QSAR studies on piperazinylalkylisoxazole analogues selectively acting on dopamine D3 receptor by HQSAR and CoMFA

QSAR studies for piperazinylalkylisoxazole analogues were conducted by hologram QSAR (HQSAR) and comparative molecular field analysis (CoMFA) to explain the binding affinities of 264 ligands acting on dopamine D(3) receptor. The HQSAR was assessed by r(2) value of 0.917 and cross validated q(2) value of 0.841. In the CoMFA, r(2) is 0.919 and cross validated q(2) is 0.727. The results provide the tools for predicting the affinity of related compounds and guiding the design of new ligands.     

Predicting anti-HIV activity of PETT derivatives: CoMFA approach

HIV-1 (Human Immunodeficiency Virus Type-1) is the pathogenic retrovirus and causative agent of AIDS. HIV-1 RT is one of the key enzymes in the duplication of HIV-1. Inhibitors of HIV-1 RT are classified as NNRTIs and NRTIs. NNRTIs bind in a region not associated with the active site of the enzyme. Within the NNRTIs category, there is a set of inhibitors commonly referred to as phenyl ethyl thiazolyl thiourea (PETT) derivatives. The present 3D QSAR study attempts to explore the structural requirements of phenyl ethyl thiazolyl thiourea (PETT) derivatives for anti-HIV activity. Based on the structures and biodata of previous PETT analogs, 3D-QSAR (CoMFA) study has been performed with a training set consisting of 60 molecules, which resulted in a reliable computational model with q(2)=0.657, S(PRESS)=0.957, r(2)=0.938, and standard error of estimation (SEE)=0.270 with the number of partial least square (PLS) components being 5. It is shown that the steric and electrostatic properties predicted by CoMFA contours can be related to the anti-HIV activity. The predictive ability of the resultant model was evaluated using a test set comprised of 11 molecules and the predicted r(2)=0.893. This model is a more significant guide to trace the features that really matter especially with respect to the design of novel compounds.     

3D—HoVAIF模型用于八角茴香油成分色谱保留时间研究

本文采用GC/MS测定了八角茴香油中各组分,应用本实验室新近提出的三维原子场全息作用矢量(3D-HoVAIF)对鉴定的48个挥发性有机物的结构进行了表征,并分别采用了偏最小二乘回归(PLS)与多元线性回归(MLR)进行了建模研究.结果表明,3D-HoVAIF能够较好地表征茴香油中各组分的化学结构,所建模型具有良好的估计能力与稳定性.     

Comparative molecular field analysis and comparative molecular similarity indices analysis of human thymidine kinase 1 substrates

Thymidine kinase 1 (TK1) is a key target for antiviral and anticancer chemotherapy. Three-dimensional quantitative structure-activity relationship (3D-QSAR) using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) techniques was applied to analyze the phosphorylation capacity of a series of 31 TK1 substrates. The optimal predictive CoMFA model with 26 molecules provided the following values: cross-validated r(2) (q(2))=0.651, non-cross-validated r(2)=0.980, standard error of estimate (s)=0.207, F=129.3. For the optimal CoMSIA model the following values were found: q(2)=0.619, r(2)=0.994, s=0.104, F=372.2. The CoMSIA model includes steric, electrostatic, and hydrogen bond donor fields. The predictive capacity of both models was successfully validated by calculating known phosphorylation rates of five TK1 substrates that were not included in the training set. Contour maps obtained from CoMFA and CoMSIA models correlated with the experimentally developed SAR.     

Isolation and characterization of an angiotensin converting enzyme substrate from vitellogenic ovaries of Neobellieria bullata

Vitellogenic ovaries of the gray fleshfly Neobellieria bullata contain a variety of unidentified substances that interact, either as a substrate or as an inhibitor, with angiotensin converting enzyme (ACE). We here report the isolation and characterization of the first ACE interactive compound hereof. This 1312.7 Da peptide with the sequence NKLKPSQWISL, is substrate to both insect and human ACE. It is a novel peptide that shows high sequence similarity to a sequence at the N-terminal part of dipteran yolk polypeptides (YPs). We propose to call it N. bullata ovary-derived ACE interactive factor or Neb-ODAIF. Both insect and human ACE hydrolyze Neb-ODAIF by sequentially cleaving off two C-terminal dipeptides. K(m) values of Neb-ODAIF and Neb-ODAIF(1-9) (NKLKPSQWI) for human somatic ACE (sACE) are 17 and 81 microM, respectively. Additionally, Neb-ODAIF(1-7) (NKLKPSQ) also interacts with sACE (K(m/i)=90 microM). These affinity-constants are in range with those of the physiological ACE substrates and suggest the importance of Neb-ODAIF and its cleavage products in the elucidation of the physiological role of insect ACE. Alternatively, they can serve as lead compounds in the development of new drugs against ACE-related diseases in humans.     

