SYNTHESIS AND BIOLOGICAL ACTIVITY OF CYCLIC ADP-CARBOCYCLIC-RIBOSE ANALOGS: STRUCTURE-ACTIVITY RELATIONSHIP AND CONFORMATIONAL ANALYSIS OF N-1-CARBOCYCLIC-RIBOSE MOIETY

Several cyclic ADP-carbocyclic-ribose analogs 3–10 modified in the N-1-carbocyclic-ribose moiety were synthesized. Their Ca²⁺-releasing activity was estimated in sea urchin eggs to show that the 3″-deoxy analog 6 shows 5 times more potent activity than cADPcR, but the 2″,3″-didieoxy-2″,3″-unsunsaturated analog 3 has very weak activity. We also calculated their stable conformation and found that 3 and 6 were significantly different in their stable conformation.     

A DFT/ab initio study of hydrogen bonding and conformational preference in model cellobiose analogs using B3LYP/6-311++G**

A series of beta-cellobiose analogs were studied at the B3LYP/6-311++G** level of theory to isolate and understand how the various electronic components of the beta-(1-->4)-linked disaccharide, cellobiose, contribute to the energetic stability of the molecule in vacuo. Previous studies on beta-cellobiose (see accompanying paper) showed that the most energetically stable conformation was that in which the dihedral angle phi (phi(H)) was 'flipped' by approximately 180 degrees relative to the 'normal' form. From our examination of eight sets of structures in which different combinations of functional hydroxyl and hydroxymethyl groups were removed, it was determined that only beta-cellobiose and one other analog (analog 7, beta-xylobioside), an analog in which both hydroxymethyl groups were removed but the exocyclic hydroxyl groups retained, can form a 'cooperative' hydrogen-bonding network. Only in these two molecules did we find continuous synergistic 'communication' through hydrogen bonding from one sugar moiety to the other. This 'cooperative' hydrogen bonding energetically stabilizes the 'flipped' conformation of beta-cellobiose and beta-xylobioside, while the other analogs studied were unable to form a 'cooperative' grouping of hydrogen bonds and thus were more stable in their 'normal' conformational state.     

A new class of biflavonoids: 2'-hydroxygenistein dimers from the roots of white lupin

Two novel isoflavonoid dimers presumably originating from 2'-hydroxygenistein, 5,7,4'-trihydroxycoumaranochroman-4-one-(3-->5"')-5",7",2"'4"'- tetrahydroxyisoflavone (1, lupinalbisone A) and 5,7,4'-trihydroxycoumaranochroman-4-one-(3-6")-5",7",2"',4"'-te trahydroxyisoflavone (2, lupinalbisone B) were isolated from the roots of Lupinus albus L., and their structures involving relative stereochemistry were elucidated by spectroscopic methods. Using horse radish peroxidase and 2'-hydroxygenistein (3) as the substrate revealed the formation of these dimers together with 5,7,4'-trihydroxycoumaronochromone (4, lupinalbin A). Dimerization of 3 caused a remarkable increase of antifungal activity.     

Synthesis of some newer derivatives of substituted quinazolinonyl-2-oxo/thiobarbituric acid as potent anticonvulsant agents

