Docking small ligands in flexible binding sites

A novel procedure for docking ligands in a flexible binding site is presented. It relies on conjugate gradient minimization, during which nonbonded interactions are gradually switched on. Short Monte Carlo minimization runs are performed on the most promising candidates. Solvation is implicitly taken into account in the evaluation of structures with a continuum model. It is shown that the method is very accurate and can model induced fit in the ligand and the binding site. The docking procedure has been successfully applied to three systems. The first two are the binding of progesterone and 5β-androstane-3,17-dione to the antigen binding fragment of a steroid binding antibody. A comparison of the crystal structures of the free and the two complexed forms reveals that any attempt to model binding must take protein rearrangements into account. Furthermore, the two ligands bind in two different orientations, posing an additional challenge. The third test case is the docking of N^α-(2-naphthyl-sulfonyl-glycyl)-D -para-amidino-phenyl-alanyl-piperidine (NAPAP) to human α-thrombin. In contrast to steroids, NAPAP is a very flexible ligand, and no information of its conformation in the binding site is used. All docking calculations are started from X-ray conformations of proteins with the uncomplexed binding site. For all three systems the best minima in terms of free energy have a root mean square deviation from the X-ray structure smaller than 1.5 Å for the ligand atoms. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 21–37, 1998     

Conformational analysis of polypropylene chains bound to model catalytic sites

The models of catalytic sites for isospecific Ziegler-Natta polymerization proposed previously (edges and reliefs on lateral surfaces of violet TiCl₃) are compared in order to verify their validity in the presence of long alkyl groups and of analyzing the conformational constraints imposed by the TiCl₃ surface on the growing chain. Our results indicate that sites on edges of lateral surfaces parallel or nearly parallel to the c axis may be not suitable for the coordination of long alkyl chains; the coordination of long alkyl chains at less hindered sites, such as edges of inclined lateral surfaces or reliefs, do not involve any increase of repulsive interactions for an isobutyl group. Further, these latter sites allow the optimum spiralization of the chain at a very early stage of growth, and their isospecific behaviour is not affected by the presence of configuration defects in the growing chain.     

Conformational analysis of a flexible oligosaccharide using residual dipolar couplings.

We present a new approach to the analysis of the conformational and the motional properties of an oligosaccharide, methyl 3,6-di-O-(alpha-D-mannopyranosyl)-alpha-D-mannopyranoside. The approach relies on an order matrix analysis of residual dipolar couplings in the solution state. By combining a number of different types of couplings, (1)D(CH), (2)D(CH), and D(HH), an order matrix is solved for each ring of the trimannoside. The resulting order parameters indicate the internal motion at the alpha (1,3) linkage to be limited, while significant motion is suggested at the alpha (1,6) linkage. Two structures for the trimannoside were determined by aligning the order tensor principal axes obtained from two different orienting media, bicelles and phage. The very similar conformations at the alpha (1,3) linkage of these two structures confirm that the internal motion at the alpha (1,3) linkage is small and the conformation is a good representation of a single preferred structure. The different conformations at the alpha (1,6) linkage suggest that the motional amplitudes are large and the conformations must be viewed as virtual conformers. Compared with traditional NMR methods, data acquisition is easy and data analysis is straightforward.     

Hammerhead: fast,fully automated docking of flexible ligands to protein binding sites

Background: Molecular docking seeks to predict the geometry and affinity of the binding of a small molecule to a given protein of known structure. Rigid docking has long been used to screen databases of small molecules, because docking techniques that account for ligand flexibility have either been too slow or have required significant human intervention. Here we describe a docking algorithm, Hammerhead, which is a fast, automated tool to screen for the binding of flexible molecules to protein binding sites.Results: We used Hammerhead to successfully dock a variety of positive control ligands into their cognate proteins. The empirically tuned scoring function of the algorithm predicted binding affinities within 1.3 log units of the known affinities for these ligands. Conformations and alignments close to those determined crystallographically received the highest scores. We screened 80 000 compounds for binding to streptavidin, and biotin was predicted as the top-scoring ligand, with other known ligands included among the highest-scoring dockings. The screen ran in a few days on commonly available hardware.Conclusions: Hammerhead is suitable for screening large databases of flexible molecules for binding to a protein of known structure. It correctly docks a variety of known flexible ligands, and it spends an average of only a few seconds on each compound during a screen. The approach is completely automated, from the elucidation of protein binding sites, through the docking of molecules, to the final selection of compounds for assay.     

