Propyl Linker Research Articles

Role of Amine Structure on Carbon Dioxide Adsorption from Ultradilute Gas Streams such as Ambient Air

A fundamental study on the adsorption properties of primary, secondary, and tertiary amine materials is used to evaluate what amine type(s) are best suited for ultradilute CO(2) capture applications. A series of comparable materials comprised of primary, secondary, or tertiary amines ligated to a mesoporous silica support via a propyl linker are used to systematically assess the role of amine type. Both CO(2) and water adsorption isotherms are presented for these materials in the range relevant to CO(2) capture from ambient air and it is demonstrated that primary amines are the best candidates for CO(2) capture from air. Primary amines possess both the highest amine efficiency for CO(2) adsorption as well as enhanced water affinity compared to other amine types or the bare silica support. The results suggest that the rational design of amine adsorbents for the extraction of CO(2) from ambient air should focus on adsorbents rich in primary amines.

Chemoselective Staudinger-phosphite reaction of symmetrical glycosyl-phosphites with azido-peptides and polygycerols

In this paper we present the synthesis of glyco-phosphoramidate conjugates as easily accessible analogs of glyco-phosphorous esters via the Staudinger-phosphite reaction. This protocol takes advantage of synthetically accessible symmetrical carbohydrate phosphites in good overall yields, in which ethylene or propylene linkers can be introduced between phosphorous and galactose or lactose moieties. The phosphites were finally applied for the chemoselective reaction with azido-peptides and polyazido(poly)glycerols.

DNA duplexes and triplex-forming oligodeoxynucleotides incorporating modified nucleosides forming stable and selective triplexes

We have previously reported DNA triplexes containing the unnatural base triad G-PPI·C3, in which PPI is an indole-fused cytosine derivative incorporated into DNA duplexes and C3 is an abasic site in triplex-forming oligonucleotides (TFOs) introduced by a propylene linker. In this study, we developed a new unnatural base triad A-ψ·C(R1) where ψ and C(R1) are base moieties 2'-deoxypseudouridine and 5-substituted deoxycytidine, respectively. We examined several electron-withdrawing substituents for R1 and found that 5-bromocytosine (C(Br)) could selectively recognize ψ. In addition, we developed a new PPI derivative, PPI(Me), having a methyl group on the indole ring in order to achieve selective triplex formation between DNA duplexes incorporating various Watson-Crick base pairs, such as T-A, C-G, A-ψ, and G-PPI(Me), and TFOs containing T, C, C(Br), and C3. We studied the selective triplex formation between these duplexes and TFOs using UV-melting and gel mobility shift assays.

Structure–activity relationship studies of S1P agonists with a dihydronaphthalene scaffold

Structure-activity relationship (SAR) of sphingosine-1-phosphate receptor agonists with a dihydronaphthalene scaffold was investigated. Compound 1 was modified to improve S1P(1) agonistic activity and in vivo peripheral lymphocyte lowering (PLL) activity without impairing selectivity over S1P(3) agonistic activity. A detailed SAR study of the terminal lipophilic part revealed that the introduction of substituents on the propylene linker and the terminal benzene ring influences in vitro and PLL activities. Compound 6n bearing a (S)-methyl group at the 2-position on the propylene linker and chlorine at the para-position on the terminal benzene ring showed potent hS1P(1) agonistic activity with excellent selectivity over hS1P(3) and in vivo PLL activity in mice.

Analogues of σ Receptor Ligand 1-Cyclohexyl-4-[3-(5-methoxy-1,2,3,4-tetrahydronaphthalen-1-yl)propyl]piperazine (PB28) with Added Polar Functionality and Reduced Lipophilicity for Potential Use as Positron Emission Tomography Radiotracers

1-Cyclohexyl-4-[3-(5-methoxy-1,2,3,4-tetrahydronaphthalen-1-yl)propyl]piperazine 1 (PB28) represents an excellent lead candidate for therapeutic and/or diagnostic applications in oncology. However, because its utility is limited by its relatively high degree of lipophilicity, novel analogues of 1 with reduced lipophilic character were designed by substituting methylene groups with more polar functional groups in the propylene linker and at the tetralin C4 position. For the chiral analogues, separate enantiomers exhibited substantial and roughly equal affinities within a given receptor subtype, with the greatest difference observed for compound 9 at σ(1) (7.5-fold; (-)-(S)-9 K(i) = 94.6 nM, (+)-(R)-9 K(i) = 12.6 nM). Compound (-)-(S)-9 was also found to be the most σ(2)-selective agent (σ(2) K(i) = 5.92 nM), to possess a lipophilicity consistent with entry into tumor cells (log D(7.4) = 2.38), and to show minimal antiproliferative activity. However, (-)-(S)-9 exhibited moderate activity (EC(50) = 8.1 μM) at the P-gp efflux pump.