5-[1'-[3"-Aminoacetyl-2"-methyl-6",8"-dihalosubstitutedquinazolin-4"(3"H)-onyl]-thiosemicarbazido]-2-oxo/thiobarbituric acids 3a-3h and 5-[2'-amino-5'-[3"-aminomethylene-2"-methyl-6",8"-dihalosubstitutedquinazolin-4"(3"H)-onyl]-1',3',4'-thiadiazol-2'-yl]-2-oxo/thiobarbituric acid 5a-5h were prepared by incorporating 1-[3'-aminoacetyl-2'-methyl-6",8"-dihalosubstituted-quinazolin-4'(3'H)-onyl]-thiosemicarbazides 2a-2d and 2-amino-5-[3'-aminomethylene-2'-methyl-6',8'-dihalosubstituted-quinazolin-4'(3'H)-onyl]-1,3,4-thiadiazoles 4a-4 h respectively at 5(th) position of 2-oxo/thiobarbituric acids (via Mannich reaction). All the newly synthesized compounds were screened for their anti-convulsant activity in MES and PTZ models and were compared with standard drugs phenytoin sodium and sodium valproate. Interestingly, these compounds were found to be devoid of sedative and hypnotic activities when tested. Out of the compounds studied, the most active compound 5h, that is 5-[2'-amino-5'-[3"-aminomethylene-2"-methyl-6",8"-dibromoquinazolin-4"(3"H)-onyl]-1',3',4'-thiadiazol-2'-yl]-2-thiobarbituric acid showed activity (90%) more potent than the standard drug.     

Spectroscopic identification of new ellagitannins and a trigalloyl-glucosylkaempferol from an extract of Euphorbia cotinifolia L. with antitumour and antioxidant activity

From an extract of leaves and small branches of Euphorbia cotinifolia L., 17 polyphenols were isolated including two new ellagitannins and a trigalloyl-glucosylkaempferol. Based on extensive spectral data (UV, ESI-MS, 1H NMR, DEPT and 1D/2D NMR) and chemical studies, their structures were characterized as 1-O-galloyl-3,6-hexahydroxydiphenoyl-D-B1,4-glucopyranose (5), 1-O-galloyl-3,6-valoneoyl-D-B1,4-glucopyranose (6), and kaempferol 3-O-(2",3",6"-tri-O-galloyl)-beta-D-glucopyranoside (13). Biological evaluation indicated that the 80% aqueous methanol extract (AME), chloroform extract (CE), and some pure compounds have potent scavenging activity in the DPPH assay with SC50 values lower than that of ascorbic acid, especially 5, 7-9, and a mixture of hyperin 6"-gallate (11) and isoquercitrin 6"-gallate (12). Moreover, using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) cell viability assay, 6 and 8 exhibited the highest inhibition of human hepatocellular carcinoma cells (Hep-G2), while AME, CE, 5, 7, 9, and the mixture of 11 and 12 were found to be moderate growth inhibitors according to their IC50 values. In addition, AME, 5, and 8 exhibited significant antiproliferative activity against colon carcinoma cells (HCT-116); however, CE and the other examined compounds displayed moderate to low antitumour activity against HCT-116 cells.     

Prenylated flavonoids from Deguelia hatschbachii and their systematic significance in Deguelia

Chemical investigation of dichloromethane and petrol extracts from the roots of D. hatshbachii A. M. G. Azevedo furnished thirteen compounds from which five are described for the first time and their structures were determined to be 3-(4'-hydroxyphenyl)-5-methoxy-6-( 3,3-dimethylallyl)-2"2"-dimethylchromene-(5",6":8,7)-3-(propyl-2-one)-4H-1-benzo-2,3-dihydropyran-2,4-dione; 6,4'-dihydroxy-3-(3,3-dimethylallyl)-2",2"-dimethylchromene (5",6":5,4)-2-methoxy deoxybenzoin; 6.4'-dihydroxy-3-(3,3-dimethylallyl)-2",2"-dimethylchromene (5",6":5,4)-2-methoxy-8-(propyl-2-one) deoxybenzon; 6-(3,3-dimethylallyl)-2",2"-dimethylchromene (5",6":4.5)-4'-hydroxy-3-methoxy stilbene and 3,5-dimethoxy-4'-hydroxy-4-(3,3-dimethylallyl) stilbene by spectral analysis (UV, IR, MS and ID- and 2D- NMR experiments). The root extracts and some isolated compounds were bioactive, as revealed by bioautography and brine shrimp lethality assays.     

