CXCR4 as possible druggable target linking inflammatory bowel disease and Parkinson's disease.

Parkinson's disease (PD) is a chronic, progressive, and second most prevalent neurological disorder affecting the motor system. It has been found that people suffering with inflammatory bowel disease (IBD) are at 22% more risk for PD. In the current study, we have established a molecular link between gut and brain. The microarray gene expression datasets of Homo sapiens were obtained from Gene Expression Omnibus Database. Major genes involved in gut-brain connection were found to be CXCR4, LRRK2, APOE, SNCA, IL6, HIF-1α, ABCA1 etc. The common biological pathways linking both the pathologies were found to be HIF-signaling, cytokines interactions, JAK-STAT pathway, cholesterol metabolism, apoptosis and CXCR4 signaling which modulates the synaptic function and neuronal survival in the mature brain. It is known that flavonoid-rich foods throughout life hold the potential to limit the inflammation, neurodegeneration and, to prevent the age-dependent cognitive impairment. Therefore, the potential receptor, CXCR4 was used further for docking with twenty-seven phytochemicals from 5 different classes of Flavonoids found in several dietary items. Docking studies of the top scoring compounds were compared with a known inhibitor (BPRCX807) of receptor CXCR4 (IC50 = 40.4 ± 8.0 nM). The study indicates that Flavan-3-ol families of flavonoids are the best fit and finest dietary supplements for improving brain health. Hence the food items like Pistachio nuts, hazelnuts, Green Tea, walnuts, etc. should be incorporated more in the diet of healthy people as well as in IBD and PD patients to prevent inflammation in gut and brain damage from oxidative stress.

An in silico approach to identify potential medicinal plants for treating Alzheimer disease: a case study with acetylcholinesterase.

Alzheimer's disease (AD) is a progressive neurological disorder affecting an estimated 10 million people worldwide. There is no cure for AD, and only a handful of drugs are known to provide some relief of the symptoms. The prescription drug donepezil has been widely used to treat to slow the progression and onset of the disease; however, the unpleasant side effects have paved the way to find alternative medicines. Many herbs are known to improve brain function, but evidence of medicinal plants that can treat AD is limited due to the lack of concrete rational evidences. Moreover, the traditional method of randomly screening plant extract against AD targets takes time and resources. In this study, a receptor-based in silico method has been implemented which serves to accelerate the process of identification of medicinal plants useful for treatment of AD. A database of natural compounds was compiled to identify hits against acetylcholinesterase (AChE). Receptor-based pharmacophore screening was performed, and selected hits were subjected to docking and molecular dynamics simulations. Molecular Mechanics/Generalized Born surface area (MM/GBSA) calculations were carried out to identify the best scoring hits further. In vitro assays were done for the plant extracts containing the top-scoring hits against AChE. Three plant extracts showed favorable inhibitory activity.Communicated by Ramaswamy H. Sarma.

RAPD, ISSR, and SCoT markers based genetic stability assessment of micropropagated Dendrobium fimbriatum Lindl. var. oculatum Hk. f.- an important endangered orchid.

Dendrobium fimbriatum is an ornamental and medicinal orchid listed in the Red data book of IUCN. Phytohormones' effect on the in vitro regeneration of the orchid was studied using Mitra medium supplemented with different growth regulators. KN produced effective shoot formation when present alone or in combination with IBA or NAA. The shooting was gradually increased when KN concentration was increased from 0.8 to 4.8 mg L-1, but the opposite response was observed with BAP at higher concentration (4.8 mg L-1). IBA either in combination with BAP or KN promoted effective root development and multiplication. Micropropagated orchids grown in the basal medium devoid of any phytohormone showed 100% monomorphism, while low genetic polymorphism of 1.52% (RAPD-Random Amplification of Polymorphic DNA), 1.19% (ISSR-Inter Simple Sequence Repeat) and 3.97% (SCoT-Start Codon Targeted) was exhibited among the regenerants propagated in the hormone enriched medium. UPGMA (Unweighted pair group method using arithmetic averages) dendrograms showed the grouping of mother plant (MP) with the in vitro regenerants. The principal coordinate analysis (PCoA) further confirmed the clustering patterns as determined by the cluster analysis. The study reported for the first time the successful in vitro propagation of Dendrobium fimbriatum and their genetic stability assessment using molecular markers.

Discovery of dual cation-π inhibitors of acetylcholinesterase: design, synthesis and biological evaluation.

