Identification of antiviral phytochemicals from cranberry as potential inhibitors of SARS-CoV-2 main protease (Mpro).

Cranberry phytochemicals are known to possess antiviral activities. In the current study, we explored the therapeutic potential of cranberry against SARS-CoV-2 by targeting its main protease (Mpro) enzyme. Firstly, phytochemicals of cranberry origin were identified from three independent databases. Subsequently, virtual screening, using molecular docking and molecular dynamics simulation approaches, led to the identification of three lead phytochemicals namely, cyanidin 3-O-galactoside, ß-carotene and epicatechin. Furthermore, in vitro enzymatic assays revealed that cyanidin 3-O-galactoside had the highest inhibitory potential with IC50 of 9.98 µM compared to the other two phytochemicals. Cyanidin 3-O-galactoside belongs to the class of anthocyanins. Anthocyanins extracted from frozen cranberry also exhibited the highest inhibitory potential with IC50 of 23.58 µg/ml compared to the extracts of carotenoids and flavanols, the class for ß-carotene and epicatechin, respectively. Finally, we confirm the presence of the phytochemicals in the cranberry extracts using targeted LC-MS/MS analysis. Our results, therefore, indicate that the identified cranberry-derived bioactive compounds as well as cranberry could be used for therapeutic interventions against SARS-CoV-2.

Electrochemical Synthesis of 2-Aryl-3-(2-aminoaryl)quinoxalines via Oxidative Dearomatization/Ring-Opening/Cyclization Cascade Sequence of 2-Arylindoles with 1,2-Diaminoarenes.

A straightforward method has been developed to synthesize 2-aryl-3-(2-aminoaryl) quinoxalines from 2-arylindoles and 1,2-diaminoarenes under mild electrochemical conditions. The reaction proceeds through in situ generations of 2-arylindole-3-ones under electrochemical oxidative dearomatization of 2-arylindoles, followed by a ring opening-cyclization sequence with 1,2-diaminoarenes. A series of 2-aryl-3-(2-aminoaryl) quinoxalines have been prepared with moderate to good yields (up to 75%).

Electrochemical Oxidative Addition of Nucleophiles on 2-Arylindoles: Synthesis of C2-Heteroquaternary Indolin-3-ones.

An electrochemical method has been developed to synthesize 2,2-disubstituted indolin-3-ones under mild conditions. A series of nucleophiles have been added to the 2-arylindole-3-ones, generated in situ under metal-free electrochemical oxidative dearomatization of 2-arylindoles, to afford 2,2-disubstituted 3-carbonyl indoles with heteroquaternary centers in 57-79% yields.

Enantioselective Direct Synthesis of C3-Hydroxyalkylated Pyrrole via an Amine-Catalyzed Aldol/Paal-Knorr Reaction Sequence.

Creating functionality with chirality at position C3 of pyrrole is challenging. An operationally simple organocatalytic method has been developed to generate functionality with a chiral tertiary/quaternary stereocenter at position C3 of pyrrole. The process proceeds through an amine-catalyzed direct aldol reaction of succinaldehyde with various acceptor carbonyls, followed by a Paal-Knorr reaction with a primary amine in the same pot. A series of chiral C3-hydroxyalkylated N-alkyl/Ar/H-pyrroles have been synthesized for the first time with good to high yields and excellent enantioselectivity.

PIFA-promoted intramolecular oxidative cyclization of pyrrolo- and indolo[1,2-a]quinoxalino-appended porphyrins: an efficient synthesis of meso,ß-pyrrolo- and indolo[1,2-a]quinoxalino-fused porphyrins.

We have developed an efficient protocol for the synthesis of meso,ß-pyrrolo- and indolo[1,2-a]quinoxalino-fused porphyrin systems 7-9 by PIFA-promoted intramolecular oxidative cyclization of easily accessible meso-pyrrolo- and indolo[1,2-a]quinoxalino-appended porphyrins 6a-j. The absorption spectra of meso,ß-pyrrolo- and indolo[1,2-a]quinoxalino-fused porphyrins 7-9 displayed bathochromic shifted (100-150 nm) and broadened Soret bands and Q bands in addition to intense band near IR region. The indolo[1,2-a]quinoxalino-fused porphyrin 9bZn with lower fluorescence quantum yield (0.003) and reduced energy gap (∼1.3 eV) was found to sensitize singlet oxygen effectively.

Catalyst-free direct regiospecific multicomponent synthesis of C3-functionalized pyrroles.

