Synthesis and conformational analysis of stevastelin C3 analogues and their activity against the dual-specific vaccina H1-related phosphatase

The biological activity of macrocyclic natural products depends on their conformational properties. For both the elucidation of enzyme binding affinities as well as the development of selective drugs, rigid macrocyclic scaffolds carry high potential. In this study, 13-membered cyclodepsipeptides based on the structure of naturally occurring stevastelins were studied in detail. Six diastereomeric stevastelin C3 analogues and four phosphorylated derivatives were synthesized. The synthesis of linear precursors was achieved on solid support by starting from stereoisomerically pure 2-methyl-3-hydroxy acids. Subsequent macro-lactamization gave the cyclic depsipeptides in very good yields (36-62%). The conformational space of these stevastelin C3 analogues was computationally investigated. On the basis of NMR spectroscopic data, homogeneous conformations were determined for each benzylated depsipeptide and the influence of phosphorylation on the overall conformation was investigated. Importantly, phosphorylation was found to significantly weaken the conformational preferences of the 13-membered depsipeptides. Finally, the cyclic depsipeptides were tested for activity against phosphatases. Inhibitory activity on vaccina H1-related phosphatase was observed depending on the derivatization of the cycles. The activity profiles are discussed in the light of the structural data.     

Synthesis and Conformational Preferences of a Potential beta-Sheet Nucleator Based on the 9,9-Dimethylxanthene Skeleton

A 4,5-disubstituted-9,9-dimethylxanthene-based amino acid (10) has been synthesized for incorporation into peptide sequences which have a propensity to adopt beta-sheet structure. Molecular dynamics studies support the FT-IR and NMR results which demonstrate that amides based on this residue utilize the NH and the C=O from the xanthene residue to form an intramolecular hydrogen bond (13-membered ring), unlike the previously studied dibenzofuran-based amino acid residues in which the NH and the C=O of the attached amide groups participate in intramolecular hydrogen bonding (15-membered ring). Interestingly, residue 10 derivatized as a simple amide prefers to adopt a trans conformation where the aliphatic side chains are placed on opposite sides of the plane of the 9,9-dimethylxanthene ring system. This is different than the conformational preferences of the dibenzofuran-based amino acids which adopt a cis conformation that is preorganized to nucleate beta-sheet formation. It will be interesting to see how these conformational differences effect nucleation in aqueous solution.     

Novel antibacterial macrolides: synthesis of 15-membered diolides

Novel 15-membered macrolides possessing the dilactone skeleton, diolides 13a and 13b, have been synthesized in our research program aimed at finding new antibacterial macrolides. Key strategic elements of the approach include the ring-expanding reaction of 13-membered dilactones, prepared from erythromycin A (Ery-A), to 15-membered dilactones via intramolecular translactonization. The absolute configuration at the regenerated C-8 position of the new diolides was determined by chemical transformation, leading to the corresponding lactam analogues, whose stereochemistry is known in the literature. For further confirmation, X-ray analysis was performed. The X-ray structure determination of 13a revealed a backbone conformation similar to that of Ery-A. Novel 15-membered diolide 13a and the 11,12-diol 18 exhibited antibacterial activities comparable to that of Ery-A.     

Design, synthesis, and biological evaluation of novel C14-C3'BzN-linked macrocyclic taxoids

Novel macrocyclic paclitaxel congeners were designed to mimic the bioactive conformation of paclitaxel. Computational analysis of the "REDOR-Taxol" structure revealed that this structure could be rigidified by connecting the C14 position of the baccatin moiety and the ortho position of C3'N-benzoyl group (C3'BzN), which are ca. 7.5 A apart, with a short linker (4-6 atoms). 7-TES-14beta-allyloxybaccatin III and (3R,4S)-1-(2-alkenylbenzoyl)-beta-lactams were selected as key components, and the Ojima-Holton coupling afforded the corresponding paclitaxel-dienes. The Ru-catalyzed ring-closing metathesis (RCM) of paclitaxel-dienes gave the designed 15- and 16-membered macrocyclic taxoids. However, the RCM reaction to form the designed 14-membered macrocyclic taxoid did not proceed as planned. Instead, the attempted RCM reaction led to the occurrence of an unprecedented novel Ru-catalyzed diene-coupling process, giving the corresponding 15-membered macrocyclic taxoid (SB-T-2054). The biological activities of the novel macrocyclic taxoids were evaluated by tumor cell growth inhibition (i.e., cytotoxicity) and tubulin-polymerization assays. Those assays revealed high sensitivity of cytotoxicity to subtle conformational changes. Among the novel macrocyclic taxoids evaluated, SB-T-2054 is the most active compound, which possesses virtually the same potency as that of paclitaxel. The result may also indicate that SB-T-2054 structure is an excellent mimic of the bioactive conformation of paclitaxel. Computational analysis for the observed structure-activity relationships is also performed and discussed.     