Nodulisporic acid side-chain modifications: access to the 2", 3", 4", and 6" registers

Efficient routes to access the 2", 3", 4", and 6" registers of the nodulisporic acid (NsA) side chain are disclosed. A mild one-carbon, Ph(2)CdoublebondNCH(2)CtriplebondN mediated homologation of NsA's 3"-aldehyde permitted access to the 4"-register. Curtius reaction of NsA's 3"-acid yielded the corresponding 2"-aldehyde 4 from which the unnatural Delta(2",3")-olefin isomer 2b was obtained. In addition, Arndt-Eistert reactions of the parent NsA permitted a one-carbon homologation to the 6" register. These efforts identified new analogues with significant flea activity and illustrated the biological significance of unsaturation at the 1",2" register.     

Antinematodal activities of ingenane diterpenes from Euphorbia kansui and their derivatives against the pine wood nematode (Bursaphelenchus xylophilus)

Under the bioassay-guided method, two diterpenes, 3-O-(2",3"-dimethylbutanoyl)-13-O-dodecanoylingenol (1) and 3-O-(2",3"-dimethylbutanoyl)-13-O-decanoylingenol (2) isolated from Euphorbia kansui, showed a pronounced antinematodal activity against the nematode Bursaphelenchus xylophilus at the same minimum effective dose (MED) of 5 microg per cotton ball and still displayed antinematodal activity at a dose of 2.5 microg per cotton ball. Compounds 3-6 were obtained, and the structure of the new compound 6 was elucidated based on 1D- and 2D-NMR analyses and physicochemical data. Preliminary structure-biological activity relationships of ingenane-type compounds were deduced.     

Environment-dependent conformation and antimicrobial activity of a gramicidin S analog containing leucine and lysine residues

An analog of gramicidin S, cyclo(-L-Leu-L-Lys-L-Leu-D-Leu-L-Leu-)2, in which four out of five amino acid components of gramicidin S were substituted, has been synthesized. This analog assumes a conformation similar to that of gramicidin S in acidic liposomes and a random conformation in neutral liposomes. The antimicrobial activity of this analog corresponded to one-fourth of that of gramicidin S. A possible mechanism for conformational changes in acidic liposomes is discussed.     

Role of peptide backbone conformation on biological activity of chemotactic peptides

To investigate the role of peptide backbone conformation on the biological activity of chemotactic peptides, we synthesized a unique analog of N-formyl-Met-Leu-Phe-OH incorporating the C alpha,alpha disubstituted residue, dipropylglycine (Dpg) in place of Leu. The conformation of the stereochemically constrained Dpg analog was examined in the crystalline state by x-ray diffraction and in solution using NMR, IR, and CD methods. The secretagogue activity of the peptide on human neutrophils was determined and compared with that of a stereochemically constrained, folded type II beta-turn analog incorporating 1-aminocyclohexanecarboxylic acid (Ac6c) at position 2 (f-Met-Ac6c-Phe-OMe), the parent peptide (f-Met-Leu-Phe-OH) and its methyl ester derivative (f-Met-Leu-Phe-OMe). In the solid state, the Dpg analog adopts an extended beta-sheet-like structure with an intramolecular hydrogen bond between the NH and CO groups of the Dpg residue, thereby forming a fully extended (C5) conformation at position 2. The phi and psi values for Met and Phe residues are significantly lower than the values expected for an ideal antiparallel beta conformation causing a twist in the extended backbone both at the N and C termini. Nuclear magnetic resonance studies suggest the presence of a significant population of the peptide molecules in an extended antiparallel beta conformation and the involvement of Dpg NH in a C5 intramolecular hydrogen bond in solutions of deuterated chloroform and deuterated dimethyl sulfoxide. IR studies provide evidence for the presence of an intramolecular hydrogen bond in the molecule and the antiparallel extended conformation in chloroform solution. CD spectra in methanol, trifluoroethanol, and trimethyl phosphate indicate that the Dpg peptide shows slight conformational flexibility, whereas the folded Ac6c analog is quite rigid. The extended Dpg peptide consistently shows the highest activity in human peripheral blood neutrophils, being approximately 8 and 16 times more active than the parent peptide and the folded Ac6c analog, respectively. However, the finding that all four peptides have ED50 (the molar concentration of peptide to induce half-maximal enzyme release) values in the 10(-8)-10(-9) M range suggests that an induced fit mechanism may indeed be important in this ligand-receptor interaction. Moreover, it is also possible that alterations in the backbone conformation at the tripeptide level may not significantly alter the side chain topography and/or the accessibility of key functional groups important for interaction with the receptor.     