Conformational energy penalties of protein-bound ligands

The conformational energies required for ligands to adopt their bioactive conformations were calculated for 33 ligand–protein complexes including 28 different ligands. In order to monitor the force field dependence of the results, two force fields, MM3 and AMBER, were employed for the calculations. Conformational analyses were performed in vacuo and in aqueous solution by using the generalized Born/solvent accessible surface (GB/SA) solvation model. The protein-bound conformations were relaxed by using flat-bottomed Cartesian constraints. For about 70% of the ligand–protein complexes studied, the conformational energies of the bioactive conformations were calculated to be 3 kcal/mol. It is demonstrated that the aqueous conformational ensemble for the unbound ligand must be used as a reference state in this type of calculations. The calculations for the ligand–protein complexes with conformational energy penalties of the ligand calculated to be larger than 3 kcal/mol suffer from uncertainties in the interpretation of the experimental data or limitations of the computational methods. For example, in the case of long-chain flexible ligands (e.g. fatty acids), it is demonstrated that several conformations may be found which are very similar to the conformation determined by X-ray crystallography and which display significantly lower conformational energy penalties for binding than obtained by using the experimental conformation. For strongly polar molecules, e.g. amino acids, the results indicate that further developments of the force fields and of the dielectric continuum solvation model are required for reliable calculations on the conformational properties of this type of compounds.     

Conformational analysis of nucleic acid molecules with flexible furanose rings in dihedral angle space

The computational algorithm that works in the coordinate space of dihedral angles (i.e., bond lengths and bond angles are kept fixed and only rotatable dihedral angles are treated as independent variables) is extended to deal with the pseudorotational m otion of furanose rings by introducing a variable of pseudorotation. Then, this algorithm is applied to a distance geometry calculation that generates three-dimensional (3D) structures that are consistent with given constraints of interatomic distances. This method efficiently generates 3D structures of an RNA hairpin loop which satisfy a set of experimental NMR data. © 1996 by John Wiley & Sons, Inc.     

Conformational analysis and the binding sites of nitrilotriacetamide: A computational study

The conformational analysis of nitrilotriacetamide has been carried out computationally, at both the semi‐empirical AM1 and density functional theory (DFT) (B3LYP/6‐31+G*) levels of theory. The lowest‐energy conformation predicted with the Monte Carlo search method, using the AM1 model, has two amide functionalities aligned on the same side; however, the DFT calculations at B3LYP/6‐31+G* predicted the global minimum with all three acetamide functionalities on the same side in the gas phase. In the aqueous phase, the DFT results predicted the orientations of amides similar to that of the reported crystal structure. The rotation barriers to transition to different low‐energy conformers of nitrilotriacetamide are lower in energy (5.0 kcal/mol) in water. The molecular electrostatic isopotentials (MESP) generated for the selected conformers at DFT level show that the nitrilotriacetamide could interact more effectively with the sodium chloride surface than that of its monomeric unit nitrilomonoacetamide. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Synthesis of new macromolecular, functionalized carboxylic-acid-PEG-DHLA surface ligands

An efficient method for the synthesis of new macromolecular surface ligands for quantum dots functionalization has been developed. The new ligands contain a dihydrolipoic acid unit which is connected to either a mono- or a diacid terminal function by a PEG chain.     

