The synthesis of (−)-varitriol and (−)-3′-epi-varitriol via a Ramberg-Bäcklund route

A concise route to the anti-tumour natural product (−)-varitriol, together with its novel isomer (−)-3′-epi-varitriol, is described using a Horner-Wadsworth-Emmons (HWE)/conjugate addition/Ramberg-Bäcklund sequence as the cornerstone. The flexibility of the synthetic route has been demonstrated by the preparation of novel varitriol analogues.     

Synthesis of tricyclic analogues of methyllycaconitine using ring closing metathesis to append a B ring to an AE azabicyclic fragment

The synthesis of several ABE tricyclic analogues of the alkaloid methyllycaconitine 1 is reported. The analogues contain two key pharmacophores: a homocholine motif formed from a tertiary N-ethyl amine in a 3-azabicyclo[3.3.1]nonane ring system and a 2-(3-methyl-2,5-dioxopyrrolidin-1-ly)benzoate ester 4. The synthesis of the ABE tricyclic analogues of MLA 1 began with selective allylation at C-3 of 3 to produce allyl beta-keto ester 4. Double Mannich reaction of 4 with ethylamine and formaldehyde produced bicyclic amine 5 The C-9 ketone of bicyclic amine 5 was selectively reduced to form bicyclic alcohols 6 and 7 which were subsequently allylated to form dienes 8 and 9. Ring closing metathesis of dienes 8 and 9 afforded tricyclic ethers 11 and 12, respectively, the C-8 ester of which was reduced to a hydroxymethyl group to form ABE tricyclic analogues 13 and 14. Addition of allylmagnesium bromide to the C-9 ketone of 20 afforded dienes 21 and 22, which underwent ring closing metathesis to form tricyclic esters 23 and 24, respectively. Reduction of the C-8 ethyl ester of 23 and 24 to a hydroxymethyl group afforded diols 25 and 26 respectively. The 2-(3-methyl-2,5-dioxopyrrolin-1-ly)benzoate ester was introduced by conversion of alcohols 13, 14, 25 and 26, to the anthranilate esters 16, 17, 27 and 28 using N-(trifluoroacetyl)anthranilic acid 15 followed by fusion with methylsuccinic anhydride to afford the substituted anthranilates 18, 19, 29 and 30 containing the key 2-(3-methyl-2,5-dioxopyrrolidin-1-ly)benzoate ester pharmacophore.     

Model systems for flavoenzyme activity: a tuneable intramolecularly hydrogen bonded flavin-diamidopyridine complex

We report the electrochemically tuneable intramolecular hydrogen bonding interactions between a covalently linked flavin-diamidopyridine unit.     

Delineation of RAID1, the RACK1 interaction domain located within the unique N-terminal region of the cAMP-specific phosphodiesterase, PDE4D5

Background  

The cyclic AMP specific phosphodiesterase, PDE4D5 interacts with the β-propeller protein RACK1 to form a signaling scaffold complex in cells. Two-hybrid analysis of truncation and mutant constructs of the unique N-terminal region of the cAMP-specific phosphodiesterase, PDE4D5 were used to define a domain conferring interaction with the signaling scaffold protein, RACK1.     

Ferrocene incorporating host-guest dyads with electrochemically controlled three-pole hydrogen bonding properties

We describe the electrochemically controlled hydrogen bonding interactions between the isobutyl flavin/2,6-diferrocenylamidopyridine (2·5) and 9,10-phenanthrenequinone/1-ferrocenyl-3-hexylurea (4·6) dyads. Cyclic and square wave voltammetry studies have shown that the binding efficiencies between these moieties can be electrochemically actuated in non-polar (CH₂Cl₂ for 2·5) or polar (DMF for 4·6) organic solvents between three distinct states.     

Advances in coupling a commercial total organic carbon analyser with an isotope ratio mass spectrometer to determine the isotopic signal of the total dissolved nitrogen pool

A new method has been developed to analyse 15N of the total dissolved nitrogen (TDN) pool. The method operates on a commercial total organic carbon (TOC) analyser coupled to an elemental analyser/isotope ratio mass spectrometer (EA-IRMS). Nitrogen compounds are combusted to nitric oxide (NO) and nitrogen dioxide (NO2) by high-temperature catalytic oxidation (HTCO), after which the NOx gas is transferred to an EA-IRMS for isotopic nitrogen analysis. The system is described, including five modifications of the system in order to overcome analytical problems. First, flow paths were modified to run both systems on helium as carrier gas, while complete sample oxidation was maintained. Secondly, the catalyst structure was adapted to allow high injection volumes at the given backpressures delivered by the EA system. Thirdly, we installed a Permapure dehumidification system as the standard Peltier element did not satisfy dehumidification requirements. Finally, we prevented the inflow of atmospheric nitrogen into the system. In a final stage, we are planning to automate the coupled system in order to run a continuous batch of up to 60 samples. We have obtained satisfactory results on the accuracy and precision of 180+/-1 per thousand potassium nitrate samples (IAEA, USGS-32). Running a batch of five samples resulted in a mean isotopic value of 178.8 per thousand with a standard deviation of 2.8 per thousand. Some important issues could not yet be addressed here, and will have to be evaluated once the system is running on a continuous base. However, the results appear promising and this system has the potential to become a method for TD15N analysis. An appropriate TD15N analysis method might open new challenges in aquatic and terrestrial ecosystem nitrogen studies, including a more comprehensive study of the dissolved organic nitrogen pool.     

