Quantitative characterization of protein tertiary motifs

Dimerization of 2-naphthalenecarbonitrile (2-NpCN) mediated by cucurbit[8]uril (CB[8]) has been investigated employing the density functional theory. Different structures of 2-NpCN dimers were generated by combining monomers in anti-head-to-head (A), anti-head-to-tail (B) and syn-head-to-tail (C) fashion. All these dimeric structures possess rigid cube-like architecture. On confinement within the CB[8] dimer A turns out to be the lowest energy structure. Calculated ¹H NMR spectra revealed that the 2-NpCN dimer exhibits large shielding for aromatic protons consistent with the experiment. The protons attached to cubane moiety on the other hand, led to down-field signals. Dimerization mediated with CB[8] cavitand is further accompanied by the frequency up-shift (blue shift) of methylene stretching vibration in its infrared spectra.

Peptidomimetic 2-cyanopyrrolidines as potent selective cathepsin L inhibitors

Cathepsins have been found to have important physiological roles. The implication of cathepsin L in various types of cancers is well established. In a search for selective cathepsin L inhibitors as anticancer agents, a series of 2-cyanoprrolidine peptidomimetics, carrying a nitrile group as warhead, were designed. Two series of compounds, one with a benzyl moiety and a second with an isobutyl moiety at P₂ position of the enzyme were synthesized. The synthesized compounds were evaluated for inhibitory activity against human cathepsin L and cathepsin B. Although, none of the compounds showed promising inhibitory activity, (E)N-{(S)1-[(S)2-cyano-1-pyrrolidinecarbonyl]-3-methylbutyl}-2,3-diphenylacrylamide (24) with an isobutyl moiety at P₂ was found to show selectivity as a cathepsin L inhibitor (Ki 5.3 μM for cathepsin L and Ki > 100 μM for cathepsin B). This compound could act as a new lead for the further development of improved inhibitors within this inhibitor type.     

Statistics of catalytic domain sequences in protein kinases vs non-kinases

The catalytic regions of Protein Kinases are known to have similarity in primary chains. However, it is not known whether there is a signature profile specific to a particular catalytic region? Whether the signature profile, if any, is unique to a protein kinases family in a particular species or in a group of species? We have attempted analyzing some of these aspects by statistical data mining using an authentic and exhaustive database of Protein Kinases. The results reveal interesting features and provide some new directions to look at their applications.     

Polymerase chain reaction analysis of transgenic plants contaminated byAgrobacterium

Agrobacterium-mediated genetic transformation is a method of choice for the development of transgenic plants. The presence of latentAgrobacterium that multiplies in the plant tissue in spite of antibiotic application confounds the results obtained by polymerase chain reaction (PCR) analysis of putative transgenic plants. The presence ofAgrobacterium can be confirmed by amplification of eitherAgrobacterium chromosomal genes or genes present out of transfer DNA (T-DNA) in the binary vector. However, the transgenic nature ofAgrobacterium-contaminated transgenic plants cannot be confirmed by PCR. Here we report a simple protocol for PCR analysis ofAgrobacterium-contaminated transgenic plants. This protocol is based on denaturation and renaturation of DNA. The contaminating plasmid vector becomes double-stranded after renaturation and is cut by a restriction enzyme having site(s) within the PCR amplicon. As a result, amplification by PCR is not possible. The genomic DNA with a few copies of the transgene remains single-stranded and unaffected by the restriction enzyme, leading to amplification by PCR. This protocol has been successfully tested with 4 different binary vectors and 3Agrobacterium tumefaciens strains: EHA105, LBA4404, and GV3101.     

Site specific chemical delivery of NSAIDs to inflamed joints: synthesis, biological activity and gamma-imaging studies of quaternary ammonium salts of tropinol esters of some NSAIDs or their active metabolites

Quaternized tropinol ester derivatives of some commonly used non-steroidal anti-inflammatory drugs (NSAIDs) or their active metabolites, were prepared and studied for their anti-inflammatory activity in a chronic inflammation model and for inflamed tissue tropism. The quaternized esters were radiolabeled with 99mTechnetium (99mTc) and their selective localization in the inflamed tissue was traced using scintigraphy. In the chronic arthritis rodent model, most of the quaternized esters exhibited anti-inflammatory effect comparable to their respective parent drugs. In the gamma-imaging studies only the quaternary derivatives exhibited selective accumulation into the inflamed tissue unlike the parent NSAIDs or the unquaternized tropinol esters. This work is a step ahead in the direction of use of quaternary ammonium ester derivatives for site specific chemical delivery of commonly used NSAIDs to the inflamed tissues to minimize their GIT side effect or other systemic toxicities.     

In vitro plantlet regeneration from mature zygotic embryos of Pinus wallichiana A.B. Jacks

 Plantlet regeneration was achieved in blue pine (Pinus wallichiana A.B. Jacks) by organogenesis of mature zygotic embryos. The effect of various basal media and five cytokinins on adventitious bud induction, development and elongation was investigated. Half-strength Douglas fir cotyledon revised medium (DCR) supplemented with 2.5 μm N⁶-benzyladinine (BA) and 0.025 μM thidiazuron was found to be most effective in inducing adventitious buds. The effect of a BA pulse treatment was also tested, and the bud-forming capacity of each treatment was quantified. The elongation of adventitious buds was achieved on hormone-free half-strength DCR medium containing 2% sucrose and 0.05% activated charcoal. Rooting was induced in the elongated shoots with a 6-h treatment of indoleacetic acid and indolebutyric acid solutions (1 mM each). Rooted shoots were transplanted in the greenhouse for hardening and their survival percentage was 64.4 after 5 weeks and 45.7 after 6 months. Received: 11 September 1998 / Revision received: 10 February 1999 / Accepted: 26 February 1999     

Role of Vanadium (V) in the Differentiation of C3H10t1/2 Cells Towards Osteoblast Lineage: A Comparative Analysis with Other Trace Elements

In recent time, vanadium compounds are being used as antidiabetic drug and in orthopedic implants. However, the exact role of this incorporated vanadium in improving the quality of bone structure and morphology is not known. The impact of vanadium ion was studied and compared to other trace metal ions with respect to the proliferation and osteoblast differentiation of C3H10t1/2 cells. Toxicity profile of these trace metal ions revealed a descending toxicity trend of Fe²⁺ > Zn²⁺ > Cu²⁺ > Co²⁺ > Mn²⁺ > V⁵⁺ > Cr²⁺. The effect of vanadium and other trace metal ions on osteoblast differentiation was evaluated by culturing the cells for 10 days in osteoblastic medium supplemented with different trace ions at concentrations lower than their cytotoxic doses. The results indicated that vanadium has maximum impact on the induction of osteoblast differentiation by upregulating alkaline phosphatase activity and mineralization by up to 145 and 150 %, respectively (p?<?0.05), over control. Cu²⁺ and Zn²⁺ had a mild inhibitory effect, while Mn²⁺, Fe²⁺, and Co²⁺ demonstrated a clear decrease in osteoblast differentiation when compared to the control. The data as presented here demonstrate that orthopedic implants, if supplemented with trace metals like vanadium, may provide a source of better model for bone formation and its turnover.