02064nas a2200253 4500008004100000022001400041245013500055210006900190260009300259300001200352490000700364520103800371653004301409653003301452653001301485653003701498100002501535700002301560700002401583700002501607700002301632700002501655856013001680 2012 eng d a1469-066700aZoom-in - a targeted database search for identification of glycation modifications analyzed by untargeted tandem mass spectrometry0 aZoomin a targeted database search for identification of glycatio a6 CHARLTON MILL, CHARLTON, CHICHESTER,, W SUSSEX PO18 0HY, ENGLANDbIM PUBLICATIONScJAN a475-4810 v183 a

Post-translational modifications (PTMs) are very important to biological function, however their identification and characterization is technically challenging. In this study, we have identified glycation modifications by nano LC-MSE, a data independent acquisition work flow, followed by database search using the Protein Lynx Global Server (PLGS). PLGS search with a complete human protein database hardly identified glycation modifications in a glycated human serum albumin (HSA), which was detected to be glycated by western blotting with advanced glycation end products (AGE) antibody and fluorescence spectroscopy. To overcome this difficulty, ``Zoom-In'' approach, a targeted database search was used to identify glycation modifications in a glycated HSA, which were further manually validated. This approach was useful for identification of glycation modifications from untargeted tandem mass spectrometry workflow such as MSE, but may require the development of a new algorithm or an upgrade of the existing software.

10aadvanced glycation end products (AGEs)10adata independent acquisition10aDiabetes10apost-translational modifications1 aBhonsle, Hemangi, S.1 aKorwar, Arvind, M.1 aKesavan, Suresh, K.1 aBhosale, Santosh, D.1 aBansode, Sneha, B.1 aKulkarni, Mahesh, J. uhttps://library.ncl.res.in/content/zoom-targeted-database-search-identification-glycation-modifications-analyzed-untargeted-002124nas a2200217 4500008004100000022001400041245008100055210006900136260010300205300001200308490000700320520130500327100002301632700002401655700002201679700002001701700002701721700002501748700002501773856010801798 2013 eng d a1535-947600aProteomic analysis of protease resistant proteins in the diabetic rat kidney0 aProteomic analysis of protease resistant proteins in the diabeti a9650 ROCKVILLE PIKE, BETHESDA, MD 20814-3996 USAbAMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INCcJAN a228-2360 v123 a

Glycation induced protein aggregation has been implicated in the development of diabetic complications and neurodegenerative diseases. These aggregates are known to be resistant to proteolytic digestion. Here we report the identification of protease resistant proteins from the streptozotocin induced diabetic rat kidney, which included enzymes in glucose metabolism and stress response proteins. These protease resistant proteins were characterized to be advanced glycation end products modified and ubiquitinated by immunological and mass spectrometry analysis. Further, diabetic rat kidney exhibited significantly impaired proteasomal activity. The functional analysis of identified physiologically important enzymes showed that their activity was reduced in diabetic condition. Loss of functional activity of these proteins was compensated by enhanced gene expression. Aggregation prone regions were predicted by in silico analysis and compared with advanced glycation end products modification sites. These findings suggested that the accumulation of protein aggregates is an inevitable consequence of impaired proteasomal activity and protease resistance due to advanced glycation end products modification. Molecular & Cellular Proteomics 12: 10.1074/mcp.M112.020651, 228-236, 2013.

1 aBansode, Sneha, B.1 aChougale, Ashok, D.1 aJoshi, Rakesh, S.1 aGiri, Ashok, P.1 aBodhankar, Subhash, L.1 aHarsulkar, Abhay, M.1 aKulkarni, Mahesh, J. uhttps://library.ncl.res.in/content/proteomic-analysis-protease-resistant-proteins-diabetic-rat-kidney-002257nas a2200217 4500008004100000022001400041245010300055210006900158260009100227300001200318490000600330520141100336100002301747700001901770700002501789700002501814700002201839700002501861700002501886856012801911 2014 eng d a1932-620300aMolecular investigations of protriptyline as a multi-target directed ligand in alzheimer's disease0 aMolecular investigations of protriptyline as a multitarget direc a1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USAbPUBLIC LIBRARY SCIENCEcAUG ae1051960 v93 a

