Ligplot Analysis Research Articles

Inhibitory Potential of Benzo[a]phenazin-5-ol Derivatives Against C-Kit Kinase: Molecular Docking and Prediction of ADME/Drug-Likeness Properties

Background & Objectives: C-Kit, a receptor tyrosine kinase involved in intracellular signaling, has a mutated form that significantly contributes to the development of certain cancers. This study aimed to evaluate a series of benzo[a]phenazin-5-ol-tethered tri- substituted methane derivatives as potential pharmacophores for inhibiting C-Kit kinase. Materials & Methods: Benzo[a]phenazine-5-ol derivatives were sketched and converted into Mol2 files using Marvin software. Their three dimensional (3D) structures were generated and saved in PDB format. Molecular docking studies with the C-Kit kinase (PDB code 1t46) were performed using AutoDock 4.2. Additionally, the derivatives’ physicochemical properties, ADME characteristics, and drug-likeness parameters were assessed with the SwissADME online tool. Results: Molecular docking studies of benzo[a]phenazin-5-ol derivatives ( A-L) against C-kit kinase revealed that compounds A and C exhibited greater selectivity and stronger inhibitory effects than the reference drug, Sunitinib. Ligplot analysis demonstrated that compound A formed four hydrogen bonds with Arg791(A), Ile789(A), and His790(A), while compound C formed two hydrogen bonds with Ile571(A) and Ile789(A). ADME analysis indicated that all compounds, except C, D, and I, are potential P-gp substrates. Drug-likeness analysis showed one or two violations of Lipinski’s rule of five. Conclusion: In summary, molecular docking studies identified compounds A and C as promising lead candidates for inhibiting C-kit kinase, demonstrating superior binding to the active site compared to Sunitinib. ADME and drug-likeness analysis revealed that compound A is a potential P-gp substrate with one violation of Lipinski’s rule of five, making it the closest pharmacological match to Sunitinib and a strong candidate for further investigation.

In silico molecular docking and dynamic simulation of anti-cholinesterase compounds from the extract of Catunaregam spinosa for possible treatment of Alzheimer's disease

Alzheimer's disease (AD), is characterized by a progressive loss of cognitive abilities as well as behavioral symptoms including disorientation, trouble solving problems, personality and mood changes. Acetylcholinesterase (AChE) is a promising target for symptomatic improvement in AD due to its consistent and early cholinergic deficit. This research has investigated the potential compounds from Catunaregam spinosa as AChE inhibitors as a treatment option for AD, aiming to enhance cholinergic neurotransmission and alleviate cognitive decline. Tacrine, the FDA's first approved treatment for AD, is no longer in use due to its hepatotoxicity. Box-Behnken design (BBD) modelling was used to optimise the ultrasonic extraction of alkaloids from the dried fruits of C. spinosa. GC-MS analysis revealed the presence of ninety phytoconstituents in the extract. Among them, eighty-nine new phytoconstituents are reported in this plant fruit for the first time. Out of ninety phytoconstituents, eight phytoconstituents showed the best binding affinity against the AChE enzyme, i.e., PDB IDs 1GQR, 1QTI and 4PQE of AD targets using iGEMDOCK. The lead hits were tested for their drug-like properties and atomistic binding mechanisms using in silico ADMET prediction, LigPlot analysis, and molecular dynamics simulation. The results suggest four compounds such as 1,4,7,10,13,16-hexaoxacyclooctadecane; butanoic acid, 3-methyl-2-[(phenylmethoxy)imino]-, trime; butane-1,2,3,4-tetraol; and D-(+)-ribonic acid.gamma-lactone as potent inhibitors of AChE for the possible treatment of AD.