Cleavage of an RNA Model Catalyzed by Dinuclear Zn(II) Complexes Containing Rate-Accelerating Pendants. Comparison of the Catalytic Benefits of H-Bonding and Hydrophobic Substituents

The transesterification of a simple RNA model, 2-hydroxypropyl p-nitrophenyl phosphate (2, HpNPP) promoted by seven dinuclear Zn(II) catalysts (3,4,5,6,7,8,9:Zn(II)2:(-OCH3)) based on the bis[bis(2-substituted-pyridinyl-6-methyl)]amine ligand system was investigated in methanol under sspH-controlled conditions at 25.0 ± 0.1 °C. The two metal complexing ligands were joined together via the amino N connected to a m-xylyl linker (3, 4, 5, 6, 7) where the 2-pyridinyl substituent = H, CH3, (CH)4, NH2, and NH(C═O)CH3, respectively, and a propyl linker (8, 9) where the ring substituent = H and CH3. All of the dinuclear complexes except 8:Zn(II)2 exhibit saturation kinetics for the kobs versus [catalyst] plots from which one can determine catalyst:substrate binding constants (KM), the catalytic rate constants for their decomposition (kcat), and the second order catalytic rate constants (k2cat = kcat/KM). In the case of 8:Zn(II)2, the plots of kobs versus [catalyst] as a function of sspH are linear, and the catalytic rate constants (k2cat) are defined as the gradients of the plots. Analysis of all of the data at the sspH optimum for each reaction indicates that the presence of the amino and acetamido H-bonding groups and the CH3 group provides similar increases of the kcat terms of 25−50 times that exhibited by the parent complex 3:Zn(II)2. However, in terms of substrate catalyst binding (KM), there is no clear trend that H-bonding groups or the CH3 group provides stronger binding than the parent complex. In terms of the overall second order catalytic rate constant, the CH3, amino, and NH(C═O)CH3 groups provide 20, 10, and 68 times the k2cat observed for the parent complex. In the case of 9:Zn(II)2, the presence of the methyl groups provides a 1000-fold increase in activity (judged by k2cat) over the parent complex 8:Zn(II)2. The results are interpreted to indicate that H-bonding effects may be important for catalysis and less so for substrate binding, but the steric effect and impact on the local polarity provided by a methyl substituent is just as effective and in fact may form part of the acceleratory effect attributed to H-bonding in related systems.

Abasic site-based DNA aptamers for analytical applications

We here describe a class of duplex DNA aptamers that possess an abasic site as an active cavity for binding events. A structurally optimised 23-meric duplex (5′-TCT GCG TCC AGX GCA ACG CAC AC-3′/3′-AGA CGC AGG TCT CGT TGC GTG TG-5′, X = abasic site; a propyl linker, T = receptor base) binds to riboflavin with a dissociation constant of 1.9 μM (at 20°C, pH 7.0, I = 0.11 M), and it exhibits a high selectivity for riboflavin over flavin mononucleotide and flavin adenine dinucleotide. A fluorescent signalling aptamer is also developed by the incorporation of fluorescent 2-aminopurine (2-AP) into the duplex to flank the abasic site. This 2-AP-modified abasic site-containing duplex DNA (5′-TCTGC GTCCT PXT TAACG CACAC-3′/3′-AGACG CAGGA TCA ATTGC GTGTG-5′, P = 2-AP, X = abasic site; a propyl linker, C = receptor base) is capable of selectively binding to the bronchodilator theophylline with a dissociation constant of 10 μM (at 5°C, pH 7.0, I = 0.11 M), and it is applicable to monitoring serum theophylline concentrations. In addition, we describe a design strategy for label-free aptamer-based fluorescence-signalling systems based on an abasic site-binding fluorescent ligand. A DNA aptamer against adenosine is examined as a model system, and an abasic site is designed to be incorporated into the aptamer system, so that the adenosine binding causes either a release or binding of abasic site-binding ligands with a clear fluorescent signalling. The designed system is highly selective and sensitive with a detection limit of 1–2 μM for adenosine. These results are discussed as a potential basis for the further development of an aptamer-based analytical assay.

