A pharmacoinformatic approach on Cannabinoid receptor 2 (CB2) and different small molecules: Homology modelling,molecular docking,MD simulations,drug designing and ADME analysis

CB2 receptor belongs to the family of G-protein coupled receptors (GPCRs), which extensively controls a range of pointer transduction. CB2 plays an essential role in the immune system. It also associates in the pathology of different ailment conditions. In this scenario, the synthetic drugs are inducing side effects to the human beings after the drug use. Therefore, this study is seeking novel alternate drug molecules with least side effects than conventional drugs. The alternative drug molecules were chosen from the natural sources. These molecules were selected from cyanobacteria with the help of earlier research findings. The target and ligand molecules were obtained from recognized databases. The bioactive molecules are selected from various cyanobacterial species, which are selected by their biological and pharmacological properties, after, which we incorporated to the crucial findings such as homology modelling, molecular docking, MD simulations along with absorption, distribution, metabolism, and excretion (ADME) analysis. Initially, the homology modelling was performed to frame the target from unknown sequences of CB2, which revealed 44% of similarities and 66% of identities with the A2A receptor. Subsequently, the CB2 protein molecule has docked with already known and prepared bioactive molecules, agonists and antagonist complex. In the present study, the agonists (5) and antagonist (1) were also taken for comparing the results with natural molecules. At the end of the docking analysis, the cyanobacterial molecules and an antagonist TNC-201 are revealed better docking scores with well binding contacts than the agonists. Especially, the usneoidone shows better results than other cyanobacterial molecules, and it is very close docking scores with that of TCN-201. Therefore, the usneoidone has incorporated to MD simulation with Cannabinoid receptors 2 (CB2). In MD simulations, the complex (CB2 and usneoidone) reveals better stability in 30 ns. Based on the computational outcome, we concluded that usneoidone is an effectual and appropriate drug candidate for activating CB2 receptors and it will be serving as a better component for the complications of CB2. Moreover, these computational approaches can be motivated to discover novel drug candidates in the pharmacological and healthcare sectors.     

Molecular dynamics simulation study of PTP1B with allosteric inhibitor and its application in receptor based pharmacophore modeling

Allosteric inhibition of protein tyrosine phosphatase 1B (PTP1B), has paved a new path to design specific inhibitors for PTP1B, which is an important drug target for the treatment of type II diabetes and obesity. The PTP1B_1–282-allosteric inhibitor complex crystal structure lacks α7 (287–298) and moreover there is no available 3D structure of PTP1B_1–298 in open form. As the interaction between α7 and α6–α3 helices plays a crucial role in allosteric inhibition, α7 was modeled to the PTP1B_1–282 in open form complexed with an allosteric inhibitor (compound-2) and a 5 ns MD simulation was performed to investigate the relative orientation of the α7–α6–α3 helices. The simulation conformational space was statistically sampled by clustering analyses. This approach was helpful to reveal certain clues on PTP1B allosteric inhibition. The simulation was also utilized in the generation of receptor based pharmacophore models to include the conformational flexibility of the protein-inhibitor complex. Three cluster representative structures of the highly populated clusters were selected for pharmacophore model generation. The three pharmacophore models were subsequently utilized for screening databases to retrieve molecules containing the features that complement the allosteric site. The retrieved hits were filtered based on certain drug-like properties and molecular docking simulations were performed in two different conformations of protein. Thus, performing MD simulation with α7 to investigate the changes at the allosteric site, then developing receptor based pharmacophore models and finally docking the retrieved hits into two distinct conformations will be a reliable methodology in identifying PTP1B allosteric inhibitors. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Identification of potential Gly/NMDA receptor antagonists by cheminformatics approach: a combination of pharmacophore modelling,virtual screening and molecular docking studies