Biochemical and in silico analysis of the binding mode of erastin with tubulin

Erastin (ERN) is a small molecule that induces different forms of cell death. For example, it has been reported to induce ferroptosis by disrupting tubulin subunits that maintain the voltage-dependent anion channels (VDACs) of mitochondria. Although its possible binding to tubulin has been suggested, the fine details of the interaction between ERN and tubulin are poorly understood. Using a combination of biochemical, cell-model and in silico approaches, we elucidate the interactions of ERN with tubulin and their biological manifestations. After confirming ERN's antiproliferative efficacy (IC50, 20 ± 3.2 M) and induction of cell death in the breast cancer cell line MDA-MB-231, the binding interactions of ERN with tubulin were examined. ERN bound to tubulin in a concentration-dependent manner, disorganizing the structural integrity of the protein, as substantiated via the tryptophan-quenching assay and the aniline-naphthalene sulfonate binding assay, respectively. In silico studies based on molecular docking revealed a docking score of −5.863 kcal/mol, suggesting strong binding interactions of ERN with tubulin. Additionally, molecular dynamics simulation and Molecular Mechanics Poisson–Boltzmann Surface Area (MM-PBSA) analyses evinced the binding free energy (ΔGbinding) of −31.235 kcal/mol, substantiating strong binding affinity of ERN with tubulin. Ligplot analysis showed hydrogen bonding with specific amino acids (Asn A226, Thr A223, Gln B247 and Val B355). QikProp-based ADME (absorption, distribution, metabolism and excretion) assessment showed considerable therapeutic potential for ERN. Communicated by Ramaswamy H. Sarma

Molecular Modelling and Structure Analysis of Lectins from Vigna linearis

A study was conducted during the year 2022–2023 for in silico analysis of two Vigna linearis lectins in the computer lab, CDFT, Jodhpur, Rajasthan, India. Amino acid sequences of both lectins were obtained from NCBI database and analyzed using different computational tools. Primary structure analysis using ProtParam server revealed acidic, stable and hydrophobic nature of both VLL proteins. Both proteins were predicted heavily glycosylated with a single signal peptide cleavage site (A26-A27). High sequence similarity of both VLL proteins was observed with adzuki, rice bean and moth bean lectins. Both VLL proteins had high proportions of β-sheets in their secondary structure. Good quality 3D structures for both VLL proteins were modelled using Modeller software. A Jelly roll fold, also known as β-sandwich structure was identified in the 3D structure of both VLL proteins. Profunc server annotated both lectins as a carbohydrate binding regulatory protein with significant role in plant defense (GO terms: 0065007, 0006952, 0050896, 0006950, 0009607, 0030246). Galaxy Site web server predicted galactose, A2G (2-acetamido-2-deoxy-α-D-galactopyranose), MFU (Methyl α-L-fucopyranoside) and adenine as common binding ligands for both VLL proteins. Lig Plot analysis revealed hydrogen bonding and hydrophobic interactions were the major bonding interactions between VLL proteins and putative ligands. The results of the study would provide a base for conducting future research on Vigna linearis lectins for different applications.

IDENTIFICATION AND SCREENING OF PLANT-BASED POTENT INHIBITORS AGAINST nSH2 DOMAIN OF PI3K OF BREAST CANCER USING DOCKING AND SIMULATION STUDIES

Breast cancer (BC) is a critical health issue that affects countless women, and it is the second leading reason of death worldwide. The phosphatidylinositol 3 kinases (PI3Ks) constitute a group of lipid kinases that play a role in tumorigenesis, development, migration, infiltration, programmed cell death, glycogen synthesis, DNA correction and viability by the PI3K/Akt cascade. The PI3K pathway has been linked to a variety of malignancies and increases the activation rate of cancer. Here, focus was given to the study of PI3K pathway involved in BC and emphasis was given on a particular nSH2 domain that resides in the regulatory subunit of PI3K to find a potent inhibitor. A detailed pathway and interaction study was performed from KEGG pathway database and from the cystoscope. A total list of 60 compounds, comprises phytochemicals, and herbal compounds were screened based on structural similarity and eight FDA-approved drugs were considered. The docking analysis was carried over through the AutoDock software and Ligplot analysis was performed to investigate the interaction between the nSH2 domain and the potent inhibitors. To ensure the complex stability, 20 ns of simulation run was also performed on the best complexes using GROMACS. From this study, it can be concluded that Evodia fruit has the maximum stability in the catalytic region among all the listed inhibitors against the target proteins and can act as a potent inhibitor among the others.

