Interactome based biomarker discovery for irritable bowel syndrome-A systems biology approach.

Irritable bowel syndrome (IBS) is a common functional gastrointestinal (GI) disorder around world with no standard therapy. Till date, the pathophysiology of IBS is not clearly understood due to complexity of the disease. Current study reveals the underlying mechanism of IBS using systems biological approach. The complexity of IBS was explained by constructing protein-protein interaction (PPI) network from the text mined genes/proteins. PPI network displayed 68822 interactions from 3595 proteins. IBS interactome was mapped with colon tissue interactome which resulted in a sub-network containing 153 genes. Further, MCL algorithm was applied to sub-network to identify six major clusters. These cluster genes are involved in several pathways such as MAPK, PI3K/Akt, and NF-kappa B. The obtained clustered genes were prioritized using differentially expressed transcriptome data of 45 IBS and 45 normal volunteers. Among the differentially expressed genes, FUS, UNC5CL and BCLAF1 were found in the clusters, suggesting that the identified clusters could play a potential role in the regulation of IBS. Further pathway analysis of cluster genes revealed their molecular association with IBS. Gene prioritization studies identified top 10 genes that can be used as candidate biomarkers for early diagnosis of IBS. Out of top ten genes, PRPF31 was expressed in all biofluids (serum, saliva and urine).

Whole genome sequencing of Oryza sativa L. cv. Seeragasamba identifies a new fragrance allele in rice.

Fragrance of rice is an important trait that confers a large economic benefit to the farmers who cultivate aromatic rice varieties. Several aromatic rice varieties have limited geographic distribution, and are endowed with variety-specific unique fragrances. BADH2 was identified as a fragrance gene in 2005, and it is essential to identify the fragrance alleles from diverse geographical locations and genetic backgrounds. Seeragasamba is a short-grain aromatic rice variety of the indica type, which is cultivated in a limited area in India. Whole genome sequencing of this variety identified a new badh2 allele (badh2-p) with an 8 bp insertion in the promoter region of the BADH2 gene. When the whole genome sequences of 76 aromatic varieties in the 3000 rice genome project were analyzed, the badh2-p allele was present in 13 varieties (approximately 17%) of both indica and japonica types. In addition, the badh2-p allele was present in 17 varieties that already had the loss-of-function allele, badh2-E7. Taken together, the frequency of badh2-p allele (approximately 40%) was found to be greater than that of the badh2-E7 allele (approximately 34%) among the aromatic rice varieties. Therefore, it is suggested to include badh2-p as a predominant allele when screening for fragrance alleles in aromatic rice varieties.

Identification of novel selective MMP-9 inhibitors as potential anti-metastatic lead using structure-based hierarchical virtual screening and molecular dynamics simulation.

MMP-9 is an attractive target for the development of new anticancer drugs. In the current study, pharmacophore modeling was employed using two highly active and selective gelatinase inhibitors obtained from two X-ray crystal structures (PDB IDs: and ) to identify novel selective MMP-9 inhibitors. The derived model was refined manually and also validated by the GH scoring method. The refined pharmacophore model, ADRR, was able to retrieve 86% of actives with a GH score of 0.774, indicating that the model was capable of retrieving the active MMP-9 inhibitors. ADRR was used to screen 2 838 166 unique structures. Hit filtration was carried out using a fitness score >1.5 and drug-likeness properties. Hierarchical clustering generates 33 clusters based on diversity. A total of 33 molecules were obtained and these molecules were taken for cross-docking studies with 5 subtype MMPs. Among 33 tested, 2 molecules, P10A-0000088030 (Lig-1) and P10A-0001383812 (Lig-2), were found to have the highest docking scores (-8.59 kcal mol(-1) and -8.27 kcal mol(-1)) towards MMP-9 compared with the other MMPs. Further MM-GBSA analysis was performed for two hits with 5 subtype MMPs to reveal the essential features that contribute to selectivity. The results showed that van der Waals contributions play a central role in determining the selectivity of MMP-9 inhibitors. Molecular dynamics studies were carried out for total time of 330 ns to assess the stability of ligands at the active site. MD analysis showed that binding of Lig-1 with MMP-9 is stable compared to that with Lig-2. Hence, we suggest the Lig-1 compound as a good lead in designing novel potent inhibitors of MMP-9.

