Unraveling the Interaction Mechanism of the Compounds From Cladophora sp to Recognize Prospective Larvicidal and Bactericidal Activities: In vitro and In Silico Approaches

The present investigation aims to validate the larvicidal and antibacterial potential of Cladophora sp through in vitro and in silico approaches. The presence of phytoconstituents, functional groups and the compounds responsible for antibacterial and larvicidal activity were assessed through FT-IR and GC-MS analyses which unveiled the existence of active secondary metabolites, hydroxyl, alkane and carbonyl groups. The larvicidal and antibacterial activity of algal extract were examined and revealed complete mortality and substantial zone of inhibition was observed against Culex quinquefasciatus and E. coli. To support the in vitro investigation in silico studies were performed. Molecular docking investigations of the selected compounds from GC-MS which exhibited favorable agreement with drug likeness and ADMET properties indicated robust interactions with the larvicidal and bacterial proteins showcasing considerable binding affinities. Notably, 1,2,4-Oxadiazole, 3-(1,3-benzodioxol-5-yl)-5-[(4-iodo-1H-pyrazol-1-yl) methyl]- exhibited strong interactions with the target proteins. Density Functional Theory revealed that the energy gap of the lead compound was reduced and substantiates the occurrence of intermolecular charge transfer. Molecular Dynamic simulations confirms the stability and flexibility of the lead compound. Hence, this investigation offers computational perspectives on the molecular interactions of Cladophora sp, suggesting its suitability as a promising biocontrol agent.

Virtual screening, molecular docking, molecular dynamics and quantum chemical studies on (2-methoxy-4-prop-2-enylphenyl) N-(2-methoxy-4-nitrophenyl) carbamate: a novel inhibitor of hepatocellular carcinoma

HDAC protein is associated with hepatocellular carcinoma. Different medicinal plants were selected for this study to analyze the inhibitory efficacy against the target protein, HDAC. Using virtual screening, we filtered out the best compounds, and molecular docking (XP) was carried out for the top compounds which filtered out. The molecular docking results showed that the title compound (2-methoxy-4-prop-2-enylphenyl) N-(2-methoxy-4-nitrophenyl) carbamate (MEMNC) has the highest docking score of about -7.7 kcal/mol against the targeted protein histone deacetylase (HDAC) compared with the other selected phytocompounds. From the molecular dynamics analysis, the RMSD and RMSF plots depicted the overall stability of the protein-ligand complex. Toxicity properties show the acceptable range of various kinds of toxicity that were predicted using the ProTox-II server. In addition, DFT quantum chemical and physicochemical properties of the MEMNC molecule were reported. Initially, the molecular structure of the MEMNC molecule was optimized and harmonic vibrational frequencies were calculated using DFT/B3LYP method with a cc-pVTZ basis set using Gaussian 09 program. The calculated vibrational wavenumber values were assigned based on Potential Energy Distribution calculations using the VEDA 4.0 program and correlated well with the previous literature values. The molecule has bioactivity as a result of intramolecular charge transfer interactions, as demonstrated by frontier molecular orbital analysis. Molecular electrostatic potential surface and Mulliken atomic charge distribution analyses validate the reactive sites of the molecule. Thus, the title compound can be used as a potential inhibitor of HDAC protein, which paves the way for designing novel drugs to treat Hepatocellular carcinoma.Communicated by Ramaswamy H. Sarma.

Targeting potential receptor molecules in non-small cell lung cancer (NSCLC) using in silico approaches

Introduction: Non-Small Cell Lung Cancer is the most prevalent type of cancer in lung cancer. Chemotherapy, radiation therapy, and other conventional cancer treatments have a low success rate. Thus, creating new medications is essential to halt the spread of lung cancer. Methods: In this study bioactive nature of lochnericine against Non-Small Cell Lung Cancer (NSCLC) was analyzed using various computational approaches such as quantum chemical calculations, molecular docking, and molecular dynamic simulation. Furthermore, the MTT assay shows the anti-proliferation activity of lochnericine. Results and Discussion: Using Frontier Molecular Orbital (FMO), the calculated band gap energy value associated with bioactive compounds and the molecule's potential bioactivity is confirmed. The H38 hydrogen atom and O1 oxygen atom in the molecule are effectively electrophilic, and potential nucleophilic attack sites were confirmed through analysis of the Molecular electrostatic potential surface. Furthermore, the electrons within the molecule were delocalized, which confers bioactivity on the title molecule and was authorized through Mulliken atomic charge distribution analysis. A molecular docking study revealed that lochnericine inhibits non-small cell lung cancer-associated targeted protein. The lead molecule and targeted protein complex were stable during molecular dynamics simulation studies till the simulation period. Further, lochnericine demonstrated remarkable anti-proliferative and apoptotic features against A549 lung cancer cells. The current investigation powerfully suggests that lochnericine is a potential candidate for lung cancer.

