Linker Elongation Research Articles

Effect of Linker Elongation on the VGSC Affinity and Anticonvulsant Activity among 4-Alkyl-5-aryl-1,2,4-triazole-3-thione Derivatives

The main aim of the current project was to investigate the effect of the linker size in 4-alkyl-5-aryl-1,2,4-triazole-3-thione derivatives, known as a group of antiepileptic drug candidates, on their affinity towards voltage-gated sodium channels (VGSCs). The rationale of the study was based both on the SAR observations and docking simulations of the interactions between the designed ligands and the binding site of human VGSC. HYDE docking scores, which describe hydrogen bonding, desolvation, and hydrophobic effects, obtained for 5-[(3-chlorophenyl)ethyl]-4-butyl/hexyl-1,2,4-triazole-3-thiones, justified their beneficial sodium channel blocking activity. The results of docking simulations were verified using a radioligand binding assay with [3H]batrachotoxin. Unexpectedly, although the investigated triazole-based compounds acted as VGSC ligands, their affinities were lower than those of the respective analogs containing shorter alkyl linkers. Since numerous sodium channel blockers are recognized as antiepileptic agents, the obtained 1,2,4-triazole derivatives were examined for antiepileptic potential using an experimental model of tonic–clonic seizures in mice. Median effective doses (ED50) of the compounds examined in MES test reached 96.6 ± 14.8 mg/kg, while their median toxic doses (TD50), obtained in the rotarod test, were even as high as 710.5 ± 47.4 mg/kg.

Development of Novel Quinoline-Based Sulfonamides as Selective Cancer-Associated Carbonic Anhydrase Isoform IX Inhibitors.

A new series of quinoline-based benzenesulfonamides (QBS) were developed as potential carbonic anhydrase inhibitors (CAIs). The target QBS CAIs is based on the 4-anilinoquinoline scaffold where the primary sulphonamide functionality was grafted at C4 of the anilino moiety as a zinc anchoring group (QBS 13a–c); thereafter, the sulphonamide group was switched to ortho- and meta-positions to afford regioisomers 9a–d and 11a–g. Moreover, a linker elongation approach was adopted where the amino linker was replaced by a hydrazide one to afford QBS 16. All the described QBS have been synthesized and investigated for their CA inhibitory action against hCA I, II, IX and XII. In general, para-sulphonamide derivatives 13a–c displayed the best inhibitory activity against both cancer-related isoforms hCA IX (KIs = 25.8, 5.5 and 18.6 nM, respectively) and hCA XII (KIs = 9.8, 13.2 and 8.7 nM, respectively), beside the excellent hCA IX inhibitory activity exerted by meta-sulphonamide derivative 11c (KI = 8.4 nM). The most promising QBS were further evaluated for their anticancer and pro-apoptotic activities on two cancer cell lines (MDA-MB-231 and MCF-7). In addition, molecular docking simulation studies were applied to justify the acquired CA inhibitory action of the target QBS.

Synthesis and in vitro evaluation of triphenylphosphonium derivatives of acetylsalicylic and salicylic acids: structure-dependent interactions with cancer cells, bacteria, and mitochondria

Salicylic acid (SA) remains one of the most fruitful natural compounds to generate drug molecules with versatile activities. In this study, effective synthesis of SA and acetylsalicylic acid (ASA) derivatives with a carrier triphenylphoshonium (TPP) group was proposed. A series of SA and ASA conjugates linked with the TPP group via alkyl chain linker (C3-C10) was synthesized. The conjugates showed enhanced TPP-mediated cytotoxicity towards MCF-7, Caco-2, PC-3 cells in proportion to the linker length. 7e, 8e (C9), and 7f (C10) were the most active against the cancer cells with IC50 = 0.6–1.9 µM while were less toxic for HSF. Similarly, antibacterial (bactericidal) activity of the compounds against S. aureus increased with the linker elongation. The lowest MIC for SA and ASA derivatives were 4 and 1 µM, respectively. The TPP conjugates induced early linker length-dependent mitochondria depolarization and concurrent superoxide radical production in the cancer cells. The most lipophilic conjugates were found to specifically interact with ROS probe 2′,7′-dichlorofluorescin diacetate, forming mixed aggregates with the probe and inhibiting its fluorescence upon oxidation. These interactions were exploited to probe the compounds inside living cells. The results identify 7e and 7f as promising mitochondria-modulating and anticancer agents with increased cellular availability.