BACKGROUND: Alzheimer's disease (AD) is a widespread dementia-related disease affecting mankind worldwide. A cholinergic hypothesis is considered the most effective target for treating mild to moderate AD. Present study aims to identify new scaffolds for inhibiting acetylcholinesterase activity. METHODS: To find Acetylcholinesterase (AChE) inhibitors, we computationally designed and chemically synthesized a series of cation-π inhibitors based on novel scaffolds that potentially block AChE. The cytotoxic effect of inhibitors were determined by MTT. AChE inhibition experiment was performed by Ellman and the Amplex red method in the SH-SY5Y cell line. Further, the experimental data on designed compounds corroborate with various computational studies that further elucidate the binding mode of interactions and binding affinity. RESULTS: The inhibitors were designed to promote dual binding and were incorporated with groups that may facilitate any of the cation- π, hydrophobic and hydrogen-bonding interactions with the conserved and hot-spot residues in the binding site. The inhibitors possessing pyridine-N-methylated pyridinium group and thereby involved in cation- π interactions are highly active relative to the marketed drug Donepezil as well as the designed analogs that lack the group. In vitro enzymatic Ellman assay and Amplex red assay on SH-SY5Y cell line estimated IC50 of the designed compounds in nM range with one having binding affinity higher than Donepezil. Compounds exhibit no significant toxicity up to µM range. CONCLUSIONS: Compounds possessing methylidenecyclohexanone scaffolds, with characteristic dual-binding and involving strong cation-π interactions, serves as new leads for AChE and opens a new direction for drug discovery efforts.

Efficiency of RAPD, ISSR, iPBS, SCoT and phytochemical markers in the genetic relationship study of five native and economical important bamboos of North-East India.

10 primers each of random amplified polymorphic DNA (RAPD), inter-simple sequence repeats (ISSR), inter primer binding site (iPBS) and start codon targeted (SCoT) were used to analyze genetic polymorphism and relationship between 50 genotypes of 5 economical important native bamboos (Bambusa cacharensis, B. mizorameana, Dendrocalamus manipureanus, D. hamiltonii and D. sikkimensis) of North-East India. The 40 different primers generated 111, 115, 116 and 138 polymorphic bands for RAPD, ISSR, iPBS and SCoT markers respectively. The comparative analysis of 4 marker systems based on polymorphic information content (PIC), effective multiplex ratio (EMR) and marker index (MI) values showed SCoT to be more informative with higher discriminating power than the other three markers. The correlation value (r) as determined by the Mantel test ranged from 0.60 (SCoT and RAPD) to 0.83 (iPBS and ISSR) indicating a high positive correlation between the markers. The close correspondence between the genetic matrices of RAPD, ISSR, iPBS and SCoT markers revealed the effectiveness of each marker system in determining the genetic relationship between bamboos. UPGMA (Unweighted Pair Group Arithmetic Mean Method) dendrograms generated from DNA marker analysis demonstrated species-specific clustering of different bamboo genotypes. Except for RAPD, the dendrograms of ISSR, iPBS and SCoT markers also showed a close association of bamboo genotypes based on geographical origin. Principal coordinate analysis (PCoA) revealed the distribution of different bamboo genotypes in accordance with the cluster analysis. The cluster grouping based on phytochemical study not only discriminated the different bamboo species but also illustrated a location-specific grouping of the genotypes. The bamboo clustering pattern derived from phytochemical analysis matched closely with the dendrograms generated by the DNA markers. The present investigation established the possibility of using a combined molecular and phytochemical marker approach to determine the genetic relationship between 5 native bamboos of North-East India with high precision.

The anti-oxidant enzyme, Prdx6 might have cis-acting regulatory sequence(s).

Peroxiredoxin 6 (Prdx6) is a ubiquitously expressed 1-cysteine Peroxiredoxin found throughout all phyla. In mammals, under different physiological conditions, it has evolved from a peroxidase to a multifunctional enzyme. Among the mammalian Prdx6's, human and rat Prdx6's are the most extensively studied. Our study revealed that human and rat Prdx6's exhibit differences in their peroxidase activity. These two Prdx6's have only 8% difference in their primary sequence (with 19 amino acids) with no apparent modification at any of the key conserved residues. In the present communication, we have investigated the roles of thermodynamics, structure and internal flexibility of Prdx6 to account for the difference in their peroxidase activity. We discovered that these amino acid variations have led to structural alterations in human Prdx6 so that it shows enhanced intrinsic dynamics (or flexibility) than the rat protein. We could also identify the gain of intrinsic dynamics of the catalytic site in human Prdx6 due to relocation of an important active site residue (R132) to the loop region as the most plausible reason for high catalytic activity in the human protein as compared to rat variant. Since it is the thioredoxin fold that upholds the peroxidase function, certain structural alteration in the Prdx6 structure might help to regulate the efficiency of thioredoxin folds. Our results hint that Prdx6 might have a cis-acting regulatory sequence(s).

