Molecular modelling of the differential interaction between several non-steroidal anti-inflammatory drugs and human prostaglandin endoperoxide H synthase-2 (h-PGHS-2)

The prostaglandin endoperoxide H synthase-1 (PGHS-1) and prostaglandin endoperoxide H synthase-2 (PGHS-2) are the targets of non-steroidal anti-inflammatory drugs (NSAIDs). The high degree of selectivity for inhibition of PGHS-2 shown by certain compounds appears to stem from two mechanisms (time-dependent, time-independent inhibition) by which they interact with each isoform. Molecular models of the complexes between indomethacin, fenamates, 2-phenylpropionic acids and the selective cyclooxygenase-2 (COX-2) inhibitors, with the cyclooxygenase active site of human PGHS-2 have been built by combining homology modelling, conformational searching and automated docking techniques. The stability of the resulting complexes has been assessed by molecular dynamics simulations combined with extended linear response calculations. The results allow us to identify regions of biological significance consistent with both X-ray crystallographic and kinetic results. The selective PGHS-2 inhibitors exploit the extra space of a side-pocket in the active site of PGHS-2 that is not found in PGHS-1. The results obtained point out a marked relationship between the experimental affinity and the electrostatic interaction energy alone for a series of NSAIDs. Analysis of the structural and the energetic data provides evidence supporting that network of hydrogen bonds between Tyr355, Glu524, Arg120 and Arg513 might be involved in mediating the binding of the time-dependent inhibitors of PGHS-2.     

Towards understanding the mechanism of action of the multidrug resistance-linked half-ABC transporter ABCG2: a molecular modeling study

The ATP-binding cassette protein ABCG2 is a member of a broad family of ABC transporters with potential clinical importance as a mediator of multidrug resistance. We carried out a homology and knowledge-based, and mutationally improved molecular modeling study to establish a much needed structural framework for the protein, which could serve as guidance for further genetic, biochemical, and structural analyses. Based on homology with known structures of both full-length and nucleotide-binding domains (NBD) of ABC transporters and structural knowledge of integral membrane proteins, an initial model of ABCG2 was established. Subsequent refinement to conform to the lipophilic index distributions in the transmembrane domain (TMD) and to the results of site-directed mutagenesis experiments led to an improved model. The complete ABCG2 model consists of two identical subunits facing each other in a closed conformation. The dimeric interface in the nucleotide-binding domain (NBD) involves a characteristic nucleotide sandwich and the interface in the TMD consists of the TM helices 1–3 of one subunit and the helices 5 and 6 of the other. The interface between the NBD and the TMD is bridged by the conserved structural motif between TM2 and TM3, the intracellular domain 1 (ICD1), and the terminal β-strand (S6) of the central β-sheet in the NBD. The apparent flexibility of the ICD1 may play a role in transmitting conformational changes from the NBD to the TMD or from the TMD to the NBD.     

线型聚(N-杂环化)硅烷体系的电子结构与光谱性质的比较研究

用密度泛函理论(DFT)和含时密度泛函理论(TD-DFT)对线型(N-杂环化)硅烷低聚体系与简单聚硅烷的电子结构和吸收光谱性质进行了比较研究。对各体系的基态分子结构在B3LYP/6-31G**水平上进行了全优化,讨论了电荷分布和前线分子轨道性质。在获得基态稳定构型的基础上,应用含时密度泛函理论计算了电子吸收光谱的性质。计算结果显示,当主链硅原子被氮杂环环化后,由于空间位阻作用使相邻硅硅键明显伸长,使主链结构变得松散。但同时改善了分子主链的电子离域范围,增强了分子结构的可塑性。随着氮杂环数目的增加,低聚硅烷的电子吸收光谱发生明显的红移。氮杂环的引入对聚硅烷的最大吸收光谱带影响非常大。     

卟吩结构的HARTREE-FORCK和密度泛函研究比较

采用传统的Hartree-Fock(HF)从头算和密度泛函中的B3LYP和B3PW91方法,选择了不同基组水平(STO-3G,3-21G和6-31G~*)对卟吩结构进行了全几何优化,并对得到的结果相互进行了比较,同时与实验数据进行了对照。结果表明,对于H_2P以及具有类似结构的卟啉衍生物,传统的HF方法得到的几何构型以及相关性质(核磁共振谱,NMR)并不可靠。这种体系中电子相关能是不可忽略的。在B3LYP水平上选用较小的基组3-21G得到的结果与中等基组6-31G~*差别不大,但是最小基组STO-3G得到的优化构型却是一个鞍点结构。     

