Surface activity at the planar interface in relation to the thermodynamics of intermolecular interactions in the ternary system: maltodextrin-small-molecule surfactant-legumin

We report on the effect of potato maltodextrins with variable dextrose equivalent (Paselli SA-2, SA-6 and SA-10) on the surface behavior at the air-water interface of the mixture: legumin+small-molecule surfactant. Distinct in nature small-molecule surfactants (model: sodium salt of capric acid, Na-caprate; and commercially important: a citric acid ester of monoglyceride, CITREM) have been under our consideration. The role of the structure of both of the maltodextrins and the small-molecule surfactants in the effect studied has been elucidated by measurements in a bulk aqueous medium of the enthalpy of their interaction from mixing calorimetry, value of weight average molecular weight of the maltodextrins and the thermodynamics of the pair maltodextrin-solvent and maltodextrin-protein interactions from laser static light scattering. The combined data of mixing calorimetry and light scattering suggest some complex formation between the small-molecule surfactants and the maltodextrins. Predominantly hydrophobic interactions along with hydrogen bonding form the basis of the complexes. The effect of the maltodextrins on the thermodynamics of the protein heat denaturation and thereby on the protein conformational stability in the presence of the small-molecule surfactants has been studied by differential scanning calorimetry. The interrelation between the thermodynamics of intermolecular interactions in a bulk and the surface behavior at the planar air-water interface of the ternary systems (maltodextrin+legumin+small-molecule surfactant) has been elucidated by tensiometry. The effect of the maltodextrins on the surface activity of mixtures of legumin with the small-molecule surfactants is governed by the competitive in relation to the protein interactions with the small-molecule surfactants and a subsequent change in the thermodynamic properties of the both biopolymers, which are favorable to the ternary complex formation.     

On relationships between molecular structure, interaction and surface behavior in mixture: small-molecule surfactant+protein

We report on the effect of distinct in nature small-molecule surfactants (model, a sodium salt of capric acid, Na-caprate; and commercially important, a citric acid ester of monoglyceride, CITREM; a sodium salt of stearol-lactoyl lactic acid, SSL (Na(+)); polyglycerol ester, PGE (080)) on molecular properties in a bulk and at the air-water interface of globular legumin and random-coiled micellar sodium caseinate. The role of the structure of both proteins and small-molecule surfactants in the effect studied has been elucidated by measurements in a bulk aqueous medium of the enthalpy of their interaction from mixing calorimetry, the change in value of weight average molecular weight of the proteins and the thermodynamics of the pair protein-protein interactions from laser static light scattering as well as, in addition, by measurements of the change in hydrodynamic radius for micellar sodium caseinate from laser dynamic light scattering. The effect of the small-molecule surfactants on the thermodynamics of the protein heat denaturation and thereby on the protein conformational stability has been studied by differential scanning calorimetry in the case of globular legumin. The interrelation between the effects of the small-molecule surfactants on the properties of the proteins in a bulk and at the planar air-water interface has been elucidated by tensiometry. The combined data of mixing calorimetry, differential scanning calorimetry and laser light scattering suggest some complex formation between the small-molecule surfactants and the proteins in a bulk aqueous medium. Predominantly hydrophobic interaction along with electrostatic and hydrogen bonding form the basis of the complex formation. The found effect of the small-molecule surfactants on the surface activity of their mixtures with proteins is governed primarily by both the extent of the protein association, resulting in specific hydrophobicity/hydrophilicity of the surface of the protein associates, and the specific protein conformational stability, for the globular protein, produced by the interaction between the proteins and the small-molecule surfactants.     

色谱技术在药物-血浆蛋白相互作用研究中的应用进展

小分子药物进入人体血液循环系统后与人血清白蛋白(HSA)、α₁ -酸性糖蛋白(AGP)等血浆蛋白存在广泛的相互作用,这些相互作用深刻影响药物在体内的分布及其与靶标蛋白的结合,进而影响药物效应的发挥。深入探究药物与血浆蛋白间的相互作用对于候选药物的成药性优化、新药研发、联合用药的风险评控等意义重大。而发展高效、灵敏、准确的分析检测方法是开展药物-血浆蛋白相互作用研究的关键。近年来,色谱技术由于其高通量、高分离性能、高灵敏度等特点在该领域得到了广泛的应用,包括测定血浆蛋白翻译后修饰对药物结合的影响,多种药物的竞争性结合等。其中,高效亲和色谱(HPAC)和毛细管电泳(CE)应用最为广泛,能够通过多种分析方法获取结合常数、结合位点数、解离速率常数等相互作用信息。该文着重综述了HPAC和CE在药物-血浆蛋白相互作用研究中的常用策略及最新研究进展,包括HPAC中常用的前沿色谱法、竞争洗脱法、超快亲和提取法、峰值分析法和峰衰减分析法,以及CE中常用的亲和毛细管电泳法(ACE)和毛细管电泳前沿分析法(CE-FA)等。最后,该文还对当前色谱方法存在的不足进行了总结,并对色谱技术在药物-血浆蛋白相互作用研究领域的应用前景和发展方向进行了展望。     

