Molecular assessment of protective effect of Vitex negundo in ISO induced myocardial infarction in rats.

Myocardial infarction (MI) is the one of the major causes of death worldwide, however the molecular mechanisms hidden under this disease conditions remain unknown. This demands serious attention to unravel the molecular mechanisms to identify the therapeutic strategies either to prevent or to control MI. Ayurveda is becoming one of the best alternatives for the modern medicines. On the other hand, Vitex negundo is one of the medicinally important plants used for various diseases and to date, its cardioprotective role is not fully elucidated. In the present study, we made an attempt to understand the cardiac signaling cascade of Akt1 and NF-κB in isoproterenol (ISO)-induced MI, and targeting these signaling molecules by using V. negundo leaf ethanolic extract (VNE). Our findings demonstrate that VNE significantly protects the ISO-induced MI by regulating NF-κB and Akt1experssion in rats.

Experimental and molecular docking investigation on DNA interaction of N-substituted phthalimides: antibacterial, antioxidant and hemolytic activities.

A series of Schiff base molecules derived from a phthalimide scaffold was investigated as efficient antibacterial, antioxidant and DNA-interacting agents. The spectroscopic characterization of these derivatives was studied in detail using elemental analysis and spectroscopic techniques. The DNA-binding profile of title molecules against Ct-DNA (calf thymus) was investigated by absorbance, fluorescence, hydrodynamics and thermal denaturation investigations. The bacterial inhibition potential of these molecules was investigated against Escherichia coli and Staphylococcus aureus. Molecule 3c emerged as the most active against S. aureus (IC50 : 14.8 µg/mL), whereas compounds 3a and 3b displayed potential antibacterial activities against E. coli (IC50 : 49.7 and 67.6 µg/mL). Molecular docking studies of these compounds against GlcN-6-P synthase were carried out to rationalize antibacterial efficiency of these molecules. These newly synthesized molecules were screened for their scavenging capacity against 2,2-diphenyl-1-picryl-hydrazyl (DPPH) and H2 O2 free radicals and the results were compared with ascorbic acid as synthetic antioxidant. The title molecules 3a, 3b and 3e showed less than 20% hemolysis, which indicated their significant non-toxic behavior.

Design, synthesis, and evaluation of pyrazolo-pyrazole derivatives on Methylisocitratelyase of Pseudomonas aeruginosa: in silico and in vitro study.

Pseudomonas aeruginosa is an opportunistic micro-organism causing diseases both in animals and humans. In case of human pathology, the role of P. aeruginosa is one of the major concerns in intensive care septicemia. Presently, the drug resistance strains of P. aeruginosa are arising mainly by developing multiple mechanisms due to its natural and acquired resistance to many of the antimicrobial agents commonly used in clinical practice. As a result, there is a direct need to invent new drugs so that they may restrict the outbreak of multidrug resistant strains. Virtual high-throughput insilico screening, which helps to identify the chemical ligands that bind to the enzymes, is an important tool in drug discovery and the drugs discovered in this way are clinically tested. In this study, Methylisocitratelyase (MICL), which is essential for the survival of the bacterium and which doesn't show any similarity with the humans, was selected to evaluate the functions of high-affinity inhibitors (PPI-analogs) that are identified using the virtual screening approach. By adopting the computational analysis tools, structural, functional, and inhibitor interactions of MICL against P. aeruginosa were identified. The PPIA-32 is found to be the best binding interactions with MICL. PPIA-32 reduces the binding affinity for substrate to residues required for MICL enzyme activity and also Root Mean Square Deviation simulations show the most stable nature of PPA32-MICL(complex) than that of MICL alone, thereby effectively inhibiting the growth of virulent P. aeruginosa. To our surprise, the same phenomenon is also identified with other gram-negative bacteria like Escherichia coli, Klebsiella pneumoniae, and Salmonella typhi.

Bioinformatics exploration of PAK1 (P21-activated kinase-1) revealed potential network gene elements in breast invasive carcinoma.

