Pharmacophore-based screening and drug repurposing exemplified on glycogen synthase kinase-3 inhibitors

The current study was conducted to elaborate a novel pharmacophore model to accurately map selective glycogen synthase kinase-3 (GSK-3) inhibitors, and perform virtual screening and drug repurposing. Pharmacophore modeling was developed using PHASE on a data set of 203 maleimides. Two benchmarking validation data sets with focus on selectivity were assembled using ChEMBL and PubChem GSK-3 confirmatory assays. A drug repurposing experiment linking pharmacophore matching with drug information originating from multiple data sources was performed. A five-point pharmacophore model was built consisting of a hydrogen bond acceptor (A), hydrogen bond donor (D), hydrophobic (H), and two rings (RR). An atom-based 3D quantitative structure–activity relationship (QSAR) model showed good correlative and satisfactory predictive abilities (training set \({R}^{2}= 0.904\); test set: \({Q}^{2}= 0.676\); whole data set: stability \(s = 0.803\)). Virtual screening experiments revealed that selective GSK-3 inhibitors are ranked preferentially by Hypo-1, but fail to retrieve nonselective compounds. The pharmacophore and 3D QSAR models can provide assistance to design novel, potential GSK-3 inhibitors with high potency and selectivity pattern, with potential application for the treatment of GSK-3-driven diseases. A class of purine nucleoside antileukemic drugs was identified as potential inhibitor of GSK-3, suggesting the reassessment of the target range of these drugs.     

Integration-mediated prediction enrichment of quantitative model for Hsp90 inhibitors as anti-cancer agents: 3D-QSAR study

The present study describes a systematic 3D-QSAR study consisting of pharmacophore modeling, docking, and integration of ligand-based and structure-based drug design approaches, applied on a dataset of 72 Hsp90 inhibitors as anti-cancer agents. The best pharmacophore model, with one H-bond donor (HBD), one H-bond acceptor (HBA), one hydrophobic_aromatic (Hy_Ar), and two hydrophobic_aliphatic (Hy_Al) features, was developed using the Catalyst/HypoGen algorithm on a training set of 35 compounds. The model was further validated using test set, external set, Fisher’s randomization method, and ability of the pharmacophoric features to complement the active site amino acids. Docking analysis was performed using Hsp90 chaperone (PDB-Id: 1uyf) along with water molecules reported to be crucial for binding and catalysis (Sgobba et al. ChemMedChem 4:1399–1409, 2009). Furthermore, an integration of the ligand-based as well as structure-based drug design approaches was done leading to the integrated model, which was found to be superior over the best pharmacophore model in terms of its predictive ability on internal [integrated model 2: R _(train) = 0.954, R _(test) = 0.888; Hypo-01: R _(train) = 0.912 and R _(test) = 0.819] as well as on external data set [integrated model 2: R _(ext.set) = 0.801; Hypo-01: R _(ext.set) = 0.604].     

Comparative molecular field analysis and comparative molecular similarity indices analysis of hydroxyethylamine derivatives as selective human BACE-1 inhibitor

Three-dimensional quantitative structure–activity relationship (3D-QSAR) models were developed based on comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA), on a series of 43 hydroxyethylamine derivatives, acting as potent inhibitors of β-site amyloid precursor protein (APP) cleavage enzyme (BACE-1). The crystal structure of the BACE-1 enzyme (PDB ID: 2HM1) with one of the most active compound 28 was available, and we assumed it to be the bioactive conformation of the studied series, for 3D-QSAR analysis. Statistically significant 3D-QSAR model was established on a training set of 34 compounds, which were validated by a test set of 9 compounds. For the best CoMFA model, the statistics are, r ² =  0.998, r²_cv = 0.810{r^{2}_{\rm cv} = 0.810} , n =  34 for the training set and r²_pred = 0.934{r^{2}_{\rm pred} = 0.934} , n = 9 for the test set. For the best CoMSIA model (combined steric, electrostatic, hydrophobic, and hydrogen bond donor fields), the statistics are r ² =  0.978, r²_cv = 0.754{r^{2}_{\rm cv} = 0.754} , n =  34 for the training set and r²_pred = 0.750{r^{2}_{\rm pred} = 0.750} , n =  9 for the test set. The resulting contour maps, produced by the best CoMFA and CoMSIA models, were used to identify the structural features relevant to the biological activity in this series of analogs. The data generated from the present study will further help to design novel, potent, and selective BACE-1 inhibitors.     