Multiscale Virtual Screening Optimization for Shotgun Drug Repurposing Using the CANDO Platform

Drug repurposing, the practice of utilizing existing drugs for novel clinical indications, has tremendous potential for improving human health outcomes and increasing therapeutic development efficiency. The goal of multi-disease multitarget drug repurposing, also known as shotgun drug repurposing, is to develop platforms that assess the therapeutic potential of each existing drug for every clinical indication. Our Computational Analysis of Novel Drug Opportunities (CANDO) platform for shotgun multitarget repurposing implements several pipelines for the large-scale modeling and simulation of interactions between comprehensive libraries of drugs/compounds and protein structures. In these pipelines, each drug is described by an interaction signature that is compared to all other signatures that are subsequently sorted and ranked based on similarity. Pipelines within the platform are benchmarked based on their ability to recover known drugs for all indications in our library, and predictions are generated based on the hypothesis that (novel) drugs with similar signatures may be repurposed for the same indication(s). The drug-protein interactions used to create the drug-proteome signatures may be determined by any screening or docking method, but the primary approach used thus far has been BANDOCK, our in-house bioanalytical or similarity docking protocol. In this study, we calculated drug-proteome interaction signatures using the publicly available molecular docking method Autodock Vina and created hybrid decision tree pipelines that combined our original bio- and chem-informatic approach with the goal of assessing and benchmarking their drug repurposing capabilities and performance. The hybrid decision tree pipeline outperformed the two docking-based pipelines from which it was synthesized, yielding an average indication accuracy of 13.3% at the top10 cutoff (the most stringent), relative to 10.9% and 7.1% for its constituent pipelines, and a random control accuracy of 2.2%. We demonstrate that docking-based virtual screening pipelines have unique performance characteristics and that the CANDO shotgun repurposing paradigm is not dependent on a specific docking method. Our results also provide further evidence that multiple CANDO pipelines can be synthesized to enhance drug repurposing predictive capability relative to their constituent pipelines. Overall, this study indicates that pipelines consisting of varied docking-based signature generation methods can capture unique and useful signals for accurate comparison of drug-proteome interaction signatures, leading to improvements in the benchmarking and predictive performance of the CANDO shotgun drug repurposing platform.     

Polar interactions in solid-phase extraction of basic drugs by octadecylsilanized silica

Polar interactions between basic drugs (pentacaine, propranolol, and stobadin) and C18 silanized silica are studied along with hydrophobic interactions by using elution profiles of the drugs obtained with six organic solvents. The elution ability of the liquids towards basic drugs depends positively on their proton acceptor properties and negatively on their dipole interaction properties. Addition of triethylamine, a strong proton acceptor, to the liquids improves their elution ability, resulting in practically total recovery in all instances. The shapes of elution profiles indicate the presence of multiple types of interactions between C18 silica sorbent and basic drugs, ranging from those that originate from hydrophobic interactions to those originating from solute-sorbent ionic forces.     

Thermodynamic and functional properties of legumin (11S globulin from Vicia faba) in the presence of small-molecule surfactants: effect of temperature and pH

We report on the effect of a set of water-dispersible small-molecule surfactants (the main and the longest-hydrocarbon components of which are a citric acid ester of monostearate, a sodium salt of stearol-lactoyl lactic acid, and a polyglycerol ester of stearic acid) on molecular, thermodynamic, and functional properties of the major storage protein of broad beans (Vicia faba) legumin in different molecular states (native, heated, and acid-denatured). The interaction between legumin and the surfactants has been characterized by a combination of thermodynamic methods, namely, mixing calorimetry and multiangle laser static and dynamic light scattering. It was found that hydrogen bonds, electrostatic interactions, and hydrophobic contacts provided a basis for the interactions between the surfactants and both the native and the denatured protein in aqueous medium. Intensive association of the protein molecules in a bulk aqueous medium in the presence of the surfactants was revealed by static and dynamic laser light scattering. In consequence of this, both the surface activity and the gel-forming ability of legumin increased markedly, which has been shown by tensiometry, estimation of protein foaming capacity, and steady-state viscometry. A likely molecular mechanism underlying the effects of small-molecule surfactants on legumin structure-forming properties at the interface and in a bulk aqueous medium is discussed.     

