In silico screening and covalent binding of phytochemicals of Ocimum sanctum against SARS-CoV-2 (COVID 19) main protease.

Coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has compelled the scientific community to search for an effective drug that can cure or a vaccine that can prevent the disease. Alternatively, symptomatic treatment and traditional immunity boosters are prescribed. Holy Tulsi (Ocimum sanctum) has been known as an ancient remedy for cure of common cold and respiratory ailment. Several reports have come on virtual screening of phytochemicals including those of Tulsi against various enzymes of the virus. We undertook in silico analysis of the ethanol extracted phytochemicals of Tulsi as inhibitors of SARS-CoV-2 (2019-nCoV) main protease with an approach to look into the possibility of covalent ligand binding with the catalytic residue Cys145, which makes the report unique. The results suggest that the flavonoids and polyphenolic compounds of Tulsi, have potential to covalently bind to the catalytic residue Cys145 of main protease and irreversibly inhibit the viral enzyme. Luteolin-7-O-glucuronide is specially considered for its optimum properties, namely, low toxicity (LD50 5000 mg/kg body weight), high drug-likeness score (0.71), the active site binding free energy (ΔGbind) -19.19 kcal/mol by GBSA method and covalent binding energy -24.23 kcal/mol. Further experimental validations are required to establish the theoretical findings.Communicated by Ramaswamy H. Sarma.

In Silico and In Vitro Evaluations of Fluorophoric Thiazolo-[2,3-b]quinazolinones as Anti-cancer Agents Targeting EGFR-TKD.

Epidermal growth factor receptor tyrosine kinase domain (EGFR-TKD) plays a pivotal role in cellular signaling, growth, and metabolism. The EGFR-TKD is highly expressed in cancer cells and was endorsed as a therapeutic target for cancer management to overcome metastasis, cell proliferation, and angiogenesis. The novel thiazolo-[2,3-b]quinazolinones series were strategically developed by microwave-assisted organic synthesis and multi dominos reactions aimed to identify the potent thiazolo-[2,3-b]quinazolinone inhibitor against EGFR-TKD. This study explores the binding stability and binding strength of newly developed series via molecular docking, molecular dynamics simulation, and MM/PBSA and MM/GBSA calculations. The binding interaction was observed to be through the functional groups on aryl substituents at positions 3 and 5 of the thiazolo-[2, 3-b]quinazolinone scaffold. The methyl substituents at position 8 of the ligands had prominent hydrophobic interactions corroborating their bindings similar to the reference FDA-approved drug erlotinib in the active site. ADMET predictions reveal that derivatives 5ab, 5aq, and 5bq are drug-like and may be effective in in vitro study. Molecular dynamics simulation for 100 ns of docked complexes revealed their stability at the atomistic level. The ΔGbinding of thiazolo-[2,3-b]quinazolinone was found to be 5ab - 22.45, 5aq - 22.23, and 5bq - 20.76 similar to standard drug, and erlotinib - 24.11 kcal/mol was determined by MM/GBSA method. Furthermore, the anti-proliferative activity of leads of thiazolo-[2,3-b]quinazolinones (n = 3) was studied against breast cancer cell line (MCF-7) and non-small lung carcinoma cell line (H-1299). The highest inhibitions in cell proliferation were shown by 5bq derivatives, and the IC50 was found to be 6.5 ± 0.67 µM against MCF-7 and 14.8 µM against H-1299. The noscapine was also taken as a positive control and showed IC50 at higher concentrations 37 ± 1 against MCF-7 and 46.5 ± 1.2 against H-1299.

Monte-Carlo method-based QSAR model to discover phytochemical urease inhibitors using SMILES and GRAPH descriptors.

Urease inhibitors are known to play a vital role in the field of medicine as well as agriculture. Special attention is attributed to the development of novel urease inhibitors with a view to treat the Helicobacter pylori infection. Amongst a number of urease inhibitors, a large number of molecules fail in vivo and in clinical trials due to their hydrolytic instability and toxicity profile. The search for potential inhibitors may require screening of large and diverse databases of small molecules and to design novel molecules. We developed a Monte-Carlo method-based QSAR model to predict urease inhibiting potency of molecules using SMILES and GRAPH descriptors on an existing diverse database of urease inhibitors. The QSAR model satisfies all the statistical parameters required for acceptance as a good model. The model is applied to identify urease inhibitors among the wide range of compounds in the phytochemical database, NPACT, as a test case. We combine the ligand-based and structure-based drug discovery methods to improve the accuracy of the prediction. The method predicts pIC50 and estimates docking score of compounds in the database. The method may be applied to any other database or compounds designed in silico to discover novel drugs targeting urease.Communicated by Ramaswamy H. Sarma.

Structure-based Discovery of Narirutin as a Shikimate kinase Inhibitor with Anti-tubercular Potency.

BACKGROUND: Shikimate pathway is essential for tubercular bacillus but it is absent in mammals. Therefore, Shikimate kinase and other enzymes in the pathway are potential targets for the development of novel anti-tuberculosis drugs. OBJECTIVE: In the present study, Shikimate kinase is selected as the target for in silico screening of phytochemicals with an aim to discover a novel herbal drug against Mycobacterium tuberculosis (Mtb). METHODS: A structure-based drug discovery approach is undertaken for the execution of the objective. Virtual screening of phytochemical database NPACT against the target, Shikimate kinase (PDB ID 3BAF), is carried out followed by toxicity and drug-likeness filtration. Finally, a lead, narirutin was selected for in vitro anti-tubercular study. RESULTS: Narirutin, present in citrus fruits, emerges as the lead. It is considered to be non-toxic with predicted high LD50 value, 12000 mg/kg body weight. The phytochemical is tested for its antitubercular activity in vitro. It has MIC99 62.5 µg/mL against the MtbH37Rv strain. CONCLUSION: This is the first-ever report to show anti-tuberculosis potency of narirutin.

