonstop to deal with the emergence of new viruses and subject to drug resistance. Nitrogen-containing heterocycles have compatible structures and properties with exceptional biological activity for the drug design of antiviral agents. They provided a broad spectrum of interference against viral infection at various stages, from blocking early viral entry to disrupting the viral genome replication process by targeting different enzymes and proteins of viruses. This review focused on the synthesis and application of antiviral agents derived from various nitrogen-containing heterocycles, such as indole, pyrrole, pyrimidine, pyrazole, and quinoline, within the last ten years. The synthesized scaffolds target HIV, HCV/HBV, VZV/HSV, SARS-CoV, COVID-19, and influenza viruses.

Investigation for anticancer activity of the newly synthesized p-Methoxyphenyl maleanilic acid and the diagnostic property of its 99mTc-analogue

PURPOSE

The limitations of the current chemotherapeutics are the main rational to develop and/or explore new anticancer agents and radiolabeled analogues for cancer early diagnosis.

MATERIALS AND METHODS

The newly synthesized p-methoxyphenyl maleanilic acid (MPMA) was prepared, characterized and investigated for its anticancer activity. MPMA screened in-vitro against human hepatocellular carcinoma (HepG-2), human colon carcinoma (HCT-116) and human breast carcinoma (MCF-7) cell lines. Furthermore, the in-vivo screening was performed by radiolabeling of MPMA with technetium-99m (^99mTc) and investigating its biological distribution in normal mice and solid tumor models. Moreover, MPMA and its radiolabeled analogue were docked to Y220C and Y220S mutants of p53 (p53^Y220C and p53^Y220S) in an effort to confirm their affinity to cancer as well as to investigate, virtually, the mechanism of action of MPMA.

RESULTS

The results revealed significant potency of MPMA against HepG-2 cell line (IC₅₀ = 56.2 ± 1.5 µg/mL) if compared to HCT-116 (IC₅₀ = 89.9 ± 1.8 µg/mL) and MCF-7 (IC₅₀ = 104 ± 2.7 µg/mL) cell lines. The radiolabeling yield was optimized to be 90.2 ± 2.1%. The radiolabeled MPMA showed a good localization in the site of solid tumor (15.1 ± 1.6%ID/g) at 2 h post intravenous administration to the tumor bearing mice.

CONCLUSIONS

Collectively, the findings confirmed the potential anticancer activity of MPMA and the possible use of ^99mTc-MPMA for cancer diagnosis and monitoring.

RdRp (RNA-dependent RNA polymerase): A key target providing anti-virals for the management of various viral diseases

With the arrival of the Covid-19 pandemic, anti-viral agents have regained center stage in the arena of medicine. Out of the various drug targets involved in managing RNA-viral infections, the one that dominates almost all RNA viruses is RdRp (RNA-dependent RNA polymerase). RdRp are proteins that are involved in the replication of RNA-based viruses. Inhibition of RdRps has been an integral approach for managing various viral infections such as dengue, influenza, HCV (Hepatitis), BVDV, etc. Inhibition of the coronavirus RdRp is currently rigorously explored for the treatment of Covid-19 related complications. So, keeping in view the importance and current relevance of this drug target, we have discussed the importance of RdRp in developing anti-viral agents against various viral diseases. Different reported inhibitors have also been discussed, and emphasis has been laid on highlighting the inhibitor's pharmacophoric features and SAR profile.

Bioactive pyrrole-based compounds with target selectivity

The discovery of novel synthetic compounds with drug-like properties is an ongoing challenge in medicinal chemistry. Natural products have inspired the synthesis of compounds for pharmaceutical application, most of which are based on N-heterocyclic motifs. Among these, the pyrrole ring is one of the most explored heterocycles in drug discovery programs for several therapeutic areas, confirmed by the high number of pyrrole-based drugs reaching the market. In the present review, we focused on pyrrole and its hetero-fused derivatives with anticancer, antimicrobial, and antiviral activities, reported in the literature between 2015 and 2019, for which a specific target was identified, being responsible for their biological activity. It emerges that the powerful pharmaceutical and pharmacological features provided by the pyrrole nucleus as pharmacophore unit of many drugs are still recognized by medicinal chemists.

