Noscapinoids with anti-cancer activity against human acute lymphoblastic leukemia cells (CEM): a three dimensional chemical space pharmacophore modeling and electronic feature analysis

We have identified a new class of microtubule-binding compounds—noscapinoids—that alter microtubule dynamics at stoichiometric concentrations without affecting tubulin polymer mass. Noscapinoids show great promise as chemotherapeutic agents for the treatment of human cancers. To investigate the structural determinants of noscapinoids responsible for anti-cancer activity, we tested 36 structurally diverse noscapinoids in human acute lymphoblastic leukemia cells (CEM). The IC₅₀ values of these noscapinoids vary from 1.2 to 56.0 μM. Pharmacophore models of anti-cancer activity were generated that identify two hydrogen bond acceptors, two aromatic rings, two hydrophobic groups, and one positively charged group as essential structural features. Additionally, an atom-based quantitative structure–activity relationship (QSAR) model was developed that gave a statistically satisfying result (R ² = 0.912, Q ² = 0.908, Pearson R = 0.951) and effectively predicts the anti-cancer activity of training and test set compounds. The pharmacophore model presented here is well supported by electronic property analysis using density functional theory at B3LYP/3-21*G level. Molecular electrostatic potential, particularly localization of negative potential near oxygen atoms of the dimethoxy isobenzofuranone ring of active compounds, matched the hydrogen bond acceptor feature of the generated pharmacophore. Our results further reveal that all active compounds have smaller lowest unoccupied molecular orbital (LUMO) energies concentrated over the dimethoxy isobenzofuranone ring, azido group, and nitro group, which is indicative of the electron acceptor capacity of the compounds. Results obtained from this study will be useful in the efficient design and development of more active noscapinoids.     

In silico QSAR studies of anilinoquinolines as EGFR inhibitors

Members of the epidermal growth factor receptor (EGFR) family of proteins are frequently overactive in solid tumors. A relatively new therapeutic approach to inhibit the kinase activity is the use of ATP-competitive small molecules. In silico techniques were employed to identify the key interactions between inhibitors and their protein receptors. A series of EGFR inhibitory anilinoquinolines was studied within the framework of hologram quantitative structure activity relationship (HQSAR), density functional theory (DFT)-based QSAR, and three-dimensional (3D) QSAR (CoMFA/CoMSIA). The HQSAR analysis implied that substitutions at certain sites on the inhibitors play an important role in EGFR inhibition. DFT-based QSAR results suggested that steric and electronic interactions contributed significantly to the activity. Ligand-based 3D-QSAR and receptor-guided 3D-QSAR analyses such as CoMFA and CoMSIA techniques were carried out, and the results corroborated the previous two approaches. The 3D QSAR models indicated that steric and hydrophobic interactions are dominant, and that substitution patterns are an important factor in determining activity. Molecular docking was helpful in identifying a bioactive conformer as well as a plausible binding mode. The docked geometry-based CoMFA model with steric and electrostatic fields effect gave q ² = 0.66, r ² = = 0.94 with r ² _predictive = 0.72. Similarly, CoMSIA with hydrophobic field gave q ² = 0.59, r ² = 0.85 with r ² _predictive = 0.63. Bulky groups around site 3 of ring “C”, and hydrophilic and bulky groups at position 6 of ring “A” are desirable, with a hydrophobic and electron-donating group at site 7 of ring “A” being helpful. Accordingly, potential EGFR inhibitors may be designed by modification of known inhibitors.     

Pharmacophore modeling and 3D-QSAR analysis of phosphoinositide 3-kinase p110α inhibitors

Pharmacophore modeling studies were undertaken for a series of compounds belonging several groups of phosphoinositide 3-kinase (PI3K) p110α inhibitors: 4-morpholino-2-phenylquinazolines derivatives, pyrido[3′,2′:4,5]furo-[3,2-d]pyrimidine derivatives, imidazo[1,2-a]pyridine derivatives, sulfonylhydrazone substituted imidazo[1,2-a]pyridines, and LY294002. A five-point pharmacophore with three hydrogen bond acceptors (A), one hydrophobic group (H), and one aromatic ring (R) as pharmacophore features was developed. The pharmacophore hypothesis yielded a statistically significant 3D-QSAR model, with a correlation coefficient of R ² = 0.95 for training set compounds. The model generated showed excellent predictive power, with a correlation coefficient of Q ² = 0.88 and r _pret² = 0.95 for a test set of 14 compounds. Furthermore, the structure–activity relationships of PI3K p110α inhibitors were elucidated and the activity differences between them discussed. Docking studies were also carried out wherein active and inactive compounds were docked into the active site of the PI3K p110α crystal structure to analyze PI3K p110α–inhibitor interactions. The results provide insights that will aid optimization of these classes of PI3K p110α inhibitors for better activity, and may prove helpful for further lead optimization and virtual screening.     

