Disassembly of preformed amyloid beta fibrils by small organofluorine molecules

A potential therapeutic approach for Alzheimer’s disease is to reduce the amount of toxic amyloid-beta oligomers and fibrillar amyloid plaques. In order to contribute to this approach the ability of small organofluorine compounds that were previously reported as successful inhibitors of fibrillogenesis to destabilize preformed fibrils of the amyloid-beta peptide was studied. These organofluorine molecules including chiral compounds were tested in vitro using standard methods based on Thioflavin-T (THT) fluorescence spectroscopy, atomic force microscopy (AFM) and Fourier-transform infrared spectroscopy (FTIR). It was observed that 5′-halogen substituted 3,3,3-trifluoromethyl-2-hydroxyl-(indol-3-yl)-propionic acid esters showed significant activity in the disassembly of the preformed fibrils. Since the same compounds were identified as strong fibrillogenesis inhibitors as well, this dual action makes them promising candidates for further drug development.     

The application of 19F nuclear magnetic resonance to investigate microbial biotransformations of organofluorine compounds

Fluorinated organic compounds, although rare in nature, are significant environmental contaminants owing to the numerous applications for which this class of compounds is employed. It is important that biodegradation of these compounds can be readily assessed in order to provide information on their fate in the environment. Fluorine-19 nuclear magnetic resonance (19F NMR) spectroscopy has emerged as a very useful technique to readily determine the catabolism of fluorinated aromatic compounds by microorganisms, either in whole cell or cell-free systems. The principal advantage of this technique is that fluorinated compounds can be observed directly in the culture supernatant or enzyme assay, without purification or derivatization. In this review an account of the application of 19F NMR in the study of microbial metabolism of organofluorine compounds is presented.     

Metabolism of fluoroorganic compounds in microorganisms: impacts for the environment and the production of fine chemicals

Incorporation of fluorine into an organic compound can favourably alter its physicochemical properties with respect to biological activity, stability and lipophilicity. Accordingly, this element is found in many pharmaceutical and industrial chemicals. Organofluorine compounds are accepted as substrates by many enzymes, and the interactions of microorganisms with these compounds are of relevance to the environment and the fine chemicals industry. On the one hand, the microbial transformation of organofluorines can lead to the generation of toxic compounds that are of environmental concern, yet similar biotransformations can yield difficult-to-synthesise products and intermediates, in particular derivatives of biologically active secondary metabolites. In this paper, we review the historical and recent developments of organofluorine biotransformation in microorganisms and highlight the possibility of using microbes as models of fluorinated drug metabolism in mammals.     

Natural hydrazine-containing compounds: Biosynthesis,isolation, biological activities and synthesis

Hydrazine, hydrazone and hydrazide derivatives are nitrogen–nitrogen bond containing compounds. Such molecules are relatively scarce in nature and have been isolated from plants, marine organisms and microorganisms. These compounds exhibit remarkable structural diversity and relevant biological activities. The enzymes involved in the formation of the N–N bond are still unknown, but many lines of evidence support the involvement of N-nitrosation and N-hydroxylation activating steps. Beside the challenging N–N bond, N-acylases catalyzing the C–N bond formation contribute to the chemical diversity of N–N-containing natural products (N2NP). This review examines the state of knowledge regarding the biosynthesis of N2NP, for which only two biosynthetic gene clusters have been investigated. Biological properties and chemical synthesis of hydrazines, hydrazones and hydrazides are also reported.     

