新型查尔酮衍生物抗乳腺癌活性的3D-QSAR模型构建及分子设计

为了获得较高抗乳腺癌活性的新型化合物,对18个新型查尔酮衍生物抗乳腺癌活性(pIC_(50))进行了三维定量构效关系(3D-QSAR)研究。其中14个化合物作为训练集用于构建3D-QSAR模型,其余化合物(含模板分子)作为测试集对所建模型进行验证。所建3D-QSAR模型的交叉验证系数R^(2)_(CV)为0.569,非交叉验证系数R^(2)为0.974,说明所建模型具有良好的稳定性和预测能力。该模型中立体场、静电场对pIC_(50)的贡献分别为58.8%和41.2%,表明影响该类化合物抗肿瘤活性的主要因素是取代基的疏水性、空间位阻和电荷分布。通过对模型的分析,设计了5个具有较高pIC_(50)的新化合物,有待通过后续医学实验加以验证。

Molecular characteristics and structure–activity relationships of food-derived bioactive peptides

Peptides are functional active fragments of proteins which can provide nutrients needed for human growth and development,and they also have unique physiological activity characteristics relative to proteins.Bioactive peptides contain a great deal of development potential.More specifically,food-derived bioactive peptides have the advantages of a wide variety of sources,unique structures,high efficiency and safety,so they have broad development prospects.This review provides an overview of the current advances regarding the preparation,functional characteristics,and structure–activity relationships of food-derived bioactive peptides.Moreover,the prospects for the future development and application of food-derived bioactive peptides are discussed.This review may provide a better understanding of foodderived bioactive peptides,and some constructive inspirations for further research and applications in the food industry.

Determination of structure-activity relationships between fentanyl analogs and human μ-opioid receptors based on active binding site models

Fentanyl is a potent and widely used clinical narcotic analgesic, as well as a highly selective IJ-opioid agonist. The present study established a homologous model of the human μ-opioid receptor; an intercomparison of three types of μ-opioid receptor protein sequence homologous rates was made. The secondary receptor structure was predicted, the model reliability was assessed and verified using the Ramachandran plot and ProTab analysis. The predictive ability of the CoMFA model was further validated using an external test set. Using the Surflex-Dock program, a series of fentanyl analog molecules were docked to the receptor, the calculation results from Biopolymer/SitelD showed that the receptor had a deep binding area situated in the extracellular side of the transmembrane domains （TM） among TM3, TM5, TM6, and TMT. Results suggested that there might be 5 active areas in the receptor. The important residues were Asp147, Tyr148, and Tyr149 in TM3, Trp293, and His297 in TM6, and Trp318, His319, Ile322, and Tyr326 in TM7, which were located at the 5 active areas. The best fentanyl docking orientation position was the piperidine ring, which was nearly perpendicular to the membrane surface in the 7 TM domains. Molecular dynamic simulations were applied to evaluate potential relationships between ligand conformation and fentanyl substitution.

A Systematic Review of Uric Acid Transporter 1(URAT1) Inhibitors for the Treatment of Hyperuricemia and Gout and an Insight into the Structure-activity Relationship(SAR)

Gout is caused by the deposition of uric acid as monosodium urate（MSU）. Chronic hyperuricemia is the necessary condition for MSU deposition, which arises from over-production and/or under-excretion of uric acid. Renal under-excretion of uric acid accounts for greater than 90% of the patients with hyperuricemia, making URAT1 inhibitors, which act through uricosuric effect a promising class of urate-lowering therapy（ULT）. This review aims at the summary and discussion of the latest development of URAT1 inhibitors for the treatment of hyperuricemia and gout and providing an insight into their structure-activity relationship（SAR）, which will be helpful to the design of URAT1 inhibitors for both academic research and pharmaceutical industry. The current development pipeline of URAT1 inhibitors is promising and encouraging.

Application of PCA and HCA to the Structure-activity Relationship(SAR) Study of Fluoroquinolones

Density functional theory （DFT） was used to calculate a set of molecular descri ptors （properties） for 14 fluoroquinolones with anti-B.fragilis activity. Principal component analysis （PCA） and hierarchical cluster analysis （HCA） were employed in order to reduce dimensionality and investigate which subset of variables should be more effective for classifying fluoroquinolones according to their an-B.fragilis activity degree. The PCA shows that the variables of ELUMO, AEHL, μ, Q2, Q3, Q5, Q6, QB, LogP, MR and MP are responsible for the separation between compounds with higher and lower anti-B.fragilis activities. The HCA results are similar to those obtained with PCA. By using the chemometric results, 4 synthetic compounds were analyzed through PCA and HCA, and 2 of them are proposed as active molecules against B.fragilis, which is consistent with the results of clinic experiments. The methodologies of PCA and HCA provide a reliable rule for classifying new fluoroquinolones with anti-B.fragilis activity.

