Structure-activity relationships for non-congeneric structures. Application of substructural balance method for antiallergic activity

This paper presents a new research method of structure-activity relationships (SAR) based on the concept of substructural balance. By using antiallergic activity (PCA, rat, iv) of a non-congeneric set of 267 structures, the structural feature of active group is expressed in terms of substructural balance. Each structure was expressed with 100 new substructures and the number of each substructure in a molecule was counted. The substructural balance was expressed as their ratio. Structures were classified into three groups based on their potencies (ED50), active (44), median (33) and inactive (190) group. Using two substructural ratios, 80.53% of inactive and 57.58% of median structures were excluded from those that were active. Common features of active structures were shown as a zone indicating the optimal ranges of two substructural ratios. Two substructural ratios were determined out of 4950 substructural ratios, all possible combinations of 100 substructures (100C2), by selecting the greatest discriminatory power of inactive from active structures. The substructures used in this work include: the number of bonds comprising of the longest conjugate system, the number of skeletal atoms and the numbers of electron-donor pairs at certain distances in the molecule.     

Sar modeling of unbalanced data sets

Abstract

The increased acceptance of SAR approaches to hazard identification has led us to investigate methods to improve the predictive performance of SAR models. In the present study we demonstrate that although on theoretical grounds the ratio of active to inactive chemicals in the learning set should be unity, SAR models can ?tolerate‘ an unbalanced range in ratios from 3 : 1 (i.e., 75% actives) to 1 : 2 (i.e., 33% actives) and still perform adequately. On the other hand SAR models derived from learning sets with ratios in excess of 4 : 1 (80% actives), even when corrected for the initial ratio do not perform satisfactorily.     

Application of infrared data analysis based on symbolic logic in automated structure elucidation by chemics

A computer program, IRASSL, is described for processing infrared (IR) data. The program, based on symbolic logic, is used to formulate complex relationships between substructures and their characteristic wavenumber regions. The program yields sets of substructures inferred from a correlation table prepared from accumulated IR data. The procedure is applied as an ancillary to the automated structure elucidation system CHEMICS. The introduction of the substructural information provided by IRASSL into CHEMICS as restrictions in the elucidation process produces a significant decrease in the number of candidate structures. Some examples of the application are given.     

A CoMFA analysis with conformational propensity: An attempt to analyze the SAR of a set of molecules with different conformational flexibility using a 3D-QSAR method

CoMFA analysis, a widely used 3D-QSAR method, has limitations to handle a set of SAR data containing diverse conformational flexibility since it does not explicitly include the conformational entropic effects into the analysis. Here, we present an attempt to incorporate the conformational entropy effects of a molecule into a 3D-QSAR analysis. Our attempt is based on the assumption that the conformational entropic loss of a ligand upon making a ligand-receptor complex is small if the ligand in an unbound state has a conformational propensity to adopt an active conformation in a complex state. For a QSAR analysis, this assumption was interpreted as follows: a potent ligand should have a higher conformational propensity to adopt an `active-conformation'-like structure in an unbound state than an inactive one. The conformational propensity value was defined as the populational ratio, N<sub>active</sub>/N<sub>stable</sub>, of the number of energetically stable conformers, N<sub>stable</sub>, to the number of `active-conformation'-like structures, N_active. The latter number was calculated by counting the number of conformers that satisfied the structural parameters deduced from the active conformation. A set of SAR data of imidazoleglycerol phosphate dehydratase inhibitors containing 20 molecules with different conformational flexibility was used as a training set for developing a 3D structure-activity relationship by a CoMFA analysis with the conformational propensity value. This resulted in a cross-validated squared correlation coefficient of the CoMFA model with the conformational propensity value (R ² _cross = 0.640) higher than that of the standard CoMFA model (R ² _cross = 0.431). Then we evaluated the quality of the CoMFA models by predicting the inhibitory activity for a new molecule.     