Globally Approved EGFR Inhibitors: Insights into Their Syntheses,Target Kinases,Biological Activities,Receptor Interactions,and Metabolism

Targeting the EGFR with small-molecule inhibitors is a confirmed valid strategy in cancer therapy. Since the FDA approval of the first EGFR-TKI, erlotinib, great efforts have been devoted to the discovery of new potent inhibitors. Until now, fourteen EGFR small-molecule inhibitors have been globally approved for the treatment of different types of cancers. Although these drugs showed high efficacy in cancer therapy, EGFR mutations have emerged as a big challenge for these drugs. In this review, we focus on the EGFR small-molecule inhibitors that have been approved for clinical uses in cancer therapy. These drugs are classified based on their chemical structures, target kinases, and pharmacological uses. The synthetic routes of these drugs are also discussed. The crystal structures of these drugs with their target kinases are also summarized and their bonding modes and interactions are visualized. Based on their binding interactions with the EGFR, these drugs are also classified into reversible and irreversible inhibitors. The cytotoxicity of these drugs against different types of cancer cell lines is also summarized. In addition, the proposed metabolic pathways and metabolites of the fourteen drugs are discussed, with a primary focus on the active and reactive metabolites. Taken together, this review highlights the syntheses, target kinases, crystal structures, binding interactions, cytotoxicity, and metabolism of the fourteen globally approved EGFR inhibitors. These data should greatly help in the design of new EGFR inhibitors.     

Single-molecule analysis of interaction between p53TAD and MDM2 using aerolysin nanopores

Protein–protein interactions (PPIs) are regarded as important, but undruggable targets. Intrinsically disordered p53 transactivation domain (p53TAD) mediates PPI with mouse double minute 2 (MDM2), which is an attractive anticancer target for therapeutic intervention. Here, using aerolysin nanopores, we probed the p53TAD peptide/MDM2 interaction and its modulation by small-molecule PPI inhibitors or p53TAD phosphorylation. Although the p53TAD peptide showed short-lived (<100 ms) translocation, the protein complex induced the characteristic extraordinarily long-lived (0.1 s ∼ tens of min) current blockage, indicating that the MDM2 recruitment by p53TAD peptide almost fully occludes the pore. Simultaneously, the protein complex formation substantially reduced the event frequency of short-lived peptide translocation. Notably, the addition of small-molecule PPI inhibitors, Nutlin-3 and AMG232, or Thr18 phosphorylation of p53TAD peptide, were able to diminish the extraordinarily long-lived events and restore the short-lived translocation of the peptide rescued from the complex. Taken together, our results elucidate a novel mechanism of single-molecule sensing for analyzing PPIs and their inhibitors using aerolysin nanopores. This novel methodology may contribute to remarkable improvements in drug discovery targeted against undruggable PPIs.

Using aerolysin nanopores, we probed protein–protein interaction (PPI) between p53TAD and MDM2 and its modulation by small-molecule PPI inhibitors and p53TAD phosphorylation.     

基于计算机模拟技术对JAK2抑制剂的定量构效关系、分子设计和分子动力学研究

本文选取了52个对Janus激酶2(JAK2)有抑制作用的小分子化合物,分别使用3D-QSAR中的CoMFA和CoMSIA方法构建了两个可靠的、具有预测能力的模型,并利用分子对接分析数据集化合物与JAK2蛋白的相互作用,表明化合物主要通过氢键和范德华作用与JAK2靶蛋白结合。根据3D-QSAR模型的分析结果,设计了40个化合物,利用构建的模型预测其抑制活性;使用软件预测了化合物的药代动力学(ADME)参数,开展分子对接模拟,最终选择化合物D01和D22与JAK2靶蛋白进行了分子动力学模拟研究,结果显示两个复合物结合构象稳定,与分子对接结果趋势一致。本研究的结果可以为JAK2抑制剂的研发提供一些新的思路,为临床开发此类药物提供理论支撑。     

Influence of protein–protein interactions on bulk mass transport during ultrafiltration

Bulk mass transfer limitations can have a significant effect on the flux and selectivity during membrane ultrafiltration. Most previous studies of these phenomena have employed the simple stagnant film analysis, but this model is unable to account for the effects of solute–solute interactions on mass transport. We have developed a generalized framework for multicomponent mass transfer that includes both thermodynamic and hydrodynamic (frictional) interactions. Thermodynamic (virial) coefficients were evaluated from osmotic pressure data for albumin (BSA) and immunoglobulins (IgG), while hydrodynamic interaction parameters were determined from filtrate flux data obtained in a stirred cell using fully retentive membranes. The protein concentration profiles in the bulk solution were evaluated by numerical solution of the governing continuity equations incorporating the multicomponent diffusive flux. This model was used to analyze flux and protein transmission data obtained for the filtration of BSA and IgG mixtures through partially permeable membranes. The model accurately predicted the large reduction in flux and BSA transmission upon addition of IgG. These effects were due to the coupling between BSA and IgG mass transfer caused by protein–protein interactions.     