Carbonyl Complexes of Rhodium with N-Donor Ligands: Factors Determining the Formation of Terminal versus Bridging Carbonyls

Cationic rhodium carbonyl complexes supported by a series of different N3- and N4-donor ligands were prepared, and their ability to form carbonyl-bridged species was evaluated. Complex [Rh(κ3-bpa)(cod)]+ (1+) (bpa = bis(2-picolyl)amine, cod = cis,cis-1,5-cyclooctadiene) reacts with 1 bar of CO to form a tris-carbonyl-bridged species [Rh2(κ3-bpa)2(μ-CO)3]2+ (22+), which in solution slowly decomposes to the terminal monocarbonyl complex [Rh(κ3-bpa)(CO)]+ (3+). Similar conditions lead to direct formation of a terminal monocarbonyl species, [Rh(κ3-Bu-bpa)(CO)]+ (5+), from [Rh(κ3-Bu-bpa)(cod)]+ (4+) (Bu-bpa = N-butylbis(2-picolyl)amine). Treatment of 4+ with 50 bar of CO leads to only partial conversion (∼15%) to the tris-carbonyl-bridged species [Rh2(κ3-Bu-bpa)2(μ-CO)3]2+ (62+). Stabilization of tris-carbonyl bridges can be achieved by cooperative binding. Tethering two bpa moieties with a propylene linker allows cooperative CO binding to [(CO)Rh(μ-(bis-κ3)tppn)Rh(CO)]2+, producing the tetranuclear complex [R...

Diols and anions can control the formation of an exciplex between a pyridinium boronic acid with an aryl group connected via a propylene linker

The exciplex formation between a pyridinium boronic acid and phenyl group connected via a propylene linker can be monitored using fluorescence. Addition of pinacol affords a cyclic boronate ester with enhanced Lewis acidity that increases the strength of its cation-π stacking interaction causing a four-fold fluorescence enhancement.

Synthesis and Antiviral Activity of Phthiobuzone Analogues

A series of phthiobuzone analogs, prepared from potassium phthalimide or phthalandione, have been evaluated for their antiviral activities. Among the candidates, compounds 5j and 5k, which contain the substituted 4-halogenated phenyl ring at N-4',4'' position, show more potent antiviral activity than phthiobuzone against herpes simplex virus 1 (IC(50)=8.56 and 2.85 microg/ml, respectively) and herpes simplex virus 2 (IC(50)=1.75 and 4.11 microg/ml, respectively). Compounds 9c and 9d with a propylene linker between the phthalimide and bisthiosemicarbazone moieties display similar antiviral potency against herpes simplex virus 1 (IC(50)=2.85 and 4.11 microg/ml, respectively).

(Perfluoro)sulfonic acids having an imidazolium tag as homogeneous and reusable ionophilic Brönsted acid catalysts for carboxylic acid esterification

The concept of adding a peripheral imidazolium tag to obtain ionophilic sulfonic acids has been applied to the synthesis of four Brönsted acids having perfluoroalkyl and propyl linkers. The resulting sulfonic acids were tested as homogeneous and reusable Brönsted acid for the esterification of octanoic acid by n-propanol. It was found that while perfluoroalkyl sulfonic acids exhibit low catalytic activity due to miscibility problems, propylsulfonic acids were highly active and reusable. It was concluded that no strong Brönsted sites are necessary to promote this carboxylic esterification and that the fluorous properties of the perfluroalkyl chain (>30% fluorine in the imidazolium cation) play an adverse role on the catalytic activity under the conditions used.

Nickel(II) Complexes of Monofunctionalized Pyridine-Azamacrocycles: Synthesis, Structures, Pendant Arm “On-Off” Coordination Equilibria, and Peroxidase-like Activity

Novel nickel(II) complexes of pyridine-azamacrocycles (PyMACs) with pendant arms have been synthesized using simple, direct, and selective mono-N-functionalization of PyMACs. These complexes have been characterized by spectroscopy and X-ray crystallography. Nickel(II)-PyMAC complexes with a flexible pendant arm bearing a tertiary amine, a carboxylic acid, or an amide group exhibit structural and color changes due to "on-off" arm coordination to the metal center. Five- or six-coordinate complexes with the arm bound to the nickel(II) center are high-spin, while their four-coordinate "arm-off" counterparts are low-spin. Synergistic axial coordination of acetonitrile and the amide group from the pendant arm was observed. Coordination to the nickel(II) center lowers the pK(a) of the functional group attached to the macrocycle via a propylene linker by up to 4-5 orders of magnitude. Varying hydrogen bonding and proton-donating properties of the pendant arm affects the peroxidase-like activity of Ni(II)-PyMAC complexes in the oxidation of ABTS with hydrogen peroxide.