Analyses of a Mixture of Glucosyl-Cyclomaltoheptaoses Prepared on an Industrial Scale

ABSTRACT

A mixture of glucosyl-cyclomaltoheptaoses (β-cyclodextrins, βCDs) was prepared by glucoamylolysis of a mixture of maltosyl-βCDs which was produced on an industrial scale from maltose and β CD through the reverse action of Klebsiella pneumoniae pullulanase. Glucosyl-βCDs in the mixture were separated by HPLC on a reversed phase column and their molecular weights were measured by FAB-MS. In addition, the number of side-chains in each molecule was confirmed by methylation analysis and it was proved that the mixture comprised mainly of a monoglucosyl-βCD [G-β CD] and diglucosyl-β-CDs [(G)₂-βCDs], and as a minor component triglucosyl-β CDs [(G)₃-βCDs], and that G-, (G)₂-, and (G)₃-β CDs were produced in the ratios of 50%:45%:5%. The structures of three positional isomers of (G)₂-β CD were established by HPLC analysis of partial hydrolyzates, ¹³C NMR spectroscopy, and chemical synthesis. Four regioisomeric (G)₃-β CDs which could be isolated were characterized by ¹³C NMR spectroscopy.     

Synthesis,crystal structures,in vitro anticancer,and in vivo acute oral toxicity studies of bis-imidazolium/benzimidazolium salts and respective dinuclear Ag(I)-N-heterocyclic carbene complexes

The synthesis, spectral (FT-IR and NMR), and structural studies of 1,1′-methylene linked 3,3′-2-cyanobenzyl bis-imidazolium salt (L₁) and respective dinuclear Ag(I)-NHC complex (C₁) are reported. The structures of both compounds were established through single-crystal X-ray diffraction. C₁ has a short Ag–Ag separation of 3.16?Å. Both L₁ and C₁ were tested for potential against leukemia (k562) cell line. For comparison, para-xylyl linked bis-benzimidazolium salts (L₂–L₄) and their dinuclear Ag(I)-NHC complexes (C₂–C₄) were synthesized and tested against the same cell line (K562). The IC₅₀ values proved that L₂–L₄ and C₂–C₄ are many fold more active than L₁ and C₁. The mechanism of action and structure activity relationship are discussed. In vivo oral acute toxicity study (sighting study) was carried out which depicts that 2000 mg/kg dose of selected compounds is an appropriate and safe dose for conducting main study on animals.     

Bis(oxamato)palladate(II) complexes: synthesis,crystal structure and application to catalytic Suzuki reaction

New bis(oxamato)palladate(II) complexes, [Pd(H₂O)₄][Pd(2,6-Me₂pma)₂]·2H₂O (1), (n-Bu₄N)₂[Pd(2,6-Me₂pma)₂]·2H₂O (2a), and (n-Bu₄N)₂[Pd(2,6-Me₂pma)₂]·2CHCl₃ (2b) (2,6-Me₂pma = N-2,6-dimethylphenyoxamate and n-Bu₄N⁺ = tetra-n-butylammonium), have been synthesized and the structures of 1 and 2b characterized by single-crystal X-ray diffraction. Complex 1 is a double salt constituted by tetraaquapalladium(II) cations and bis(oxamato)palladate(II) anions interlinked by hydrogen bonds. The palladium(II) ions in 1 are four-coordinate with two oxygens and two nitrogens from two fully deprotonated oxamate ligands (anion), and four water molecules (cation) building centrosymmetric square-planar surroundings. Centrosymmetric bis(oxamato)palladate(II) anions occur in 2b as in 1, the charge balance in this compound being ensured by the bulky n-Bu₄N⁺. The catalytic role of 1 and 2a for the Suzuki reaction has been investigated by using a series of aryl iodide/bromide derivatives in the conventional organic medium dimethylformamide. The tetraaquapalladium(II) unit in 1 appears to be active in the catalytic Suzuki cross-coupling reactions, but it readily decomposes to inactive palladium black.     

