Synthesis of S-mono- and S,O-bis-1,2,3-triazole linked 1,5-benzodiazepine conjugates and evaluation of their cytotoxic,anti-tyrosinase,and anti-cholinesterase activities

A series of S-mono and S,O-bis-1,2,3-triazole linked 1,5-benzodiazepines (BZD) conjugates 6a-j and 7a-j were synthesized employing “click chemistry” under microwave irradiation. The synthesized derivatives have been evaluated for their cytotoxic (MCF-7, HeLa, A549 cell lines), anti-tyrosinase and anti-cholinesterase activities. These molecules exhibited moderate to good biological activity.     

Efficient synthesis of new azo-sulfonamide derivatives and investigation of their molecular docking and cytotoxicity results

The present study focused on the synthesis, introduction and investigation of the biological effects of sulfonamide-derived products as new azo-sulfonamides (samples 1–6). In this transformation, the amine sulfonamide is first converted to the corresponding diazonium salt, which is then attacked by a nucleophilic carbon of the aromatic ring in the playing medium. All products were obtained with reasonable yields and high purity. The structure of synthesized derivatives was determined using various analytical tools including FT-IR, ¹H NMR, ¹³C NMR and XRD spectroscopy, and the synthesized products were purified and identified. Biological properties of newly synthesized azo-compounds similar to SSZAD were also investigated. These compounds were tested in terms of biological effectiveness. The results of biochemical assays show that: the products have significant biological properties. MTT toxicity of compounds in breast cancer cells (MCF-7) for compounds 1–6 according to IC₅₀ compare to Vinblastine is Vin > 5 > 4 > 6 > 2 > 3 > 1. The biochemical results obtained were analyzed by molecular docking interaction studies and showed strong hydrogen bonding with the target receptor. The docking calculation has been invoked to reveal the type of interactions that synthesized compounds can establish with the residues forming the active sites of the target proteins, 1FDW the three higher scores molecules appears to be (6 > 1 > 2), 3FC2 (the three highest binding affinities are in the order of 1 > 3 > 6), and 5GWK (three highest binding affinities are 1 > 3 > 6). The results indicate the effective interaction of all products with the targets. The molecular dynamics simulation has been invoked to study the presence of a stable system of the interacting protein–ligand.     

1,2,3-triazole derivative: Synthesis,characterization, DFT,molecular docking study and antibacterial-antileishmanial activities

In this study, 4-((1-(4-chlorobenzyl)-1H-1,2,3-triazole-4-yl)methoxy)-3-methoxybenzaldehyde (I) was synthesized and molecular structure of compound I was confirmed by FTIR and NMR (¹H and ¹³C NMR) spectroscopic methods. The geometric structure of compound I was optimized by DFT/B3LYP method using 6–311++G(d, p) basis set. The molecular docking study was carried out against six different proteins. The antibacterial and antileishmanial activities of compound I were tested by microdilution broth with Alamar blue method and minimum inhibitor concentrations (MIC) were determined. According to the test results, it was found to be effective against eleven types of bacteria at different concentrations (MIC: 312–5000 ​μg/mL). In addition, compound I was not effective against leishmania species at the concentrations that were examined.     

Phytochemical profiling,in vitro biological activities,and in-silico molecular docking studies of Typha domingensis

A comparative study between methanolic extract and n-hexane fraction of Typha domingensis (Typhaceae) was conducted for the evaluation of phytochemical potential, in vitro biological activities, and in-silico molecular docking studies. The phytochemical composition was estimated by total phenolic and total flavonoid contents, and by GC–MS analysis. Several biological activities were performed such as antioxidant assays (ABTS, FRAP, DPPH, & CUPRAC), enzyme inhibition activity (Tyrosinase, Acetylcholinesterase & Butyrylcholinesterase), thrombolytic activity, and antimicrobial activity (antibacterial & antiviral) to evaluate the medicinal importance of Typha domingensis. The results of the comparative study showed that methanolic extract has more total phenolic and total flavonoid contents (95.72 ± 5.76 mg GAE/g, 131.66 ± 7.92 mg QE/g, respectively) as compared to n-hexane fraction which confirms its maximum antioxidant potential (ABTS 114.31 ± 8.17, FRAP 116.84 ± 3.01, DPPH 283.54 ± 7.3 & CUPRAC 284.16 ± 6.5 mg TE/g). In the case of in vitro enzyme inhibition study and thrombolytic activity, better results were observed for methanolic extract. Almost similar antimicrobial patterns were observed for both methanolic extract and n-hexane fraction of Typha domingensis. The major bioactive phytochemicals identified by GC–MS were further analyzed for in-silico molecular docking studies to determine the binding affinity between ligands and the enzymes. The docking study indicated that most of the bioactive compounds showed a better binding affinity with enzymes as compared to the standard compounds (kojic acid & galantamine). The results of this study recommended that Typha domingensis has promising pharmaceutical importance and it should be further analyzed for the isolation of bioactive phytochemicals which may be useful for the treatment of several diseases.     

