scholarly journals Multi-Body Interactions in Molecular Docking Program Devised with Key Water Molecules in Protein Binding Sites

Molecules ◽  
2018 ◽  
Vol 23 (9) ◽  
pp. 2321 ◽  
Author(s):  
Wei Xiao ◽  
Disha Wang ◽  
Zihao Shen ◽  
Shiliang Li ◽  
Honglin Li
Keyword(s):  
The Other ◽  
Water Molecules ◽  
Protein Targets ◽  
Docking Simulations ◽  
Cross Docking ◽  
Docking Program ◽  
Screening Efficiency ◽  
Multi Body ◽  
Docking Accuracy ◽  
Length Optimization

Water molecules play an important role in modeling protein-ligand interactions. However, traditional molecular docking methods often ignore the impact of the water molecules by removing them without any analysis or keeping them as a static part of the proteins or the ligands. Hence, the accuracy of the docking simulations will inevitably be damaged. Here, we introduce a multi-body docking program which incorporates the fixed or the variable number of the key water molecules in protein-ligand docking simulations. The program employed NSGA II, a multi-objective optimization algorithm, to identify the binding poses of the ligand and the key water molecules for a protein. To this end, a force-field-based hydration-specific scoring function was designed to favor estimate the binding affinity considering the key water molecules. The program was evaluated in aspects of the docking accuracy, cross-docking accuracy, and screening efficiency. When the numbers of the key water molecules were treated as fixed-length optimization variables, the docking accuracy of the multi-body docking program achieved a success rate of 80.58% for the best RMSD values for the recruit of the ligands smaller than 2.0 Å. The cross-docking accuracy was investigated on the presence and absence of the key water molecules by four protein targets. The screening efficiency was assessed against those protein targets. Results indicated that the proposed multi-body docking program was with good performance compared with the other programs. On the other side, when the numbers of the key water molecules were treated as variable-length optimization variables, the program obtained comparative performance under the same three evaluation criterions. These results indicated that the multi-body docking with the variable numbers of the water molecules was also efficient. Above all, the multi-body docking program developed in this study was capable of dealing with the problem of the water molecules that explicitly participating in protein-ligand binding.

Improving protein–ligand binding prediction by considering the bridging water molecules in Autodock

2019 ◽  
Vol 18 (05) ◽  
pp. 1950027 ◽  
Author(s):  
Qiangna Lu ◽  
Lian-Wen Qi ◽  
Jinfeng Liu
Keyword(s):  
Ligand Binding ◽  
Considerable Improvement ◽  
Ligand Docking ◽  
Water Molecules ◽  
Binding Modes ◽  
Binding Prediction ◽  
Docking Simulations ◽  
Protein Ligand Interactions ◽  
Ligand Interactions ◽  
Docking Program

Water plays a significant role in determining the protein–ligand binding modes, especially when water molecules are involved in mediating protein–ligand interactions, and these important water molecules are receiving more and more attention in recent years. Considering the effects of water molecules has gradually become a routine process for accurate description of the protein–ligand interactions. As a free docking program, Autodock has been most widely used in predicting the protein–ligand binding modes. However, whether the inclusion of water molecules in Autodock would improve its docking performance has not been systematically investigated. Here, we incorporate important bridging water molecules into Autodock program, and systematically investigate the effectiveness of these water molecules in protein–ligand docking. This approach was evaluated using 18 structurally diverse protein–ligand complexes, in which several water molecules bridge the protein–ligand interactions. Different treatment of water molecules were tested by using the fixed and rotatable water molecules, and a considerable improvement in successful docking simulations was found when including these water molecules. This study illustrates the necessity of inclusion of water molecules in Autodock docking, and emphasizes the importance of a proper treatment of water molecules in protein–ligand binding predictions.

