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The bile salt export pump (BSEP in humans, Bsep in animals) is a member of the ATP-binding cassette superfamily of transport proteins. BSEP is selectively located in the apical (canalicular) domain of hepatocytes and catalyzes the rate-limiting step in bile salt secretion from hepatocytes into the bile duct. Reduction of BSEP activity by chemical inhibition leads to disturbances in bile acid trafficking, hepatocellular accumulation of bile acids (intrahepatic cholestasis), and eventually to drug-induced liver injury (DILI). A compound's potential to inhibit BSEP can be assessed by means of dedicated in vitro assays using primary or transfected cells, or cell fragments containing the transport protein. Alternatively, bile salt transport inhibition can also be assessed by measuring plasma bile salt levels in vivo. This latter, more holistic approach may represent an attractive alternative as it allows for a more physiological assessment beyond the mere inhibition of the isolated BSEP transporter. The structural diversity of compounds showing significant BSEP inhibition is rather large. Unfortunately, specific structural features responsible for BSEP inhibition have not been identified so far. Results of computational structure–activity relationship (SAR) analyses indicate that increasing molecular weight and lipophilicity favour BSEP inhibition.

The orexin system plays an important role in the regulation of wakefulness. Suvorexant, a dual orexin receptor antagonist (DORA) is approved for the treatment of primary insomnia. Herein, we outline our optimization efforts toward a novel DORA. We started our investigation with rac-[3-(5-chloro-benzooxazol-2-ylamino)piperidin-1-yl]-(5-methyl-2-[1,2,3]triazol-2-ylphenyl)methanone (3), a structural hybrid of suvorexant and a piperidine-containing DORA. During the optimization, we resolved liabilities such as chemical instability, CYP3A4 inhibition, and low brain penetration potential. Furthermore, structural modification of the piperidine scaffold was essential to improve potency at the orexin 2 receptor. This work led to the identification of (5-methoxy-4-methyl-2-[1,2,3]triazol-2-ylphenyl)-{(S)-2-[5-(2-trifluoromethoxyphenyl)-[1,2,4]oxadiazol-3-yl]pyrrolidin-1-yl}methanone (51), a potent, brain-penetrating DORA with in vivo efficacy similar to that of suvorexant in rats.

The orexin system is responsible for regulating the sleep-wake cycle. Suvorexant, a dual orexin receptor antagonist (DORA) is approved by the FDA for the treatment of insomnia disorders. Herein, we report the optimization efforts toward a DORA, where our starting point was (5-methoxy-4-methyl-2-[1,2,3]triazol-2-yl-phenyl)-{(S)-2-[5-(2-trifluoromethoxy-phenyl)-[1,2,4]oxadiazol-3-yl]-pyrrolidin-1-yl}methanone (6), a compound which emerged from our in-house research program. Compound 6 was shown to be a potent, brain-penetrating DORA with in vivo efficacy similar to suvorexant in rats. However, shortcomings from low metabolic stability, high plasma protein binding (PPB), low brain free fraction (fu brain), and low aqueous solubility, were identified and hence, compound 6 was not an ideal candidate for further development. Our optimization efforts addressing the above-mentioned shortcomings resulted in the identification of (4-chloro-2-[1,2,3]triazol-2-yl-phenyl)-{(S)-2-methyl-2-[5-(2-trifluoromethoxy-phenyl)-4H-[1,2,4]triazol-3-yl]-pyrrolidin-1-yl}l-methanone (42), a DORA with improved in vivo efficacy compared to 6.

Starting from suvorexant (trade name Belsomra), we successfully identified interesting templates leading to potent dual orexin receptor antagonists (DORAs) via a scaffold-hopping approach. Structure-activity relationship optimization allowed us not only to improve the antagonistic potency on both orexin 1 and orexin 2 receptors (Ox1 and Ox2, respectively), but also to increase metabolic stability in human liver microsomes (HLM), decrease time-dependent inhibition of cytochrome P450 (CYP) 3A4, and decrease P-glycoprotein (Pgp)-mediated efflux. Compound 80 c [{(1S,6R)-3-(6,7-difluoroquinoxalin-2-yl)-3,8-diazabicyclo[4.2.0]octan-8-yl}(4-methyl-[1,1'-biphenyl]-2-yl)methanone] is a potent and selective DORA that inhibits the stimulating effects of orexin peptides OXA and OXB at both Ox1 and Ox2. In calcium-release assays, 80 c was found to exhibit an insurmountable antagonistic profile at both Ox1 and Ox2, while displaying a sleep-promoting effect in rat and dog models, similar to that of the benchmark compound suvorexant.