An operationally simple catalyst-free protocol for the direct regiospecific synthesis of ß-(C3)-substituted pyrroles has been developed. The enamine intermediate, in situ generated from succinaldehyde and a primary amine, was trapped with activated carbonyls before the Paal-Knorr reaction in a direct multicomponent "just-mix" fashion to furnish pyrroles with overall good yields. Several C3-substituted N-alkyl/aryl/H pyrroles have been produced under open-flask conditions with high atom economy and avoiding protection-deprotection chemistry.

In silico and in vitro assays reveal potential inhibitors against 3CLpro main protease of SARS-CoV-2.

The COVID-19 pandemic, caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is not showing any sign of slowing down even after the ongoing efforts of vaccination. The threats of new strains are concerning, as some of them are more infectious than the original one. A therapeutic against the disease is, therefore, of urgent need. Here, we use the DrugBank database to screen for potential inhibitors against the 3CLpro main protease of SARS-CoV-2. Instead of using the traditional approach of computational screening by docking, we developed a kernel ridge regressor (using a part of the docking data) to predict the binding energy of ligands. We used this model to screen the DrugBank database and shortlist two lead candidates (bromocriptine and avoralstat) for in vitro enzymatic study. Our results show that the 3CLpro enzyme activity in presence of 100 µM concentration of bromocriptine and avoralstat is 9.9% and 15.9%, respectively. Remarkably, bromocriptine exhibited submicromolar IC50 of 130 nM (0.13 µM). Avoralstat showed an IC50 of 2.16 µM. Further, the interactions of both drugs with 3CLpro were analyzed using molecular dynamics simulations of 100 ns. Results indicate that both ligands are stable in the binding pocket of the 3CLpro receptor. In addition, the MM-PBSA analysis revealed that bromocriptine (-29.37 kcal/mol) has a lower binding free energy compared to avoralstat (-6.91 kcal/mol). Further, hydrogen bond analysis also showed that bromocriptine interacts with the two catalytic residues, His41 and Cys145, more frequently than avoralstat.Communicated by Ramaswamy H. Sarma.

Two-pot synthesis and photophysical studies of 1,6-disubstituted 5-aza-indoles from succinaldehyde and N-aryl propargylic-imines.

A two-pot synthesis of 5-aza-indoles has been developed from aqueous succinaldehyde and N-aryl propargylic-imines. This overall protocol involves: (i) the metal-free [3 + 2] annulation of aqueous succinaldehyde and N-aryl propargylic-imines to access 2-alkynyl-pyrrole-3-aldehydes and (ii) Ag-catalyzed 6-endo-dig-cyclization to obtain substituted 5-aza-indoles in the second pot. The 5-aza-indoles showed engaging photophysical activities, and the practicality of this pot-economic gram-scale synthesis has been demonstrated.

Asymmetric Synthesis of Bridged N-Heterocycles with Tertiary Carbon Center through Barbas Dienamine-Catalysis: Scope and Applications.

A direct aza-Diels-Alder reaction between 2-aryl-3H-indolin-3-ones and cyclic-enones has been developed to access chiral indolin-3-one fused polycyclic bridged compounds. This method proceeds via proline-catalyzed Barbas-dienamine intermediate formation from various cyclic-enones such as 2-cyclopenten-1-one, 2-cyclohexene-1-one, and 2-cycloheptene-1-one, followed by a reaction with 2-aryl-3H-indol-3-ones. Several indolin-3-ones fusing [2.2.2], [2.2.1], and [3.2.1] skeletons decorated with a tertiary carbon chiral center have been prepared. Computational studies (DFT) supported the observed stereoselectivity in the method. The synthesized compounds have shown exciting photophysical activities and selective sensing of Pd2+ and Fe3+ ions through the fluorescence quenching "switch-off" mode.

Modeling rarefied gas-solid surface interactions for Couette flow with different wall temperatures using an unsupervised machine learning technique.

In rarefied gas flows, discontinuity phenomena such as velocity slip and temperature jump commonly appear in the gas layer adjacent to a solid boundary. Due to the physical complexity of the interactions at the gas-solid interface, particularly in the case of systems with local nonequilibrium state, boundary models with limited number of parameters cannot completely describe the reflection of gas molecules at the boundary. In this work, the Gaussian mixture (GM) model, which is an unsupervised machine learning technique, is employed to construct a statistical gas-solid surface scattering model based on the collisional data obtained from molecular dynamics (MD) simulations. The GM model is applied to study Couette flow for different inert gases (Ar and He) confined between two parallel infinite gold walls at different temperatures. A direct comparison between the results obtained from the GM model and the Cercignani-Lampis-Lord (CLL) scattering kernel against the MD collisional data in terms of the distribution of the predicted postcollisional velocities, and accommodation coefficients has shown that the results from the GM model are an excellent match with the MD results outperforming the CLL scattering kernel. As an example, for He gas, while the predicted energy accommodation coefficient by the CLL model is more than two times higher than the MD predictions, the value computed by the GM model is in excellent agreement with the MD results. This superior performance of the GM model confirms its high potential to derive a generalized boundary condition in systems encountered with highly nonequilibrium and complex gas flow conditions.

