Kripamoy Aguan

Discovery of Protein Phosphorylation Motifs through Exploratory Data Analysis

Background The need for efficient algorithms to uncover biologically relevant phosphorylation motifs has become very important with rapid expansion of the proteomic sequence database along with a plethora of new information on phosphorylation sites. Here we present a novel unsupervised method, called Motif Finder (in short, F-Motif) for identification of phosphorylation motifs. F-Motif uses clustering of sequence information represented by numerical features that exploit the statistical information hidden in some foreground data. Furthermore, these identified motifs are then filtered to find “actual” motifs with statistically significant motif scores. Results and Discussion We have applied F-Motif to several new and existing data sets and compared its performance with two well known state-of-the-art methods. In almost all cases F-Motif could identify all statistically significant motifs extracted by the state-of-the-art methods. More importantly, in addition to this, F-Motif uncovers several novel motifs. We have demonstrated using clues from the literature that most of these new motifs discovered by F-Motif are indeed novel. We have also found some interesting phenomena. For example, for CK2 kinase, the conserved sites appear only on the right side of S. However, for CDK kinase, the adjacent site on the right of S is conserved with residue P. In addition, three different encoding methods, including a novel position contrast matrix (PCM) and the simplest binary coding, are used and the ability of F-motif to discover motifs remains quite robust with respect to encoding schemes. Conclusions An iterative algorithm proposed here uses exploratory data analysis to discover motifs from phosphorylated data. The effectiveness of F-Motif has been demonstrated using several real data sets as well as using a synthetic data set. The method is quite general in nature and can be used to find other types of motifs also. We have also provided a server for F-Motif at http://f-motif.classcloud.org/, http://bio.classcloud.org/f-motif/ or http://ymu.classcloud.org/f-motif/.

A coumarin based Schiff base probe for selective fluorescence detection of Al3 + and its application in live cell imaging

A new coumarin based Schiff base compound, CSB-1 has been synthesized to detect metal ion based on the chelation enhanced fluorescence (CHEF). The cation binding properties of CSB-1 was thoroughly examined in UV-vis and fluorescence spectroscopy. In fluorescence spectroscopy the compound showed high selectivity toward Al3+ ion and the Al3+ can be quantified in mixed aqueous buffer solution (MeOH: 0.01M HEPES Buffer; 9:1; v/v) at pH7.4 as well as in BSA media. The fluorescence intensity of CSB-1 was enhanced by ~24 fold after addition of only five equivalents of Al3+. The fluorescence titration of CSB-1 with Al3+ in mixed aqueous buffer afforded a binding constant, Ka=(1.06±0.2)×104M-1. The colour change from light yellow to colourless and the appearance of blue fluorescence, which can be observed by the naked eye, provides a real-time method for Al3+ sensing. Further the live cell imaging study indicated that the detection of intracellular Al3+ ions are also readily possible in living cell.

Highly Sensitive Bifunctional Probe for Colorimetric Cyanide and Fluorometric H2S Detection and Bioimaging: Spontaneous Resolution, Aggregation, and Multicolor Fluorescence of Bisulfide Adduct

A 4-methylbenzothiazole linked maleimide-based single molecular bifunctional probe 1 has been synthesized for the colorimetric and fluorometric detection of highly competitive H2S and cyanide ion in aqueous DMSO media. The probe 1 selectively detected CN- under the UV-vis spectroscopy through the rapid appearance of deep pink color. The bright pink color developed due to ICT in the moderately stable cyano substituted enolate intermediate. The absorbance titration of 1 with CN- revealed a new band at 540 nm and the nonlinear curve fitting analysis showed good fit with 1:1 model. In fluorescence channel, 1 was found to be highly selective to H2S in 50% aqueous buffer (pH 7). It exhibited ∼16-fold fluorescence intensity enhancement at 435 nm after reaction with 1 equiv of H2S due to the inhibition of PET. The 1-SH adduct showed TICT phenomenon and behaved like molecular rotor. It further displayed aggregation behavior at higher concentration and excitation wavelength dependent multicolor emission properties. Most interestingly, the spontaneous resolution of chiral S-isomer of the 1-SH adduct occurred during crystallization. The cell imaging study revealed the staining of the cell and multicolor emission in the presence of H2S.

