(E)-1-(3-Benzoyl-4-phenyl-1H-pyrrol-1-yl)-3-phenylprop-2-en-1-one

Over the last decade, there has been an increasing effort to fight inflammatory conditions establishing new multitarget approaches. Chronic inflammation is implicated in many multifactorial diseases, constituting a great economic burden and a chronic health problem. In an attempt to develop new potent multifunctional anti-inflammatory agents, a cinnamic-pyrrole hybrid (6) was synthesized and screened for its antioxidant and anti-Lipoxygenase potential. The new compound, in comparison with its pyrrole precursor (4), showed improved biological activities. In silico calculations were performed to predict its drug-likeness. The examined derivative is considered orally bioavailable according to Lipinski’s rule of five. Compound 6 could be used as a lead for the synthesis of more effective hybrids.

Structure-Based In Silico Investigation of Agonists for Proteins Involved in Breast Cancer

Cancer is recognized as one of the main causes of mortality worldwide by the World Health Organization. The high cost of currently available cancer therapy and certain limitations of current treatment make it necessary to search for novel, cost-effective, and efficient methods of cancer treatment. Therefore, in the current investigation, sixty-two compounds from five medicinal plants (Tinospora cordifolia, Ocimum tenuiflorum, Podophyllum hexandrum, Andrographis paniculata, and Beta vulgaris) and two proteins that are associated with breast cancer, i.e., HER4/ErbB4 kinase and ERα were selected. Selected compounds were screened using Lipinski’s rule, which resulted in eighteen molecules being ruled out. The remaining forty-four compounds were then taken forward for docking studies followed by molecular dynamics studies of the best screened complexes. Results showed that isocolumbin, isopropylideneandrographolide, and 14-acetylandrographolide were potential lead compounds against the selected breast cancer receptors. Furthermore, in vitro studies are required to confirm the efficacy of the lead compounds.

Promising inhibitors against main protease of SARS CoV-2 from medicinal plants: In silico identification

Some compounds reported as active against SARS CoV were selected, and docking studies were performed using the main protease of SARS CoV-2 as the receptor. The docked complex analysis shows that the ligands selectively bind with the target residues and binding affinity of amentoflavone (–10.1 kcal mol–1), isotheaflavin-3’-gallate (–9.8 kcal mol–1), tomentin A and D (–8.0 and –8.8 kcal mol–1), theaflavin-3,3’-digallate (–8.6 kcal mol–1), papyriflavonol A (–8.4 kcal mol–1), iguesterin (–8.0 kcal mol–1) and savinin (–8.3 kcal mol–1) were ranked above the binding affinity of the reference, co-crystal ligand, ML188, a furan-2-carboxamide-based compound. To pinpoint the drug-like compound among the top-ranked compounds, the Lipinski’s rule of five and pharmacokinetic properties of all the selected compounds were evaluated. The results detailed that savinin exhibits high gastrointestinal absorption and can penetrate through the blood-brain barrier. Also, modifying these natural scaffolds with excellent binding affinity may lead to discovering of anti-SARS CoV agents with promising safety profiles.

Structure-Based De Novo Design and Docking Studies of 5(S)-Methyl-L-Proline Containing Peptidomimetic Compounds as Dipeptidyl Peptidase-4 Inhibitors

Background: Diabetes affects millions of people worldwide, with predicted numbers of about 700 million adults affected by 2045. Among the several anti-diabetic drug therapies available in the market, Dipeptidyl Peptidase-4 (DPP-4) inhibitors have emerged as a promising therapeutic approach with scope for exploration in the segment of peptidomimetics. Objective: Series of proline-containing peptidomimetic compounds were designed and investigated for their drug-likeness through Lipinski’s rule of five, lead-likeness through the rule of three, predictive pharmacokinetic studies (absorption, distribution, metabolism, and excretion), and toxicity properties through in-silico approaches. The designed compounds were evaluated for their interactions with binding sites of the enzyme DPP-4 using an extra precision docking approach. Methods: Proline-containing peptidomimetic compounds were designed rationally. Drug-likeness and lead-likeness properties were calculated using Schrödinger Maestro v11.2 software. ADME and toxicity properties were predicted using PreADMET version 2.0. Docking study was performed using Schrödinger Maestro v11.2 software, and ligands for the study were designed using MarvinSketch software. Results: 5(S)-methyl-L-proline containing 17 ligands were designed. All of them were found to obey Lipinski’s rule of five. Compounds were found to have good ADME profile and low toxicity predictions. Conclusion: Four compounds were found to have good interactions with DPP-4 binding sites and hence created the scope to develop a DPP-4 inhibitors containing 5(S)-methyl-L-proline moiety.