A Novel Electron-Conformational Approach to Molecular Modeling for QSAR by Identification of Pharmacophore and Anti-Pharmacophore Shielding

Abstract

A novel method of pharmacophore identification and activity prediction in structure-activity (structure-property) relationships is worked out as an essential extension and improvement of previous publications. In this method each conformation of the molecular systems in the training set of the SAR problem is presented by both electronic structure and geometry parameters arranged in a matrix form. Multiple comparisons of these matrices for the active and inactive compounds allows one to separate a smaller number of matrix elements that are common for all the active compounds and are not present in the same arrangement in the inactive ones. This submatrix of activity represents the pharmacophore (Pha).

By introducing the Anti-Pharmacophore Shielding (APS) defined as molecular groups and competing charges outside the Pha that hinder the proper docking of the Pha with the bioreceptor, the procedure of Pha identification is essentially reduced to the treatment of a smaller number of simplest in structure most active and inactive compounds. A simple empirical scheme is suggested to estimate the APS numerically, while the contributions of different conformations of the same compound are taken into account by means of Boltzmann distribution. This enables us to make approximate quantitative predictions of activities.

In application to rice blast activity we reached an approximately 100% (within experimental error) prediction probability of the activity qualitatively (yes, no), and with r ² = 70% quantitatively.     

Synthesis,spectroscopic characterization,and antimicrobial activities of Ni(II) and Fe(II) complexes with N-(2-hydroxyethyl)-5-nitrosalicylaldimine

Metal complexes [Ni(HL1)₂H₂O] (1) and [Fe(HL1)₂] (2), where HL1 is the tridentate Schiff base N-(2-hydroxyethyl)-5-nitrosalicylaldimine, were synthesized and characterized by spectroscopic methods. The crystal structures of 1 and 2 have been determined by single crystal diffraction at 100?K. Complexes 1 and 2 have a distorted octahedral geometry. The ligand and metal complexes were screened for antibacterial and antifungal activities by the disk diffusion, microdilution broth, and single spore culture techniques. Antimicrobial activities of the ligand and its complexes have been tested against 10 bacteria, two yeast, and five filamentous fungi. The ligand and metal complexes were found to be active against all tested micro-organisms.     

The new ether derivative of phenylpropanoid and bioactivity was investigated from the leaves of Piper betle L.

Abstract

A new ether derivative of phenylpropanoid compound, γ-(γ′-isohydroxychavicol)-chavicol octanyl ether (K1) along with one known phenylpropanoid named allyl-pyrocatechol or hydroxychavicol (2) were isolated from Piper betle var. kali collected from Tumluk district, West Bengal India. We first report the presence of compound K1 in the genus Piper. Their structures were established on the basis of various spectroscopic analyses. Compounds K1 and 2 showed excellent antioxidant DPPH free radical scavenging activity with IC₅₀ values of 4.61 and 4.12?µg/mL compared to ascorbic acid as a standard antioxidant drug with IC₅₀ value of 3.42?µg/mL, respectively. Evaluation of in vitro cytotoxic activities of compounds K1 and 2 showed significant effects against human oral cancer cell lines (AW13516 and AW8507), human hepatoma cell lines (HEPG2 and PLC-PRF-5) and a human pancreatic cell line (MIA-PA-CA-2), compared to Doxorubicin^® as a standard cytotoxic drug with GI₅₀ values of <10 and 18.18?µg/mL.     

Quantitative comparison of selectivities in the polymerization of cyclic esters

Chain transfer processes (k_tr) taking place in the polymerization (anionic and pseudoanionic) of cyclic esters (lactones) are reviewed. These reactions are mostly responsible for the departure of these systems from the fully controlled (living) polymerizations. The ratios of k_p/k_tr have been determined for a number of initiating systems and the structures of the growing species are related to their selectivity, expressed by k_p/k_tr. It has been shown that the less reactive and more sterically crowded active species polymerize more selectively.     

