A novel view of modelling interactions between synthetic and biological polymers via docking

Multipoint interactions between synthetic and natural polymers provide a promising platform for many topical applications, including therapeutic blockage of virus-specific targets. Docking may become a useful tool for modelling of such interactions. However, the rigid docking cannot be correctly applied to synthetic polymers with flexible chains. The application of flexible docking to these polymers as whole macromolecule ligands is also limited by too many possible conformations. We propose to solve this problem via stepwise flexible docking. Step 1 is docking of separate polymer components: (1) backbone units (BU), multi-repeated along the chain, and (2) side groups (SG) consisting of functionally active elements (SG _F ) and bridges (SG _B ) linking SG _F with BU. At this step, probable binding sites locations and binding energies for the components are scored. Step 2 is docking of component-integrating models: [BU] _m , SG = SG _F –SG _B , BU–SG, BU–BU(SG)–BU, BU(SG)–[BU] _m –BU(SG), and [BU _var (SG _var )] _m . Every modelling level yields new information, including how the linkage of various components influences on the ligand—target contacts positioning, orientation, and binding energy in step-by-step approximation to polymeric ligand motifs. Step 3 extrapolates the docking results to real-scale macromolecules. This approach has been demonstrated by studying the interactions between hetero-SG modified anionic polymers and the N-heptad repeat region tri-helix core of the human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein gp41, the key mediator of HIV-1 fusion during virus entry. The docking results are compared to real polymeric compounds, acting as HIV-1 entry inhibitors in vitro. This study clarifies the optimal macromolecular design for the viral fusion inhibition and drug resistance prevention.     

Agonist–PPARγ interactions: Molecular modeling study with docking approach

Docking simulation of 18 agonists with the ligand binding pocket (LBP) of PPARγ has been performed. The binding conformations and binding affinities of these agonists were obtained by use of the flexible docking protocol FlexX. Test compound calculations indicated that FlexX can reproduce the binding conformation of the crystal structure (root mean square deviation = 1.43 Å); moreover, the predicted binding affinities correlate well with the activities of these agonists. The interaction model and pharmacophore of PPARγ agonists were derived and the difference in biologic activities of these agonists can be well explained. The PPARγ agonists must have both polar head and the hydrophobic tail, which form hydrogen bonds and hydrophobic contacts with hydrophilic and hydrophobic regions of the LBP of PPARγ, respectively. In addition, a suitable linker is also necessary. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 93: 405–410, 2003     

Molecular dynamics simulation of semirigid polymers

The chain rigidity of poly(p-hydroxybenzoate) was estimated through the theoretical evaluation of its persistence length (L_p). A non-Brownian molecular dynamics (MD) simulation of an isolated chain with 20 monomeric units was performed. The sampled conformational population was analyzed and the orientational correlation function between monomeric units along the chain was calculated. An algorithm based on the worm-like chain model was applied to evaluate the persistence length. The results were compared with those obtained from equilibrium models like the freely-rotating-chain and the rotational-matrix method with fluctuations. Equilibrium models give different results depending on the degree of accuracy used in describing the monomeric unit. The inclusion of thermal fluctuations is crucial to obtain realistic results. These coincide with those given by MD simulation when only nearest-neighbour orientational correlations are taken into account: inclusion of higher-order correlation terms leads to lower values of the persistence length. The origin of this discrepancy was investigated. The MD simulation results are characterized by an overrepresentation of conformations with a short end-to-end distance resulting from an anomalous energy concentration in the first bending mode of the chain. In analogy with previous simulation results from systems characterized by a week coupling amoung their degrees of freedom, failure in the energy equipartition is proposed as a likely explanation of the anomalous dynamical behaviour.     

Structural insight into the glucokinase-ligands interactions. Molecular docking study

Glucokinase (GK) plays a key role in the regulation of hepatic glucose metabolism. Inactivation of GK is associated with diabetes, and an increase of its activity is linked to hypoglycemia. Possibility to regulate the GK activity using small chemical compounds as allosteric activators induces the scientific interest to the study of the activation mechanism and to the development of new allosteric glucokinase activators.Interaction of glucokinase with ligands is the first step of the complicated mechanism of regulation of the GK functioning. In this paper, we study the interaction of GK with native (glucose) and synthetic (allosteric activators) ligands using molecular docking method. Calculations demonstrate the ability of molecular docking programs to accurately reproduce crystallized ligand poses and conformations and to calculate a free energy of binding with satisfactory accuracy. Correlation between the free energy of binding and the bioactivity of activators is discussed. These results provide a new insight into protein–ligand interactions and can be used for the engineering of new activators.     