Virtual prediction of purple rice ferulic acid as anti-inflammatory of TNF-α signaling

Purple rice is one of the main sources of ferulic acid (FA). Some studies reported anti-inflammatory properties of FA, but the interaction of FA with TNF-α signaling has not been elucidated. TNF-α is a target for anti-inflammatory drug research due to its major role in the inflammatory process. This study aims to investigate the interaction of FA with TNF-α and TNF-α receptor (TNFR) through in silico study and evaluate the drug-like properties and biological activity of FA. The interactions among FA (CID 445858), TNF-α (2AZ5), and TNFR (1NCF) were docked by Hex 8.0.0 Cuda, then visualized by Discovery Studio 2020 and LigPlot V.1.4.5. Apigenin-7-glucuronide (AG, CID 5319484) was used as the positive control. The drug-like properties were predicted by Lipinski’s rule of five and the biological activity was analyzed by PASS online. FA showed good properties as a drug-like molecule and biological activity as an anti-inflammatory. FA also showed good interaction with TNF-α and TNFR. FA bound to TNF-α at Asn92(B), Val91(B), Leu93(B), Phe124(B), Phe124(D), and Leu93(D) residues with docking energy of -214.6 kJ/mol, and bound to TNFR at Pro16(A), Glu56(B), Cys55(B), Glu54(B) residues with docking energy of -191.1 kJ/mol. FA could inhibit TNF-α – TNFR interaction by binding to TNFR at Glu54 residue, the same inhibition mechanism to AG which bind to TNFR at Glu54 and Val90. The current study shows that FA has the potential as an anti-inflammatory of TNF-α signaling and can be developed as an oral anti-inflammatory drug candidate.

In silico screening of drug inhibitors of SARS-CoV-2RNA-dependent RNA polymerase target

Objectives: the COVID-19 pandemic triggering acute respiratory syndrome has become a major global health concern. After one year into this pandemic, special therapies for COVID-19 remain an unprecedented challenge to mankind and finding drugs to treat this disease is extremely urgent. The SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) enzyme that regulates viral replication has been examined as a potential therapeutic target for the inhibition of SARS-CoV-2 infection. In this study, the authors evaluated the ability of RNA-dependent RNA polymerase drug inhibitors by using an in silico molecular docking model. Methods: the 3D structure of RdRp enzyme (PDB ID:6M71, resolution of 2.90 Å) was derived from the Protein Data Bank RCSB. The ligand structures were collected from DrugBank for the RdRp target. Molecular docking was done by AutoDock Vina software. Lipinski’s rule of five is used to compare compounds with drug-like and non-drug-like properties. Pharmacokinetic parameters of potential compounds were evaluated using the pkCSM tool. Results: based on the DrugBank database, we collected 192 antiviral molecules and compared them to remdesivir, which has inhibitory activity with this protein target. Results showed that 26 out of 192 compounds have a higher ability to inhibit the SARS-CoV-2 RdRp enzyme than remdesivir. Next, 6 drugs were selected by visually inspecting the docking results with focus on the main interaction between crucial residues at the binding site of the SARS-CoV-2 RdRp enzyme. For the visual inspection, the existence of polar interactions with ASP760 and ASP761 were utilised as the preference criterion. Finally, Lipinski’s rule of 5 criteria and absorption, distribution, metabolism, excretion and toxicity (ADMET) profile analysis suggested five drugs that have good pharmacokinetic properties. Conclusions: these drugs were dihydroergotamine, sofosbuvir, nilotinib, tipranavir, and darunavir and may be used as anti-SARS-CoV-2 agents.