1. The metabolism of the endothelin receptor antagonist macitentan has been characterized in bile duct-cannulated rats and dogs. 2. In both species, macitentan was metabolized along five primary pathways, i.e. conjugation with glucose (M9), oxidative depropylation (M6), aliphatic hydroxylation (M7), oxidative cleavage of the ethylene glycol linker (M4) and hydrolysis of the sulfamide moiety (M3). Most of the primary metabolites underwent subsequent biotransformation including conjugation with glucuronic acid or glucose, hydrolysis of the sulfamide group or secondary oxidation of the ethylene glycol moiety. 3. Though there were species differences in their relative importance, all metabolic pathways were present in rat and dog. The depropylated M6 was the only metabolite present in plasma of both species. 4. Metabolism was a prerequisite for macitentan excretion as relevant amounts of parent drug were neither detected in bile nor urine. Biliary excretion was the major elimination pathway, while renal elimination was of little importance.

Starting from a thienopiperidine lead compound with high intrinsic clearance in rat and human liver microsomes and low aqueous solubility, a novel series of 1-acyl-2-benzylpyrrolidines were discovered as potent and competitive dual orexin receptor antagonists. Metabolic stability was improved to afford oral exposure, and aqueous solubility was increased by twentyfold, providing compounds suitable for preclinical evaluation. Compound 27 showed insurmountable antagonism at both orexin 1 and orexin 2 receptor subtypes and displayed a comparable sleep-promoting effect in the rat to almorexant and suvorexant.

A series of sequences of the DNA analog bicyclo-DNA, 6-12 nucleotides in length and containing all four natural nucleobases, were prepared and their Watson-Crick pairing properties with complementary RNA and DNA, as well as in its own series, were analyzed by UV-melting curves and CD-spectroscopy. The results can be summarized as follows: bicyclo-DNA forms stable Watson-Crick duplexes with complementary RNA and DNA, the duplexes with RNA generally being more stable than those with DNA. Pyrimidine-rich bicyclo-DNA sequences form duplexes of equal or slightly increased stability with DNA or RNA, whereas purine-rich sequences show decreased affinity to complementary DNA and RNA when compared with wild-type (DNA-DNA, DNA-RNA) duplexes. In its own system, bicyclo-DNA prefers antiparallel strand alignment and strongly discriminates for base mismatches. Duplexes are always inferior in stability compared with the natural ones. A detailed analysis of the thermodynamic properties was performed with the sequence 5'-GGATGGGAG-3'x 5'-CTCCCATCC-3' in both backbone systems. Comparison of the pairing enthalpy and entropy terms shows an enthalpic advantage for DNA association (delta deltaH = -18 kcal x (mol)-1)) and an entropic advantage for bicyclo-DNA association (delta deltaS = 49 cal x K(-1) x mol(-1), leading to a delta deltaG 25 degrees C of -3.4 kcal x mol(-1) in favor of the natural duplex. The salt dependence of Tm for this sequence is more pronounced in the case of bicyclo-DNA due to increased counter ion screening from the solvent. Furthermore bicyclo-DNA sequences are more stable towards snake venom phosphodiesterase by a factor of 10-20, and show increased stability in fetal calf serum by a factor of 8 compared with DNA.

