Predicting the binding mode of known NCp7 inhibitors to facilitate the design of novel modulators

The HIV-1 nucleocapsid protein (NCp7) is an emerging target for antiretroviral therapy. Five hits have been reported to inhibit the NCp7-viral nucleic acids interaction at micromolar concentrations. We used two computationally refined structures of NCp7 as receptors to propose a reliable binding pose for these compounds, by means of computational methods. Theoretical binding modes are in agreement with available experimental data. Results lay the foundations for a rationale development of more effective NCp7 inhibitors.     

Synthesis of some acyclonucleosides with the alkylating chain of acyclovir

The synthesis of some acyclic 1-[1,2,3-triazol-(4 and 5)-ylmethyl]-1H-pyrazolo[3,4-d]pyrimidine nucleosides, via 1,3-dipolar cycloaddition reaction, from 4-substituted N₁-propargyl-1H-pyrazolo[3,4-d]pyrimidines 7a,b and azido derivative 8 is described. Compounds 7a,b and all deprotected acyclic nucleosides 11a,b, 12a,b and 13–22 were evaluated against: HIV-1, HIV-2 and a series of tumour cell-lines. No marked activity was found. Their anti-tuberculosis evaluation showed that compound 7b had marked activity.     

Selectivity between N-1 and N-7 nucleosides: regioselective synthesis of BMK-Y101, a potent cdk7 and 9 inhibitor

BMK-Y101 is a new pyrrolo[2,3-d]pyrimidine-based potent cdk7 and 9 inhibitor, which is characterized by an intriguing structural feature of N-1 nucleoside, departing from previously reported N-7 nucleoside Cdk inhibitor, xylocydine. Though N-1 nucleosides have appeared in the literature, they have often been considered as kinetic products and thus intermediates of N-7 glycosylation. In the course of the synthetic studies of xylocydine derivatives, we have developed a highly regioselective method to obtain the N-1 nucleoside. The origin of the selectivity is apparently based on the reactivity of the silylated nucleobase and the stability of the resulting N-1 nucleoside. The choice of BSA as a silylating agent was critical in securing the N-1 nucleoside, BMK-Y101. On the other hand, proper selection of reaction conditions promoting transglycosylation provides an efficient route to N-7 nucleosides.     

Synthesis and photoluminescent properties of 7-N,N-diphenylamino-3- benzoheterocyclic coumarin derivatives

Two new 7-N,N-diphenylamino-3-benzoheterocyclic coumarin derivatives containing electron-transporting benzotriazolyl or benzoxazolyl moiety, 3-(1-benzotriazole)-7-N,N-diphenylaminocoumarin (BTDC) and 3-(2-benzoxazole)-7-N,N-diphenylaminocoumarin (BODC), were synthesized and characterized by element analysis, ¹H NMR and FT-IR spectra. The UV–vis and fluorescence spectra of these coumarin derivatives were investigated. The results show that BTDC and BODC exhibit strong blue and red emissions, respectively, under ultraviolet light excitation. The relationships between the chemical structure and the fluorescence characteristics of the 7-N,N-diphenylamino-3-benzoheterocyclic coumarin derivatives are discussed. It was found that the coumarin derivative will become a high-efficiency emitting material when an amino group is attached in 7-position of the coumarin ring, and 7- strong electron donors can improve the ability of the intramolecular charge transfer of the coumarin molecules.     

Specificity of acyl transfer from 2-mercaptobenzamide thioesters to the HIV-1 nucleocapsid protein