Molecular description of pyrimidine-based inhibitors with activity against FAK combining 3D-QSAR analysis,molecular docking and molecular dynamics

Focal adhesion kinase (FAK) is a promising target for developing more effective anticancer drugs. To better understand the structure-activity relationships and mechanism of actions of FAK inhibitors, a molecular modeling study using 3D-QSAR, molecular docking, molecular dynamics simulations, and binding free energy analysis were conducted. Two types of satisfactory 3D-QSAR models were generated, comprising the CoMFA model (R²_cv = 0.528, R²_pred = 0.7557) and CoMSIA model (R²_cv = 0.757, R²_pred = 0.8362), for predicting the inhibitory activities of novel inhibitors. The derived contour maps indicate structural characteristics for substituents on the template. Molecular docking, molecular dynamic simulations and binding free energy calculations further reveal that the binding of inhibitors to FAK is mainly contributed from hydrophobic, electrostatic and hydrogen bonding interactions. In addition, some key residues (Arg14, Glu88, Cys90, Arg138, Asn139, Leu141, and Leu155) responsible for ligand-receptor binding are highlighted. All structural information obtained from 3D-QSAR models and molecular dynamics is consist with the available experimental activities. All the results will facilitate the optimization of this series of FAK inhibitors with higher inhibitory activities.     

The novel 4-hydroxyphenylpyruvate dioxygenase inhibitors in vivo and in silico approach: 3D-QSAR analysis,molecular docking,bioassay and molecular dynamics

4-Hydroxyphenylpyruvate dioxygenase (HPPD) is not only an important target enzyme for the treatment of type I tyrosinemia, but also a new target for design bleaching herbicides, and it plays key role in the biosynthesis of tocopherol and plastoquinone. Thirty-six known active pyridine derivatives were collected, and comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) models based on common skeleton were constructed to obtain novel HPPD herbicides with higher activity. Two new HPPD inhibitors were rationally designed and synthesized according to the CoMFA and CoMSIA models and verified by enzyme activity, biological assays, and molecular docking. The promising compound W1 ((E)-5-(3-(4-bromophenyl)acryloyl)-6-hydroxy-2,3-dihydropyridin-4(1H)-one) showed better AtHPPD inhibitory activity, and the bioassay results revealed that some weeds showed bleaching symptoms. The good binding stability of W1 and protein was confirmed by molecular dynamics simulation in 100 ns. These results would be highly useful in the progress of new HPPD inhibitors discovery.     

The design of fluoroquinolone-based cholinesterase inhibitors: Synthesis,biological evaluation and in silico docking studies

An enhanced acetylcholinesterase (AChE) activity is a hallmark in early stages of Alzheimer's ailment that results in decreased acetylcholine (ACh) levels, which in turn leads to cholinergic dysfunction and neurodegeneration. Consequently, inhibition of both AChE and butyrylcholinesterase (BChE) is important to prolong ACh activity in synapses for the enhanced cholinergic neurotransmission. In this study, a series of new fluoroquinolone derivatives (7a-m) have synthesized and evaluated for AChE and BChE inhibitory activities. The screening results suggested that 7 g bearing ortho fluorophenyl was the most active inhibitor against both AChE and BChE, exhibiting IC₅₀ values of 0.70 ± 0.10 µM and 2.20 ± 0.10 µM, respectively. The structure–activity relationship (SAR) revealed that compounds containing electronegative functions (F, Cl, OMe, N and O) at the ortho position of the phenyl group exhibited higher activities as compared to their meta- and/or para substituted counterparts. Molecular docking studies of synthesized compounds 7a, 7g, 7j and 7l docked into the active site of AChE and 7a-f docked into the active site of BChE revealed that these compounds exhibited conventional H-bonding along with π-π interaction with the active residues of AChE through their electronegative functions and phenyl ring, respectively. All the synthesized compounds are characterized by spectroscopic methods including FT-IR, ¹H- and ¹³C NMR as well as elemental analysis. This is the first example of fluoroquinolone-based cholinesterase inhibitors.     