Analysis Of The Interaction Of The Nucleotide Base With The Myosin Catalytic Pocket And The Effect On Substrate Efficacy

Myosin has been shown it to be a promiscuous enzyme that can utilize a number nucleotide and non-nucleoside triphosphate substrates. However, the chemomechanical efficacy of the alternative substrates varies widely. In particular, the ability of “nanalog” substrates (an amino-ethyl or -propyl linker and a substituted phenyl ring in lieu of the ribose and the nucleotide base) to completely decouple substrate hydrolysis from motility clearly indicates that the correct interaction of myosin with the ribose and base is essential for myosin function. As a first step to understand better the myosin-substrate interaction and how interactions other than with the triphosphates are essential for motility, we have used molecular dynamics simulations of the Dictyostelium ADP•BeFx x-ray structure to investigate the interactions of myosin with ATP, CTP (effective substrate) and GTP (poor substrate) docked at the active site. The simulations with ATP suggest a “troika” of conserved amino acids lining the nucleotide site that form a cyclical chain of nucleotide-protein hydrogen bonding interactions: ATP (N6) → Y135 → Y116 → N188 → ATP (N7). In the simulations, substitution of CTP at the active site maintains this coordination. Substitution of GTP at the active site perturbs the interaction. Thus the simulations suggest a set of crucial protein-substrate interactions that must be maintained for an effective substrate. The modeling has predictive power. “In silico” mutation experiments suggest that the mutation Y135K preserves troika-mediated pattern with GTP at the active site, but destroys it with ATP at the active site. The prediction would be that the Y135K mutation would make myosin a more effective GTPase and a less effective ATPase.

New Nucleotide Pairs for Stable DNA Triplexes Stabilized by Stacking Interaction

New nucleotide pairs applicable to formation of DNA triplexes were developed. We designed oligonucleotides incorporating 5-aryl deoxycytidine derivatives (dC5Ars) and cyclic deoxycytidine derivatives, dCPPP and dCPPI, having an expanded aromatic area, as the second strand. As pairing partners, two types of abasic residues (C3: propylene linker, phi: abasic base) were chosen. It was concluded that, when the 5-aryl-modified cytosine bases paired with the abasic sites in TFOs in a space-fitting manner, the stability of the resulting triplexes significantly increased. The recognition of C3 toward dC5Ars was selective because of the stacking interactions between their aromatic part and the nucleobases flanking the abasic site. These results indicate the potential utility of new nucleotide triplets for DNA triplex formation, which might expand the variety of structures and sequences and might be useful for biorelated fields such as DNA nanotechnologies.

An Engineered Mannoside Presenting Platform: Escherichia coli Adhesion under Static and Dynamic Conditions

AbstractThe study of the adhesion mechanisms of pathogens to host tissues has gained increased interest as bacterial adhesion is involved in the early stages of surface colonization and infection. Here we describe a platform to study the specific binding of the bacterium Escherichia coli (E. coli) K‐12 strain to molecularly well‐defined surfaces mimicking cellular interfaces. This approach uses a poly(ethylene glycol) brush interface, which displays synthetic determinants of the high mannose N‐linked glycans in a range of densities (3.8 × 104–1.6 × 105 mannosides µm−2) for the investigation of multivalent interactions with bacteria. The bacterial attachment is mediated by specific interactions between the adhesive protein FimH located on the tip of the bacterial type 1 pili and the mannosylated surfaces. With synthetically engineered mannoses, it is found that the number of strongly adhering bacteria is co‐regulated by many structural physical parameters. Beyond the dependency on carbohydrate density, higher numbers of E. coli attach to the branched trimannose Man(α1–3)(Man(α1–6))Man compared to the monomannose, while larger oligomannoses exposing Man(α1–2) Man at their non reducing end show low binding capacity. The linker used between the mannose moiety and PEG is also affecting the binding efficacy of E. coli. The (hydrophobic) propyl linker results in higher bacteria numbers in comparison to the (hydrophilic) tri(EG), likely a consequence of additional stabilization of the binding complex by hydrophobic interactions. Furthermore, differences are observed in bacteria attachment between stagnant and flow conditions that depend on the type of mannose ligand. Finally, a photolithographic resist lift‐off combined with site‐selective assembly of the glycopolymers is used to produce micropatterns with bacteria colonies confined to defined areas and at controlled colony numbers.

From rigid cyclic templates to conformationally stabilized acyclic scaffolds. Part I: The discovery of CCR3 antagonist development candidate BMS-639623 with picomolar inhibition potency against eosinophil chemotaxis

Conformational analysis of trans-1,2-disubstituted cyclohexane CCR3 antagonist 2 revealed that the cyclohexane linker could be replaced by an acyclic syn-α-methyl-β-hydroxypropyl linker. Synthesis and biological evaluation of mono- and disubstituted propyl linkers support this conformational correlation. It was also found that the α-methyl group to the urea lowered protein binding and that the β-hydroxyl group lowered affinity for CYP2D6. Ab initio calculations show that the α-methyl group governs the spatial orientation of three key functionalities within the molecule. α-Methyl-β-hydroxypropyl urea 31 with a chemotaxis IC 50 = 38 pM for eosinophils was chosen to enter clinical development for the treatment of asthma.