The HIV-1 nucleocapsid protein (NCp7) is a small, highly conserved protein with two zinc-binding domains that are essential for the protein's function. Molecules that bind to and inactivate NCp7 are currently being evaluated as new antiviral drugs. In particular, derivatives based on a 2-mercaptobenzamide thioester template have been shown to specifically eject zinc from the C-terminal zinc-binding domain (ZD2) of NCp7 via acyl transfer from the thioester to a cysteine sulfur. In this study, mutational analysis of the NCp7 amino acid sequence has been used to investigate the specificity of the interaction between ZD2 and a 2-mercaptobenzamide thioester compound using UV-vis spectroscopy and mass spectrometry to monitor the rate of metal ejection from NCp7 mutant peptides and sites of acylation, respectively. We were able to extend the previously reported mechanism of action of these thioester compounds to include a secondary S to N intramolecular acyl transfer that occurs after the primary acyl transfer from the thioester to a cysteine side chain in the protein. Structural models of the thioester/ZD2 complex were then examined to identify the most likely binding orientation. We determined that position x+1 (where x is Cys36) needs to be an aromatic residue for reactivity and a hydrogen-bond donor in position x+9 is important for optimal reactivity. A basic residue (lysine or arginine) is required at position x+2 for the correct fold, while a lysine residue is needed for reactivity involving S to N acyl transfer. We report highly specific interactions between 2-mercaptobenzamide thioester compounds and NCp7 that offer a structural basis for refining and designing new antiretroviral therapeutics, directed toward a target that is resistant to viral mutation.     

Targeting a Dark Excited State of HIV‐1 Nucleocapsid by Antiretroviral Thioesters Revealed by NMR Spectroscopy

HIV‐1 nucleocapsid (NCp7) is a two Cys₂HisCys zinc knuckle (N‐Zn and C‐Zn) protein that plays a key role in viral replication. NCp7 conformational dynamics is characterized by NMR relaxation dispersion and chemical exchange saturation transfer measurements. While the N‐Zn knuckle is conformationally stable, the C‐Zn knuckle interconverts on the millisecond timescale between the major state, in which the zinc is coordinated by three cysteines and a histidine, and two folded minor species (with populations around 1 %) in which one of the coordination bonds (Cys413‐Sγ‐Zn or His421‐N?2‐Zn) is hydrolyzed. These findings explain why antiretroviral thioesters specifically disrupt the C‐Zn knuckle by initial acylation of Cys413, and show that transient, sparsely‐populated (“dark”), excited states of proteins can present effective targets for rational drug design.     

Synthesis of fluorescent fluorene–isoindole-containing mono- and oligomers

Novel fluorene–isoindole-containing light-emitting mono- and oligomers were prepared. The synthesis of the monomers N-(4-bromo-phenyl)-2-(7-bromo-9,9-diethylfluoren-2-yl)-isoindole-1-carboxamide, N-(7-bromo-9,9-dibutylfluoren-2-yl)-2-(7-bromo-9,9-dibutylfluoren-2-yl)-isoindole-1-carboxamide, and N-[7-bromo-9,9-bis(2-ethylhexyl)-fluoren-2-yl]-2-[7-bromo-9,9-bis(2-ethylhexyl)-fluoren-2-yl]-isoindole -1-carboxamide was carried out by a three-component reaction of ortho-phthalaldehyde with the corresponding amine and isocyanide partners. The Ni(0) mediated polymerization reactions of the obtained monomers gave the corresponding mixture of oligomers from two up to twelve repeat units. The optical properties were also studied and it was found that the phenylene-containing oligomer emitted green light in dichloromethane solution, while both difluorene-containing oligomers, under the same conditions, proved to be blue light-emitters with good quantum efficiency.     

Cytotoxicity evaluation of coumarin derivatives containing 4-bromophenyl or anthracene moieties

The cytotoxic properties of four synthesized coumarin derivatives containing 4-bromophenyl or anthracene moieties against the human hepatocellular carcinoma cell lines (HepG-2) were investigated in vitro by use of the sulforhodamine B (SRB) assay. The four coumarin derivatives are 3-(4-bromophenyl)-benzo[5,6]coumarin (1a), 3-(4-bromophenyl)-7-(N,N-diethylamino)coumarin (1b), 3-(4-(anthracen-10-yl)phenyl)-benzo[5,6]coumarin (2a), and 3-(4-(anthracen-10-yl)phenyl)-7-(N,N-diethylamino)coumarin (2b). The preliminary results indicate that 1a, 2a, and 2b have significant cytotoxicity against HepG-2 whereas 1b has a growth-promotion effect.     

