Computational molecular perspectives on novel carbazole derivative as an anti-cancer molecule against CDK1 of breast and colorectal cancers via gene expression studies, novel two-way docking strategies, molecular mechanics and dynamics.

With increase in cancer incidences, alternative strategies for disease management are of utmost importance. Carbazole, is a compound that is being studied extensively as an anti-cancer compound. In this work, we aimed to investigate a carbazole derivative against specific cancer types such as breast and colorectal, based on the off-target analyses of carbazole derivative. The present work shortlisted 6 proteins that have an association in both cancer types, and then employed two different molecular docking strategies to examine the binding stability of carbazole derivative: a blind-docking state, where the pockets were undefined and mutation-docking state, where possible mutations were induced within the proteins. The results showed that CDK1 bound best in both states to carbazole derivative, and performed better than an array of positive controls. Molecular dynamic simulations at 100 ns further proved its stability, with carbazole derivative-CDK1-blind and mutated complex having RMSD values between 3.2 and 3.6 Å, and 2.8-3.2 Šrespectively. Molecular-mechanics generalized born and surface area solvation disclosed free energy of binding for the complexes as -28.79 ± 3.97 kcal/mol and -31.86 ± 5.09 kcal/mol respectively, with carbazole derivative bound stably within the binding pocket at every 10 ns of the 100 ns trajectory. Radial distribution functions showed that the bell curve was well within 6 Å, thus showing that carbazole derivative and its atoms do not deviate away from the pocket, suggesting its ability to be used as a good anti-cancer compound against breast and colorectal.

Comprehending interaction mechanism of natural actives of Colchicum autumnale L. for rheumatoid arthritis using integrative chemoinformatic approaches.

This research delves into the realm of therapeutic potential within natural compounds derived from Colchicum autumnale L., emphasizing a holistic perspective on medications used in human therapy. Rather than confining the study to their primary actions, the research endeavors to unveil molecular targets for these natural compounds, with a specific focus on their potential applicability in the treatment of rheumatoid arthritis (RA). The study focuses on understanding interactions between specific natural actives that target RA. Fifteen RA target proteins were identified from OMIM, GeneScan and PharmaGKB. Their structures were downloaded from RCSB PDB. Two active components of C. autumnale L. were chosen for mass spectrometry investigation. Ligand characteristics were determined using the ADMETlab and SwissADME software tools. Molecular docking was performed, and the top three complexes were simulated for 200 ns, along with identification of free binding energies. The compounds ß-sitosterol-IL-10 (-6.50 kcal/mol), colchicine-IL-10 (-6.01 kcal/mol), linoleic acid-IL-10 (-7.22 kcal/mol) and linoleic acid-IL-10 (-7.22 kcal/mol) exhibited best binding energies. ß-Sitosterol and colchicine showed the highest stability in simulations, confirmed by molecular mechanics free energy binding calculations. This work provides insights into the molecular interaction of natural compounds against RA targets, offering potential therapeutic anti-RA medications.Communicated by Ramaswamy H. Sarma.

Repurposing of known drugs for COVID-19 using molecular docking and simulation analysis.

We selected fifty one drugs already known for their potential disease treatment roles in various studies and subjected to docking and molecular docking simulation (MDS) analyses. Five of them showed promising features that are discussed and suggested as potential candidates for repurposing for COVID-19. These top five compounds were boswellic acid, pimecrolimus, GYY-4137, BMS-345541 and triamcinolone hexacetonide that interacted with the chosen receptors 1R42, 4G3D, 6VW1, 6VXX and 7MEQ, respectively with binding energies of -9.2 kcal/mol, -9.1 kcal/mol, -10.3 kcal/mol, -10.1 kcal/mol and -8.7 kcal/mol, respectively. The MDS studies for the top 5 best complexes revealed binding features for the chosen receptor, human NF-kappa B transcription factor as an important drug target in COVID-19-based drug development strategies.

Exploring the Synergistic Mechanism of AP2A2 Transcription Factor Inhibition via Molecular Modeling and Simulations as a Novel Computational Approach for Combating Breast Cancer: In Silico Interpretations.

