Alkaloids conformations

Besides the use of novel fiinctionahty that is beyond rational design by synthetic chemists, nature is unsurpassed at the display of chemical information in three-dimensional space. For example, despite intensive efforts, there is no standard algorithm for translating a linear peptide into a small-molecule peptidomimetic. Meanwhile, numerous natural scaffolds perform this task efficiently, as in the opium alkaloids conformational mimicry of the enkephaUns. We will never know what revolutionary new scaffolds and pharmacophores will be lost if natural product screening is discontinued. 

Application of NMR spectroscopy to heterocyclic chemistry has developed very rapidly during the past 15 years, and the technique is now used almost as routinely as H NMR spectroscopy. There are four main areas of application of interest to the heterocyclic chemist (i) elucidation of structure, where the method can be particularly valuable for complex natural products such as alkaloids and carbohydrate antibiotics (ii) stereochemical studies, especially conformational analysis of saturated heterocyclic systems (iii) the correlation of various theoretical aspects of structure and electronic distribution with chemical shifts, coupling constants and other NMR derived parameters and (iv) the unravelling of biosynthetic pathways to natural products, where, in contrast to related studies with " C-labelled precursors, stepwise degradation of the secondary metabolite is usually unnecessary. 

Sencor — see l,2,4-Triazin-5-one, 4-amino-6-t-butyl-3-methylthio-Senecio alkaloids structure, 7, 658 Senepoxide, 7, 192 Senkirkine conformation, 7, 703 structure, 7, 658 Sensitizing dyes... 

Work also prepared a series of carbinolamines and polyamines without a quinoline nucleus but, in other respects, conforming in type and range of molecular weight, with quinoline compounds known to possess plasmocidal activity. As none of these were active, it seems clear that the quinoline nucleus in the cinchona alkaloids and in certain synthetic anti-malarials is a potent factor in the production of plasmocidal action. Later the same author made (1942) a series of lepidylamine derivatives of the form R. Q. CHj. NH[CH2] . NEtj, which were found to be inactive, in spite of their similarity to the active examples of the type R. Q. NH[CH2] . NEt2 prepared by Magidson and Rubtzow. Rubtzow (1939) has also shown that an isomeride of dihydroquinine (II) with the quinuclidine nucleus attached via the carbinol group at C in the quinoline nucleus was inactive in an infection of Plasmodium prcecox in finches. 

Conformational study of geissoschizine isomers and their model compounds (geissoschizine is the indolo[2,3-fl]quinolizidine derivative considered to be an important participant of indole alkaloids biogenesis) 99H(51)649. 

Vinylindoles have been studied extensively and used in the synthesis of carbazoles, alkaloids and other classes of pharmacologically active compounds. MMX force field calculations have shown that coplanar s-cis and. s-trans conformations of 3-vinylindole (84, Figure 2.11) are the most stable conformers they exhibit only slight differences in their thermodynamic stabilities [86]. 

Poly(dG-dC) poly(dG-dC) and its methylated analogue structures assume left-handed conformation (Z-DNA) in high molar sodium salt (Na", K" ), in low molar divalent cations (Ca", Mg", Ni ), micromolar concentrations of hexaamine cobalt chloride (Co(NH3)6)Cl3 and in millimolar concentrations of polyamines. In order to analyse the binding of berberine to Z-form DNA, Kumar et al. [186] reported that the Z-DNA structure of poly(dG-dC) poly(dG-dC) prepared in either a high salt concentration (4.0 M) or in 40 mM (Co(NH3)6)Cl3 remained invariant in the presence of berberine up to a nucleotide phosphate/alkaloid molar ratio of 0.8 and suggested that berberine neither bormd to Z-form DNA nor converted the Z-DNA to the... 

In order to develop compounds that can selectively target duplex RNA, Sinha et al. [ 194] studied the interaction of berberine with two different conformations of poly(rC) poly(rG) structures. Poly(rC) poly(rG) has been shown [15,215] to exist in two conformations depending on the pH of the solution, the A-form at physiological pH and the protonated form at pH 4.3. These two conformations have been characterized to have clearly defined but distinctly different circular dichroic and absorption spectral characteristics. Both the A-form and the protonated form of the RNA induced moderate hypochromic change and bathochromic shifts in the absorption maxima peaks at 344 nm and 420 nm of the alkaloid with three isosbestic points centered around 357,382 and 448 nm. Binding of berberine to both forms enhanced the fluorescence intensity, which was higher with the protonated form than with the A-from, suggesting clear differences in the nature of orientation... 

Taxonomically close to the Annonaceae, the Lauraceae family abounds with apor-phinoid alkaloids. A remarkable advance in the search for topoisomerase inhibitors from Lauraceae has been provided by Woo et al. (6). Using DNA-unwinding assay and structural modeling, they showed that dicentrine can attain a relatively planar conformation and molecular bulk which allow it to occupy the active site of topoisomerase II which becomes inactive. The requirement of a suboptimal conformation to achieve DNA binding appears to make dicentrine less potent against topoisomerase II than the... 

Molecular mechanics (MM) calculations have been employed for determining dihedral angles and to establish a comparison with values calculated from coupling constants, during conformational studies of tricyclic and tetracyclic quinolizidine alkaloids. The MM results had to be treated with care, as they sometimes predicted ring conformations different to those supported by experimental data <1999JST215>. 

Cytisine is a tricyclic quinolizidine alkaloid that binds with high affinity and specificity to nicotinic acetylcholine receptors. In principle, this compound can exist in several conformations, but semi-empirical calculations at the AM 1 and PM3 levels have shown that stmctures 19 and 20 are more stable than other possible conformers by more than 50 kcalmol-1. Both structures differ by 3.7 kcalmol 1 at the AMI level and 2.0 kcalmol 1 at the PM3 level, although this difference is much smaller when ab initio calculations are employed <2001PJC1483>. This conclusion is in agreement with infrared (IR) studies and with H NMR data obtained in CDCI3 solution, which are compatible with an exo-endo equilibrium < 1987JP21159>, although in the solid state cytisine has an exo NH proton (stmcture 19) (see Section 12.01.3.4.2). 

Bisquinolizidine alkaloids have also been widely studied by this technique. For instance, the crystal structure of (—)-A16(17 ,-dehydrolupaninium perchlorate 23 was obtained from sealed-tube and synchroton X-ray diffraction data, and showed that the A, B, C, and D rings assume distorted half-chair, chair, distorted sofa, and chair conformations, respectively it was also used to determine the most precise dimensions so far known for the iminium group <1999JST245>. The crystal structure of quinolizinium hexafluorophosphate has also been studied <2001CSC174>. 

More recently, infrared data have found further application in conformational studies of complex quinolizine derivatives, such as the previously mentioned alkaloid cytisine 9. Comparison of experimental values for the and t co) frequencies with the theoretical values obtained from semi-empirical calculations for... 

Sequential pyrrolidine and hydantoin ring-forming reactions via intramolecular [2+3] cycloaddition have been applied to the stereoselective solid-phase synthesis of conformationally constrained tricyclic triazacyclopenta [C]pentalene scaffold 43 < 1999JOC8342>. These novel compounds 43 share the structural complexity characteristic of certain alkaloid natural products, angular triquinanes. The retrosynthetic analysis is shown in Scheme 87. 

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