Comparative co-expression analysis of RNA-Seq transcriptome revealing key genes, miRNA and transcription factor in distinct metabolic pathways in diabetic nerve, eye, and kidney disease

Asmy, Veerankutty Subaida Shafna,Natarajan, Jeyakumar Korea Genome Organization 2022 Genomics & informatics Vol.20 No.3

Diabetes and its related complications are associated with long term damage and failure of various organ systems. The microvascular complications of diabetes considered in this study are diabetic retinopathy, diabetic neuropathy, and diabetic nephropathy. The aim is to identify the weighted co-expressed and differentially expressed genes (DEGs), major pathways, and their miRNA, transcription factors (TFs) and drugs interacting in all the three conditions. The primary goal is to identify vital DEGs in all the three conditions. The overlapped five genes (AKT1, NFKB1, MAPK3, PDPK1, and TNF) from the DEGs and the co-expressed genes were defined as key genes, which differentially expressed in all the three cases. Then the protein-protein interaction network and gene set linkage analysis (GSLA) of key genes was performed. GSLA, gene ontology, and pathway enrichment analysis of the key genes elucidates nine major pathways in diabetes. Subsequently, we constructed the miRNA-gene and transcription factor-gene regulatory network of the five gene of interest in the nine major pathways were studied. hsa-mir-34a-5p, a major miRNA that interacted with all the five genes. RELA, FOXO3, PDX1, and SREBF1 were the TFs interacting with the major five gene of interest. Finally, drug-gene interaction network elucidates five potential drugs to treat the genes of interest. This research reveals biomarker genes, miRNA, TFs, and therapeutic drugs in the key signaling pathways, which may help us, understand the processes of all three secondary microvascular problems and aid in disease detection and management.

Synthesis, Characterization and Biological Activities of 4-(p-Chlorophenyl)-1-(pyridin-2-yl)thiosemicarbazide and Its Metal Complexes

Hassanien, Mohammad M.,Mortada, Wael I.,Hassan, Ali M.,El-Asmy, Ahmed A. Korean Chemical Society 2012 대한화학회지 Vol.56 No.6

New series of metal complexes of Co(II), Ni(II), Cu(II), Zn(II), Pd(II) and Pt(II) with 4-(p-chlorophenyl)-1-(pyridin-2-yl)thiosemicarbazide (HCPTS) have been synthesized and characterized by elemental analyses, magnetic moment, spectra (IR, UV-Vis, $^1H$ NMR, mass and ESR) and thermal studies. The IR data suggest different coordination modes for HCPTS which behaves as a monobasic bidentate with all metal ions except Cu(II) and Zn(II) which acts as a monobasic tridentate. Based on the electronic and magnetic studies, Co(II), Cu(II), Pd(II) and Pt(II) complexes have square - planner, Ni(II) has mixed stereochemistry (tetrahedral + square planar), while Zn(II) is tetrahedral. Molar conductance in DMF solution indicates the non-ionic nature of the complexes. The ESR spectra of solid copper(II) complex show $g_{\parallel}$ (2.2221) > $g_{\perp}$ (2.0899) > 2.0023 indicating square-planar structure and the presence of the unpaired electron in the $d_x2_{-y}2$ orbital with significant covalent bond character. The thermal stability and degradation kinetics of the ligand and its metal complexes were studied by TGA and DTA and the kinetic parameters were calculated using Coats-Redfern and Horowitz-Metzger methods. The complexes have more antibacterial activity against some bacteria than the free ligand. However, the ligand has high anticancer activities against HCT116 (human colon carcinoma cell line) and HEPG2 (human liver hepatocellular carcinoma cell line) compared with its complexes.

Synthesis, biochemistry, and in silico investigations of isatin-based hydrazone derivatives as monoamine oxidase inhibitors

Maliyakkal Naseer,Oh Jong Min,Kumar Sunil,Gahori Prashant,Tengli Anandkumar,Beeran Asmy Appadath,Kim Hoon,Mathew Bijo 한국응용생명화학회 2024 Applied Biological Chemistry (Appl Biol Chem) Vol.67 No.-