Identification of single- and multiple-class specific signature genes from gene expression profiles by group marker index.

Informative genes from microarray data can be used to construct prediction model and investigate biological mechanisms. Differentially expressed genes, the main targets of most gene selection methods, can be classified as single- and multiple-class specific signature genes. Here, we present a novel gene selection algorithm based on a Group Marker Index (GMI), which is intuitive, of low-computational complexity, and efficient in identification of both types of genes. Most gene selection methods identify only single-class specific signature genes and cannot identify multiple-class specific signature genes easily. Our algorithm can detect de novo certain conditions of multiple-class specificity of a gene and makes use of a novel non-parametric indicator to assess the discrimination ability between classes. Our method is effective even when the sample size is small as well as when the class sizes are significantly different. To compare the effectiveness and robustness we formulate an intuitive template-based method and use four well-known datasets. We demonstrate that our algorithm outperforms the template-based method in difficult cases with unbalanced distribution. Moreover, the multiple-class specific genes are good biomarkers and play important roles in biological pathways. Our literature survey supports that the proposed method identifies unique multiple-class specific marker genes (not reported earlier to be related to cancer) in the Central Nervous System data. It also discovers unique biomarkers indicating the intrinsic difference between subtypes of lung cancer. We also associate the pathway information with the multiple-class specific signature genes and cross-reference to published studies. We find that the identified genes participate in the pathways directly involved in cancer development in leukemia data. Our method gives a promising way to find genes that can involve in pathways of multiple diseases and hence opens up the possibility of using an existing drug on other diseases as well as designing a single drug for multiple diseases.

Identification of molecular descriptors for design of novel Isoalloxazine derivatives as potential Acetylcholinesterase inhibitors against Alzheimer's disease.

In Alzheimer’s disease (AD), the level of Acetylcholine (ACh) neurotransmitter is reduced. Since Acetylcholinesterase (AChE) cleaves ACh, inhibitors of AChE are very much sought after for AD treatment. The side effects of current inhibitors necessitate development of newer AChE inhibitors. Isoalloxazine derivatives have proved to be promising (AChE) inhibitors. However, their structure–activity relationship studies have not been reported till date. In the present work, various quantitative structure–activity relationship (QSAR) building methods such as multiple linear regression (MLR), partial least squares ,and principal component regression were employed to derive 3D-QSAR models using steric and electrostatic field descriptors. Statistically significant model was obtained using MLR coupled with stepwise selection method having r2 = .9405, cross validated r2 (q2) = .6683, and a high predictability (pred_r2 = .6206 and standard error, pred_r2se = .2491). Steric and electrostatic contribution plot revealed three electrostatic fields E_496, E_386 and E_577 and one steric field S_60 contributing towards biological activity. A ligand-based 3D-pharmacophore model was generated consisting of eight pharmacophore features. Isoalloxazine derivatives were docked against human AChE, which revealed critical residues implicated in hydrogen bonds as well as hydrophobic interactions. The binding modes of docked complexes (AChE_IA1 and AChE_IA14) were validated by molecular dynamics simulation which showed their stable trajectories in terms of root mean square deviation and molecular mechanics/Poisson–Boltzmann surface area binding free energy analysis revealed key residues contributing significantly to overall binding energy. The present study may be useful in the design of more potent Isoalloxazine derivatives as AChE inhibitors.