The Gly/NMDA receptor has become known as potential target for the management of neurodegenerative diseases. Discovery of Gly/NMDA antagonists has thus attracted much attention in recent years. In the present research, a cheminformatics approach has been used to determine structural requirements for Gly/NMDA antagonism and to identify potential antagonists. Here, 37 quinoxaline derivatives were selected to develop a significant pharmacophore model with good certainty. The selected model was validated by leave-one-out cross-validation, an external test set, decoy set and Y-randomization test. Applicability domain was verified by the standardization approach. The validated 3D-QSAR model was used to screen virtual hits from the ZINC database by pharmacophore mapping. Molecular docking was used for assessment of receptor–ligand binding modes and binding affinities. The GlideScore and molecular interactions with critical amino acids were considered as crucial features to identify final hits. Furthermore, hits were analysed for in silico pharmacokinetic parameters and Lipinski’s rule of five, demonstrating their potential as drug-like candidates. The PubChem and SciFinder search tools were used to authenticate the novelty of leads retrieved. Finally, five different leads have been suggested as putative novel candidates for the exploration of potent Gly/NMDA receptor antagonists.     

Tin(IV) complex of 3,4-dihydroxybenzaldehyde 4-ethylthiosemicarbazone: Synthesis,spectral studies and molecular modeling

The tin(IV) complex with 3,4-dihydroxybenzaldehyde 4-ethylthiosemicarbazone, [Sn(BETSC)Cl₂] has been synthesised and characterized using elemental analysis, Fourier transform infrared spectroscopy (FT-IR), UV-vis and NMR spectra. Theoretical calculations have also been performed by B3LYP method using LANL2DZ basis set. The assignments of bands observed in FT-IR spectrum for H₂BETSC and its Sn(IV) complex have been made using DFT method. Some significant differences in vibrational structures between the H₂BETSC and [Sn(BETSC)Cl₂] have been observed and discussed. Molecular docking was performed for the ligand H₂BETSC against dihydrofolate reductase (DHFR).     

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.     

New salen-type manganese(III) Schiff base complexes derived from meso-1,2-diphenyl-1,2-ethylenediamine: In vitro anticancer activity,mechanism of action,and molecular docking studies

Four new manganese(III) Schiff base complexes (1–4) were synthesized and characterized. The complexes have general formula [MnClL^x] in which L represents a Schiff base ligand derived from condensation of meso-1,2-diphenyl-1,2-ethylenediamine with salicylaldehyde or its 3-OMe-, 5-Br-, or 5-OMe-derivatives (x = 1–4, respectively). The crystal structure of [MnClL¹] (1) was characterized by X-ray crystallography. The in vitro anticancer activity of these complexes was evaluated by MTT and apoptosis assays against human breast (MCF-7) and liver (Hep G2) cancer cells. The complexes exhibited considerable antiproliferative activity against both cell lines (IC₅₀ = 10.8–21.02 μM) comparable to cis-platin, except 4 (MCF-7). The highest activity was found for 1 with IC₅₀ values of 13.62 μM (MCF-7) and 10.8 μM (Hep G2). Flow cytometry experiments showed that 1 induced apoptosis on MCF-7 tumor cell line. Docking simulations using AUTODOCK were also carried out. The results showed that all complexes fitted into the minor groove region of DNA.     

Molecular docking,dynamics simulations and 3D-QSAR modeling of arylpiperazine derivatives of 3,5-dioxo-(2H,4H)-1,2,4-triazine as 5-HT1AR agonists

Serotonin receptor, 5-HT_1AR, agonists and partial agonists have established drug candidates for psychiatric and neurologic disorders. Recently, we reported the synthesis and evaluation of arylpiperazine derivatives of 3,5-dioxo-(2H,4H)-1,2,4-triazine as 5-HT_1AR ligands. Herein, we generated a homology model of the receptor and docked the ligands against it, predicted the stability of the receptor model and complexes by molecular dynamics and generated a 3D-QSAR model for the arylpiperazine derivatives of 3,5-dioxo-(2H,4H)-1,2,4-triazine. The model suggests the hydrophobic part that arises from the aromatic region and the electron withdrawing parts play a vital role in the agonist activity of the lead molecules.     

