Design, synthesis and evaluation of naphthalene-2-carboxamides as reversal agents in MDR cancer

A novel class of molecules with structure N-[3-(4-substituted-1-piperazinyl) propyl]-6-methoxy naphthalene-2-carboxamides were designed by generating a pharmacophore for potent MDR reversal activity, using Elacridar (GF 120918) as a query molecule and using MOE software. They were synthesized by condensing 6-methoxynaphthalene-2-carboxylic acid with N-[3-(4-substituted-1-piperazinyl) propyl] amines in the presence of DCC in DMF. They were evaluated in P388 murine lymphocytic leukemia cell line (P388) in vitro using SRB assay for cytotoxicity and in adriamycin-resistant P388 murine lymphocytic leukemia cell line (P388/ADR) using MTT assay for resistant reversal activity. Test compounds were non-toxic at the doses studied (upto 80 microg/ml). They effectively reversed adriamycin resistance at the doses studied (40 and 80 microg/ml). The percentage enhancement in adriamycin activity was in the range 33.58 -90.67 (at 40 microg/ml) and 8.80-46.04 (at 80 microg/ml) and the corresponding reversal potency values were in the range 1.33-1.90 and 1.08-1.46, respectively. Test compounds 2, 3, and 5 exhibited better activity as compared to the standard resistant reversal agent (Verapamil), at same concentration.     

Bovine Serum Albumin Binding and Drug Delivery Studies with PVA-Ferrofluid

This paper describes a single-step method for the biomimetic synthesis of stably suspended magnetite nanoparticles in poly(vinyl alcohol) termed ferrofluids. The challenge is to synthesize water based stable magnetic colloids with a control over the particle size and morphology for biomedical applications. The polymer possibly plays a dual role of a surfactant and a functionalizing agent. Transmission electron microscopy, infrared spectroscopy and vibrating sample magnetometry were used to investigate the properties of the synthesized ferrofluids. It has a strong affinity towards the tryptophan residues in bovine serum albumin protein as determined from the fluorescence emission studies. For in vivo applications this could indirectly mean a resistance to immune response and thus ensure long-term circulation. The ability of the synthesized ferrofluid to bind a che-motherapeutic drug ceftriaxone and its ionic release was observed. The polymer hydroxyl group allows drug-binding and the magnetic property allows targeting to specific sites. Magnetic hybrid fluids with combined advantages of magnetism and polymer open up new perspectives for applications.     

CD4 binding site antibodies inhibit human immunodeficiency virus gp120 envelope glycoprotein interaction with CCR5

The human immunodeficiency virus type 1 (HIV-1) gp120 exterior glycoprotein is conformationally flexible. Upon binding the host cell receptor, CD4, gp120 assumes a conformation that is able to bind the chemokine receptors CCR5 or CXCR4, which act as coreceptors for the virus. CD4-binding-site (CD4BS) antibodies are neutralizing antibodies elicited during natural infection that are directed against gp120 epitopes that overlap the binding site for CD4. Recent studies (S. H. Xiang et al., J. Virol. 76:9888-9899, 2002) suggest that CD4BS antibodies recognize conformations of gp120 distinct from the CD4-bound conformation. This predicts that the binding of CD4BS antibodies will inhibit chemokine receptor binding. Here, we show that Fab fragments and complete immunoglobulin molecules of CD4BS antibodies inhibit CD4-independent gp120 binding to CCR5 and cell-cell fusion mediated by CD4-independent HIV-1 envelope glycoproteins. These results are consistent with a model in which the binding of CD4BS antibodies limits the ability of gp120 to assume a conformation required for coreceptor binding.     

Dissecting the genetic complexity of the association between human leukocyte antigens and rheumatoid arthritis

Rheumatoid arthritis (RA) is an inflammatory disease with a complex genetic component. An association between RA and the human leukocyte antigen (HLA) complex has long been observed in many different populations, and most studies have focused on a direct role for the HLA-DRB1 "shared epitope" in disease susceptibility. We have performed an extensive haplotype analysis, using 54 markers distributed across the entire HLA complex, in a set of 469 multicase families with RA. The results show that, in addition to associations with the DRB1 alleles, at least two additional genetic effects are present within the major histocompatibility complex. One of these lies within a 497-kb region in the central portion of the HLA complex, an interval that excludes DRB1. This genetic risk factor is present on a segment of a highly conserved ancestral A1-B8-DRB1*03 (8.1) haplotype. Additional risk genes may also be present in the HLA class I region in a subset of DRB1*0404 haplotypes. These data emphasize the importance of defining haplotypes when trying to understand the HLA associations with disease, and they clearly demonstrate that such associations with RA are complex and cannot be completely explained by the DRB1 locus.     

Leukocyte-derived matrix metalloproteinase-9 mediates blood-brain barrier breakdown and is proinflammatory after transient focal cerebral ischemia

Results of recent studies reveal vascular and neuroprotective effects of matrix metalloproteinase-9 (MMP-9) inhibition and MMP-9 gene deletion in experimental stroke. However, the cellular source of MMP-9 produced in the ischemic brain and the mechanistic basis of MMP-9-mediated brain injury require elucidation. In the present study, we used MMP-9-/- mice and chimeric knockouts lacking either MMP-9 in leukocytes or in resident brain cells to test the hypothesis that MMP-9 released from leukocytes recruited to the brain during postischemic reperfusion contributes to this injury phenotype. We also tested the hypothesis that MMP-9 promotes leukocyte recruitment to the ischemic brain and thus is proinflammatory. The extent of blood-brain barrier (BBB) breakdown, the neurological deficit, and the volume of infarction resulting from transient focal stroke were abrogated to a similar extent in MMP-9-/- mice and in chimeras lacking leukocytic MMP-9 but not in chimeras with MMP-9-containing leukocytes. Zymography and Western blot analysis from these chimeras confirmed that the elevated MMP-9 expression in the brain at 24 h of reperfusion is derived largely from leukocytes. MMP-9-/- mice exhibited a reduction in leukocyte-endothelial adherence and a reduction in the number of neutrophils plugging capillaries and infiltrating the ischemic brain during reperfusion; microvessel immunopositivity for collagen IV was also preserved in these animals. These latter results document proinflammatory actions of MMP-9 in the ischemic brain. Overall, our findings implicate leukocytes, most likely neutrophils, as a key cellular source of MMP-9, which, in turn, promotes leukocyte recruitment, causes BBB breakdown secondary to microvascular basal lamina proteolysis, and ultimately contributes to neuronal injury after transient focal stroke.     

