Synthesis, NMR kinetics and dynamic structure of a 17-mer heptaloop RNA hairpin carrying a 3-N-methyluridine nucleotide residue in the loop region.

A 17-mer RNA hairpin (5'GGGAGUXAGCGGCUCCC3') carrying 3-N-methyluridine (m3U) at position X (m3U7-RNA), designed to represent the anticodon stem-loop (ACSL) region of tRNAs to study an open loop state (O-state), was synthesized, purified by HPLC, and characterized by MALDI-ToF_MS and NMR methods. 1H-NMR data revealed primary (P-state in 56.1%), secondary (S-state in 43.9%) and tertiary (∼5-6%) ACSL conformations. Exchange rate constant (kex) for interconversion between P and S states is 112 sec-1 (<Δω ∼454 rad/sec), confirming a slow exchange regime between the two states. Forward (kPS) and backward (kSP) rate constants are 49.166 sec-1 and 62.792 sec-1, respectively, leading to a longer life-time (20.339 msec) for the P-state and a shorter life-time (15.926 msec) for the S-state. In accordance with conformational populations determined by 1H-NMR, dynamics of the P/S/tertiary states of m3U7-RNA and its wild-type counterpart (wt-RNA) were studied by three independent MD production simulations. Cluster analysis revealed that wt-RNA reflects the structural characteristics of the ACSL region of tRNAs. The P-state of m3U7-RNA was found to be structurally similar to wt-RNA but lacks an intraloop H-bond between m3U7 and C10 (U33 and nt36 in tRNAs). In the S-state of m3U7-RNA, m3U7 flips out of the loop region. O-state loop conformations of m3U7-RNA were also clustered (4.8%), wherein the loop nucleotides m3U7.A8.G9.C10.G11 stack one after another. We propose that the O-state of m3U7-RNA is the most suitable conformation that makes the loop accessible for complementary nucleotides and for non-enzymatic primordial replication of small circular RNAs.Communicated by Ramaswamy H. Sarma.

Preliminary results of a novel quorum sensing inhibitor against pneumococcal infection and biofilm formation with special interest to otitis media and cochlear implantation.

The purpose of the study is to assess the effect of a novel quorum sensing inhibitor (QSI), coded as 'yd 47', against otitis media and biofilm formation on Cochlear implants (CIs). Small pieces cut from cochlear implant were implanted under the skin in the retroauricular area on both sides of four guinea pigs. The implant pieces in the study and control sides were implanted in Streptococcus pneumoniae strain solution and saline, respectively. The right and left middle ears were also instilled with a solution containing pneumococci and saline, respectively. The animals were only given an intraperitoneal 'yd 47' twice daily for three months to be assessed later with electron microscopy. Clinical examination with palpation, inspection and otoscopy did not reveal any sign of implant infection or otitis media. In the study and control implant materials, soft tissues around the implant and tympanic membranes, there was no biofilm formation by pneumococci. Contamination by various cells and some rod-shaped bacteria (not diplococcic) were seen in some of the materials. In conclusion, the novel QSI seems promising in the prevention of otitis media and biofilm formation on CIs by pneumococci.

Use of the parmbsc0 force field and trajectory analysis to study the binding of netropsin to the DNA fragment (5'CCAATTGG)(2) in the presence of excess NaCl salt in aqueous solution.

The parmbsc0 force field was applied to study in detail the binding of netropsin, at a salt concentration of 0.28M Na(+), to the minor groove of an 8-mer (5'CCAATTGG)(2) DNA duplex forming a netropsin·DNA complex which previously has been characterized by X-ray crystallography, albeit with the use of closely related DNA duplexes. The X-ray structure revealed that the terminal guanidinium and amidinium groups of netropsin interact with the extreme ends of the palindromic AATT sequence of the receptor DNA. The parmbsc0 parameters of B-DNA and AMBER v9 parameters of netropsin generated a stable 6ns molecular dynamics (MD) trajectory for a 1:1 class I binding motif of this complex. Trajectory analysis for the salt and hydration effects on the binding of netropsin to the 8-mer DNA duplex revealed that 18 water molecules and 2 Na(+) are displaced from the DNA upon netropsin binding. A hydration density map of the complex parallels the X-ray data showing that two structured water molecules are localized near the netropsin guanidinium and amidinium groups forming H-bond bridges between the receptor and the ligand.

NMR and amber analysis of the neamine pharmacophore for the design of novel aminoglycoside antibiotics.