Synthesis, characterization, antiproliferative and molecular docking study of new half sandwich Ir(III), Rh(III) and Ru(II) complexes.

The new carbazole N,N' ligand containing [(η(5)-C5Me5)MCl(L)]PF6, (M=Ir (1) and Rh (2)) and [(η(6)-C6H6)RuCl(L)]PF6 (3) (C5Me5=pentamethylcyclopentadienyl, L=9-ethyl-N-(pyridine-2-yl methylene)-9H-carbazole-3-amine) complexes has been synthesized and characterized by (1)H NMR, (13)C NMR, 2D NMR, melting point analysis, electronic absorption, infrared spectroscopy, HR-Mass spectroscopy and elemental analyses. The crystal structure of the [(η(5)-C5Me5)RhCl(L)]PF6 has been confirmed by single crystal XRD. The anticancer study of the synthesized complexes 1-3 clearly showed a potent inhibitor of human breast cancer cells (MCF-7) under in vitro conditions. The inhibitory concentrations (IC50) of the complexes 1-3 were determined at low (5, 6 and 8µM) concentration against the MCF-7 human breast cancer cell line. Further cytotoxic, cell cycle and nuclear studies confirmed that the novel half sandwich Ir(III), Rh(III) and Ru(II) complexes could be effective against MCF-7 human breast cancer cell proliferation. Moreover the results indicate that anticancer in vitro activity of complexes 1-3 falls in the order of 1>2>3. A molecular docking study of the complexes 1-3 showed the nature of binding energy, H-bond and hydrophobic interactions with the cyclooxygenase-2 (COX-2) receptor.

Identification of Potent Virtual Leads Specific to S1' Loop of ADAMTS4: Pharmacophore Modeling, 3D-QSAR, Molecular Docking and Dynamic Studies.

ADAMTS4 (Aggrecanase-1) is an important enzyme, which belongs to ADAMTS family. Aggrecanase-1 is involved in aggrecan degradation of articular cartilage in osteoarthritis and rheumatoid arthritis. Overall variability of S1' domain of ADAMTS4 has been the main selectivity determinant to design the unique inhibitors. 34 inhibitors from Binding database and literature were used to develop the pharmacophore model. The five featured pharmacophore model AHHRR had the best survival score of 3.493 and post-hoc score of 2.545, indicating that the model is highly reliable. The 3D-QSAR acquired had excellent r(2) value of 0.99 and GH score of 0.839. The validated pharmacophore model was used for insilico screening of Asinex and ZINC database for finding the potential lead compounds. ZINC00987406 and ASN04459656 which pose high glide score i.e >7 Kcal/mol and H-bond and hydrophobic interactions in the S1'loop residues of ADAMTS4 were subjected to Molecular Dynamics Simulation studies. Molecular dynamic simulation result indicates that the RMSD and RMSF of backbone atoms for the above complexes were within the limit of 2.0 A˚. These compounds can be potential candidates for osteoarthritis by inhibiting ADAMTS4.

Homology modeling and in silico site directed mutagenesis of pyruvate ferredoxin oxidoreductase from Clostridium thermocellum.

Pyruvate ferredoxin oxidoreductase is the crucial enzyme that involves in bioethanol synthesis pathway of Clostridium thermocellum. It is an ethanologenic organism but has been investigated less on its enzyme structure. The amino acid sequence of Pyruvate ferredoxin oxidoreductase was derived from UNIPROT and the screened crystal structure was taken as the template for homology modeling using MODELLER 9V11. The model was loop refined and was validated using RMSD, ProSA and PROCHECK. The docking and per residue interaction studies were carried out to elucidate the interaction energies of amino acid residues with pyruvate. To enhance the binding of pyruvate with the enzyme, mutation studies were carried out by replacing Thr31 as it had a less interaction energy. Out of 10 mutants, T31N, T31Q and T31G were selected using potential energy and the residual energy calculations. Five nanoseconds explicit MD simulations were run for apo, wild type and mutants T31N, T31Q and T31G using Desmond. RMSD, RMSF, distance plots and H-bonds analysis proved T31G to be a favorable mutant for binding of pyruvate. Thus, modeling PFOR would help in profound understanding of its structural clefts and mutation studies would aid in improving the enzyme efficiency.

Molecular docking and dynamics simulation study on the influence of Zn2+ on the binding modes of aggrecanase with its inhibitors.