Support vector machine-based method for subcellular localization of human proteins using amino acid compositions, their order, and similarity search

Here we report a systematic approach for predicting subcellular localization (cytoplasm, mitochondrial, nuclear, and plasma membrane) of human proteins. First, support vector machine (SVM)-based modules for predicting subcellular localization using traditional amino acid and dipeptide (i + 1) composition achieved overall accuracy of 76.6 and 77.8%, respectively. PSI-BLAST, when carried out using a similarity-based search against a nonredundant data base of experimentally annotated proteins, yielded 73.3% accuracy. To gain further insight, a hybrid module (hybrid1) was developed based on amino acid composition, dipeptide composition, and similarity information and attained better accuracy of 84.9%. In addition, SVM modules based on a different higher order dipeptide i.e. i + 2, i + 3, and i + 4 were also constructed for the prediction of subcellular localization of human proteins, and overall accuracy of 79.7, 77.5, and 77.1% was accomplished, respectively. Furthermore, another SVM module hybrid2 was developed using traditional dipeptide (i + 1) and higher order dipeptide (i + 2, i + 3, and i + 4) compositions, which gave an overall accuracy of 81.3%. We also developed SVM module hybrid3 based on amino acid composition, traditional and higher order dipeptide compositions, and PSI-BLAST output and achieved an overall accuracy of 84.4%. A Web server HSLPred (www.imtech.res.in/raghava/hslpred/ or bioinformatics.uams.edu/raghava/hslpred/) has been designed to predict subcellular localization of human proteins using the above approaches.     

Photocurable hard and porous biomaterials from ROMP precursors cross-linked with diyl radicals

A combination of (ROMP) ring-opening metathesis polymerization and diradical (diyl) cross-linking provides a new access to hard biomaterials and potential artificial bone replacements. ROMP was used to construct soft and pliable linear polymers bearing photolabile diazene functions. After treatment with light, a nitrogen aerosol is released throughout the polymer to create desirable porosity, cross-linking, and hardening in a single step. Nonpolymeric mechanistic work supporting these studies was also examined.     

Real value prediction of solvent accessibility in proteins using multiple sequence alignment and secondary structure

The present study is an attempt to develop a neural network-based method for predicting the real value of solvent accessibility from the sequence using evolutionary information in the form of multiple sequence alignment. In this method, two feed-forward networks with a single hidden layer have been trained with standard back-propagation as a learning algorithm. The Pearson's correlation coefficient increases from 0.53 to 0.63, and mean absolute error decreases from 18.2 to 16% when multiple-sequence alignment obtained from PSI-BLAST is used as input instead of a single sequence. The performance of the method further improves from a correlation coefficient of 0.63 to 0.67 when secondary structure information predicted by PSIPRED is incorporated in the prediction. The final network yields a mean absolute error value of 15.2% between the experimental and predicted values, when tested on two different nonhomologous and nonredundant datasets of varying sizes. The method consists of two steps: (1) in the first step, a sequence-to-structure network is trained with the multiple alignment profiles in the form of PSI-BLAST-generated position-specific scoring matrices, and (2) in the second step, the output obtained from the first network and PSIPRED-predicted secondary structure information is used as an input to the second structure-to-structure network. Based on the present study, a server SARpred (http://www.imtech.res.in/raghava/sarpred/) has been developed that predicts the real value of solvent accessibility of residues for a given protein sequence. We have also evaluated the performance of SARpred on 47 proteins used in CASP6 and achieved a correlation coefficient of 0.68 and a MAE of 15.9% between predicted and observed values.     

Characterisation of the nuclear proteome of a dehydration‐sensitive cultivar of chickpea and comparative proteomic analysis with a tolerant cultivar

Water deficit or dehydration hampers plant growth and development, and shrinks harvest size of major crop species worldwide. Therefore, a better understanding of dehydration response is the key to decipher the regulatory mechanism of better adaptation. In recent years, nuclear proteomics has become an attractive area of research, particularly to study the role of nucleus in stress response. In this study, a proteome of dehydration‐sensitive chickpea cultivar (ICCV‐2) was generated from nuclei‐enriched fractions. The LC‐MS/MS analysis led to the identification of 75 differentially expressed proteins presumably associated with different metabolic and regulatory pathways. Nuclear localisation of three candidate proteins was validated by transient expression assay. The ICCV‐2 proteome was then compared with that of JG‐62, a tolerant cultivar. The differential proteomics and in silico analysis revealed cultivar‐specific differential expression of many proteins involved in various cellular functions. The differential tolerance could be attributed to altered expression of many structural proteins and the proteins involved in stress adaptation, notably the ROS catabolising enzymes. Further, a comprehensive comparison on the abiotic stress‐responsive nuclear proteome was performed using the datasets published thus far. These findings might expedite the functional determination of the dehydration‐responsive proteins and their prioritisation as potential molecular targets for better adaptation.