Synthesis and Anticonvulsant Activity of 9-Alkoxy-6,7-dihydro-2H-benzo[c][1,2,4]triazolo[4,3-a]azepin-3[5H]-ones

A series of novel 9-alkoxy-6,7-dihydro-2H-benzo[c][1,2,4]triazolo[4,3-a]azepin-3(5H)-one derivatives was designed and synthesized starting from 2,3,4,5-tetrahydro-7-hydroxy-1H-2-benzazepin-1-one. The structures of these compounds were confirmed by mass, ¹H NMR infrared spectra, and elemental analysis. Their anticonvulsant activity was evaluated by maximal electroshock (MES) test, and their neurotoxic effects were determined by the rotarod neurotoxicity test. The results shown that 3k was the most active compound with median effective dose (ED₅₀) of 27.3 mg/kg, median toxicity dose (TD₅₀) of 118.3 mg/kg, and protective index (PI) of 4.3. Possible structure–activity relationship is discussed.     

Models for the active site in galactose oxidase: Structure, spectra and redox of copper(II) complexes of certain phenolate ligands

Galactose oxidase (GOase) is a fungal enzyme which is unusual among metalloenzymes in appearing to catalyse the two electron oxidation of primary alcohols to aldehydes and H₂O₂. The crystal structure of the enzyme reveals that the coordination geometry of mononuclear copper(II) ion is square pyramidal, with two histidine imidazoles, a tyrosinate, and either H₂O (pH 7.0) or acetate (from buffer,pH 4-5) in the equatorial sites and a tyrosinate ligand weakly bound in the axial position. This paper summarizes the results of our studies on the structure, spectral and redox properties of certain novel models for the active site of the inactive form of GOase. The monophenolato Cu(II) complexes of the type [Cu(L1)X][H(L1) = 2-(bis(pyrid-2-ylmethyl)aminomethyl)-4-nitrophenol and X⁻ = Cl⁻ 1, NCS⁻ 2, CH₃COO⁻ 3, ClO₄ ⁻ 4] reveal a distorted square pyramidal geometry around Cu(II) with an unusual axial coordination of phenolate moiety. The coordination geometry of 3 is reminiscent of the active site of GOase with an axial phenolate and equatorial CH₃COO⁻ ligands. All the present complexes exhibit several electronic and EPR spectral features which are also similar to the enzyme. Further, to establish the structural and spectroscopic consequences of the coordination of two tyrosinates in GOase enzyme, we studied the monomeric copper(II) complexes containing two phenolates and imidazole/pyridine donors as closer structural models for GOase. N,N-dimethylethylenediamine and N,N’-dimethylethylenediamine have been used as starting materials to obtain a variety of 2,4-disubstituted phenolate ligands. The X-ray crystal structures of the complexes [Cu(L5)(py)], (8) [H₂(L5) = N,N-dimethyl-N’,N’-bis(2-hydroxy-4-nitrobenzyl) ethylenediamine, py = pyridine] and [Cu(L8)(H₂O)] (11), [H₂(L8) = N,N’-dimethyl-N,N’-bis(2-hydroxy-4-nitrobenzyl)ethylenediamine] reveal distorted square pyramidal geometries around Cu(II) with the axial tertiary amine nitrogen and water coordination respectively. Interestingly, for the latter complex there are two different molecules present in the same unit cell containing the methyl groups of the ethylenediamine fragmentcis to each other in one molecule andtrans to each other in the other. The ligand field and EPR spectra of the model complexes reveal square-based geometries even in solution. The electrochemical and chemical means of generating novel radical species of the model complexes, analogous to the active form of the enzyme is presently under investigation.     