Total synthesis and molecular target of largazole, a histone deacetylase inhibitor

Full details of the concise and convergent synthesis (eight steps, 19% overall yield), its extension to the preparation of a series of key analogues, and the molecular target and pharmacophore of largazole are described. Central to the synthesis of largazole is a macrocyclization reaction for formation of the strained 16-membered depsipeptide core followed by an olefin cross-metathesis reaction for installation of the thioester. The biological evaluation of largazole and its key analogues, including an acetyl analogue, a thiol analogue, and a hydroxyl analogue, suggested that histone deacetylases (HDACs) are molecular targets of largazole and largazole is a class I HDAC inhibitor. In addition, structure-activity relationship (SAR) studies revealed that the thiol group is the pharmacophore of the natural product. Largazole's HDAC inhibitory activity correlates with its antiproliferative activity.     

Synthesis of new crown ethers and their metal complexes: 1H and 13C NMR study

A new type of crown ethers containing a diphenyl ether unit has been prepared, the ring size ranging from 12 to 36. ¹H and ¹³C NMR spectra of both free ligands and their metal-ion complexes have been recorded. For 18- and 21-membered compounds a general downfield shift was observed for both methylene and aromatic proton resonances on metal-ion complexation. The stoichiometry of K⁺ and Na⁺ complexes was deduced from chemical shift dependence on metal-ion concentration. The K⁺ and Na⁺ complexes of 18- and 21-membered rings have a guest to host ratio of 1:1, whereas the K⁺ salt of the 15-membered ring exists as a 1:2 complex in solution. The ¹H shift observed on salt formation was attributed to electric-field and conformational effects. The ¹³C resonances for the aryl carbons, C-1, C-2 and C-3, and the α-methylene carbon in 15- and 18-membered rings were shifted upfield when an equivalent amount of KSCN was added in CDCI_3?DMSO-d₆. The shift changes were independent of the anion, and similar results were obtained for SCN^?, Br^?, and I^? salts. The upfield shift is explained by conformational factors. The spectral changes were slight for 12- and 36-membered rings. In 15- and 18-membered rings, complexation induces conformational changes which force the C-α carbon into the plane of the benzene ring. The solution conformation of these molecules is discussed.     

Cytotoxic alkaloids motuporamines A-C: synthesis and structural verification

[formula: see text] The unusual structure and biological properties of the marine alkaloids motuporamines A-C, as well as the uncertainty as to the position of the olefin within the ring of motuporamine C, led us to synthesize these compounds. The strategy utilized the ring-closing metathesis reaction to form the 14- and 15-membered rings and Michael addition and amidation chemistry to introduce the spermine-like unit. The syntheses, structure assignment verifications, and also the determination of the position of the olefin in motuporamine C are described.     