Alzheimer's disease (AD) is a complex neurodegenerative disorder involving multiple cellular and molecular processes. The discovery of drug molecules capable of targeting multiple factors involved in AD pathogenesis would greatly facilitate in improving therapeutic strategies. The repositioning of existing non-toxic drugs could dramatically reduce the time and costs involved in developmental and clinical trial stages. In this study, preliminary screening of 140 FDA approved nervous system drugs by docking suggested the viability of the tricyclic group of antidepressants against three major AD targets, viz. Acetylcholinesterase (AChE), beta-secretase (BACE-1), and amyloid beta (A beta) aggregation, with one member, protriptyline, showing highest inhibitory activity. Detailed biophysical assays, together with isothermal calorimetry, fluorescence quenching experiments, kinetic studies and atomic force microscopy established the strong inhibitory activity of protriptyline against all three major targets. The molecular basis of inhibition was supported with comprehensive molecular dynamics simulations. Further, the drug inhibited glycation induced amyloid aggregation, another important causal factor in AD progression. This study has led to the discovery of protriptyline as a potent multi target directed ligand and established its viability as a promising candidate for AD treatment.

1 aBansode, Sneha, B.1 aJana, Asis, K.1 aBatkulwar, Kedar, B.1 aWarkad, Shrikant, D.1 aJoshi, Rakesh, S.1 aSengupta, Neelanjana1 aKulkarni, Mahesh, J. uhttps://library.ncl.res.in/content/molecular-investigations-protriptyline-multi-target-directed-ligand-alzheimers-disease-001713nas a2200205 4500008004100000022001400041245006000055210006000115260011000175300001600285490000600301520095000307100002401257700002901281700002301310700002101333700003701354700002501391856009101416 2015 eng d a2046-206900aInvestigation of antiglycation activity of isoprenaline0 aInvestigation of antiglycation activity of isoprenaline aTHOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLANDbROYAL SOC CHEMISTRYcMAR a25051-250580 v53 a

Advanced glycation end products (AGEs) are implicated in pathogenesis of diabetes and its complications. In this study, we report the ability of isoprenaline to inhibit the AGE modification of protein by fluorescence spectroscopy and western blotting. Isoprenaline was more effective in inhibiting AGE modification than aminoguanidine, a well known glycation inhibitor. Further, we show that isoprenaline inhibits at Amadori product formation during glycation reaction by various techniques such as MALDI-TOF-MS, LC-MS/MS, and fructosamine assay. Mass spectrometric analysis of the glycation reaction mixture incubated with isoprenaline suggested that it forms adducts with glucose and thus inhibits glycation. The finding of the additional property of isoprenaline of inhibiting glycation suggests that it is a potential candidate for drug repositioning for the treatment of diabetes and its complications, as it is an FDA approved drug.

1 aKolekar, Yogesh, M.1 aVannuruswamy, Garikapati1 aBansode, Sneha, B.1 aSanthakumari, B.1 aThulasiram, Hirekodathakallu, V.1 aKulkarni, Mahesh, J. uhttps://library.ncl.res.in/content/investigation-antiglycation-activity-isoprenaline-002643nas a2200301 4500008004100000022001400041245005500055210005500110260006700165300001200232490000700244520171800251653001701969653001201986653001401998653001102012653002002023653000902043100002502052700002302077700002102100700002402121700002102145700003602166700002802202700002502230856008602255 2015 eng d a1615-985300aInvestigation of phosphoproteome in RAGE signaling0 aInvestigation of phosphoproteome in RAGE signaling a111 RIVER ST, HOBOKEN 07030-5774, NJ USAbWILEY-BLACKWELLcJAN a245-2590 v153 a

The receptor for advanced glycation end products (RAGE) is one of the most important proteins implicated in diabetes, cardiovascular diseases, neurodegenerative diseases, and cancer. It is a pattern recognition receptor by virtue of its ability to interact with multiple ligands, RAGE activates several signal transduction pathways through involvement of various kinases that phosphorylate their respective substrates. Only few substrates have been known to be phosphorylated in response to activation by RAGE (e.g., nuclear factor kappa B); however, it is possible that these kinases can phosphorylate multiple substrates depending upon their expression and localization, leading to altered cellular responses in different cell types and conditions. One such example is, glycogen synthase kinase 3 beta which is known to phosphorylate glycogen synthase, acts downstream to RAGE, and hyperphosphorylates microtubule-associated protein tau causing neuronal damage. Thus, it is important to understand the role of various RAGE-activated kinases and their substrates. Therefore, we have reviewed here the details of RAGE-activated kinases in response to different ligands and their respective phosphoproteome. Furthermore, we discuss the analysis of the data mined for known substrates of these kinases from the PhosphoSitePlus (http://www.phosphosite.org) database, and the role of some of the important substrates involved in cancer, diabetes, cardiovascular diseases, and neurodegenerative diseases. In summary, this review provides information on RAGE-activated kinases and their phosphoproteome, which will be helpful in understanding the possible role of RAGE and its ligands in progression of diseases.