The sphingosine-1-phosphate (S1P) type 1 receptor (S1P1R) is a novel therapeutic target in lymphocyte-mediated autoimmune diseases. S1P1 receptor desensitization caused by synthetic S1P1 receptor agonists prevents T-lymphocyte egress from secondary lymphoid organs into the circulation. The selective S1P1 receptor agonist ponesimod, which is in development for the treatment of autoimmune diseases, efficiently reduces peripheral lymphocyte counts and displays efficacy in animal models of autoimmune disease. Using ponesimod and the natural ligand S1P, we investigated the molecular mechanisms leading to different signaling, desensitization and trafficking behavior of S1P1 receptors. In recombinant S1P1 receptor-expressing cells, ponesimod and S1P triggered Gαi protein-mediated signaling and β-arrestin recruitment with comparable potency and efficiency, but only ponesimod efficiently induced intracellular receptor accumulation. In human umbilical vein endothelial cells (HUVEC), ponesimod and S1P triggered translocation of the endogenous S1P1 receptor to the Golgi compartment. However, only ponesimod treatment caused efficient surface receptor depletion, receptor accumulation in the Golgi and degradation. Impedance measurements in HUVEC showed that ponesimod induced only short-lived Gαi protein-mediated signaling followed by resistance to further stimulation, whereas S1P induced sustained Gαi protein-mediated signaling without desensitization. Inhibition of S1P lyase activity in HUVEC rendered S1P an efficient S1P1 receptor internalizing compound and abrogated S1P-mediated sustained signaling. This suggests that S1P lyase - by facilitating S1P1 receptor recycling - is essential for S1P-mediated sustained signaling, and that synthetic agonists are functional antagonists because they are not S1P lyase substrates.

Plasma cells (PCs) are terminally differentiated cells of the B-cell lineage that secrete antibodies at a high rate and are thought to lack the expression of the B-cell receptor (BCR). Here, we report that human IgA and IgM, unlike IgG, PCs express a membrane functional BCR associated with the Igα/Igβ heterodimer. BCR cross-linking on IgA and IgM PCs led to Ca(2+) mobilization and extracellular signal-regulated kinase 1/2 and AKT phosphorylation and impacted survival of IgA PCs. These findings demonstrate a significant difference between human IgG, IgM, and IgA PCs and suggest that the IgA PC repertoire may be modulated by specific antigens with implications for the regulation of the mucosal immune system.

The endothelin peptides bind to two receptors found on cells of vasculature and in tissues. While the endothelin-A (ETA)-receptor is predominantly expressed in vascular smooth muscle cells, the endothelin-B (ETB)-receptor is also found in endothelial cells, fibroblasts, and neuronal cells. Activation of the endothelin system plays a driving role in several chronic cardiovascular diseases and several endothelin receptor antagonists (ERAs) (bosentan (6), ambrisentan (83) and macitentan (43)) have successfully been introduced as oral treatments for the life threatening condition of pulmonary arterial hypertension (PAH). This digest highlights the medicinal chemistry of the pyrimidine based ERAs 6 and 43 and describes the story that started with bosentan and culminated in macitentan (43). A condensed overview of the competitive landscape in the field of ERAs puts the different strategies and tactics applied by the medicinal chemists involved in this endeavor into perspective.

The crystal structure of the duplex formed by oligo(2',3'-dideoxy-beta-d-glucopyranosyl)nucleotides (homo-DNA) revealed strongly inclined backbone and base-pair axes [Egli,M., Pallan,P.S., Pattanayek,R., Wilds,C.J., Lubini,P., Minasov,G., Dobler,M., Leumann,C.J. and Eschenmoser,A. (2006) Crystal structure of homo-DNA and nature's choice of pentose over hexose in the genetic system. J. Am. Chem. Soc., 128, 10847-10856]. This inclination is easily perceived because homo-DNA exhibits only a modest helical twist. Conversely, the tight coiling of strands conceals that the backbone-base inclinations for A- (DNA and RNA) and B-form (DNA) duplexes differ considerably. We have defined a parameter eta(B) that corresponds to the local inclination between sugar-phosphate backbone and base plane in nucleic acid strands. Here, we show its biological significance as a predictive measure for the relative strand polarities (antiparallel, aps, or parallel, ps) in duplexes of DNA, RNA and artificial nucleic acid pairing systems. The potential of formation of ps duplexes between complementary 16-mers with eight A and U(T) residues each was investigated with DNA, RNA, 2'-O-methylated RNA, homo-DNA and p-RNA, the ribopyranosyl isomer of RNA. The thermodynamic stabilities of the corresponding aps duplexes were also measured. As shown previously, DNA is capable of forming both ps and aps duplexes. However, all other tested systems are unable to form stable ps duplexes with reverse Watson-Crick (rWC) base pairs. This observation illustrates the handicap encountered by nucleic acid systems with inclinations eta(B) that differ significantly from 0 degrees to form a ps rWC paired duplex. Accordingly, RNA with a backbone-base inclination of -30 degrees , pairs strictly in an aps fashion. On the other hand, the more or less perpendicular orientation of backbone and bases in DNA allows it to adopt a ps rWC paired duplex. In addition to providing a rationalization of relative strand polarity with nucleic acids, the backbone-base inclination parameter is also a determinant of cross-pairing. Thus, systems with strongly deviating eta(B) angles will not pair with each other. Nucleic acid pairing systems with significant backbone-base inclinations can also be expected to display different stabilities depending on which terminus carries unpaired nucleotides. The negative inclination of RNA is consistent with the higher stability of duplexes with 3'- compared to those with 5'-dangling ends.