Insight into shock-induced chemical reaction from the perspective of ring strain and rotation of chemical bonds

Density functional theory BLYP/DNP and hyperhomodesmotic equations were employed to calculate ring strain energy, the bond dissociation energy of X–NO₂ (X=C, N) and the charges on the nitro groups of several four-membered and six-membered heterocycle compounds. BLYP/DNP and LST/QST + CG method were also applied to calculate bond rotational energy of X–NO₂ (X=C, N) of above mentioned compounds. It indicated that ring strain energy of four-membered heterocycle nitro compounds is apparently higher than that of six-membered heterocycle nitro compounds. Predictably, ring-opening reactions may preferentially occur for those compounds containing higher ring strain energy under shock. In addition, C–NO₂ bonds in these compounds may rotate easier than N–NO₂ bonds in response to the external shock. As for N–NO₂ bonds in these compounds, they also respond to the external shock by the rotation of N–NO₂ bonds, once to the saddle point of the rotational energy barrier, the whole molecule will become relaxed, N–NO₂ bond becomes weaker and eventually leads to the breakage. When one ?C=O, ?C=NH or ?NH₂ group is introduced to the six-membered heterocycle, the charges on the nitro groups of the new compound decrease drastically, and ring strains increase remarkably. It can be predicted that the new compounds will be more sensitive to shock, and the viewpoint is confirmed by the experimental results of shock sensitivity (small scale gap test) of several explosives.     

Noble gas inserted compounds of borazine and its derivative B<Subscript>3</Subscript>N<Subscript>3</Subscript>R<Subscript>6</Subscript>: structures and bonding

Quantum chemistry computations were performed at the MP2 and B3LYP levels of theory using the basis sets aug-cc-pVDZ and def2-TZVPPD to study the noble gas (Ng) compounds formed by insertion of a Ng atom (Kr, Xe, Rn) into the B–H/F and N–H/F bonds of inorganic benzene B₃N₃H₆ and its fluorine derivative B₃N₃F₆. The geometrical structures were optimized and vibrational analysis was carried out to demonstrate these structures being local minima on the potential energy surface. The thermodynamic properties of the formation process of Ng compounds were calculated. A series of theoretical methods based on the wavefunction analysis, including NBO, AIM and ELF methods and energy decomposition analysis, was used to investigate the bonding nature of the noble gas atoms and the properties of the Ng compounds. The N–Ng bond was found to be stronger than the B–Ng bond, but the B–Ng bond is of typical covalent character and σ-donation from the Ng atom to the ring B atom makes the predominant contribution towards stability of the B-Ng bond. NICS calculation shows that these Ng-containing compounds are of weak π-aromaticity.     

A refined parameterization of the analytical Cd–Zn–Te bond-order potential

This paper reports an updated parameterization for a CdTe bond order potential. The original potential is a rigorously parameterized analytical bond order potential for ternary the Cd–Zn–Te systems. This potential effectively captures property trends of multiple Cd, Zn, Te, CdZn, CdTe, ZnTe, and Cd_1-xZn_xTe phases including clusters, lattices, defects, and surfaces. It also enables crystalline growth simulations of stoichiometric compounds/alloys from non-stoichiometric vapors. However, the potential over predicts the zinc-blende CdTe lattice constant compared to experimental data. Here, we report a refined analytical Cd–Zn–Te bond order potential parameterization that predicts a better CdTe lattice constant. Characteristics of the second potential are given based on comparisons with both literature potentials and the quantum mechanical calculations.     

Synthesis and properties of macrolones characterized by two ether bonds in the linker

In this paper synthesis of macrolones 1–18 starting from azithromycin is reported. Two key steps in the construction of the linker between macrolide and quinolone moiety, are formation of central ether bond by alkylation of unactivated OH group, and formation of terminal C–C bond at 6-position of the quinolone unit. Due to the difficulty in formation of these two bonds the study of alternative synthetic methodologies and optimization of the conditions for the selected routes was required. Formation of C-4″-O-ether bond was completed by modified Michael addition, whereas O-alkylation via diazonium cation proved to be the most effective in formation of the central allylic or propargylic ether bond. Comparison of Heck and Sonogashira reaction revealed the former as preferred route to the C–C bond formation at C(6) position of the quinolone unit. Most of the target compounds exhibited highly favorable antibacterial activity against common respiratory pathogens, without significant cytotoxicity profile when tested in vitro on eukaryotic cell lines.     

