Oxalic acid as a dual C1 surrogate for heterogeneous palladium-catalyzed tandem four-component quinazolinone synthesis.

Herein, a heterogeneous Pd/C-catalyzed direct one-step four-component double carbonylative approach for cascade synthesis of 2-aryl quinazolinones has been reported for the first time starting from 2-iodoaniline derivatives and aryl iodides. The given reaction involves the simultaneous implementation of two different gaseous surrogates i.e., ammonium carbamate as an NH3 precursor and oxalic acid as a bi-functional reagent acting as a CO as well as a C-atom surrogate under ligand-free conditions.

Pd/C-Catalyzed Carbonylative Amidation for the Synthesis of 2-Carboxamidocyclohexane-1,3-diones.

Herein, a first-ever heterogeneous Pd/C-catalyzed single-step tandem approach for the synthesis of 2-carboxamidocyclohexane-1,3-diones via direct carbonylative C-H amidation of cyclohexane-1,3-diones is reported. The reaction progressed under base-, oxidant-, and ligand-free conditions employing oxalic acid as a CO surrogate and sodium azide as a nitrogen precursor in a double-layer vial system.

An unconventional iron oxide catalyst for 5-hydroxymethylfurfural oxidation to 2,5-diformylfuran.

Commonly used magnetic iron oxide (γ-Fe2O3) was examined for the first time as an unconventional catalyst for 5-hydroxymethylfurfural (5-HMF) oxidation to 2,5-diformylfuran (DFF). Fascinatingly, the magnetic support showed remarkable catalytic activity for this conversion, especially in nanoscale size (≤50 nm). The developed mild reagent system consisting of γ-Fe2O3 and molecular O2 in xylene solvent delivered DFF with 94% selectivity and 82% conversion at 135 °C for 12 h. A deep inspection of the mechanistic study through IR and XPS analysis revealed a phase transition (γ-Fe2O3 to Fe3O4) during the reaction, and then its reversal to the parent form after catalyst activation. The loss in crystallinity and increase in the particle size of the catalyst after the reaction were explicitly analysed by XRD and TEM studies, respectively. The excellent activity of the catalyst was even noticed by a recyclability test for six cycles. The method avoided the requirement of high-pressure equipment, costly noble and transition metals, and harsh basic environments.

Supported Palladium-Catalyzed Tandem Synthesis of 2-(Alkylamino/amino)-3-arylquinazolin-4(3H)-ones Employing CO Source.

Herein, we demonstrated heterogeneous and recyclable polystyrene-supported palladium (Pd@PS) nanoparticles (NPs) catalyzed tandem addition and intramolecular aminocarbonylative cyclization approach for the synthesis of potentially bioactive 2-(alkylamino/amino)-3-arylquinazolin-4(3H)-one analogues from 2-iodophenylcarbodiimides employing amines as nucleophiles and oxalic acid as an ex-situ CO alternative. Various cyclic/acyclic primary and secondary amines were employed and selectively produced substituted 2-(alkylamino)-3-arylquinazolin-4(3H)-ones in good to excellent yields. In addition, we extended the developed strategy to fix two ammonium carbamate and oxalic acid as gaseous NH3 and CO sources respectively, for the synthesis of 2-amino-3-arylquinazolin-4(3H)-one derivatives. Furthermore, gram scale applicability, diverse substrate scope and high recyclability of the Pd@PS catalyst were the major achievements of the developed protocol.

Mechanochemical Approach towards Multi-Functionalized 1,2,3-Triazoles and Anti-Seizure Drug Rufinamide Analogs Using Copper Beads.

Highly regiospecific, copper-salt-free and neat conditions have been demonstrated for the 1,3-dipolar azide-alkyne cycloaddition (AAC) reactions under mechanochemical conditions. A group of structurally challenging alkynes and heterocyclic derivatives was efficiently implemented to achieve highly functionalized 1,4-disubstituted-1,2,3-triazoles in good to excellent yield by using the Cu beads without generation of unwanted byproducts. Furthermore, the high-speed ball milling (HSBM) strategy has also been extended to the synthesis of the commercially available pharmaceutical agent, Rufinamide, an antiepileptic drug (AED) and its analogues. The same strategy was also applied for the synthesis of the Cl-derivative of Rufinamide. Analysis of the single crystal XRD data of the triazole was also performed for the final structural confirmation. The Cu beads are easily recoverable from the reaction mixture and used for the further reactions without any special treatment.