Rational Design of CYP3A4 Inhibitors: A One-Atom Linker Elongation in Ritonavir-Like Compounds Leads to a Marked Improvement in the Binding Strength.

Inhibition of the major human drug-metabolizing cytochrome P450 3A4 (CYP3A4) by pharmaceuticals and other xenobiotics could lead to toxicity, drug–drug interactions and other adverse effects, as well as pharmacoenhancement. Despite serious clinical implications, the structural basis and attributes required for the potent inhibition of CYP3A4 remain to be established. We utilized a rational inhibitor design to investigate the structure–activity relationships in the analogues of ritonavir, the most potent CYP3A4 inhibitor in clinical use. This study elucidated the optimal length of the head-group spacer using eleven (series V) analogues with the R1/R2 side-groups as phenyls or R1–phenyl/R2–indole/naphthalene in various stereo configurations. Spectral, functional and structural characterization of the inhibitory complexes showed that a one-atom head-group linker elongation, from pyridyl–ethyl to pyridyl–propyl, was beneficial and markedly improved Ks, IC50 and thermostability of CYP3A4. In contrast, a two-atom linker extension led to a multi-fold decrease in the binding and inhibitory strength, possibly due to spatial and/or conformational constraints. The lead compound, 3h, was among the best inhibitors designed so far and overall, the strongest binder (Ks and IC50 of 0.007 and 0.090 µM, respectively). 3h was the fourth structurally simpler inhibitor superior to ritonavir, which further demonstrates the power of our approach.

Linker Expansion and Its Impact on Switchability in Pillared-Layer MOFs

Linker elongation is an important method to systematically adjust porosity and pore size in isoreticular MOFs. In flexible structures, this approach opens the possibility for the systematic analysis of the building blocks and their contribution to the overall flexible behavior enabling tuning of the framework responsivity toward molecular stimuli. In this work, we report two new compounds isoreticular to the highly flexible pillared layer structure DUT-8(Ni) ([Ni2(2,6-ndc)2(dabco)]n, 2,6-ndc = 2,6-naphthalenedicarboxylate, dabco = 1,4-diazabicylo[2.2.2]octane). Aromatic linker 2,6-ndc was substituted by longer carboxylic linkers, namely, 4,4'-biphenyldicarboxylate (4,4'-bpdc) and 4,4'-stilbenedicarboxylate (4,4'-sdc), while the dabco pillar was retained. The structural response of the new compounds toward the desolvation and adsorption of various fluids was studied using advanced in situ PXRD techniques, demonstrating distinct differences in the flexible behavior of three compounds and disclosing the impact of linker structure on the framework response. Theoretical calculations provide mechanistic insights and an energetic rationale for the pronounced differences in switchability observed. The energetics of linker bending and linker-linker dispersion interactions govern the phase transitions in investigated MOFs.

Hydrogen bonding in triols on the triphenylphosphine oxide platform in crystal and solution: Effect of linker length

The structure of tripodal phosphoryl alkanols [2-HO(CH2)nOC6H4]3P = O (n = 2, 3, 4) have been studied in crystal and solution by X-ray diffraction and FTIR. Linker length in the phosphoryl alkanols has a dramatic effect on their supramolecular structure in crystal and the type of hydrogen bonding in solution. It has been shown that compounds with n = 2 and 4 in crystal form linear and zigzag chains, respectively, while compound with n = 3 produces ribbons united into 2D networks. IR spectral study indicates that solutions of the triols contain monomers with intramolecular simple or bifurcate association of PO and OH groups, linear and cyclic dimers. The concentration of molecules with bifurcate bond decreases upon linker elongation. The studied compounds showed insignificant anticancer activity.