Chk2抑制剂2-芳香基苯并咪唑类化合物活性的CoMFA研究

利用比较分子力场分析(CoMFA)法,研究训练集中的37个Chk2抑制剂2-芳香基苯并咪唑类化合物的生物活性,考察了互变异构对抑制剂活性的影响,建立了主成分为4的三维定量结构-活性关系模型.模型的交叉和非交叉验证回归系数(q2、r2)分别为0.660和0.908,是稳定性较高和预测能力较好的模型,立体场对活性的影响比静电场大.模型可用于指导设计新的Chk2抑制剂.     

In silico study of subtilisin-like protease 1 (SUB1) from different Plasmodium species in complex with peptidyl-difluorostatones and characterization of potent pan-SUB1 inhibitors

Plasmodium falciparum subtilisin-like protease 1 (SUB1) is a novel target for the development of innovative antimalarials. We recently described the first potent difluorostatone-based inhibitors of the enzyme ((4S)-(N-((N-acetyl-l-lysyl)-l-isoleucyl-l-threonyl-l-alanyl)-2,2-difluoro-3-oxo-4-aminopentanoyl)glycine (1) and (4S)-(N-((N-acetyl-l-isoleucyl)-l-threonyl-l-alanylamino)-2,2-difluoro-3-oxo-4-aminopentanoyl)glycine (2)). As a continuation of our efforts towards the definition of the molecular determinants of enzyme-inhibitor interaction, we herein propose the first comprehensive computational investigation of the SUB1 catalytic core from six different Plasmodium species, using homology modeling and molecular docking approaches. Investigation of the differences in the binding sites as well as the interactions of our inhibitors 1,2 with all SUB1 orthologues, allowed us to highlight the structurally relevant regions of the enzyme that could be targeted for developing pan-SUB1 inhibitors. According to our in silico predictions, compounds 1,2 have been demonstrated to be potent inhibitors of SUB1 from all three major clinically relevant Plasmodium species (P. falciparum, P. vivax, and P. knowlesi). We next derived multiple structure-based pharmacophore models that were combined in an inclusive pan-SUB1 pharmacophore (SUB1-PHA). This latter was validated by applying in silico methods, showing that it may be useful for the future development of potent antimalarial agents.     

N-甲基-2-(5-甲基-噻吩)-吡咯并[3,4]C60(MTPC)衍生物的分子结构和几何构型的理论研究

用半经验AM1法研究N-甲基-2-(5-甲基,噻吩)-吡咯并[3,4]C_(60)(MTPC)衍生物的分子轨道,电荷分布,几何构型。计算结果显示,分子(C)具有较低的跃迁能。HOMO轨道主要分布在杂环上,LUMO轨道则主要分布在C_(60)上。电荷从富电子的噻吩环向缺电子体C_(60)种转移。预测(C)可能在基态下产生长寿命的电荷分离态。     

(OsB)_n(n=1-6)团簇结构与稳定性的第一性原理研究

基于第一性原理,采用密度泛函理论(DFT)中的广义梯度近似(GGA)对(OsB)_n(n=1-6)团簇各种可能的构型进行了几何结构优化,得出了各团簇的最稳定构型,并对最稳定构型的能量、结合能、二阶能量差分、能隙等性质进行了理论研究。研究结果表明:n=2、3时,体系的基态结构分别为棱形和锅盖形;n=4时,体系的基态结构是对称性为T_d的立方体形状,是本文对称性最高的构型;从n=4开始立方体构型主导着团簇基态结构的生长行为,表明团簇的稳定性不仅与团簇的尺寸大小有关,还与团簇的对称性有关。团簇(OsB)_4的能隙、结合能与能量的二阶差分比邻近的值都大,说明团簇(OsB)_4有较高的稳定性,n=4是团簇的幻数。     

Exploring the molecular basis of the enantioselective binding of penicillin G acylase towards a series of 2-aryloxyalkanoic acids: a docking and molecular dynamics study

In the present paper, molecular modeling studies were undertaken in order to shed light on the molecular basis of the observed enantioselectivity of penicillin G acylase (PGA), a well known enzyme for its industrial applications, towards 16 racemic 2-aryloxyalkanoic acids, which have been reported to affect several biological systems. With this intention docking calculations and MD simulations were performed. Docking results indicated that the (S)-enantiomers establish several electrostatic interactions with SerB1, SerB386 and ArgB263 of PGA. Conversely, the absence of specific polar interactions between the (R)-enantiomers and ArgB263 seems to be the main reason for the different binding affinities observed between the two enantiomers. Results of molecular dynamics simulations demonstrated that polar interactions are responsible for both the ligand affinity and PGA enantiospecificity. Modeling calculations provided possible explanations for the observed enantioselectivity of the enzyme that rationalize available experimental data and could be the basis for future protein engineering efforts.     