Theoretical study of hydrogen bond interactions of fluvastatin with <Emphasis Type="BoldItalic">ι</Emphasis>-carrageenan and <Emphasis Type="Italic">λ</Emphasis>-carrageenan

The binding of the reductase inhibitor drug fluvastatin, hydroxy-3-methylglutaryl coenzyme A, with the hydrophilic ι- or λ-carrageenan polymers, serving as potential controllers of the drug’s release rate, have been studied at the density functional level of theory with the B3LYP exchange correlation functional. Three low energy conformers of fluvastatin have been calculated. The vibrational spectroscopic properties calculated for the most stable conformer were in satisfactory agreement with the experimental data. A series of hydrogen bonded complexes of the most stable conformer of fluvastatin anion with low molecular weight models of the polymers have been fully optimized. In almost all, intermolecular H-bonds are formed between the sulfate groups of ι- or λ-carrageenan and fluvastatin’s hydroxyls, resulting in a red shift of the fluvastatin’s O − H stretching vibrations. Cooperative intramolecular H-bonds within fluvastatin or ι-, λ-carrageenan are also present. The BSSE and ZPE corrected interaction energies were estimated in the range 281–318 kJ mol⁻¹ for ι-carrageenan - fluvastatin and 145–200 kJ mol⁻¹ for λ-carrageenan - fluvastatin complexes. The electron density (ρ _bcp) and Laplacian (∇² ρ _bcp) properties at critical points of the intermolecular hydrogen bonds, estimated by AIM (atoms in molecules) calculations, have a low and positive character (∇² ρ _bcp > 0), consistent with the electrostatic character of the hydrogen bonds. The structural and energetic data observed, as well as the extent of the red shift of the fluvastatin’s O − H stretching vibrations upon complex formation and the properties of electron density show a stronger binding of fluvastatin to ι- than to λ-carrageenan.     

Comparison of aromatic monomers in lignocellulosic biomass prehydrolysates

Differences in the relative toxicity of xylose-rich prehydrolysates derived from woody and herbaceous feedstocks are likely due to the relative abundance of a variety of inhibitory compounds. Acetate, as well as several aromatic monomers, has been shown to be an inhibitor of the xylose-fermenting yeast, Pichia stipitis. Comparative information on the concentration of known and likely inhibitors, other than acetate, is lacking. The present study provides data on the aromatic monomer composition of representative herbaceous and woody prehydrolysates. Dilute-acid prehydrolysates were prepared from three feedstocks; two herbaceous, corn stover and switchgrass (Panicum virgatum L.), and one woody (poplar). The prehydrolysates were neutralized with Ca(OH)₂ extracted with ethyl acetate, trimethylsilylated, and analyzed by GC-MS. Fourteen aromatic monomers were tentatively identified by comparison with published mass spectra. The concentrations of the aromatic monomers totalled 112, 141 and 247 mg L⁻¹ for corn stover, switchgrass and poplar prehydrolysates, respectively. This is also the order of increasing inhibition of growth and ethanol productivity observed for Pichia fermentations. The woody prehydrolysate contained approximately four-fold more syringyl-based monomers than did the herbaceous prehydrolysates, while guaiacyl-containing compounds were more evenly distributed. Received 24 April 1998/ Accepted in revised form 8 June 1998     

Crystal structure and conformational analysis of s-cis-(acetylacetonato)(ethylenediamine-N,N′-diacetato)-chromium(III)