Pyranosyl-RNA (qp-RNAq) is an oligonucleotide system isomeric to natural RNA and composed of the very same building blocks as RNA. Its generational, chem., and informational properties are deemed to be those of an alternative nucleic acid system that could have been a candidate in Nature's evolutionary choice of the mol. basis of genetic function. We consider the study of the chem. of p-RNA as etiol. relevant in the sense that knowledge of its structural, chem., and informational properties on the chem. level offers both a perspective and ref. points for the recognition of specific structural assets of the RNA structure that made it the (supposedly) superior system among possible alternatives and, therefore, the system that became part of biol. as we know it today. The paper describes the chem. synthesis of b-D- (and -L)-ribopyranosyl-(4'->2')-oligonucleotide sequences, presents a resume of their structural and chem. properties, and cautiously discusses what we may and may not have learned from the pyranosyl isomer of RNA with respect to the conundrum of RNA's origin. [on SciFinder (R)]

The competitive endothelin receptor antagonists (ERA) bosentan and ambrisentan, which have long been approved for the treatment of pulmonary arterial hypertension, are characterized by very short (1 min) occupancy half-lives at the ET(A) receptor. The novel ERA macitentan, displays a 20-fold increased receptor occupancy half-life, causing insurmountable antagonism of ET-1-induced signaling in pulmonary arterial smooth muscle cells. We show here that the slow ET(A) receptor dissociation rate of macitentan was shared with a set of structural analogs, whereas compounds structurally related to bosentan displayed fast dissociation kinetics. NMR analysis showed that macitentan adopts a compact structure in aqueous solution and molecular modeling suggests that this conformation tightly fits into a well-defined ET(A) receptor binding pocket. In contrast the structurally different and negatively charged bosentan-type molecules only partially filled this pocket and expanded into an extended endothelin binding site. To further investigate these different ET(A) receptor-antagonist interaction modes, we performed functional studies using ET(A) receptor variants harboring amino acid point mutations in the presumed ERA interaction site. Three ET(A) receptor residues significantly and differentially affected ERA activity: Mutation R326Q did not affect the antagonist activity of macitentan, however the potencies of bosentan and ambrisentan were significantly reduced; mutation L322A rendered macitentan less potent, whereas bosentan and ambrisentan were unaffected; mutation I355A significantly reduced bosentan potency, but not ambrisentan and macitentan potencies. This suggests that--in contrast to bosentan and ambrisentan--macitentan-ET(A) receptor binding is not dependent on strong charge-charge interactions, but depends predominantly on hydrophobic interactions. This different binding mode could be the reason for macitentan's sustained target occupancy and insurmountable antagonism.

[formula: see text] The L-alpha-lyxopyranosyl (4'-->3') oligonucleotide system shows cooperative base-pairing in spite of containing only five instead of the usual six covalent bonds per repetitive backbone unit. In contrast, corresponding D-beta-ribofuranosyl (4'-->3') oligonucleotides do not show adenine-thymine pairing under comparable conditions. The difference in pairing behavior relates to the conformation of the two systems' vicinal 3',4'-phosphodiester substituents, which is diaxial in the lyxopyranosyl system and 3'-axial-4'-equatorial in the ribopyranosyl system.