Peptide inhibitors against SARS-CoV-2 2'-O-methyltransferase involved in RNA capping: A computational approach.

The COVID-19 pandemic is still evolving and is caused by SARS-CoV-2. The 2'-O-methyltransferase (nsp16) enzyme is crucial for maintaining the stability of viral RNA for effective translation of viral proteins and its life cycle. Another protein, nsp10, is important for enzymatic activity of nsp16. Any disturbance in the interaction between nsp16 and nsp10 may affect viral replication fidelity. Here, five peptide inhibitors, derived from nsp16, were designed and assessed for their effectiveness in binding to nsp10 using molecular dynamics simulation. The inhibitors were derived from the nsp10/nsp16 binding interface. Post-simulation analysis showed that inhibitors 2 and 5 were stable and bind to the nsp16 interacting region of nsp10 which could potentially prevent the interaction between the two proteins. The proposed peptides are useful starting points for the development of therapeutics to manage the spread of COVID-19.

Direct catalytic synthesis of ß-(C3)-substituted pyrroles: a complementary addition to the Paal-Knorr reaction.

The synthesis of ß-(C3)-functionalized pyrroles is a challenging task and requires a multistep protocol. An operationally simple direct catalytic synthesis of ß-substituted pyrroles has been developed. This one-pot multicomponent method combined aqueous succinaldehyde as 1,4-dicarbonyl, primary amines, and isatins to access hydroxyl-oxindole ß-tethered pyrroles. Direct synthesis of the ß-substituted free NH-pyrrole is the central intensity of this work. DFT-calculations and preliminary mechanism investigation support the possible reaction pathway.

Direct Amine-Catalyzed Enantioselective Synthesis of Pentacyclic Dibenzo[b,f][1,4]oxazepine/Thiazepine-Fused Isoquinuclidines along with DFT Calculations.

A direct protocol for the asymmetric synthesis of dibenzoxazepine/thiazepine-fused [2.2.2] isoquinuclidines is developed. The reaction proceeds through a proline-catalyzed direct Mannich reaction followed by an intramolecular aza-Michael cascade sequence between 2-cyclohexene-1-one and various tricyclic imines, like dibenzoxazepines/thiazepines, as an overall [4 + 2] aza-Diels-Alder reaction. A series of pentacyclic isoquinuclidines have been prepared, with complete endo-selectivity, in good to high yields and excellent enantioselectivity (>99:1). Density functional theory (DFT) calculations further support the observed high stereochemical outcome of the reaction.

Sequential multicomponent site-selective synthesis of 4-iodo and 5-iodopyrrole-3-carboxaldehydes from a common set of starting materials by tuning the conditions.

A simple and straightforward method for the synthesis of 4-iodo and 5-iodopyrrole-3-carboxaldehydes is developed from a common set of starting materials by tuning the reaction conditions. This sequential multicomponent protocol involves I2-mediated regioselective C4-iodination and aromatization of intermediate dihydropyrrole, generated through proline-catalyzed direct Mannich reaction-cyclization sequence between succinaldehyde and imines, to access 4-iodopyrroles. While aerobic oxidative aromatization of dihydropyrrole to pyrrole followed by NIS-mediated regioselective iodination furnished 5-iodopyrroles in a two-pot fashion. A series of site-selective C4/C5-iodopyrroles have been synthesized in good to high yields (up to 78%) and DFT calculations of these compounds were also performed.

Enantio- and Diastereoselective Two-Pot Synthesis of Isoquinuclidines from Glutaraldehyde and N-Aryl Imines with DFT Calculations.

A pot-economic method for the enantio- and diastereoselective synthesis of a [2.2.2] azabicyclic isoquinuclidine system is developed. This protocol involves the proline-catalyzed direct Mannich reaction-cyclization/IBX-mediated site-selective oxidation/NaBH4-reduction sequence between glutaraldehyde and imines to generate in situ chiral 1,2-DHPs, followed by the diastereoselective Diels-Alder reaction with N-aryl maleimides furnishing isoquinuclidines in overall five steps. A variety of isoquinuclidines having five-contiguous chiral centers, including an all-carbon quaternary, were prepared with high yields (up to 78%) and excellent stereoselectivity (>50:1 dr, and up to >99:1 er). DFT calculations support the observed high stereoselective reaction outcome.