The crystal structure of [Cr(edda)(acac)] (edda = ethylediamine-N,N′-diacetate; acac = acetylacetonato) has been determined by a single crystal X-ray diffraction study at 150 K. The chromium ion is in a distorted octahedral environment coordinated by two N and two O atoms of chelating edda and two O atoms of acac, resulting in s-cis configuration. The complex crystallizes in the space group P2₁/c of the monoclinic system in a cell of dimensions a = 10.2588(9), b = 15.801(3), c = 8.7015(11) ?, β =101.201(9)° and Z = 4. The mean Cr-N(edda), Cr-O(edda) and Cr-O(acac) bond distances are 2.0829(14), 1.9678(11) and 1.9477(11) ? while the angles O-Cr-O of edda and O-Cr-O of acac are 171.47(5) and 92.72(5)°, respectively. The crystal structure is stabilized by N–H⋯O hydrogen bonds linking [Cr(edda)(acac)] molecules in distinct linear strands. The visible electronic and IR spectroscopic properties are also discussed. An improved, physically more realistic force field, Vibrationally Optimized Force Field (VOFF), capable of reproducing structural and vibrational properties of [Cr(edda)(acac)] was developed and its transferability demonstrated on selected chromium(III) complexes with similar ligands.     

Conformational changes in the archaerhodopsin-3 proton pump: detection of conserved strongly hydrogen bonded water networks

Archaerhodopsin-3 (AR3) is a light-driven proton pump from Halorubrum sodomense, but little is known about its photocycle. Recent interest has focused on AR3 because of its ability to serve both as a high-performance, genetically-targetable optical silencer of neuronal activity and as a membrane voltage sensor. We examined light-activated structural changes of the protein, retinal chromophore, and internal water molecules during the photocycle of AR3. Low-temperature and rapid-scan time-resolved FTIR-difference spectroscopy revealed that conformational changes during formation of the K, M, and N photocycle intermediates are similar, although not identical, to bacteriorhodopsin (BR). Positive/negative bands in the region above 3,600 cm^− 1, which have previously been assigned to structural changes of weakly hydrogen bonded internal water molecules, were substantially different between AR3 and BR. This included the absence of positive bands recently associated with a chain of proton transporting water molecules in the cytoplasmic channel and a weakly hydrogen bonded water (W401), which is part of a hydrogen-bonded pentagonal cluster located near the retinal Schiff base. However, many of the broad IR continuum absorption changes below 3,000 cm^− 1 assigned to networks of water molecules involved in proton transport through cytoplasmic and extracellular portions in BR were very similar in AR3. This work and subsequent studies comparing BR and AR3 structural changes will help identify conserved elements in BR-like proton pumps as well as bioengineer AR3 to optimize neural silencing and voltage sensing.     

A MP2 and DFT study of the aromatic character of polyphosphaphospholes. Is the pyramidality the only factor to take into consideration?

A comprehensive MP2/6-311 + G(d,p) and B3LYP/6-311 + G(d,p) study of the aromatic character of phospholes, P _n (CH)_4-n PH with n = 0-4 was conducted. For this purpose, the structures for these compounds were optimized at both theoretical levels and different magnetic properties (magnetic susceptibility anisotropy, χ_anis, and the nucleus-independent chemical shifts, NICS) were evaluated. For comparison, these magnetic properties were also calculated in the optimized structures with planarity constraints. We have also applied the ACID (anisotropy of the current-induced density) method in this analysis. The main conclusions are the aromatic character of these compounds, the relationship between aromaticity and planarity and the importance of other factors in this aromaticity.     

Pharmacophore mapping of a series of pyrrolopyrimidines,indolopyrimidines and their congeners as multidrug-resistance-associated protein (MRP1) modulators

Pharmacophore mapping studies were undertaken for a series of molecules belonging to pyrrolopyrimidines, indolopyrimidines and their congeners as multidrug resistance-associated protein (MRP1) modulators. A five-point pharmacophore with two hydrogen bond acceptors (A), one lipophilic/hydrophobic group (H), one positive ionic feature (P) and one aromatic ring (R) as pharmacophoric features was developed. The pharmacophore hypothesis yielded a statistically significant 3D-QSAR model, with a correlation coefficient of r ² = 0.799 for training set molecules. The model generated showed excellent predictive power, with a correlation coefficient Q ² = 0.679 for an external test set of 20 molecules. The pharmacophore was further validated using four structurally diverse compounds with MRP1 modulatory activity. These compounds mapped well onto four of the five features of the pharmacophore. The pharmacophore proposed here was then utilised for the successful retrieval of active molecules with diverse chemotypes from database search. The geometry and features of pharmacophore are expected to be useful for the design of selective MRP1 inhibitors. Figure Alignment of multidrug resistance-associated protein (MRP1) inhibitors with the developed pharmacophore. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

A MP2 and DFT study of the influence of complexation on the aromatic character of phosphole

This work is focused in three topical subjects: intermolecular interactions, metal ions, and aromaticity. A comprehensive MP2/6-31 + G* and B3LYP/6-31 + G* study of the influence of cation-π interactions on the aromatic character of phosphole was conducted. For this purpose, the structures of complexes were optimized at both theoretical level and different magnetic properties were evaluated. The main conclusion is the increase of the aromatic character of the phosphole when complexes with Li⁺, Be²⁺, and Al³⁺ are formed.     