Benchmarking the ability of novel compounds to inhibit SARS-CoV-2 main protease using steered molecular dynamics simulations.

BACKGROUND: The SARS-CoV-2 main protease (Mpro) is an attractive target in the COVID-19 drug development process. It catalyzes the polyprotein's translation from viral RNA and specifies a particular cleavage site. Due to the absence of identical cleavage specificity in human cell proteases, targeting Mpro with chemical compounds can obstruct the replication of the virus. METHODS: To explore the potential binding mechanisms of 1,2,3-triazole scaffolds in comparison to co-crystallized inhibitors 11a and 11b towards Mpro, we herein utilized molecular dynamics and enhanced sampling simulation studies. RESULTS AND CONCLUSION: All the 1,2,3-triazole scaffolds interacted with catalytic residues (Cys145 and His41) and binding pocket residues of Mpro involving Met165, Glu166, Ser144, Gln189, His163, and Met49. Furthermore, the adequate binding free energy and potential mean force of the topmost compound 3h was comparable to the experimental inhibitors 11a and 11b of Mpro. Overall, the current analysis could be beneficial in developing the SARS-CoV-2 Mpro potential inhibitors.

Identification of 11ß-HSD1 inhibitors through enhanced sampling methods.

Aminoarylbenzosuberene (AAB) molecules were chosen for in silico analysis to develop effective and more competent 11ß-hydroxysteroid dehydrogenase (11ß-HSD1) protein inhibitors. The AAB4 molecule was shown to have stronger interactions and binding affinity than standard inhibitors (co-crystallized molecules). These results were based on conventional, steered and enhanced umbrella sampling simulations.

Identification of acridinedione scaffolds as potential inhibitor of DENV-2 C protein: An in silico strategy to combat dengue.

Dengue is a prominent viral disease transmitted by mosquitoes to humans that affects mainly tropical and subtropical countries worldwide. The global spread of dengue virus (DENV) is mainly occurred by Aedes aegypti and Aedes albopictus mosquitoes. The dengue virus serotypes-2 (DENV-2) is a widely prevalent serotype of DENV, that causes the hemorrhagic fever and bleeding in the mucosa, which can be fatal. In the life cycle of DENV-2, a structural capsid (DENV-2 C) protein forms the nucleocapsid assembly and bind to the viral progeny RNA. For DENV-2 maturation, the nucleocapsid is a vital component. We used virtual ligand screening to filter out the best in-house synthesized acridinedione analogs (DSPD molecules) that could efficiently bind to DENV-2 C protein. The molecular docking and dynamics simulations studies were performed to analyze the effect of DSPD molecules on DENV-2 C protein after binding. Our findings showed that DSPD molecules strongly interacted with DENV-2 C protein, as evident from molecular interactions and several time-dependent molecular dynamics-driven analyses. Moreover, this study was also supported by the thermodynamic binding free energy and steered molecular dynamics simulations. Therefore, we intend to suggest that the DSPD3 molecule could be used as a potential therapeutic molecule against dengue complications as compared to the cocrystallized inhibitor ST-148. However, further studies are required to demonstrate the ability of DSPD3 to induce DENV-2 C tetramer formation.

Identification of selective cyclin-dependent kinase 2 inhibitor from the library of pyrrolone-fused benzosuberene compounds: an in silico exploration.

The over-expression of cyclin-dependent kinase 2 is related to multiple cancers, which has led them to be a widely researched topic for nearly two decades. The prime focus of the present research is to design new potent and specific inhibitors against CDK2 to suppress cancer cell proliferation. In this study, we have chosen Flavopiridol, SU9516, and CVT-313 as standard inhibitors to compare with in-house synthesized pyrrolone-fused benzosuberene (PBS) compounds. We scrutinized Ligand2 as a selective inhibitor of CDK2 without off-target binding (CDK1 and CDK9) based on ligand efficiency and binding affinity. Interpretation of dynamic simulations and binding free energy studies unveiled that Ligand2 has a stable and equivalent free energy to standard inhibitors. These outcomes led towards positioning a potential natural molecule as selective inhibitor for CDK2 with low side effects.

Supported Palladium Catalyzed Carbonylative Coupling Reactions using Carbon Monoxide as C1 Source.