The dependence of the solution structure of neamine on pH was determined by NMR and AMBER molecular dynamics methods at pD 3.3, pD 6.5, and pD 7.4 in D(2)O at 25°C. Unlike neamine structures at pD 3.3 and 6.5, which essentially showed only one conformer, slowly exchanging primary, P-state, and secondary, S-state, neamine conformers populated on the NMR time scale at ~80% and ~20%, respectively, were detected at pD 7.4 with kinetic constants k(on(P→S))=1.9771s(-1) and k(off(S→P))=1.1319s(-1). A tertiary, T-state, neamine species populated at ~3% was also detected by NMR at pD 7.4. The pKa values determined by NMR titration experiments are pKa1 6.44±0.13 for N3 of ring-II, pKa2 7.23±0.09 for N2' of ring-I, pKa3 7.77±0.19 for N1 of ring-II, and pKa4 8.08±0.15 for N6' of ring-I. Ring-I and ring-II of the P-state neamine and ring-I of the S and T-states of neamine possess the (4)C(1) chair conformation between pD 3.3 and pD=7.4. In contrast, ring-II of the S and T-states of neamine most likely adopt the (6)rH(1) half-chair conformation. The P and S-states of neamine exhibit a negative syn-ψ glycosidic geometry. The exocyclic aminomethyl group of ring-I adopts the gt exocyclic rotamer conformation around physiological pHs while the gg exocyclic rotamer conformation predominates in acidic solutions near and below pH 4.5. Neamine exists in the P-state as a mixture of tetra-/tri-/di-protonated species between pD 4.5 and pD 7.4, while the S-state neamine exist only in a di-protonated species around physiological pDs. The existence of the S-state neamine may facilitate binding of neamine-like aminoglycosides by favorable entropy of binding to the A-site of 16S ribosomal RNA, suggesting that novel aminoglycoside compounds carrying a S-state neamine pharmacophore can be developed.

Synthesis and biological evaluation of 4,5-diphenyloxazolone derivatives on route towards selective COX-2 inhibitors.

A series of 3-unsubstituted/substituted-4,5-diphenyl-2-oxo-3H-1,3-oxazole derivatives were prepared as selective cyclooxygenase-2 (COX-2) inhibitors. Among the synthesized compounds, 4-(4-phenyl-3-methyl-2-oxo-3H-1,3-oxazol-5-yl)benzensulfonamide (compound 6) showed selective COX-2 inhibition with a selectivity index of >50 (IC(50)COX-1=>100 microm, IC(50)COX-2=2 microm) in purified enzyme (PE) assay. Compound 6 also exhibited selective COX-2 inhibition in human whole blood assay. Molecular docking studies showed that 6 can be docked into the COX-2 binding site thus providing the molecular basis for its activity.

Antiviral and antimicrobial activities of new nitrobutane derivatives.

It is known that some addition products of beta-nitrostyrenes exhibit potent antimicrobial activity. In order to investigate the effects of structural modifications on the biological properties, some new Michael type addition products of beta-ethyl-beta-nitrostyrenes were synthesized. In this study, eight new 1-[(2-aminophenyl)thio]-1-phenyl-2-nitrobutane (2) derivatives were synthesized by addition of 2-aminothiophenol to the double bond of beta-ethyl-beta-nitrostyrenes (1). The chemical structures were proved by IR and 1H-NMR data and by elemental analysis. Antimicrobial activities of the synthesized compound were investigated against Escherichia coil, Pseudomonas aeruginosa, Proteus mirabilis, Enterococcus faecalis, Bacillus subtilis, Staphylococcus aureus, Candida albicans by the microdilution method. In addition, the newly synthesized compounds were studied for antiviral activities. All of them were found to be almost 100 fold more active than the standard compound aciclovir (CAS 59277-89-3).

Synthesis and analgesic and anti-inflammatory activity of some new (6-acyl-2-benzoxazolinone and 6-acyl-2-benzothiazolinone derivatives with acetic acid and propanoic acid residues.

In this study for developing potent analgesic and anti-inflammatory compounds, we synthesized 6-acyl-2-benzoxazolinone and 6-acyl-2-benzothiazolinone derivatives with acetic acid and propanoic acid side chain, and performed preliminary screening of their in vivo analgesic and anti-inflammatory activities at a single dose of 100 mg/kg inmice by a p-benzoquinone-induced writhing test and a Carrageenaninduced hind paw edema model, respectively. We also determined their gastric ulceration effects in the tested animals. Propanoic acid derivatives were generally found to have higher analgesic and anti-inflammatory activities, and among them, 3-(6-benzoyl-2-benzothiazolinon-3-yl)propanoic acid (Compound 4 a) exhibited the highest analgesic and anti-inflammatory activity. However, all compounds showed lower anti-inflammatory effects than we observed for indomethacin at 10 mg/kg dose. Consequently, 6-acyl-2-benzoxazolinone/2-benzothiazolinones having propanoic acid side chain might lead to further studies for developing better candidates with potent analgesic and anti-inflammatory effects while acetic acid derivatives do not exhibit comparable satisfactory features.