On quantitative structure-activity relationships between hydrazine derivatives and β irradiation

In this study, solutions of hydrazine and its derivatives were irradiated using a pulsed electron beam to determine the half-reaction time of radiolysis. 3 D structures of the hydrazine derivatives were optimized, and their energies were calculated using density functional theory with the B3 LYP method and 6-311 +(3 d, 3 p) basis set.For the first time, the 3 D quantitative structure-activity relationship(QSAR) equation describing the relationship between the hydrazine derivative structures and rate of radiolysis has been established using SPSS software.Pearson correlation analysis revealed a close correlation between the total energies of the molecules and half-reaction times. In the QSAR equation, Y =-7583.464 +54.687 X_1+94333.586 X_2,Y,X_1,and X_2 are the half-reaction time, total energy of the molecule, and orbital transition energy, respectively. The significance levels of the regression coefficients were 0.006 and 0.031, i.e., both less than 0.05. Thus, this model fully explains the relationship between hydrazine derivatives and β radiolysis stability.The results show that the total energy of the molecule and orbital transition energy are the main factors that influence the β radiolysis stability of these hydrazine derivatives.

向列相液晶分子结构与黏度关系研究及BPNN-QSAR模型建立

用于光学、微波通信调谐等器件的向列相液晶材料需要具备高响应速度来实现应用需求.液晶器件响应速度与液晶的旋转黏度、液晶的双折射率等因素相关.微波器件用向列相液晶,常采用大π-电子共轭体系、大极性基团来提高液晶分子的双折射率和介电各向异性,实现宽相位调制量,也因此增大了液晶材料黏度,影响了微波器件的响应速度.本文以液晶黏度因素为主线,对本课题组设计合成的42种向列相液晶在25℃时的黏度用旋转流变仪进行测试,从液晶化合物的结构角度分析影响液晶黏度的因素.首次建立向列相液晶分子结构与黏度的BPNN-QSAR定量构效模型,模型测试组预测值跟真实值之间的相关系数q^(2)=0.607>0.5,说明模型可用于液晶化合物的黏度性能预测,并对影响黏度性能的分子结构描述符进行了探讨.从实际应用出发结合本课题研究,设计了两个系列7个大双折射率液晶分子,BPNN模型测试黏度量度小于同类型分子,实验测试值与模型测试值相近.

Quantitative Structure-activity Relationship(QSAR) Study of Toxicity of Substituted Aromatic Compounds to Photobacterium Phosphoreum

With the artificial neural network（ANN） method combined with the multiple linear regression（MLR）,based on a series of quantum chemical descriptors and molecular connectivity indexes,quantitative structure-activity relationship（QSAR） models to predict the acute toxicity（-lgEC50） of substituted aromatic compounds to Photobacterium phosphoreum were established.Four molecular descriptors that appear in the MLR model,namely,the second order valence molecular connectivity index（2XV）,the energy of the highest occupied molecular orbital（EHOMO）,the logarithm of n-octyl alcohol/water partition coefficient（logKow） and the Connolly molecular area（MA）,were inputs of the ANN model.The root-mean-square error（RMSE） of the training and validation sets of the ANN model are 0.1359 and 0.2523,and the correlation coefficient（R） is 0.9810 and 0.8681,respectively.The leave-one-out（LOO） cross validated correlation coefficient（Q L2OO） of the MLR and ANN models is 0.6954 and 0.6708,respectively.The result showed that the two methods are complementary in the calculations.The regression method gave support to the neural network with physical explanation,and the neural network method gave a more accurate model for QSAR.In addition,some insights into the structural factors affecting the acute toxicity and toxicity mechanism of substituted aromatic compounds were discussed.