Conformational properties of macromolecular pyramoids and their potential use as nano-containers

We study the macroscopic behavior of a pyramid-like nano-construct made of linear macromolecular chains. The average mean square end-to-end distances of the six edges of the pyramoid are evaluated by means of the Gaussian chain model and are found smaller than those of free chains because of architecture confinement. We also evaluate the average areas of the four faces which give a first estimate of the open windows towards the interior space of the macromolecular construct and its loading capacity. The average volume of the polymeric nano-container, which provides a measure of its interior emptiness and carrying ability, is estimated as well. The density of monomers at each point of the construct shows the three-dimensional character of the nano-cage and the location of its entrances and voids.     

Conformational analysis of 5-H-dibenzo[a,d]cycloheptene derivatives with flexible amino-substituted side-chains by means of lanthanide induced shifts (LIS). Conformational analysis of highly flexible structures,part III

Summary TheLIS data of 5-(3-N,N-dimethylaminopropyl)-5H-dibenzo[a,d]cycloheptene (1), 5-(3-N,N-dimethyl-and 5-(3-N-methylaminopropylidene)-10,11-dihydro-5H-dibenzo[a,d]-cycloheptene (2,2a) and 5-(3-N,N-dimethylaminopropyl)-10,11-dihydro-5H-dibenzo[a,d]cycloheptene (3) were used to calculate populations of possible conformers in solution. The substrate geometries of the particular conformers were taken from force field calculations. ALIS simulation program was used which is able to handle up to four possible conformations. The limits and special features of the method for highly flexible structures — especially for the case that the coordinating group is within a flexible chain — are discussed.

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Konformationsanalyse von 5-H-Dibenzo[a,d]cyclohepten-Derivaten mit flexiblen aminosubstituierten Seitenketten mittels Lanthaniden-induzierter Verschiebungen. Konformationsanalyse hochflexibler Strukturen, 3. Mitt.

Zusammenfassung DieLIS-Werte von 5-(3-N,N-Dimethylaminopropyl)-5H-dibenzo[a,d]-cyclohepten (1), 5-(3-N,N-Dimethyl- bzw. 5-(3-N-Methylaminopropyliden)-10,11-dihydro-5H-dibenzo[a,d]-cyclohepten (2 bzw.2a) und 5-(3-N,N-Dimethylaminopropyl)-10,11-dihydro-5H-dibenzo[a,d]cyclohepten (3) wurden zur Berechnung von Populationen bevorzugter Konformerer herangezogen. Die Geometrien der einzelnen Konformeren wurden aus Force-Field-Rechnungen entnommen. Es wurde einLIS-Programm verwendet, das bei der Simulation bis zu vier Konformationen berücksichtigen kann. Die Grenzen der Anwendbarkeit der Methode — insbesondere die speziellen Probleme die auftreten, wenn die Koordinationsstelle innerhalb einer flexiblen Kette liegt — werden diskutiert.

     

Conformational analysis: crystallographic,NMR, and molecular mechanics studies of flexible sulfonic esters

Two novel X-ray structures of the sulfonic ester derivatives 2-(6-iodo-1,3-benzodioxol-5-yl)ethyl 4-nitrobenzenesulfonate, 3, and 2-(6-iodo-1,3-benzodioxol-5-yl)ethyl 4-methylbenzenesulfonate, 4, have been obtained in a study aimed at analyzing the structures and conformations of sulfonic ester derivatives that are routinely used in alkaloid syntheses. The crystal structure of 4 is highly unusual, containing four independent molecules that belong to two distinct conformational types: (1) a hairpin conformation (stabilized mainly by intramolecular pi-stacking) and (2) a stepped conformation (stabilized mainly by intermolecular pi-stacking). Compound 3, on the other hand, crystallizes exclusively as the hairpin conformer. New MM+ force field parameters for sulfonic esters have been developed using the X-ray data, empirical rules, and DFT calculations to estimate the bond dipole parameters. Grid searches of conformational space for 3 and 4 using MM methods show that there are several gas-phase conformations within 5 kcal/mol of the global minimum and that the lowest energy conformations (by approximately 4.6 kcal/mol) are of the hairpin type. Analysis of the MM conformational energies suggests that the dominant intramolecular interaction stabilizing the hairpin conformations of 3 and 4 is van der Waals attraction. Moreover, the lattice energies for packing the hairpin conformations of 3 and 4 are approximately 4 kcal/mol more favorable than for the stepped conformations. Various intermolecular interactions contribute to the complexity of the observed crystal structures of 3 and 4, including electrostatic attraction between O and I atoms in neighboring molecules. Langevin dynamics (LD) simulations at several temperatures (6.0 ns, friction coefficient = 2.5 ps(-1)) indicate that the conformational exchange rates are approximately 10(10)-10(11) s(-1) over the temperature range 213-400 K, accounting for the temperature-independent (1)H NMR spectra of 3 and 4.     