The synthesis of anti-fixed 3-methyl-3-deaza-2'-deoxyadenosine and other 3H-imidazo[4,5-c]pyridine analogs

Rotation of a heterocyclic base around a glycosidic bond allows the formation of syn and anti conformations in nucleosides. The syn conformation has been observed primarily in purine-purine mismatches in DNA duplexes. Such mismatches give rise to false positive oligonucleotide hybridization in DNA-based diagnostics. Here we describe the synthesis of an analog of 2'-deoxyadenosine that retains its Watson-Crick functional groups, but cannot form the syn conformation. In this analog, the N3 atom of 2'-deoxyadenosine is replaced by a C-CH3 group to give 7-methyl-1-beta-D-deoxyribofuranosyl-1H-imidazo[4,5-c]pyridin-4-ylamine or 3-methyl-3-deaza-2'-deoxyadenosine (3mddA). This modification sterically prevents the syn conformation and 3mddA becomes an anti-fixed nucleoside analog of 2'-deoxyadenosine. The synthesis and conformational analysis of 3mddA and several analogs with an 3H-imidazo[4,5-c]pyridine skeleton are described, as well as their potential applications.     

Conformational analysis corresponding to intra-chain disulfide bridged peptides in proteins of known three-dimensional structure

We have carried out a systematic analysis in order to evaluate whether Intra-Chain Disulfide Bridged Peptides (ICDBPs) observed in proteins of known three-dimensional structure adopt structurally similar conformations as they may correspond to structural/functional motifs. 406 representative ICDBPs comprising between 3 to 17 amino acid residues could be classified according to peptide sequence length and main-chain secondary structure conformation into 146 classes. ICDBPs comprising 6 amino acid residues are maximally represented in the Protein Data Bank. They also represent the maximum number of main-chain secondary structure conformational classes. Individual ICDBPs in each class represent different protein superfamilies and correspond to different amino acid sequences. We identified 145 ICDBP pairs that had not less-than 0.5 A root mean square deviation value corresponding to their equivalent peptide backbone atoms. We believe these ICDBPs represent structural motifs and possible candidates in order to further explore their structure/function role in the corresponding proteins. The common conformational classes observed for ICDBPs defined according to the main-chain secondary structure conformations; H (helix), B (residue in a isolated beta bridge), C (coil), E (extended beta strand), G (3(10) helix), I (pi helix), S (bend), T (hydrogen-bonded turn) were; "CHHH", "CTTC", "CSSS" and "CSSC" (for ICDBP length 4), "CSSCC" (length 5), "EETTEE", "CCSSCC", "CCSSSC" (length 6), "EETTTEE" (length 7), "EETTTTEE" (length 8), "EEEETTEEEE" (length 10), "EEEETTTEEEE" (length 11) and "EEEETTTTEEEE" (length 12).     

Role of cell displacement, cell division, and fragment size in pattern formation during embryonic retinal regeneration in Xenopus

Studies on the regenerating vertebrate retina provide, for the first time, a detailed view of how cells respond to removal of 2/3 of the eyebud, how their displacements, new juxtapositions, and extra mitotic activity correlate with stable changes in the retinotectal projection. They provide insight into how retinal ganglion cells encode "position", and how they use this information to form specific neural connectivity patterns.     