P21-activated kinase-1 (PAK1) is an enzyme associated with multiple metabolic networks and different types of cancers. Hence, there is a need to study the global network map of PAK1 to understand its role and regulatory mechanisms by means of its significant molecular interactive partners. This will help to explore its global biological functions in breast cancer. In view of this, we obtained the gene expression data-sets of PAK1 from The Cancer Genome Atlas-cBioportal and GeneCards databases and found that 91 PAK1-related genes are associated with breast cancer. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway investigations of 91 genes via Database for Annotation Visualization and Integrated Discovery bioinformatics resource revealed that, PAK1 being a major kinase is associated with several metabolic pathways and involved in phosphorylation, signal transduction, apoptosis, biosynthesis and majorly cancer-related cell signalling pathways. The PAK1 interaction network derived from STRING and Cytoscape revealed that the genes Signal-Transducer-and-Activator-of-Transcription-3 (STAT3), Cyclin-D1 (CCND1), Mitogen-activated protein kinase-1 (MAPK1), Ras-Homolog-Family-Member-A (RHOA) and Catenin-beta-1 have high degrees of interaction where CCND1, MAPK1 and RHOA have direct interaction with PAK1. Finally, the global expression map of PAK1 and its related genes was derived as topological frame that helped to explore and investigate PAK1 interactions. Further, the molecular modelling studies of PAK1 with its major interacting partners RHOA and STAT3 helped to explore the key interactive residues of PAK1 structure. This information can be used to develop novel therapeutic and control strategies against breast cancer.

Inhibition of Mycobacterium-RmlA by Molecular Modeling, Dynamics Simulation, and Docking.

The increasing resistance to anti-tb drugs has enforced strategies for finding new drug targets against Mycobacterium tuberculosis (Mtb). In recent years enzymes associated with the rhamnose pathway in Mtb have attracted attention as drug targets. The present work is on α-D-glucose-1-phosphate thymidylyltransferase (RmlA), the first enzyme involved in the biosynthesis of L-rhamnose, of Mtb cell wall. This study aims to derive a 3D structure of RmlA by using a comparative modeling approach. Structural refinement and energy minimization of the built model have been done with molecular dynamics. The reliability assessment of the built model was carried out with various protein checking tools such as Procheck, Whatif, ProsA, Errat, and Verify 3D. The obtained model investigates the relation between the structure and function. Molecular docking interactions of Mtb-RmlA with modified EMB (ethambutol) ligands and natural substrate have revealed specific key residues Arg13, Lys23, Asn109, and Thr223 which play an important role in ligand binding and selection. Compared to all EMB ligands, EMB-1 has shown better interaction with Mtb-RmlA model. The information thus discussed above will be useful for the rational design of safe and effective inhibitors specific to RmlA enzyme pertaining to the treatment of tuberculosis.

A transcriptional repressive role for epithelial-specific ETS factor ELF3 on oestrogen receptor alpha in breast cancer cells.

Oestrogen receptor-α (ERα) is a ligand-dependent transcription factor that primarily mediates oestrogen (E2)-dependent gene transcription required for mammary gland development. Coregulators critically regulate ERα transcription functions by directly interacting with it. In the present study, we report that ELF3, an epithelial-specific ETS transcription factor, acts as a transcriptional repressor of ERα. Co-immunoprecipitation (Co-IP) analysis demonstrated that ELF3 strongly binds to ERα in the absence of E2, but ELF3 dissociation occurs upon E2 treatment in a dose- and time-dependent manner suggesting that E2 negatively influences such interaction. Domain mapping studies further revealed that the ETS (E-twenty six) domain of ELF3 interacts with the DNA binding domain of ERα. Accordingly, ELF3 inhibited ERα's DNA binding activity by preventing receptor dimerization, partly explaining the mechanism by which ELF3 represses ERα transcriptional activity. Ectopic expression of ELF3 decreases ERα transcriptional activity as demonstrated by oestrogen response elements (ERE)-luciferase reporter assay or by endogenous ERα target genes. Conversely ELF3 knockdown increases ERα transcriptional activity. Consistent with these results, ELF3 ectopic expression decreases E2-dependent MCF7 cell proliferation whereas ELF3 knockdown increases it. We also found that E2 induces ELF3 expression in MCF7 cells suggesting a negative feedback regulation of ERα signalling in breast cancer cells. A small peptide sequence of ELF3 derived through functional interaction between ERα and ELF3 could inhibit DNA binding activity of ERα and breast cancer cell growth. These findings demonstrate that ELF3 is a novel transcriptional repressor of ERα in breast cancer cells. Peptide interaction studies further represent a novel therapeutic option in breast cancer therapy.