Synthesis,urease inhibitory activities,and molecular docking studies of two Cu(II) complexes

Two mononuclear copper(II) complexes, [Cu(C₄H₃N₂O₂)₂?·?4H₂O] (1) and [Cu(C₁₂H₁₁N₂O₂Cl₂)₂] (2), were synthesized and structurally characterized by single-crystal X-ray analysis. The copper(II) adopts a square-planar environment in 1, while the geometry in 2 can be described as distorted square-pyramidal. Complexes 1 and 2 were evaluated for their inhibitory activities against jack bean urease in vitro and both were found to have strong inhibitory activities comparable to that of acetohydroxamic acid. A docking simulation was performed to position 2 into the jack bean urease active site to determine the probable binding conformation.     

Synthesis,anticancer activity,and molecular docking of new pyrazolo[1,5-a]pyrimidine derivatives

The reaction of 3-aminopyrzoles with dimethylamino-acrylonitrile derivatives was utilized for the production of new functionalized pyrazolopyrimidine compounds 4a-c and 6a-c. The structures of the obtained pyrazolopyrimidines were characterized by the different spectroscopic measurements (IR, NMR, and mass analyses). The DFT quantum chemical calculations were applied to the determination of the HOMO-LUMO energies and Mulliken atomic charges. The investigated derivatives exhibited a low HOMO-LUMO energy gap, ranging from 2.70 to 2.34 eV, 4c and both 4b and 6b, respectively. Furthermore, the anticancer activities of the synthesized compounds have also been investigated against four cancer cells as well as normal cells (WI38). The investigated compounds demonstrated an impressive cytotoxic effect on MCF-7 and Hep-2 cells. On comparison with 5-fluorouracil, pyrazolopyrimidines 6a–c showed promising cytotoxic action against MCF-7 and Hep-2, with IC₅₀ values of 18.31–26.51 and 24.15–27.16 μM, respectively. Molecular docking of the prepared pyrazolopyrimidines 4 and 6 with the crystal structure of the KDM5A protein, obtained from the PDB, revealed the types of the protein's binding sites.     

Molecular docking,HOMO-LUMO and quantum chemical computation analysis of anti-glyoximehydrazone derivatives containing pyrazolone moiety and their transition metal complexes

In this study, in order to obtain biologically active compounds, a series of anti-glyoximehydrazone ligands bearing vic-dioxime, hydrazone, and pyrazole moieties and their (O•••H–O) bridged nickel(II), cobalt(II) and copper(II) metal complexes were prepared. Further, the molecular docking studies were carried out on those ligands and their nickel(II), cobalt(II) and copper(II) metal complexes to analyze the interaction with EGFR Kinase domain complexed with tak-285 (PDB ID: 3POZ) and human androgen receptor T877A mutant (PDB ID:2OZ7). In addition, the compounds were optimized by using B3LYP/6-311G+(d,p) level of Density Functional Theory (DFT) to evaluate the HOMO–LUMO contours and quantum chemical parameters. Also, bioactivity analysis were performed.Metal complexes had higher binding affinities against 3POZ and 2OZ7. The most promising compounds for 3POZ were nickel(II) and copper(II) metal complexes. However, for the 2OZ7 target receptor, cobalt(II) and copper(II) metal complexes were the possible hit compounds. Furthermore, cobalt(II) metal complex of ligand two was found to be the most reactive one among others. Moreover, it had the highest ω which is related to a potent higher electrophilic character. It was determined that all the compounds had moderate bioactivity.In conclusion, nickel(II), cobalt(II), and copper(II) complexes could be powerful hit compounds for anti-cancer drug discovery studies.     