Replication (single-turnover) of pyranosyl-RNA (p-RNA) sequences can be accomplished reliably by template-directed ligation of 2',3'-cyclophosphates of short oligomers. The ligation process was studied using (mostly) octamers as templates and tetramers as ligands. The transcription of the sequence pr(GGGCGGGC) into the (antiparallel) complementary sequence pr(GCCCGCCC) by ligation of 2 mols. of pr(GCCC)-2',3'-cp was investigated in detail. In aq. 1.5 M LiCl soln. of pH 8.5 at room temp. (0.45 mM ligand, 0.15 mM template), the reaction proceeds in up to 60% yield within a week. It is limited by concomitant hydrolysis of cyclophosphate groups of both reactant and ligation product as the only efficient side reaction, the latter occurring .apprx.3 times more slowly than ligation. No ligation at all is obsd. in the absence of template. The reaction is highly regioselective: the (4'->2') phosphodiester junction is formed exclusively; no isomeric (4'->3') junctions are found. For ligation to occur, template and ligand must be homochiral and must have the same sense of chirality; with chiro-diastereoisomeric tetramer-2',3'-cyclophosphates contg. a single enantio-ribopyranosyl unit, no ligation is obsd., except to a minor extent in the case of the diastereoisomer that has that unit at the 4'-end. Observations made in expts. involving 6 different octamer templates contg. isomeric base sequences indicate that the ligation process does not tolerate a mismatch at ligation sites. However, ligation still takes place when a mismatch occurs at either end of the (octamer) template. Ligation efficiencies differ widely, depending on the nature, as well as the sequence, of participating bases. These differences can be understood qual. by considering the relative stability of ternary pre-ligation complexes, together with the differences in interstrand base stacking at ligation sites. Dominance of the latter over intrastrand base stacking is the feature of the p-RNA structure that appears to det. most of the characteristic properties of p-RNA. As regards the etiol. context of this work on nucleic-acid alternatives, it is essential that the chem. properties found for p-RNA be compared with the corresponding properties of RNA. In the RNA series, the 2 ligations of the replicative cycle r(GGGCGGGC) .tautm. r(GCCCGCCC) using the corresponding ribofuranosyl-tetramer 2',3'-cyclophosphates as ligands are found to proceed also, though somewhat less efficiently than in the p-RNA series; however, the ligation step produces exclusively the unnatural (5'->2') phosphodiester junctions instead of the natural (5'->3') junctions. This is in sharp contrast to p-RNA, where template-controlled 2',3'-cyclophosphate ligations produce the 'correct' phosphodiester junctions. [on SciFinder (R)]

Synthetic sphingosine 1-phosphate receptor 1 modulators constitute a new class of drugs for the treatment of autoimmune diseases. Sphingosine 1-phosphate (S1P) signaling, however, is also involved in the development of fibrosis. Using normal human lung fibroblasts, we investigated the induction of fibrotic responses by the S1P receptor (S1PR) agonists S1P, FTY720-P, ponesimod, and SEW2871 and compared them with the responses induced by the known fibrotic mediator TGF-β1. In contrast to TGF-β1, S1PR agonists did not induce expression of the myofibroblast marker α-smooth muscle actin. However, TGF-β1, S1P, and FTY720-P caused robust stimulation of extracellular matrix (ECM) synthesis and increased pro-fibrotic marker gene expression including connective tissue growth factor. Ponesimod showed limited and SEW2871 showed no pro-fibrotic potential in these readouts. Analysis of pro-fibrotic signaling pathways showed that in contrast to TGF-β1, S1PR agonists did not activate Smad2/3 signaling but rather activated PI3K/Akt and ERK1/2 signaling to induce ECM synthesis. The strong induction of ECM synthesis by the nonselective agonists S1P and FTY720-P was due to the stimulation of S1P2 and S1P3 receptors, whereas the weaker induction of ECM synthesis at high concentrations of ponesimod was due to a low potency activation of S1P3 receptors. Finally, in normal human lung fibroblast-derived myofibroblasts that were generated by TGF-β1 pretreatment, S1P and FTY720-P were effective stimulators of ECM synthesis, whereas ponesimod was inactive, because of the down-regulation of S1P3R expression in myofibroblasts. These data demonstrate that S1PR agonists are pro-fibrotic via S1P2R and S1P3R stimulation using Smad-independent pathways.

Background: The natural nucleic acids (DNA and RNA) can adopt a variety of structures besides the antiparallel double helix described by Watson and Crick, depending on base sequence and solvent conditions. Specifically base-paired DNA structures with regular backbone units include left-handed and parallel duplexes and triple and quadruple helical arrangements. Given the base-pairing pattern of the natural bases, preferences for how single strands associate are determined by the structure and flexibility of the sugar-phosphate backbone. We set out to determine the role of the backbone in complex formation by designing DNA analogs with well defined modifications in backbone structure. Results: We recently developed a DNA analog (bicyclo-DNA) in which one (γ) of the six torsion angles (a-ζ) describing the DNA-backbone conformation is fixed in an orientation that deviates from that observed in B-DNA duplexes by about +100°, a shift from the synclinal to the antiperiplanar range. Upon duplex formation between homopurine and homopyrimidine sequences, this analog preferentially selects the Hoogsteen and reversed Hoogsteen mode, forming A-T and G-C + base pairs. Base-pair formation is highly selective, but degeneracy is observed with respect to strand orientation in the duplex. Conclusions: The flexibility and orientation of the DNA backbone can influence the preferences of the natural bases for base-pairing modes, and can alter the relative stability of duplexes and triplexes.