Studies have shown that transcription factor AP2A2 (activator protein-2 alpha-2) is involved in the expression of DLEC1, a tumor suppressor gene, which, when mutated, will cause breast cancer and is thus an excellent target for breast cancer studies. Therefore, in the present research, a synergistic approach toward combating breast cancer is proposed by blocking AP2A2 factor, and allowing the cancer cells to be sensitive to anti-cancer drugs. The effect of AP2A2 on breast cancer was first understood via gene analysis from cBioPortal. AP2A2 was then modeled using RaptorX and its structure was validated from Ramachandran plots. Using all ligands from MolPort database, molecular docking was performed against AP2A2, from which the top three best docked ligands were studied for toxicity in humans using Protox-II. Once the ligands passed these tests, the best complexes were simulated at 200ns in Desmond Maestro, to comprehend their stabilities, followed by the computations of free energies of binding via Molecular mechanics- Generalized Born Solvent Accessibility method (MM-GBSA). The results showed that molecules MolPort-005-945-556 (sachharolipids), MolPort-001-741-124 (flavonoids), and MolPort-005-944-667 (lignan glycosides) with AP2A2 passed toxicity evaluation and belonged to toxicity classes 6, 5, and 5, respectively, with good docking energies. 200 ns simulations revealed stable complexes with slight conformational changes. Stability of ligands was confirmed via snapshots at every 20 ns of the trajectory. Radial distribution of these molecules against the protein revealed very slight deviation from binding pocket. Additionally, the free binding energies for these complexes were found to be - 54.93 ± 12.982 kcal/mol, - 44.39 ± 14.393 kcal/mol, and - 66.51 ± 13.522 kcal/mol, respectively. A preliminary computational validation of the inability of AP2A2 to bind to DLEC1 in the presence of ligands offers beneficial insights into the potential of these ligands. Therefore, this study sheds light on the potential natural molecules that could stably block AP2A2 with least deviation and act in synergy to aid anti-cancer drugs work on breast cancer cells.

Apoptotic Factors and Mitochondrial Complexes Assist Determination of Strain-Specific Susceptibility of Mice to Parkinsonian Neurotoxin MPTP.

Identification of genetic mutations in Parkinson's disease (PD) promulgates the genetic nature of disease susceptibility. Resilience-associated genes being unknown till date, the normal genetic makeup of an individual may be determinative too. Our earlier studies comparing the substantia nigra (SN) and striatum of C57BL/6J, CD-1 mice, and their F1-crossbreds demonstrated the neuroprotective role of admixing against the neurotoxin MPTP. Furthermore, the differences in levels of mitochondrial fission/fusion proteins in the SN of parent strains imply effects on mitochondrial biogenesis. Our present investigations suggest that the baseline levels of apoptotic factors Bcl-2, Bax, and AIF differ across the three strains and are differentially altered in SN following MPTP administration. The reduction in complex-I levels exclusively in MPTP-injected C57BL/6J reiterates mitochondrial involvement in PD pathogenesis. The MPTP-induced increase in complex-IV, in the nigra of both parent strains, may be compensatory in nature. The ultrastructural evaluation showed fairly preserved mitochondria in the dopaminergic neurons of CD-1 and F1-crossbreds. However, in CD-1, the endoplasmic reticulum demonstrated distinct luminal enlargement, bordering onto ballooning, suggesting proteinopathy as a possible initial trigger.The increase in α-synuclein in the pars reticulata of crossbreds suggests a supportive role for this output nucleus in compensating for the lost function of pars compacta. Alternatively, since α-synuclein over-expression occurs in different brain regions in PD, the α-synuclein increase here may suggest a similar pathogenic outcome. Further understanding is required to resolve this biological contraption. Nevertheless, admixing reduces the risk to MPTP by favoring anti-apoptotic consequences. Similar neuroprotection may be envisaged in the admixed populace of Anglo-Indians.

Deciphering the interaction mechanism of natural actives against larval proteins of Aedes aegypti to identify potential larvicides: a computational biology analysis.

Aedes aegypti is the target for repellents to curb incidences of vector-borne diseases. Stopping breeding of this mosquito species at its larval stages helps in controlling spread of insect-borne diseases. Therefore, the present study focused on deciphering the mechanism of interaction of selected natural actives against larval proteins of A. aegypti to identify potential natural alternative larvicides. 65 larval proteins were identified from literature, whose structures were modelled and validated using RaptorX and ProCheck. 11 natural actives were selected for predicting their ligand properties and toxicities via Toxicity Estimation Software Tool and ProTox-II. Molecular docking studies were carried out using POAP followed by 100 ns molecular dynamic simulation studies for top three best docked complexes to better understand the robustness of docking, complex stabilities and molecular mechanisms of interactions. Toxicity predictions revealed that 6 molecules belonged to toxicity class 4, and five to toxicity class 5, implying that they were all safe to use. Complexes goniothalamin-translation elongation factor (-10 kcal/mol), andrographolide-acetyl-CoA C-myristoyltransferase (-9.2 kcal/mol) and capillin-translation elongation factor (-8.4 kcal/mol) showed best binding energies. When simulated, capillin-translation elongation factor showed most stability, while the remaining two also evidenced robust docking. Evolutionary studies for top two larval proteins disclosed 100 other insect species in which these proteins can be targeted using various larvicides. Protein-protein interaction network analysis revealed several protein pathways that might be affected due to aforesaid naturals. Therefore, this study provides computational insights into the molecular interaction of naturals against larval proteins, acting as potential natural larvicides.Communicated by Ramaswamy H. Sarma.