Dehydration induced loss of photosynthesis in Arabidopsis leaves during senescence is accompanied by the reversible enhancement in the activity of cell wall ß-glucosidase.

The physiology of loss of photosynthetic production of sugar and the consequent cellular sugar reprogramming during senescence of leaves experiencing environmental stress largely remains unclear. We have shown that leaf senescence in Arabidopsis thaliana causes a significant reduction in the rate of oxygen evolution and net photosynthetic rate (Pn). The decline in photosynthesis is further aggravated by dehydration. During dehydration, primary photochemical reaction of thylakoids and net photosynthesis decrease in parallel with the increase in water deficit. Senescence induced loss in photosynthesis is accompanied by a significant increase in the activity of cell wall hydrolyzing enzyme such as ß-glucosidase associated with cell wall catabolism. The activity of this enzyme is further enhanced when the senescing leaves experience dehydration stress. It is possible that both senescence and stress separately or in combination result in the loss in photosynthesis which could be a signal for an enhancement in the activity of ß-glucosidase that breaks down cell wall polysaccharides to sugar to sustain respiration for metabolic activities of plants experiencing stress. Thus dehydration response of cell wall hydrolases of senescing leaves is considered as plants' strategy to have cell wall polysaccharides as an alternative energy source for completion of energy requiring senescence process, stress survival and maintenance of recovery potential of energy deficit cells in the background of loss in photosynthesis. Withdrawal of stress (rehydration) distinctly exhibits recovery of photosynthesis and suppression of enzyme activity. Retention of the signaling for sugar reprogramming through breakdown of cell wall polysaccharides in the senescing leaves exposed to severe drought stress suggests that senescing leaves like mature ones possess potential for stress recovery. The precise mechanism of stress adaptation of senescing leaves is yet to be known. A significant accumulation of anthocyanin and flavonoids may be an indicator of stress adaptation of senescing leaves. In addition, stress induced enhancement of nonphotochemical quenching (NPQ), a stress protection provision in green plants, also suggests the potential of the leaves to develop adaptational mechanism to counter the dehydration stress.

Damage of photosynthetic apparatus in the senescing basal leaf of Arabidopsis thaliana: a plausible mechanism of inactivation of reaction center II.

Significant decline in oxygen evolution and DCPIP photoreduction and a marginal restoration of the later with DPC as an electron donor suggest the inactivation of reaction center of photosystem II. The declines in the height of thermoluminescence bands support the view and the damage of reaction center II could be central to the senescence process in Arabidopsis leaves. The enhancement in the number of reduced quinones, signifying a loss in redox homeostasis in the electron transport chain between photosystem II and I leads to the creation of an energy imbalance. The view is supported by the decline in actual quantum yield of photosystem II in the light adapted state and maximum quantum yield of primary photochemistry in the dark adapted state of chlorophyll fluorescence. An increase in chlorophyll a fluorescence polarization and decline in carotenoid to chlorophyll energy transfer efficiency suggest the perturbation in thylakoid structure. A plausible mechanism illustrating the senescence mediated inactivation of oxygen evolving complex has been proposed.

A molecular model of artificial photosynthesis: Mn-Ca binuclear complex for photosynthetic oxidation of water.

The redox active component of oxygenic photosynthetic reaction center II contains metal cluster Mn4-Ca, where two H2O are oxidized to O2 and four H+ ions are liberated. A binuclear Mn-Ca metal center binding one substrate H2O on each ion is proposed to be the minimal unit of the redox center. A model for the water oxidizing metal cluster is built with molecular modeling software (HyperChem 8.0 Pro). Mn, being a transitional metal with variable valency is redox active, while Ca is redox inert. Formation and deprotonation of H2O+ on MnIII may be favorable compared to Ca. Deprotonation of H2O+ yields a stable species HO(-) on MnIV by transfer of one electron from MnIII as a consequence of first photoact. Similarly, during second photoact, it may lead to formation of MnV = O. The O-O bond may be formed in the third photoact between O on Mn and H2O on Ca. Subsequently, HO2*(-) may be formed, leading to formation of O2. Molecular models are built for each transition states.

Senescence-induced loss in photosynthesis enhances cell wall beta-glucosidase activity.

A link between senescence-induced decline in photosynthesis and activity of beta-glucosidase is examined in the leaves of Arabidopsis. The enzyme is purified and characterized. The molecular weight of the enzyme is 58 kDa. It shows maximum activity at pH 5.5 and at temperature of 50 degrees C. Photosynthetic measurements and activity of the enzyme are conducted at different developmental stages including senescence of leaves. Senescence causes a significant loss in total chlorophyll, stomatal conductance, rate of evaporation and in the ability of the leaves for carbon dioxide fixation. The process also brings about a decline in oxygen evolution, quantum yield of photosystem II (PS II) and quantum efficiency of PS II photochemistry of thylakoid membrane. The loss in photosynthesis is accompanied by a significant increase in the activity of the cell wall-bound beta-glucosidase that breaks down polysaccharides to soluble sugars. The loss in photosynthesis as a signal for the enhancement in the activity of the enzyme is confirmed from the observation that incubation of excised mature leaves in continuous dark or in light with a photosynthesis inhibitor 3-(3,4-dichlorophenyl)-1, 1-dimethylurea (DCMU) that leads to sugar starvation enhances the activity of the enzyme. The work suggests that in the background of photosynthetic decline, the polysaccharides bound to cell wall that remains intact even during late phase of senescence may be the last target of senescing leaves for a possible source of sugar for remobilization and completion of the energy-dependent senescence program.