Discovery of sulfone-resistant dihydropteroate synthase (DHPS) as a target enzyme for kaempferol, a natural flavanoid.

Kaempferol is a ubiquitous flavonoid, found in various plants having a wide range of known pharmacological activities, including antioxidant, antiinflammatory, anticancer, antiallergic, antidiabetic, neuroprotective, cardioprotective and antimicrobial activities. Nonetheless various evidence suggest that kaempferol is also able to interact with many unknown therapeutic targets modulating signalling pathways, thus providing an opportunity to explore the potential target space of kaempferol. In this study, we have employed various ligand-based approaches to identify the potential targets of kaempferol, followed by validations using modelling and docking studies. Molecular dynamics, free energy calculations, volume and residue contact map analyses were made to delineate the cause of drug-resistance among mutants. We have discovered dihydropteroate synthase (DHPS) as a novel potential therapeutic target for kaempferol. Further studies employing molecular dynamics simulations and binding free energies indicate that kaempferol has potential to inhibit even the sulfone-resistant DHPS mutants, which makes it a very attractive antibiotic agent. The identification of natural-product based kaempferol opens up the door for the design of antibiotics in a quick and high throughput fashion for identifying antibiotic leads.

Studies on conformational changes induced by binding of pendimethalin with human serum albumin.

Pendimethalin (PND) is a widely used herbicide in modern means of agricultural practices. So, its toxic residues exist extensively in the environment and can enter human body. Therefore, the in vitro interaction of PND with human serum albumin (HSA) has been explored by employing various biophysical, molecular docking and dynamics simulation studies as well as enzyme kinetics to unravel its binding mechanism. The binding constant of the PND-HSA complex was about 104 M-1 using Fluorescence quenching spectra. The negative value of Gibbs free energy change (ΔG0 = -32.0 kJ mol-1) indicates this interaction is a spontaneous process. A large negative ΔH0 and positive ΔS0 suggests that hydrophobic interactions and H-bonding are involved in the binding process of PND with HSA. The binding of PND can cause conformational and micro-environmental changes in HSA molecule, as shown by various biophysical and molecular dynamics simulation studies. The site marker competition and molecular docking and simulation experiments affirmed that the binding of PND to HSA occurs at or near site I. Esterase-like activity of HSA exhibited decline in the presence of PND revealed the direct involvement of Lys199 of subdomain IIA (Sudlow's site I) in the binding process.

MedPServer: A database for identification of therapeutic targets and novel leads pertaining to natural products.

Natural products have been the source of treatment for various human diseases from time immemorial. Interests in natural product-based scaffolds for the discovery of modern drugs have grown in recent years. However, research on exploring the traditional medicinal systems for modern therapeutics is severely limited due to our incomplete understanding of the therapeutic mechanism of action. One possible solution is to develop computational approaches, based on ligand- and structure-based screening tools, for fast and plausible target identification, leading to elucidation of the therapeutic mechanism. In the present work, we present two methods based on shape-based and pharmacophore search to predict targets of natural products and elucidate their mechanism, and to identify natural product-based leads. These methods were tested on an in-house developed database of medicinal plants that include information from a largely unexplored North-East region of India, known as one of the twelve mega biodiversity regions. However, depending on the choice of the lead molecules, any existing databases can be used for screening. MedPServer is an open access resource available at http://bif.uohyd.ac.in/medserver/.

3D-QSAR and molecular docking studies of 2-pyrimidinecarbonitrile derivatives as inhibitors against falcipain-3.

The three dimensional-quantitative structure activity relationship (3D-QSAR) studies were performed on a series of falcipain-3 inhibitors using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) techniques. A training set containing 42 molecules served to establish the QSAR models. The optimum CoMFA and CoMSIA models obtained for the training set were statistically significant with cross-validated correlation coefficients r(cv)(2) (q(2)) of 0.549 and 0.608, and conventional correlation coefficients (r(2)) of 0.976 and 0.932, respectively. An independent test set of 12 molecules validated the external predictive power of both models with predicted correlation coefficients (r(pred)(2)) for CoMFA and CoMSIA as 0.697 and 0.509, respectively. The docking of inhibitors into falcipain-3 active site using GOLD software revealed the vital interactions and binding conformation of the inhibitors. The CoMFA and CoMSIA field contour maps agree well with the structural characteristics of the binding pocket of falcipain-3 active site, which suggests that the information rendered by 3D-QSAR models and the docking interactions can provide guidelines for the development of improved falcipain-3 inhibitors.