1-(4-硝基苯基)-3-(5,6-二甲基-1,2,4三氮唑)-三氮烯质子迁移的理论研究

采用密度泛函B3LYP在6-31G*基组下,对有机显色剂1-(4-硝基苯基)-3-(5,6-二甲基-1,2,4三氮唑)-三氮烯(NPDMTT)的各种可能结构进行质子迁移的3种可能途径:(a)分子内质子迁移,(b)水助质子迁移,(c)甲醇助质子转移的计算,得到了各种途径异构体的相对能,获得了它们的互变异构过程的活化能、活化吉布斯自由能和质子转移反应的速率常数等性质。计算结果表明,分子内质子转移形成的各种异构体相对能量较大,当水分子或甲醇分子参与反应时,异构体的相对能量明显减小,但无论是孤立分子、一水合物还是一甲醇合物,其最稳定的异构体都相同,均为A2。溶剂化效应对异构化能垒的影响较大。最稳定的异构体分子内质子转移在N11和N13间转移的速控步骤的活化能为130.9 kJ.mol-1,反应速度常数为2.172×10-11s-1;当水分子参与反应以双质子转移机理异构化时,活化能显著降低,有利于三氮异构化,其中异构体质子在N11和N13间转移的速控步骤的活化能为22.55 kJ.mol-1,反应速度常数为3.617×107s-1;当醇分子参与反应以双质子转移机理异构时,活化能减小得更多,其中异构体质子在N11和N13间转移的速控步骤的活化能为2.384 kJ.mol-1,反应速度常数为9.032×1011s-1。计算结果还表明,氢键作用在增大NPDMTT一水合物和NPDMTT一甲醇合物相对稳定性、降低质子转移异构化反应活化能等方面起着重要作用。     

H…Cl(O),π…π作用的三维配合物[Cu(phen)2Cl(ClO4)]n的结构和量子化学研究

通过Cu(ClO4)2和phen(phen=1,10-邻啡罗啉)合成配合物[Cu(phen)2Cl(ClO4)]n,并表征其结构,晶体结构为单斜晶系,空间群为P21／c,晶体学参数:a=1．2666(2)nm,b=1．1219(2)nm,c=1．7225(2)nm,β=111．462(8)°,V=2．2779 (6)nm3,wR=0．071。在晶体中两个邻啡罗啉氮与中心铜离子配位形成2个五元环,4个氮和氯原子与中心铜形成变形四面锥,配合物之间邻近邻啡罗啉的芳环通过π…π作用形成一维结构,通过Cl…H和O…H“氢键”作用形成三维结构,邻近邻啡罗啉的芳环相互平衡组成π…π作用形成一维结构。量子化学(HF／LanL2DZ)计算表明,在配合物中HOMO电子(由铜原子的d轨道、氯和氮的p轨道)向LUMO和LUMO-1(碳原子的p轨道)转移。     

Toward the three-dimensional structure and lysophosphatidic acid binding characteristics of the LPA4/p2y9/GPR23 receptor: A homology modeling study