Zinc plays a vital role in structural organization, regulation of function and stabilization of the folded protein, which ultimately activates or inactivates the binding sites of the protein. Its transition makes a major change in the protein and its binding affinity. The ligand binding aggrecanases can be influenced by Zn2+ ions; therefore the study focuses on checking the binding mode in the presence and absence of zinc using Docking and Molecular dynamics simulation. The crystal structure with zinc was considered as wild type (ADAMTS-4-1Zn2+, ADAMTS-5-1Zn2+) and the crystal structure without zinc was considered as the mutant type (ADAMTS-4-0Zn2+, ADAMTS-5-0Zn2+). Mutations were made manually by deleting the zinc atom. ADAMTS-4-1Zn2+ had the best Glide score of -12.66 kcal·mol−1, whereas ADAMTS-4-0Zn2+ had -11.69 kcal·mol−1. ADAMTS-4-1Zn2+ had the best glide energy of -72.29 kcal·mol−1, whereas ADAMTS-4-0Zn2+ had-68.44 kcal·mol−1. ADAMTS-4-1Zn2+ had the best glide e-model of -116.34, whereas ADAMTS-4-0Zn2+ had -104.264. The RMSD value for ADAMTS-4-1Zn2+ and ADAMTS-4-0Zn2+ was 1.9. These results suggested that the absence of zinc decreases the binding affinity of ADAMTS-4 with its inhibitor. ADAMTS-5-1Zn2+ had the best Glide score of -8.32 kcal·mol−1, whereas ADAMTS-5-0Zn2+ had -6.62 kcal·mol−1. ADAMTS-5-1Zn2+ had the best glide energy of -70.28 kcal·mol−1, whereas ADAMTS-5-0Zn2+ had -66.02 kcal·mol−1. ADAMTS-5-1Zn2+ had the best glide e-model of-108.484, whereas ADAMTS-5-0Zn2+ had -93.81. The RMSD value for ADAMTS-5-1Zn2+ and ADAMTS-5-0Zn2+ was 0.48Å. These results confirmed that the absence of zinc decreased the binding affinity of ADAMTS-5 with its inhibitor whereas the presence extended the docking energy range and strengthened the binding affinity. Per-residue interaction study, MM-GBSA and Molecular Dynamics showed that all the four complexes underwent extensive structural changes whereas the complex with zinc was stable throughout the simulation period.

Combined structure- and ligand-based pharmacophore modeling and molecular dynamics simulation studies to identify selective inhibitors of MMP-8.

Matrix metalloproteinase-8 (MMP-8) is the key mediator in initiating type I collagen degradation and is associated with rheumatoid arthritis. In the present study, a pharmacophore hypothesis was developed based on selective non zinc binding inhibitors of MMP-8. The pharmacophore hypothesis was refined manually and validated by observing structures and the interactions of MMP-8 inhibitors. The refined pharmacophore model was able to discriminate the non-zinc binding inhibitors of MMP-8 with respect to other inhibitors. Hence this study proposes a combined structure- and ligand-based pharmacophore model that is suitable for retrieving the novel inhibitors of MMP-8. The pharmacophore hypothesis AADRH was used as query for retrieving potential compounds from the Zinc database and hits were selected based on the catalytic selective amino acid residues of Arg 222, and Tyr 227. We identified six compounds as potent inhibitors and their selectivity profile were checked against different subtypes of MMPs using the cross-docking method. Molecular dynamics results indicated that ZINC 00673680 forms a stable interaction with the key amino acid residues and avoids the zinc atom with a distance of 5.49 Å. Our computational study might be useful for further development of selective MMP-8 inhibitors.

E-pharmacophore and molecular dynamics study of flavonols and dihydroflavonols as inhibitors against dihydroorotate dehydrogenase.