10.1002/hlca.19950780816.abs A conformational analysis of the (3′S,5′R)-2′-deoxy-3′,5′-ethano-α-D-ribonucleosides (a-D-bicyclodeoxynucleosides) based on the X-ray analysis of N4-benzoyl-α-D-(bicyclodeoxycytidine) 6 and on 1H-NMR analysis of the α-D-bicyclodeoxynucleoside derivatives 1-7 reveals a rigid sugar structure with the furanose units in the l′-exo/2′-endo conformation and the secondary OH groups on the carbocyclic ring in the pseudoequatorial orientation. Oligonucleotides consisting of α-D-bicyclothymidine and α-D-bicyclodeoxyadenosine were successfully synthesized from the corresponding nucleosides by phosphoramidite methodology on a DNA synthesizer. An evaluation of their pairing properties with complementary natural RNA and DNA by means of UV/melting curves and CD spectroscopy show the following characteristics: i) α-bcd(A10) and α-bcd(T10) (α = short form of α-D)efficiently form complexes with complementary natural DNA and RNA. The stability of these hybrids is comparable or slightly lower as those with natural β-d(A10) or β-d(T10)( β = short form ofβ-D). ii) The strand orientation in α-bicyclo-DNA/β-DNA duplexes is parallel as was deduced from UV/melting curves of decamers with nonsymmetric base sequences. iii) CD Spectroscopy shows significant structural differences between α-bicyclo-DNA/β-DNA duplexes compared to α-DNA/β-DNA duplexes. Furthermore, α-bicyclo-DNA is ca. 100-fold more resistant to the enzyme snake-venom phosphodiesterase with respect to β-DNA and about equally resistant as α-DNA.

A review and discussion, with 42 refs. Base pairing in p-RNA (b-D-ribopyranosyl-(4'->2')-oligonucleotides) is not only stronger than in DNA and RNA, but also more selective in the sense that it is strictly confined to the Watson-Crick mode. Homopurine sequences (tested up to decamers) exist as single strands under conditions where they undergo reverse-Hoogsteen self-pairing in homo-DNA or Hoogsteen self-pairing in DNA. This exceptional pairing selectivity is rationalized as hinging on 2 structural features of p-RNA: the large inclination between backbone axis and base-pair axes in p-RNA duplexes, and the higher rigidity of the p-RNA backbone compared with RNA, DNA, and homo-DNA. The most important consequence of the pairing selectivity refers to the potential of p-RNA to replicate. Replicative copying of sequence information by nonenzymic template-controlled ligation is not hampered by self-pairing of guanine-rich templates, as it is known to be the case in the RNA series. Two replicative cycles are demonstrated in which G-rich p-RNA-octamer templates induce sequence-selective ligation of tetramer-2'-phosphate derivs. to complementary C-rich octamer sequences, and in which the latter, with comparable efficiency, induce corresponding ligation reactions back to the original G-rich octamers. Ligation is most satisfactorily achieved after pre-activation of the 2'-phosphate groups as 2',3'-cyclophosphate derivs.; in this version, the process does not proceed as oligocondensation, but as a genuine oligomerization. This is of considerable promise for the search for potentially natural conditions under which homochiral p-RNA strands might self-assemble and self-replicate. [on SciFinder (R)]

Institute of Pathology (M.B.), CH-6601 Locarno, Switzerland; Department of Nuclear Medicine and Thyroid Centre (S.S., L.G.), Oncology Institute of Southern Switzerland, CH-6500 Bellinzona, Switzerland; Department of General and Visceral Surgery (M.B.), Ente Ospedaliero Cantonale, CH-6501 Bellinzona, Switzerland; Endocrine Private Practice (F.C.), CH-6900 Lugano, Switzerland; and Department of General Surgery (F.F.), Ente Ospedaliero Cantonale, CH-6850 Mendrisio, Switzerland

