Molecular recognition in the sphingosine 1-phosphate receptor family

Computational modeling and its application in ligand screening and ligand receptor interaction studies play important roles in structure-based drug design. A series of sphingosine 1-phosphate (S1P) receptor ligands with varying potencies and receptor selectivities were docked into homology models of the S1P_1–5 receptors. These studies provided molecular insights into pharmacological trends both across the receptor family as well as at single receptors. This study identifies ligand recognition features that generalize across the S1P receptor family, features unique to the S1P₄ and S1P₅ receptors, and suggests significant structural differences of the S1P₂ receptor. Docking results reveal a previously unknown sulfur–aromatic interaction between the S1P₄ C5.44 sulfur atom and the phenyl ring of benzimidazole as well as π–π interaction between F3.33 of S1P_1,4,5 and aromatic ligands. The findings not only confirm the importance of a cation–π interaction between W4.64 and the ammonium of S1P at S1P₄ but also predict the same interaction at S1P₅. S1P receptor models are validated for pharmacophore development including database mining and new ligand discovery and serve as tools for ligand optimization to improve potency and selectivity.     

Molecular recognition of docosahexaenoic acid by peroxisome proliferator-activated receptors and retinoid-X receptor alpha

The family of peroxisome proliferator-activated receptors (PPARs) is the molecular target of synthetic antidiabetic and hypolipidemic drugs. The side effects of these drugs are limiting their use in patients with high lipid levels. Natural compounds, like Docosahexaenoic acid (DHA) from fish oil, have beneficial effects in the treatment of metabolic diseases, and several DHA derivatives are known to activate PPAR genes. Experimental studies on affinities of DHA and its derivatives for PPARs are not available. In the present study we are therefore using computational docking, molecular dynamics simulation, and several scoring programs to predict affinities and binding modes of DHA for PPARs and retinoid-X receptor alpha, which is the DNA binding partner of PPARs. The calculations indicated that DHA binds to PPARs and the retinoid-X receptor alpha with high affinity, and that different PPARs exhibited different structural effects on the first four carbons atoms of DHA. Our data indicate that the beneficial health effects of DHA may be obtained by high affinity binding to the PPARs.     

Molecular basis of the recognition of FMN by a HAD phosphatase TON_0338

The haloalkaloic acid dehalogenase (HAD) phosphatase from Thermococcus onnurineus NA1 (TON_0338), has phosphatase activity the flavin mono-nucleotide (FMN). The molecular origin and structural motifs for the activity deficiency of double-tryptophan mutant have not been rationalized at atomic resolution. Molecular dynamics (MD) simulations and the molecular mechanics/Generalized-Born surface area (MM/GBSA) free energy calculations were used to explore the effects of mutations on the changes in both structural flexibility and conformational dynamics. The non-polar solvation energy plays an indispensable role in the binding process of TON_0338 and FMN. The tryptophan sandwich structure provides a primary function to anchor FMN and keeps FMN well bound to TON_0338. The double-tryptophan mutation has influences on the secondary structures of TON_0338 and changes the conformation, which would lead to reduced activity of W58A/W61A-FMN binding. The present study provides important insights into the structure-function relationships of TON_0338 protein, which could contribute to further understanding about the HAD phosphatases.     

Molecular recognition pattern of cytotoxic alkaloid vinblastine with multiple targets

Vinblastine (VLB), a cytotoxic alkaloid is used extensively against various cancer types and the crystal structure of its tubulin complex is already known. Multitarget affinity of vinblastine has been investigated and the nature of binding with biological receptors namely, duplex DNA and Human serum albumin (HSA) has been compared to the binding characteristics of its known complex with natural high affinity receptor tubulin using molecular docking and QM–MM calculations. VLB is found to interact with DNA as well as HSA protein, though, with weaker affinity as compared to tubulin. Analysis of various docked complexes revealed that the H-bonds and cation–pi bonds do not have significant contribution to the binding interactions and despite its large size, VLB remains in relaxed conformation and fits in the hydrophobic regions on the receptors.     

Molecular modeling of sigma 1 receptor ligands: a model of binding conformational and electrostatic considerations

We have performed molecular modeling studies on several sigma 1 specific ligands, including PD144418, spipethiane, haloperidol, pentazocine, and others to develop a pharmacophore for sigma 1 receptor-ligand binding, under the assumption that all the compounds interact at the same receptor binding site. The modeling studies have investigated the conformational and electrostatic properties of the ligands. Superposition of active molecules gave the coordinates of the hypothetical 5-point sigma 1 pharmacophore, as follows: R1 (0.85, 7.26, 0.30); R2 (5.47, 2.40, -1.51); R3 (-2.57, 4.82, -7.10); N (-0.71, 3.29, -6.40); carbon centroid (3.16, 4.83, -0.60), where R1, R2 were constructed onto the aromatic ring of each compound to represent hydrophobic interactions with the receptor; and R3 represents a hydrogen bond between the nitrogen atom and the receptor. Additional analyses were used to describe secondary binding sites to electronegative groups such as oxygen or sulfur atom. Those coordinates are (2.34, 5.08, -4.18). The model was verified by fitting other sigma 1 receptor ligands. This model may be used to search conformational databases for other possibly active ligands. In conjunction with rational drug design techniques the model may be useful in design and synthesis of novel sigma 1 ligands of high selectivity and potency. Calculations were performed using Sybyl 6.5.     