Intercalation Processes in Cobalt Substituted Nickel Oxyhydroxides

1990 ◽  
Vol 210 ◽  
Author(s):  
Claude Delmas
Keyword(s):  
Ir Spectroscopy ◽  
Mechanical Treatment ◽  
Positive Charge ◽  
Van Der Waals ◽  
The Other ◽  
Hydrolysis Reaction ◽  
Water Molecules ◽  
Layered Oxides ◽  
Experimental Conditions ◽  
Cobalt Ions

AbstractChimie douce reactions (hydrolysis and reduction) from layered oxides : NaNiO2, NaxCoO2 and NaNil-xCoxO2 lead to numerous oxyhydroxides and hydroxides which differ by the composition of the intersheet space.According to the experimental conditions of the hydrolysis reaction, the oxyhydroxides can be unhydrated or intercalated with one or two layers of water molecules. From the most hydrated phases, the other ones can be obtained by chemical, thermal and even mechanical treatment.The reduction of Co-substituted nickel oxyhydroxides leads to hydroxides in which nickel and cobalt ions are respectively divalent and trivalent. In order to compensate the excess of positive charge in the (Ni, Co)O2 sheet, anions (OH-, CO32-, SO42-, NO3-) are inserted in the Van der Waals gap.For the highest anion amounts, well ordered α*-type materials are obtained. Water molecules are simultaneously inserted in the interslab space. Their structure is strongly related to the hydrotalcite one. When the amouit of anions in the intersheet space is not sufficient, interstratified materials are obtained. In this case the (Ni,Co)(OH)2 slabs are separated by a layer of CO32- anions and water molecules (α*-type) or by an empty Van der Waals gap (β(II)-type). The amount of α*-type planes in the structure increases with the cobalt amount. All these materials have been characterized by IR spectroscopy which allows to detect the existence of two types of O-H bonds (free in α*-type plane or hydrogen bonded in ²(II)-type plane).

scholarly journals Removal of Chromium from Aqueous Solution Using Modified Pomegranate Peel:Mechanistic and Thermodynamic Studies

2009 ◽  
Vol 6 (s1) ◽  
pp. S153-S158 ◽  
Author(s):  
Tariq S. Najim ◽  
Suhad A. Yassin
Keyword(s):  
Activation Energy ◽  
Solid Solution ◽  
Aqueous Solution ◽  
Adsorption Process ◽  
Batch Process ◽  
The Other ◽  
Water Molecules ◽  
Pomegranate Peel ◽  
Solution Interface ◽  
Adsorbent Surface

Modified pomegranate peel (MPGP) and formaldehyde modified pomegranate peel (FMPGP) were prepared and used as adsorbent for removal of Cr(VI) ions from aqueous solution using batch process. The temperature variation study of adsorption on both adsorbents revealed that the adsorption process is endothermic, from the positive values of ∆H˚. These values lie in the range of physisorption. The negative values of ∆G˚ show the adsorption is favorable and spontaneous. On the other hand, these negative values increases with increase in temperature on both adsorbents, which indicate that the adsorption is preferable at higher temperatures. ∆S˚ values showed that the process is accompanied by increase in disorder and randomness at the solid solution interface due to the reorientation of water molecules and Cr(VI) ions around the adsorbent surface. The endothermic nature of the adsorption was also confirmed from the positive values of activation energy, Ea, the low values of Ea confirm the physisorption mechanism of adsorption. The sticking probability, S*, of Cr(VI) ion on surface of both adsorbents showed that the adsorption is preferable due to low values of S*(0< S*< 1 ), but S*values are lower for FMPGP indicating that the adsorption on FMPGP is more preferable .

scholarly journals Two New Polyiodides in the 4,4´-Bipyridinium Diiodide/Iodine System

2012 ◽  
Vol 67 (1) ◽  
pp. 5-10
Author(s):  
Guido J. Reiss ◽  
Martin van Megen
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Complex I ◽  
The Other ◽  
Cyclic Dimer ◽  
Water Molecules ◽  
Spectroscopic Methods ◽  
Halogen Bonds ◽  
One Dimensional ◽  
Hydroiodic Acid

The reaction of bipyridine with hydroiodic acid in the presence of iodine gave two new polyiodide-containing salts best described as 4,4´-bipyridinium bis(triiodide), C10H10N2[I3]2, 1, and bis(4,4´-bipyridinium) diiodide bis(triiodide) tris(diiodine) solvate dihydrate, (C10H10N2)2I2[I3]2 · 3 I2 ·2H2O, 2. Both compounds have been structurally characterized by crystallographic and spectroscopic methods (Raman and IR). Compound 1 is composed of I3 − anions forming one-dimensional polymers connected by interionic halogen bonds. These chains run along [101] with one crystallographically independent triiodide anion aligned and the other triiodide anion perpendicular to the chain direction. There are no classical hydrogen bonds present in 1. The structure of 2 consists of a complex I144− anion, 4,4´-bipyridinium dications and hydrogen-bonded water molecules in the ratio of 1 : 2 : 2. The I144− polyiodide anion is best described as an adduct of two iodide and two triiodide anions and three diiodine molecules. Two 4,4´-bipyridinium cations and two water molecules form a cyclic dimer through N-H· · ·O hydrogen bonds. Only weak hydrogen bonding is found between these cyclic dimers and the polyiodide anions.

