Exploring the potential of 3'-O-carboxy esters of thymidine as inhibitors of ribonuclease A and angiogenin

In this study, compounds with a carboxy ester in lieu of the phosphate ester at the 3'-position have been employed to inhibit the ribonucleolytic activity of ribonuclease A (RNase A). Phosphates at the 3'-position of pyrimidine bases are well-known inhibitors of the protein. We have investigated the inhibition of RNase A by 3'-O-carboxy esters of thymidine. The compounds behave as competitive inhibitors with inhibition constants ranging from 42 to 95 microM. The mode of inhibition has also been confirmed by (1)H NMR studies of the active site histidines of RNase A. Docking studies have further substantiated the experimental results. The compounds are also found to inhibit the ribonucleolytic activity of angiogenin, a homologous protein and potent inducer of blood vessel formation.     

Interface of apoptotic protein complexes has distinct properties

Apoptosis is a programmed mechanism of cell death that is a normal component of development and health of multi-cellular organisms. In this study, we ask if interface properties of apoptotic protein complexes are different from protein complexes in general. We find that although in apoptotic protein complexes the overall distribution of interface size, surface complementarity, hydrogen bonding, hydrophobicity are similar to general interface properties, apoptotic complexes tend to have more fragmented interfaces and different secondary structural preferences. The statistics on the number of interfaces where specific amino acid(s) occur with significantly enhanced frequency suggest that Arg, Met and Asp are most important functional residues. The role of Met is believed to be unique, as evidenced from the existing data on hot spot potential of residues. These findings together provide insight into the possible role of various physico-chemical attributes at the protein interface in regulation of the apoptosis process.     

Morphology of the archaellar motor and associated cytoplasmic cone in Thermococcus kodakaraensis

Archaeal swimming motility is driven by archaella: rotary motors attached to long extracellular filaments. The structure of these motors, and particularly how they are anchored in the absence of a peptidoglycan cell wall, is unknown. Here, we use electron cryotomography to visualize the archaellar basal body in vivo in Thermococcus kodakaraensis KOD1. Compared to the homologous bacterial type IV pilus (T4P), we observe structural similarities as well as several unique features. While the position of the cytoplasmic ATPase appears conserved, it is not braced by linkages that extend upward through the cell envelope as in the T4P, but rather by cytoplasmic components that attach it to a large conical frustum up to 500 nm in diameter at its base. In addition to anchoring the lophotrichous bundle of archaella, the conical frustum associates with chemosensory arrays and ribosome‐excluding material and may function as a polar organizing center for the coccoid cells.     

Effect of Ayurvedic mercury preparation Makaradhwaja on geriatric canine--a preliminary study

Makaradhwaja, an alchemical Ayurvedic mercury preparation is used as stimulant and vitalizer. Towards veterinary practices, the acceptability, tolerability and toxicity studies were undertaken in geriatric pet dogs aged more than 10 years irrespective of breed and sex for future use. Makaradhwaja (2.5 mg/kg) was used with honey once daily for 30 days. Before and after treatment, blood was collected for hematological studies as well as liver, kidney function and anti-oxidant activity. In control group, honey itself showed no appreciable change whereas, Makaradhwaja lowered neutrophil and total leucocyte count. Serum cholesterol, urea, glucose, alanine amino transferase, aspartate amino transferase, sodium, phosphorus and calcium were decreased. Haemoglobin and serum creatinine were significantly increased. There was appreciable physical, behavioral and body weight change including quality of life. The dose was used in replication of human dose (125 mg/50 kg). Anti-oxidant study showed significant increase of lipid per oxidation in experimental group while the values of ABTS radical cation decolorisation assay although decreased but did not show any significant changes. Decrease of serum urea and increase of serum creatinine could not be explained on single dose response. Different dose study could only explain the optimum dose to be required in canine practices.     

Isolation and Characterization of Chromium(VI)-Reducing Bacteria from Tannery Effluents

Two chromium-resistant bacteria (IFR-2 and IFR-3) capable of reducing/transforming Cr(VI) to Cr(III) were isolated from tannery effluents. Isolates IFR-2 and IFR-3 were identified as Staphylococcus aureus and Pediococcus pentosaceus respectively by 16S rRNA gene sequence analyses. Both isolates can grow well on 2,000 mg/l Cr(VI) (as K₂Cr₂O₇) in Luria-Bertani (LB) medium. Reduction of Cr(VI) was found to be growth-associated in both isolates and IFR-2 and IFR-3 reduced 20 mg/l Cr(VI) completely in 6 and 24 h respectively. The Cr(VI) reduction due to chromate reductase activity was detected in the culture supernatant and cell lysate but not at all in the cell extract supernatant of both isolates. Whole cells of IFR-2 and IFR-3 converted 24 and 30% of the initial Cr(VI) concentration (1 mg/l) in 45 min respectively at 37°C. NiCl₂ stimulated the growth of IFR-2 whereas HgCl₂ and CdCl₂ significantly inhibited the growth of both isolates. Optimum temperature and pH for growth of and Cr(VI) reduction by both isolates were found to be between 35 and 40°C and pH 7.0 to 8.0. The two bacterial isolates can be good candidates for detoxification of Cr(VI) in industrial effluents.     