Exploring ligand recognition and ion flow in comparative models of the human GABA type A receptor

We present two comparative models of the GABA(A) receptor. Model 1 is based on the 4-A resolution structure of the nicotinic acetylcholine receptor from Torpedo marmorata and represents the unliganded receptor. Two agonists, GABA and muscimol, two benzodiazepines, flunitrazepam and alprazolam, together with the general anaesthetic halothane, have been docked to this model. The ion flow is also explored in model 1 by evaluating the interaction energy of a chloride ion as it traverses the extracellular, transmembrane and intracellular domains of the protein. Model 2 differs from model 1 only in the extracellular domain and represents the liganded receptor. Comparison between the two models not only allows us to explore commonalities and differences with comparative models of the nicotinic acetylcholine receptor, but also suggests possible protein sub-domain interactions with the GABA(A) receptor not previously addressed.     

Plan parsing for intended response recognition in discourse1

In a discourse the hearer must recognize the response intended by the speaker. To perform this recognition, the hearer must ascertain what plans the speaker is undertaking and how the utterances in the discourse further that plan. To do so, the hearer can parse the initial intentions (recoverable from the utterance) and recognize the plans the speaker has in mind and intends the hearer to know about. This paper reports on a theory of parsing the intentions in discourse. It also discusses the role of another aspect of discourse, discourse markers, that are valuable to intended response recognition.     

Molecular graphics approach to bacterial AcrB protein-beta-lactam antibiotic molecular recognition in drug efflux mechanism

AcrAB-TolC is the most important multidrug efflux pump system of Gram-negative bacteria, responsible for their resistance to lipophilic and amphiphilic drugs. In this work, a molecular graphics study of the pump components AcrB and TolC, 16 beta-lactam antibiotics and 7 other substrates, as well as of AcrB-substrate complexes, was performed in order to give a mechanistic proposal for the efflux process at molecular level. AcrAB-TolC is a proton-dependent electromechanical device which opens to extrude drugs from the bacterial periplasm and perhaps cytoplasm, by means of a series of structural changes within the complex and its components AcrA, AcrB and TolC. These changes are initiated by protonation and disruption of salt bridges and certain hydrogen bonds, and are followed by conformational changes in which a number of intra- and interchain interactions are rearranged. Molecular properties of beta-lactams accounting for their lipophilicity, shape/conformation and other sterical features, polar/charge group distribution and other electronic properties, and hydrogen bonding potency determine their interaction with polar headpieces of the inner membrane, recognition and binding to receptors of AcrB and TolC. The orientation of the beta-lactam molecular dipoles with respect the efflux system is maintained during the drug efflux. Elongated cylinder-like beta-lactam antibiotics with lipophylic side chains, a significantly negative component of the dipole moment and low hydrogen bonding capacity seem to be good substrates of AcrAB-TolC.     

Insights into protein-carbohydrate recognition: A novel binding mechanism for CBM family 43

Despite the growing number of carbohydrate-binding modules (CBMs) that are being uncovered, information on the structural determinants for the sugar-binding regions at atomic resolution is scarce. It is widely accepted that aromatic and H-bonding interactions govern these processes, and reported simulations and theoretical calculations are valuable tools to quantify and understand these interactions. We present here a computational model derived from experimental data that provide a unique atomistic picture of an uncharacterized binding mode of laminarin to the CBM family 43. The present study, which is among the first describing an isolated CBM with the bound carbohydrate, is complemented with quantum mechanical calculations. This allows us to attribute certain experimental observations (binding affinities) to key interactions (H-bonds and aromatic stacking), on the basis of NMR-driven docking structure.     