The synthesis of a new type of oligonucleotide (‘bicyclooligodeoxynucleotide’ = bcd(Xn)) displaying less conformational flexibility in its sugar-phosphate backbone is described, and a characterization of the pairing properties and energetics of the decamers bcd(T10) and bcd (A10) with each other and with complementary RNA and DNA sequences by UV-spectroscopic and calorimetric techniques is given. The results can be summarized as follows: (i) bcd(T10) pairs less strongly to complementary RNA and DNA, whereas bcd(A10) forms stronger duplexes relative to the natural system. (ii) bcd(A10) discriminates between a complementary oligodeoxynucleotide with a mismatch in the center in the same way as d(A10), indicating equal base-pairing selectivity. (iii) bcd(A10) forms more stable triplexes with d(T10) of the pyrimidine-purine-pyrimidine (py · pu · py) motif than d(A10). (iv) The stability of duplexes containing a bicyclic strand is more sensitive towards salt concentration. The higher sensitivity in bcd(A10) containing duplexes is due to a higher differential cation uptake. (v) Differential scanning calorimetric (DSC) analysis of duplex-formation enthalpies shows ΔHvH in all duplexes containing bicyclooligonucleotides to be more negative than ΔHcal, which is compatible with the formation of catenated structures. (vi) Isothermal titration calorimetry (ITC) provides a complete set of thermodynamic data including duplex and triplex association constants for the systems d(A10)/d(T10), bcd(A10)/d(T10), d(A10)/bcd(T10), bcd(A10)/bcd(T10). (vii) All duplexes containing bicyclic strands show a (numerically) reduced pairing entropy term with respect to that of the natural system. (viii) Enthalpies from DSC and ITC are similar, suggesting that the enthalpic contribution from ordered single strands to the overall duplex-formation enthalpy plays a minor role in the duplexes investigated.

We describe the synthesis of 2′-deoxy-3′,5′-ethano-D-ribonucleosides 1–8 (= (5′,8′-dihydroxy-2′-oxabicyclo-[3.3.0]oct-3′-yl)purines or -pyrimidines) of the nucleobases adenine, thymine, cytosine, and guanine. They differ from natural 2′-deoxyribonucleosides only by an additional ethylene bridge between the centers C(3′) and C(5′). The configuration at these centers (3S,5′R) was chosen as to match the geometry of a repeating nucleoside unit in duplex DNA as close as possible. These nucleosides were designed to confer, as constituents of an oligonucleotide chain, a higher degree of preorganization of a single strand for duplex formation with respect to natural DNA, thus leading to an entropic advantage for the pairing process. The synthesis of these ‘bicyclonucleosides’ was achieved by construction of an enantiomerically pure carbohydrate precursor 18/19 (Schemes 1), which was then converted to the corresponding nucleosides by known methods in nucleoside synthesis (Schemes 2 and 3). In all cases, both anomeric forms of the nucleosides were obtained in pure crystalline form, the relative configuration of which was established by 1H-NMR-NOE spectroscopy. A conformational analysis of the nucleosides with β-configuration at the anomeric center by means of X-ray and 1H-NMR (including NOE) spectroscopy show the furanose part of the molecules to adopt uniformly a 1′exo-conformation with the base substituents preferentially in the anti-range in the pyrimidine nucleosides (anti/syn ca. 2:1) distribution in the purine nucleosides (in solution).

Since its discovery in 1988 by Yanagisawa et al., endothelin (ET), a potent vasoconstrictor, has been widely implicated in the pathophysiology of cardiovascular, cerebrovascular, and renal diseases. Many research groups have embarked on the discovery and development of ET receptor antagonists for the treatment of such diseases. While several compounds, e.g., ambrisentan 2, are in late clinical trials for various indications, one compound (bosentan, Tracleer) is being marketed to treat pulmonary arterial hypertension. Inspired by the structure of ambrisentan 2, we designed a novel class of ET receptor antagonists based on a 1,3,4,5-tetrahydro-1H-benzo[e][1,4]diazepin-2-one scaffold. Here, we report on the preparation as well as the in vitro and in vivo structure-activity relationships of these derivatives. Potent dual ET(A)/ET(B) receptor antagonists with affinities in the low nanomolar range have been identified. In addition, several compounds efficiently reduced arterial blood pressure after oral administration to Dahl salt sensitive rats. In this animal model, the efficacy of the benzo[e][1,4]diazepin-2-one derivative rac-39au was superior to that of racemic ambrisentan, rac-2.

