What induces pocket openings on protein surface patches involved in protein–protein interactions?

We previously showed for the proteins BCL-X_L, IL-2, and MDM2 that transient pockets at their protein–protein binding interfaces can be identified by applying the PASS algorithm to molecular dynamics (MD) snapshots. We now investigated which aspects of the natural conformational dynamics of proteins induce the formation of such pockets. The pocket detection protocol was applied to three different conformational ensembles for the same proteins that were extracted from MD simulations of the inhibitor bound crystal conformation in water and the free crystal/NMR structure in water and in methanol. Additional MD simulations studied the impact of backbone mobility. The more efficient CONCOORD or normal mode analysis (NMA) techniques gave significantly smaller pockets than MD simulations, whereas tCONCOORD generated pockets comparable to those observed in MD simulations for two of the three systems. Our findings emphasize the influence of solvent polarity and backbone rearrangements on the formation of pockets on protein surfaces and should be helpful in future generation of transient pockets as putative ligand binding sites at protein–protein interfaces. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Inhibition of protein interactions: co-crystalized protein–protein interfaces are nearly as good as holo proteins in rigid-body ligand docking

Modulating protein interaction pathways may lead to the cure of many diseases. Known protein–protein inhibitors bind to large pockets on the protein–protein interface. Such large pockets are detected also in the protein–protein complexes without known inhibitors, making such complexes potentially druggable. The inhibitor-binding site is primary defined by the side chains that form the largest pocket in the protein-bound conformation. Low-resolution ligand docking shows that the success rate for the protein-bound conformation is close to the one for the ligand-bound conformation, and significantly higher than for the apo conformation. The conformational change on the protein interface upon binding to the other protein results in a pocket employed by the ligand when it binds to that interface. This proof-of-concept study suggests that rather than using computational pocket-opening procedures, one can opt for an experimentally determined structure of the target co-crystallized protein–protein complex as a starting point for drug design.     

Synthesis,characterization and biological screening studies of mixed ligand complexes using flavonoids as precursors

Flavonoids are a group of plant phenolics that provide various health benefits through cell signalling pathways and antioxidant effects. In the present study, a new series of mixed ligand complexes of Co(II), Ni(II), Cu(II) and Zn(II) were synthesized by incorporating curcumin and quercetin flavonoid precursors. The structural features of the synthesized complexes were explored using elemental analysis, thermogravimetric analysis, UV–visible, infrared, NMR, mass and electron paramagnetic resonance spectral analyses and conductivity measurements. These data support an octahedral geometry of the synthesized complexes. In silico biological activity score for the ligand was predicted using PASS online software. ADMET properties were studied using VLS3D online software. Anti‐inflammatory and antioxidant activities were experimentally validated which prove that theoretical predictions are in agreement with the experimental results. Interestingly the synthesized complexes interact with calf thymus DNA through groove binding mode. Moreover, they have good potential to cleave pUC19 DNA. Minimum inhibitory concentration values of the synthesized complexes reveal that they have better antimicrobial efficacy than the ligands.     

Coarse‐grained molecular dynamics simulations of protein–ligand binding

Coarse‐grained molecular dynamics (CGMD) simulations with the MARTINI force field were performed to reproduce the protein–ligand binding processes. We chose two protein–ligand systems, the levansucrase–sugar (glucose or sucrose), and LinB–1,2‐dichloroethane systems, as target systems that differ in terms of the size and shape of the ligand‐binding pocket and the physicochemical properties of the pocket and the ligand. Spatial distributions of the Coarse‐grained (CG) ligand molecules revealed potential ligand‐binding sites on the protein surfaces other than the real ligand‐binding sites. The ligands bound most strongly to the real ligand‐binding sites. The binding and unbinding rate constants obtained from the CGMD simulation of the levansucrase–sucrose system were approximately 10 times greater than the experimental values; this is mainly due to faster diffusion of the CG ligand in the CG water model. We could obtain dissociation constants close to the experimental values for both systems. Analysis of the ligand fluxes demonstrated that the CG ligand molecules entered the ligand‐binding pockets through specific pathways. The ligands tended to move through grooves on the protein surface. Thus, the CGMD simulations produced reasonable results for the two different systems overall and are useful for studying the protein–ligand binding processes. © 2014 Wiley Periodicals, Inc.     