柔性对接算法用于β-环糊精和胆汁酸的分子识别研究

为了研究β-环糊精与胆汁酸形成包结物的稳定性和分子识别机制，采用自行研制的柔性对接算法对β-环糊精和不同胆汁酸的分子识别进行了分子力学模拟，并和刚性对接方式进行了比较。结果表明：柔性对接优化得到的结构比相应的刚性对接得到的结构更合理；包结物的稳定性随着胆汁酸所含羟基数目的增加而降低；对于含有相同羟基数目的胆汁酸，羟基的位置及其取向对包结物的稳定性也存在影响；范德华能和去溶剂化能是影响包结物稳定性的主要因素。     

Molecular basis of agonicity and antagonicity in the androgen receptor studied by molecular dynamics simulations

Treatment of prostate cancer patients with antiandrogens is initially successful, though the therapy often becomes refractory over the time. This mechanism is not fully understood, but the presence of androgen receptor (AR) mutant forms which are activated by antiandrogens and other endogenous ligands, and overexpression of the receptor have been suggested. In an attempt to explain the molecular basis for agonicity and antagonicity in the androgen receptor, and the changes on biological activity of subtle modifications at the ligand and receptor (mutations) level, molecular dynamics simulations were performed on the androgen receptor wild type (WT), and T877A and W741 mutant forms, complexed with several non-steroidal androgens. The stabilizing role of residues from helices 3, 5, 11 and 12 was observed in non-steroidal androgens R-3, S-1, and R-bicalutamide and hydroxyflutamide in resistant mutations. In the AR WT antiandrogen R-bicalutamide complex, destabilization of M895 by both W741 and the sulfonyl linkage of the ligand may be responsible for reported antagonism. Changes in the ligand or mutations alleviating this effect were observed to stabilize the receptor in the active conformation, thus developing resistance to R-bicalutamide. The results presented provide a plausible explanation for the molecular basis of agonicity and antagonicity in the androgen receptor, and complement previous studies using static crystal structures, incorporating for the first time protein dynamics into the analysis. Thus, our results provide a valuable framework for the structure-based design of improved antiandrogens.     

流感病毒A型核酸内切酶与羟基嘧啶酮衍生物识别的分子动力学模拟

流感病毒A型核酸内切酶(Influenza A Endonuclease,IAE)是目前抗流感新药物研发的重要靶标。本文对IAE单体及其与羟基嘧啶酮衍生物(Hydroxy pyrimidine-ketone derivatives,HPD)抑制剂的复合物分别进行了2.1 ns的分子动力学模拟。从能量角度详细分析了IAE与HPD识别的关键残基,并对IAE-HPD复合物和IAE单体进行了成簇和自由能曲面计算,得到了HPD结合导致IAE的构象变化,主要是H41~Y48段α螺旋的去螺旋化以及H41等氨基酸残基的空间结构变化。优化后的结合模式表明,HPD与IAE识别主要是依靠一个双金属螯合的作用力以及周围残基的范德华相互作用力。模拟结果对于更深入理解IAE的结构特点以及与HPD的分子识别机制具有指导意义,为后续基于结构的抗流感病毒药物设计具有参考作用。     

Sphingosine 1-phosphate pKa and binding constants: intramolecular and intermolecular influences

The dissociation constant for an ionizable ligand binding to a receptor is dependent on its charge and therefore on its environmentally-influenced pKa value. The pKa values of sphingosine 1-phosphate (S1P) were studied computationally in the context of the wild type S1P1 receptor and the following mutants: E3.29Q, E3.29A, and K5.38A. Calculated pKa values indicate that S1P binds to S1P1 and its site mutants with a total charge of -1, including a +1 charge on the ammonium group and a -2 charge on the phosphate group. The dissociation constant of S1P binding to these receptors was studied as well. The models of wild type and mutant proteins originated from an active receptor model that was developed previously. We used ab initio RHF/6-31+G(d) to optimize our models in aqueous solution, where the solvation energy derivatives are represented by conductor-like polarizable continuum model (C-PCM) and integral equation formalism polarizable continuum model (IEF-PCM). Calculation of the dissociation constant for each mutant was determined by reference to the experimental dissociation constant of the wild type receptor. The computed dissociation constants of the E3.29Q and E3.29A mutants are three to five orders of magnitude higher than those for the wild type receptor and K5.38A mutant, indicating vital contacts between the S1P phosphate group and the carboxylate group of E3.29. Computational dissociation constants for K5.38A, E3.29A, and E3.29Q mutants were compared with experimentally determined binding and activation data. No measurable binding of S1P to the E3.29A and E3.29Q mutants was observed, supporting the critical contacts observed computationally. These results validate the quantitative accuracy of the model.     