Fluorescence emission detection of single-nucleotide polymorphisms by a naphthyridine-benzofurazan conjugate

We have successfully developed a class of ligand that exhibits a fluorescence-enhancement upon binding to pyrimidine bases opposite an AP site in DNA duplexes. The present ligand, Naph-c3-DBD, in which DBD (7-N,N-dimethylaminosulfonylbenzo-2-oxa-1,3-diazole) is connected to 2-amino-7-methyl-1,8-naphthyridine by a propylene linker, is capable of selectively binding to pyrimidine bases over purine bases, and the binding event is accompanied by a significant enhancement of emission due to the DBD moiety (emission maximum at 597 nm). The response of the ligand is almost specific to pyrimidine bases, making it possible to detect pyrimidine/purine transversion.

A posteriori design of crystal contacts to improve the X-ray diffraction properties of a small RNA enzyme.

The hairpin ribozyme is a small catalytic RNA comprising two helix-loop-helix domains linked by a four-way helical junction (4WJ). In its most basic form, each domain can be formed independently and reconstituted without a 4WJ to yield an active enzyme. The production of such minimal junctionless hairpin ribozymes is achievable by chemical synthesis, which has allowed structures to be determined for numerous nucleotide variants. However, abasic and other destabilizing core modifications hinder crystallization. This investigation describes the use of a dangling 5'-U to form an intermolecular U.U mismatch, as well as the use of synthetic linkers to tether the loop A and B domains, including (i) a three-carbon propyl linker (C3L) and (ii) a nine-atom triethylene glycol linker (S9L). Both linker constructs demonstrated similar enzymatic activity, but S9L constructs yielded crystals that diffracted to 2.65 A resolution or better. In contrast, C3L variants diffracted to 3.35 A and exhibited a 15 A expansion of the c axis. Crystal packing of the C3L construct showed a paucity of 6(1) contacts, which comprise numerous backbone to 2'-OH hydrogen bonds in junctionless and S9L complexes. Significantly, the crystal packing in minimal structures mimics stabilizing features observed in the 4WJ hairpin ribozyme structure. The results demonstrate how knowledge-based design can be used to improve diffraction and overcome otherwise destabilizing defects.

In vitro activity of novel dual action MDR anthranilamide modulators with inhibitory activity on CYP-450 (Part 2)

Synthesis and in vitro cytotoxicity assays of new anthranilamide MDR modulators have been performed to assess their inhibition potency on the P-glycoprotein (P-gp) transporter. Previous studies showed that the replacement of the aromatic spacer group between nitrogen atoms (N 1 and N 2) in the P-gp inhibitor XR9576 with ethyl or propyl chain is optimal for P-gp inhibition potency. To confirm that observation, the ethyl or the propyl linker arm was replaced with a pyrrolidine or an alicyclic group such as cyclohexyl. In addition, an arylpiperazinyl group and two methoxyl groups onto the anthranilic part were introduced to assess their effect on the anti P-gp activity. Five molecules were prepared and evaluated on CEM/VLB500. All new anthranilamides were more potent than verapamil, most of them exhibited a lower cytotoxicity than XR9576. Compound 5 was the most potent and its inhibition activity was similar to XR9576. Interestingly, in vitro biotransformation studies of compounds 4 and 5 using human CYP-450 isoforms revealed, that conversely to XR9576, compounds 4 and 5 inhibited CYP3A4, an enzyme that colocalizes with P-gp in the intestine and contributes to tumor cell chemoresistance by enhancing the biodisposition of numerous drugs, notably paclitaxel. In that context, 5 might be suitable for further drug development.

LNA (locked nucleic acid) and analogs as triplex-forming oligonucleotides

The triplex-forming abilities of some conformationally restricted nucleotide analogs are disclosed and compared herein. 2'-Amino-LNA monomers proved to be less stabilising to triplexes than LNA monomers when incorporated into a triplex-forming third strand. N2'-functionalisation of 2'-amino-LNA monomers with a glycyl unit induced the formation of exceptionally stable triplexes. Nucleotide analogs containing a C2',C3'-oxymethylene linker (E-type furanose conformation) or a C2',C4'-propylene linker (N-type furanose conformation) had no significant effect on triplex stability proving that conformational restriction per se is insufficient to stabilise triplexes.