Lattice Expansion and Contraction in Metal-Organic Frameworks by Sequential Linker Reinstallation

Summary Isoreticular expansion of metal-organic frameworks (MOFs) by linker elongation often leads to interpenetration or other undesired structures. Here we report a sequential linker labilization and reinstallation method to expand the unit cell dimensions of MOFs while manipulating the framework structure and interpenetration. A stable Zr-based MOF was initially synthesized as a template. Subsequently, labile linkers with imine bonds were post-synthetically introduced into the structure to destabilize the Zr-MOF. Eventually, gradual dissociation of the imine-based linkers and reinstallation of longer linkers into the defective spaces lead to the formation of non-interpenetrated isoreticular Zr-MOFs with progressively increased pore sizes. Similarly, lattice contraction can also be realized by incorporating shorter linkers. In addition to providing a powerful tool that yields control over the structures and functions of MOFs, this work also highlights new opportunities by combining the dynamic covalent chemistry with coordination chemistry in MOFs.

Tunable Metal-Catalyzed Heterocyclization Reactions of Allenic Amino Alcohols: An Experimental and Theoretical Study.

Controlled preparation of 2,5-dihydro-1H-pyrroles, 3,6-dihydro-2H-pyrans, and pyrroles has been achieved through switchable chemo- and regioselectivity in the metal-catalyzed heterocyclization reactions of allenic amino alcohols. The gold-catalyzed cycloisomerization reaction of α-amino-β-hydroxyallenes was effective as 5-endo cyclization by addition of amino functionality to the distal allene carbon to yield enantiopure 2,5-dihydro-1H-pyrroles, whereas their palladium-catalyzed cyclizative coupling reactions furnished 3,6-dihydro-2H-pyrans through a chemo- and regioselective 6-endo cycloetherification. Conversely, the gold-catalyzed heterocyclization reaction of β-amino-γ-hydroxyallenes generated exclusively pyrrole derivatives. These results could be explained through a chemo- and regioselective 5-exo aminocyclization to the central allene carbon followed by aromatization. Chemo- and regioselectivity depend on both linker elongation as well as the type of catalyst. This behavior can be justified by means of density functional theory calculations.

Enhanced Charge Separation Efficiency in Pyridine-Anchored Phthalocyanine-Sensitized Solar Cells by Linker Elongation.

A series of zinc phthalocyanine sensitizers (PcS22-24) having a pyridine anchoring group are designed and synthesized to investigate the structural dependence on performance in dye-sensitized solar cells. The pyridine-anchor zinc phthalocyanine sensitizer PcS23 shows 79 % incident-photon to current-conversion efficiency (IPCE) and 6.1 % energy conversion efficiency, which are comparable with similar phthalocyanine dyes having a carboxylic acid anchoring group. Based on DFT calculations, the high IPCE is attributed with the mixture of an excited-state molecular orbital of the sensitizer and the orbitals of TiO2 . Between pyridine and carboxylic acid anchor dyes, opposite trends are observed in the linker-length dependence of the IPCE. The red-absorbing PcS23 is applied for co-sensitization with a carboxyl-anchor organic dye D131 that has a complementary spectral response. The site-selective adsorption of PcS23 and D131 on the TiO2 surface results in a panchromatic photocurrent response for the whole visible-light region of sun light.