Non-cholinergic Effects of Huperzine A: Beyond Inhibition of Acetylcholinesterase

The use of acetylcholinesterase inhibitors to decrease the breakdown of the neurotransmitter acetylcholine has been the main symptomatic therapy for mild to moderate Alzheimer’s patients, though the etiology of Alzheimer’s disease remains unclear and seems to involve multiple factors. Further evidence has indicated that some of these acetylcholinesterase inhibitors also have non-cholinergic functions on the pathogenesis of Alzheimer’s disease including the formation and deposition of β-amyloid. Huperzine A, a potent and reversible inhibitor of acetylcholinesterase that was initially isolated from a Chinese herb, has been found to improve cognitive deficits in a broad range of animal models and has been used for Alzheimer’s disease treatment in China. The novel neuroprotective effects of huperzine A might yield beneficial effects in Alzheimer’s disease therapy and provide a potential template for the design of new selective and powerful anti-Alzheimer’s drugs. The present paper gives an overview on the neuroprotective effects of huperzine A beyond its acetylcholinesterase inhibition. These effects include regulating β-amyloid precursor protein metabolism, protecting against β-amyloid-mediated oxidative stress and apoptosis. The structure–function relationship of huperzine A is also discussed.     

A transketolase mutant of Corynebacterium glutamicum

A transketolase mutant was first isolated from Corynebacterium glutamicum, an organism of industrial importance. The mutant strain exhibited an absolute requirement for shikimic acid or the aromatic amino acids and vitamins for growth, and also failed to grow on ribose or gluconic acid as sole carbon source, even with the aromatic supplement. All of these defective properties were fully restored in spontaneous revertants, indicating the existence of a single transketolase in C. glutamicum that was indispensable both for aromatic biosynthesis and for utilization of these carbohydrates in vivo. The transketolase mutant accumulated ribulose extracellularly when cultivated in glucose medium with shikimic acid, but no ribose was detected. Received: 10 April 1998 / Received revision: 26 May 1998 / Accepted: 14 June 1998     

A cluster of charged and aromatic residues in the C-terminal portion of maltoporin participates in sugar binding and uptake

The maltoporin LamB of Escherichia coli K12 is a trimeric protein which facilitates the diffusion of maltose and maltodextrins through the bacterial outer membrane, and also acts as a non-specific porin for small hydrophilic molecules as well as a receptor for phages. Loop L9 (residues 375 to 405) is the most distal and largest surface-exposed loop of LamB. It comprises a central portion, which varies in size and sequence in the maltoporins of known sequence, flanked by two conserved regions containing charged and aromatic residues. In order to identify the residues within the proximal region that are specifically involved in sugar utilization, we used site-directed mutagenesis to change, individually, each of the charged (five) and aromatic (three) residues in the region 371 to 379 into alanine. None of the eight single amino acid substitutions affected the phage receptor activity of LamB. In contrast, they all affected, to variable extents, maltoporin functions. For all the mutants, very good correlations were observed between the effects on sugar binding and on in vivo uptake. In no case were maltoporin functions completely abolished. Mutants E374 A and W376 A were the most impaired (with over 60% reduction in dextrin binding and in vivo uptake of maltose and maltopentaose). These two mutations also led to an increased bacterial sensitivity to bacitracin and vancomycin. The functional and structural implications are discussed. Received: 29 April 1998 / Accepted: 23 July 1998     

Use of molecular modeling, docking, and 3D-QSAR studies for the determination of the binding mode of benzofuran-3-yl-(indol-3-yl)maleimides as GSK-3β inhibitors

Molecular modeling and docking studies along with three-dimensional quantitative structure relationships (3D-QSAR) studies have been used to determine the correct binding mode of glycogen synthase kinase 3β (GSK-3β) inhibitors. The approaches of comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) are used for the 3D-QSAR of 51 substituted benzofuran-3-yl-(indol-3-yl)maleimides as GSK-3β inhibitors. Two binding modes of the inhibitors to the binding site of GSK-3β are investigated. The binding mode 1 yielded better 3D-QSAR correlations using both CoMFA and CoMSIA methodologies. The three-component CoMFA model from the steric and electrostatic fields for the experimentally determined pIC₅₀ values has the following statistics: R²(cv) = 0.386 nd SE(cv) = 0.854 for the cross-validation, and R² = 0.811 and SE = 0.474 for the fitted correlation. F (3,47) = 67.034, and probability of R² = 0 (3,47) = 0.000. The binding mode suggested by the results of this study is consistent with the preliminary results of X-ray crystal structures of inhibitor-bound GSK-3β. The 3D-QSAR models were used for the estimation of the inhibitory potency of two additional compounds.     