Molecular modeling and docking studies of new antimicrobial antipyrine-thiazole hybrids

A series of new antipyrine incorporated thiazole derivatives having phenoxyacetamide moiety as a link bridge was synthesized. The synthetic strategy involves condensation of the precursor N-(4-antipyrinyl)-2-(4-formylphenoxy)acetamide with thiosemicarbazide followed by heterocyclization of the produced thiosemicarbazone with various α-halogenated carbonyl compounds (namely; 4-chlorophenacyl bromide, ethyl bromoacetate, 3-chloroacetylacetone and ethyl 4-chloroacetoacetate). Moreover, the quantum chemical calculations at DFT/B3LYP level were used to determine the HOMO-LUMO energies and Fukui’s indices toward nucleophilic, electrophilic and radical attacks. The investigated compounds were arranged due to HOMO-LUMO energy gap as following 6 < 5 < 7 < 3 < 2 < 4 < 8. The synthesized antipyrinyl-thiazole hybrids were screened to evaluate their antibacterial and antifungal efficacies. Using Chloramphenicol as reference material, the synthesized antipyrinyl-thiazole hybrids were revealed a remarkable activity against S. aureus than B. subtilis, as example for Gram’s positive strains. The antipyrine-thiazole compounds 3, 4, 6 and 8 exhibited significant MIC values. However, the antipyrine-thiazole hybride 4 displayed reputable activities against Gram’s negative strains S. typhimurium and E. coli, respectively, in comparison with Cephalothin. Likewise, the compounds 7 and 8 were demonstrated respectable antifungal efficacy toward C. albicans in contrast to cycloheximide grade. The theoretical molecular docking studies were applied to simulate reactivity of the synthesized antipyrine-thiazole hybrids against contrasting binding sites for both of Staphylococcus aureus “Homo sapiens” (pdb: 3HUN) protein and E.coli “Homo sapiens” (PDB: 2EXB) protein. The theoretical and practical antibacterial and antifungal activities result in this work designated a proper agreement.     

Comparing ligand interactions with multiple receptors via serial docking

Standard uses of ligand-receptor docking typically focus on the association of candidate ligands with a single targeted receptor, but actual applications increasingly require comparisons across multiple receptors. This study demonstrates that comparative docking to multiple receptors can help to select homology models for virtual compound screening and to discover ligands that bind to one set of receptors but not to another, potentially similar, set. A serial docking algorithm is furthermore described that reduces the computational costs of such calculations by testing compounds against a series of receptor structures and discarding a compound as soon as it fails to satisfy specified bind/no bind criteria for each receptor. The algorithm also realizes substantial efficiencies by taking advantage of the fact that a ligand typically binds in similar conformations to similar receptors. Thus, once detailed docking has been used to fit a ligand into the first of a series of similar receptors, much less extensive calculations can be used for the remaining structures.     

Molecular modeling and dynamics of neuropeptide Y

Summary A combination of molecular modeling and molecular dynamics (MD) is used to determine a theoretical structure for neuropeptide Y (NPY). Starting with the X-ray structure for avian pancreatic polypeptide (APP), the substituted amino acids were mutated, the side chains oriented to local potential energy minima, and the entire structure minimized and subjected to an MD simulation. Comparison of the resulting NPY structure with APP X-ray and MD results showed secondary structural elements to be maintained and RMS fluctuations to be similar, although differences in both were observed. The approach presented offers a means to study the structure-function relationships of NPY and other similar polypeptides when combined with pharmacological measurements.Abbreviations NPY Neuropeptide Y - APP Avian pancreatic polypeptide - ABNR Adopted-basis Newton Raphson - MD Molecular dynamics     