The carbonylative reactions of aryl halides, boronic acids, amines, activated alkene and alkynes under CO and supported palladium catalyzed conditions are very popular reactions for the synthesis of bioactive molecules, pharmaceuticals, polymers, peptides, intermediates and fine chemicals synthesis. Due to cost effectiveness and easy handling of recyclable supported palladium catalyst, it became more popular among researchers either working in academic institute or industry. In recent years, irrespective of poisoning effect of CO with palladium as major limitation, several advancements have been done through surface selection, designing and condition improvement to achieve high yield in the area of carbonylative coupling reactions. We hope this review will be helpful as a ready reference of last 20 years in the field of CO insertion reactions using diverse range of supported palladium catalysts under carbon monoxide or its sources as C1 source.

Free Amine, Hydroxyl and Sulfhydryl Directed C-H Functionalization and Annulation: Application to Heterocycle Synthesis.

Transition metal-catalyzed direct C-H bond functionalization is recognized as an efficient strategy to assemble heterocyclic frameworks. For this purpose, directing groups (DGs) installation on an organic molecule has remained a widely exploited strategy for the years. The installation of directing groups, especially for the amine, alcohol and thiol containing reactants and their removal after the reaction need additional steps. In this regard, the use of free amine, hydroxyl and sulfhydryl as directing groups in native form is advantageous and in recent times, these transformations have stirred undisputable advancements for applications to heterocycle synthesis. In this review, the aromatic sp2 -C attached free amine, hydroxyl and sulfhydryl as native functionalities are shown to be useful for the construction of five to seven-membered N-, O- and S-heterocycles.

Pd-Catalysed Decarbonylation Free Approach to Carbonylative Esterification of 5-HMF to Its Aryl Esters Synthesis Using Aryl Halides and Oxalic Acid as C1 Source.

A decarbonylation free, polystyrene-supported, Pd (Pd@PS)-catalysed carbonylative esterification of the hydroxy group of 5-hydroxymethyl furfural (5-HMF) to its corresponding aryl esters has been developed. The use of Pd@PS, oxalic acid as CO source, and aryl halides was first explored for the aryl ester of 5-HMF synthesis. Here, we investigated the vital role of a polystyrene support to avoid the commonly known decarbonylation of 5-HMF. The reaction exhibits vast substrate scope with comparably good yield and catalyst recyclability.

A computational approach for rational discovery of inhibitors for non-structural protein 1 of SARS-CoV-2.

BACKGROUND: Non-structural protein 1 (Nsp1), a virulence agent of SARS-CoV-2, has emerged as an important target for drug discovery. Nsp1 shuts down the host gene function by associating with the 40S ribosomal subunit. METHODS: Molecular interactions, drug-likeness, physiochemical property predictions, and robust molecular dynamics (MD) simulations were employed to discover novel Nsp1 inhibitors. In this study, we evaluated a series of molecules based on the plant (Cedrus deodara) derived α,ß,γ-Himachalenes scaffolds. RESULTS: The results obtained from estimated affinity and ligand efficiency suggested that BCH10, BCH15, BCH16, and BCH17 could act as potential inhibitors of Nsp1. Moreover, MD simulations comprising various MD driven time-dependent analyses and thermodynamic free energy calculations also suggested stable protein-ligand complexes and strong interactions with the binding site. Furthermore, the selected molecules passed drug likeliness parameters and the physiochemical property analysis showed acceptable bioactivity scores. CONCLUSION: The structural parameters of dynamic simulations revealed that the reported molecules could act as lead compounds against SARS-CoV-2 Nsp1 protein.

Plant-based analogues identified as potential inhibitor against tobacco mosaic virus: A biosimulation approach.

Benzosuberene compounds with a pyrrolone group adhered to it are compounds extracted from the oils of Cedrus deodara plant, that bear inhibitory capabilities. Tobacco mosaic virus is known to affect crop production every year. The currently known inhibitors against TMV have a weak inhibition effect and also tend to be toxic towards non-target living organisms as well as the environment. Thus, the requirement of non-toxic potent inhibitors is the need of the hour, which led us to test our benzosuberene molecules on the binding site of TMV and check their affinity as well as stability. The non-toxic nature of these molecules has already been experimentally established. Through in-silico analysis involving docking and simulation experiments, we compared the interaction pattern of these ligand molecules with the already present inhibitors. Our investigation proved that the reported ligands (ligands 3, 7, 9, and 17 obtained -177.103, -228.632, -184.134, and - 188.075 kJ/mol binding energies, respectively) interacted with the binding site of TMV much efficiently than the known inhibitors (Ribavirin and Zhao et al. 2020 obtained 121.561 and - 221.393 kJ/mol binding energies, respectively). Moreover, they acquired a stable conformation inside the binding pocket, where a higher number of binding site residues contributed towards interaction. Thus, their structural framework can be optimized for the exploration of their antiviral properties to develop potent botanical viricides against plant virus infection.