Ten isatin-based hydrazone derivatives were synthesized using two subseries, IA (isatin + acetophenone) and IB (isatin + benzaldehyde), and evaluated for their monoamine oxidases (MAOs) inhibitory activity. All the compounds showed stronger MAO-A inhibition than MAO-B, and the IB series showed more effective MAO-A inhibitory activity than IA series. Compound IB4 most potently inhibited MAO-A (half maximal inhibitory concentration IC 50  = 0.015 µM), followed by IB3 (IC 50  = 0.019 µM). On the contrary, compound IB3 showed the highest MAO-B inhibition (IC 50  = 0.068 µM), followed by IB4 (IC 50  = 1.87 µM). Compound IB3 and IB4 had low selectivity indices of 3.68 and 8.50, respectively. Structurally, the methyl group of IA series decreased the inhibition of both MAO-A and MAO-B. Among them, IB3 and IB4 (4-Cl and 4-Br in B-ring, respectively) showed higher MAO-A and MAO-B inhibition than the other substitutions. Inhibition constant K i values of IB3 and IB4 for MAO-A were 0.0088 and 0.0063 µM, respectively, and those for MAO-B were 0.048 and 0.060 µM, respectively. IB3 and IB4 were competitive, reversible inhibitors of MAO-A and MAO-B. Molecular docking analysis predicted that IB3 and IB4 formed stable hydrogen bonds between Asn181 and the NH atom of isatin in the ligand-protein complex. Dynamic analysis revealed that IB3 and IB4 are stable with both MAO isoforms. These observations suggest IB3 and IB4 are potent and reversible MAO-A and MAO-B inhibitors and both compounds can be used as therapeutic agents for neurological disorders. Ten isatin-based hydrazone derivatives were synthesized using two subseries, IA (isatin + acetophenone) and IB (isatin + benzaldehyde), and evaluated for their monoamine oxidases (MAOs) inhibitory activity. All the compounds showed stronger MAO-A inhibition than MAO-B, and the IB series showed more effective MAO-A inhibitory activity than IA series. Compound IB4 most potently inhibited MAO-A (half maximal inhibitory concentration IC50 = 0.015 μM), followed by IB3 (IC50 = 0.019 μM). On the contrary, compound IB3 showed the highest MAO-B inhibition (IC50 = 0.068 μM), followed by IB4 (IC50 = 1.87 μM). Compound IB3 and IB4 had low selectivity indices of 3.68 and 8.50, respectively. Structurally, the methyl group of IA series decreased the inhibition of both MAO-A and MAO-B. Among them, IB3 and IB4 (4-Cl and 4-Br in B-ring, respectively) showed higher MAO-A and MAO-B inhibition than the other substitutions. Inhibition constant Ki values of IB3 and IB4 for MAO-A were 0.0088 and 0.0063 μM, respectively, and those for MAO-B were 0.048 and 0.060 μM, respectively. IB3 and IB4 were competitive, reversible inhibitors of MAO-A and MAO-B. Molecular docking analysis predicted that IB3 and IB4 formed stable hydrogen bonds between Asn181 and the NH atom of isatin in the ligand-protein complex. Dynamic analysis revealed that IB3 and IB4 are stable with both MAO isoforms. These observations suggest IB3 and IB4 are potent and reversible MAO-A and MAO-B inhibitors and both compounds can be used as therapeutic agents for neurological disorders.

Precipitation–deposition assisted fabrication and characterization of nano-sized zinc manganite

N.M. Deraz,Ahmed A. Abdeltawab,M.M. Selim,O. El-Shafey,A.A. El-Asmy,Salem S Al-Deyab 한국공업화학회 2014 Journal of Industrial and Engineering Chemistry Vol.20 No.5

Catalytic and structural investigations of nano-sized zinc manganite (ZnMn2O4) powders have been determined. These manganites were prepared by precipitation–deposition route followed by heating at 400, 600, and 800℃. The final products were characterized X-ray diffraction, scanning electron microscopy (SEM), transmission electron microscopy (TEM), and energy dispersive X-ray (EDX). The catalytic activity of the as prepared systems was measured by the hydrogen peroxide decomposition in aqueous solution over the solid surface at 30–50℃. The results showed that the calcination temperature affects the different characteristics of the investigated solids.

APPLICATION OF POLYCULTURE USING STRATIFIED DOUBLE NET CAGE AT TELUK AWERANGE, SOUTH SULAWESI, INDONESIA

Sapto P. Putro,Agung Sudaryono,Rahmansyah, Suminto,Asmi Citra Malina,Rahmansyah,Lydeman 한국수산과학회 양식분과 2015 한국수산과학회 양식분과 학술대회 Vol.2015 No.5

Protein <i>S</i>-Glutathionylation Mediates Macrophage Responses to Metabolic Cues from the Extracellular Environment

Ullevig, Sarah L.,Kim, Hong Seok,Short, John D.,Tavakoli, Sina,Weintraub, Susan T.,Downs, Kevin,Asmis, Reto Mary Ann Liebert 2016 Antioxidants & redox signaling Vol.25 No.15