Evaluation of xanthene-appended quinoline hybrids as potential leads against antimalarial drug targets.

A series of fused heterocycle xanthene-appended quinoline 6a-n was successfully synthesized with regioselectivity and characterized using IR, 1H NMR, 13C NMR, and mass spectral data. Molecular docking was performed to find the binding efficacy of all these newly synthesized compounds towards thirteen antimalarial drug targets. Molecular dynamics simulation was carried out to predict the stability of the ligand-bound complex in a solvent medium. Blind and site-directed docking with compounds 6a-n against 13 drug targets revealed most of the ligands to have a good binding affinity with the targets. Analysis on the basis of binding energy, binding modalities of the ligands, intermolecular interactions, and pharmacophore, we identified only one of the ligand-receptor complexes to provide better results. Molecular dynamic simulation of the selected receptor-ligand complex revealed that the synthesized compound had a better binding affinity with the receptor than the native ligand complex. Further analysis of the synthesized ligand in the laboratory may prove promising results in the search for potential antimalarial drugs.

Identification of zebrafish fumarate hydratase active site by molecular docking and simulation studies.

Fumarate hydratase (FH), one of the members of TCA cycle, acts as a catalyte for the synthesis of malate from fumarate. FH has been proposed to play as a tumour suppressor leading to the pathogenicity of leiomyomas, renal cell carcinoma and paraganglioma. Mutations in the active site of FH lead to alteration in the protein structure. Similarly, binding of several chemical inhibitors to the active site also leads to the disruption of protein structural integrity thereby leading to protein dysfunction. Therefore, in order to address this mechanism leading to cancer, the binding efficiency of potential human FH inhibitor citrate to zebrafish fh has been extensively analysed in this study by molecular docking and simulation experiments followed by quantification of fumarate hydratase enzyme activity to validate and confirm the findings. Molecular docking revealed stronger interaction of zebrafish fh protein with inhibitor citrate when compared to natural substrate fumarate. Study on the dynamics of docked structures further confirmed that citrate was found to possess more binding affinity than fumarate. In vitro biochemical analysis also revealed concentration dependent potential inhibitory effect of citrate on zebrafish fh, thus confirming the findings of the in-silico experiments.Communicated by Ramaswamy H. Sarma.

Evaluation of peptide designing strategy against subunit reassociation in mucin 1: A steered molecular dynamics approach.

Subunit reassociation in mucin 1, a breast cancer tumor marker, is reported as one of the critical factors for its cytoplasmic activation. Inhibition of its heterodimeric association would therefore result in loss of its function and alter disease progression. The present study aimed at evaluating peptide inhibitor designing strategies that may serve as antagonist against this receptor-ligand alliance. Several peptides and their derivatives were designed based on native residues, subunit interface, hydrogen bonding and secondary structure. Docking studies with the peptides were carried on the receptor subunit and their binding affinities were evaluated using steered molecular dynamics simulation and umbrella sampling. Our results showed that among all the different classes of peptides evaluated, the receptor based peptide showed the highest binding affinity. This result was concurrent with the experimental observation that the receptor-ligand alliance in mucin 1 is highly specific. Our results also show that peptide ligand against this subunit association is only stabilized through native residue inter-protein interaction irrespective of the peptide structure, peptide length and number of hydrogen bonds. Consistency in binding affinity, pull force and free energy barrier was observed with only the receptor derived peptides which resulted in favorable interprotein interactions at the interface. Several observations were made and discussed which will eventually lead to designing efficient peptide inhibitors against mucin 1 heterodimeric subunit reassociation.

Systematic prioritization of functional hotspot in RIG-1 domains using pattern based conventional molecular dynamic simulation.