Estimation of important binding sites in compounds that interact with proteins

Proteins are one of the important substances in understanding biological activity, and many of them express the function by binding to other proteins or small molecules (ligands) on the molecular surface. This interaction often occurs in the hollows (pockets) on the molecular surface of the protein. It is known that when pockets are similar in structure and physical properties, they are likely to express similar functions and to bind similar ligands. Therefore, exploring the similarity of the structure and physical properties in pockets is very useful because it leads to the discovery of new ligands that are likely to bind. In addition, exploring the important structure when binding to the protein significant spot in the ligand will provide useful knowledge for the development of new ligands.In this study, we propose a method to search for proteins containing pockets that are structurally and physically similar to significant spot in the pocket of the analyzed protein, and to extract significant spots in the ligands that bind to them. We use feature points as data. Feature points are the 3-dimensional points that are extracted from 3D structure data of proteins with feature values quantifying hydrophobicity and electrostatic potential. The corresponding feature points are extracted by comparing structurally and physically the pockets of the search target proteins with the significant spot of the analyzed protein. By evaluating the similarity based on the comparison results of the feature values given to the extracted feature points, we search for proteins that are similar to the analyzed protein. From the ligands that bind to the searched proteins, atoms that are near the protein pocket and similar to the atoms in ligand binding to the analyzed protein are extracted. The site constituted by the extracted atoms is defined as a significant spot in the ligand.As a result of classifying ligands binding to the protein by using the extracted significant spot in the ligand, the effectiveness of the proposed method was confirmed.     

Reverse Spin‐Crossover and High‐Pressure Kinetics of the Heme Iron Center Relevant for the Operation of Heme Proteins under Deep‐Sea Conditions

By design of a heme model complex with a binding pocket of appropriate size and flexibility, and by elucidating its kinetics and thermodynamics under elevated pressures, some of the pressure effects are demonstrated relevant for operation of heme‐proteins under deep‐sea conditions. Opposite from classical paradigms of the spin‐crossover and reaction kinetics, a pressure increase can cause deceleration of the small‐molecule binding to the vacant coordination site of the heme‐center in a confined space and stabilize a high‐spin state of its Fe center. This reverse high‐pressure behavior can be achieved only if the volume changes related to the conformational transformation of the cavity can offset the volume changes caused by the substrate binding. It is speculated that based on these criteria nature could make a selection of structures of heme pockets that assist in reducing metabolic activity and enzymatic side reactions under extreme pressure conditions.     

Localized Mixed‐Valence and Redox Activity within a Triazole‐Bridged Dinucleating Ligand upon Coordination to Palladium

The new dinucleating redox‐active ligand ( L^H4 ), bearing two redox‐active NNO‐binding pockets linked by a 1,2,3‐triazole unit, is synthetically readily accessible. Coordination to two equivalents of Pd^II resulted in the formation of paramagnetic (S= ) dinuclear Pd complexes with a κ²‐N,N′‐bridging triazole and a single bridging chlorido or azido ligand. A combined spectroscopic, spectroelectrochemical, and computational study confirmed Robin–Day Class II mixed‐valence within the redox‐active ligand, with little influence of the secondary bridging anionic ligand. Intervalence charge transfer was observed between the two ligand binding pockets. Selective one‐electron oxidation allowed for isolation of the corresponding cationic ligand‐based diradical species. SQUID (super‐conducting quantum interference device) measurements of these compounds revealed weak anti‐ferromagnetic spin coupling between the two ligand‐centered radicals and an overall singlet ground state in the solid state, which is supported by DFT calculations. The rigid and conjugated dinucleating redox‐active ligand framework thus allows for efficient electronic communication between the two binding pockets.     