Protein interactions of phosphatase and tensin homologue (PTEN) and its cancer-associated G20E mutant compared by using stable isotope labeling by amino acids in cell culture-based parallel affinity purification

The tumor suppressor PTEN (phosphatase and tensin homologue) negatively regulates the PI3K pathway through its lipid phosphatase activity and is one of the most commonly lost tumor suppressors in human cancers. Though the tumor suppressive function involves the lipid phosphatase-dependent and -independent activities of PTEN, the mechanism leading to the phosphatase-independent function of PTEN is understood poorly. Some PTEN mutants have lipid phosphatase activity but fail to suppress cell growth. Here, we use a cancer-associated mutant, G20E, to gain insight into the phosphatase-independent function of PTEN by investigating protein-protein interactions using MS-based stable isotope labeling by amino acids in cell culture (SILAC). A strategy named parallel affinity purification (PAP) and SILAC has been developed to prioritize interactors and to compare the interactions between wild-type and G20E PTEN. Clustering of the prioritized interactors acquired by the PAP-SILAC approach shows three distinct clusters: 1) wild-type-specific interactors, 2) interactors unique to the G20E mutant, and 3) proteins common to wild-type and mutant. These interactors are involved mainly in cell migration and apoptosis pathways. We further demonstrate that the wild-type-specific interactor, NUDTL16L1, is required for the regulatory function of wild-type PTEN in cell migration. These findings contribute to a better understanding of the mechanisms of the phosphatase-dependent and -independent functions of PTEN.     

QSAR study on adenosine kinase inhibition of pyrrolo[2,3-d]pyrimidine nucleoside analogues using the hansch approach

QSAR studies on series of pyrrolo[2,3-d]pyrimidine nucleoside analogues were performed for their adenosine kinase (AK) inhibitory activity using the Hansch approach. Significant correlations were obtained with hydrophobic parameter at position 'X'. Electronic and steric parameters on pyrimidine and pyrrole rings found to play an important role in the ligand-receptor interactions with the active sites of the enzyme. Presence of bulkier groups at 'X' and 'Y' positions seems to protect the title compounds from biodegradation, as is evident from their positive sterimol steric parameter B1 at these positions.     

Isg15 controls p53 stability and functions

Degradation of p53 is a cornerstone in the control of its functions as a tumor suppressor. This process is attributed to ubiquitin-dependent modification of p53. In addition to polyubiquitination, we found that p53 is targeted for degradation through ISGylation. Isg15, a ubiquitin-like protein, covalently modifies p53 at 2 sites in the N and C terminus, and ISGylated p53 can be degraded by the 20S proteasome. ISGylation primarily targets a misfolded, dominant-negative p53, and Isg15 deletion in normal cells results in suppression of p53 activity and functions. We propose that Isg15-dependent degradation of p53 represents an alternative mechanism of controlling p53 protein levels, and, thus, it is an attractive pathway for drug discovery.     

Ubiquitination and proteasomal degradation of ATG12 regulates its proapoptotic activity

During macroautophagy, conjugation of ATG12 to ATG5 is essential for LC3 lipidation and autophagosome formation. Additionally, ATG12 has ATG5-independent functions in diverse processes including mitochondrial fusion and mitochondrial-dependent apoptosis. In this study, we investigated the regulation of free ATG12. In stark contrast to the stable ATG12–ATG5 conjugate, we find that free ATG12 is highly unstable and rapidly degraded in a proteasome-dependent manner. Surprisingly, ATG12, itself a ubiquitin-like protein, is directly ubiquitinated and this promotes its proteasomal degradation. As a functional consequence of its turnover, accumulation of free ATG12 contributes to proteasome inhibitor-mediated apoptosis, a finding that may be clinically important given the use of proteasome inhibitors as anticancer agents. Collectively, our results reveal a novel interconnection between autophagy, proteasome activity, and cell death mediated by the ubiquitin-like properties of ATG12.     

Crystal Structures of HIV-1 gp120 Envelope Glycoprotein in Complex with NBD Analogues That Target the CD4-Binding Site

Efforts to develop therapeutic agents that inhibit HIV-1 entry have led to the identification of several small molecule leads. One of the most promising is the NBD series, which binds within a conserved gp120 cavity and possesses para-halogen substituted aromatic rings, a central oxalamide linker, and a tetramethylpiperidine moiety. In this study, we characterized structurally the interactions of four NBD analogues containing meta-fluoro substitution on the aromatic ring and various heterocyclic ring replacements of the tetramethylpiperidine group. The addition of a meta-fluorine to the aromatic ring improved surface complementarity and did not alter the position of the analogue relative to gp120. By contrast, heterocyclic ring replacements of the tetramethylpiperidine moiety exhibited diverse positioning and interactions with the vestibule of the gp120 cavity. Overall, the biological profile of NBD-congeners was modulated by ligand interactions with the gp120-cavity vestibule. Herein, six co-crystal structures of NBD-analogues with gp120 provide a structural framework for continued small molecule-entry inhibitor optimization.