Comprehensive Molecular Interaction Studies to Construe the Repellent/Kill Activity of Geraniol During Binding Event Against Aedes aegypti Proteins.

Aedes aegypti is an etiological agent for dengue, chikungunya, zika, and yellow fever viruses. With the advent of the use of natural alternatives as repellents, their precise mode of action during the event of binding is still unclear. Geraniol is one such bioactive natural that has been previously shown to have some insecticide properties. Thus, the present study aimed to understand the mechanism of the binding event of geraniol with the whole proteome of A. aegypti. Twenty protein target categories were shortlisted for the mosquito, wherein the proteins were downloaded with respect to the reference proteome. Conserved domain analysis was performed for the same using the CDD search tool to find the proteins that have common domains. 309 proteins were modeled using RaptorX standalone tool, and validated using Ramachandran plots from SAVES v6.0 from ProCheck. These modeled and validated proteins were then docked against geraniol, using POAP software, for understanding the binding energies. The top 3 best-docked complexes were then analyzed for their stabilities and event of binding via 100 ns simulation studies using DESMOND's Maestro environment. The docking results showed that the geraniol-voltage-gated sodium channel had the best energy of - 7.1 kcal/mol, followed by geraniol-glutathione-S-transferase (- 6.8 kcal/mol) and geraniol-alpha esterase (- 6.8 kcal/mol). The simulations for these 3 complexes revealed that several residues of the proteins interacted well with geraniol at a molecular level, and all three docked complexes were found to be stable when simulated (RMSD: 16-18 Å, 3.6-4.8 Å, 4.8-5.6 Å, respectively). Thus, the present study provides insights into the mechanism of the binding event of geraniol with the major A. aegypti targets, thereby, assisting the use of geraniol as a natural repellent.

Lack of IDH1 mutation in astroblastomas suggests putative origin from ependymoglial cells?

Astroblastomas are extremely rare neuroepithelial tumors of uncertain histogenesis, affecting children and young adults, and constitute a new addition to the WHO 2000 classification of CNS tumors. We report the largest series of nine cases diagnosed in a single institute over the last 13 years and review published literature. Mean age at presentation was 12.8 years (range: 22 months to 27years). Seven out of nine cases were supratentorial (frontal/frontoparietal - three, parieto-occipital - three, parafalcine - one), one was intraventricular and another was optochaismatic/suprasellar. Five cases were high grade (anaplastic) astroblastomas with Ki-67 labeling index of 8-10%. Immunohistochemical and ultrastructural evidence suggesting origin from cells intermediate between ependymocytes and astrocytes is presented. The histogenetic origin of these tumors remains speculative. But the lack of Isocitrate dehydrogenase 1 (IDH1) mutation as detected by immunohistochemistry in this study, which is similar to ependymomas supports putative origin from ependymoglial cells. Out of the nine cases, recurrence was noted in one case, 12 months after gross total resection with progression to high grade in the recurrent tumor. There is no recommended treatment protocol due to the rarity of this entity and prognostic factors are yet to be established.

Enhanced methanol production in plants provides broad spectrum insect resistance.