Volatile anesthetic binding to proteins is influenced by solvent and aliphatic residues

The main objective of this work was to characterize VA binding sites in multiple anesthetic target proteins. A computational algorithm was used to quantify the solvent exclusion and aliphatic character of amphiphilic pockets in the structures of VA binding proteins. VA binding sites in the protein structures were defined as the pockets with solvent exclusion and aliphatic character that exceeded minimum values observed in the VA binding sites of serum albumin, firefly luciferase, and apoferritin. We found that the structures of VA binding proteins are enriched in these pockets and that the predicted binding sites were consistent with experimental determined binding locations in several proteins. Autodock3 was used to dock the simulated molecules of 1,1,1,2,2-pentafluoroethane, difluoromethyl 1,1,1,2-tetrafluoroethyl ether, and sevoflurane and the isomers of halothane and isoflurane into these potential binding sites. We found that the binding of the various VA molecules to the amphiphilic pockets is driven primarily by VDW interactions and to a lesser extent by weak hydrogen bonding and electrostatic interactions. In addition, the trend in Delta G binding values follows the Meyer-Overton rule. These results suggest that VA potencies are related to the VDW interactions between the VA ligand and protein target. It is likely that VA bind to sites with a high degree of solvent exclusion and aliphatic character because aliphatic residues provide favorable VDW contacts and weak hydrogen bond donors. Water molecules occupying these sites maintain pocket integrity, associate with the VA ligand, and diminish the unfavorable solvation enthalpy of the VA. Water molecules displaced into the bulk by the VA ligand may provide an additional favorable enthalpic contribution to VA binding. Anesthesia is a component of many health related procedures, the outcomes of which could be improved with a better understanding of the molecular targets and mechanisms of anesthetic action.     

Quantum mechanics approaches to drug research in the era of structural chemogenomics

The rapid growth of the available crystallographic information about proteins and binding pockets creates remarkable opportunities for enriching the drug research pipelines with computational prediction of novel protein–ligand interactions. While ab initio quantum mechanical (QM) approaches are known to provide unprecedented accuracy in structure‐based binding energy calculations, they are limited to only small systems of dozens of atoms. In the structural chemogenomics era, it is critical that new approaches are developed that enable application of QM methodologies to noncovalent interactions in systems as large as protein–ligand complexes and conformational ensembles. This perspective highlights recent advances towards bridging the gap between high‐accuracy and high‐volume computations in drug research. © 2013 Wiley Periodicals, Inc.     

A nonredundant structure dataset for benchmarking protein‐RNA computational docking

Protein–RNA interactions play an important role in many biological processes. The ability to predict the molecular structures of protein–RNA complexes from docking would be valuable for understanding the underlying chemical mechanisms. We have developed a novel nonredundant benchmark dataset for protein–RNA docking and scoring. The diverse dataset of 72 targets consists of 52 unbound–unbound test complexes, and 20 unbound–bound test complexes. Here, unbound–unbound complexes refer to cases in which both binding partners of the cocrystallized complex are either in apo form or in a conformation taken from a different protein–RNA complex, whereas unbound–bound complexes are cases in which only one of the two binding partners has another experimentally determined conformation. The dataset is classified into three categories according to the interface root mean square deviation and the percentage of native contacts in the unbound structures: 49 easy, 16 medium, and 7 difficult targets. The bound and unbound cases of the benchmark dataset are expected to benefit the development and improvement of docking and scoring algorithms for the docking community. All the easy‐to‐view structures are freely available to the public at http://zoulab.dalton.missouri.edu/RNAbenchmark/ . © 2012 Wiley Periodicals, Inc.     