Comparative docking and CoMFA analysis of curcumine derivatives as HIV-1 integrase inhibitors

The docking studies and comparative molecular field analysis (CoMFA) were performed on highly active molecules of curcumine derivatives against 3′ processing activity of HIV-1 integrase (IN) enzyme. The optimum CoMFA model was selected with statistically significant cross-validated r² value of 0.815 and non-cross validated r ² value of 0.99. The common pharmacophore of highly active molecules was used for screening of HIV-1 IN inhibitors. The high contribution of polar interactions in pharmacophore mapping is well supported by docking and CoMFA results. The results of docking, CoMFA, and pharmacophore mapping give structural insights as well as important binding features of curcumine derivatives as HIV-1 IN inhibitors which can provide guidance for the rational design of novel HIV-1 IN inhibitors.     

Identification of dual Acetyl-CoA carboxylases 1 and 2 inhibitors by pharmacophore based virtual screening and molecular docking approach

Acetyl-CoA carboxylase (ACC) is a crucial metabolic enzyme that plays a vital role in obesity-induced type 2 diabetes and fatty acid metabolism. To identify dual inhibitors of Acetyl-CoA carboxylase1 and Acetyl-CoA carboxylase2, a pharmacophore modelling approach has been employed. The best HypoGen pharmacophore model for ACC2 inhibitors (Hypo1_ACC2) consists of one hydrogen bond acceptor, one hydrophobic aliphatic and one hydrophobic aromatic feature, whereas the best pharmacophore (Hypo1_ACC1) for ACC1 consists of one additional hydrogen-bond donor (HBD) features. The best pharmacophore hypotheses were validated by various methods such as test set, decoy set and Cat-Scramble methodology. The validated pharmacophore models were used to screen several small-molecule databases, including Specs, NCI, ChemDiv and Natural product databases to identify the potential dual ACC inhibitors. The virtual hits were then subjected to several filters such as estimated $\text{ IC}_{50}$ value, quantitative estimation of drug-likeness and molecular docking analysis. Finally, three novel compounds with diverse scaffolds were selected as potential starting points for the design of novel dual ACC inhibitors.     

Identification of new novel scaffold for Aurora A inhibition by pharmacophore modeling and virtual screening

Aurora kinases belong to family of highly conserved serine/threonine protein kinases that are involved in diverse cell cycle events and play a major role in regulation of cell division. Abnormal expression of Aurora kinases may lead to cancer; hence, these are considered as a potential target in cancer treatment. In this research article, we identified three novel Aurora A inhibitors using modern computational tools. A four-point common 3D pharmacophore hypothesis of Aurora A (AurA) inhibitors was developed using a diverse set of 55 thienopyrimidine derivatives. A three-dimensional quantitative structure–activity relationship (3D-QSAR) study was carried out using atom-based alignment of diverse set of 55 molecules to evaluate the structure– activity relationships. Docking and 3D-QSAR studies were performed with the 3D structure of AurA to evaluate the generated pharmacophore. The pharmacophore model and 3D-QSAR results complemented the results of our docking study. The pharmacophore hypothesis, which yields the best results, was used to screen the Zinc ‘clean drug-like’ database. Various database filters such as 3D-arrangement of pharmacophoric features, predicted activity and binding interaction score were used to retrieve hits having potential AurA inhibition activity.     