A Structure-activity Relationship (SAR) Study of Fluoroquinolones with Biological Activity against Anti-S.pneumoniae

Structure-activity relationship techniques were employed to classify fluoroquinolones against S.pneumoniae. Density functional theory （DFT） was used to calculate a set of molecular descriptors （properties） for eighteen fluoroquinolones. The descriptors were further analyzed using the principal component analysis （PCA）, hierarchical cluster analysis （HCA） and K-nearest neighbor （KNN） chemometeric method. The PCA and HCA methods are quite efficient to classify the eighteen compounds into two groups （active and inactive） according to their degrees of anti- S.pneumoniae activity. The classified result is consistent with the clinic experimental result. The PCA shows that the variables Q3 （net charge on atom 3）, QA （net charge on ring A）, QB （net charge on ring B）, VOL （molecular volume） and A （surface area） are found to be responsible for the separation between compounds with higher and lower anti-S.pneumoniae.

Structure-activity relationships regarding the antioxidant effects of the flavonoids on human erythrocytes

The effects of eleven flavonoids on lipid peroxidation, protein degradation, deformability and osmotic fragility of human erythrocytes exposed in vitro to 10 mM H2O2 for 60 min at 37 oC have been studied. The following flavonoids;quercetin, rutin and morin significantly protected eryt-hrocytes against lipid peroxidation caused by H2O2. This inhibition of lipid peroxidation could be explained by the presence of at least two hydroxyl groups in ring B of the flavonoid structure, regardless of their positions. However, the flavonoids;quercetin, 3,5,7-trihy- droxy-4'-methoxy flavone-7-rutinoside and 3- hydroxy flavone significantly protected eryt-hrocytes against protein degradation. This inhibition could also be explained by the presence of a hydroxyl group at C-3 in ring C of the flavonoid structure. Quercetin and 3,5,7-trihydroxy-4'- methoxy flvone-7-rutinoside significantly protected erythrocytes against loss of deformability and increased osmotic fragility, indicating that the loss of erythrocyte deformability and the increase in osmotic fragility of erythrocytes exposed to H2O2 are related to protein degradation rather than to lipid peroxidation. The other flavonoids (chrysin, 2-carboxy ethyl dihydroxy flavone, apigenin, cirsimaritin, α-naphto flavone and flavanone) failed to protect erythrocytes against the observed oxidative damages. The results demonstrate the importance of the chemical groups substituted on the basic skeleton of the flavonoids in dictating the type of antioxidant activity, and also demonstrate the hemorheological potentials of flavonoids that have particular protein-antioxidant activities.

Some substrates of P-glycoprotein targeting <i>β</i>-amyloid clearance by quantitative structure-activity relationship (QSAR)/membrane-interaction (MI)-QSAR analysis

The pathogenesis of Alzheimer’s disease (AD) putatively involves a compromised blood-brain barrier (BBB). In particular, the importance of brain-to-blood transport of brain-derived metabolites across the BBB has gained increasing attention as a potential mechanism in the pathogenesis of neurodegenerative disorders such as AD, which is characterized by the aberrant polymerization and accumulation of specific misfolded proteins, particularly β-amyloid (Aβ), a neuropathological hallmark of AD. P-glycoprotein (P-gp), a major component of the BBB, plays a role in the etiology of AD through Aβ clearance from the brain. Our QSAR models on a series of purine-type and propafenone-type substrates of P-gp showed that the interaction between P-gp and its modulators depended on Molar Refractivity, LogP, and Shape Attribute of drugs it transports. Meanwhile, another model on BBB partitioning of some compounds revealed that BBB partitioning relied upon the polar surface area, LogP, Balaban Index, the strength of a molecule combined with the membrane-water complex, and the changeability of the structure of a solute-membrane-water complex. The predictive model on BBB partitioning contributes to the discovery of some molecules through BBB as potential AD therapeutic drugs. Moreover, the interaction model of P-gp and modulators for treatment of multidrug resistance (MDR) indicates the discovery of some molecules to increase Aβ clearance from the brain and reduce Aβ brain accumulation by regulating BBB P-gp in the early stages of AD. The mechanism provides a new insight into the therapeutic strategy for AD.

Application of PCA and HCA to the Structure-Activity Relationship Study of Fluoroquinolones

用密度泛函理论计算了12种具有抗肺炎链球菌的氟诺喹酮类药物分子的分子特性.利用主成分分析和分层聚类分析方法来简化氟诺喹酮类药物数据库的维数.主成分分析法表明,变量 E_(LUMO)、 Q_3、Q_5、Q_A、lgP、MR、VOL、ΔE_(HL)能够有效地对抗肺炎链球菌的氟诺喹酮类药物进行分类.分层聚类方法的结果和主成分分析方法的结果一致.这表明两种方法都能够对新的具有抗肺炎链球菌的氟诺喹酮类药物的分类提供一个可信的规律.利用主成分分析法和分层聚类分析法对其他6个氟诺喹酮类药物分子进行分析,结果都表明有两个药物分子具有较强的抗肺炎链球菌活性.此结果和临床结果相吻合.