Conformational analysis of oleandomycin and its 8-methylene-9-oxime derivative by NMR and molecular modelling

Conformations of the 14-membered macrolide antibiotic oleandomycin and its 8-methylene-9-oxime derivative were determined in various solvents. The experimental NMR data--coupling constants and NOE contacts--were compared with the results of molecular modelling--molecular mechanics calculations and molecular dynamics simulations. The conformational changes, on the right-hand side of the 14-membered ring, affected mostly the 3JH2,H3 values and NOE crosspeaks H3 or H4 to H11. Oleandomycin was found to be present predominantly in the C3-C5 folded-in conformations in DMSO-d6 solution, whereas in buffered D2O, acetone-d6 and CDCl3, there was a mixture of folded-in and folded-out conformational families. The predominant conformation of the 8-methylene-oleandomycin-9-oxime derivative in solution was a folded-out one although different amounts of folded-in conformation were also present depending on the solvent. Oleandrose and desosamine sugar moieties adopted the usual and expected chair conformation. The conformation around the glycosidic bonds, governing the relative orientation of sugars vs. the lactone ring, showed a certain flexibility within two conformationally close families. We believe that by combining the experimental NMR data and the molecular modelling techniques, as reported in this paper, we have made significant progress in understanding the conformational behaviour and properties of macrolides. Our belief is based on our own current studies on oleandomycins as well as on the previously reported results and best practices concerning other macrolides. A rational for macrolide conformational studies and advances in methodology has been suggested accordingly.     

Double-helical cyclic peptides: design, synthesis, and crystal structure of figure-eight mirror-image conformers of adamantane-constrained cystine-containing cyclic peptide cyclo (Adm-Cyst)(3)

A large number of macrocycles containing alternating repeats of cystine diOMe(-NH-CH(CO(2)Me)-CH(2)-S-)(2) and either a conformationally rigid aromatic/alicyclic moiety or a flexible polymethylene unit (X) in the cyclic backbone with ring size varying from 13- to 78-membered have been examined by spectral ((1)H NMR, FT-IR, CD) and X-ray crystallography studies for unusual conformational preferences. While (1)H NMR measurements indicated a turnlike conformation for all macrocycles, stabilized by intramolecular NH.CO hydrogen bonding, as also supported by FT-IR spectra in chloroform, convincing proof for beta-turn structures was provided by circular dichroism studies. Single-crystal X-ray studies on 39-membered cyclo (Adm-L-Cyst)(3) revealed a double-helical fold (figure-eight motif) for the macrocycle. Only a right-handed double helix was seen in the macrocycle constructed from L-cystine. The mirror-image macrocycle made up of D-cystine units exhibited a double helix with exactly the opposite screw sense, as expected. The enantiomeric figure-eights were stabilized by two intramolecular NH. CO hydrogen bonds and exhibited identical (1) H NMR and FT-IR spectra. The CD spectra of both isomers had a mirror-image relationship. The present results have clearly brought out the importance of cystine residues in inducing turn conformation that may be an important deciding factor for the adoption of topologically important structures by macrocycles containing multiple S-S linkages.     

Synthesis and Anti‐tumor Evaluation of B‐ring Modified Caged Xanthone Analogues of Gambogic Acid

Gambogic acid (GA, 1 ), the most prominent member of Garcinia natural products, has been reported to be a promising anti‐tumor agent. Previous studies have suggested that the planar B ring and the unique 4‐oxa‐tricyclo[4.3.1.0^3,7]dec‐2‐one caged motif were essential for anti‐tumor activity. To further explore the structure‐activity relationship (SAR) of caged Garcinia xanthones, two new series of B‐ring modified caged GA analogues 13a – 13e and 15a – 15e were synthesized utilizing a Claisen/Diel‐Alder cascade reaction. Subsequently, these compounds were evaluated for their in vitro anti‐tumor activities against A549, MCF‐7, SMMC‐7721 and BGC‐823 cancer cell lines by MTT assay. Among them, 13b – 13e exhibited micromolar inhibition against several cancer cell lines, being approximately 2–4 fold less potent in comparison to GA. SAR analysis revealed that the peripheral gem‐dimethyl groups are essential for maintaining anti‐tumor activity and substituent group on C1 position of B‐ring has a significant effect on potency, while modifications at C‐2, C‐3 and C‐4 positions are relatively tolerated. These findings will enhance our understanding of the SAR of Garcinia xanthones and lead to the development of simplified analogues as potential anti‐tumor agents.     