A series of compounds structurally related to bosentan 1 featuring an unsaturated side chain at position 6 of the core pyrimidine have been studied for their potential to block the ET A and ET B receptor. Incorporation of a 2-butyne-1,4-diol linker bearing a pyridyl carbamoyl moiety led to in vitro highly potent endothelin receptor antagonists (e.g., 70 and 75 ). The propargyl derivative 26 significantly reduced blood pressure in in vivo model studies with hypertensive salt-sensitive Dahl rats.

Modification of the structure of bosentan 1, the first marketed endothelin receptor antagonist (Tracleer™), by introduction of a second sulfonamide function at the alkoxy side chain, led to bis-sulfonamides 2. This allowed to prepare dual ETA/ETB as well as ETB receptor selective antagonists, which could serve as tools to investigate the pharmacological consequences of selective ETB receptor blockade.

The ( l )-α-lyxopyranosyl-(4′→3′)-oligonucleotide system—a member of a pentopyranosyl oligonucleotide family containing a shortened backbone—is capable of cooperative base-pairing and of cross-pairing with DNA and RNA. In contrast, corresponding ( d )-β-ribopyransoyl-(4′→3′)-oligonucleotides do not show base-pairing under similar conditions. We conclude that oligonucleotide systems can violate the ‘six-bonds-per-backbone-unit’ rule by having five bonds instead, if their vicinally bound phosphodiester bridges can assume an antiperiplanar conformation. An additional structural feature that seems relevant to the cross-pairing capability of the ( l )-α-lyxopyranosyl-(4′→3′)-oligonucleotide system is its (small) backbone/basepair axes inclination. An inclination which is similar to that in B-DNA seems to be a prerequisite for an oligonucleotide system's capability to cross-pair with DNA.

Background: Why did Nature choose furanosyl-RNA and not pyranosyl-RNA as her molecular genetic system? An experimental approach to this problem is the systematic comparison of the two isomeric oligonucleotide systems with respect to the chemical properties that are fundamental to the biological role of RNA, such as base pairing and nonenzymic replication. Pyranosyl-RNA has been found to be not only a stronger, but also a more selective pairing system than natural RNA; both form hairpin structures with comparable ease. Base sequences of pyranosyl-RNA can be copied by template-controlled replicatioe ligation of short activated oligomers (e.g. tetramer-2′,3′-cyclophosphates) under mild and potentially natural conditions. The copying proceeds with high regio-selectivity as well as chiroselectivity: homochiral template sequences mediate the formation of the correct (4′→2′)-phosphodiester junction between homochiral tetramer units provided they have the same sense of chirality as the template. How could homochiral template sequences assemble themselves in the first place? Results: Higher oligomers of pyranosyl-RNA can self-assemble in dilute solutions under mild conditions by ligative oligomerization of tetramer-2′,3′-cyclophosphates containing hemi self-complementary base sequences. The only side reaction that effectively competes with ligation is hydrolytic deactivation of 2′,3′-cyclophosphate end groups. The ligation reaction is highly chiroselective; it is slower by at least two orders of magnitude when one of the (d)-ribopyranosyl units of a homochiral (d)-tetramer-2′,3′-cyclophosphate is replaced by a corresponding (l)-unit, except when the (l)-unit is at the 4′ end of the tetramer and carries a purine, when the oligomerization rate can be ∼ 10% of that shown for a homochiral isomer. The oligomerization of homochiral tetramers is not, or only weakly, inhibited by the presence of the non-oligomerizing diastereomers. Conclusions: Available data on the chiroselective self-directed oligomerization of tetramer-2′,3′-cyclophosphates allow us to extrapolate that sets of tetramers with different but mutually fitting base sequences can be expected to co-oligomerize stochastically and generate sequence libraries consisting of predominantly homochiral (d)- and (l)-oligomers, starting from the racemic mixture of tetramers containing all possible diastereomers. Such a capability of an oligonucleotide system deserves special attention in the context of the problem of the origin of biomolecular homochirality: breaking molecular mirror symmetry by de-racemization is an intrinsic property of such a system whenever the constitutional complexity of the products of co-oligomerization exceeds a critical level.