In- Silico Drug Design and Molecular Docking Studies of Poly ADP-Ribose Polymerase (PARP-1) Inhibitors as Anticancer Agents

Background of the Topic: Drug discovery employs bioinformatics and computational biology (CADD) approaches for the identification and optimization of lead compounds. The PARP-1 is the member of the PARP family. PARP-1 is the enzyme that repairs the DNA damage in cancer cell hence it is selected as the target for the study. PARP inhibitors were shown the prominent results in the treatment of different kinds of malignancies due to loss of function of BRCA1/2 genes.
 Methodology: Based on literature review, database search, ADME and MD simulation, top 10 selected ligands were screened and tested against PARP-1 (4R6E) protein using molecular docking (Glide and Gold software), protein ligand interaction by LIGPLOT analysis. Molecular simulation studies were performed using DESMOND software afterwards on the top compound (CHEMBL378794).
 Results: All top 10 compounds showed binding affinity based inhibitory potential against the PARP-1 protein. The highest binding affinities from top 10 compounds towards anticancer targets were exhibited by CHEMBL378794 and CHEMBL245559. 
 Discussion: The comparative analysis of 4R6E and the identified hits using MD simulation exhibited better stability of the binding domain with these molecules suggesting their strong interaction and selectivity towards PARP-1. 
 Conclusion: This study showed the significant results in cancer treatment and their strong interaction with PARP-1 binding BRCT domain. Hence, these molecules could further be carried forward to explore their potency against PARP-1 sensitive cancer.

Appraisal of the Possible Role of PPARγ Upregulation by CLA of Probiotic Pediococcus pentosaceus GS4 in Colon Cancer Mitigation.

The prevalence of colon cancer (CC) is increasing at the endemic scale, which is accompanied by subsequent morbidity and mortality. Although there have been noteworthy achievements in the therapeutic strategies in recent years, the treatment of patients with CC remains a formidable task. The current study focused on to study role of biohydrogenation-derived conjugated linoleic acid (CLA) of probiotic Pediococcus pentosaceus GS4 (CLAGS4) against CC, which induced peroxisome proliferator-activated receptor gamma (PPARγ) expression in human CC HCT-116 cells. Pre-treatment with PPARγ antagonist bisphenol A diglycidyl ether has significantly reduced the inhibitory efficacy of enhanced cell viability of HCT-116 cells, suggesting the PPARγ-dependent cell death. The cancer cells treated with CLA/CLAGS4 demonstrated the reduced level of Prostaglandin E2 PGE2 in association with reduced COX-2 and 5-LOX expressions. Moreover, these consequences were found to be associated with PPARγ-dependent. Furthermore, delineation of mitochondrial dependent apoptosis with the help of molecular docking LigPlot analysis showed that CLA can bind with hexokinase-II (hHK-II) (highly expressed in cancer cells) and that this association underlies voltage dependent anionic channel to open, thereby causing mitochondrial membrane depolarization, a condition that initiates intrinsic apoptotic events. Apoptosis was further confirmed by annexin V staining and elevation of caspase 1p10 expression. Taken all together, it is deduced that, mechanistically, the upregulation of PPARγ by CLAGS4 of P. pentosaceus GS4 can alter cancer cell metabolism in association with triggering apoptosis in CC.

Structure Based Drug Designing of Histone Deacetylase-2 inhibitors as an Anticancer Agents