Chalcone derivatives as novel,potent and selective inhibitors against human Notum:Structure–activity relationships and biological evaluations

Human Notum(hNotum)inhibitors could be used for treating Wnt signalling-associated diseases including colorectal cancer.Herein,two series of chalcone derivatives were designed and synthesized aiming to find selective and potent hNotum inhibitors.Structure–activity relationship(SAR)studies showed that 2-methoxyl and 5-bromine substitutions on A-ring significantly enhanced anti-hNotum effect,while 4’-ethoxyl and 3’-alkyl substitutions on B-ring were beneficial for hNotum inhibition.Among all tested chalcones,B11 displayed the most potent anti-Notum effect(IC_(50)=3.6 nmol/L),good selectivity,excellent chemical stability and suitable metabolic stability.Further investigations showed that B11 acted as a competitive inhibitor of hNotum,while this agent(5μmol/L)significantly weaken the migration abilities of colorectal cancer cells.Collectively,this study deciphers the SARs of chalcones as hNotum inhibitors and reports a novel and potent hNotum inhibitor with the anti-migration effect on colorectal cancer cells,which offers a promising lead compound to develop novel anti-cancer agents.

Quinoline-based anti-MRSA agents: Current development, structure-activity relationships, and mechanisms

Methicillin-resistant Staphylococcus aureus (MRSA), the most common pathogen in hospital and community environments, can cause serious and even fatal infections. The antibiotics currently used for clinical treatment of MRSA have developed resistance, and there is an urgent need to develop new antimicrobials to treat infections caused by MRSA strains. Quinoline analogues play an important role in the development of antimicrobials. Herein, we discussed the current development of antibacterial activities of quinoline analogues, mainly for anti-MRSA activity, and their structure-activity relationships (SARs) from the perspective of using the quinoline nucleus to search for novel potential anti-MRSA candidates. Additionally, the mechanisms of some representative quinoline analogues against MRSA were clarified. Altogether, this review could provide further insights for the rational development of quinoline-based antibacterial drugs, especially against MRSA.

Structure and Anti-HIV Activity of Betulinic Acid Analogues

Firstly discovered in 1980s, human immunodeficiency virus （HIV） continues to affect more and more people. However, there is no effective drug available for the therapy of HIV infection. Betulinic acid existing in various medicinal herbs and fruits exhibits multiple biological effects, especially its outstanding anti-HIV activity, which has drawn the attentions of many pharmacists. Among the derivatives of betulinic acid, some compounds exhibited inhibitory activities at the nanomolar concentration, and have entered phase II clinical trials. This paper summarizes the current investigations on the anti-HIV activity of betulinic acid analogues, and provides valuable data for subsequent researches.

Quantitative structure-activity relationship study on the biodegradation of acid dyestuffs

Quantitative structure-biodegradability relationships （QSBRs） were established to develop predictive models and mechanistic explanations for acid dyestuffs as well as biological activities. With a total of four descriptors, molecular weight （MW）, energies of the highest occupied molecular orbital （EHOMO）, the lowest unoccupied molecular orbital （ELUMO）, and the excited state （EES）, calculated using quantum chemical semi-empirical methodology, a series of models were analyzed between the dye biodegradability and each descriptor. Results showed that EHOMO and Mw were the dominant parameters controlling the biodegradability of acid dyes. A statistically robust QSBR model was developed for all studied dyes, with the combined application of EHOMO and Mw. The calculated biodegradations fitted well with the experimental data monitored in a facultative-aerobic process, indicative of the reliable prediction and mechanistic character of the developed model.

Quantitative Structure-activity Relationship Study on the Antioxidant Activity of Carotenoids

Carotenoids are a family of effective active oxygen scavengers, which can reduce the danger of occurrence of chronic diseases such as cardiovascular disease, cataract, cancer, and so on. The quantitative structure-activity relationship （QSAR） equation between carotenoids and antioxidant activity was established by quantum chemistry AM1, molecular mechanism （MM＋） and stepwise regression analysis methods, and the model was evaluated by leave-one-out approach. The results showed that the significant molecular descriptors related to the antioxidant activity of carotenoids were the energy difference （E_HL） between the lowest unoccupied molecular orbital （LUMO） and the highest occupied molecular orbital （HOMO） and ionization energy （Eiso）. The model showed a good predictive ability （Q^2 〉 0.5）.