Benzosuberene-sulfone analogues synthesis from Cedrus deodara oil and their therapeutic evaluation by computational analysis to treat type 2 diabetes.

Benzosuberene-sulfone (BSS) analogues have been semi-synthesized following green approaches from himachalenes, which has been extracted from essential oil of Cedrus deodara. In this process, benzosuberene in presence of different aryl or alkyl sodium sulfinates, I2 and potassium persulfate (K2S2O8) in acetonitrile-water solvent conditions gave BSS-analogues at room temperature. Under this reaction, a facile endocyclic ß-H elimination has been noticed for BSS-analogues synthesis instead of vinyl sulfones and the reason may be due to its specific structure and electronic environment. The BSS-compounds were obtained with moderate to excellent yields under mild conditions. All the compounds were computationally subjected to drug likeliness and toxicity prediction studies. Further, the synthesized molecules were evaluated under in-silico studies for their binding affinity towards the native Peroxisome Proliferator-Activated Receptor Gamma (PPARG), and two PPARG mutants (R357A and V290M). Both the mutant forms of PPARG are deficient in eliciting a response to treatment with full and partial agonists. Our computational studies suggested that the molecule 3q performed better than the standard drug (Rosiglitazone) in all three protein structures. This implies that our suggested molecule could act as a more potent antagonist to native PPARG and could also be developed to treat type-2 diabetes patients with R357A and V290M mutations, which didn't elicit any response to currently available drugs in the market.

Application of cyclohexane-1,3-diones for six-membered oxygen-containing heterocycles synthesis.

Cyclohexan-1,3-dione derivatives are versatile scaffolds for the synthesis of a variety of value-added organic molecules including heterocycles and natural products. Six-membered oxygen heterocycles prepared from cyclohexan-1,3-diones are of much importance as they are intermediate for the synthesis of a number of natural products and several other valuable bioactive molecules which shows anti-viral, anti-bacterial, analgesic, antimalarial, anti-inflammatory, anti-allergic, anti-tumor and anti-cancer activities. These advantages have inspired us to write a detailed survey on the newly developed methods which are very essential in the construction of six-membered oxygen heterocycles. Further, the versatility in the chemistry of cyclohexan-1,3-dione and its derivatives is due to the presence of highly active methylene moiety and its active di-carbonyl groups. Recently, reactions of cyclohexane-1,3-dione and its derivatives with other substrates for instance aldehydes, malononitriles, NMSM, chalcones, isatin etc. have been established for the construction of a variety of six-membered oxygen heterocycles. The studies reported in this review article involved the synthesis of six-membered oxygen-containing heterocycles which includes 4H-chromen-5(6H)-one, 2H-xanthen-1(9H)-one, 2H-xanthen-1,8(5H,9H)-dione, 6H-chromen-2,5-dione derivatives and natural products having six-membered oxygen heterocycles from cyclohexane-1,3-dione and its derivatives as one of the substrate.

Identification of naturally originated molecules as γ-aminobutyric acid receptor antagonist.

γ-aminobutyric acid, being a principle neuromediator in humans controlling the inhibition signals, acts on the ligand-gated pentameric type A receptors to transmit their response. Any dysfunction of these receptors leads to neurological disorders and mental illness. Benzodiazepine has been used extensively for the treatment of these disorders, which shows its effect by reducing the threshold concentration of γ-aminobutyric acid required to activate the receptor. Being a central nervous system depressant, benzodiazepine is also a common substance of abuse along with other recreational drugs that show affinity towards the benzodiazepine binding site. Flumazenil is considered the first line of treatment for the overdose of these substances, which competes with them to bind with the receptor having a higher binding affinity towards the receptor. Like most of the synthetic drugs, Flumazenil also has some side-effects associated with it. Here we focus our work towards finding specific naturally originated antagonist of the benzodiazepine binding site to suggest an alternative for Flumazenil by performing various computational analysis like docking experiments followed by simulations and molecular mechanics poisson-boltzmann surface area analysis. Molecular docking experiments filtered out four ligand molecules specific for the benzodiazepine binding site, namely, ligand-1,7,9 and 17. Further, molecular dynamics simulations showed ligand-17 to have stable conformation in the binding site as well as a lower binding free energy as compared to Flumazenil. Due to its natural origin, ligand-17 is supposed to have lower side effects; therefore, its backbone can be further explored to develop specific antagonists of benzodiazepines. Communicated by Ramaswamy H. Sarma.