10aCell biology10aDisease10aGlycation10aKinase10aPhosphoproteome10aRAGE1 aBatkulwar, Kedar, B.1 aBansode, Sneha, B.1 aPatil, Gouri, V.1 aGodbole, Rashmi, K.1 aKazi, Rubina, S.1 aChinnathambi, Subashchandrabose1 aShanmugam, Dhanasekaran1 aKulkarni, Mahesh, J. uhttps://library.ncl.res.in/content/investigation-phosphoproteome-rage-signaling-002873nas a2200325 4500008004100000022001400041245012300055210006900178260006700247300001200314490000700326520171600333653003602049653001002085653002702095653001102122653001402133653001302147653001502160100002502175700002102200700002102221700002702242700003902269700002302308700003602331700002502367700002402392856013102416 2015 eng d a1474-971800aRifampicin reduces advanced glycation end products and activates DAF-16 to increase lifespan in Caenorhabditis elegans0 aRifampicin reduces advanced glycation end products and activates a111 RIVER ST, HOBOKEN 07030-5774, NJ USAbWILEY-BLACKWELLcJUN a463-4730 v143 a

Advanced glycation end products (AGEs) are formed when glucose reacts nonenzymatically with proteins; these modifications are implicated in aging and pathogenesis of many age-related diseases including type II diabetes, atherosclerosis, and neurodegenerative disorders. Thus, pharmaceutical interventions that can reduce AGEs may delay age-onset diseases and extend lifespan. Using LC-MSE, we show that rifampicin (RIF) reduces glycation of important cellular proteins in vivo and consequently increases lifespan in Caenorhabditis elegans by up to 60%. RIF analog rifamycin SV (RSV) possesses similar properties, while rifaximin (RMN) lacks antiglycation activity and therefore fails to affect lifespan positively. The efficacy of RIF and RSV as potent antiglycating agents may be attributed to the presence of a p-dihydroxyl moiety that can potentially undergo spontaneous oxidation to yield highly reactive p-quinone structures, a feature absent in RMN. We also show that supplementing rifampicin late in adulthood is sufficient to increase lifespan. For its effect on longevity, rifampicin requires DAF-18 (nematode PTEN) as well as JNK-1 and activates DAF-16, the FOXO homolog. Interestingly, the drug treatment modulates transcription of a different subset of DAF-16 target genes, those not controlled by the conserved Insulin-IGF-1-like signaling pathway. RIF failed to increase the lifespan of daf-16 null mutant despite reducing glycation, showing thereby that DAF-16 may not directly affect AGE formation. Together, our data suggest that the dual ability to reduce glycation in vivo and activate prolongevity processes through DAF-16 makes RIF and RSV effective lifespan-extending interventions.

10aadvanced glycation end products10aaging10aCaenorhabditis elegans10aDAF-1610aGlycation10alifespan10arifampicin1 aGolegaonkar, Sandeep1 aTabrez, Syed, S.1 aPandit, Awadhesh1 aSethurathinam, Shalini1 aJagadeeshaprasad, Mashanipalya, G.1 aBansode, Sneha, B.1 aSampathkumar, Srinivasa-Gopalan1 aKulkarni, Mahesh, J.1 aMukhopadhyay, Arnab uhttps://library.ncl.res.in/content/rifampicin-reduces-advanced-glycation-end-products-and-activates-daf-16-increase-lifespan-001692nas a2200205 4500008004100000022001400041245007700055210006900132260011000201300001600311490000600327520089700333100002301230700002501253700002501278700001901303700002501322700002501347856011401372 2015 eng d a2046-206900aTolbutamide induces conformational change and promotes albumin glycation0 aTolbutamide induces conformational change and promotes albumin g aTHOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLANDbROYAL SOC CHEMISTRYcAPR a40070-400750 v53 a

Tolbutamide is a first generation sulfonylurea drug used for the treatment of type II diabetes. In the present study, the effect of tolbutamide on albumin conformation was investigated using BSA as a model protein. The binding of tolbutamide induced a conformational change in albumin, which was confirmed by thioflavin T assay, ANS assay, and CD spectroscopy. Computer simulations suggested that the binding of tolbutamide increases the solvent accessibility of lysine residues, the hotspots of glycation. Furthermore, the change in conformation of albumin facilitates increased glycation, which was observed by AGE specific fluorescence and the results were corroborated by mass spectrometric analysis. This study suggested that tolbutamide enhances albumin glycation by inducing conformational change in BSA and hence could be a potential risk factor if used for a prolonged period.