QSAR Studies on the Inhibitory Activityof Levofloxacin-thiadiazole HDACi Conjugates to Histone Deacetylases

A molecular electronegativity distance vector(M)based on 13 atomic types has been used to describe the structures of 19 conjugates(LHCc)of levofloxacin-thiadiazole HDAC inhibitor(HDACi)and related inhibitory activities(pH,i=1,2,6)of LHCc against histone deacetylases(HDACs,such as HDAC1,HDAC2 and HDAC6).The quantitative structure-activity relationships(QSAR)were established by using leaps-and-bounds regression analysis for the inhibitory activities(pH)of 19 above compounds to HDAC1,HDAC2 and HDAC6 along with M.The correlation coefficients(R~2)and the leave-one-out(LOO)cross validation Rfor the pH,pHand pHmodels were 0.976 and 0.949;0.985 and 0.977;0.976 and 0.932,respectively.The QSAR models had favorable correlations,as well as robustness and good prediction capability by R~2,F,R~2,A,Fand Vtests.Validated by using 3876 training sets,the models have good external prediction ability.The results indicate that the molecular structural units:–CH–(g=1,2),–NH,–OH,=O,–O–and–S–are the main factors which can affect the inhibitory activity of pH,pHas well as pHbioactivities of these compounds directly.Accordingly,the main interactions between HDACs inhibitor and HDACs are hydrophobic interaction,hydrogen bond,and coordination with Znto form compounds,which is consistent with the results in reports.

基于极限梯度提升算法和特征筛选方法的羊角月牙藻(Selenastrum capricornutum)急性毒性定量构效关系(QSAR)模型的建立与应用

藻类是水生食物网中主要的初级生产者,对水生生态系统的可持续性起着重要作用。随着社会发展、工业进步和人类活动,大量化学品被释放到水生环境中,对藻类产生了极大的威胁。若藻类受到危害势必会影响其他水生生物,因此有必要开展藻类的毒性评估。藻类的毒性评估需要大量的毒性数据,通过实验的方法获得水生毒性数据成本较高且比较耗时,定量构效关系(QSAR)是解决这类问题的一种良好的替代方法。本研究基于Web of Science与中国知网数据库文献中的53条急性毒性数据,利用极限梯度提升(XGB)算法和特征筛选方法建立了羊角月牙藻(Selenastrum capricornutum)急性毒性的QSAR模型。最优模型的训练集决定系数(R^(2)_(TR))达到了0.97,验证集决定系数(Q^(2)_(EXT))达到了0.78,留一法交叉验证系数(Q^(2)_(LOO))也达到了0.51,表明建立的QSAR模型具有较好的拟合优度、稳健性和预测能力。机理解释结果表明,化合物的拓扑电荷数、总原子序数和电负性是影响羊角月牙藻急性毒性的关键因素。在此基础上,采用建立的QSAR模型和EPI Suite分别预测了16种典型多环芳烃(PAHs)对藻类的急性毒性,并对其进行了毒性分级。研究结果为藻类的急性毒性数据的获取提供了一个高效预测工具,有利于加快化学品的水环境风险评估工作。

New Descriptors of Amino Acids and Its Applications to Peptide Quantitative Structure-activity Relationship

A new set of descriptors, HSEHPCSV （component score vector of hydrophobic, steric, and electronic properties together with hydrogen bonding contributions）, were derived from principal component analyses of 95 physicochemical variables of 20 natural amino acids separately according to different kinds of properties described, namely, hydrophobic, steric, and electronic properties as well as hydrogen bonding contributions. HSEHPCSV scales were then employed to express structures of angiotensin-converting enzyme inhibitors, bitter tasting thresholds and bactericidal 18 peptide, and to construct QSAR models based on partial least square （PLS）. The results obtained are as follows： the multiple correlation coefficient （R2cum） of 0.846, 0.917 and 0.993, leave-one-out cross validated Q2cm of 0.835, 0.865 and 0.899, and root-mean-square error for estimated error （RMSEE） of 0.396, 0.187and 0.22, respectively. Satisfactory results showed that, as new amino acid scales, data of HSEHPCSV may be a useful structural expression methodology＇for the studies on peptide QSAR （quantitative structure-activity relationship） due to many advantages such as plentiful structural information, definite physical and chemical meaning and easy interpretation.