THE SYNTHESIS OF ANTI-FIXED 3-METHYL-3- DEAZA-2′-DEOXYADENOSINE AND OTHER 3H-IMIDAZO[4,5-c]PYRIDINE ANALOGS

ABSTRACT

Rotation of a heterocyclic base around a glycosidic bond allows the formation of syn and anti conformations in nucleosides. The syn conformation has been observed primarily in purine-purine mismatches in DNA duplexes. Such mismatches give rise to false positive oligonucleotide hybridization in DNA-based diagnostics. Here we describe the synthesis of an analog of 2′-deoxyadenosine that retains its Watson-Crick functional groups, but cannot form the syn conformation. In this analog, the N3 atom of 2′-deoxyadenosine is replaced by a C-CH₃ group to give 7-methyl-1-β-D-deoxyribofuranosyl-1H-imidazo[4,5-c]pyridin-4-ylamine or 3-methyl-3-deaza-2′-deoxyadenosine (3mddA). This modification sterically prevents the syn conformation and 3mddA becomes an anti-fixed nucleoside analog of 2′-deoxyadenosine. The synthesis and conformational analysis of 3mddA and several analogs with an 3H-imidazo[4,5-c]pyridine skeleton are described, as well as their potential applications.     

Glyco-optimization of aminoglycosides: new aminoglycosides as novel anti-infective agents

Glyco-optimization (OPopS) of aminoglycosides has been performed by replacing the existing sugar moiety with a variety of sugar derivatives. Glycosylation of the 6-position of nebramine provided a library of novel 4,6-linked aminoglycosides (AMGs). Among them, compounds 8b,g,i,l, and 8u with 2"-amino, 2",3"-diamino, 2",4"-diamino, 3",4"-diamino, 3"-amino groups, respectively, showed significant antimicrobial activity against Gram-(+) and -(-) bacteria. Several were particularly potent against Pseudomonus aeruginosa with MICs in the 1-2 microg/mL range.     

An analog of 1alpha,25-dihydroxy-19-norvitamin D3 with the 1alpha-hydroxy group fixed in the axial position lacks biological activity in vitro

The relationship between the A-ring chair conformation of vitamin D compounds and their ability to bind the vitamin D receptor (VDR) has long attracted the attention of many researchers. It was established that in the crystalline complexes of hVDRmt with the natural hormone, 1alpha,25-dihydroxyvitamin D(3) (1), and its side-chain analogs the vitamins exist in beta-chair form with an equatorial orientation of 1alpha-OH. However, with all these ligands the interconversion between both A-ring forms would be possible in solution. In an attempt to verify the conformation of vitamin D compounds required for binding the VDR we prepared analog 4, characterized by the presence of an axial 1alpha-hydroxy group. Since the additional ring connecting 3beta-oxygen and C-2 prevents A-ring conformational flexibility, the synthesized vitamin 4 can exist exclusively in the alpha-chair form. The geometrical isomer 5 with a free 3beta-OH group was also obtained. The analog 5 binds very poorly to VDR, whereas the vitamin 4 is practically devoid of binding ability. Both compounds also show very low HL-60-differentiating activity. When tested in vivo in mice the analogs 4 and 5 exhibit significant calcemic responses with analog 4 showing more activity than analog 5.     

Flavonoids from the roots of Millettia erythrocalyx

From the roots of Millettia erythrocalyx, 6-methoxy-[2",3":7,8]-furanoflavanone, 2,5-dimethoxy-4-hydroxy-[2",3":7,8]-furanoflavan, and 3,4-methylenedioxy-2',4'-dimethoxychalcone were isolated, along with ten other known flavonoids. Their structures were elucidated on the basis of analyses of their spectroscopic data.     