The geometry of the nitroguanyl fragment in the simplest nitroguanidine derivatives in the absence of intermolecular interactions: The gas electron diffraction data on 1,1,3,3-tetramethyl-2-nitroguanidine

The structures and force fields of the equilibrium forms of 2-nitroguanidine (1), 1,1,3,3-tetramethyl-2-nitroguanidine (2), and nitroguanyl azide (3) were determined in the MP2(full)/6-311G(3df, 2p) approximation; wagging-inversion motions of the N amine atoms were studied. The internal rotation potential function of the NO₂ group was calculated for 1. Similar functions for 1 and 2 were also obtained in the MP2(full)/6-311G(d, p) approximation. Direct one-dimensional problems for a nonrigid model were solved by the variational method, and the distribution of torsional levels was obtained. In the region of potential minimum, rotation in both molecules had the character of large-amplitude motions. For the first time, electron diffractions data were obtained at 100°C for molecule 2 without noticeable traces of substance decomposition. A structural r _e analysis was performed using the model of large-amplitude motions for characteristic NO₂ group torsional vibrations. Vibrational corrections to internuclear distances and mean amplitudes were calculated taking into account nonlinear kinematic effects using the force fields obtained in this work. The geometry of molecule 2 calculated in the MP2(full)/6-311G(3df, 2p) approximation well corresponds to the gas electron diffraction data. The parameters of molecule 2 in the crystalline phase, however, differ substantially from the parameters of the free molecule. This corresponds with the suggestion of the influence of intermolecular H-bonds involving the imine nitrogen atom and nitro groups oxygen atoms.     

Influence of F and CF3 Groups at the C=C Double Bond on the Structure and Properties of Protonated Forms of Olefin‐Series Compounds: an MP2 ab initio Study

The ab initio MP2 method using the 6–31G^* basis set with full geometry optimization was employed to calculate the protonated fluoroolefin molecules (F)_i(H)_jC=C(F)_k(H)_l (A) and (CF₃)_i(F)_jC=C(CF₃)_k×(F)_l (B), where i + j = k + l = 2. It is shown that a proton is attached to a carbon atom that is linked to fewer fluorine atoms as substituents. In series A, the proton affinity (PA:rpar; passes through a maximum as the number of fluorine atoms in the molecule increases. The highest PA is found for the 1,1difluoroethylene molecule (182.6 kcal/mole). In series B, the PA decreases monotonically, assuming an anomalously low value for the tetra(trifluoromethyl)ethylene molecule (114.7 kcal/mole). The obtained results are compared with Hartree–Fock calculations; the Hartree–Fock method is inadequate for predicting the structures of the carbocations examined.     

Synthesis of Novel 3-(5-(Alkyl/arylthio)-1,3,4-Oxadiazol-2-yl)-8-Phenylquinolin-4(1H)-One Derivatives as Anti-HIV Agents

Novel quinolone derivatives featuring an 1,3,4-oxadiazole ring as a metal-chelating component and a benzyl group base on HIV-1 integrase inhibitors pharmacophore were designed and synthesized. An antiviral assay revealed that most analogues inhibited HIV-1 replication in the cell culture. Our results showed that compounds bearing small alkyl groups as R group were inactive in anti-HIV-1 assay, whereas compounds possessing benzyl or substituted benzyl at the same position showed good anti-HIV activity with the range of 20–57% at 100 μM concentration. Among them, 3-(5-((2-fluorobenzyl)thio)-1,3,4-oxadiazol-2-yl)-8-phenylquinolin-4-(1H)-one (compound 13) showed reasonable cell-based antiviral activity (EC₅₀ = 50 μM) with no considerable cytotoxicity (CC₅₀ > 100 μM) in the cell viability assay, suggesting that it may be amenable to further development for identifying new anti-HIV-1 agents. Docking studies using the later crystallographic data available for PFV integrase corroborate favorable binding to the active site of HIV integrase, providing a basis for the design of more potent analogues.     