Protein family classification and functional annotation

With the accelerated accumulation of genomic sequence data, there is a pressing need to develop computational methods and advanced bioinformatics infrastructure for reliable and large-scale protein annotation and biological knowledge discovery. The Protein Information Resource (PIR) provides an integrated public resource of protein informatics to support genomic and proteomic research. PIR produces the Protein Sequence Database of functionally annotated protein sequences. The annotation problems are addressed by a classification-driven and rule-based method with evidence attribution, coupled with an integrated knowledge base system being developed. The approach allows sensitive identification, consistent and rich annotation, and systematic detection of annotation errors, as well as distinction of experimentally verified and computationally predicted features. The knowledge base consists of two new databases, sequence analysis tools, and graphical interfaces. PIR-NREF, a non-redundant reference database, provides a timely and comprehensive collection of all protein sequences, totaling more than 1,000,000 entries. iProClass, an integrated database of protein family, function, and structure information, provides extensive value-added features for about 830,000 proteins with rich links to over 50 molecular databases. This paper describes our approach to protein functional annotation with case studies and examines common identification errors. It also illustrates that data integration in PIR supports exploration of protein relationships and may reveal protein functional associations beyond sequence homology.     

Five-coordinate Fe(III)NO and Fe(II)CO porphyrinates: where are the electrons and why does it matter?

Recent years have seen dramatic growth in our understanding of the biological roles of nitric oxide (NO). Yet, the fundamental underpinnings of its reactivities with transition metal centers in proteins and enzymes, the stabilities of their structures, and the relationships between structure and reactivity remains, to a significant extent, elusive. This is especially true for the so-called ferric heme nitrosyls ([FeNO](6) in the Enemark-Feltham scheme). The Fe-CO and C-O bond strengths in the isoelectronic ferrous carbonyl complexes are widely recognized to be inversely correlated and sensitive to structural, environmental, and electronic factors. On the other hand, the Fe-NO and N-O bonds in [FeNO](6) heme complexes exhibit seemingly inconsistent behavior in response to varying structure and environment. This report contains resonance Raman and density functional theory results that suggest a new model for FeNO bonding in five-coordinate [FeNO](6) complexes. On the basis of resonance Raman and FTIR data, a direct correlation between the nu(Fe)(-)(NO) and nu(N)(-)(O) frequencies of [Fe(OEP)NO](ClO(4)) and [Fe(OEP)NO](ClO(4)).CHCl(3) (two crystal forms of the same complex) has been established. Density functional theory calculations show that the relationship between Fe-NO and N-O bond strengths is responsive to FeNO electron density in three molecular orbitals. The highest energy orbital of the three is sigma-antibonding with respect to the entire FeNO unit. The other two comprise a lower-energy, degenerate, or nearly degenerate pair that is pi-bonding with respect to Fe-NO and pi-antibonding with respect to N-O. The relative sensitivities of the electron density distributions in these orbitals are shown to be consistent with all published indicators of Fe-N-O bond strengths and angles, including the examples reported here.     

Hydrogen bonding in redox-modulated molecular recognition. An experimental and theoretical investigation

Two receptors, a diaminotriazine derivative (DAT) and diamidopyridine (DAP), are complementary to the electroactive naphthalimide (N) through three-point hydrogen bonding. The association constants of the two receptors were evaluated for both the fully oxidized and the radical anion forms of N. In the oxidized state, the two receptors displayed identical binding constants. Diamidopyridine, however, lowers the reduction potential of naphthalimide to a far greater extent than does diaminotriazine, indicating a greater affinity for diamidopyridine by naphthalimide in the radical anion form. This behavior was mirrored by EPR experiments that showed small deviations from the hyperfine coupling pattern of N(red) in the presence of DAT, with greater effects seen for the N(red).DAP complex. Computational simulations using the UB3LYP/6-311+G(d,p)//UHF/6-31G(d) hybrid gave theoretical hyperfine constants in good quantitative agreement with the experimental results. Using this correlation, we determined that electrostatics and hydrogen bond polarizability play key roles in controlling redox-modulated molecular recognition.