Exploring new chemical space by stereocontrolled diversity-oriented synthesis

Natural products that act as highly specific, small-molecule protein-binding agents and as modulators of protein-protein interactions are highly complex and exhibit functional groups with three-dimensional and stereochemical diversity. The complex three-dimensional display of chiral functional groups appears to be crucial for exhibiting specificity in protein binding and in differentiating between closely related proteins. The development of methods that allow a high-throughput access to three-dimensional, skelatally complex, polycyclic compounds having few asymmetric diversity sites is essential and a highly challenging task. In the postgenomic chemical biology age, in which there is a great desire to understand protein-protein interactions and to dissect protein networking-based signaling pathways by small molecules, the need for developing "stereocontrolled, diversity-oriented synthesis" methods to generate natural product-like libraries is of utmost importance.     

Identification of the Binding Site of Brucella VirB8 Interaction Inhibitors

Secretion systems translocate virulence factors of many bacterial pathogens, enabling their survival inside the host organism. Consequently, inhibition strongly attenuates pathogenicity and can be considered a target for novel antimicrobial drugs. The type IV secretion system (T4SS) of the intracellular pathogen Brucella is a prerequisite for its virulence, and in this work we targeted the interactions of the?essential assembly factor protein, VirB8, using small-molecule inhibitors. High-throughput screening identified several potent and specific inhibitors, and the target-binding site of these inhibitors was identified by X-ray crystallography, in?silico docking, and analysis of the derivates of the inhibitor B8I-2. VirB8 interaction inhibitors bind to a surface groove opposite to the dimerization interface, and by varying the binding-site residues, we were able to determine which residues are required for inhibitor activity. E115 and K182 were found to be especially important, and changes at R114, Y229, and L151 also reduced inhibitor efficiency.     

Binding of biguanides to β-lactoglobulin: molecular-docking and molecular dynamics simulation studies

Biguanides are a class of drugs derived from biguanide and they are the most widely used drugs for diabetes mellitus or pre-diabetes treatment. An investigation of their interaction and a transport protein such as β-lactoglobulin (BLG) at atomic level could be a valuable factor in controlling their transport to biological sites. Molecular-docking and molecular dynamics simulation methods were used to study the interaction of metformin, phenformin and buformin as biguanides and BLG as transport protein. The molecular-docking results revealed that these biguanides bind to BLG and that the BLG affinity for binding the biguanides decreases in the following order: phenformin — buformin — metformin. The docking results also show the hydrophobic interactions to have a significant role in the BLG-biguanides complex stability. Analysis of molecular dynamic simulation trajectories shows that the root mean square deviation of various systems attained equilibrium and fluctuated around the mean value at various times. The time evolution of the radius of gyration and the total solvent-accessible surface of the protein showed that BLG and BLG-biguanide complexes became stable at approximately 2500 ps and that there was not any conformational change in the BLG-biguanide complexes. In addition, the profiles of atomic fluctuations show the rigidity of the ligand-binding site during the simulation.     

A computational analysis of the binding model of MDM2 with inhibitors

Abstract  

It is a new and promising strategy for anticancer drug design to block the MDM2-p53 interaction using a non-peptide small-molecule inhibitor. We carry out molecular dynamics simulations to study the binding of a set of six non-peptide small-molecule inhibitors with the MDM2. The relative binding free energies calculated using molecular mechanics Poisson–Boltzmann surface area method produce a good correlation with experimentally determined results. The study shows that the van der Waals energies are the largest component of the binding free energy for each complex, which indicates that the affinities of these inhibitors for MDM2 are dominated by shape complementarity. The A-ligands and the B-ligands are the same except for the conformation of 2,2-dimethylbutane group. The quantum mechanics and the binding free energies calculation also show the B-ligands are the more possible conformation of ligands. Detailed binding free energies between inhibitors and individual protein residues are calculated to provide insights into the inhibitor-protein binding model through interpretation of the structural and energetic results from the simulations. The study shows that G1, G2 and G3 group mimic the Phe19, Trp23 and Leu26 residues in p53 and their interactions with MDM2, but the binding model of G4 group differs from the original design strategy to mimic Leu22 residue in p53.     