Probing the Subunit-Subunit Interaction of the Tetramer of E. coli KDO8P Synthase by Electrospray Ionization Mass Spectrometry

Escherichia coli 3-Deoxy-D-manno-octulosonate 8-phosphate (KDO8P) synthase catalyzes the condensation reaction between D-arabinose 5-phosphate (A5P) and phosphoenolpyruvate (PEP) to form KDO8P and inorganic phosphate (Pi). This enzyme exists as a tetramer in solution, which is important for catalysis. Two different states of the enzyme were obtained: i) PEP-bound and ii) PEP-unbound. The effect of the substrates and products on the overall structure of KDO8P synthase in both PEP-bound and unbound states was examined using electrospray ionization mass spectrometry. The analysis of our data showed that the complexes of the PEP-unbound enzyme with PEP (or Pi) favored the formation of monomers, while the complexes with A5P (or KDO8P) mainly favored dimers. The PEP-bound enzyme was found to exist in the monomer and dimer with a small amount of the tetramer, whereas the PEP-unbound form primarily exists in the monomer and dimer, and no tetramer was observed, suggesting that the bound PEP have a role in stabilization of the tetrameric structure. Taken together, the results imply that the addition of the substrates or products to the unbound enzyme may alter the subunit-subunit interactions and/or conformational change of the protein at the active site, and this study also demonstrates that the electrospray ionization mass spectrometric method may be a powerful tool in probing the subunit-subunit interactions and/or conformational change of multi-subunit protein upon binding to ligand.     

Standard free energy of releasing a localized water molecule from the binding pockets of proteins: double-decoupling method

Localized water molecules in the binding pockets of proteins play an important role in noncovalent association of proteins and small drug compounds. At times, the dominant contribution to the binding free energy comes from the release of localized water molecules in the binding pockets of biomolecules. Therefore, to quantify the energetic importance of these water molecules for drug design purposes, we have used the double-decoupling approach to calculate the standard free energy of tying up a water molecule in the binding pockets of two protein complexes. The double-decoupling approach is based on the underlying principle of statistical thermodynamics. We have calculated the standard free energies of tying up the water molecule in the binding pockets of these complexes to be favorable. These water molecules stabilize the protein-drug complexes by interacting with the ligands and binding pockets. Our results offer ideas that could be used in optimizing protein-drug interactions, by designing ligands that are capable of targeting localized water molecules in protein binding sites. The resulting free energy of ligand binding could benefit from the potential free energy gain accompanying the release of these water molecules. Furthermore, we have examined the theoretical background of the double-decoupling method and its connection to the molecular dynamics thermodynamic integration techniques.     

Connectivity and binding‐site recognition: Applications relevant to drug design

Here, we describe a family of methods based on residue–residue connectivity for characterizing binding sites and apply variants of the method to various types of protein–ligand complexes including proteases, allosteric‐binding sites, correctly and incorrectly docked poses, and inhibitors of protein–protein interactions. Residues within ligand‐binding sites have about 25% more contact neighbors than surface residues in general; high‐connectivity residues are found in contact with the ligand in 84% of all complexes studied. In addition, a k‐means algorithm was developed that may be useful for identifying potential binding sites with no obvious geometric or connectivity features. The analysis was primarily carried out on 61 protein–ligand structures from the MEROPS protease database, 250 protein–ligand structures from the PDBSelect (25%), and 30 protein–protein complexes. Analysis of four proteases with crystal structures for multiple bound ligands has shown that residues with high connectivity tend to have less variable side‐chain conformation. The relevance to drug design is discussed in terms of identifying allosteric‐binding sites, distinguishing between alternative docked poses and designing protein interface inhibitors. Taken together, this data indicate that residue–residue connectivity is highly relevant to medicinal chemistry. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Synthesis,characterization, spectroscopic and theoretical studies of transition metal complexes of new nano Schiff base derived from l‐histidine and 2‐acetylferrocene and evaluation of biological and anticancer activities