Ruthenium(II) Complex-Based Luminescent Bifunctional Probe for Ag+ and Phosphate Ions: Ag+-Assisted Detection and Imaging of rRNA

A new bis-heteroleptic Ru(II) complex (1) of benzimidazole-substituted 1,2,3-triazole pyridine ligand has been designed and constructed for the photoluminescent detection of cationic and anionic analytes, Ag+ and phosphate ions. Compound, 1[PF6]2 was fully characterized by various spectroscopic techniques and the solid-state structure was determined via single-crystal X-ray diffraction. The cation and anion sensing properties in 50% aqueous buffer (pH 9.2) and pure acetonitrile were carefully examined in photoluminescence (PL) spectroscopy. The 1[PF6]2 was found to be highly selective to pyrophosphate; PPi/HP2O73- and H2PO4- ions in CH3CN. It showed ∼10-fold PL intensity enhancement at 583 nm in the presence of only 1 and 2 equiv of PPi and H2PO4- ions, respectively. The PL titrations of 1[PF6]2 with PPi and H2PO4- in CH3CN furnished the association constant (Ka = 3.3 × 103 M-1 and 6.8 × 103 M-1) and the detection limit was as low as 5.73 and 5.19 ppb, respectively. The 1[PF6]2 also selectively detected Ag+ over other competitive cations through the luminescence light up in 50% aqueous buffer (pH 9.2) media. The PL titration of 1[PF6]2 with Ag+ showed ∼8-fold luminescence enhancement at 591 nm and yielded association constant, Ka = 3.5 × 104 M-1 and the detection limit was determined to be 5.05 ppb. A new cation sensing mechanism has been established where the Ag+ ion is detected in photoluminescence spectroscopy through the unique cyclometalated Ag+-triazolide complex formation. The high selectivity of 1[PF6]2 for phosphates and Ag+ was established by PL in the presence of various competing ions. Finally, for biological application, the cytotoxicity study was performed. The probe showed low cytotoxicity and was suitable for intracellular Ag+ imaging. The cell imaging and in vitro photoluminescence study revealed that the probe stained the cell nucleoli and specifically bind with ribosomal RNA (rRNA) and, therefore, it can also serve as a luminescent probe for rRNA in the presence of Ag+.

Pyruvate dehydrogenase complex deficiency and its relationship with epilepsy frequency--An overview.

The pyruvate dehydrogenase complex (PDHc) is a member of a family of multienzyme complexes that provides the link between glycolysis and the tricarboxylic acid (TCA) cycle by catalyzing the physiologically irreversible decarboxylation of various 2-oxoacid substrates to their corresponding acyl-CoA derivatives, NADH and CO2. PDHc deficiency is a metabolic disorder commonly associated with lactic acidosis, progressive neurological and neuromuscular degeneration that vary with age and gender. In this review, we aim to discuss the relationship between occurrence of epilepsy and PDHc deficiency associated with the pyruvate dehydrogenase complex (E1α subunit (PDHA1) and E1β subunit (PDHB)) and PDH phosphatase (PDP) deficiency. PDHc plays a crucial role in the aerobic carbohydrate metabolism and regulates the use of carbohydrate as the source of oxidative energy. In severe PDHc deficiency, the energy deficit impairs brain development in utero resulting in physiological and structural changes in the brain that contributes to the subsequent onset of epileptogenesis. Epileptogenesis in PDHc deficiency is linked to energy failure and abnormal neurotransmitter metabolism that progressively alters neuronal excitability. This metabolic blockage might be restricted via inclusion of ketogenic diet that is broken up by β-oxidation and directly converting it to acetyl-CoA, and thereby improving the patients health condition. Genetic counseling is essential as PDHA1 deficiency is X-linked. The demonstration of the X-chromosome localization of PDHA1 resolved a number of questions concerning the variable phenotype displayed by patients with E1 deficiency. Most patients show a broad range of neurological abnormalities, with the severity showing some dependence on the nature of the mutation in the Elα gene, while PDHB and PDH phosphatase (PDP) deficiencies are of autosomal recessive inheritance. However, in females, the disorder is further complicated by the pattern of X-chromosome inactivation, i.e., unfavorable lyonization. Furthermore research should focus on epileptogenic animal models; this might pave a new way toward identification of the pathophysiology of this challenging disorder.