Background and purpose- Histone deacetylase 2 (HDAC2) in tumour development and carcinogenesis as a promising therapeutic target for cancer treatment. HDAC-2 belongs to class I histone deacetylase and acts as a transcriptional repressor through the deacetylation of lysine residues present at the N-terminal tail of histone proteins (H2A, H2B, H3 and H4). They are overexpressed in various solid tumours like cutaneous t cell lymphoma, colorectal, prostate cancer, lung cancer, breast cancer, gastric cancer, liver cancer and medulloblastoma. Hence, targeting HDAC-2 could be rewarding strategy to combat cancer. The goal of the research is to design, develop and identification of molecules through docking, Ligplot, ADMET properties and dynamic studies. Objective- To update HDAC-2 databases as a resource for Structure based drug designing. Validation of model by understanding the interaction pattern with known inhibitors. To identify selective and trapping HDAC-2 inhibitors by targeting the catalytic domain through structure-based pharmacophore study. To design novel HDAC inhibitors (HDACi) analogues for further generation of new compounds through software. Molecular dynamics simulations for most active compound. Methods- In the present study HDAC-2 protein (PDB-4LY1) from RCSB PDB screened and retrieved. The different set of data for ligand preparation were downloaded from CHEMBL, NCI, Anticancer databases and FDA approved drugs of HDACi were downloaded from PubChem. The compounds were screened with two software Schrodinger and gold. The multiset framework combining ligand preparation, protein preparation, grid generation, ADMET prediction, molecular docking, Ligplot analysis and molecular dynamics (MD) simulation studies was performed to find the potential compound with HDAC-2 binding affinity. Result- The optimised compound shows high docking score from ChEMBL (-14.078) and NCI library it shows (-12.083) as compared to reference drug Panobinostat (-9.157). binding energy, hydrogen bonding and hydrophobic interaction against the reference compound. 20 compounds were selected as the best HDAC2 inhibitors based on the glide score, binding energy, hydrogen bonding, hydrophobic interaction. Top two compound show Ligplot analysis. Then the one highest docked compound shows dynamic study at 50ns shows binding stability with the inhibitor. Finally find its ADMET property. Conclusion- The virtual screening of drugs through software is ongoing process and 20 modified analogues those which satisfied all the screening results have been found to be better than the conventional drugs available. Further, synthesis, in vivo and cytotoxic studies of synthesised molecules are under process. KEYWORDS- Histone acetylase, histone deacetylase, histone deacetylase-2, molecular dynamics, 4LY1, ADME property, histone deacetylase inhibitor, Optimized Potential for Liquid Simulation 3e, high throughput virtual screening, standard precision, extra precision.

In silico molecular docking analysis for potential anti-Alzheimer's compounds from the methanolic leaf extract of Erythroxylum monogynum using Gas chromatography–mass spectrometry

BackgroundAlzheimer's disease is the major cause of dementia by two main factors includes an accumulation of acetylcholinesterase enzyme at cholinergic synapse and deposition of β-amyloid protein at neurofibrillary tangles. The present investigation explores the binding affinities of phytoconstituents present in the methanolic leaf extract of Erytrhroxylum monogynum identified by gas chromatography-mass spectrometry against selected targets, i.e., β-amyloid and acetylcholinesterase. ObjectivesThe main objective of present study was to explore anti-Alzheimer's potential of phytoconstituents from methanolic leaf extract of Erytrhroxylum monogynum. MethodsErytrhroxylum monogynum leaf material was subjected to Soxhlet extraction by three different solvents, namely n-hexane, chloroform and methanol. The methanolic leaf extract was subjected to Gas chromatography–mass spectrometric analysis for identification of novel phytoconstituents and chromatogram revealed the presence of 45 novel phytoconstituents. These phytoconstituents were not reported earlier from any part of this plant material. These phytoconstituents were explored for their anti-Alzheimer’s potential by iGEMDOCK software against selected targets, namely recombinant human acetylcholinesterase (protein data bank ID: 3LII) and β-amyloid (protein data bank ID: 2LMN). ResultsFrom the results of docking analysis, the top five phytoconstituents with the highest binding affinity towards the selected targets were further subjected to ADMET prediction by in silico admetSAR web portal. ConclusionsMolecular docking analysis revealed the presence of 7 phytoconstituents are having the highest binding affinity towards the selected targets when compared to their respective standard compounds namely 9, 12-octa-decadienoic acid, methyl ester, (E, E); octadecanoic acid, methyl ester; hexadecanoic acid, 2-hydroxy-1-(hydroxymethyl) ethyl ester; 3, 6-ditigloyloxy-7-hydroxytropane; 3, 7,11, 15-tetramethyl-2-hexa-decen-1-ol; neophytadiene and phytol. The lead hits were further subjected to LigPlot analysis to understand their intermolecular interactions. Thus the result collectively obtained from the in silico studies using computational approaches may become prospective novel lead compounds against the selected targets of Alzheimer's disease.

Application of In silico Methods in the Design of Drugs for Neurodegenerative Diseases.