Understanding how the herpes thymidine kinase orchestrates optimal sugar and nucleobase conformations to accommodate its substrate at the active site: a chemical approach

The herpes virus thymidine kinase (HSV-tk) is a critical enzyme for the activation of anti-HSV nucleosides. However, a successful therapeutic outcome depends not only on the activity of this enzyme but also on the ability of the compound(s) to interact effectively with cellular kinases and with the target viral or cellular DNA polymerases. Herein, we describe the synthesis and study of two nucleoside analogues built on a conformationally locked bicyclo[3.1.0]hexane template designed to investigate the conformational preferences of HSV-tk for the 2'-deoxyribose ring. Intimately associated with the conformation of the 2'-deoxyribose ring is the value of the C-N torsion angle chi, which positions the nucleobase into two different domains (syn or anti). The often-conflicting sugar and nucleobase conformational parameters were studied using North and South methanocarbadeoxythymidine analogues (6 and 7), which forced HSV-tk to make a clear choice in the conformation of the substrate. The results provide new insights into the mechanism of action of this enzyme, which cannot be gleaned from a static X-ray crystal structure.     

Zooxanthellamide Cs: vasoconstrictive polyhydroxylated macrolides with the largest lactone ring size from a marine dinoflagellate of Symbiodinium sp

Zooxanthellamide Cs (ZAD-Cs), C(128)H(220)N(2)O(53)S(2) (ca. 2.7 kDa), was obtained from a cultured marine dinoflagellate of the genus Symbiodinium as an inseparable isomeric mixture of polyhydroxylated 61- to 66-membered macrolides. The chemical structures of the components were clarified by detailed 2D NMR analysis to be the macrolactonized analogues of zooxanthellamide A (ZAD-A), which had been previously isolated from the same microalgae. Chemical lability of ZAD-Cs suggests that ZAD-A is an artifact derived from ZAD-Cs during the isolation steps. Three of the components possess the largest (63-, 64-, and 66-membered) ring sizes found to date among the natural macrolides. ZAD-Cs exhibited higher vasoconstrictive activity than that of the zooxanthellatoxins, the first vasoconstrictive macrolides from Symbiodinium sp. The structure-activity relationship suggests that the huge macrolactone structure is important for biological activity. The relationship between the structures of the polyol metabolites and the phylogenetic systematics of Symbiodinium sp. is also discussed.     

Cystobactamid 507: Concise Synthesis,Mode of Action,and Optimization toward More Potent Antibiotics

Lack of new antibiotics and increasing antimicrobial resistance are among the main concerns of healthcare communities nowadays, and these concerns necessitate the search for novel antibacterial agents. Recently, we discovered the cystobactamids—a novel natural class of antibiotics with broad-spectrum antibacterial activity. In this work, we describe 1) a concise total synthesis of cystobactamid 507, 2) the identification of the bioactive conformation using noncovalently bonded rigid analogues, and 3) the first structure–activity relationship (SAR) study for cystobactamid 507 leading to new analogues with high metabolic stability, superior topoisomerase IIA inhibition, antibacterial activity and, importantly, stability toward the resistant factor AlbD. Deeper insight into the mode of action revealed that the cystobactamids employ DNA minor-groove binding as part of the drug–target interaction without showing significant intercalation. By designing a new analogue of cystobactamid 919-2, we finally demonstrated that these findings could be further exploited to obtain more potent hexapeptides against Gram-negative bacteria.     

Conformational behavior of dodecyldiamine inside the confined space of montmorillonites

We have investigated the change of the intercalated amount and conformational behavior of dodecyldiamine (C(12)H(28)N(2), di-C(12)amine) inside the confined space of the montmorillonite (MMT) intergallery at different pHs of the intercalation solution (H(2)O/ethanol/Na(+)-MMT/di-C(12)amine), and these results were compared with those of dodecylmonoamine (C(12)H(27)N, mono-C(12)amine). The mono-C(12)amine with one end-functional amine (-NH(2)) has a constant intercalated amount independent of the pH of the intercalation solution, confirming the tail conformation in the MMT intergallery. On the other hand, the intercalated amount of di-C(12)amines remains quite low at low pH due to the long-range Coulombic repulsion among protonated amines. The di-C(12)amines dominantly take the bridge conformation inside the MMT intergallery up to pH 9.5 and adopt a fraction of the tail conformation at pH 11.5, which is verified by Fourier transform infrared spectra with an abrupt frequency shift of the CH(2) stretching band and the emergence of a new NH(2) scissoring band at 1598 cm(-)(1) related to unanchored free amines. The d-spacing and the square of the half-width at half-maximum of the MMT based on X-ray diffraction measurements are also constant up to pH 9.5, while these two variables are suddenly increased at pH 11.5. The bridge conformation of di-C(12)amines in the confined space of the MMT intergallery prevents poly(ethylene oxide) chains from intercalation into the MMT intergallery, called the gluing effect.     