Mechanistic Validation of an Ergogenic T. arjuna Standardized Extract (Oxyjun®) Using a Molecular Docking Approach

The bark of the tree Terminalia arjuna commonly referred as Arjuna is widely used in Ayurveda as a therapeutic agent for heart disease. More recently, a proprietary botanical extract of T. arjuna with tradename, Oxyjun®, demonstrated cardiotonic and ergogenic benefits for the first time in a younger and healthier population. However, the mechanism of action and biological actives of this novel sports ingredient were not clear. A molecular docking approach was adopted to understand the protein-ligand interactions and establish the most probable mechanism(s) of cardio vascular actions of the phytoconstituents of the T. arjuna standardized extract (TASE). Twenty-one phytochemicals (ligands) were chosen from Arjuna and their binding affinities against eight proteins serving cardiovascular functions (target proteins) were investigated. Autodock Vina was used to carry out the molecular docking studies. Potential efficacy in humans was assessed on the basis of ADMET properties and Lipinski’s Rule of 5. We found that arjunic acid, arjungenin, arjunetin, arjunglucoside1, chrysin, kaempferol, luteolin, rhamnetin and taxifolin demonstrated good docking scores and bioactivity.

COMPUTATIONAL SCREENING AND MOLECULAR DOCKING OF LICHEN SECONDARY METABOLITES AGAINST SEVERE ACUTE RESPIRATORY SYNDROME-COV-2 MAIN PROTEASE AND SPIKE PROTEIN

Objective: At present, the coronavirus disease (COVID)-19 pandemic is increasing global health concerns. This coronavirus outbreak is caused by severe acute respiratory syndrome coronavirus (SARS-CoV)-2. Since, no specific antiviral for treatment against COVID-19, so identification of new therapeutics is an urgent need. The objective of this study is to the analysis of lichen compounds against main protease and spike protein targets of SARS-CoV-2 using in silico approach. Methods: A total of 108 lichen compounds were subjected to ADMET analysis and 14 compounds were selected based on the ADMET properties and Lipinski’s rule of five. Molecular docking was performed for screening of selected individual lichen metabolites against the main protease and spike proteins of SARS-CoV-2 by Schrodinger Glide module software. Results: Among the lead compounds, fallacinol showed the highest binding energy value of −11.83 kcal/mol against spike protein, 4-O-Demethylbarbatic acid exhibited the highest dock score of −11.67 kcal/mol against main protease. Conclusion: This study finding suggests that lichen substances may be potential inhibitors of SARS-CoV-2.

IN SILICO DESIGN OF BENOXAZOLE BEARING AZETIDINONE DERIVATIVES AS VEGFR-2 AGONIST IN CANCER

Objective: Cancer is a group of disease characterized by uncontrolled growth of cells. The objective of the study includes the in silico designing of benzoxazole bearing azetidinone derivatives as Vascular Endothelial Growth Factor 2 in cancer. Methods: In silico design of proposed derivatives was conducted using tools such as AutoDock Vina, ACD Lab ChemSketch ver. 12.0, Prediction of Activity Spectra for Substances online, molinspiration, and Swiss ADME. The derivatives obeying Lipinski’s Rule of Five in accordance with molinspiration were selected for docking studies. Results: The data obtained from molinspiration revealed that the designed derivatives have physical and chemical properties meant for an orally bioavailable drug. From the docking studies derivatives BT1 and BT5 showed high docking score which indicate that these derivatives possess high affinity and high polar interaction towards protein 4DBN. Conclusion: The designed benzoxazole bearing azetidinone derivatives were found to possess good binding affinity and good interaction in the binding pocket of the target 4DBN. Therefore, these derivatives are expected to exhibit good anticancer property with minimal side effects.