Neurodegenerative diseases are complex disorders that cause neuron loss, brain aging and ultimately lead to death. These diseases are difficult to treat because of the complex nature of the nervous system, and the available medicines are unable to heal them effectively. This fact implies the need for novel therapeutics to be designed that are ready to stop or a minimum of retard the neurodegeneration process. These days, Computer-Assisted Drug Design (CADD) approaches are a passage to extend the drug development efficiency and to reduce time and cost because traditional drug discovery is both time-consuming as well as costly. Computational or in silico methods came up with powerful tools in drug design against neurodegenerative diseases. This review presents the approaches and theoretical basis of CADD. Also, the successful applications of various in silico studies, including homology modeling, molecular docking, Quantitative Structure-Activity Relationship (QSAR), Molecular Dynamic (MD), De novo drug design, Pharmacophore-based drug design, Virtual Screening (VS), LIGPLOT Analysis, In silico ADMET and drug safety prediction, for treating neurodegenerative diseases have also been included in this review. Major emphasis is given to Alzheimer's disease and Parkinson's disease because these two are the most familiar neurodegenerative diseases.

Inhibitory Potential Of Black Seed (Nigella Sativa L.) Bioactive Compounds Towards Main Protease Of SARS-CoV-2 : In Silico Study

COVID-19, caused by SARS-CoV-2, has become a massive worldwide concern of the 21st century. One potential strategy to block the biochemical pathway of SARS-CoV-2 was by inhibiting the main protease (Mpro), which is a key enzyme on viral replication. Black seed (Nigella sativa L.) has a long history for its use as a traditional medicine. Therefore, we hypothesised that the black seed contains numerous active compounds that could potentially confer inhibitory activity against SARS-CoV-2 viral Mpro. In this study, 24 active compounds from black seed were tested. Compounds were screened using Lipinski's Rules and admetSAR, then docked to viral Mpro 7BQY by AutoDockTools-1.5.6 and AutoDock Vina using a site directed docking approach resulting in affinity energy (∆G) and binding data. We found that the most potential active compound of N. sativa is 3-[(4-Methylphenyl)sulfanyl]-1,3-diphenyl-1-propanone, since its affinity energy was -7.6 kCal.mol-1. Its similarity to N3 inhibitor based on Ligplot analysis and DS were 86.7% and 76.19%, respectively, and the occupancy on binding site based on Ligplot analysis and DS were 90.91% and 81.82%, respectively. These findings can be used as a starting point for further investigation using in vitro and in vivo studies.

In silico exploration of anti-Alzheimer's compounds present in methanolic extract of Neolamarckia cadamba bark using GC–MS/MS

Alzheimer’s disease (AD) can be treated by the inhibition of Beta Amyloid protein (Aβ) and inhibition of Acetylcholinesterase (ACHE). Anti-Alzheimer’s potential phytoconstituents from Neolamarckia cadamba methanolic bark extracts were identified through GC–MS/MS analysis and in silico molecular docking analysis. Powdered bark sample was subjected to extract by soxhlet extractor with n-hexane, chloroform and methanol solvents respectively. The methanolic extract was taken for GC–MS/MS analysis, the observed chromatogram was revealed the presence of 61 constituents in the methanolic extract, 59 new phytoconstituents were identified which were not reported earlier as constituents any part of N. cadamba. GC–MS/MS detected phytoconstituents were analysed through the docking analysis by iGEMDOCK software against Aβ (PDB ID: 2LMN) and ACHE (PDB ID: 3LII) and compared with standard known inhibitors of galantamine and curcumin. Docking analysis binding energy was determined and verified by Discovery studio visulaizer. Both inhibition assay top 5 best dock energy compounds were analysed through the in silico modeling through admetSAR web portal for parameters of intestinal absorption, blood brain barrier permeation, carcinogencity, and acute oral toxicity were determined. From that heptadecanoic acid, 16-methyl-, methyl ester; beta-sitosterol acetate and octadecanoic acid, 2-hydroxy-, methyl ester inhibitors were identified. Further the top lead successful compound of each target molecular interactions were detected by LigPlot analysis. From this research these three compounds are best to treat AD than standard. Isolation of individual compounds would, however, help to find new compounds for other diseases and lead molecules for AD were identified.