DiHydroOrotate DeHydrogenase [huDHODH] is a therapeutic target for Rheumatoid arthritis [RA]. Leflunomide [A771726] is a widely used synthetic inhibitor against huDHODH. We to find more efficient lead like compounds. A four featured E-Pharmacophore A1D4H6R7 was built based on the inhibitor A771726. This pharmacophore was validated by checking its ability to identify known highly active inhibitors of huDHODH and assigning higher fitness scores to them. A reverse validation was also performed where random 4 featured pharmacophores were built and its efficiency in identifying actives was compared with our E-Pharmacophore. Our Epharmacophore was very efficient, since it passed both validations by picking the known active molecules with high fitness scores. This validated E- pharmacophore was searched against the KEGG phytochemicals subset database. This search resulted in 18 molecules which were subjected to docking with huDHODH. The molecules with docking score greater than that of A771726 were selected. The docking results were further validated using MM/GBSA which gave similar ranking with high binding free energy values. The four molecules 6-Methoxytaxifolin, Rhamnetin, Rhamnazin and Pinoquercetin were taken for explicit 3ns simulation and it was observed that all four molecules had acceptable RMSD values and stable interactions. Thus our study, suggests four phytomolecules that might inhibit huDHODH more efficiently than A771726. Interestingly, some of the obtained hits have already been proven in vitro anti-inflammatory activity which confirms that, the developed E-pharmacophore can be used to identify novel small molecules against inflammatory target, huDHODH.

Discovery of potent inhibitor for matrix metalloproteinase-9 by pharmacophore based modeling and dynamics simulation studies.

Matrix metalloproteinase-9 (MMP-9) is an attractive target for anticancer therapy. In the present study ligand based pharmacophore modeling was performed to elucidate the structural elements for a diverse class of MMP-9 inhibitors. The pharmacophore model was validated through Güner-Henry (GH) scoring method. The final pharmacophore model consisted of three hydrogen bond acceptors (HBA), and two ring aromatic regions (RA). This model was utilized to screen the natural compound database to seek novel compounds as MMP-9 inhibitors. The identified hits were validated using molecular docking and molecular dynamics simulation studies. Finally, one compound named Hinokiflavone from Juniperus communis had high binding free energy of -26.54kJ/mol compared with the known inhibitors of MMP-9. Cytotoxicity for hinokiflavone was evaluated by MTT assay. Inhibition of MMP-9 in the presence of hinokiflavone was detected by gelatin zymography and gelatinolytic inhibition assay. Results revealed that the natural compounds derived based on the developed pharmacophore model would be useful for further design and development of MMP-9 inhibitors.

Potent inhibitors precise to S1' loop of MMP-13, a crucial target for osteoarthritis.

Matrix metalloproteinase-13 (MMP-13) is the primary MMP involved in cartilage degradation through its particular ability to cleave type-II collagen. This protein is expressed by chondrocytes and synovial cells in human osteoarthritis and rheumatoid arthritis; hence, it is an attractive target for the treatment of arthritic diseases. Currently available inhibitors lack specificity for metalloproteinase because of a common Zn binding site in MMPs; thus, there is a need to identify selective MMP-13 inhibitors for osteoarthritis therapy. Because selectivity is the major concern, both ligand-based and protein-based pharmacophore methodologies were used to identity potent and selective MMP-13 inhibitors. Different hypotheses were validated, and the best hypothesis was used to screen Zinc (natural and chemical) databases to seek novel scaffolds as MMP-13 inhibitors. The identified hits were validated using different strategies, such as Glide Standard precision, extra precision, E-model energies and receiver operating curve (ROC). In addition, potent inhibitors were selected based on two criteria: a similar binding mode as that of the active site PB3 crystal ligand and crucial amino acid interactions that are catalytically important for the function of MMP-13. The candidate potent inhibitors ZINC 02535232, ZINC 08399795, ZINC 12419118 and ZINC 00624580 nearly reproduced the H-bond interactions formed in the crystal structure of 1XUC with reasonable RMSD values exhibiting a novel interaction pattern that was not previously observed in MMP-13 inhibitors. The identified potent hits with diverse chemical scaffolds may be useful in designing new MMP-13 inhibitors.

Lead identification and optimization of novel collagenase inhibitors; pharmacophore and structure based studies.

In this study, chemical feature based pharmacophore models of MMP-1, MMP-8 and MMP-13 inhibitors have been developed with the aid of HypoGen module within Catalyst program package. In MMP-1 and MMP-13, all the compounds in the training set mapped HBA and RA, while in MMP-8, the training set mapped HBA and HY. These features revealed responsibility for the high molecular bioactivity, and this is further used as a three dimensional query to screen the knowledge based designed molecules. These pharmacophore models for collagenases picked up some potent and novel inhibitors. Subsequently, docking studies were performed for the potent molecules and novel hits were suggested for further studies based on the docking score and active site interactions in MMP-1, MMP-8 and MMP-13.