BACKGROUND: Retinoic acid inducible gene 1 (RIG-1), multi-domain protein has a role-play in detecting viral nucleic acids and stimulates the antiviral response. Dysfunction of this protein due to mutations makes the route vulnerable to viral diseases. AIM: Identification of functional hotspots that maintains conformational stability in RIG-1 domains. METHODS: In this study, we employed a systematic in silico strategy on RIG-1 protein to understand the mechanism of structural changes upon mutation. We computationally investigated the protein sequence signature for all the three domains of RIG-1 protein that encloses the mutation within the motif. Further, we carried out a structural comparison between RIG-1 domains with their respective distant orthologs which revealed the minimal number of interactions required to maintain its structural fold. This intra-protein network paved the way to infer hotspot residues crucial for the maintenance of the structural architecture and folding pattern. KEY FINDINGS: Our analysis revealed about 40 hotspot residues that determine the folding pattern of the RIG-1 domains. Also, conventional molecular dynamic simulation coupled with essential dynamics provides conformational transitions of hot spot residues among native and mutant structures. Structural variations owing to hotspot residues in mutants again confirm the significance of these residues in structural characterization of RIG-1 domains. We believe our results will help the researchers to better comprehend towards regulatory regions and target-binding sites for therapeutic design within the pattern recognition receptor proteins. SIGNIFICANCE: Our protocol employed in this work describes a novel approach in identifying signature residues that would provide structural insights in protein folding.

Casting the critical regions in nucleotide binding oligomerization domain 2 protein: a signature mediated structural dynamics approach.

Nucleotide binding oligomerization domain 2 (NOD2), a protein involved in the first line defence mechanism has a pivotal role in innate immunity. Impaired function of this protein is implicated in disorders such as Blau syndrome and Crohn's disease. Since an altered function is linked to protein's structure, we framed a systematic strategy to interpret the structure-function relationship of the protein. Initiated with mutation-based pattern prediction and identified a distant ortholog (DO) of NOD2 from which the intra-residue interaction network was elucidated. The network was used to identify hotspots that serve as critical points to maintain the stable architecture of the protein. Structural comparison of NOD2 domains with a DO revealed the minimal number of intra-protein interactions required by the protein to maintain the structural fold. In addition, the conventional molecular dynamics simulation emphasized the conformational transitions at hot spot residues between native NOD2 domains and its respective mutants (G116R, R42W and R54A) structures. The analysis of intra-protein interactions globally and the displacement of residues locally around the mutational site revealed loss of several critical bonds and residues vital for the protein's function. Conclusively we report, about 10 residues in leucine-rich repeat, 13 residues in NOD and 6 residues in CARD domain are required by the NOD2 to maintain its function. This protocol will help the researchers to achieve for more prospective studies to attest druggable site utility in discovering novel drug candidates.

Ab initio coordination chemistry for nickel chelation motifs.

Chelation therapy is one of the most appreciated methods in the treatment of metal induced disease predisposition. Coordination chemistry provides a way to understand metal association in biological structures. In this work we have implemented coordination chemistry to study nickel coordination due to its high impact in industrial usage and thereby health consequences. This paper reports the analysis of nickel coordination from a large dataset of nickel bound structures and sequences. Coordination patterns predicted from the structures are reported in terms of donors, chelate length, coordination number, chelate geometry, structural fold and architecture. The analysis revealed histidine as the most favored residue in nickel coordination. The most common chelates identified were histidine based namely HHH, HDH, HEH and HH spaced at specific intervals. Though a maximum coordination number of 8 was observed, the presence of a single protein donor was noted to be mandatory in nickel coordination. The coordination pattern did not reveal any specific fold, nevertheless we report preferable residue spacing for specific structural architecture. In contrast, the analysis of nickel binding proteins from bacterial and archeal species revealed no common coordination patterns. Nickel binding sequence motifs were noted to be organism specific and protein class specific. As a result we identified about 13 signatures derived from 13 classes of nickel binding proteins. The specifications on nickel coordination presented in this paper will prove beneficial for developing better chelation strategies.

Kinetic study of adsorption of arsenic onto New Zealand Ironsand (NZIS).

New Zealand Ironsand (NZIS), an iron-rich sand ubiquitous to the coast of the North Island of New Zealand was examined for the removal of arsenic (both As (III) and As (V)) by adsorption. Batch experiments were performed to evaluate the adsorption kinetics at three different pH conditions (3.0, 7.5 and 11.0). In addition, a column test was conducted to obtain the breakthrough curve and appraise the arsenic removal capacity of NZIS used as a filter media. The kinetic study showed that a very long contact time (>144 h) was needed to reach equilibrium and the nature of the adsorption was well described (R(2) value more than 0.96 at each pH condition) with a pseudo-second-order adsorption kinetic model for both As (III) and As (V). In column tests, a pore volume (PV) of 700 and 400 yielded a total arsenic level less than the WHO guideline value of 10 µg/L for As (III) and As (V), respectively.