In Silico Molecular Docking Analysis of Potential Anti-Alzheimer's Compounds Present in Chloroform Extract of Carissa carandas Leaf Using Gas Chromatography MS/MS

Background: The current treatment of Alzheimer's disease (AD) is far from adequate. AD can be treated by inhibiting either β-amyloid protein deposition or acetylcholinesterase enzyme activity. Many treatments for AD are directed at these 2 targets. In the present study, the phytoconstituents of Carissa carandas chloroform leaf extract were identified by gas chromatography-MS/MS analysis, and in silico molecular docking studies were performed to evaluate their potential against AD.Objectives: The present study aimed to identify the possible anti-Alzheimer's activity of novel phytoconstituents isolated from C carandas.Methods: The powdered leafy material was subjected to successive Soxhlet extraction using 3 different solvents: n-hexane, chloroform, and methanol. The chloroform extract was subjected to gas chromatography-MS/MS analysis, and the observed chromatogram revealed the presence of 48 chemical constituents. Among them, 42 new phytoconstituents are reported in this plant for the first time. The gas chromatography-MS/MS–identified phytoconstituents were evaluated by iGEMDOCK software against AD targets of β-amyloid fibril (protein data bank ID: 2LMN) and recombinant human acetylcholinesterase (protein data bank ID: 3LII) ligands, and their anti-AD potential were compared with those of known inhibitors of galantamine and curcumin.Results: On the basis of results from both docking assays, the 5 compounds with the highest docking energy were further analyzed using in silico admetSAR web portal modeling for the evaluation of parameters such as intestinal absorption, blood-brain barrier permeation, carcinogenicity, and acute oral toxicity.Conclusions: The chloroform leaf extract of C carandas was found to contain constituents that have affinities for the 2 targets tested; that is, amyloid β and acetylcholinesterase. The best docking scores were found for 7 compounds: 1-heneicosanol; N-nonadecanol-1; cholesta-4,6-dien-3-ol, (3beta); di-n-octyl phthalate; 7,9-di-tert-butyl-1-oxaspiro(4,5)deca-6,9-diene-2,8-dione; 6-undecyl-5,6-dihydro-2H-pyran-2-one, and phenol, 2,4-di-t-butyl-6-nitro compounds, and these compounds were therefore suggested to be promising anti-AD lead compounds. Further, the target leads were subjected to ligplot analysis for their 2-dimensional representation of hydrogen bonding and hydrophobic interactions. Thus, the results obtained from the in silico study of C carandas leaf extract using these computational approaches indicate the presence of phytoconstituents that have affinities for the selected 2 targets of AD. (Curr Ther Res Clin Exp. 2020; 81:XXX–XXX)

Targeting Trypanothione Reductase of Leishmanial major to Fight Against Cutaneous Leishmaniasis.

1.2-2.0 million cases of leishmaniasis occur annually throughout the world. The available drugs like Amphotericin B, antimonials and miltefosine are unable to fulfill the need due to less effectiveness, high toxicity, resistance, high cost and complex route of administration. Leishmania survives inside the macrophages through different evasion mechanisms; one of that is activation of its trypanothione reductase enzyme which neutralizes the reactive oxygen species generated inside the macrophages to kill the parasites. This enzyme is unique and absent in human, therefore in this study I targeted it for screening of new inhibitors to fight against leishmaniasis. Homology modeling of Leishmania major trypanothione reductase was performed using Phyre2 server. The homology based modelled protein was validated with PROCHECK analysis. Ligplot analysis was performed to predict the active residues inside the binding pocket. Further, virtual screening of ligand library containing 113 ligands from PubChem Bioassay was performed against the target using AutoDock Vina Tool. Top five ligands showed best binding affinity. The molecule having PubChem CID: 10553746 showed highest binding affinity of -11.3 kcal/mol. Over all this molecule showed highest binding affinity and moderate number of hydrogen bonds. Hopefully, this molecule will be able to block the activity of target enzyme, trypanothione reductase of Leishmania major effectively and may work as new molecules to fight against cutaneous leishmanaisis. This study will help the researchers to identify the new molecules which can block the activity of leishmanial-trypanothione reductase, a novel enzyme of trypanosomatids. These screened inhibitors may also be effective not only in leishmaniasis but also other trypanosomatid-mediated infectious diseases.