Evaluation of DNA Binding, Radicals Scavenging and Antimicrobial Studies of Newly Synthesized N-Substituted Naphthalimides: Spectroscopic and Molecular Docking Investigations.

In this study, we investigated a new series of naphthalimide based Schiff base compounds as potential DNA binding, antioxidant and antimicrobial agents. The structural characterization of synthesized compounds was carried out with the aid of elemental analysis and spectroscopic techniques (UV-vis., IR, (1)H and (13)C NMR). The DNA binding properties of target compounds against Ct-DNA (calf thymus) have been investigated in detail by numerous biophysical techniques (UV-vis, fluorescence, ethidium bromide displacement assay, Time resolved fluorescence, viscosity, cyclic voltammetry and circular dichorism) and the evidences have suggested that the test compounds could interact with DNA via intercalative binding. The extent of DNA binding (Kb) of these compounds follow the order of 3b (3.33 × 10(4) M(-1)) > 3a (2.25 × 10(4) M(-1)) > 3c (2 × 10(4) M(-1)), suggesting that compound 3b binds more strongly to Ct- DNA than the compounds 3a and 3c. Molecular docking results further support intercalative binding of test compounds with DNA. The binding energies of docked compounds (3a-3c) were found to be -8.20 to -8.69 kcal/ mol, suggesting greater binding affinity to Ct-DNA. The synthesized compounds displayed potential antimicrobial activities against Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae and Salmonella typhimurium. Compound 3c has emerged as most active against all the four tested bacterial strains with MIC value in the range of 0.031-0.062 mg/mL. In the mutagenicity studies, all the test compounds were found to be non-mutagenic both in the presence and absence of metabolic activation. Furthermore, the antioxidant activity experiments show that these compounds exhibited potential scavenging activities against DPPH and H2O2 radicals.

A New Isoindoline Based Schiff Base Derivative as Cu(II) Chemosensor: Synthesis, Photophysical, DNA Binding and Molecular Docking Studies.

A new chemo sensor 2-(4-methylbenzylideneamino)-isoindoline-1,3-dione (PDB) was synthesized and characterized by UV-Vis., IR, (1)H NMR, (13)C NMR spectral and elemental analysis. Its photophysical properties in organic solvents with different polarity were studied. The sensitivity of the PDB in different pH solutions was investigated and the results indicated that PDB would be able to act as an efficient "off-on-off" switch for pH. This chemosensor displayed high selectivity towards Cu(2+) in the presence of metal ions Ba(2+), Cd(2+), Co(2+), Hg(2+), Ni(2+), Pb(2+), K(+) and Zn(2+) in DMF/H2O solution. Furthermore DNA binding and molecular docking studies were also carried out to investigate the biological potential of the test compound. The interaction of compound (PDB) with Ct-DNA was examined by absorption, CD spectroscopy, cyclic voltammetry and viscosity measurements. In silico studies revealed that the test compound (PDB) showed good affinity towards the target receptor d (CGCGAATTCGCG)2 with the binding energy of -7.70 kcal/mol.

Molecular modeling and docking studies of O-succinylbenzoate synthase of M. tuberculosis--a potential target for antituberculosis drug design.