De novo design of N-(pyridin-4-ylmethyl)aniline derivatives as KDR inhibitors: 3D-QSAR, molecular fragment replacement, protein-ligand interaction fingerprint, and ADMET prediction

Vascular endothelial growth factor (VEGF) and its receptor tyrosine kinase VEGFR-2 or kinase insert domain receptor (KDR) have been identified as promising targets for novel anticancer agents. To achieve new potent inhibitors of KDR, we conducted molecular fragment replacement (MFR) studies for the understanding of 3D-QSAR modeling and the docking investigation of arylphthalazines and 2-((1H-Azol-1-yl)methyl)-N-arylbenzamides-based KDR inhibitors. Two favorable 3D-QSAR models (CoMFA with q ², 0.671; r ², 0.969; CoMSIA with q ², 0.608; r ², 0.936) have been developed to predict the biological activity of new compounds. The new molecular database generated by MFR was virtually screened using Glide (docking) and further evaluated with CoMFA prediction, protein?Cligand interaction fingerprint (PLIF) and ADMET analysis. 44 N-(pyridin-4-ylmethyl)aniline derivatives as novel potential KDR inhibitors were finally obtained. In this paper, the work flow developed could be applied to de novo drug design and virtual screening potential KDR inhibitors, and use hit compounds to further optimize and design new potential KDR inhibitors.     

Absolute cross sections of electron attachment to molecular clusters. Part II: Formation of (H2O) N? , (N2O) N? , and (N2) N?

Absolute cross sections σ⁻(E, N) of electron attachment to clusters (H₂O) _N , (N₂O) _N , and (N₂) _N for varying electron energy E and cluster size N are measured by using crossed electron and cluster beams in a vacuum. Continua of σ⁻(E) are found that correlate well with the functions of electron impact excitation of molecules’ internal degrees of freedom. The electron is attached through its solvation in a cluster. In the formation of (H₂O) _N ⁻ , (N₂O) _N ⁻ , and (N₂) _N ⁻ , the curves σ⁻(N) have a well-defined threshold because of a rise in the electron thermalization and solvation probability with N. For (H₂O)₉₀₀, (N₂O)₃₅₀, and (N₂)₂₆₀ clusters at E = 0.2 eV, the energy losses by the slow electron in the cluster are estimated as 3.0 × 10⁷, 2.7 × 10⁷, and 6.0 × 10⁵ eV/m, respectively. It is found that the growth of σ⁻ with N is the fastest for (H₂O) _N and (N₂) _N clusters at E → 0 as a result of polarization capture of the s-electron. Specifically, at E = 0.1 eV and N = 260, σ⁻ = 3.0 × 10⁻¹³ cm² for H₂O clusters, 8.0 × 10⁻¹⁴ cm² for N₂O clusters, and 1.4 × 10⁻¹⁵ cm² for N₂ clusters; at E = 11 eV, σ⁻ = 9.0 × 10⁻¹⁶ cm² for (H₂O)₂₀₀ clusters, 2.4 × 10⁻¹⁴ cm² for (N₂O)₃₅₀ clusters, and 5.0 × 10⁻¹⁷ cm² for (N₂)₂₆₀ clusters; finally, at E = 30 eV, σ⁻ = 3.6 × 10⁻¹⁷ cm² for (N₂O)₁₀ clusters and 3.0 × 10⁻¹⁷ cm² for (N₂)₁₂₅ clusters. Original Russian Text ? A.A. Vostrikov, D.Yu. Dubov, 2006, published in Zhurnal Tekhnicheskoĭ Fiziki, 2006, Vol. 76, No. 12, pp. 1–15.     

Polarized absorption spectra of Co2+ in Na2Cd3Cl8 single crystals

Summary The polarized optical absorption spectra of Na₂Cd₃Cl₈: Co²⁺ in the range of 15 000 to 40 000 cm⁻¹ down to 15 K are reported. The Co²⁺ ion is found to occupy the Cd²⁺ sites in octahedral geometry and the spectra are interpreted satisfactorily in terms of a cubic ligand field model including spin-orbit coupling. The observed crystal field spectra are well reproduced withB=745 cm⁻¹,C=3410 cm⁻¹,Dq=700 cm⁻¹ and ζ (spin-orbit interaction) =520 cm⁻¹. No spectral evidence for tetragonal distortion is observed.     