1 aBansode, Sneha, B.1 aBatkulwar, Kedar, B.1 aWarkad, Shrikant, D.1 aJana, Asis, K.1 aSengupta, Neelanjana1 aKulkarni, Mahesh, J. uhttps://library.ncl.res.in/content/tolbutamide-induces-conformational-change-and-promotes-albumin-glycation-002342nas a2200265 4500008004100000022001400041245016300055210006900218260012700287300001200414490000700426520130200433653001301735653001301748653001701761653001401778653001101792653001901803100002601822700002501848700002301873700002501896700002501921856013001946 2016 eng d a1138-754800aDietary flaxseed oil and fish oil ameliorates renal oxidative stress, protein glycation, and inflammation in streptozotocin-nicotinamide-induced diabetic rats0 aDietary flaxseed oil and fish oil ameliorates renal oxidative st aCAMPUS UNIV, CARRETERA DEL SADAR S-N, APARTADO 177, 31080 PAMPLONA, SPAINbSERVICIO PUBLICACIONES UNIVERSIDAD NAVARRAcJUN a327-3360 v723 a

Protective and prophylactic effects of omega-3 fatty acids on oxidative stress and inflammation are well known. We assessed beneficial effects of flaxseed oil and fish oil on streptozotocin (65 mg/kg; i.p.)-nicotinamide (110 mg/kg; i.p.) induced diabetic rats by studying renal expression of antioxidant and inflammatory genes. Diabetic rats given 10 % flaxseed oil or 10 % fish oil diet for 35 days showed significant decrease in renal lipid peroxidation. Flaxseed oil diet resulted in up-regulation of renal superoxide dismutase-1 (SOD-1) (activity and expression) and glutathione peroxidase-1 (GPx-1) expression. Furthermore, both diets up-regulated catalase (CAT) (activity and expression) and down-regulated heme oxygenase-1 (HO-1) expression. Both diets were able to limit the renal advanced glycation end products (AGEs) formation and reduced receptor of AGE (RAGE) protein expression significantly. Expressions of interleukin-6 (IL-6) and NF-kappa B p65 subunit were down-regulated significantly by flaxseed oil or fish oil diet. The histological tubular injuries were also lowered by both diets. These results suggest that dietary omega-3 fatty acids may slow the progression of diabetic nephropathy (DN) associated with oxidative stress, glycation, and inflammation in the kidney.

10aDiabetes10aFish oil10aFlaxseed oil10aGlycation10aKidney10aStreptozotocin1 aJangale, Nivedita, M.1 aDevarshi, Prasad, P.1 aBansode, Sneha, B.1 aKulkarni, Mahesh, J.1 aHarsulkar, Abhay, M. uhttps://library.ncl.res.in/content/dietary-flaxseed-oil-and-fish-oil-ameliorates-renal-oxidative-stress-protein-glycation-and02932nas a2200313 4500008004100000022001400041245013200055210006900187260000800256520189100264653001602155653001302171653001102184653000902195653003302204653002302237653000902260653002102269100002202290700002502312700002302337700001902360700002602379700002702405700001702432700002002449700002502469856012402494 2020 eng d a0739-110200aDiscovery of potential multi-target-directed ligands by targeting host-specific SARS-CoV-2 structurally conserved main protease0 aDiscovery of potential multitargetdirected ligands by targeting  cMAY3 a