New approach to isolate mesenchymal stem cell (MSC) from human umbilical cord blood

HUCB (human umbilical cord blood) has been frequently used in clinical allogeneic HSC (haemopoietic stem cell) transplant. However, HUCB is poorly recognized as a rich source of MSC (mesenchymal stem cell). The aim of this study has been to establish a new method for isolating large number of MSC from HUCB to recognize it as a good source of MSC. HUCB samples were collected from women following their elective caesarean section. The new method (Clot Spot method) was carried out by explanting HUCB samples in mesencult complete medium and maintained in 37°C, in a 5% CO2 and air incubator. MSC presence was established by quantitative and qualitative immunophenotyping of cells and using FITC attached to MSC phenotypic markers (CD29, CD73, CD44 and CD105). Haematopoietic antibodies (CD34 and CD45) were used as negative control. MSC differentiation was examined in neurogenic and adipogenic media. Immunocytochemistry was carried out for the embryonic markers: SOX2 (sex determining region Y-box 2), OLIG-4 (oligodendrocyte-4) and FABP-4 (fatty acid binding protein-4). The new method was compared with the conventional Rosset Sep method. MSC cultures using the Clot Spot method showed 3-fold increase in proliferation rate compared with conventional method. Also, the cells showed high expression of MSC markers CD29, CD73, CD44 and CD105, but lacked the expression of specific HSC markers (CD34 and CD45). The isolated MSC showed some differentiation by expressing the neurogenic (SOX2 and Olig4) and adipogenic (FABP-4) markers respectively. In conclusion, HUCB is a good source of MSC using this new technique.     

3D-QSAR analysis of sialyltransferase inhibitors

A predictive 3D-QSAR model that correlates the biological activities with the chemical structures of a series of sialyltransferase inhibitors, exemplified by the sugar:nucleotide derivatives, was developed by means of comparative molecular field analysis (CoMFA). The resulting cross-validated value (q(2)=0.629), non-cross-validated value (r(2)=0.965) and standard error of estimate (SEE=0.288) indicate that the obtained pharmacophore model indeed mimics the steric and electrostatic environment where inhibitors bind to the enzyme. The developed model also possesses promising predictive ability as discerned by the testing on the external test set, and should be useful to further understand the molecular nature of inhibitor-enzyme interactions and to aid in the design of more potent sialyltransferase inhibitors.     

Genetic and alkaloid analysis of Menispermum dauricum DC. by RAPD and HPLC

The aim of the present work was to determine whether dauricine could be used as a taxonomic marker for Menispermum dauricum DC., and to explore the correlation among RAPD, ecological markers and chemical markers. To this end, the chemical and genetic differences of 173 individual samples of M. dauricum from nine different sources were studied based on the relevant ecological factors including longitude, latitude, annual precipitation, mean temperature, annual accumulated temperature and mean sea level. The contents of dauricine in the sample rhizomes were assayed by HPLC with photodiode array detection. The leaves from the same sample were assayed using randomly amplified polymorphism DNA (RAPD). The genetic distances were then compared. Hierarchical cluster analysis and multiple linear stepwise regression analysis were used in the statistical analysis. The results indicated that the contents of dauricine were respectively correlated with the genetic distance (r = 1.000), longitude (r = 0.849), latitude (r = 0.861), annual precipitation (r = 0.903), mean temperature(r = 0.912), annual accumulated temperature (r = 0.919) and mean sea level (r = 0.925). It is concluded that the content of dauricine in M. dauricum is significantly correlated with genetic distance and ecological factors, and may be used as the taxonomic marker.     