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Pyrrole nucleus is one of the most explored heterocycle in drug discovery.

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Pyrrole derivatives exhibit antitumor, antimicrobial and antiviral activities.

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Targets involved in their biological activities were identified.

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SAR to underline their most important features were discussed.

Acid-Catalyzed Multicomponent Rearrangements via 2-((Quinoxalin-3(4H)-on-2-yl)(aryl)methylene)malononitriles, Generated In Situ, for Divergent Synthesis of Pyrroles with Different Substitution Patterns

New three-component domino reactions, providing divergent approaches to multifunctionalized pyrroles with different substitution patterns, have been established (47 examples). In this work, a new rearrangement of quinoxalinones with the participation of the in situ-generated 2-en-1-imine moiety of the substituent at C3 makes it possible to construct two new heterocyclic systems, namely, a benzimidazolone and a pyrrole, simultaneously under one-pot reaction conditions. The reaction is easy to perform simply by mixing three common reactants of acetic acid with heating. Secondary amines or primary alcohols as the third component of the reaction, along with quinoxalin-3(4H)-ones and malononitrile, not only initiate the rearrangement but also are responsible for the nature of substituents at position 5 of the pyrrole ring in the newly formed new biheterocyclic system. The reaction proceeds smoothly and can be finished within 7 h, which makes workup convenient to give up to 97% chemical yields.

Design, synthesis and in vitro apoptotic mechanism of novel pyrrolopyrimidine derivatives

In this work we described the synthesis and evaluation of cytotoxic and apoptotic activity of novel pyrrolopyrimidine derivatives against A549, PC3 and MCF-7 cells. Among the synthesized compounds, 6b, 8a, 9a and 7a, 8b displayed the significant cytotoxic activities against A549 and PC3 cells with IC₅₀ value of 0.35, 1.48, 1.56 and 1.04, 1.89 µM, respectively. It was found that A549 cells were more sensitive to synthesized compounds than PC3 and MCF-7 cells. In order to evaluate the mechanism of cytotoxic activity in A549, compounds 6b, 8a and 9a were selected for further studies. Annexin V binding assay and western blot analysis results revealed that 6b, 8a and 9a induced apoptosis in A549 cells by intrinsic apoptotic pathway through the activation pro-apoptotic proteins such as Bim, Bax, Bak, Puma and deactivation of anti-apoptotic proteins including Bcl-2, Mcl-1 and Bcl-XL accompanied by the activation of caspase-3, caspase-9 and cleavage of PARP. Also, compounds 6b, 8a and 9a triggered apoptosis in HCT116 wt cells via activation of caspase-3 and caspase-9, but not in HCT116 Bax/Bak KO cells, indicating resistance to 6b, 8a and 9a treatment.

Evaluation of novel pyrrolopyrimidine derivatives as antiviral against gastroenteric viral infections

Viral gastroenteritis is a major global public-health threat. All age groups are susceptible for this infection, but its most serious consequences affect children. Rotavirus, Coxsackievirus and Adenovirus are the most common viruses that cause gastroenteritis. Herein, we synthesized novel pyrrole, pyrrolo[2,3‑d]pyrimidine and pyrrolo[3,2‑e][1,2,4]triazolo[4,3‑c]pyrimidine derivatives. The non-toxic doses of these compounds were determined using BGM cell lines. We examined all the new compounds for their anti-viral activities against Rotavirus Wa strain and Coxsackievirus B4. Compounds 2a, 2d, 5a, 5c, 5d, 7b, 7j, 7n, 14b, 14c, 14e and 14f exhibited significant antiviral activity. We interpreted the action of these compounds using molecular docking against the homology models of viral polymerase enzymes of these viruses. RMSD value of 5d/Coxsackievirus was higher than the RMSD value for 5d/rotavirus and hence better as a stability parameter, which can be correlated to the biological activity.