Constrained Dipeptide Surrogates: 5- and 7-Hydroxy Indolizidin-2-one Amino Acid Synthesis from Iodolactonization of Dehydro-2,8-diamino Azelates

The constrained dipeptide surrogates 5- and 7-hydroxy indolizidin-2-one N-(Boc)amino acids have been synthesized from L-serine as a chiral educt. A linear precursor ∆⁴-unsaturated (2S,8S)-2,8-bis[N-(Boc)amino]azelic acid was prepared in five steps from L-serine. Although epoxidation and dihydroxylation pathways gave mixtures of hydroxy indolizidin-2-one diastereomers, iodolactonization of the ∆⁴-azelate stereoselectively delivered a lactone iodide from which separable (5S)- and (7S)-hydroxy indolizidin-2-one N-(Boc)amino esters were synthesized by sequences featuring intramolecular iodide displacement and lactam formation. X-ray analysis of the (7S)-hydroxy indolizidin-2-one N-(Boc)amino ester indicated that the backbone dihedral angles embedded in the bicyclic ring system resembled those of the central residues of an ideal type II’ β-turn indicating the potential for peptide mimicry.     

Chiral sulfamide-catalyzed asymmetric Michael addition of protected 3-hydroxypropanal to β-nitrostyrenes

Organocatalytic asymmetric Michael addition of 3-(OTBS)-propanal to β-nitrostyrenes catalyzed by chiral sulfamides was investigated. Good d.r. (up to 80:20) and excellent enantioselectivities (up to >99% ee) were achieved. Both the N-[(1R,2R)-2-aminocyclohexyl]-N’-(phenylmethyl)sulfamide 7b and the novel chiral N-[(1R,2R)-2-aminocyclohexyl]-N’-[3,5-bis(trifluoromethyl)phenyl]sulfamide 7a were identified as efficient primary amine organocatalysts.     

First stereoselective synthesis of serinol-derived malyngamides and their 1′-epi-isomers

A stereoselective synthesis of 1a {N-[(1R)-2-hydroxy-1-methoxy-methyl ethyl]-(4E,7S)-7-methoxy-4-eicosenamide} has been accomplished in 10 steps from 1-tetradecanol for the first time in 28% overall yield. The key steps involved the coupling reaction of a chiral alkyne with a protected bromide in the presence of t-BuLi, as well as the amidation reaction of (4E,7S)-7-methoxyeicos-4-enoic acid with (R)-methoxyamino alcohol. Acetylation of 1a finished the preparation of 1b {N-[(1S)-2-acetyloxy-1-methoxy-methyl ethyl]-(4E,7S)-7-methoxy-4-eicosenamide}. Their 1′-epi-isomers have also been synthesized with a similar strategy.     

Super/Subcritical Fluid Chromatography Separations with Four Synthetic Polymeric Chiral Stationary Phases

New synthetic polymeric chiral selectors were developed recently as chiral stationary phases. They were tested with supercritical fluid mobile phases made of CO₂ plus an alcohol modifier and 0.2% v/v trifluoroacetic acid. The polymeric N,N′-(1S,2S)-1,2-cyclohexanediyl-bis-2-propenamide (P-CAP), the polymeric N,N′-[(1R,2R)]-1,2-diphenyl-1,2-ethanediyl] bis-2-propenamide (P-CAP-DP), the polymeric trans-9,10-dihydro-9,10-ethanoanthracene-(11S,12S)-11,12-dicarboxylic acid bis-4-vinylphenylamide (DEABV) and the polymeric N,N′-[(1R,2R)-1,2-diphenyl-1,2-ethanediyl] bis-4-vinylbenzamide (DPEVB) were bonded to 5 μm silica particles and used to prepare four columns that were tested with a set of 88 chiral compounds with a wide variety of chemical functionalities. All 88 test compounds were separated on one or more of these “related” polymeric CSPs. Forty-three enantiomeric pairs were separated in SFC conditions by only one of the CSPs. Twenty pairs were separated by two CSPs and 18 and 7 enantiomeric pairs were separated by 3 and all 4 CSPs, respectively. The three P-CAP, P-CAP-DP and DEABV CSPs have equivalent success being able to separate 49 enantiomeric pairs of the studied set with respectively 12, 14 and 20 at baseline (R _s  > 1.5). The DPEVB CSP was significantly less efficient separating only 18 chiral compounds with only one at baseline. The great advantage of the SFC mobile phases is the rapid separation, witch most achieved in less than 5 min.     