A selectivity study on mTOR/PI3Kα inhibitors by homology modeling and 3D-QSAR

The phosphatidylinositol-3-kinase (PI3K)/Akt/mammalian target of rapamycin (mTOR) signaling pathway plays a critical role in the regulation of cellular growth, survival and proliferation. mTOR and PI3K have attracted particular attention as cancer targets. These kinases belong to the phosphatidylinositol-3-kinase-related kinase (PIKK) family and therefore have considerable homology in their active sites. To accelerate the discovery of inhibitors with selective activity against mTOR and PI3K as cancer targets, in this work, a homology model of mTOR was developed to identify the structural divergence in the active sites between mTOR and PI3Kα. Furthermore, two highly predictive comparative molecular similarity index analyses (CoMSIA) models were built based on 304 selective inhibitors docked into mTOR and PI3Kα, respectively (mTOR: q ² = 0.658, r _pre² = 0.839; PI3Kα: q ² = 0.540, r _pre² = 0.719). The results showed that steric and electrostatic fields have an important influence on selectivity towards mTOR and PI3Kα—a finding consistent with the structural divergence between the active sites. The findings may be helpful in investigating selective mTOR/PI3Kα inhibitors.     

Viability and thermal stability of a strain of Saccharomyces cerevisiae freeze-dried in different sugar and polymer matrices

The viability and thermal stability of a freeze-dried yeast strain were studied in relation to some physical properties of the matrices in which the cells were freeze-dried. Samples of inoculum with solutions of the matrix components [polyvinylpyrrolidone (PVP), maltose, trehalose, maltodextrins, or mixtures of maltodextrin and trehalose] and controls without matrices were freeze-dried and then equilibrated at several relative humidities. Viability was determined before and after freeze-drying and after heat treatment (100 min at 70 °C). Freeze-drying with trehalose, PVP, maltose or 1.8-kDa maltodextrin, and mixtures of maltodextrin/trehalose increased viability in comparison with controls. The 3.6-kDa maltodextrin was ineffective at protecting the cells during freeze-drying. The glass transition temperature (T _g), which depends on moisture content, was indicated as a possible factor to determine the stability of labile materials. Protective effects of the excipients during thermal treatment were analysed in relation to the physical changes (collapse or structural shrinkage) which were dependent on the T _g of the systems. The presence of a certain amount of amorphous disaccharides during freeze-drying and heating was found to be a critical factor for ensuring cell viability, which was protected even in rubbery (above T _g) matrices. Received: 4 December 1998 / Received last revision: 2 March 1999 / Accepted: 14 March 1999     

Elucidation of binding mode and three dimensional quantitative structure–activity relationship studies of a novel series of protein kinase B/Akt inhibitors

Protein kinase B (PKB; also known as Akt kinase) is located downstream in the PI-3 kinase pathway. Overexpression and constitutive activation of PKB/Akt leads to human prostate, breast and ovarian carcinomas. A series of 69 PKB/Akt inhibitors were examined to explore their binding modes using FlexX, and three-dimensional quantitative structure–activity relationship (3D-QSAR) studies based on comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were performed to provide structural insights into these compounds. CoMFA produced statistically significant results, with cross-validated q ² and non-cross validated correlation r ² coefficients of 0.53 and 0.95, respectively. For CoMSIA, steric, hydrophobic and hydrogen bond acceptor fields jointly yielded ‘leave one out’ q ²  = 0.51 and r ²  = 0.84. The predictive power of CoMFA and CoMSIA was determined using a test set of 13 molecules, which gave correlation coefficients, of 0.58 and 0.62, respectively. Molecular docking revealed that the binding modes of these molecules in the ATP binding sites of the Akt kinase domain were very similar to those of the co-crystallized ligand. The information obtained from 3D contour maps will allow the design of more potent and selective Akt kinase inhibitors.