Synthesis, crystallization, XRD, Hirshfeld surface, vibrational spectra, and quantum chemical studies and Computational investigation of Caffeinium bisulfate: a new noncentrosymmetric form

Crystals of caffienium bisulfate were grown by solution growth technique. The vibrational spectra were scaled by adopting FT-IR and FT-Raman spectroscopy with the wide range, between 4000-400 cm^-1. X-ray diffraction study exhibited that the functional group such as N-H….O hydrogen bonds played an effective role in generating hydrogen-bonded crystal packing, pre-dominant. The examined molecules showed an interconnection of anions, by the O-H…O hydrogen bonds, establishing a chain C (4) motif, extending along the b-axis of the unit cell. Further, anions have shown interaction with cations, through N-H…O hydrogen bond, resulting from a ring R₁² (4) motif. The formed ring and chain motifs manifested an alternate hydrophilic stratum at z = ¼ and ¾. Geometrical optimization of tester molecule was done with Density Functional Theory (DFT) employing B3LYP function along with Hartree-Fock (HF) using 6-311++G(d,p) level basis set. Optimum molecular geometry and calculated database on the vibrational spectra were critically analyzed by comparing with experimental findings, resulting in a good correlating exhibited among them. Natural Bond Orbital (NBO) study revealed that hyper conjugation affinities and intermolecular charge transfer (ICT). An advanced technique such as HOMO-LUMO plot was performed to understand the chemical hardness, electro negativity and chemical efficacy of the tested molecules. The results showed that the occurrence of lower band gap value in the frontier orbital was responsible for the possible biological activities of the study materials. Bioinformatics analysis is applied for analyzing the biological activity of CAFSUL against Alzheimer's disease through computational methods.Communicated by Ramaswamy H. Sarma.

Molecular docking and dynamic simulations of Ocimum basilicum compounds against HCC and structural, vibrational, quantum, and chemical investigation of campesterol

Hepatocellular carcinoma (HCC) is a pervasive type of liver malignant growth and the third-driving reason for disease-related overall mortality with an expanding pervasiveness worldwide. Besides, no successful treatment can be utilized on patients with the cutting-edge or metastatic illness. Some of the natural therapeutics are paved the way for developing potential inhibitors for many types of cancer. Ocimum basilicum is one of the most well-known herbs, which contains numerous therapeutic properties and is widely used for various health issues. This study focused on its valuable medicinal property against HCC via in silico approach. Bioactive constituents from O. basilicum is subjected to molecular docking and dynamics study for 100 ns against the HCC targets (FGFR1, FGFR2, FGFR3, and FGFR4), and the selected lead compounds showed better interactions, docking score, obeys Lipinski's rule of five, highest occupied molecular orbital, lowest unoccupied molecular orbital hypothesis, protein-complex stability throughout the simulation period and the pharmacophoric features were analysed. Out of selected seven compounds, Campesterol revealed its potential therapeutic activity (Docking score - FGFR1 - 8.59 Kcal/Mol, FGFR2 - 7.11 Kcal/Mol, FGFR3 - 10.53 Kcal/Mol and FGFR4 - 9.17 Kcal/Mol, respectively. And also, it maintains good stability with the targets without any fluctuations. So, we concluded our findings that Campesterol is considered as, such a promising and potential inhibitor for HCC.Communicated by Ramaswamy H. Sarma.

Screening and identification of potential inhibitor for visceral leishmaniasis (VL) through computational analysis

Aim

The aim of this investigation is to detect potential inhibitor for visceral leishmaniasis through computational analysis.

Background

Leishmaniasis is categorized as a vector born pathogenic infection prevalent in tropical, subtropical, and in Mediterranean zones spread by intra-macrophage protozoa. The clinical syndrome of leishmaniasis is divided into the following type’s namely cutaneous leishmaniasis, mucocutaneous leishmaniasis, visceral leishmaniasis, and dermal leishmaniasis. Trypanothione synthetase is a key enzyme involving in glutathione biosynthesis as well as hydrolysis. Trypanothione is one of the promising drug targets for parasites. Parasites are inimitable with concern to their dependence on trypanothione to regulate intracellular thiol-redox balance in fighting against oxidative stress and biochemical anxiety. However, trypanothione synthetase was presumed as the target therapeutic alternate in VL therapy.