Evaluation of the abilities of ��-cyclodextrin to form complexes by surface plasmon resonance with a Biacore? system

Although phase-solubility studies have often been used to evaluate the interaction of cyclodextrins (CDs) with various drugs, hundreds of milligrams of both CD and drug are required to prepare a phase diagram. A method that would require considerably less material for evaluating complex formation between a CD and guest compound is therefore needed. We previously reported the detection of the interactions between ??-CD and various drugs using a Biacore^® system. In this study, we succeeded in immobilizing 6-monodeoxy-6-monoamino-??-CD on the gold surface of a sensor chip and in detecting the interactions between the immobilized ??-CD and various drugs. The interaction processes were kinetically analyzed using Biacore^®. The surface plasmon resonance sensorgrams indicated that the association and dissociation rates of the interactions between ??-CD and drugs were faster than those between ??-CD and drugs. Although the association constants calculated from the sensorgrams were smaller than those calculated from phase-solubility studies, good correlation was shown between these data.     

亲和毛细管电泳法和荧光法研究氟喹诺酮类药物与牛血清白蛋白的相互作用

分别采用亲和毛细管电泳法和荧光法对6种氟喹诺酮类药物(司帕沙星、洛美沙星、左氧氟沙星、诺氟沙星、培氟沙星和氟罗沙星)与牛血清白蛋白的相互作用进行考察. 结合比均为1∶1, 结合常数在104 L/mol量级, 热力学参数表明体系间的相互作用力以范德华作用力和氢键力为主. 另外, 亲和毛细管电泳实验结果表明, 缓冲溶液pH值和离子强度增大会造成结合常数在一定程度上的减小, 使相互作用减弱. 同时, 荧光猝灭实验结合紫外光谱扫描说明体系间为静态猝灭. 所得到的数据对进一步研究氟喹诺酮类药物的作用机理、提高药效和开发新一代氟喹诺酮类药物具有一定的参考意义.     

Visualizing an Ultra‐Weak Protein–Protein Interaction in Phosphorylation Signaling

Proteins interact with each other to fulfill their functions. The importance of weak protein–protein interactions has been increasingly recognized. However, owing to technical difficulties, ultra‐weak interactions remain to be characterized. Phosphorylation can take place via a K_D≈25 mM interaction between two bacterial enzymes. Using paramagnetic NMR spectroscopy and with the introduction of a novel Gd^III‐based probe, we determined the structure of the resulting complex to atomic resolution. The structure accounts for the mechanism of phosphoryl transfer between the two enzymes and demonstrates the physical basis for their ultra‐weak interaction. Further, molecular dynamics (MD) simulations suggest that the complex has a lifetime in the micro‐ to millisecond regimen. Hence such interaction is termed a fleeting interaction. From mathematical modeling, we propose that an ultra‐weak fleeting interaction enables rapid flux of phosphoryl signal, providing a high effective protein concentration.     

NSAIDs interactions with membranes: a biophysical approach

This work focuses on the interaction of four representative NSAIDs (nimesulide, indomethacin, meloxicam, and piroxicam) with different membrane models (liposomes, monolayers, and supported lipid bilayers), at different pH values, that mimic the pH conditions of normal (pH 7.4) and inflamed cells (pH 5.0). All models are composed of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) which is a representative phospholipid of most cellular membranes. Several biophysical techniques were employed: Fluorescence steady-state anisotropy to study the effects of NSAIDs in membrane microviscosity and thus to assess the main phase transition of DPPC, surface pressure-area isotherms to evaluate the adsorption and penetration of NSAIDs into the membrane, IRRAS to acquire structural information of DPPC monolayers upon interaction with the drugs, and AFM to study the changes in surface topography of the lipid bilayers caused by the interaction with NSAIDs. The NSAIDs show pronounced interactions with the lipid membranes at both physiological and inflammatory conditions. Liposomes, monolayers, and supported lipid bilayers experiments allow the conclusion that the pH of the medium is an essential parameter when evaluating drug-membrane interactions, because it conditions the structure of the membrane and the ionization state of NSAIDs, thereby influencing the interactions between these drugs and the lipid membranes. The applied models and techniques provided detailed information about different aspects of the drug-membrane interaction offering valuable information to understand the effect of these drugs on their target membrane-associated enzymes and their side effects at the gastrointestinal level.