Radioiodination and biological distribution of a new s-triazine derivative for tumor uptake evaluation

A newly synthesized s-triazine derivative 1,1',1″-(((1,3,5-triazine-2,4,6-triyl) tris (azanediyl)) tris (benzene-4,1-diyl))tris (ethan-1-one), (1), was synthesized as a part of an ongoing research for development of novel s-triazine-based radiopharmaceuticals. In-vitro cell viability assay against different human cancer cell lines showed very promising inhibitory activity of the synthesized compound. This finding encouraged the radioiodination of 1 to study the degree of its localization in tumor site for evaluating the possibility of its use as a tumor imaging agent. The biodistribution study showed good localization of the radioiodinated derivative 2 at tumor site following i.v. administration in solid tumor-bearing mice. Finally, in a trial to understand the mechanism of the anticancer effect exerted by 1, a target prediction study and a docking study were performed. The results of the first study showed that focal adhesion kinase is a possible target for compound 1 and the docking study confirmed successful binding of both compound 1 and its radioiodinated derivative 2 to the binding site of focal adhesion kinase. As a conclusion, the results of this study suggest that, compound 2 could be used as a potential agent for tumor imaging after preclinical trials.

Quantum molecular modeling of hepatitis C virus inhibition through non-structural protein 5B polymerase receptor binding of C5-arylidene rhodanines

We have carried out high-level quantum chemical computations followed by molecular docking studies on a set of 17C₅-arylidene rhodanine isomers to provide insights into the binding modes with different reported binding pockets of the nonstructural protein 5B (NS5B) polymerase that contribute to the hepatitis C virus (HCV) inhibition. We optimized the multi-target profile of the selected rhodanine analogs to investigate potential non-nucleotide inhibitors (NNIs) by quantum chemical optimization of the 18 isomers followed by docking with quantum chemically optimized structures of each isomer with NS5B polymerase at multiple binding pockets. The binding affinities of the PP-I, PP-II and TP-II pockets of NS5B polymerase were analyzed for all the 17 isomers of 2-[(5Z)-5-(2,4-dichlorobenzylidene)-4-oxo-2-thioxo-1,3-thiazolidin-3-yl]-3-phenylpropanoic acid. On the basis of binding propensity at the different pockets and inhibitor constants, we ranked these isomers as potential candidates for the HCV inhibition. We have identified four isomers as promising NNIs of NS5B polymerase with comparable binding and inhibition to the standard (1,3) dichloro substituted isomer that exhibits in vitro activity and several other isomers as candidates in a "multi-targeted drug" approach.

A multi-component synthesis of N-substituted 2-amino-3-cyano pyrroles via ring-opening of nitroepoxides

A multi-component synthesis of N-substituted 2-amino-3-cyano pyrroles from nitroepoxides, amines and malononitrile has been demonstrated.

Molecular simulations to delineate functional conformational transitions in the HCV polymerase

Hepatitis C virus (HCV) is a global health concern for which there is no vaccine available. The HCV polymerase is responsible for the critical function of replicating the RNA genome of the virus. Transitions between at least two conformations (open and closed) are necessary to allow the enzyme to replicate RNA. In this study, molecular dynamic simulations were initiated from multiple crystal structures to understand the free energy landscape (FEL) explored by the enzyme as it interconverts between these conformations. Our studies reveal the location of distinct states within the FEL as well as the molecular interactions associated with these states. Specific hydrogen bonds appear to play a key role in modulating conformational transitions. This knowledge is essential to elucidate the role of these conformations in replication and may also be valuable in understanding the basis by which this enzyme is inhibited by small molecules. © 2016 Wiley Periodicals, Inc.