Plants naturally emit methanol as volatile organic compound. Methanol is toxic to insect pests; but the quantity produced by most of the plants is not enough to protect them against invading insect pests. In the present study, we demonstrated that the over-expression of pectin methylesterase, derived from Arabidopsis thaliana and Aspergillus niger, in transgenic tobacco plants enhances methanol production and resistance to polyphagous insect pests. Methanol content in the leaves of transgenic plants was measured using proton nuclear spectroscopy (1H NMR) and spectra showed up to 16 fold higher methanol as compared to control wild type (WT) plants. A maximum of 100 and 85% mortality in chewing insects Helicoverpa armigera and Spodoptera litura larvae was observed, respectively when fed on transgenic plants leaves. The surviving larvae showed less feeding, severe growth retardation and could not develop into pupae. In-planta bioassay on transgenic lines showed up to 99 and 75% reduction in the population multiplication of plant sap sucking pests Myzus persicae (aphid) and Bemisia tabaci (whitefly), respectively. Most of the phenotypic characters of transgenic plants were similar to WT plants. Confocal microscopy showed no deformities in cellular integrity, structure and density of stomata and trichomes of transgenic plants compared to WT. Pollen germination and tube formation was also not affected in transgenic plants. Cell wall enzyme transcript levels were comparable with WT. This study demonstrated for the first time that methanol emission can be utilized for imparting broad range insect resistance in plants.

Fabry's disease: An ultrastructural study of nerve biopsy.

Fabry's disease, an X linked recessive disorder caused by the deficiency of alpha-galactosidase A (alpha-gal A), leads to progressive accumulation of glycosphingolipids. We report this rare disease in a 19-year-old boy who presented with angiokeratomas, paresthesia and corneal opacities, and nerve biopsy revealed by electron microscopy lamellated inclusions in the smooth muscle, perineurial and endothelial cells characteristic of Fabry's disease.

Localization of ferrochelatase in Plasmodium falciparum.

Our previous studies have demonstrated de novo haem biosynthesis in the malarial parasite (Plasmodium falciparum and P. berghei). It has also been shown that the first enzyme of the pathway is the parasite genome-coded ALA (delta-aminolaevulinate) synthase localized in the parasite mitochondrion, whereas the second enzyme, ALAD (ALA dehydratase), is accounted for by two species: one species imported from the host red blood cell into the parasite cytosol and another parasite genome-coded species in the apicoplast. In the present study, specific antibodies have been raised to PfFC (parasite genome-coded ferrochelatase), the terminal enzyme of the haem-biosynthetic pathway, using recombinant truncated protein. With the use of these antibodies as well as those against the hFC (host red cell ferrochelatase) and other marker proteins, immunofluorescence studies were performed. The results reveal that P. falciparum in culture manifests a broad distribution of hFC and a localized distribution of PfFC in the parasite. However, PfFC is not localized to the parasite mitochondrion. Immunoelectron-microscopy studies reveal that PfFC is indeed localized to the apicoplast, whereas hFC is distributed in the parasite cytoplasm. These results on the localization of PfFC are unexpected and are at variance with theoretical predictions based on leader sequence analysis. Biochemical studies using the parasite cytosolic and organellar fractions reveal that the cytosol containing hFC accounts for 80% of FC enzymic activity, whereas the organellar fraction containing PfFC accounts for the remaining 20%. Interestingly, both the isolated cytosolic and organellar fractions are capable of independent haem synthesis in vitro from [4-14C]ALA, with the cytosol being three times more efficient compared with the organellar fraction. With [2-14C]glycine, most of the haem is synthesized in the organellar fraction. Thus haem is synthesized in two independent compartments: in the cytosol, using the imported host enzymes, and in the organellar fractions, using the parasite genome-coded enzymes.

Light microscopical and ultrastructural studies on the vas deferens of the lizard Mabuya carinata.

Adult male lizards (Mabuya carinata) were studied during breeding and non breeding seasons to determine the regional and seasonal differences if any in the vas deferens and to compare ultrastructural features of luminal epithelial cells with those of endotherms. The vas deferens of the lizard is a convoluted tube extending from the epididymis to the hemipenis passing over the kidney. Based on morphometric data of luminal diameter and epithelial cell height three distinct regions viz; proximal, middle and distal regions were identified in the vas deferens. The epithelium is surrounded by a thin layer of lamina propria, many layers of circular smooth muscle fibers and an outer layer of visceral pleuro peritoneum. Based on cell and nuclear morphology and ultrastructure, five different cell types viz; principal cell, basal cell, mitochondria rich cell, halo cell and narrow cell were identified in the epithelium during both breeding and non breeding season. Principal cells and basal cells were more abundant in both seasons. The types of luminal epithelial cells of vas deferens of M. carinata and their ultrastructural features are similar to those of mammals. Further, vas deferens of M. carinata differs from mammals in having only circular smooth muscles in contrast to circular and longitudinal muscles of mammalian vas deferens. To the best of our knowledge this is the first report describing cell types of vas deferens, their ultrastructure and ultrastructural seasonal variations in reptiles.