Docking analysis of hexanoic acid and quercetin with seven domains of polyketide synthase A provided insight into quercetin-mediated aflatoxin biosynthesis inhibition in Aspergillus flavus

Studies on phytochemicals as anti-aflatoxigenic agents have gained importance including quercetin. Thus, to understand the molecular mechanism behind inhibition of aflatoxin biosynthesis by quercetin, interaction study with polyketide synthase A (PksA) of Aspergillus flavus was undertaken. The 3D structure of seven domains of PksA was modeled using SWISS-MODEL server and docking studies were performed by Autodock tools-1.5.6. Docking energies of both the ligands (quercetin and hexanoic acid) were compared with each of the domains of PksA enzyme. Binding energy for quercetin was lesser that ranged from - 7.1 to - 5.25kcal/mol in comparison to hexanoic acid (- 4.74 to - 3.54kcal/mol). LigPlot analysis showed the formation of 12H bonds in case of quercetin and 8H bonds in hexanoic acid. During an interaction with acyltransferase domain, both ligands showed H bond formation at Arg63 position. Also, in product template domain, quercetin creates four H bonds in comparison to one in hexanoic acid. Our quantitative RT-PCR analysis of genes from aflatoxin biosynthesis showed downregulation of pksA, aflD, aflR, aflP and aflS at 24h time point in comparison to 7h in quercetin-treated A. flavus. Overall results revealed that quercetin exhibited the highest level of binding potential (more number of H bonds) with PksA domain in comparison to hexanoic acid; thus, quercetin possibly inhibits via competitively binding to the domains of polyketide synthase, a key enzyme of aflatoxin biosynthetic pathway. Further, we propose that key enzymes from aflatoxin biosynthetic pathway in aflatoxin-producing Aspergilli could be explored further using other phytochemicals as inhibitors.

In vitro and In silico Antigout arthritic activities of Ethanolic and Aqueous stem extracts of Cissus quadrangularis - A TLR2 and TLR4 Receptor approach

The in vitro anti-gout arthritic activity of ethanolic and aqueous extracts of Cissus quadrangularis stem was evaluated in terms of inhibition of xanthine oxidase, proteinase enzyme, protein denaturation and membrane stabilization. The Monosodium Urate (MSU) up-regulated expression patterns of toll like receptors namely TLR-2and TLR-4 were analyzed. The molecular docking was performed to select the antagonistic phyto ligand for receptors since their activation leads to the destructive immunological reactions occurring in gouty arthritis. The in vitro anti-gout arthritic activities were estimated using standard protocols. The MSU crystal induced toll like receptors gene expression was analyzed. Molecular docking and LIGPLOT analysis was performed with the GCMS derived phyto constituents in the ethanolic extract of Cissus quadrangularis with the receptors to find the interactions. Colchicine was used as a positive drug in the study. Among the two extracts, ethanolic extract revealed better in-vitro anti arthritic activity in the present investigation. Out of the GCMS derived 13 phyto components, based on docking score three main components namely Pentadecanoic acid, 14-methyl,-methyl ester,10-Octadecenoic acid, methyl ester, 4-one,2-(3,4-dihydroxyphenyl)-2,3-dihydro-3,5,7-trihydroxy showed better antagonistic action in the LIGPLOT analysis. It may be concluded these three ligands may further developed as a potential anti gouty arthritic drug

Structural investigations on mechanism of lapatinib resistance caused by HER-2 mutants.

HER-2 belongs to the human epidermal growth factor receptor (HER) family. Via different signal transduction pathways, HER-2 regulates normal cell proliferation, survival, and differentiation. Recently, it was reported that MCF10A, BT474, and MDA-MB-231 cells bearing the HER2 K753E mutation were resistant to lapatinib. Present study revealed that HER-2 mutant K753E showed some contrasting behaviour as compared to wild, L768S and V773L HER-2 in complex with lapatinib while similar to previously known lapatinib resistant L755S HER-2 mutant. Lapatinib showed stable but reverse orientation in binding site of K753E and the highest binding energy among studied HER2-lapatinib complexes but slightly lesser than L755S mutant. Results indicate that K753E has similar profile as L755S mutant for lapatinib. The interacting residues were also found different from other three studied forms as revealed by free energy decomposition and ligplot analysis.