Molecular dynamics simulations of peptide-surface interactions

Proteins, which are bioactive molecules, adsorb on implants placed in the body through complex and poorly understood mechanisms and directly influence biocompatibility. Molecular dynamics modeling using empirical force fields provides one of the most direct methods of theoretically analyzing the behavior of complex molecular systems and is well-suited for the simulation of protein adsorption behavior. To accurately simulate protein adsorption behavior, a force field must correctly represent the thermodynamic driving forces that govern peptide residue-surface interactions. However, since existing force fields were developed without specific consideration of protein-surface interactions, they may not accurately represent this type of molecular behavior. To address this concern, we developed a host-guest peptide adsorption model in the form of a G(4)-X-G(4) peptide (G is glycine, X is a variable residue) to enable determination of the contributions to adsorption free energy of different X residues when adsorbed to functionalized Au-alkanethiol self-assembled monolayers (SAMs). We have previously reported experimental results using surface plasmon resonance (SPR) spectroscopy to measure the free energy of peptide adsorption for this peptide model with X = G and K (lysine) on OH and COOH functionalized SAMs. The objectives of the present research were the development and assessment of methods to calculate adsorption free energy using molecular dynamics simulations with the GROMACS force field for these same peptide adsorption systems, with an oligoethylene oxide (OEG) functionalized SAM surface also being considered. By comparing simulation results to the experimental results, the accuracy of the selected force field to represent the behavior of these molecular systems can be evaluated. From our simulations, the G(4)-G-G(4) and G(4)-K-G(4) peptides showed minimal to no adsorption to the OH SAM surfaces and the G(4)-K-G(4) showed strong adsorption to the COOH SAM surface, which is in agreement with our SPR experiments. Contrary to our experimental results, however, the simulations predicted a relatively strong adsorption of G(4)-G-G(4) peptide to the COOH SAM surface. In addition, both peptides were unexpectedly predicted to adsorb to the OEG surface. These findings demonstrate the need for GROMACS force field parameters to be rebalanced for the simulation of peptide adsorption behavior on SAM surfaces. The developed methods provide a direct means of assessing, modifying, and validating force field performance for the simulation of peptide and protein adsorption to surfaces, without which little confidence can be placed in the simulation results that are generated with these types of systems.     

Molecular modeling and docking of new 2-acetamidothiazole-based compounds as antioxidant agents

The highly versatile, 2-chloroacetamido-5-(4-chlorophenylazo)thiazole (2) was synthesized and used as a precursor for the production of five 2-(2-substitutedacetamido)thiazole compounds by its reaction with different types of nucleophiles such as piperidine, morpholine, 2-mercaptobenzothiazole, 4,6-dimethyl-2-mercaptonicotinonitrile and 6-amino-2-mercapto pyrimidin-4-ol. DFT/B3LYP calculations of the isolated derivatives showed that their HOMO consisted mainly of the non-bonding lone pairs of heteroatoms while LUMO were π*-orbitals of the 2-acetamido-5-(4-chlorophenylazo)thiazole moiety. Despite the close energy gap values (ΔE_H-L) of the investigated compounds, the data showed that thiazole-pyrimidine derivative 8 has the highest energy gap while the thiazole-piperidine derivative 3a was the lowest. The DPPH antioxidant activity examination results, in comparison to BHT (Butylated hydroxytoluene) and Ascorbic acid as controls, showed that sulfide compounds 4, 6, and 8 had more respectable inhibitions (IC₅₀ = 24.17–32.26 µg/mL). Moreover, the molecular docking studies of the synthesized derivatives using protein (PDB Code-2Y9X) indicated that the sulfide compounds 4, 6, and 8 had a superior binding score, ?6.3934, ?6.5735, and ?7.2835 kcal/mol, respectively. The docking results were satisfactory, and they matched the antioxidant investigation's conclusions.     

Molecular imprinted polymers as synthetic receptors for the analysis of myco- and phyco-toxins

Continuous exposure to low doses of myco- and phyco-toxins poses severe risks to human health. Contemporary analytical methods have the sensitivity required for contamination detection and quantification, but direct application of these methods on real samples can be rarely performed because of matrix complexity. Thus, selective analytical methods, relying on intelligent functional materials are needed. Recent years have seen the increasing use of molecular imprinted polymers in contaminant analysis because these materials seem to be particularly suitable for applications where analyte selectivity is essential. In this review, several applications of molecular imprinted polymers in myco- and phyco-toxin contamination analysis will be discussed.     

Molecular modeling and thermoanalytical studies of thermophysical properties of some polymers

The results of computational modeling and experimental data on some thermophysical properties of selected polymers were compared. Different engineering polymers, e.g. polycarbonates and terephthalate polyesters, were considered and their glass transition temperatures and thermal stabilities were determined, by using thermoanalytical methods, e.g. DSC and TG. Measurements were carried out with Perkin-Elmer DSC 7 and TGA 7 instruments. Molecular modeling and computer calculations were performed at the Interdisciplinary Computer Modeling Center (ICM) of Warsaw University, using a Cray El 98 computer and the Insight II software of BIOSYM Technologies Inc. Reasonably good agreement was found between the experimental and calculated values of the glass transition temperatures of the investigated polymers, e.g. for poly(butylene terephthalate)T _g (calc.)=74C andT _g (experim.)=70C. Discrepancies were observed for the temperature of half decompositionT _d,1/2, some of them can be explained by effects of polymer molecular weight and/or char-forming effects.Polymer modeling computations were performed at the Interdisciplinary Computer Modeling Center (ICM) of the Warsaw University, where a CRAY EL 98 computer and the software of BIOSYM Technologies, Inc. were used.     