新型双膦酸酯杯[4]吡咯过渡受体离子对识别的理论计算

含有2个膦酸酯基团的芳环扩展的新型杯[4]吡咯系列化合物可以作为客体烷基铵/鏻氯盐的离子对受体。使用量子力学计算和新的非共价弱相互作用分析方法研究了过渡受体io的离子对识别行为。计算的离子对结合能表明,io与四级鏻氯盐和一级铵氯盐的优势结合模式分别为分离式和接触式,阳离子-π和氢键分别在其中起主导作用。结合前面的计算结果,发现三种受体对于这2种氯盐的结合能力顺序与实验结果完全一致,io在其中显示出明显的过渡性质。对几何构型、弱相互作用和基于自然键轨道的电荷转移进行了分析,阐释了io具有过渡性质的原因。本项工作进一步揭示了新型双膦酸酯杯[4]吡咯受体离子对识别机制,为设计基于杯[4]吡咯的离子对受体提供了理论基础。     

Immobilization of a boronic receptor for fructose recognition: influence on the photoinduced electron transfer process

The work presented here describes the synthesis on different solid supports of a luminescent probe, dansylphenylboronic acid (DPBA) for use in fructose recognition. While in aqueous solution DPBA changes its fluorescence in response to added fructose via a photoinduced electron transfer (PET) mechanism, we have found that once immobilized the fructose binding event could not be monitored by a change in fluorescence. It was observed, however, that the immobilized DPBA displayed enhanced acidity upon binding of fructose. The system was indeed selective for fructose in competitive binding experiments, preferring fructose over glucose. It is demonstrated that design of immobilized fluorescent sensors for fructose, based on a PET mechanism, is not an easy task due to the chemical and spectral changes experienced by the fluorescent probe upon immobilization.     

Molecular dynamics simulation using the cray-1 vector processing computer

Algorithms are presented which enable molecular dynamics simulations of liquids to be performed most efficiently on the Cray-1 vector processing computer. For 256 atoms interacting via the Lennard-Jones potential the CPU time per step of the simulation is 22 ms.     

Syntactic pattern recognition for the recognition of bright spots

Syntactic pattern recognition techniques are applied to the analysis of one-dimensional seismic traces and two-dimensional seismograms for the detection of bright spots. The calculation between error probability and Levenshtein distance is proposed. The system for two-dimensional seismic analysis includes three kinds of string distance computation to test the continuity of a bright spot pattern.     

一种语音识别中核心词快速模型优化方法

针对国网客服电话语音识别在特定领域核心词识别效果差的问题,提出一种基于HCLG领域词权重增强和领域词纠正的方法,能够实时并快速地添加领域词,从而动态地优化语言模型,提升语音识别效果。将该模型和算法优化应用在国网客服中心电话语音的咨询、维修、投诉等各种领域场景中,其语音识别结果都得到大幅改善。     

Pattern recognition in a compartmental model of a CA1 pyramidal neuron.

Computer simulation of a CA1 hippocampal pyramidal neuron is used to estimate the effects of synaptic and spatio-temporal noise on such a cell's ability to accurately calculate the weighted sum of its inputs, presented in the form of transient patterns of activity. Comparison is made between the pattern recognition capability of the cell in the presence of this noise and that of a noise-free computing unit in an artificial neural network model of a heteroassociative memory. Spatio-temporal noise due to the spatial distribution of synaptic input and quantal variance at each synapse degrade the accuracy of signal integration and consequently reduce pattern recognition performance in the cell. It is shown here that a certain degree of asynchrony in action potential arrival at different synapses, however, can improve signal integration. Signal amplification by voltage-dependent conductances in the dendrites, provided by synaptic NMDA receptors, and sodium and calcium ion channels, also improves integration and pattern recognition. While the biological sources of noise are significant when few patterns are stored in the associative memory of which the cell is a part, when large numbers of patterns are stored the noise from the other stored patterns comes to dominate the pattern recognition process. In this situation, the pattern recognition performance of the pyramidal cell is within a factor of two of that of the computing unit in the artificial neural network model.     

Molecular dynamics at the receptor level of immunodominant myelin oligodendrocyte glycoprotein 35–55 epitope implicated in multiple sclerosis

Multiple Sclerosis (MS) is a common autoimmune disease whereby myelin is destroyed by the immune system. The disease is triggered by the stimulation of encephalitogenic T-cells via the formation of a trimolecular complex between the Human Leukocyte Antigen (HLA), an immunodominant epitope of myelin proteins and T-cell Receptor (TCR). Myelin Oligodendrocyte Glycoprotein (MOG) is located on the external surface of myelin and has been implicated in MS induction. The immunodominant 35–55 epitope of MOG is widely used for in vivo biological evaluation and immunological studies that are related with chronic Experimental Autoimmune Encephalomyelitis (EAE, animal model of MS), inflammatory diseases and MS. In this report, Molecular Dynamics (MD) simulations were used to explore the interactions of MOG_35–55 at the receptor level. A detailed mapping of the developed interactions during the creation of the trimolecular complex is reported. This is the first attempt to gain an understanding of the molecular recognition of the MOG_35–55 epitope by the HLA and TCR receptors. During the formation of the trimolecular complex, the residues Arg⁴¹ and Arg⁴⁶ of MOG_35–55 have been confirmed to serve as TCR anchors while Tyr⁴⁰ interacts with HLA. The present structural findings indicate that the Arg at positions 41 and 46 is a key residue for the stimulation of the encephalitogenic T-cells.