The effect of substitution on protonation sites: evidence for protonation at N(3) in N(7)-substituted adenine

Several experimental and theoretical studies have shown that N(1) is the first site for protonation in adenine and N(9)-substituted adenine derivatives. N(7) is considered the site for the second protonation to yield dipositive cations. Results are reported here which indicate that this protonation pattern is altered in N(7)-substituted adenine derivatives. In particular, an X-ray diffraction analysis of the structure of 7-methyladenine dihydrochloride, [C₆N₅H₇]Cl₂, definitively shows that the sites for protonation are N(3), as opposed to N(1), and N(9). Theoretical calculations of the molecular electrostatic potential in various systems suggest that such changes in preferred protonation sites should be expected, in general, when a modification of the molecular structure creates adjacent sites with similar reactivity, such as the N(3) and N(9) sites in 7-methyladenine.     

Preparation, structure and photoluminescence properties of Eu and Ce-doped SrYSi4N7

Undoped and Eu²⁺ or Ce³⁺-doped SrYSi₄N₇ were synthesized by solid-state reaction method at 1400-1660 °C under nitrogen/hydrogen atmosphere. The crystal structure was refined from the X-ray powder diffraction data by the Rietveld method. SrYSi₄N₇ and EuYSi₄N₇, being isotypic with the family of compounds MYbSi₄N₇ (M=Sr, Eu, Ba) and BaYSi₄N_7, crystallize with the hexagonal symmetry: space group P6₃mc (No. 186), Z=2, a=6.0160 (1) Å, c=9.7894 (1) Å, V=306.83(3) Å³; and a=6.0123 (1) Å, c=9.7869 (1) Å, V=306.37(1) Å³, respectively. Photoluminescence properties have been studied for Sr_1−xEu_xYSi₄N₇ (x=0-1) and SrY_1−xCe_xSi₄N₇ (x=0-0.03) at room temperature. Eu²⁺-doped SrYSi₄N₇ shows a broad yellow emission band peaking around 548-570 nm, while Ce³⁺-doped SrYSi₄N₇ exhibits a blue emission band with a maximum at about 450 nm. SrYSi₄N₇:Eu²⁺ can be very well excited by 390 nm radiation, which makes this material attractive as conversion phosphor for LED lighting applications.     

Isolation of highly pure erlotinib hydrochloride by recrystallization after nucleophilic substitution of an impurity with piperazine

Optimized synthesis and purification of erlotinib hydrochloride (N-(3-ethynylphenyl)-6,7-bis(2-methoxyethoxy)quinazoline-4-amine hydrochloride) were studied. Highly polar piperazine was used in a nucleophilic substitution reaction with the chlorinated intermediate byproduct N-(3-ethynylphenyl)-6(2-chloroethoxy)-7-(2-methoxyethoxy)quinazolin-4-amine hydrochloride. As a result, N-(3-ethynylphenyl)-6(2-chloroethoxy)-7-(2-methoxyethoxy)quinazolin-4-amine hydrochloride was completely transformed to N-(3-ethynylphenyl)-6(2-piperzinoethoxy)-7-(2-methoxyethoxy)quinazolin-4-amine hydrochloride. The polarity of N-(3-ethynylphenyl)-6(2-piperzinoethoxy)-7-(2-methoxyethoxy)quinazolin-4-amine hydrochloride was changed, and its molecule was enlarged. It was easy to remove this larger, more polar, compound by recrystallization. Highly pure erlotinib hydrochloride was obtained with low impurity content (<1 %). The purity of erlotinib hydrochloride was >99.9 %.     