CoMFA and CoMSIA 3D-QSAR analysis of diaryloxy-methano-phenanthrene derivatives as anti-tubercular agents

Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) based on three-dimensional quantitative structure-activity relationship (3D-QSAR) studies were conducted on a series (44 compounds) of diaryloxy-methano-phenanthrene derivatives as potent antitubercular agents. The best predictions were obtained with a CoMFA standard model (q (2)=0.625, r (2)=0.994) and with CoMSIA combined steric, electrostatic, and hydrophobic fields (q (2)=0.486, r (2)=0.986). Both models were validated by a test set of seven compounds and gave satisfactory predictive r (2) values of 0.999 and 0.745, respectively. CoMFA and CoMSIA contour maps were used to analyze the structural features of the ligands to account for the activity in terms of positively contributing physicochemical properties: steric, electrostatic, and hydrophobic fields. The information obtained from CoMFA and CoMSIA 3-D contour maps can be used for further design of phenanthrene-based analogs as anti-TB agents. 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. Further analysis of these interaction-field contour maps also showed a high level of internal consistency. This study suggests that introduction of bulky and highly electronegative groups on the basic amino side chain along with decreasing steric bulk and electronegativity on the phenanthrene ring might be suitable for designing better antitubercular agents.     

3D QSAR studies on T-type calcium channel blockers using CoMFA and CoMSIA

Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were performed on a series of isoxazolyl compounds as a potent T-type calcium channel blockers. A set of 24 structurally similar compounds served to establish the model. Four different conformations of the most active compound were used as template structures for the alignment, three of which were obtained from Catalyst pharmacophore modeling and one by using SYBYL random search option. All CoMFA and CoMSIA models gave cross-validated r(2) (q(2)) value of more than 0.5 and conventional r(2) value of more than 0.85. The predictive ability of the models was validated by an external test set of 10 compounds, which gave satisfactory pred r(2) values ranging from 0.577 to 0.866 for all models. Best predictions were obtained with CoMFA std model of Conformer no: 3 alignment (q(2)=0.756, r(2)=0.963), giving predictive r(2) value of 0.866 for the test set. CoMFA and CoMSIA contour maps were used to analyze the structural features of the ligands accounting for the activity in terms of positively contributing physicochemical properties: steric, electrostatic, hydrophobic and hydrogen bonding fields.     

Non-nucleoside HIV-1 reverse-transcriptase inhibitors. Part 10. Synthesis and anti-HIV activity of 5-alkyl-6-(1-naphthylmethyl)pyrimidin-4(3H)-ones with a mono- or disubstituted 2-amino function as novel 'dihydro-alkoxy-benzyl-oxopyrimidine' (DABO) analogues

A series of structurally related 2,5-disubstituted 6-(1-naphthylmethyl)-pyrimidin-4(3H)-ones, compounds 6a-6r, were synthesized and evaluated for their in vitro anti-HIV activities in MT-4 cells. Most of the new compounds investigated showed moderate-to-good activities against wild-type HIV-1, with IC(50) values in the range 5.64-0.21 microM. Compound 6d was the most potent congener (IC(50)=0.21 microM, SI=724) in inhibiting HIV-1 replication, which is ca. 25 times more effective than the reference compound 2',3'-dideoxyinosine (DDI). Preliminary structure-activity relationship (SAR) studies revealed that both modulation of the amino function at C(2) and of the alkyl group at C(5) of the pyrimidine ring are crucial for high anti-HIV-1 activity.     

Inhibitor analysis of angiotensin I-converting and kinin-degrading activities of bovine lung and testicular angiotensin-converting enzyme.

Inhibition of bovine lung and testicular angiotensin-converting enzyme (ACE) by some well-known ACE inhibitors (lisinopril, captopril, enalapril), new substances (Nalpha-carboxyalkyl dipeptides PP-09, PP-35, and PP-36), and phosphoramidon was investigated using Cbz-Phe-His-Leu and FA-Phe-Phe-Arg (C-terminal analogs of angiotensin I and bradykinin, respectively) as the substrates. The somatic (two domains) and testicular (single domain) isoenzymes demonstrated different kinetic parameters for hydrolysis of these substrates. All of the inhibitors were competitive inhibitors of both ACE isoforms, and the Ki values were substrate-independent. The relative potencies of the inhibitors for both enzymes were: lisinopril > captopril > PP-09 > enalapril > PP-36 > PP-35 > phosphoramidon. The inhibition efficiency of PP-09 was comparable with those of the well-known ACE inhibitors. Captopril was more effectively bound to the somatic ACE (Ki = 0.5 nM) than to the testicular isoform (Ki = 6.5 nM).     