Molecular modeling of interactions between L-lysine and functionalized quartz surfaces

Molecular modeling techniques have been used to investigate the interaction of L-lysine in aqueous medium with silanol and methyl sites onto quartz substrates. The substrate effect has been studied for partially hydrophilic surfaces formed by silanol and methyl groups with a ratio of 1:5 and hydrophobic fully methylated surfaces. Molecular dynamics and static calculations indicate that L-lysine does not show any significant interaction with fully methylated surfaces, while its interaction with hydroxylated/methylated surfaces is dominated by electrostatic and H-bond terms. Accordingly, on fully methylated surfaces there is no preferential orientation of L-lysine with respect to the surface, while for hydroxylated/methylated surfaces the L-lysine-surface interaction mainly depends on the molecular orientation, with a preferred geometry involving the ammonium group pointing toward the silanol site. The structure of water shells around L-lysine molecules was shown to be strongly affected by the relative hydrophilic/hydrophobic character of the surfaces. In particular, the order is almost completely lost for partially hydrophilic surfaces, while well-defined hydration shells around L-lysine are obtained for hydrophobic surfaces.     

基于分子对接的thanatin与NDM-1分子动力学模拟研究

耐碳青霉烯类抗生素的超级细菌给人类健康带来了严重威胁,其所携带的金属 β-内酰胺酶编码基因是耐药性的主要来源。NDM-1作为其中传播最广、活性最强的 β-内酰胺酶,其抑制剂的研发刻不容缓。具有广谱作用的抗菌肽thanatin对NDM-1展现出了较好的抑制效果,但抑制机理并不清楚。本文使用HPEPDOCK与Rosetta FlexPepDock服务器,将thanatin与NDM-1进行了分子对接,并使用Desmond软件包对对接模型进行了分子动力学模拟。结果表明,thanatin与NDM-1活性中心的Zn2+ 并无直接相互作用,而作为竞争性抑制剂结合于NDM-1的活性口袋,阻止抗生素分子进入活性口袋与Zn2+ 结合,从而抑制NDM-1的水解活性。本文为研发有效的NDM临床抑制剂探索了可行的方法。     

Probing interfacial interactions and dynamics of polymers enclosed in boron nitride nanotubes

Understanding interfacial interactions in polymer systems is crucial for their applicability for instance in adhesives and coatings. Enclosing polymers in a cylindrical volume provides a system for studying interactions dictated by a continuous interfacial layer and a bulk-like volume in the middle of the cylinders. Here, we describe a simple method for enclosing polymers into boron nitride nanotubes (BNNTs) and establishing the effect of the interfacial interactions on the glass transition temperature (T_g) of the polymers by infrared spectroscopy. The volume of the inner channel is large in comparison to the volume of the loaded polymer coils, allowing the polymer to expand along the inner channel, resulting in the effect of interfacial interactions on polymer dynamics dominating over confinement effects. As examples, we loaded poly(4-vinyl pyridine), poly(methyl methacrylate), poly(vinyl pyrrolidone), and poly(disperse red 1 acrylate) in BNNTs. The strongest interaction between the studied polymer and BNNTs was observed for poly(4-vinyl pyridine), which also caused a significant increase of T_g. In addition to characterizing the effect of interfacial interactions on the thermal transitions of the polymers, this method, which is generalizable to most soluble polymer materials, can be used for studying photoinduced transitions in photoactive polymers thanks to the transparency of the BNNTs at visible wavelengths.     

Molecular modeling to rationalize ligand-support interactions in affinity chromatography

The development of rational design criteria for synthetic-ligand-based affinity chromatography requires a basic comprehension of all the factors influencing the binding capacity and selectivity of the stationary phase. In this work, molecular dynamics simulations are systematically used to investigate the impact of structural modifications of spacer and ligand on ligand-support interactions. The investigated ligands are characterized by a triazine core bi-functionalized with two amino acid side chains aimed at representing a range of hydrophobic/hydrophilic characters. As spacers both literature (1-2-diaminoethane and 1,4-substituted [1,2,3]-triazole) and speculative oligopeptidic molecules (Gly-[Ala]4-Gly, Gly-[Lys]4-Gly, and Gly-[Glu]4-Gly) have been considered to address the role of charges distribution, rigidity, and structural complexity. In this investigation, the spacer emerged as a key component: on the one hand, the choice of a proper spacer allows improving the hydrophilic character of the ligand-spacer adduct without compromising the structure of the affinity ligand, while on the other hand the use of structurally complex spacers induces spacer-support interactions that enhance the degree of solvation of the ligand regardless of its hydrophobic character. These findings suggest that the use of structured spacers could represent a viable pathway for tailoring the performances of affinity chromatography stationary phases.     