Comparative Study of Reversible Organofluorine Ammonium Inhibitors of Cholinesterases of Different Animals

A group of organofluorine ammonium compounds, trimethyltrifluoromethylammonium, diethylmethyltrifluoromethylammonium, hexa(difluoromethylene)-bis(trimethylammonium), their non-substituted analogs as well as bis-onium organosilicone, phenyliodonium, and triphenylphosphonium derivatives were tested as reversible inhibitors of acetylcholinesterase of human erythrocytes, butyrylcholinesterase of horse blood serum, cholinesterase of brain of the frog Rana temporaria and cholinesterases of optic ganglion of the Pacific squid Todarodes pacificus. By the method of molecular mechanics, differences were revealed in conformational mobility of interonium chain and in geometric parameters of the studied compounds. It was shown that introduction of fluorine atoms into the inhibitor molecule affected only their interaction with the Pacific squid cholinesterase. It was possible to separate effects of the onium atom nature and of the interonium chain structure in the inhibitor molecule on the anticholinesterase potency.     

Synthesis of H-bonding probes of α7 nAChR agonist selectivity

The α7 subtype of the nicotinic acetylcholine receptor (nAChR) is the target of studies aimed at identifying features that will lead to the development of selective therapeutics. Five arylidine anabaseines, three with pyridine rings and two with the pyrrole rings, were synthesized in 35–65% yield via aldol condensation. The compounds are homologs of benzylidine anabaseine and were chosen for synthesis because they provide either a hydrogen bond acceptor (pyridines) or hydrogen bond donor (pyrroles) that may interact with the receptor within the benzylidine selectivity motif. Initial analysis of the new compounds at 100 μM concentration reveal that the two pyrrole anabaseines are good partial agonists of the α7 nAChR, having 40% of the efficacy of ACh, efficacy comparable to 4OH-GTS-21, and dramatically enhanced efficacy relative to the 2- and 4-pyridinyl compounds. The pyrrole compounds were confirmed to be α7 selective, displaying preference for this receptor over muscle and heteromeric neuronal receptor subtypes.     

Organocatalyzed Solvent Free and Efficient Synthesis of 2,4,5‐Trisubstituted Imidazoles as Potential Acetylcholinesterase Inhibitors for Alzheimer's Disease

The catalytic potential of pyridine‐2‐carboxlic acid has been evaluated for efficient, green and solvent free synthesis of 2,4,5‐trisubstituted imidazole derivatives 3a – 3m . The compounds 3a – 3m were synthesized by one pot condensation reaction of substituted aromatic aldehydes, benzil, and ammonium acetate in good to excellent yields (74–96 %). To explore the potential of these compounds against Alzheimer's disease, their inhibitory activities against acetylcholinesterase (AChE) were evaluated. In this series of compounds, compound 3m , bearing one ethoxy and a hydroxy group on the phenyl ring on 2,4,5‐trisubstituted imidazoles, proved to be a potent AChE inhibitor (102.56±0.14). Structure–activity relationship (SAR) of these compounds was developed. Molecular dockings were carried out for the compounds 3m , 3e , 3k , 3c , 3a , 3d , 3j , and 3f in order to further investigate the binding mechanism. The inhibitor molecule was molecularly docked with acetylcholinesterase to further study its binding mechanism. The amino group of the compound 3m forms an H‐bond with the oxygen atom of the residue (i. e., THR121) which has a bond length of 3.051 Å.     

Investigation of Beckett–Casy model 2: Synthesis of novel 15–16 nornaltrexone derivatives and their pharmacology

We synthesized novel 15–16 nornaltrexone derivatives 9, 11 and 22 to examine the importance of the cavity in the Beckett–Casy model, which was proposed to interact with the 15–16 ethylene moiety in the morphine structure. All the synthesized compounds showed lower affinities for the opioid receptor than did the naltrexone (10). The binding affinities of 14-OH derivatives 11, in which the rotation of the 9–17 bond would be restricted by an intramolecular hydrogen bond, was improved compared to the corresponding 14-H derivatives 9. Compound 22 whose 9–17 bond was strictly fixed by the ethylene bridge hardly bound to the opioid receptor. Compound 26 also showed very weak binding affinity in spite of the existence of the 15–16 ethylene unit. We proposed an important role for the orientation of the lone electron pair on the 17-nitrogen rather than the significance of the cavity in the Beckett–Casy model.     