A tetranuclear carbonyl fluoro rhenium(I) cluster, [Re(CO)3F]4,4H2O

1981 ◽  
Vol 34 (4) ◽  
pp. 737 ◽  
Author(s):  
E Horn ◽  
MR Snow
Keyword(s):  
Hydrogen Bonding ◽  
Title Compound ◽  
The Other ◽  
Water Molecules ◽  
Molecular Symmetry ◽  
Group 14 ◽  
Full Matrix ◽  
Abstraction Reaction ◽  
R Value ◽  
Silver Fluoride

The title compound has been prepared from Re(CO)5Br by a bromide-abstraction reaction with silver fluoride. It completes the series of known halide clusters of the type [Re(CO)3X]4 (where X = halide). The crystals are tetragonal, space group 14, with a 11.716(5), c 8.988(3) �, and Z 2. The structure was refined by full-matrix least-squares to an R value of 0.027 for 1380 observed reflections. The molecules are cubane-type clusters of Re(CO)3 groups at one set of corners interpenetrated with fluorine atoms at the other set. The clusters exhibit the molecular symmetry 43m. Each of the fluorine atoms is involved in μ3 type bridging with the rhenium atoms at an average bonding distance of 2.200(5) �. The clusters are held together by hydrogen bonding of fluoride to water molecules.

Crystal Structure of Calcium Picrate Pentahydrate: A New Eight-Coordinate Stereochemistry for [M(bidentate)2(unidentate)4]

1979 ◽  
Vol 32 (2) ◽  
pp. 301 ◽  
Author(s):  
V Diakiw ◽  
TW Hambley ◽  
DL Kepert ◽  
CL Raston ◽  
AH White
Keyword(s):  
Crystal Structure ◽  
Water Molecule ◽  
Single Crystal ◽  
Title Compound ◽  
Lattice Site ◽  
The Other ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
Triangular Face ◽  
X Ray

The crystal structure of the title compound, Ca(C6H2N307)2,5H2O, has been determined by single-crystal X-ray diffraction at 295(1) K and refined by least squares to a residual of 0.049 for 1513 'observed' reflections. Crystals are orthorhombic, Pmab, a 24.169(6), b l0.292(7), c 8.554(2) �, Z 4. The stereochemistry about the calcium has not been observed previously for the system [M(bidentate)2- (unidentate)4]; in the present structure, the calcium is coordinated by a pair of bidentate picrate ligands and the four water molecules in an array in which three of the water molecules occupy a triangular face of a square antiprism, the overall array having m symmetry. The remaining water molecule occupies a lattice site with no close interaction with the other species.

A novel one-dimensional CoIIcoordination polymer:catena-poly[[hexaaquacobalt(II)] [[diaquabis(sulfato-κO)cobalt(II)]-μ-4,4′-bipyridine-κ2N:N′] [[triaqua(sulfato-κO)cobalt(II)]-μ-4,4′-bipyridine-κ2N:N′]]

2012 ◽  
Vol 68 (9) ◽  
pp. m265-m268 ◽  
Author(s):  
Kai-Long Zhong ◽  
Ming-Yi Qian
Keyword(s):  
Crystal Structure ◽  
Three Dimensional ◽  
The Other ◽  
Water Molecules ◽  
Supramolecular Network ◽  
Sulfate Ion ◽  
Sulfate Ions ◽  
One Dimensional ◽  
The Third ◽  
Hydrogen Bonding Interactions

The title compound, {[Co(H2O)6][Co(SO4)(C10H8N2)(H2O)3][Co(SO4)2(C10H8N2)(H2O)2]}n, contains three crystallographically unique CoIIcentres, all of which are in six-coordinated environments. One CoIIcentre is coordinated by two bridging 4,4′-bipyridine (4,4′-bipy) ligands, one sulfate ion and three aqua ligands. The second CoIIcentre is surrounded by two N atoms of two 4,4′-bipy ligands and four O atoms,i.e.two O atoms from two monodentate sulfate ions and two from water molecules. The third CoIIcentre forms part of a hexaaquacobalt(II) ion. In the crystal structure, there are two different one-dimensional chains, one being anionic and the other neutral, and adjacent chains are arranged in a cross-like fashion around the mid-point of the 4,4′-bipy ligands. The structure features O—H...O hydrogen-bonding interactions between sulfate anions and water molecules, resulting in a three-dimensional supramolecular network.