Objective

The important objective of this current investigation is to identify or analyze the potential inhibitor for V. leishmaniasis through computational approaches which include virtual screening, molecular docking, ADME prediction, and molecular dynamic simulation.

Methods

An investigation was performed to develop a 3D protein structure, using computational screening among associated similar structured proteins from popular compound database banks such as Specs, Maybridge, and Enamine, to detect novel staging with a series of validation for emerging innovative drugs molecules. Modeled protein ligand complex was further analyzed to know the binding ability of the complex. Molecular dynamics were performed to ascertain its stability at 50 ns.

Results

Trypanothione synthetase overall ability in the outcome of series of analysis. Among three database compounds screened, the compound from the Specs database exhibited the better protein-ligand docking scores and fulfilled the drug-like properties through ADMET analysis, and the docked complexes had better stability throughout the simulation. Besides, the other two database leads fulfilled the pharmacological properties, and the complexes were stable in the simulation.

Conclusion

By analyzing the various compounds from different databases, we concluded that the Specs database compound exhibits potential activity against the target protein and is considered a promising inhibitor for trypanothione synthetase.

Anticarcinogenic Efficacy of Fucoxanthin on HepG2 Cell Lines

Introduction: Hepatocellular Carcinoma (HCC) is considered one of the deadliest cancers which grow rapidly worldwide. Fucoxanthin can be acquired from edible brown seaweeds, reported that fucoxanthin has numerous physiological functions and biological abilities, and various medicinal properties. Aim: To evaluate the anti-carcinogenic efficiency of fucoxanthin against the Human Hepatoma Cell Line (HepG2). Materials and Methods: This in-vitro examination and research was carried from June 2018 to August 2018, at Alagappa University, Karaikudi, Tamil Nadu, India. Fucoxanthin at different concentrations was taken to demonstrate its antiproliferative potential and its cytotoxic effect. In this present examination, based on the outcome of the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl2H-tetrazolium bromide (MTT) assay, 80 µM and 100µM were chosen for further in-vitro studies. It was noted that remarkable leakage of Lactate Dehydrogenase (LDH) and a noteworthy decrease in the Glutathione (GSH) content of 80µ M and 100µM of fucoxanthin treated HepG2 cells. Under light and fluorescence microscopic examination, there was a significant reduction in cell growth and cell proliferation in the fucoxanthin-treated HepG2 cells. Data were presented as the mean±standard deviation. The one-way analysis of variance (ANOVA) and Tukey’s multiple comparison method were used to find the level of significance. Results: The human HepG2 to be studied and analysed were divided into group I: control group; group II: comprising those cells treated with fucoxanthin in concentration of 80 µM; group III: comprising those cells treated with fucoxanthine in concentration of 100 µM. The results of the MTT assay put forward that fucoxanthin has the cytotoxic and anti-proliferative potential against HepG2 further fucoxanthin significantly alter the marker enzymes level (p-value <0.05). The therapeutic efficiency of fucoxanthin might be due to the antioxidant effect of the bioactive compound. In this present investigation, the results of in-vitro studies, fucoxanthin strongly put forward that it has potential anticarcinogenic efficacy against the hepatic tumour (p-value <0.05). Conclusion: The results of this analysis undoubtedly symbolise that fucoxanthin has anti-oxidant activity and anti-carcinogenic efficacy against primary liver cancer HCC. Due to their therapeutic efficacy, may be considered as an excellent candidate against HCC.

Inhibition of Quorum Sensing and Biofilm Formation in Chromobacterium violaceum by Fruit Extracts of Passiflora edulis

Chromobacterium violaceum (C. violaceum) is a Gram-negative, rod-shaped facultatively anaerobic bacterium implicated with recalcitrant human infections. Here, we evaluated the anti-QS and antibiofilm activities of ethyl acetate extracts of Passiflora edulis (P. edulis) on the likely inactivation of acyl-homoserine lactone (AHL)-regulated molecules in C. violaceum both by in vitro and in silico analyses. Our investigations showed that the sub-MIC levels were 2, 1, and 0.5 mg/mL, and the concentrations showed a marked reduction in violacein pigment production by 75.8, 64.6, and 35.2%. AHL quantification showed 72.5, 52.2, and 35.9% inhibitions, inhibitions of EPS production (72.8, 36.5, and 25.9%), and reductions in biofilm formation (90.7, 69.4, and 51.8%) as compared to a control. Light microscopy and CLSM analysis revealed dramatic reduction in the treated biofilm group as compared to the control. GC-MS analysis showed 20 major peaks whose chemical structures were docked as the CviR ligand. The highest docking score was observed for hexadecanoic acid, 2-hydroxy-1-(hydroxymethyl) ethyl ester bonds in the active site of CviR with a binding energy of -8.825 kcal/mol. Together, we found that hexadecanoic acid, 2-hydroxy-1-(hydroxymethyl) ethyl ester remarkably interacted with CviR to inhibit the QS system. Hence, we concluded that hexadecanoic acid, 2-hydroxy-1-(hydroxymethyl) ethyl ester of P. edulis could likely be evaluated for treating C. violaceum infections.

