The outbreak of COVID-19 caused by SARS-CoV-2 virus continually led to infect a large population worldwide. Currently, there is no specific viral protein-targeted therapeutics. The Nucleocapsid (N) ...protein of the SARS-CoV-2 virus is necessary for viral RNA replication and transcription. The C-terminal domain of N protein (CTD) involves in the self-assembly of N protein into a filament that is packaged into new virions. In this study, the CTD (PDB ID: 6WJI) was targeted for the identification of possible inhibitors of oligomerization of N protein. Herein, multiple computational approaches were employed to explore the potential mechanisms of binding and inhibitor activity of five antiviral drugs toward CTD. The five anti-N drugs studied in this work are 4E1RCat, Silmitasertib, TMCB, Sapanisertib, and Rapamycin. Among the five drugs, 4E1RCat displayed highest binding affinity (-10.95 kcal/mol), followed by rapamycin (-8.91 kcal/mol), silmitasertib (-7.89 kcal/mol), TMCB (-7.05 kcal/mol), and sapanisertib (-6.14 kcal/mol). Subsequently, stability and dynamics of the protein-drug complex were examined with molecular dynamics (MD) simulations. Overall, drug binding increases the stability of the complex with maximum stability observed in the case of 4E1RCat. The CTD-drug complex systems behave differently in terms of the free energy landscape and showed differences in population distribution. Overall, the MD simulation parameters like RMSD, RMSF, Rg, hydrogen bonds analysis, PCA, FEL, and DCCM analysis indicated that 4E1RCat and TMCB complexes were more stable as compared to silmitasertib and sapanisertib and thus could act as effective drug compounds against CTD.
Communicated by Ramaswamy H. Sarma
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Molecular docking provides a computationally efficient way to predict the atomic structural details of protein-RNA interactions (PRI), but accurate prediction of the three-dimensional structures and ...binding affinities for PRI is still notoriously difficult, partly due to the unreliability of the existing scoring functions for PRI. MM/PBSA and MM/GBSA are more theoretically rigorous than most scoring functions for protein-RNA docking, but their prediction performance for protein-RNA systems remains unclear. Here, we systemically evaluated the capability of MM/PBSA and MM/GBSA to predict the binding affinities and recognize the near-native binding structures for protein-RNA systems with different solvent models and interior dielectric constants (
). For predicting the binding affinities, the predictions given by MM/GBSA based on the minimized structures in explicit solvent and the GB
model with
= 2 yielded the highest correlation with the experimental data. Moreover, the MM/GBSA calculations based on the minimized structures in implicit solvent and the GB
model distinguished the near-native binding structures within the top 10 decoys for 117 out of the 148 protein-RNA systems (79.1%). This performance is better than all docking scoring functions studied here. Therefore, the MM/GBSA rescoring is an efficient way to improve the prediction capability of scoring functions for protein-RNA systems.
Cancer is a life-threatening disease and is the second leading cause of death worldwide. Although many drugs are available for the treatment of cancer, survival outcomes are very low. Hence, rapid ...development of newer anticancer agents is a prime focus of the medicinal chemistry community. Since the recent past, computational methods have been extensively employed for accelerating the drug discovery process. In view of this, in the present study we performed 2D-QSAR (Quantitative Structure-Activity Relationship) analysis of a series of compounds reported with potential anticancer activity against breast cancer cell line MCF7 using QSARINS software. The best four models exhibited a
value of 0.99. From the generated QSAR equations, a series of pyrimidine-coumarin-triazole conjugates were designed and their MCF7 cell inhibitory activities were predicted using the QSAR equations. Furthermore, molecular docking studies were carried out for the designed compounds using AutoDock Vina against dihydrofolate reductase (DHFR), colchicine and vinblastine binding sites of tubulin, the key enzyme targets in breast cancer. The most active compounds identified through these computational studies will be useful for synthesizing and testing them as prospective novel anti-breast cancer agents.
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•High-precision performance of the derived simplified electromagnetic force/torque models is illustrated via numerical analysis.•The soft docking process is divided into three successive maneuvers ...with predefined time.•An improved finite time sliding mode control strategy is developed to satisfy good orbit-attitude tracking performance.
In this paper, the simplified electromagnetic force/torque model and coupled orbit-attitude dynamics modeling in spacecraft electromagnetic docking are investigated, and an improved sliding mode control scheme based on planned trajectory is proposed. In this scenario, the docking two spacecraft are equipped with four energized solenoids with iron cores fixed in the body frame, and small-angle hypothesis is used to derive the simplified electromagnetic force/torque model, based on which the coupled orbit-attitude dynamics equation is established. With trajectory planning of relative orbit and attitude, where the tracking process of coupled orbit-attitude is divided into three successive parts with predefined time using three characteristic time instants, a sliding mode control strategy is proposed to solve the tracking problem. Simulation results illustrate the simplification rationality of electromagnetic force/torque model, and the good tracking performance of coupled orbit-attitude tracking controller at predefined time.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
In this study, new 7-chloro-4-aminoquinoline-benzimidazole compounds were synthesized and characterized by NMR, MS, and elemental analysis. These novel hybrids differ in the type of linker and in the ...substituent on the benzimidazole moiety. Their antiproliferative activities were evaluated on one non-tumor (MDCK1) and seven selected tumor (CaCo-2, MCF-7, CCRF-CEM, Hut78, THP-1, and Raji) cell lines by MTT test and flow cytometry analysis. The compounds with different types of linkers and an unsubstituted benzimidazole ring,
,
, and
showed strong cytotoxic activity (the GI
ranged from 0.4 to 8 µM) and effectively suppressed the cell cycle progression in the leukemia and lymphoma cells. After 24 h of treatment, compounds
and
induced the disruption of the mitochondrial membrane potential as well as apoptosis in HuT78 cells. The drug-like properties and bioavailability of the compounds were calculated using the Swiss ADME web tool, and a molecular docking study was performed on tyrosine-protein kinase c-Src (PDB: 3G6H). Compound
showed good solubility and permeability and bound to c-Src with an energy of -119.99 kcal/mol, forming hydrogen bonds with Glu310 and Asp404 in the active site and other residues with van der Waals interactions. The results suggest that compound
could be a leading compound in the further design of effective antitumor drugs.