3-D-QSAR CoMFA and CoMSIA studies on tetrahydrofuroyl-L-phenylalanine derivatives as VLA-4 antagonists

Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were performed on tetrahydrofuroyl-L-phenylalanine derivatives as VLA-4 antagonists. The best CoMFA and CoMSIA models that were generated using atom based alignment from a training set of twenty five tetrahydrofuroyl-L-phenylalanine derivatives, are six-component models with good statistics; CoMFA: r(2)(cv)=0.366, r(2)=0.983, s=0.099, F=172.661 and PRESS=4.435; CoMSIA: r(2)(cv)=0.528, r(2)=0.995, s=0.054, F=577.87 and PRESS=3.563. Both of these 3-D-QSAR models were validated using a test set of eleven compounds, whose predicted pIC(50) values fall within one log unit of the actual pIC(50). The contour diagrams obtained for the various CoMFA and CoMSIA field contributions can be mapped back onto structural features to explain the activity trends of the molecules analysed. Based on the spatial arrangement of the various field contributions, novel molecules with improved activity can be designed.     

3D-QSAR Study on dihydro-1,3,5-triazines and their spiro derivatives as DHFR inhibitors by comparative molecular field analysis (CoMFA)

A 3D-QSAR/CoMFA was performed for a series of triazine and its spiro derivative based DHFR inhibitors displaying IC(50) values ranging from 0.002 to 58.8 μM. Analyses resulted in a reliable computational model with the parameters of n=46, r(2)=0.986, q(2)=0.724, SE=0.164, F=275.889. It is shown that the steric and electrostatic properties predicted by CoMFA contours can be related to the DHFR inhibitory activity. The predictive ability of the resultant model was evaluated using a test set comprised of 18 molecules and the results show that the CoMFA model is able to correctly predict the poor inhibitory activities of the compounds in the testing set. This model is a significant guide to trace the features that really matter especially with respect to the design of novel compounds.     

Dye-induced aggregation of single stranded RNA: a mechanistic approach

The binding of proflavine (D) to single stranded poly(A) (P) was investigated at pH 7.0 and 25 degrees C using T-jump, stopped-flow and spectrophotometric methods. Equilibrium measurements show that an external complex PD(I) and an internal complex PD(II) form upon reaction between P and D and that their concentrations depend on the polymer/dye concentration ratio (C(P)/C(D)). For C(P)/C(D)<2.5, cooperative formation of stacks external to polymer strands prevails (PD(I)). Equilibria and T-jump experiments, performed at I=0.1M and analyzed according to the Schwarz theory for cooperative binding, provide the values of site size (g=1), equilibrium constant for the nucleation step (K( *)=(1.4+/-0.6)x10(3)M(-1)), equilibrium constant for the growth step (K=(1.2+/-0.6)x10(5)M(-1)), cooperativity parameter (q=85) and rate constants for the growth step (k(r)=1.2x10(7)M(-1)s(-1), k(d)=1.1 x 10(2)s(-1)). Stopped-flow experiments, performed at low ionic strength (I=0.01 M), indicate that aggregation of stacked poly(A) strands do occur provided that C(P)/C(D)<2.5.     

3D-QSAR design of novel antiepileptic sulfamides

A three-dimensional quantitative structure-activity relationship method, the comparative molecular field analysis (CoMFA), was applied to design new anticonvulsant symmetric sulfamides. The training set (27 structures) was comprised by traditional and new-generation anticonvulsant (AC) ligands that exhibit a potent activity in MES test. Physicochemical determinants of binding, such as steric and electrostatic properties, were mapped onto the molecular structures of the set, in order to interpret graphically the CoMFA results in terms of field contribution maps. The 3D-QSAR models demonstrate a good ability to predict the activity of the designed compounds (r(2)=0.967, q(2)=0.756).     

近红外光谱测定灵芝子实体多糖含量

灵芝具有多种药理活性,多糖是其主要活性成分之一.目前灵芝多糖的定量常采用的比色法,使用比较繁琐,也缺乏一定的安全环保性.应用近红外光谱对灵芝进行多糖定量分析,发现对子实体直接分析存在定量不准的问题.为了快速准确地评估灵芝子实体多糖含量,本研究采用对灵芝子实体水提物进行近红外光谱检测与分析,由此建立了较好的定量模型.该模...