Evaluation of acridinedione analogs as potential SARS-CoV-2 main protease inhibitors and their comparison with repurposed anti-viral drugs.

BACKGROUND: The main protease (Mpro) of SARS-CoV-2 is involved in the processing of vital polypeptides required for viral genome replication and transcription and is one of the best-characterized targets to inhibit the progression of SARS-CoV-2 in infected individuals. METHODS: We screened a set of novel classes of acridinediones molecules to efficiently bind and inhibit the activity of the SARS-CoV-2 by targeting the Mpro. The repurposed FDA-approved antivirals were taken as standard molecules for this study. Long term (1.1 µs) MD simulations were performed to analyze the conformational space of the binding pocket of Mpro bound to the selected molecules. RESULTS: The molecules DSPD-2 and DSPD-6 showed more favorable MM-PBSA interaction energies and were seated more deeply inside the binding pocket of Mpro than the topmost antiviral drug (Saquinavir). Moreover, DSPD-5 also exhibited comparable binding energy to Saquinavir. The analysis of per residue contribution energy and SASA studies indicated that the molecules showed efficient binding by targeting the S1 subsite of the Mpro binding pocket. CONCLUSION: The DSPD-2, DSPD-6, and DSPD-5 could be developed as potential inhibitors of SARS-CoV-2. Moreover, we suggest that targeting molecules to bind effectively to the S1 subsite could potentially increase the binding of molecules to the SARS-CoV-2 Mpro.

Discovery and in silico evaluation of aminoarylbenzosuberene molecules as novel checkpoint kinase 1 inhibitor determinants.

Checkpoint kinase 1 (CHK1) is an essential kinase with a critical function in cell cycle arrest. Several potent inhibitors targeting CHK1 have been published, but most of them have failed in clinical trials. Acknowledging the emerging consequence of CHK1 inhibitors in medication of cancer, there is a demand for widening the chemical range of CHK1 inhibitors. In this research, we considered a set of in-house plant based semi-synthetic aminoarylbenzosuberene molecules as potential CHK1 inhibitors. Based on a combined computational research that consolidates molecular docking and binding free energy computations we recognized the crucial determinants for their receptor binding. The drug likeness of these molecules were also scrutinized based on their toxicity and bioavailibilty profile. The computational strategy indicates that the Bch10 could be regarded as a potential CHK1 inhibitor in comparison with top five co-crystallize molecules. Bch10 signifies a promising outlet for the development of potent inhibitors for CHK1.

Supported palladium catalyzed aminocarbonylation of aryl iodides employing bench-stable CO and NH3 surrogates.

A simple, efficient and phosphine free protocol for carbonylative synthesis of primary aromatic amides under polystyrene supported palladium (Pd@PS) nanoparticle (NP) catalyzed conditions has been demonstrated. Herein, instead of using two toxic and difficult to handle gases simultaneously, we have employed the solid, economical, bench stable oxalic acid as the CO source and ammonium carbamate as the NH3 source in a single pot reaction. For the first time, we have applied two non-gaseous surrogates simultaneously under heterogeneous catalyst (Pd@PS) conditions for the synthesis of primary amides using an easy to handle double-vial (DV) system. The developed strategy showed a good functional group tolerance towards a wide range of aryl iodides and afforded primary aromatic amides in good yields. The Pd@PS catalyst was easy to separate and can be recycled up to four consecutive runs with small loss in catalytic activity. We have successfully extended the scope of the methodology to the synthesis of isoindole-1,3-diones from 1,2-dihalobenzene, 2-halobenzoates and 2-halobenzoic acid following double and single carbonylative cyclization approaches.