Human serum albumin reduces the potency of acetylcholinesterase inhibitor based drugs for Alzheimer's disease

Human serum albumin (HSA) induced modulation of acetylcholinesterase (AChE) inhibition activity of four well-known cholinergic inhibitors like tacrine hydrochloride (TAC), donepezil hydrochloride monohydrate (DON), (-) Huperzine A (HuPA), eserine (ESE) was monitored quantitatively by Ellmans method. Kinetic analysis of enzyme hydrolysis reaction revealed that while the mechanism of inhibition does not change significantly, the inhibition efficiency changes drastically in presence of HSA, particularly for DON and TAC. However, interestingly, no notable difference was observed in the cases of HuPA and/or ESE. For example, the IC50 value of AChE inhibition increases by almost 135% in presence of ∼250 μM HSA (IC50 = 159 ± 8 nM) while comparing with aqueous buffer solution of pH 8.0 (IC50 = 68 ± 4 nM) in DON. On the other hand, the change is almost insignificant (<10%) in case of HuPA under the similar condition. The experimentally observed difference in the extent of modulatory effect was correlated with the sequestration ability of HSA towards different drugs predicted from molecular docking calculations. The result in this study demonstrates the importance to consider the plasma protein binding tendency of a newly synthesized AD drug before claiming its potency over the existing one. Further, development of new and intelligent delivery medium that shields the administered drugs from serum adsorption may reduce the optimal drug dose requirement.

Correlation of cholinergic drug induced quenching of acetylcholinesterase bound thioflavin-T fluorescence with their inhibition activity

The development of new acetylcholinesterase inhibitors (AChEIs) and subsequent assay of their inhibition efficiency is considered to be a key step for AD treatment. The fluorescence intensity of thioflavin-T (ThT) bound in the active site of acetylcholinesterase (AChE) quenches substantially in presence of standard AChEI drugs due to the dynamic replacement of the fluorophore from the AChE active site as confirmed from steady state emission as well as time-resolved fluorescence anisotropy measurement and molecular dynamics simulation in conjunction with docking calculation. The parametrized % quenching data for individual system shows excellent correlation with enzyme inhibition activity measured independently by standard Ellman AChE assay method in a high throughput plate reader system. The results are encouraging towards design of a fluorescence intensity based AChE inhibition assay method and may provide a better toolset to rapidly evaluate as well as develop newer AChE-inhibitors for AD treatment.

Aggregation-Induced Emission-Active Ruthenium(II) Complex of 4,7-Dichloro Phenanthroline for Selective Luminescent Detection and Ribosomal RNA Imaging

The development of red emissive aggregation-induced emission (AIE) active probes for organelle-specific imaging is of great importance. Construction of metal complex-based AIE-active materials with metal-to-ligand charge transfer (MLCT), ligand-to-metal charge transfer (LMCT) emission together with the ligand-centered and intraligand (LC/ILCT) emission is a challenging task. We developed a red emissive ruthenium(II) complex, 1[PF6]2, and its perchlorate analogues of the 4,7-dichloro phenanthroline ligand. 1[PF6]2 has been characterized by spectroscopic and single-crystal X-ray diffraction. Complex 1 showed AIE enhancement in water, highly dense polyethylene glycol media, and also in the solid state. The possible reason behind the AIE property may be the weak supramolecular π···π, C-H···π, and C-Cl···H interactions between neighboring phen ligands as well as C-Cl···O halogen bonding (XB). The crystal structures of the two perchlorate analogues revealed C-Cl···O distances shorter than the sum of the van der Waals radii, which confirmed the XB interaction. The AIE property was supported by scanning electron microscopy, transmission electron microscopy, dynamic light scattering, and atomic force microscopy studies. Most importantly, the probe was found to be low cytotoxicity and to efficiently permeate the cell membrane. The cell-imaging experiments revealed rapid staining of the nucleolus in HeLa cells via the interaction with nucleolar ribosomal ribonucleic acid (rRNA). It is expected that the supramolecular interactions as well as C-Cl···O XB interaction with rRNA is the origin of aggregation and possible photoluminescence enhancement. To the best of our knowledge, this is the first report of red emissive ruthenium(II) complex-based probes with AIE characteristics for selective rRNA detection and nucleolar imaging.