A new Schiff base derived from the condensation of 2‐acetylferrocene with l ‐histidine was prepared and characterized using elemental analyses and spectroscopic methods. Cr(III), Mn(II), Fe(III), Co(II), Ni(II), Cu(II), Zn(II) and Cd(II) complexes of the Schiff base were prepared and characterized using various physicochemical methods such as elemental analysis, Fourier transform infrared and UV–visible spectroscopies, molar conductance, thermal analysis and scanning electron microscopy (SEM). Both ligand and complexes were investigated for their biological and anticancer activities. The elemental analyses showed that complexes were formed in a metal‐to‐ligand ratio of 1:1 stoichiometry. The spectral analyses proved that the ligand was tridentate and all complexes had an octahedral geometry, except the Zn(II) complex that was tetrahedral. SEM showed that the ligand and its Cd(II) complex were of nanometric structure. The molecular and electronic structure of the free ligand was optimized theoretically and the quantum chemical parameters were calculated. The molecular structure can be used to investigate the coordination sites and the total charge density around each atom. According to anticancer studies, Cd(II) complex was recommended to be used as anti‐breast cancer drug as it had very low IC₅₀ (3.5 μg ml^?1). Molecular docking was used to predict the binding between the free ligand and its Cd(II) complex and crystal structure of Staphylococcus aureus (PDB ID: 3Q8u), receptors of breast cancer mutant oxidoreductase (PDB ID: 3Hb5) and crystal structure of Escherichia coli (PDB ID: 3 T88) and to identify the binding mode and the crucial functional groups interacting with the three proteins.     

Two‐dimensional replica‐exchange method for predicting protein–ligand binding structures

We have developed a two‐dimensional replica‐exchange method for the prediction of protein–ligand binding structures. The first dimension is the umbrella sampling along the reaction coordinate, which is the distance between a protein binding pocket and a ligand. The second dimension is the solute tempering, in which the interaction between a ligand and a protein and water is weakened. The second dimension is introduced to make a ligand follow the umbrella potential more easily and enhance the binding events, which should improve the sampling efficiency. As test cases, we applied our method to two protein‐ligand complex systems (MDM2 and HSP 90‐alpha). Starting from the configuration in which the protein and the ligand are far away from each other in each system, our method predicted the ligand binding structures in excellent agreement with the experimental data from Protein Data Bank much faster with the improved sampling efficiency than the replica‐exchange umbrella sampling method that we have previously developed. © 2013 Wiley Periodicals, Inc.     

Variation of free‐energy landscape of the p53 C‐terminal domain induced by acetylation: Enhanced conformational sampling

The C‐terminal domain (CTD) of tumor suppressor protein p53 is an intrinsically disordered region that binds to various partner proteins, where lysine of CTD is acetylated/nonacetylated and histidine neutralized/non‐neutralized. Because of the flexibility of the unbound CTD, a free‐energy landscape (FEL) is a useful quantity for determining its statistical properties. We conducted enhanced conformational sampling of CTD in the unbound state via virtual system coupled multicanonical molecular dynamics, in which the lysine was acetylated or nonacetylated and histidine was charged or neutralized. The fragments were expressed by an all‐atom model and were immersed in an explicit solvent. The acetylation and charge‐neutralization varied FEL greatly, which might be convenient to exert a hub property. The acetylation slightly enhanced alpha‐helix structures that are more compact than sheet/loop conformations. The charge‐neutralization produced hairpins. Additionally, circular dichroism experiments confirmed the computational results. We propose possible binding mechanisms of CTD to partners by investigating FEL. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

8‐Hydroxy Quinoline Derivatives as Auxiliary Ligands for Red‐Emitting Cyclic‐Platinum Phosphorescent Complexes: Synthesis and Properties

Heavy metal complexes exhibit high phosphorescent efficiency and have been used extensively for electrophosphorescent emitters in the past 16 years. In 2006, we initially reported the use of the popular ligand, 8‐hydroxyquinoline (Q) to coordinate with the heavy metal ions and obtained the red‐infrared phosphorescent emission. In this paper, 8‐hydroxyquinoline has been modified at the 5‐position by electron‐donating and attracting groups and platinum complexes based on 2‐phenylpyridine and 8‐hydroxyquinoline derivatives were synthesized. The electron‐withdrawing group CF ₃ and NO ₂ lowers the HOMO level of the Q ligand and results in a N^O centered enhanced red‐infrared phosphorescence emission. The complex with CF ₃ modification exhibits the highest phosphorescence quantum yield in solid state with a life time of 1.17 μs.