Menaquinone is a lipid-soluble naphthoquinone that is essential for various pivotal functions of bacteria. Naphthoquinone is synthesized from chorismate of the shikimate pathway in microorganisms. Due to its absence in humans and animals, menaquinone biosynthesis has been an attractive target for development of antibiotics against a number of important microbial pathogens, such as Mycobacterium tuberculosis (Mtb). In shikimate pathway, O-succinylbenzoate synthase (OSBS) plays a major role and is one of the major potential drug targets. For Mtb-OSBS, a systematic study was conducted to get an insight about Mtb-OSBS enzyme and the corresponding inhibitors using in silico methods. The 3-D model of Mtb-OSBS was built using structure coordinates of Thermobifida fusca. O-succinylbenzoate synthase, the model, was further refined. The active site amino acids have been identified by comparing the template sequence with the Mtb-OSBS sequence. We identified that Lys(108), Asn(140), Asp(138), Lys(110), Glu(189), Ser(236), Asp(188), Arg(27), Tyr(52), and Ser(237) are highly conserved, and these may play a vital role as active residues, similar to that in template protein. As per the competitive binding of substrate (2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC)), we screened the SHCHC through AutoDock 4.0. The SHCHC molecule was further modified structurally and optimized through PRODRG server. Docking of the 12 lead molecules for best interactions with Mtb-OSBS has given an insight that all the lead molecules have shown interactions with active site amino acids of Mtb-OSBS. MD simulation analysis report has shown the stable conformation annotations of Mtb-OSBS. These hypothetical studies create another way to develop more potential drugs against the deadly mycobacterium.

Experimental and computational studies on newly synthesized resveratrol derivative: a new method for cancer chemoprevention and therapeutics?

Nature has been a provenance of medicinal agents for thousands of years. Resveratrol (RESL) is a naturally occurring polyphenolic compound in food stuffs such as peanuts, seeds, berries, grapes, and beverages (red wine). RESL has received significant attention due to a plethora of in vitro and in vivo reports on its cancer chemopreventive and therapeutic properties. In the present study, diacetate RESL derivative (RESL43) was synthesized. The RESL43 displayed potent cytotoxicity and triggered apoptosis in U937 cells as evidenced by poly (ADP-ribose) polymerase (PARP) cleavage, DNA fragmentation, morphological changes, and activation of FasR and FasL genes. The electrophoretic mobility shift assay revealed the suppression NFkB activity in U937 cells after treatment with RESL43 in corroboration with the deactivation of NFkB dependent genes such as IL-8, TNFR, and TNFα. Furthermore, molecular docking and dynamics studies have shown that RESL and RESL43 might exert their inhibitory activity on NFkB by altering the intramolecular binding abilities between DNA and NFkB. Taken together, RESL43 can have greater putative activity than parental RESL in a context of cancer chemoprevention and therapeutics. We suggest that the diacetate resveratrol derivative RESL43 warrants further evaluation in preclinical and clinical bridging studies in the near future.

Synthesis and biological activity of new resveratrol derivative and molecular docking: dynamics studies on NFkB.

Resveratrol (RVS) is a naturally occurring antioxidant, able to display an array of biological activities. In the present investigation, a new derivative of RVS, RVS(a), was synthesized, and its biological activity was determined on U937 cells. It was observed that RVS(a) showed pronounced activity on U937 cells than RVS. RVS(a) is able to induce apoptosis in tumor cell lines through subsequent DNA fragmentation. From the EMSA results, it was evident that RVS(a) was able to suppress the activity of NFkB by interfering its DNA binding ability. Furthermore, the molecular interaction analysis (docking and dynamics) stated that RVS(a) has strong association with the IkB-alpha site of NFkB compared with RVS; this binding nature of RVS(a) might be prevent the NFkB binding ability with DNA. The present findings represent the potential activity of propynyl RVS on U937 cells and signifying it as a one of putative chemotherapeutic drugs against cancer.

Design and evaluation of new chemotherapeutics of aloe-emodin (AE) against the deadly cancer disease: an in silico study.

The Bcl-2 family proteins include pro- and antiapoptotic factors acting as critical arbiters of apoptotic cell death decisions in most circumstances. Evasion of apoptosis is one of the hallmarks of cancer, relevant to tumorigenesis as well as resistance to cytotoxic drugs, and deregulation of Bcl-2 proteins was observed in many cancers. Since Bax-mediated induction of apoptosis is a crucial mechanism in cancerous cells, we aimed at conducting in silico analysis on Bax in order to predict the possible interactions for anticancer agents. The present report depicts the binding mode of aloe-emodin and its structurally modified derivatives onto Bax. The structural information about the binding site of Bax for docked compounds obtained from this study could aid in screening and designing new anticancer agents or selective inhibitors for chemotherapy against Bax.