Chiral recognition by 1H-NMR,EPR, and ENDOR spectroscopy

Chiral recognition with magnetic methods requires the formation of diastereomers. Due to the variety of appropriate reactions, hydrogen bond formation, esterification, and acetalization as well as host–guest interactions were chosen for basic investigations. The results obtained indicate that in the case of diamagnetic compounds the chemical shifts and for paramagnetic compounds the β-proton coupling constants are the most useful parameters. By combination of both pieces of information, assignment of the absolute configuration was achieved. © 1993 Wiley-Liss, Inc.     

Polyphenol fatty acid esters as serine protease inhibitors: a quantum-chemical QSAR analysis

We investigated the ability of polyphenol fatty acid esters to inhibit the activity of serine proteases trypsin, thrombin, elastase and urokinase. Potent protease inhibition in micromolar range was displayed by rutin and rutin derivatives esterified with medium and long chain, mono- and polyunsaturated fatty acids (1e–m), followed by phloridzin and esculin esters with medium and long fatty acid chain length (2a–d, 3a–d), while unmodified compounds showed only little or no effect. QSAR study of the compounds tested provided the most significant parameters for individual inhibition activities, i.e. number of hydrogen bond donors for urokinase, molecular volume for thrombin, and solvation energy for elastase. According to the statistical analysis, the action of elastase inhibitors is opposed to those of urokinase and thrombin. Cluster analysis showed two groups of compounds: original polyphenols together with rutin esters with short fatty acid chain length and rutin esters with long fatty acid chain length.     

3-Acyl-5-hydroxybenzofuran derivatives as potential anti-estrogen breast cancer agents: A combined experimental and theoretical investigation

We first report the application of 3-acyl-5-hydroxybenzofurans as a scaffold to develop potential drugs for breast cancer. Seven novel derivative compounds were synthesized by using a microwave-assisted synthesis method. Those compounds exhibited different antiproliferation against human breast cancer MCF-7 cells, with the best activity of IC₅₀ = 43.08 μM for compound 1. A Quantum Mechanics Polarized Ligand Docking (QPLD) study was carried out to investigate the binding interactions between these compounds and estrogen receptor alpha (ERα). The simulation results showed that the trend of receptor–ligand binding interactions was same as that of their antiproliferative activities. A detailed analysis indicated that compound 1 possesses the highest Van der Waals and hydrogen bond interactions compared to the other six compounds and better inhibitors are achievable by enhancing the hydrogen bond interactions. Based on these results, we addressed that 3-acyl-5-hydroxybenzofuran is an attractive scaffold for designing drugs against breast cancer.     

Crystal Structure and Conformation of 8-(2-Hydroxyethylamino) and 8-(Pyrrolidin-1-yl) Adenosines

In the course of investigation of 8-alkylamino substituted adenosines, the title compounds were synthesized as potential partial agonists for adenosine receptors. The structure determination of these compounds was carried out with the X-ray crystallography study. Crystals of 8-(2-hydroxyethylamino)adenosine are monoclinic, space group P 2₁; a = 7.0422(2), b = 11.2635(3), c = 8.9215(2) Å, β = 92.261(1)°, V = 707.10(3) ų, Z = 2; R-factor is 0.0339. The nucleoside is characterized by the anti conformation; the ribose ring has the C(2′)-endo conformation and gauche–gauche form across C(4′)–C(5′) bond. The molecular structure is stabilized by intramolecular hydrogen bond of N–H·O type. Crystals of 8-(pyrrolidin-1-yl)adenosine are monoclinic, space group C 2; a = 19.271(1), b = 7.3572(4), c = 11.0465(7) Å, β = 103.254(2)°, V = 1524.4(2) ų, Z = 4; R-factor is 0.0498. In this compound, there is syn conformation of the nucleoside; the ribose has the C(2′)-endo conformation and gauche–gauche form across C(4′)–C(5′) bond. The molecular structure is stabilized by intramolecular hydrogen bond of O–H·N type. For both compounds, the branching net of intermolecular hydrogen bonds occur in the crystal structures.     