Lysophosphatidic acid (LPA) is a naturally occurring phospholipid that initiates a broad array of biological processes, including those involved in cell proliferation, survival and migration via activation of specific G protein-coupled receptors located on the cell surface. To date, at least five receptor subtypes (LPA_1–5) have been identified. The LPA_1–3 receptors are members of the endothelial cell differentiation gene (Edg) family. LPA₄, a member of the purinergic receptor family, and the recently identified LPA₅ are structurally distant from the canonical Edg LPA_1–3 receptors. LPA₄ and LPA₅ are linked to G_q, G_12/13 and G_s but not G_i, while LPA_1–3 all couple to G_i in addition to G_q and G_12/13. There is also evidence that LPA₄ and LPA₅ are functionally different from the Edg LPA receptors. Computational modeling has provided useful information on the structure–activity relationship (SAR) of the Edg LPA receptors. In this work, we focus on the initial analysis of the structural and ligand-binding properties of LPA₄, a prototype non-Edg LPA receptor. Three homology models of the LPA₄ receptor were developed based on the X-ray crystal structures of the ground state and photoactivated bovine rhodopsin and the recently determined human β₂-adrenergic receptor. Docking studies of LPA in the homology models were then conducted, and plausible LPA binding loci were explored. Based on these analyses, LPA is predicted to bind to LPA₄ in an orientation similar to that reported for LPA_1–3, but through a different network of hydrogen bonds. In LPA_1–3, the ligand polar head group is reported to interact with residues at positions 3.28, 3.29 and 7.36, whereas three non-conserved amino acid residues, S114(3.28), T187(EL2) and Y265(6.51), are predicted to interact with the polar head group in the LPA₄ receptor models.     

苯与羰基钼相互作用的密度泛函研究

用密度泛函理论在B3LYP/LANL2DZ基组水平上自由优化(η~x-C_6H_6)Mo(CO)_n(x=1-6;n=1-5)复合物体系的可能构型及计算相互作用能,探索不同羰基数对复合物稳定性、苯和羰基钼相互作用的影响,并分析苯和羰基钼相互作用的NBO。结论(1)苯以η~6与Mo(CO)_n(n=1-3)配位形成的复合物比较稳定,但η~6配位复合物CO的个数越多,则越不稳定;(2)复合物1、2、3和10中,Mo(CO)_n与苯的相互作用拉动电荷由苯的π键电子向Mo(CO)_n的σ_(Mo-CO)~*键转移,而在复合物7中,苯的π键电子向Mo(CO)_n中Mo的孤对电子轨道d转移。     

3个[AlB5O7（OH）6]2-簇的电子结构和红外光谱的DFT研究

采用密度泛函(DFT)方法,在B3LYP/6-311g*基组下,对3个[AlB5O7(OH)6]2-簇(I, II, III)的电子结构、稳定性和红外光谱进行了理论研究。结果显示3个簇中优化的键长和键角值与wiberg键级有关。[AlB5O7(OH)6]2-(I)的带宽最大,能量最低,稳定性最高。红外光谱研究显示BO3、BO4和AlO4基团振动频率的大小为BO3>BO4>AlO4,且BO3基团的振动强度也最大。此外,研究也显示非端基B-O键的振动频率较端基B-O键的振动频率大。     

CO_2和CH_4分子在Ni(111)表面吸附的分子模拟研究

采用蒙特卡洛方法模拟退火计算了CH_4和CO_2在Ni催化剂表面竞争吸附的等量吸附热和等温吸附线,结果表明,较优的操作参数为:温度范围:1000 K~1150 K,压力:101.33 kPa,CO_2/CH_4:大于1.00。随后通过分子动力学模拟计算了CH_4和CO_2解离过程中产生的自由基在Ni(111)表面的吸附行为,其中CH_3、CH和C倾向于吸附在fcc位点,而H更易于在hcp位发生吸附,CH_2在桥位的吸附最优。同时吸附能的绝对值的顺序是:CH_2CH_4CH_3CHCH,吸附能的绝对值越大,相应的吸附构象越稳定。而CO_2和CO倾向于吸附在桥位,O更易于在顶位发生吸附,OH在hop位点的吸附最优。     

C22 BxNy(x+y=2)全部异构体和分子离子芳香性的研究

用拓扑共振能(TRE)和百分拓扑共振能(%TRE)方法,研究从富勒烯C24(D6)产生异质富勒烯C22N2,C22B2和C22BN的所有异构体,研究阳离子和阴离子的芳香性.分析C22BxNy中杂原子取代位置和稳定性之间的关系.结果,中性状态和阳离子状态中,各异构体的TRE都为负数具有反芳香性.但它们的高价阴离子的TRE都为正数则有芳香性.中性状态中,稳定性顺序为:C22N2(1-19)>C22BN(39-64)>C24>C22B2(20-38).形成闭壳层结构时稳定性顺序为:C22B8-2(20-38>C6-24>C22BN6-(39-64)>C22N4-2(1-19).无论在中性状态还是闭壳层结构,当N原子取代C2类碳原子,B原子取代C1类碳原子时最稳定.理论上,预测C22BxNy的高价阴离子有合成的可能性.