Synthesis of Hafnium(IV) Polyaminoacetates

The interaction of hafnium(IV) salts (oxide-dichloride, chloride, and bromide) with nitrilotriacetic acid (NTA), diethylenetriamminepentaacetic acid (DTPA), 1,2-diaminocyclohexanetetraacetic acid (CDTA), 1,3-dipropylmino-2-hydroxy N,N,N′,N′-tetraacetic acid (dpta), and N-(2-hydroxyethyl)ethylenediamine triacetic acid (HEDTA) has been studied. The corresponding complexes Na₂[Hf(NTA)₂]·3H₂O (1), Na[HfDTPA]·3H₂O (2), [HfCDTA(H₂O)₂] (3), and Na[Hf₂(dpta)₂]·7.5H₂O·0.5C₂H₅OH (4) have been isolated and characterized and their structures have been determined by single crystal X-ray diffraction. Biological studies of [HfCDTA(H₂O)₂] have shown that in 5% glucose solution this complex has low toxicity and good contrasting ability.     

Molecular recognition of biotin, barbital and tolbutamide with new synthetic receptors

We have measured, by means of NMR titrations, the binding constants for the complexes between hosts N,N′-bis(6-methylpyridin-2-yl)-1,3-benzenedicarboxamide (7) and 4-chloro-N,N′-bis(6-methylpyridin-2-yl)-2,6-pyridinedicarboxamide (8, hydrated) with biotin methyl ester (1), N,N′-dimethylurea (2), 2-imidazolidone (3), N,N′-trimethylenurea (4), barbital (5) and tolbutamide (6) as guests. Molecular Mechanics calculations (Monte Carlo Conformational Search, AMBER and OPLS force fields, MacroModel v.8.1) on the complexes formed between the foregoing guests and hosts 7 and 8, comparatively with 4-oxo-N,N′-bis(6-methylpyridin-2-yl)-1,4-dihydro-2,6-pyridinedicarboxamide (9a) have been carried out in order to determine the correlation between experimental and theoretical results and to understand the behaviour of the designed new hosts. Finally we have performed single point DFT [B3LYP/6-31G(d,p)] calculations on the optimised Molecular Mechanics geometries for the complexes between hosts 7-9 and water.     

New 1,2-disubstituted ferrocenyl stibines containing N-heterocyclic pendant arm: Sb-N hypervalent compounds

New 1,2-disubstituted ferrocenyl stibines viz. containing -CH₂NR or -CH₂NHR pendant arm at the ortho-position have been synthesized and characterized by various physicochemical methods. These new ferrocenylstibines were prepared by the nucleophilic substitution reaction of diphenyl[(N,N,N-trimethylaminomethylferrocenyl)iodide]stibine by different primary amines and secondary heterocyclic amines viz. furan-2-ylmethylamine, p-aminoacetophenone, 3-(1-hydroxyethyl)-aniline, 4-hydroxypiperidine, 1-ethylpiperazine and 4-(4-bromophenyl)-4-hydroxypiperidine. Molecular structure of stibine (2), (3), (5) and (7) have been determined by X-ray crystallography. Stibine (2), (5) and (7) show a weak hypervalent Sb-N interaction while stibine (3) does not show this interaction in solid state.     

Synthesis,crystal structures and photoluminescence of 7-(N,N′-diethylamino)-3-phenylcoumarin derivatives

Two new coumarin derivatives, 7-(N,N′-diethylamino)-3-(4-hydroxyphenyl)-coumarin and 7-(N,N′-diethylamino)-3-(4-bromophenyl)-coumarin, were synthesized successfully. Their structures were verified by single crystal X-ray crystallography. The UV–vis absorption and fluorescence of the compounds were discussed. The compounds exhibit strong blue emission under ultraviolet light excitation. The molecular structures, the lowest energy transitions and the UV–vis spectra of 7-(N,N′-diethylamino)-3-(4-hydroxyphenyl)-coumarin and 7-(N,N′-diethylamino)-3-(4-bromophenyl)-coumarin have been studied with density functional theory (DFT) and time-dependent density functional theory (TD-DFT) at B3LYP/6-31G(d) level.