Identifying dual leucine zipper kinase (DLK) inhibitors using e-pharamacophore screening and molecular docking

Alzheimer's is a neural disorder causing gradual loss in structure and function of nerve cell. To treat such disorders, c-Jun N-terminal Kinase (JNK) Pathway inhibitors were developed by representing chemical compounds that were used to inhibit the JNK signaling pathways. DLK is the stress sensor and implicating as regulatory factor in JNK pathway. Therefore, in the present investigation, pharmacophore screening was tried to identify the chemical compounds that involving inhibition of DLK proteins. To explore the pharmacophore region and mode of binding with DLK protein, N- (I H-pyrazol-3-y l) pyridin-2-aminer inhibitors were docked with DLK. Results reveal the information on the interaction mechanism of protein and ligand with chemical characteristics required to inhibit DLK protein. Such predicted information (AAAARH) was used as query to find out potential novel lead compounds sourced from public database. As an outcome of 65 compounds were listed based on the fitness score (2≥), and were subjected to glide HTVS.SP and XP. Best performing 5 lead compounds were shortlisted for dynamic simulations. This exhibited a constant RMSD over 20 ns of timescale.

Identification of novel inhibitor targeting Fyn kinase using molecular docking analysis

Identification of tyrosine Fyn kinase inhibitor is recognized as an effective and feasible therapeutic measure in reducing consequences of memory loss disorder Alzheimer's. The present investigation has been attempted with an objective to find out a novel potent inhibitor with similar homological structure to Fyn kinase using structure based in silico screening measure. Such derived structure was compared with natural data base pool and were systematically analyzed. Ligand based interaction was also tested and evaluated. We applied a molecular dynamic simulation technique to validate the stability of the identified complexes and to understand the ligand binding mechanism. Results provide information on the characteristics of novel and potent inhibitor for tyrosinase Fyn kinase protein so as to develop an innovative strategy to treat AD.

Insights from the Molecular modeling, docking analysis of illicit drugs and Bomb Compounds with Honey Bee Odorant Binding Proteins (OBPs)

Analysis of honeybee PBPs is of interest in the development of Biosensor applications. We described the predicted binding of 19 such compounds with 43-honey bee OBPs using molecular modeling, docking and phylogenetic analysis. Therefore, training the honeybees using preferred compounds formulate the bees to identify the illicit drugs and bomb compounds. Consequently, high docking score produced complex such OBP16-N-Phenyl-2-Napthalamine (-12.25k/mol), 3BJH-Crack Cocaine (-11.75k/mol), OBP10-Methadone (- 11.71k/mol), 1TUJ-Dronobinal Cannabis (-11.66k/mol), OBP13-Plasticizer (-11.27k/mol) and OBP24-Ecstasy (-10.89 k/mol) can be used to identify the compounds using biosensor application. The chemical reaction of the compounds for olfactory sensory was analyzed using DFT (Density Functional Theory) studies. Some of these compounds show high binding OBPs across distant phylogeny.

Influence of limonin on Wnt signalling molecule in HepG2 cell lines

OBJECTIVE

The role of limonin as potent anti carcinogenic, apoptosis and chemotherapeutic agents has been supported by limited studies.

MATERIALS AND METHODS

In this study, limonin is identified as a potent anti proliferative agent against human hepatoma HepG2 cells based on the cell viability study, LDH leakage assay. Induction of apoptosis in HepG2 cells by limonin was evidenced by western blot analysis of Bax, Cyclin D1, Caspase 3 and Caspase9.

RESULTS

Since Wnt signalling is involved in the initiation and sustaining of hepatocellular carcinoma we studied differential expression of LRP5, LRP6 and DKK wnt players.

CONCLUSION

Limonin found to down regulate these players which forms a rationale for further investigation on effect on limonin in cancer therapy.