In silico identification and in vitro antiviral validation of potential inhibitors against Chikungunya virus

Journal of Computer-Aided Molecular Design - The Chikungunya virus (CHIKV) has become endemic in the Africa, Asia and Indian subcontinent, with its continuous re-emergence causing a significant...     

Five- and six-membered conformationally locked 2',4'-carbocyclic ribo-thymidines: synthesis, structure, and biochemical studies

Two unusual reactions involving the 5-hexenyl or the 6-heptenyl radical cyclization of a distant double bond at C4' and the radical center at C2' of the ribofuranose ring of thymidine have been used as key steps to synthesize North-type conformationally constrained cis-fused bicyclic five-membered and six-membered carbocyclic analogues of LNA (carbocyclic-LNA-T) and ENA (carbocyclic-ENA-T) in high yields. Their structures have been confirmed unambiguously by long range 1H-13C NMR correlation (HMBC), TOCSY, COSY, and NOE experiments. The carbocyclic-LNA-T and carbocyclic-ENA-T were subsequently incorporated into the antisense oligonucleotides (AONs) to show that they enhance the Tm of the modified AON/RNA heteroduplexes by 3.5-5 degrees C and 1.5 degrees C/modification for carbocyclic-LNA-T and carbocyclic-ENA-T, respectively. Whereas the relative RNase H cleavage rates with carbocyclic-LNA-T, carbocyclic-ENA-T, aza-ENA-T, and LNA-T modified AON/RNA duplexes were found to be very similar to that of the native counterpart, irrespective of the type and the site modification in the AON strand, a single incorporation of carbocyclic-LNA and carbocyclic-ENA into AONs leads to very much more enhanced nuclease stability in the blood serum (stable >48 h) as compared to that of the native (fully degraded <3 h) and the LNA-modified AONs (fully degraded <9 h) and aza-ENA ( approximately 85% stable in 48 h). Clearly, remarkably enhanced lifetimes of these carbocyclic-modified AONs in the blood serum may produce the highly desired pharmacokinetic properties because of their unique stability and consequently a net reduction of the required dosage. This unique quality as well as their efficient use as the AON in the RNase H-promoted cleavage of the target RNA makes our carbocyclic-LNA and carbocyclic-ENA modifications excellent candidates as potential antisense therapeutic agents.     

Carba-LNA-5MeC/A/G/T modified oligos show nucleobase-specific modulation of 3'-exonuclease activity, thermodynamic stability, RNA selectivity, and RNase H elicitation: synthesis and biochemistry

Using the intramolecular 5-exo-5-hexenyl radical as a key cyclization step, we previously reported an unambiguous synthesis of carba-LNA thymine (cLNA-T), which we subsequently incorporated in antisense oligonucleotides (AON) and investigated their biochemical properties [J. Am. Chem. Soc.2007, 129 (26), 8362-8379]. These cLNA-T incorporated oligos showed specific RNA affinity of +3.5-5 °C/modification for AON:RNA heteroduplexes, which is comparable to what is found for those of LNAs (Locked Nucleic Acids). These modified oligos however showed significantly enhanced nuclease stability (ca. 100 times more) in the blood serum compared to those of the LNA modified counterparts without compromising any RNase H recruitment capability. We herein report the synthesis of 5-methylcytosine-1-yl ((Me)C), 9-adeninyl (A), and 9-guaninyl (G) derivatives of cLNA and their oligonucleotides and report their biochemical properties as potential RNA-directed inhibitors. In a series of isosequential carba-LNA modified AONs, we herein show that all the cLNA modified AONs are found to be RNA-selective, but the magnitude of RNA-selectivity of 7'-R-Me-cLNA-G (cLNA-G) (ΔT(m) = 2.9 °C/modification) and intractable isomeric mixtures of 7'-(S/R)-Me-cLNA-T (cLNA-T, ΔT(m) = 2.2 °C/modification) was found to be better than diastereomeric mixtures of 7'-(S/R)-Me-cLNA-(Me)C with trace of cENA-(Me)C (cLNA-(Me)C, ΔT(m) = 1.8 °C/modification) and 7'-R-Me-cLNA-A (cLNA-A, ΔT(m) = 0.9 °C/modification). cLNA-(Me)C modified AONs however exhibited the best nuclease stability, which is 4-, 7-, and 20-fold better, respectively, than cLNA-T, cLNA-A, and cLNA-G modified counterparts, which in turn was more than 100 times stable than that of the native. When the modification sites are appropriately chosen in the AONs, the cLNA-A, -G, and -(Me)C modified sites in the AON:RNA hybrids can be easily recognized by RNase H, and the RNA strand of the hybrid is degraded in a specific manner, which is important for the design of oligos for therapeutic purposes. The cLNA-(Me)C modified AON/RNA, however, has been found to be degraded 4 times faster than cLNA-A and G modified counterparts. By appropriately choosing the carba-LNA modification sites in AON strands, the digestion of AON:RNA can be either totally repressed or be limited to cleavage at specific sites or at a single site only (similar to that of catalytic RNAzyme or DNAzyme). Considering all physico- and biochemical aspects of cLNA modified oligos, the work suggests that the cLNA modified antisense oligos have the potential of being a promising therapeutic candidate due to their (i) higher nucleobase-specific RNA affinity and RNA selectivity, (ii) greatly improved nuclease stability, and (iii) efficient RNase H recruitment capability, which can induce target RNA cleavage in a very specific manner at multiple or at a single site, in a designed manner.     