Synthesis and pharmacological analysis of high affinity melatonin receptor ligands

We report the synthesis and radioligand binding analysis of a series of naphthalenic melatonin receptor ligands, N-[2-(7-alkoxy-2-methoxy-1-naphthyl)ethyl]propionamide. This series of ligands exhibits subpicomolar binding affinity to both MT1 and MT2 melatonin receptors expressed in chinese hamster ovary (CHO) cells.     

Guest-dependent flexible coordination networks with fluorinated ligands

Guest-dependent flexible coordination networks are formed from 1,4-bis(4-pyridylmethyl)tetrafluorobenzene (bpf), 4,4'-bis(4-pyridylmethyl)octafluorobiphenyl (bpfb), 2,6-bis(4-pyridylmethyl)hexafluoronaphthalene (2,6-bpfn), and 2,7-bis(4-pyridylmethyl)hexafluoronaphthalene (2,7-bpfn) with Cd(NO3)2 in the presence of various organic compounds. The reaction of bpf affords one-dimensional cyclic chains, two-dimensional rhombus grid sheets, and three-dimensional diamond frameworks with threefold interpenetration. The reaction of bpfb mainly affords two-dimensional rhombus grid sheets with twofold parallel interpenetration. The reaction of 2,6-bpfn affords a one-dimensional ladder and two-dimensional rhombus grid, twisted grid, and herringbone sheets. The reaction of 2,7-bpfn affords two-dimensional rhombus grid sheets and grid sheets with dumbbell-shaped cavities. This diversity of network topologies is induced by interactions between the guest molecules and the flexible ligand frameworks.     

Conformational studies of novel estrogen receptor ligands by 1D and 2D NMR spectroscopy and computational methods

The solution conformations of the novel estrogen receptor ligands (17α,20E)‐(p‐trifluoromethylphenyl)vinylestradiol ( 1 ) and (17α,20E)‐(o‐trifluoromethylphenyl)vinylestradiol ( 2 ) were investigated in 2D and 1D NOESY studies and by comparison of ¹³C NMR chemical shifts with theoretical shieldings. The ¹H and ¹³C assignments of 1 and 2 were determined by DEPT, COSY and HMQC experiments. The conformations of the 17α‐phenylvinyl substituents of 1 and 2 are of interest because of their differing receptor binding affinities and effects in in vivo uterotrophic growth assays. A statistical method of evaluating contributing conformers of 1 and 2 from predicted ¹³C shifts of possible structures correlated fairly well with conformational conclusions derived from the NOE data. The 17α substituents of 1 and 2 apparently exist in similar conformational equilibria, suggesting that while 1 and 2 would occupy a similar receptor volume, interactions with the protein may shift the equilibrium and thereby influence the expression of the ligand. Copyright © 2003 John Wiley & Sons, Ltd.     

Development of multivalent macromolecular ligands for enhanced detection of biological targets

Macromolecular conjugates enable simultaneous binding of multiple ligands on one biological entity and these polyvalent interactions can be collectively stronger than the corresponding monovalent ligands. We have synthesized macromolecules and conjugated them with a lectin (Helix Pomatia lectin, HPA), and an antibody, both with shown affinities to certain bacteria. The binding ability was studied by flow cytometry and the results showed that the affinity of the biomolecules was greatly enhanced due to the polyvalent effect.