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has resulted in the current COVID-19 pandemic. Worldwide this disease has infected over 2.5 million individuals with a mortality rate ranging from 5 to 10%. There are several efforts going on in the drug discovery to control the SARS-CoV-2 viral infection. The main protease (M-Pro) plays a critical role in viral replication and maturation, thus can serve as the primary drug target. To understand the structural evolution of M-Pro, we have performed phylogenetic and Sequence Similarity Network analysis, that depicted divergence of Coronaviridae M-Pro in five clusters specific to viral hosts. This clustering was corroborated with the comparison of M-Pro structures. Furthermore, it has been observed that backbone and binding site conformations are conserved despite variation in some of the residues. These attributes can be exploited to repurpose available viral protease inhibitors against SARS-CoV-2 M-Pro. In agreement with this, we performed screening of similar to 7100 molecules including active ingredients present in the Ayurvedic anti-tussive medicines, anti-viral phytochemicals and synthetic anti-virals against SARS-CoV-2 M-Pro as the primary target. We identified several natural molecules like delta-viniferin, myricitrin, taiwanhomoflavone A, lactucopicrin 15-oxalate, nympholide A, afzelin, biorobin, hesperidin and phyllaemblicin B that strongly binds to SARS-CoV-2 M-Pro. Intrestingly, these molecules also showed strong binding with other potential targets of SARS-CoV-2 infection like viral receptor human angiotensin-converting enzyme 2 (hACE-2) and RNA dependent RNA polymerase (RdRp). We anticipate that our approach for identification of multi-target-directed ligand will provide new avenues for drug discovery against SARS-CoV-2 infection. Communicated by Ramaswamy H. Sarma

10aCoronavirus10aCOVID-1910ahACE-210aMPro10amulti-target-directed ligand10aprotease inhibitor10aRdRp10aSARS-CoV-2 virus1 aJoshi, Rakesh, S.1 aJagdale, Shounak, S.1 aBansode, Sneha, B.1 aShankar, Shiva1 aTellis, Meenakshi, B.1 aPandya, Vaibhav, Kumar1 aChugh, Anita1 aGiri, Ashok, P.1 aKulkarni, Mahesh, J. uhttps://library.ncl.res.in/content/discovery-potential-multi-target-directed-ligands-targeting-host-specific-sars-cov-202638nas a2200277 4500008004100000022001400041245011500055210006900170260000900239300001100248490000900259520174400268653000802012653001302020653001402033653001802047653001202065653000902077100002202086700002302108700002102131700003202152700002202184700002502206856012902231 2021 eng d a0925-443900aMolecular investigation of glycated insulin-induced insulin resistance via insulin signaling and AGE-RAGE axis0 aMolecular investigation of glycated insulininduced insulin resis cFEB  a1660290 v18673 a

Hyperglycemic condition in diabetes promotes glycation of various plasma proteins including insulin. Glycation of insulin has been reported to reduce its biological activity. Reduced biological activity of glycated insulin could be either due to reduced affinity for the insulin receptor and impaired insulin signaling, or it can act as a ligand for the receptor for advanced glycation end products (RAGE) and activates oxidative stress and pro-inflammatory pathways leading to insulin resistance. This study investigates the effect of glycated insulin on both insulin and RAGE signaling. Glycated insulin treatment to Chinese hamster ovary (CHO-IR-GLUT4) cells stably expressing insulin receptor (IR) and glucose transporter fused with a green fluorescent protein (GLUT4-GFP) resulted in the impairment of insulin signaling, as the phosphorylation of IR and AKT significantly reduced, which affected GLUT4 translocation and glucose uptake. Moreover, it also activated RAGE signaling as observed by increased expression of NADPH oxidase accompanied by an increase in reactive oxygen species (ROS). Immunofluorescence study indicated the translocation of NF-kappa B to the nucleus upon treatment of glycated insulin. This was associated with increased RAGE expression, Caspase 3, and cell death. Downregulation of RAGE with the losartan treatment restored the impaired insulin signaling and glucose uptake. Additionally, in silico study demonstrated that glycated insulin has reduced binding affinity to insulin receptor and increased binding affinity to RAGE. Overall, this study demonstrates the role of glycated insulin in exacerbating insulin resistance by impairing insulin signaling as well as stimulating AGE-RAGE signaling.

10aAGE10aDiabetes10aGlycation10aHyperglycemia10ainsulin10aRAGE1 aWalke, Prachi, B.1 aBansode, Sneha, B.1 aMore, Nikita, P.1 aChaurasiya, Arvindkumar, H.1 aJoshi, Rakesh, S.1 aKulkarni, Mahesh, J. uhttps://library.ncl.res.in/content/molecular-investigation-glycated-insulin-induced-insulin-resistance-insulin-signaling-and