Molecular docking and dynamic simulation of approved drugs targeting against spike protein (6VXX) of 2019-nCoV (novel coronavirus)

The 2019-nCoV has triggered a global public health emergency due to its rapid spread, resulting in a pandemic situation. Because of its ability to bind with the host cell receptor ACE-2, the spike protein of the 2019-nCoV is a critical factor in viral infection. The current study aims to investigate the molecular-docking of the spike protein (6VXX) using PyRx for FDA-approved drugs available for the treatment of SARS-1 and MERS, with the hypothesis that these drugs could be suggested for the treatment of 2019-nCoV or not. A phylogenetic analysis of 2019-nCoV in relation to SARS-1 and MERS confirmed the validation. The positive result urged the Multiple Sequence Alignment analysis of the top five affected countries, with China serving as a control, using WHO available reference data to determine the rate of mutant variation. The docking results revealed that the top ten drugs with the highest binding affinity rate are also used for Hepatitis-C virus treatment, and the Molecular Dynamic Simulation was carried out for the drug Paritaprevir, which had the highest binding affinity rate, using Gromacs. The results indicated that the drug Paritaprevir could be used as a potential target against the 2019-nCoV Spike protein.     

Investigation on the isoform selectivity of novel kinesin-like protein 1 (KIF11) inhibitor using chemical feature based pharmacophore,molecular docking,and quantum mechanical studies

Kinesin-like protein (KIF11) is a molecular motor protein that is essential in mitosis. Removal of KIF11 prevents centrosome migration and causes cell arrest in mitosis. KIF11 defects are linked to the disease of microcephaly, lymph edema or mental retardation. The human KIF11 protein has been actively studied for its role in mitosis and its potential as a therapeutic target for cancer treatment. Pharmacophore modeling, molecular docking and density functional theory approaches was employed to reveal the structural, chemical and electronic features essential for the development of small molecule inhibitor for KIF11. Hence we have developed chemical feature based pharmacophore models using Discovery Studio v 2.5 (DS). The best hypothesis (Hypo1) consisting of four chemical features (two hydrogen bond acceptor, one hydrophobic and one ring aromatic) has exhibited high correlation co-efficient of 0.9521, cost difference of 70.63 and low RMS value of 0.9475. This Hypo1 is cross validated by Cat Scramble method; test set and decoy set to prove its robustness, statistical significance and predictability respectively. The well validated Hypo1 was used as 3Dquery to perform virtual screening. The hits obtained from the virtual screening were subjected to various scrupulous drug-like filters such as Lipinski’s rule of five and ADMET properties. Finally, six hit compounds were identified based on the molecular interaction and its electronic properties. Our final lead compound could serve as a powerful tool for the discovery of potent inhibitor as KIF11 agonists.     

Green synthesis of selenium based N-heterocyclic carbene compounds; structural,in-vitro anticancer and molecular docking studies

Benzimidazolium salts (3−6) were synthesized as stable N-Heterocyclic Carbene (NHC) precursors and their selenium-NHC compounds/Selenones (7−10) were prepared using water as a solvent. Characterization of each of the synthesized compounds was carried out by various analytical and spectroscopic (FT-IR, ¹H-, ¹³C NMR) methods. X-ray crystallographic analyses of single crystals obtained for salts 3 and 5 were carried out. Synthesized salts and their Se-NHCs were tested in-vitro for their anticancer potential against Cervical Cancer Cell line from Henrietta Lacks (HeLa), Breast cancer cell line (MDA-MB-231), Adenocarcinoma cell line (A549) and human normal endothelial cell line (EA.hy926). MTT assay was used for analysis and compared with standard drug 5-flourouracil. Benzimidazolium salts (3−6) and their selenium counter parts (7−10) were found potent anticancer agents. Salt 3–5 were found to be potent anticancer against HeLa with IC₅₀ values 0.072, 0.017 and 0.241 μM, respectively, which are less than standard drug (4.9 μM). The Se-NHCs (7–10) had also shown significant anticancer potential against HeLa with IC₅₀ values less than standard drug. Salts 3, 4 against EA.hy926, compounds 3,5,6, and 10 against MDA-MB-321, and compounds 4, 10 against A-549 cell line were found more potent anticancer agents with IC₅₀ values less than standard drug. Molecular docking for (7−10) showed their good anti-angiogenic potential having low binding energy and significant inhibition constant values with VEGFA (vascular endothelial growth factor), EGF (human epidermal growth factor), COX1 (cyclooxygenase-1) and HIF (hypoxia inducible factor).     