Modification of nanostructured states in ion-implanted platinum

The formation of nanostructures in subsurface volumes of Pt as a result of the implantation of Ar⁺ ions (E = 30 keV, F = 10¹⁶−10¹⁸ cm⁻²) was studied by the method of field ion microscopy. This phenomenon was observed at distances not less than 60 nm from the irradiated surface of the metal (at F = 10¹⁸ cm⁻²). It was established that the optimum regime for obtaining nanocrystalline structures in subsurface volumes of ion-implanted platinum is irradiation to F = 10¹⁷ cm⁻² (E = 30 keV, j = 200 μA cm⁻²). In such a regime, the formation of nanoblock structures is observed at distances not less than 20 nm from the irradiated surface, rather than the formation of vacancy pores.     

吡啶并嘧啶类Wee1激酶衍生物的三维定量构效关系与分子对接

采用比较分子场分析方法(CoMFA)和比较分子相似性指数分析方法(CoMSIA)对一系列吡啶并嘧啶类衍生物进行了三维定量构效关系(3D-QSAR)研究,建立了CoMFA和CoMSIA两种模型. 所构建的最佳模型的交叉验证相关系数分别为0.707和0.645,非交叉验证系数分别是0.964和0.972,模型的一些外部验证表明两个模型合理、可靠,并具有良好的预报能力. 同时,用分子对接的方法分析了该类化合物与Wee1激酶结构的作用模式,结果进一步表明,在R1和R5取代基上引入正电性基团,R2为体积小的电负性基团,同时选择体积中等和强的推电子的R3但亲水性的X取代基,能有效改善这类化合物的抑制活性.     

EPR studies of Cu2+ and V4+ ions in phosphate glasses

Two lead-phosphate glass systems doped with both copper and vanadium ions in different ratios were studied by EPR (electron paramagnetic resonance) method. EPR spectra and parameters (g_‖ = 2.44, g_⊥ = 2.08 andA _‖ = 117.6 · 10⁻⁴ cm⁻¹) obtained for x(CuO · V₂O₅)(l−x)[2P₂O₅ · PbO] glasses withx ≤ 10 mol% suggest a tetrahedral (Td) coordination of Cu²⁺ ions and not a tetragonally elongated octahedron as has been assumed in previous works. The ground state of the paramagnetic electron is thed _xy copper orbital with a 4p_z contribution of 6%. For 20 ≤x ≤ 40 mol% a broad line (ΔB = 307 G) characteristic for clustered ions appears atg = 2.18. The V⁴⁺ ions are evidenced only in the spectra of x(CuO · 2V₂O₅)(1 −x)[2P₂O₅ · PbO] glasses and the resonance parameters suggest a pentacoordinated C_4v local symmetry for these ions. The hyperfine structures characteristic for Cu²⁺ and V⁴⁺ ions disappear for 10 ≤x ≤ 40 mol% due to the mixed exchange Cu²⁺−V⁴⁺ pair formation in these glasses.     

Surface vibrations and the nature of the adsorption state: C2H2 on Pt(111)

Molecular vibrations of C₂H₂ and C₂D₂ adsorbed on Pt(111) at 140 K and ∼300K have been measured by high resolution electron energy loss spectroscopy. The comparison of C₂H₂ and C₂D₂ spectra allows an unambiguous assignment of the observed losses to the excitation of C−H bending, C−H stretching, and C−C stretching modes of nondissociatively adsorbed acetylene. From the relative intensities of losses the hybridisation state is determined to be nearsp ². The C−C stretching frequency indicates a C−C bond order of ∼1.8.