Modular Synthesis of Elongated Phosphonate Bipyridines

AbstractThe synthesis and the photophysical properties of a series of bpy‐R2 derivatives L1–L3 (bpy = 2,2′‐bipyridine, R represents the substitution at the 4‐ and 4′‐positions of the bpy) are described. R includes phosphonic ester groups as precursors for potent phosphonate anchoring groups, which enable immobilization on transition metal oxide semiconductor surfaces for applications like dye‐sensitized solar cells (DSSCs) or dye‐sensitized photoelectrosynthesis cells (DSPECs). The ligands L1–L3 differ in the length of conjugated linker units between bpy core and anchoring groups. Phenylene and triazole moieties serve as building blocks for linker elongation. The resulting adjustability of the distance between semiconductor and chromophore represents a viable route to improve cell efficiency, as it will allow tuning of charge carrier recombination and dye aggregation. Furthermore the photophysical studies of the free ligands reveal a pronounced effect of the aryl substitution. The solid‐state structures of L1 and L2 are reported within this contribution, enabling the determination of distances between bipyridine nitrogen donor and anchoring group.

Methane Adsorption in Metal–Organic Frameworks Containing Nanographene Linkers: A Computational Study

Metal–organic framework (MOF) materials are known to be amenable to expansion through elongation of the parent organic linker. For a family of model (3,24)-connected MOFs with the rht topology, in which the central part of organic linker comprises a hexabenzocoronene unit, the effect of the linker type and length on their structural and gas adsorption properties is studied computationally. The obtained results compare favorably with known MOF materials of similar structure and topology. We find that the presence of a flat nanographene-like central core increases the geometric surface area of the frameworks, sustains additional benzene rings, and promotes linker elongation and the efficient occupation of the void space by guest molecules. This provides a viable linker modification method with potential for enhancement of uptake for methane and other gas molecules.

Covalent conjugation of avidin with dye-doped silica nanopaticles and preparation of high density avidin nanoparticles as photostable bioprobes

Progress in biomedical imaging depends on the development of bioprobes with a high sensitivity and stability. Fluorescent silica nanoparticles (NPs) covalent conjugation of avidin has been proposed for cancer cells imaging by fluorescence microscopy. Uniform silica NPs were prepared using water-in-oil (W/O) microemulsion methods and primary amine groups were introduced onto the surface of the NPs by condensation of tetraethyl orthosilicate (TEOS). Optically stable organic dyes, tris(2,2'-bipyridyl) dichlororuthenium(II) hexahydrate (Rubpy), were doped inside the silica NPs. The amine functions were transferred to carboxyl groups coupled with a linker elongation. Avidin was immobilized at the surface of the NPs by covalent binding to the carboxyl linkers. The binding capacity of the avidin-covered NPs for ligand biotin was quantified by titration with biotin(5-fluorescein) conjugate to 1.25 biotin binding sites/100nm2. We used biotinylated antibody and cell recognition by fluorescence microscopy imaging technique. The lung carcinoma cells were identified easily with high efficiency using these antibody-coated NPs. By comparison with fluorescein isothiocyanate (FITC), dye-doped silica NPs display dramatically increased stability of fluorescence as well as photostability, as compared to the common organic dye, when under continuous irradiation.

Controlled surface functionalization of silica-coated magnetic nanoparticles with terminal amino and carboxyl groups

General and versatile methods for the functionalization of superparamagnetic, silica-coated, maghemite nanoparticles by surface amino and/or carboxyl groups have been established. The nanoparticles were synthesized using co-precipitation from aqueous solutions and coated with a thin layer of silica using the hydrolysis and condensation of tetraethoxysilane (TEOS). For the amino functionalization, 3-(2-aminoethylamino)propylmethyldimethoxysilane (APMS) was grafted onto the nanoparticle surfaces in their aqueous suspensions. The grafting process was followed by measurements of the ζ-potential and a determination of the concentration of the surface amino groups with conductometric titrations. The surface concentration of the amino groups could be varied by increasing the amount of APMS in the grafting process up to approximately 2.3 –NH2 groups per nm2. The carboxyl functionalization was obtained in two ways: (i) by a ring-opening linker elongation reaction of the surface amines at the functionalized nanoparticles with succinic anhydride (SA) in non-aqueous medium, and (ii) by reacting the APMS and SA first, followed by grafting of the carboxyl-terminated reagent onto the nanoparticle surfaces. Using the first method, the SA only reacted with the terminal primary amino groups (–NH2) of the surface-grafted APMS molecules. Infra-red spectroscopy (ATR FTIR) and mass spectrometry (HRMS) showed that the second method enables the bonding of up to two SA molecules per one APMS molecule, since the SA reacted with both the primary (–NH2) and secondary amino (–NH–) groups of the APMS molecule. When using both methods, the ratio between the surface amino and carboxyl groups can be controlled.