Low bias electron scattering in structure-identified single wall carbon nanotubes: role of substrate polar phonons

We have performed temperature-dependent electrical transport measurements on known structure single wall carbon nanotubes at low bias. The experiments show a superlinear increase in nanotube resistivity with temperature, which is in contradiction with the linear dependence expected from nanotube acoustic-phonon scattering. The measured electron mean free path is also much lower than expected, especially at medium to high temperatures (>100 K). A theoretical model that includes scattering due to surface polar phonon modes of the substrates reproduces the experiments very well. The role of surface phonons is further confirmed by resistivity measurements of nanotubes on aluminum nitride.     

Strong electric field modulation of transport in PVDF/MWCNT nanocomposite near the percolation threshold

A nanocomposite comprising of multiwalled carbon nanotubes (MWCNT) embedded in ferroelectric Poly(vinylidene fluoride) PVDF polymer matrix is examined for electric field induced transport modulation. The pulsed laser deposition (PLD) grown thin films of the nanocomposite with different MWCNT content were characterized. When used as a channel layer in a field effect transistor configuration, a strong electric field modulation of the transport was realized just below the percolation threshold. We believe that this nanocomposite non-percolating channel concept can provide several opportunities for FET devices for organic electronics.     

Nickel–Schiff base complex catalyzed C–S cross-coupling of thiols with organic chlorides

We report an efficient, mild and convenient synthetic protocol for the C–S cross-coupling reaction of various aryl, benzyl, allyl chlorides and thiols using 5 mol % Nickel–Schiff base catalyst with NaOH as the base, in DMF at 70 °C. Using this protocol, we have shown that a variety of aryl sulfides can be synthesized in excellent yields from readily available organic chlorides and thiols.     

Applicability of waste materials--bottom ash and deoiled soya--as adsorbents for the removal and recovery of a hazardous dye, brilliant green

Deoiled soya, an agricultural waste material, and bottom ash, a waste of power plants, have been successfully used for the removal and recovery of the hazardous water-soluble dye brilliant green from water. To remove the dye from water, batch adsorption studies have been carried out by observing the effects of pH, concentration, amounts of adsorbents, size of adsorbent particles, etc. Attempts have also been made to monitor the adsorption process through Langmuir, Freundlich, Tempkin, and D-R adsorption isotherm models. Relevant thermodynamic parameters have also been calculated from these models. The adsorption process has been found endothermic and feasible at all the temperatures. The kinetics of the adsorption was also recorded and indicates pseudo-second-order kinetics in both cases. Kinetic operations also reveal the involvement of a film diffusion mechanism for the deoiled soya adsorption at all the temperatures, while bottom ash undergoes through a particle diffusion mechanism at only 30 °C and at higher temperatures a film diffusion mechanism operates. Bulk removal of the dye has been carried out through column studies for both adsorbents. Attempts have also been made to recover the dye from exhausted columns by eluting sulfuric acid of pH 3.     

Selective recognition of H2PO4- by a cholestane-imidazole-zinc ensemble

A new facile amphiphile cholestane-based zinc complex 4 containing a 3-aminopropylimidazole moiety at the 3α and 7α positions of cholestane was designed and synthesized. Recognition selectivity of the new receptor 4 with various anions was assessed by ¹H NMR titration. Dihydrogen phosphate showed the highest binding affinity among all the tested anions (K_a = 4.4 × 10⁵ M^?1).     

Nonvanishing of Siegel Poincaré series

We prove that, under suitable conditions, certain Siegel Poincaré series of exponential type of even integer weight and degree 2 do not vanish identically. We also find estimates for twisted Kloosterman sums and Salié sums in all generality.     

Interactions of drugs and an oligonucleotide with charged membranes analyzed by immobilized liposome chromatography

We studied the effect of charged lipids or detergent on the retention of drugs and an oligonucleotide by immobilized liposome chromatography to characterize solute-membrane interactions. This is a novel approach in analysis of oligonucleotide-liposome interactions. The charged lipids (phosphatidylserine or distearoyltrimethylammoniumpropane) or detergent (sodium dodecylsulfate) interacted electrostatically in a concentration-dependent matter with the solutes. The oligonucleotide ions presumably bound to the liposomes by multipoint interactions, which was saturable. Sodium dodecylsulfate seemed to affect the drug-membrane interactions more strongly than phosphatidylserine did, probably due to different positioning in the bilayer.