Synthesis,crystal structure and properties of two terbium complexes with 2,2′-bipyridine

Two new complexes {[Tb(2-IBA)₃ · 2,2′-bipy]₂ · C₂H₅OH} (1) and [Tb(2-ClBA)₃ · 2,2′-bipy]₂ (2) (2-IBA = 2-iodobenzoate; 2-ClBA = 2-chlorobenzoate; 2,2′-bipy = 2,2′-bipyridine) were prepared and their crystal structures determined by X-ray diffraction. Complex 1 is composed of two types of binuclear molecules, [Tb(2-IBA)₃ · 2,2′-bipy]₂ (a) and [Tb(2-IBA)₃ · 2,2′-bipy]₂ (b), and an uncoordinated ethanol molecule. In molecule (a), two Tb³⁺ ions are linked by four 2-IBA groups, all bidentate-bridging. In molecule (b), two Tb³⁺ ions are held together by four 2-IBA groups in two coordination modes, bidentate-bridging and chelating-bridging. In the two molecules, each Tb³⁺ ion is further bonded to one chelating 2-IBA group and one chelating 2,2′-bipy molecule, resulting in coordination numbers of eight for (a) and nine for (b). The structural characteristics of 2 are similar to that of molecule (b) in 1. The two complexes, 1 and 2, both emit strong green fluorescence under ultraviolet light with the ⁵D₄ → ⁷F _j (j = 6–3) emission of Tb³⁺ ion observed.     

Synthesis and crystal structure of two praseodymium 2-iodobenzoic acid complexes

Two new complexes, {[Pr(2-IBA)₃?·?2,2′-bipy]₂·[Pr(2-IBA)₃?·?2,2′-bipy]₂?·?0.5C₂H₅OH?·?H₂O} (1) and [Pr(2-IBA)₃?·?phen]₂ (2) (2-IBA?=?2-iodobenzoate; 2,2′-bipy?=?2,2′-bipyridine; phen?=?1,10-phenanthroline) were synthesized, and their crystal structures were determined by X-ray diffraction. Complex 1 consists of two binuclear molecules [Pr(2-IBA)₃?·?2,2′-bipy]₂ (a) and [Pr(2-IBA)₃?·?2,2′-bipy]₂ (b), half uncoordinated ethanol and one uncoordinated water. In the two molecules (a) and (b), the coordination environment of central ions is similar. The Pr1³⁺ ion in molecule (a) and Pr2³⁺ ion in molecule (b) are nine-coordinate with seven oxygen atoms from five 2-IBA ligands and two nitrogen atoms from one 2,2′-bipy molecule. The crystal structure of complex 2 is similar to that of binuclear [Pr(2-IBA)₃?·?2,2′-bipy]₂ in complex 1.     

Synthesis,Structure, and Properties of Nickel(II) and Cobalt(II) Coordination Compounds with Optically Active Diaminodioxime (H2L) Derived from 3-Carene. Molecular and Crystal Structures of the [Ni(H2L)(NO3)]NO3 and [Ni(HL)]ClO4 · H2O Complexes

Nickel(II) and cobalt(II) complexes with optically active diaminodioxime (H₂L, the derivative of 3-carene) of the compositions [Ni(H₂L)NO₃]NO₃ (I), Ni(H₂L)Cl₂ (II), [Ni(HL)]ClO₄ · H₂O (III), and Co(H₂L)Cl₂ (IV), were synthesized. According to X-ray diffraction data, the structures of the paramagnetic compound I and diamagnetic complex III are ionic. In the cation of I, the distorted NiN₄O₂ octahedron is formed by the N atoms of the tetradentate cyclic ligand (H₂L molecule) and by the O atoms of NO₃ ^–; anion functioning as bidentate cyclic ligands. In the cation of III, the NiN₄ coordination unit is a distorted square formed upon coordination of the tetradentate cyclic ligand, HL^–; anion. The data of magnetochemistry and UV-Vis, IR, and Raman spectroscopy suggest that paramagnetic complexes II and IV contain a distorted octahedral polyhedron MCl₂N₄ (M = Ni, Co).