Structural Factors that Distinguish Dopamine D1 and D2 Agonists

To determine the structural features responsible for their selectivity as dopamine D1 agonists, a conformational analysis has been performed on an analog of nomifensine, dihydrexidine, a benzergoline, and an isochroman using the MM2-87 program. The preferred three dimensional structure of the hydroxylated phenyl ring of the nomifensine analog was found to differ from the other compounds with a substantial energy barrier to achieving the planar conformation of the other compounds which may explain its weak potency for D1 receptors. The preferred three dimensional structures of dihydrexidine and the benzergoline were found to differ significantly despite their molecular similarity. These conformational differences were also evident in crystal structures of the compounds or their analogs. The hypothesis that an equatorial ammonium hydrogen (or amine lone pair) is required for D1 agonist selectivity was tested by performing calculations on N-methyl equatorial and N-methyl axial analogs of the compounds. Calculations were also performed on nonselective dopamine agonists (apomorphine and 5,6-diOH- and 6,7-diOH aminotetralin) and dopamine D2-selective agonists ((+)-PHNO and an analog of quinpirole). The energy difference for the N-methyl axial conformations (or their equivalent) were found to be relatively small for the nonselective agonists and more substantial for the D2-selective agonists. This suggests that D2-selectivity may be associated with the relative unfavorability of the N-methyl axial conformation and provides an explanation for the decreased potency of tertiary amine analogs of the D1-selective agonists. In the benzergoline, where the energy difference is computed to be smaller, the addition of the N-methyl group appears to have a smaller deleterious effect on D1 activity. An N-methyl axial conformation has also been observed for the benzergoline in the crystal state suggesting that this conformation is energetically accessible.     

Three isoflav-3-enes and a 2-arylbenzofuran from the root bark of Erythrina burttii

From the root bark of Erythrina burttii three isoflav-3-enes, 7,4'-dihydroxy-2'-methoxy-6-(1",1"-dimethylallyl)isoflav-3-ene (trivial name, burttinol-A), 4'-hydroxy-2'-methoxy-2",2"-dimethylpyrano[5",6":8,7]isoflav-3-ene (trivial name, burttinol-B), 7,4'-dihydroxy-2'-methoxy-8-(3",3"-dimethylallyl)isoflav-3-ene (trivial name, burttinol-C), and 2-arylbenzofuran, 6,4'-dihydroxy-2'-methoxy-5-(1",1"-dimethylallyl)-2-arylbenzofuran (trivial name, burttinol-D) were isolated. In addition, the known compounds, abyssinone V-4'-methyl ether, bidwillol A, calopocarpin, erybraedin A, erythrabyssin II, isobavachalcone, phaseollidin and phaseollin were identified. The structures were determined on the basis of spectroscopic evidence.     

Systematic synthesis of four epicatechin series procyanidin trimers and their inhibitory activity on the Maillard reaction and antioxidant activity

A systematic synthesis of four natural epicatechin series procyanidin trimers [[4,8:4",8"]-2,3-cis-3,4-trans: 2",3"-cis-3",4"-trans: 2,3-trans-(-)-epi-catechin-(-)-epicatechin-(+)-catechin, [4,8:4",8"]-2,3-cis-3,4-trans: 2",3"-cis-3",4"-trans: 2,3-cis-tri-(-)-epicatechin: procyanidin C1, [4,8:4",8"]-2,3-cis-3,4-trans: 2",3"-trans-3",4"-trans: 2,3-trans-(-)-epicatechin-(+)-catechin-(+)-catechin: procyanidin C4, and [4,8:4",8"]-2,3-cis-3,4-trans: 2",3"-trans-3",4"-trans: 2,3-cis-(-)-epicatechin-(+)-catechin-(-)-epicatechin] is described. Condensation of (2R,3R,4S)-5,7,3'4'-tetra-O-benzyl-4-(2"-ethoxyethyloxy)flavan derived from (-)-epicatechin as an electrophile with the dimeric nucleophiles in the presence of TMSOTf followed by deprotection yielded trimers. Inhibitory activities on the Maillard reaction and antioxidant activity on lipid peroxide of the synthesized oligomers were also investigated.