Cell-based assays and molecular simulation reveal that the anti-cancer harmine is a specific matrix metalloproteinase-3 (MMP-3) inhibitor

The biological activities of harmine have been a much clearer picture in recent years, which include anti-tumor, anti-inflammation and cytotoxic properties. Numerous in vitro and in vivo animal models have confirmed its activities, but its mode of action remains a relative unsolved issue. We therefore investigated harmine for its effects on MMP-3 and the molecular interaction was also simulated. The human glioma cancer cell line, U-87 MG cells, was subjected to different concentrations (1–10 μM) of harmine for 24 h. Methylthiazol tetrazolium (MTT) test, half maximal inhibitory concentration (IC50), western blot analysis, enzyme-linked immunosorbent assay and molecular docking through BIOVIA DiscoveryStudio™ were performed. These results showed that although harmine stimulation in vitro has very little or no effects on MMP-3 expression by U-87 MG cells, the treatment of harmine decreases MMP-3 activity in a dose dependent manner. It was further calculated that 7.9 μM is the IC50 towards MMP-3. Using a molecular dynamic simulation approach, we identified the N2, methyl of C1 and benzene ring of harmine interact with Zn²⁺ (2.4 Å), His205 (2.4 Å) and His211 (2.4 Å) as well as Val163 (2.7 Å) at the active site of MMP-3, respectively, and thus conferred a striking specific binding advantage. Taken altogether, the present study evidences that harmine acts as an MMP-3 inhibitor specially targeting the enzymatic active site and possibly efficiently ameliorates MMP-3-driven malignant and inflammatory diseases.     

Discovery of potential inhibitors targeting the kinase domain of polynucleotide kinase/phosphatase (PNKP): Homology modeling,virtual screening based on multiple conformations,and molecular dynamics simulation

In recent years, the level of interest has been increased in developing the DNA-repair inhibitors, to enhance the cytotoxic effects in the treatment of cancers. Polynucleotide kinase/phosphatase (PNKP) is a critical human DNA repair enzyme that repairs DNA strand breaks by catalyzing the restoration of 5’-phosphate and 3’-hydroxyl termini that are required for subsequent processing by DNA ligases and polymerases. PNKP is the only protein that repairs the 3′-hydroxyl group and 5′-phosphate group, which depicts PNKP as a potential therapeutic target. Besides, PNKP is the only DNA-repair enzyme that contains the 5′-kinase activity, therefore, targeting this kinase domain would motivate the development of novel PNKP-specific inhibitors. However, there are neither crystal structures of human PNKP nor the kinase inhibitors reported so far. Thus, in this present study, a sequential molecular docking-based virtual screening with multiple PNKP conformations integrating homology modeling, molecular dynamics simulation, and binding free energy calculation was developed to discover novel PNKP kinase inhibitors, and the top-scored molecule was finally submitted to molecular dynamics simulation to reveal the binding mechanism between the inhibitor and PNKP. Taken together, the current study could provide some guidance for the molecular docking based-virtual screening of novel PNKP kinase inhibitors.     

Synthesis,molecular modeling of N-acyl benzoazetinones and their docking simulation on fungal modeled target

A series of stable N-acyl benzoazetinones have been synthesized in moderate to good yields (58–85%) from easily available substrates such as 2-(N-acyl) amino benzoic acids through intramolecular amidation under mild conditions. These geometry-optimized benzoazetinones were docked in the model target of P450, class CYP53A15, a benzoate 4-monooxygenase abundantly found in the genome of ascomycetes and Basidiomycetes classes of pathogenic fungi. Low per residue root-mean-square deviation (RMSD) of modeled structure of the enzyme indicated similar topology as template (4D6Z.pdb). Observed score judges site-specific docking, and the interaction of quantum mechanically optimized benzoazetinone derivatives with the target enzyme. These results suggest that 3i is the best antifungal agent. The specific hydrophobic substituent in the benzoazetinones contributed to the stability of ligand–target complex. Overall, the study provided insight into the specificity of the site-specific interactions, thereby, facilitating the possibility of development of broad-spectrum antifungal agents against opportunistic and infectious fungi.     