Effects of disordered interchain interactions on polaron dynamics in semiconducting polymers

Polaron dynamics in a system of two randomly coupled polymer chains is simulated using a nonadiabatic evolution method. The simulations are performed within the framework of the Su-Schrieffer-Heeger model modified to include disordered interchain interactions and an external electric field. By analysing the polaron velocity statistically, we find that the polaron motion is determined by the competition between the electric field and the disordered interchain interactions. Polaron dynamics are classified into two types, weak-coupling dynamics and strong-coupling dynamics. It is found that the strength of interchain interactions is the dominant factor controlling charge propagation in weak-coupling dynamics, whereas the effects of disorder are dominant in strong-coupling dynamics. The charge carriers tend to have higher mobility for stronger interchain coupling, and interchain coupling disorder can be favorable for charge transport depending on the coupling strength and the electric field.     

Molecular dynamics simulations of the interactions between platinum clusters and carbon platelets

Molecular dynamics simulations have been performed with two reactive force fields to investigate the structure of a Pt100 cluster adsorbed on the three distinct sides of a carbon platelet. A revised Reax force field for the carbon-platinum system is presented. In the simulations, carbon platelet edges both with and without hydrogen termination have been studied. It is found that the initial mismatch between the atomic structure of the platelet egde and the adsorbed face of the Pt100 cluster leads to a desorption of a few platinum atoms from the cluster and the subsequent restructuring of the cluster. Consequently, the average Pt-Pt bond length is enlarged in agreement with experimental results. This change in the bond length is supposed to play an important role in the enhancement of the catalytic activity, which is demonstrated by studying the changes in the bond order of the platinum atoms. We found an overall shift to lower values as well as a loss of the well-defined peak structure in the bond-order distribution.     

Molecular properties of conjugates formed by synthetic hydrophilic polymers and sterically hindered phenols

Water-soluble conjugates are prepared via the chemical modification of poly(vinyl alcohol) and poly(ethylene glycol) by antioxidants taken from the family of sterically hindered phenols. The effects of the degree of substitution of conjugates on the dimensions of molecules and their aggregates are studied by viscometry and light scattering in dilute solutions. It is shown that an increase in the amount of antioxidant groups incorporated into the poly(vinyl alcohol) chain leads to a decrease in the dimensions of single conjugate molecules owing to attraction of hydrophobic groups. Poly(ethylene glycol) molecules carrying end groups of sterically hindered phenols form micellar aggregates that are absent in the solution of the initial polymer. The mean number of molecules involved in such an aggregate is 83. It is found that the presence of hydrophobic end groups in poly(ethylene glycol) molecules causes a sharp reduction in the lower critical solution temperature of a solution relative to that of the initial polymer.     

Molecular dynamics of solid polymers as revealed by deuteron NMR

Pulsed deuteron NMR spectroscopy is described, which has recently been developed to become a powerful tool for studying molecular dynamics in solid polymers. It is shown that by analyzing the line shapes of²H absorption spectra and spectra obtained via solid echo and spin alignment, respectively, both type and timescale of rotational motions can be determined over an extraordinary wide range of characteristic frequencies, approximately 10 MHz to 1 Hz. By applying these techniques to selectively deuterated polymers, motional mechanisms involving different segments of the monomer unit can be monitored. In addition, motional heterogeneities in glassy polymers can be detected. The information about polymer dynamics available now is illustrated by a number of experimental examples. The chain motion in the amorphous regions of linearpolyethylene is discussed in detail and it is shown that it can clearly be distinguished from the chain motion of an amorphous polymer above the glass transition, wherepolystyrene is used as an example. Localized motions in the glassy state are illustrated through the jump motion phenyl groups exhibit both in the main chain (polycarbonate) and as a side group (polystyrene). The latter polymers also serve as examples for detecting motional heterogeneity. Finally, the mobility in novel classes of systems,liquid crystalline polymers andpolymer model membranes as revealed by²H NMR are described.