Synthesis,resolution, and absolute stereochemistry of (-)-blestriarene C

A naturally occurring 1,1'-biphenanthrene, blestriarene C (1), was prepared in 13 steps and 30% overall yield. The key steps are the ester-mediated nucleophilic aromatic substitution on 2,6-di-tert-butyl-4-methoxyphenyl 5-isopropoxy-2-methoxybenzoate (4) by 2-methoxy-4-methoxymethoxy-6-methylphenylmagnesium bromide (5) and a novel intramolecular cyclization of the resulting 4-isopropoxy-2'-methoxy-4'-methoxymethoxy-6'-methylbiphenyl-2-carboxylic ester 14 to 7-isopropoxy-4-methoxy-2-(methoxymethoxy)phenanthren-9-ol (15). The racemic blestriarene C was optically resolved by chiral HPLC on a preparative scale to give several 10-mg yields of both the enantiomers in up to 95% ee. The absolute stereochemistry was determined to be S(a)-(-) by the axial chirality recognition method, which was based on the stereospecific formation of a 12-membered cyclic diester containing two biaryl-o,o'-diyl unites joined by ester -CO(2)- linkages. The validity of the method was confirmed by an X-ray crystallographic analysis and ab initio conformational analyses of such 12-membered cyclic diesters. It was found that blestriarene C and its 7,7'-diisopropyl ether 2 underwent rapid photoracemization even under ambient light exposure.     

Aigialomycins A-E, new resorcylic macrolides from the marine mangrove fungus Aigialus parvus

Aigialomycins A-E (2-6), new 14-membered resorcylic macrolides, were isolated together with a known hypothemycin (1) from the mangrove fungus, Aigialus parvus BCC 5311. Structures of these compounds, including absolute configuration, were elucidated by spectroscopic methods, chemical conversions, and X-ray crystallographic analysis. Hypothemycin and aigialomycin D (5) exhibited in vitro antimalarial activity with IC(50) values of 2.2 and 6.6 microg/mL, respectively, while other analogues were inactive. Cytotoxicities of these compounds were also evaluated.     

Cyclic triureas--synthesis, crystal structures and properties

The synthesis of 24-membered macrocycles is described, in which rigid xanthene units (X) and/or diphenyl ether units (D) as flexible analogues are linked via urea groups. All four possible combinations (XXX, XXD, XDD, DDD) have been obtained with yields of 40-72% for the cyclisation step. In two cases, the respective cyclic hexamers (XXDXXD, XXXXXX) were also isolated. Two compounds have been characterised by a single crystal X-ray analysis of the free triurea (XXD, XDD) and one example (DDD) by its complex with tetrabutylammonium chloride. It shows the chloride anion in the centre of the macrocycle, held by six NH...Cl- hydrogen bonds. The interaction with various other anions has been studied by 1H NMR. Complexation constants for chloride, bromide and acetate have been measured for all trimers by UV spectrophotometry. Molecular dynamics simulations have been carried out to determine the conformation of the free receptors in chloroform and acetonitrile. They show that in chloroform, intramolecular hydrogen bonding occasionally facilitated by trans-->cis isomerisation of an amide bond dominates the conformation of the macrocycles while in acetonitrile (the solvent used for complexation measurements), the ligating urea NH protons are properly arranged for the complexation of anions, however, their strong solvation is counteractive to the complexation.     