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The new Corona-virus, recently called the severe acute respiratory syndrome Coronavirus (SARS-CoV-2) appears for the first time in China and more precisely in Wuhan (December 2019). This disease can ...be fatal. Seniors, and people with other medical conditions (diabetes, heart disease...), may be more vulnerable and become seriously ill. This is why research into drugs to treat this infection remains essential in several research laboratories. Natural herbal remedies have long been the main, if not the only, remedy in the oral tradition for treating illnesses. Modern medicine has known its success thanks to traditional medicine, the effectiveness of which derives from medicinal plants. The objective of this study is to determine if the components of natural origin have an anti-viral effect and which can prevent humans from infection by this coronavirus using the most reliable method is molecular docking, which used to find the interaction between studied molecules and the protein, in our case we based on the inhibitor of Coronavirus (nCoV-2019) main protease. The results of molecular docking showed that among 67 molecules of natural origin, three molecules (Crocin, Digitoxigenin, and β-Eudesmol) are proposed as inhibitors against the coronavirus based on the energy types of interaction between these molecules and studied protein.
Communicated by Ramaswamy H. Sarma
Highlights
Determine natural compounds that can have an anti-viral effect and which can prevent humans from infection by this coronavirus;
Molecular docking to find interaction between the molecules studied and the receptor of COVID-19;
The synthesis of these molecules and the evaluation of their in vitro activity against SARS-Cov-2 could be interesting.
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A series of thieno2,3‐dpyrimidines were designed and synthesized as epidermal growth factor receptor (EGFR) inhibitors. These compounds were tested for their ability to inhibit MCF‐7 and A549 cancer ...cells. The most active compound, 12c, inhibited the growth of both cell lines, with IC50 values of 15.67 and 12.16 μM, respectively. It was found that 12c had inhibitory effects on both EGFRWT and EGFRT790M isoforms, with inhibitory partialities of 37.50 and 148.90 nM, respectively. Additionally, 12c was found to be safer than erlotinib against normal cell lines (IC50 = 38.61 μM). Compound 12c induced early and late apoptosis in A549 cells and arrested cell growth at G1 and G2/M phases. 12c was also found to increase caspases 3 and 8 ratios. Molecular docking indicated the correct binding modes of the synthesized compounds. MD simulations, MM‐GBSA, and PLIP studies confirmed the precise binding of 12c to the EGFR protein over 100 ns.
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•Up to 51 different compounds were identified in the horchata infusion.•The infusion is predicted to have anti-inflammatory and antioxidant effects.•Horchata contains potential inhibitors of the ...SARS-CoV-2 Mpro and PLpro enzymes.
Bioactive plant-derived molecules have emerged as therapeutic alternatives in the fight against the COVID-19 pandemic. In this investigation, principal bioactive compounds of the herbal infusion “horchata” from Ecuador were studied as potential novel inhibitors of the SARS-CoV-2 virus. The chemical composition of horchata was determined through a HPLC-DAD/ESI-MSn and GC–MS analysis while the inhibitory potential of the compounds on SARS-CoV-2 was determined by a computational prediction using various strategies, such as molecular docking and molecular dynamics simulations. Up to 51 different compounds were identified. The computational analysis of predicted targets reveals the compounds’ possible anti-inflammatory (no steroidal) and antioxidant effects. Three compounds were identified as candidates for Mpro inhibition: benzoic acid, 2-(ethylthio)-ethyl ester, l-Leucine-N-isobutoxycarbonyl-N-methyl-heptyl and isorhamnetin and for PLpro: isorhamnetin-3-O-(6-Orhamnosyl-galactoside), dihydroxy-methoxyflavanone and dihydroxyphenyl)-5-hydroxy-4-oxochromen-7-yloxy-3,4,5-trihydroxyoxane-2-carboxylic acid. Our results suggest the potential of Ecuadorian horchata infusion as a starting scaffold for the development of new inhibitors of the SARS-CoV-2 Mpro and PLpro enzymes.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
This study included synthesis of new serotonin derivatives in which imidazolidine rings are present in their structures. The final imidazolidine derivatives compounds were synthesized by reaction of ...synthesized
Schiff bases derivatives of serotonin with the glycine (NH2-CH2COOH) in presence of tetrahydrofuran (THF) as a solvent. The imidazolidine derivatives were identified by physical characteristics, FT-IR spectroscopy and 1H- NMR spectroscopy. Biological activities against two Gram negative (Klebsiella and E. coli) and two Gram positive (Streptococcus pyogenes and Staphylococcus aureus) bacteria were also distinguished. All the synthesized compounds III(a-d) exhibit moderate activities on four types of bacteria comparing with the activity of standard drug (Trimethoprim) but the highest activities of these compounds occur on Streptococcus pyogenes and their least activities occur on E. coli. The synthesized compounds were studied for the molecular docking to know the interaction and affinity of binding between them and bacteria
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