Mechanism of arginine regulation of acetylglutamate synthase, the first enzyme of arginine synthesis

N-acetyl-l-glutamate synthase (NAGS), the first enzyme of arginine biosynthesis in bacteria/plants and an essential urea cycle activator in animals, is, respectively, arginine-inhibited and activated. Arginine binds to the hexameric ring-forming amino acid kinase (AAK) domain of NAGS. We show that arginine inhibits Pseudomonas aeruginosa NAGS by altering the functions of the distant, substrate binding/catalytic GCN5-related N-acetyltransferase (GNAT) domain, increasing KmGlu, decreasing Vmax and triggering substrate inhibition by AcCoA. These effects involve centrally the interdomain linker, since we show that linker elongation or two-residue linker shortening hampers and mimics, respectively, arginine inhibition. We propose a regulatory mechanism in which arginine triggers the expansion of the hexameric NAGS ring, altering AAK–GNAT domain interactions, and the modulation by these interactions of GNAT domain functions, explaining arginine regulation.

Preparation and self-assembly of carboxylic acid-functionalized silica

A simple method for the fabrication of silica nanoparticle film based on the covalent-bonding interaction between carboxylic acid-functionalized silica nanoparticles (SiO 2–COOH) and amino-terminated silicon wafer was developed. Prior to assembly, silica nanoparticles with an average diameter 80 nm were prepared using the Stöber method, amino-functionalized silica nanoparticles (SiO 2–NH 2) were prepared by a silanization with 3-aminopropyltriethoxysilane (APTES), while carboxylic acid-functionalized silica nanoparticles (SiO 2–COOH) were prepared by a ring opening linker elongation reaction of the amine functions with succinic anhydride, at the same time, amino-terminated silicon wafer (Si–NH 2) was obtained by self-assembling 3-aminopropyltriethoxysilane, then one layer relative close-packed carboxylic acid-functionalized silica nanoparticles (SiO 2–COOH) was arranged on silicon wafer through amidation reaction under DCC coupling agent.

Controlled Surface Functionalization of Silica Nanospheres by Covalent Conjugation Reactions and Preparation of High Density Streptavidin Nanoparticles

Silica nanoparticles with a diameter of 100 nm were covalently modified at their surface by adjustable amounts of amine and carboxyl functional groups. Bioconjugation studies of two proteins, streptavidin and streptactin, with the functional nanoparticles resulted in optimum binding of the proteins to a long-chain carboxyl-terminated linker. The surface functionalization of the nanoparticles was monitored by a variety of independent methods, including zeta-potential measurements, dynamic light scattering (DLS), scanning electron microscopy (SEM), particle charge detection titrations (PCD) and elemental analysis. At the surface of the nanoparticles, a functional surface group density of 1.8 amino groups per nm2 was realized. The amine functions were quantitatively transferred to carboxyl groups coupled with a linker elongation. Streptavidin was immobilized by covalent binding to the carboxyl linkers and resulted in a protein density at the surface of the nanoparticles that was three times higher than the highest binding densities at nanoparticles published to date. The binding capacity of the streptavidin-covered nanoparticles for ligand biotin was quantified by titration with biotin-4-fluorescein to 2.5 biotin binding sites per 100 nm2.