Macromolecular chirality induction on optically inactive poly(4-carboxyphenyl isocyanide) with chiral amines: a dynamic conformational transition of poly(phenyl isocyanide) derivatives

Optically active polyisocyanides (poly(iminomethylenes)) have been prepared with much interest in developing new functional materials. Polyisocyanides have been considered to have a stable 4(1) helical conformation even in solution when they have a bulky side group. However, the conformational characteristics of poly(phenyl isocyanide) (PPI) derivatives are still under debate. We now report that an optically inactive PPI derivative, poly(4-carboxyphenyl isocyanide) (poly-1), shows optical activity in the polymer backbone induced by external, chiral stimuli through acid-base interactions under thermodynamic control and exhibits induced circular dichroism (ICD) in the UV-visible region in DMSO. The ICD intensities of the poly-1-chiral amine complexes in DMSO gradually increased with time, and, in one case, the value reached 3 times that of the original value after 2 months at 30 degrees C. The conformational changes also occurred very slowly for poly-1 alone and its ethyl ester with time on the basis of (1)H NMR spectroscopic analysis. These results indicate that PPIs bearing a less bulky substituent may not have a 4(1) helical conformation but have a different type of prochiral conformation, for instance, an s-trans (zigzag) structure which may transform to a dynamic, one-handed helical conformation when the PPIs have a functional group capable of interacting with chiral compounds. The mechanism of helicity induction on poly-1 through a dynamic conformational transition is discussed on the basis of the above results together with molecular dynamic simulation results for PPI.     

Conformationally constrained macrocycles that mimic tripeptide beta-strands in water and aprotic solvents

The beta-strand conformation is unknown for short peptides in aqueous solution, yet it is a fundamental building block in proteins and the crucial recognition motif for proteolytic enzymes that enable formation and turnover of all proteins. To create a generalized scaffold as a peptidomimetic that is pre-organized in a beta-strand, we individually synthesized a series of 15-22-membered macrocyclic analogues of tripeptides and analyzed their structures. Each cycle is highly constrained by two trans amide bonds and a planar aromatic ring with a short nonpeptidic linker between them. A measure of this ring strain is the restricted rotation of the component tyrosinyl aromatic ring (DeltaG(rot) 76.7 kJ mol(-1) (16-membered ring), 46.1 kJ mol(-1) (17-membered ring)) evidenced by variable temperature proton NMR spectra (DMF-d(7), 200-400 K). Unusually large amide coupling constants ((3)J(NH-CHalpha) 9-10 Hz) corresponding to large dihedral angles were detected in both protic and aprotic solvents for these macrocycles, consistent with a high degree of structure in solution. The temperature dependence of all amide NH chemical shifts (Deltadelta/T 7-12 ppb/deg) precluded the presence of transannular hydrogen bonds that define alternative turn structures. Whereas similar sized conventional cyclic peptides usually exist in solution as an equilibrium mixture of multiple conformers, these macrocycles adopt a well-defined beta-strand structure even in water as revealed by 2-D NMR spectral data and by a structure calculation for the smallest (15-membered) and most constrained macrocycle. Macrocycles that are sufficiently constrained to exclusively adopt a beta-strand-mimicking structure in water may be useful pre-organized and generic templates for the design of compounds that interfere with beta-strand recognition in biology.     

Design, synthesis, and biological evaluation of HSP90 inhibitors based on conformational analysis of radicicol and its analogues

The molecular chaperone HSP90 is an attractive target for chemotherapy because its activity is required for the functional maturation of a number of oncogenes. Among the known inhibitors, radicicol, a 14-member macrolide, stands out as the most potent. A molecular dynamics/minimization of radicicol showed that there were three low energy conformers of the macrocycle. The lowest of these is the bioactive conformation observed in the cocrystal structure of radicicol with HSP90. Corresponding conformational analyses of several known analogues gave a good correlation between the bioactivity and the energy of the bioactive conformer, relative to other conformers. Based on this observation, a number of proposed analogues were analyzed for their propensity to adopt the bioactive conformation prior to synthesis. This led to the identification of pochonin D, a recently isolated secondary metabolite of Pochonia chlamydosporia, as a potential inhibitor of HSP90. Pochonin D was synthesized using polymer-bound reagents and shown to be nearly as potent an HSP90 inhibitor as radicicol.