Anthocyanin rich extract of Brassica oleracea L. alleviates experimentally induced myocardial infarction.

Cardioprotective potential of anthocyanin rich red cabbage extract (ARCE) was assessed in H2O2 treated rat neonatal cardiomyoblasts (H9c2 cells) and isoproterenol (ISO) induced rodent model of myocardial infarction. H2O2 treated H9c2 cells recorded cytotoxicity (48–50%) and apoptosis (57.3%), the same were reduced in presence of ARCE (7–10% & 12.3% respectively). Rats pretreated with ARCE for 30 days followed by ISO treatment recorded favourable heart: body weight ratio as compared to ISO treated group. Also, the mRNA levels of enzymatic antioxidants (sod and catalase) and apoptotic genes (bax and bcl-2) in ARCE+ISO treated group were similar to the control group suggesting that ARCE pretreatment prevents ISO induced depletion of enzymatic antioxidants and apoptosis. Histoarchitecture of ventricular tissue of ISO treated group was marked by infracted areas (10%) and derangement of myocardium whereas, ARCE+ISO treated group (4.5%) recorded results comparable to control (0%). ARCE+ISO treated group accounted for upregulation of caveolin-3 and SERCA2a expression as compared to the ISO treated group implying towards ARCE mediated reduction in membrane damage and calcium imbalance. Molecular docking scores and LigPlot analysis of cyanidin-3-glucoside (-8.7 Kcal/mol) and delphinidin-3-glucoside (-8.5 Kcal/mol) showed stable hydrophobic and electrostatic interactions with β1 adrenergic receptor. Overall this study elucidates the mechanism of ARCE mediated prevention of experimentally induced myocardial damage.

Natural polyphenolic inhibitors against the antiapoptotic BCL-2

The apoptotic mechanism is regulated by the BCL-2 family of proteins, such as BCL-2 or Bcl-xL, which block apoptosis while Bad, Bak, Bax, Bid, Bim or Hrk induce apoptosis. The overexpression of BCL-2 was found to be related to the progression of cancer and also providing resistance towards chemotherapeutic treatments. In the present study, we found that all polyphenols (apigenin, fisetin, galangin and luteolin) bind to the hydrophobic groove of BCL-2 and the interaction is stable throughout MD simulation run. Luteolin was found to bind with highest negative binding energy and thus, claimed highest potency towards BCL-2 inhibition followed by fisetin. The hydrophobic interactions were found to be critical for stable complex formation as revealed by the vdW energy and ligplot analysis. Finally, on the basis of data obtained during the study, it can be concluded that these polyphenols have the potential to be used as lead molecules for BCL-2 inhibition.

Secretory expression, characterization and docking study of glucose-tolerant β-glucosidase from B. subtilis

The thermostable, glucose tolerant β-glucosidase gene (bgl) of Glycoside hydrolase family 1, isolated from Bacillus subtilis, was cloned and overexpressed in Escherichia coli. The bgl has open reading frame of 1407bp, encoding 469 amino acids with predicted molecular weight of 53kDa. The recombinant protein (BGL) was purified 10.76 fold to homogeneity with specific activity of 54.04U/mg and recovery of 38.67%. The purified BGL was optimally active at pH 6.0 and temperature 60°C. The enzyme retained more than 85% of maximum activity after 1h preincubation at 60°C. The kinetic analysis indicated that BGL has highest catalytic efficiency (Kcat/Km) against p-nitrophenyl-β-d-xylopyranoside (654.58mM−1s−1) followed by p-nitrophenyl-β-d-glucopyranoside (292.53mM−1s−1) and p-nitrophenyl-β-d-galactopyranoside (61.17mM−1s−1). The Ki value for glucose and δ-gluconolactone was determined to be 1.9mM and 0.018mM, respectively. The BGL exhibited high tolerance against detergents and organic solvents. The homology modeling revealed that protein has 19 α-helices and 4 β-sheets and adopted (α/β)8 TIM barrel structure. Substrate docking and LigPlot analysis depicted the amino acids of active site involved in hydrogen bonding and hydrophobic interactions with substrates. The efficient BGL secretion with exploration of structural and functional relationship offer vistas for large scale production and various industrial applications.