Conformation of dipeptides

The amide bond in L ,L - and L ,D -α-chloropropionylalanine methyl ester is shown to be trans by molar polarization and infrared spectroscopy. In these dipeptide diastereoisomer analogues, therefore, differences in physical properties, i.e., melting points, crystalline forms, gas chromatographic mobilities, etc., depend on preferred molecular conformations and not peptide bond configuration. Nuclear magnetic resonance spectra of both compounds were identical, indicating that no major chemical environment differences exist, which might have resulted from dissimilar side group interactions. Based on the data reported here and those of others, most dipeptide conformations can be eliminated because of contradiction with limits set by experimental or theoretical considerations. Of the remaining conformational possibilities, a single pair accounts for observed physical differences in dipeptide diastereoisomers, free or blocked. The preferred form contains α-hydrogens trans to each other and in the plane of the peptide bond. In this conformation, R¹–R² and amino–carboxyl distances are minimal in L ,D diastereomers and maximal in L ,L forms.     

Design and synthesis of boron containing monosaccharides by the hydroboration of d-glucal for use in boron neutron capture therapy (BNCT)

Boron neutron capture therapy (BNCT) is one of the radiotherapies that involves the use of boron-containing compounds for the treatment of cancer. Boron-10 (¹⁰B) containing compounds that can accumulate in tumor tissue are expected to be suitable agents for BNCT. We report herein on the design and synthesis of some new BNCT agents based on a d-glucose scaffold, since glycoconjugation has been recognized as a useful strategy for the specific targeting of tumors. To introduce a boryl group into a d-glucose scaffold, we focused on the hydroboration of d-glucal derivatives, which have a double bond between the C1 and C2 positions. It was hypothesized that a C–B bond could be introduced at the C2 position of d-glucose by the hydroboration of d-glucal derivatives and that the products could be stabilized by conversion to the corresponding boronic acid ester. To test this hypothesis, we prepared some 2-boryl-1,2-dideoxy-d-glucose derivatives as boron carriers and evaluated their cytotoxicity and cellular uptake activity to cancer cells, especially under hypoxic conditions.     

Nonorthogonal tight-binding model with H–C–N–O parameterisation

A parametric nonorthogonal tight-binding model (NTBM1) with the set of parameters for H–C–N–O systems is presented. This model compares well with widely used semi-empirical AM1 and PM3/PM7 models but contains less fitting parameters per atom. All NTBM1 parameters are derived based on a criterion of the best agreement between the calculated and experimental values of bond lengths, valence angles and binding energies for various H–C–N–O molecules. Results for more than 200 chemical compounds are reported. Parameters are currently available for hydrogen, carbon, nitrogen, oxygen atoms and corresponding interatomic interactions. The model has a good transferability and can be used for both relaxation of large molecular systems (e.g., high-molecular compounds or covalent cluster complexes) and long-timescale molecular dynamics simulation (e.g., modelling of thermal decomposition processes). The program package based on this model is available for download at no cost from http://ntbm.info.     

The nature of M-O bond in MOX4 compounds (M = Os, Ru; X = F, Cl, Br, I)

The nature of M-O bond in MOX₄ compounds (where M = Ru or Os and X = F, Cl, Br or I) was analyzed by density functional theory methods at the BP86/LANL2DZ level of theory. The obtained charge density was analyzed by Fermi hole analysis, natural bond order (NBO) analysis and atoms-in-molecules (AIM)-based methods. The M-O bond is essentially a triple bond, although strongly polarized. The clearest differences in bonding between the Ru and Os compounds can be found in the M-O σ bonds, where in the Os compounds we find more charge density resting close to O.