Biology subjects

Hannan, M. A.

Publications and source records attributed to Hannan, M. A..

4 recordsLinked to original sources

bioRxiv2023

Identification of Therapeutic Leads from Ficus hispida Fruit Phytochemicals against Prostate Cancer Using Pharmacoinformatic and Molecular Dynamics Simulation Approach

Prostate cancer is one of the leading causes of death and the most common cancer type in men. In this study, potential leads from the phytochemicals of Ficus hispida fruit were screened using in silico tools against androgen receptor (AR), a known target for prostate cancer. PASS online and ADMET tools were used to screen specific phytochemicals that are relevant to prostate cancer treatment and have drug-like properties. Of 13, a total of 10 phytochemicals passed PASS online and ADMET screening. Next, a total of three phytochemicals, including nodakenetin (CID: 26305), isowigtheone hydrate (CID: 66728267), and 7-hydroxycoumarin (CID: 5281426) were selected based on their docking scores (-9.946 to -7.653 kcal/mol) and relevance to selective bioactivity. The MD simulation further confirmed the binding stability of these three phytochemicals with their target AR protein and determined that the main amino acid residues mainly responsible for this stability including RMSD, RMSF, and post simulation binding free energies. These findings suggest that these three phytochemicals of Ficus hispida fruit can further be developed as prospective therapeutics against prostate cancer.

bioinformatics↗

bioRxiv2020

In silico chemical profiling and identification of neuromodulators from Curcuma amada targeting Acetylcholinesterase

Curcuma amada or Mango ginger, a member of the Zingiberaceae family, has been revealed as a beneficiary medicinal plant having diverse pharmacological activities against a wide range of diseases. Due to having neuromodulation properties of this plant, the present study characterized the secondary metabolites of Curcuma amada for their drug-likeness properties, identified potent hits by targeting Acetylcholinesterase (AChE) and revealed neuromodulatory potentiality by network pharmacology approaches. Here in silico ADMET analysis was performed for chemical profiling, and molecular docking and molecular dynamics simulations were used to hit selection and binding characterizations. Accordingly, ADMET prediction showed that around 87.59% of compounds processed drug-likeness activity, where four compounds have been screened out by molecular docking. Guided from induced-fit docking, molecular dynamics simulations revealed phytosterol and curcumin derivatives as the most favorable AChE inhibitors with the highest binding energy, as resulted from MM-PBSA analysis. Furthermore, all of the four hits were appeared to modulate several signaling molecules and intrinsic cellular pathways in network pharmacology analysis, which are associated with neuronal growth survival, inflammation, and immune response, supporting their capacity to revert the condition of neuro-pathobiology. Together, the present in silico based characterization and system pharmacology based findings demonstrate Curcuma amada, as a great source of neuromodulating compounds, which brings about new development for complementary and alternative medicine for the prevention and treatment of neurodegenerative disorders.

bioinformatics↗

bioRxiv2018

The genome-wide, multi-layered architecture of chromosome pairing in early Drosophila embryos

Genome organization involves cis and trans chromosomal interactions, both implicated in gene regulation, development, and disease. Here, we focused on trans interactions in Drosophila, where homologous chromosomes are paired in somatic cells from embryogenesis through adulthood. We first addressed the long-standing question of whether pairing extends genome-wide and, to this end, developed a haplotype-resolved Hi-C approach that uses a new strategy to minimize homolog misassignment and thus robustly distinguish trans-homolog from cis contacts. This approach revealed striking genome-wide pairing in Drosophila embryos. Moreover, we discovered pairing to be surprisingly structured, with trans-homolog domains and interaction peaks, many coinciding with the positions of analogous cis features. We also found a significant correlation between pairing and the chromatin accessibility mediated by the pioneer factor Zelda. Our findings reveal a complex, highly structured organization underlying homolog pairing, first discovered more than a century ago.\n\nOne Sentence SummaryA robust approach for haplotype-resolved Hi-C reveals highly-structured homolog pairing in early stage Drosophila embryos.

genetics↗

bioRxiv2018

Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling

Chromosome structure is thought to be crucial for proper functioning of the nucleus. Here, we present a method for visualizing chromosomal DNA at super-resolution and then integrating Hi-C data to produce three-dimensional models of chromosome organization. We begin by applying Oligopaint probes and the single-molecule localization microscopy methods of OligoSTORM and OligoDNA-PAINT to image 8 megabases of human chromosome 19, discovering that chromosomal regions contributing to compartments can form distinct structures. Intriguingly, our data also suggest that homologous maternal and paternal regions may be differentially organized. Finally, we integrate imaging data with Hi-C and restraint-based modeling using a method called integrative modeling of genomic regions (IMGR) to increase the genomic resolution of our traces to 10 kb.\n\nOne Sentence SummarySuper-resolution genome tracing, contact maps, and integrative modeling enable 10 kb resolution glimpses of chromosome folding.

genetics↗