Impaired T-cell survival promotes mucosal inflammatory disease in SHIP1-deficient mice.

T cells have a critical role in immune surveillance at mucosal surfaces. SHIP1(-/-) mice succumb to mucosal inflammatory disease that afflicts the lung and small intestine (SI). The basis of this condition has not been defined. Here we show that SHIP1 is required for the normal persistence and survival of T cells in mucosal tissues. We find that CD4 and CD8 effector T cells are reduced; however, Treg cells are increased in the SI and lungs of SHIP1(-/-) and CD4CreSHIP(flox/flox) mice. Furthermore, a subset of T cells in the SI of SHIP1(-/-) mice are FasL(+) and are more susceptible to extrinsic cell death. Mechanistic analyses showed that SHIP1 associates with the death receptor CD95/Fas and treatment with a Caspase 8 inhibitor prevents SHIP1 inhibitor-mediated T-cell death. Notably, mucosal inflammation in SHIP1(-/-) mice is reduced by treatment with a Caspase 8 inhibitor. We also find that the incidence of Crohn's disease (CD) and pneumonia is significantly increased in mice with dual T and myeloid lineage SHIP1 deletion but not in single lineage-deleted mice. Thus, by promoting survival of protective T cells, thereby preventing an inflammatory myeloid response, SHIP1 maintains an appropriate balance of innate immune function at mucosal surfaces necessary for immune homeostasis.

Prostaglandin E2 receptors have differential effects on Leishmania major infection.

Through their receptors, prostaglandins play crucial roles in various infections. Although prostaglandin E2 (PGE2) is implicated as a susceptibility factor in Leishmania infection, the relative contributions of its four receptors--EP1, EP2, EP3 and EP4--to this infection remain unknown. We report that Leishmania major infection of BALB/c-derived peritoneal macrophages up-regulated EP1 and EP3 expressions but down-regulated EP2 and EP4 expressions. EP2 and EP4 agonists reduced parasite load, but EP1 and EP3 agonists increased parasite load in macrophages in vitro. Agonists of EP2 and EP4, antagonists of EP1 and EP3, or lentivirally expressed EP1-shRNA and EP3-shRNA significantly reduced parasite burden in susceptible BALB/c mice. These novel data suggest differential regulation and counteractive functions of EP receptor subsets.

Pattern prediction and coordination geometry analysis from cadmium-binding proteins: a computational approach.

Cadmium toxicity has been reported to have major health effects including carcinogenicity, respiratory disorders, kidney failure, neurotoxicity and liver dysfunction. Understanding the nature of the association of cadmium with biomolecules has thus become imperative and a key factor in predicting the phenomena behind predisposition to disease. Accordingly, a computational investigation of cadmium-binding characteristics was performed using about 140 cadmium-bound structures and 34 cadmium-binding sequences. The metal-coordinating architecture defining the chelate loops, residue arrangement, secondary-structural characteristics, distances and angles were analyzed. Binding patterns were predicted based on the probability of occurrence of residues within the coordination distance and were further corroborated with sequence patterns obtained from cadmium-binding proteins. About 56 different chelate loops were identified. Based on these chelate loops, putative cadmium-binding patterns were derived that resembled short-length motifs, namely Y-X-G-X-G, Q-X(9)-E, E-X(2)-E-X(2)-E and T-X(5)-E-X(2)-E, which were observed within the conserved regions of the cadmium-binding proteins. The poorer conservation of residues around these motifs resulted in a deviating pattern against the coordination loops. These structure-based motifs are proposed to be an efficient tool in building chelators for the effective removal of cadmium.

Robotically assisted biliary pancreatic diversion with a duodenal switch: a new technique.