Ligand Hyperfine Interaction in the Complex [Mn(H2O)6] ++ in La2(Mg,Mn)3(NO3)12·24H2O

1969 ◽  
Vol 24 (11) ◽  
pp. 1746-1751 ◽  
Author(s):  
D. van Ormondt ◽  
R. de Beer ◽  
M. Brouha ◽  
F. de Groot
Keyword(s):  
Simple Model ◽  
Water Molecule ◽  
Hyperfine Interaction ◽  
Principal Direction ◽  
The Other ◽  
Water Molecules ◽  
Manganese Ion ◽  
Interaction Tensor ◽  
Principal Directions

Abstract The elements of the hyperfine interaction (h.f.i.) between the manganese ion and the protons in the complex [Mn(H2O)6]++ in one of the two possible sites in La2(Mg, Mn)3(NO3)12 · 24 H2O have been measured with ENDOR at 15 to 20 K. The six water molecules in the complex at the chosen site are equivalent for reasons of symmetry.One principal direction of the h.f.i. tensor of each proton is found to be perpendicular to the Mn, O line. With the assumption that each proton is located in the plane of the other two principal directions of its interaction tensor the positions of the protons are evaluated from the anisotropic parts of the h.f.i. tensors. In this calculation the effect of covalency on the anisotropic h.f.i. is ac-counted for with the aid of a simple model.The isotropic h.f.i.'s with the two protons of a water molecule appear to be very nearly equal (+ 0.890 MHz for both). This latter result is remarkable in view of the fact that one proton is distinctly nearer to the manganese ion than the other.

scholarly journals Bis[tris(propane-1,3-diamine-κ2N,N′)nickel(II)] diaquabis(propane-1,3-diamine-κ2N,N′)nickel(II) hexabromide dihydrate

2014 ◽  
Vol 70 (6) ◽  
pp. m227-m228 ◽  
Author(s):  
Aymen Yangui ◽  
Walid Rekik ◽  
Slim Elleuch ◽  
Younes Abid
Keyword(s):  
Hydrogen Bonds ◽  
Title Compound ◽  
General Position ◽  
Three Dimensional ◽  
The Other ◽  
Octahedral Coordination ◽  
Water Molecules ◽  
Coordination Environment ◽  
Lattice Water ◽  
Dimensional Network

In the title compound, [Ni(C3H10N2)3]2[Ni(C3H10N2)2(H2O)2]Br6·2H2O, one Ni2+cation, located on an inversion centre, is coordinated by four N atoms from two ligands and by two water O atoms. The other Ni2+cation, located in a general position, is coordinated by six N atoms from three ligands. In both cases, the Ni2+cation has an octahedral coordination environment. The overall structural cohesion is ensured by three types of hydrogen bonds, N—H...Br, O—H...Br and O—H...O, which connect the two types of complex cations, the bromide counter-anions and the lattice water molecules into a three-dimensional network.

Protein environment affects the water–tryptophan binding mode. MD, QM/MM, and NMR studies of engrailed homeodomain mutants

2018 ◽  
Vol 20 (18) ◽  
pp. 12664-12677 ◽  
Author(s):  
Nad'a Špačková ◽  
Zuzana Trošanová ◽  
Filip Šebesta ◽  
Séverine Jansen ◽  
Jaroslav V. Burda ◽  
...  
Keyword(s):  
Amino Acids ◽  
Lone Pair ◽  
Binding Mode ◽  
The Other ◽  
Water Molecules ◽  
Interaction Type ◽  
Nmr Studies ◽  
Engrailed Homeodomain ◽  
The One ◽  
Protein Environment

Water molecules can interact with the π-face of tryptophan either forming an O–H⋯π hydrogen bond or by a lone-pair⋯π interaction. Surrounding amino acids can favor the one or the other interaction type.

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