Design,cytotoxic effects on breast cancer cell line (MDA-MB 231), and molecular docking of some maleimide-benzenesulfonamide derivatives

A group of novel maleimide-benzenesulfonamide derivatives 3a-d was designed and synthesized for their evaluation as a potential anti-breast cancer agent. The structures of these derivatives were confirmed by their ¹H, ¹³C NMR, Mass, FT-IR spectral data, and melting points. The cytotoxic activity (in vitro) of the selected molecules against MDA-MB231 ​cell line was evaluated by MTT method. Among them, compounds 3a and 3d exhibited a significant cytotoxicity with the IC₅₀ value of 1.61 and 1.26 ​μM, respectively, whereas compounds 3b and 3c showed a moderate cytotoxicity with IC₅₀ values of 0.45 and 1.12 ​μM, respectively against MDA-MB231 ​cells. Docking modeling of the synthesized compounds 3a-d into binding sites of human aromatase protein (PDB ID: 4GL7) was performed to investigate if these derivatives possess analogous binding mode to breast cancer proteins. Docking results showed these compounds have efficient interactions such as hydrogen bonding, Van der Waals interactions, and hydrophobic interactions with the active site residues of the aromatase protein (PDB ID: 4GL7). The low binding energies and a number of hydrogen bonding indicated that the maleimide-benzenesulfonamide derivatives might be considered as a promising anti-breast cancer agent with further developments in drug discovery.     

Medicinal plant phytochemicals and their inhibitory activities against pancreatic lipase: molecular docking combined with molecular dynamics simulation approach

Obesity is the worst health risk worldwide, which is linked to a number of diseases. Pancreatic lipase is considered as an affective cause of obesity and can be a major target for controlling the obesity. The present study was designed to find out best phytochemicals against pancreatic lipase through molecular docking combined with molecular dynamics (MD) simulation. For this purpose, a total of 3770 phytochemicals were docked against pancreatic lipase and ranked them on the basis of binding affinity. Finally, 10 molecules (Kushenol K, Rosmarinic acid, Reserpic acid, Munjistin, Leachianone G, Cephamycin C, Arctigenin, 3-O-acetylpadmatin, Geniposide and Obtusin) were selected that showed strong bonding with the pancreatic lipase. MD simulations were performed on top five compounds using AMBER16. The simulated complexes revealed stability and ligands remained inside the binding pocket. This study concluded that these finalised molecules can be used as drug candidate to control obesity.     

Identification of novel Plasmodium falciparum PI4KB inhibitors as potential anti-malarial drugs: Homology modeling,molecular docking and molecular dynamics simulations

The current study was set to discover selective Plasmodium falciparum phosphatidylinositol-4-OH kinase type III beta (pfPI4KB) inhibitors as potential antimalarial agents using combined structure-based and ligand-based drug discovery approach. A comparative model of pfPI4KB was first constructed and validated using molecular docking techniques. Performance of Autodock4.2 and Vina4 software in predicting the inhibitor-PI4KB binding mode and energy was assessed based on two Test Sets: Test Set I contained five ligands with resolved crystal structures with PI4KB, while Test Set II considered eleven compounds with known IC50 value towards PI4KB. The outperformance of Autodock as compared to Vina was reported, giving a correlation coefficient (R²) value of 0.87 and 0.90 for Test Set I and Test Set II, respectively. Pharmacophore-based screening was then conducted to identify drug-like molecules from ZINC database with physicochemical similarity to two potent pfPI4KB inhibitors –namely cpa and cpb. For each query inhibitor, the best 1000 hits in terms of TanimotoCombo scores were selected and subjected to molecular docking and molecular dynamics (MD) calculations. Binding energy was then estimated using molecular mechanics–generalized Born surface area (MM-GBSA) approach over 50 ns MD simulations of the inhibitor-pfPI4KB complexes. According to the calculated MM-GBSA binding energies, ZINC78988474 and ZINC20564116 were identified as potent pfPI4KB inhibitors with binding energies better than those of cpa and cpb, with ΔG_binding ≥ −34.56 kcal/mol. The inhibitor-pfPI4KB interaction and stability were examined over 50 ns MD simulation; as well the selectivity of the identified inhibitors towards pfPI4KB over PI4KB was reported.     