BACKGROUND: Minimally invasive surgical techniques decrease the length of hospitalization and the morbidity for general surgery procedures. Application of minimally invasive techniques to obesity surgery had previously been limited to stapled techniques used primarily for the Roux-en-Y gastric bypass and laparoscopic band placement. The authors present the technique for totally intracorporeal robotically assisted biliary pancreatic diversion with a duodenal switch (BPD/DS) using five ports. METHODS: After development of the technique in animal and human cadaver models, the da Vinci robot was first used in October 2000 to perform BPD/DS using five ports and a totally intracorporeal technique. Patient selection was based on standard surgery guidelines for the morbidly obese. RESULTS: This technique was applied for 47 patients with a mean body mass index (BMI) of 45 kg/m2 and a mean age of 38 +/- 10 years. The median operating time was 514 min (range, 370-931 min). The median operative time for the last 10 patients was 379 min (range, 370-582 min). Three patients underwent conversion to open surgery, and four patients experienced postoperative leaks with no mortality. CONCLUSION: The safety, feasibility, and reproducibility of a minimally invasive robotic surgical approach to complex abdominal operations such as BPD/DS is demonstrated. The BPD/DS allows for a sutured bowel anastomosis similar to the open technique using a minimal number of small access ports.

Phacoemulsification combined with silicone oil removal through a posterior capsulorhexis.

PURPOSE: To evaluate the technique of silicone oil removal through a posterior capsulorhexis combined with phacoemulsification and intraocular lens (IOL) implantation. SETTING: Dr. Rajendra Prasad Center for Ophthalmic Sciences, New Delhi, India. METHODS: Fifteen eyes of 15 patients had phacoemulsification with removal of silicone oil, which had been used for intraocular tamponade after a previous pars plana vitrectomy. Eyes with a stable retina were included in the series. In all eyes, the silicone oil was removed through a planned posterior capsulorhexis after phacoemulsification. The parameters evaluated were the primary diagnosis, duration between silicone oil instillation and phacoemulsification, type of cataract, preoperative and postoperative best corrected visual acuities (BCVAs), and complications such as frequency of retinal redetachment and secondary cataract. RESULTS: Vitreoretinal surgery with silicone oil instillation was performed for rhegmatogenous-tractional detachment resulting from Eales' disease in 6 eyes and from proliferative diabetic retinopathy in 2 eyes, for primary rhegmatogenous retinal detachment in 6 eyes, and for traumatic rhegmatogenous detachment in 1 eye. The mean duration between the silicone oil instillation and phacoemulsification was 7.5 months +/- 3.8 (SD). Fourteen eyes had posterior subcapsular cataract, and 10 had nuclear sclerosis. Preoperative BCVA was worse than 6/60 in all eyes. The BCVA was 6/60 or better in 9 eyes after a minimum follow-up of 6 months. Two eyes had choroidal detachment in the early postoperative period. No eye had vitreous hemorrhage, retinal redetachment, secondary cataract, clinically significant endothelial decompensation or macular edema, or a dislocated IOL. CONCLUSION: The results indicate that silicone oil removal through a posterior capsulorhexis during phacoemulsification is a viable option and can be performed in selected cases of cataract with previous silicone oil instillation and a stable retina.

Long-term outcome of simultaneous kidney-pancreas transplantation: analysis of 61 patients with more than 5 years follow-up.

BACKGROUND: The long-term outcome of simultaneous kidney pancreas transplant recipients is not well established. METHODS: We retrospectively reviewed all patients who underwent simultaneous kidney-pancreas transplantation with bladder drainage at our center between January 1989 and December 1991. A total of 57 patients (93%) were alive with functioning grafts 1 year after transplantation and were followed for a minimum of 5 years. These patients formed the study group. RESULTS: Five-year actual patient, kidney and pancreas survival rates were 95%, 85%, and 88%, respectively. Fasting serum glucose fell from 198 mg/dL preoperatively to 94 mg/dL and remained stable thereafter. Glycohemoglobin levels decreased from 9.8% preoperatively to 4.8% 1 year after transplantation and remained normal thereafter. Kidney function remained good, with mean serum creatinine of 2.0 and creatinine clearance of 56 ml/min throughout the follow-up period. Hospital admissions decreased significantly with increasing time after transplantation from a mean of 1.2 admissions per patient in the 1st year to a mean of 0.2 admissions per patient 6 years after transplantation. Of the readmissions, 42% were for <48 hr and the most common reasons for readmission were infection, surgery, and dehydration. Mean systolic blood pressure decreased from 166 mm Hg before the transplant to 142 mm Hg 1 year after the transplant. CONCLUSIONS: Simultaneous kidney pancreas transplantation is a safe and effective method to treat advanced diabetic nephropathy and is associated with stable metabolic function, decreased cholesterol, improved hypertension control, improved rehabilitation over time, and little morbidity or mortality after the 1st year.