Synthesis,Computational, Electronic spectra,and molecular docking studies of 4-((diphenylmethylene)amino)-N-(pyrimidin-2-yl)benzenesulfonamide

The 4-((diphenylmethylene)amino)-N-(pyrimidin-2-yl)benzenesulfonamide (BENDA) was synthesized and characterized by the Infrared, UV-Visible, and NMR analysis. Using density functional theory, the current work is a set of theoretical studies on BENDA. The compound molecular structure and geometry were defined using DFT. Topological studies, like ELF, LOL, ALIE, and RDG studies, were done with the Multiwfn-3.8 to find the main binding areas and weak interactions in the molecule. Using the IEFPCM solvation model was used to study the calculated UV-Visible spectrum. The HOMO-LUMO, MEP, and NLO properties were carried out in the gas phase. The NBO calculations are used to study how charges move between and within the molecule and the stability of this molecule. A pharmacological analysis is done using an online tool like Swiss-ADME, to see if the molecule could be a potential drug candidate; this evaluation looks at the drug-likeness, ADME, and eco-friendly toxicity properties of the BENDA molecule. Auto-dock suite and Discovery studio Visualizer are used to do molecular docking against 5UVC protein.     

Synthesis,characterization, computational,excited state properties,wave function,and molecular docking studies of (E)-4-((2-hydroxybenzylidene)amino)N-(thiazol-2-yl) benzenesulfonamide

The compound (E)-4-((2-hydroxybenzylidene)amino)N-(thiazol-2-yl) benzene sulfonamide (SATH) was synthesized and characterized by the Infrared, UV–Visible, and NMR analysis. Using density functional theory, the current work is a set of theoretical studies on SATH. The compound molecular structure and geometry were defined using DFT. Topological studies, like ELF, LOL, ALIE, and RDG studies, were done with the Multiwfn-3.8 to find the main binding areas and weak interactions in the molecule. Using the IEFPCM solvation model was used to study the calculated UV–Visible spectrum. The HOMO-LUMO, MEP, and NLO properties were carried out DFT/B3LYP/cc-pVDZ basis set in the gas phase. The NBO calculations are used to study how charges move between and within the molecule and the stability of this molecule. A pharmacological analysis is done using an online tool like Swiss-ADME, to see if the molecule could be a potential drug candidate; this evaluation looks at the drug-likeness, ADME, and eco-friendly toxicity properties of the PFPT molecule. Auto-dock suite and Discovery studio Visualizer are used to do molecular docking against 6ZZB protein.     

Synthesis,computational, molecular docking studies and photophysical properties of (Z)-N-(pyrimidin-2-yl)-4-(thiophen-2-ylmethylene)amino) benzenesulfonamide

The (Z)-N-(pyrimidin-2-yl)-4-(thiophen-2-ylmethylene)amino) benzenesulfonamide (TH2DA) were synthesized and characterized by the Infrared, UV–Visible, and NMR analysis. Using density functional theory, the current work is a set of theoretical studies on TH2DA. The compound molecular structure and geometry were defined using DFT. Topological studies, like ELF, LOL, ALIE, and RDG studies, were done with the Multiwfn-3.8 to find the main binding areas and weak interactions in the molecule. Using the IEFPCM solvation model were used to study the calculated UV–Visible spectrum. The HOMO-LUMO, MEP, and NLO properties were carried out in the gas phase. The NBO calculations are used to study how charges move between and within the molecule and stability of this molecule. A pharmacological analysis is done using online tool like Swiss-ADME, to see if the molecule could be potential drug candidate; this evaluation looks at the drug-likeness, ADME and eco-friendly toxicity properties of the TH2DA molecule. Auto-dock suite and Discovery studio Visualizer are used to do molecular docking studies.