Sulfamide-substituted-BODIPY based fluorescence drugs: Synthesis,spectral characteristics,molecular docking,and bioactivity

BODIPY derivatives have attracted much attention in the field of biological probes, but probes with a single imaging function are no longer innovative. In this paper, two multifunctional sulfonamide-BODIPY derivatives were designed and synthesized. Photophysical properties, cytotoxicity, in vitro and in vivo imaging, apoptosis, cell cycle, and molecular docking simulation were studied. The results showed that the compound had low cytotoxicity to normal cells, but had strong inhibitory effect on tumor cells. The IC₅₀ value of compound 3 on HCT-116 cells was 58.61 ± 4.91 μmol/L, and 4 on HeLa cells was 52.29 ± 10.93 μmol/L. Cell imaging and mice experiments demonstrated that the probe had excellent biocompatibility and potential tumor targeting; and in vivo imaging of mice at different time periods showed that the fluorescence intensity of probes in subcutaneous lung tumor gradually increased with the extension of time. In addition, the flow cytometry analysis of 3 showed that the G1 phase of HCT-116 cells was inhibited and apoptosis of tumor cells was promoted. In molecular docking simulation, sulfonamide-BODIPY derivatives had high affinity scores with CDK2: −8.0 and −8.4 kcal·mol⁻¹, and the multiple interactions with receptors provided conditions for the probes to recognize tumor cells.     

Comprehensive structural analysis of the open and closed conformations of Theileria annulata enolase by molecular modelling and docking

Theileria annulata is an apicomplexan parasite which is responsible for tropical theileriosis in cattle. Due to resistance of T. annulata against commonly used antitheilerial drug, new drug candidates should be identified urgently. Enolase might be a druggable protein candidate which has an important role in glycolysis, and could also be related to several cellular functions as a moonlight protein. In this study; we have described three-dimensional models of open and closed conformations of T. annulata enolase by homology modeling method for the first time with the comprehensive domain, active site and docking analyses. Our results show that the enolase has similar folding patterns within enolase superfamily with conserved catalytic loops and active site residues. We have described specific insertions, possible plasminogen binding sites, electrostatic potential surfaces and positively charged pockets as druggable regions in T. annulata enolase.     

Synthesis,molecular docking,and inhibitory activity of a Ni Schiff-base complex against urease

A Ni(II) Schiff-base complex, Ni(C₁₄H₁₀NOBr₂)₂, was synthesized and structurally characterized by single-crystal X-ray analysis. Its inhibitory activity against Helicobacter pylori urease was evaluated in vitro and showed strong inhibitory activity against H. pylori urease compared with acetohydroxamic acid (IC₅₀ = 42.12 µmol L^?1), which is a positive reference. A docking analysis using the autodock 4.0 program could explain the inhibitory activity of the complex against urease.     

A comparative study of 5- fluorouracil,doxorubicin, methotrexate,paclitaxel for their inhibition ability for Mpro of nCoV: Molecular docking and molecular dynamics simulations

The new corona virus (nCoV) is aetiological agent responsible for the viral pneumonia epidemic. Three is no specific therapeutic medicines available for the treatment of this condition and also effective treatment choices are few. In this work, authors tried to investigate few potential of repurposing drugs (5- fluorouracil, doxorubicin, methotrexate and paclitaxel) against the main protease (Mpro) of nCoV by the computational tools. Molecular docking was performed to screen out the best compound and doxorubicin was found to have minimum binding energy ?121.89 kcal/mol. To further study, molecular dynamics (MD) simulations were performed at 300 K and the result successfully corroborate the energy obtained by molecular docking. Further, temperature dependent MD simulations of the best molecule, that is, doxorubicin based on results of docking, was performed to check the variation in structural changes in Mpro of nCoV at 290 K, 310 K, 320 K and 325 K. It is found that doxorubicin binds effectively with Mpro of nCoV at 290 K. Further, ADME properties of the 5- fluorouracil, doxorubicin, methotrexate and paclitaxel were also evaluated to understand the bioavailability.