Concept: Computational chemistry
: This paper introduces a subdomain chemistry format for storing computational chemistry data called CompChem. It has been developed based on the design, concepts and methodologies of Chemical Markup Language (CML) by adding computational chemistry semantics on top of the CML Schema. The format allows a wide range of ab initio quantum chemistry calculations of individual molecules to be stored. These calculations include, for example, single point energy calculation, molecular geometry optimization, and vibrational frequency analysis. The paper also describes the supporting infrastructure, such as processing software, dictionaries, validation tools and database repositories. In addition, some of the challenges and difficulties in developing common computational chemistry dictionaries are discussed. The uses of CompChem are illustrated by two practical applications.
BACKGROUND: Recently, various metallocenes were synthesized and analyzed by biological activity point of view (such as antiproliferative properties): ruthenocenes, cobaltoceniums, titanocenes, zirconocenes, vanadocenes, niobocenes, molibdocenes etc. Two main disadvantages of metallocenes are the poor hydrosolubility and the hydrolytic instability. These problems could be resolved in two ways: synthetically modifying the structure or finding new formulations with enhanced properties. The aqueous solubility of metallocenes with cytostatic activities could be enhanced by molecular encapsulation in cyclodextrins, as well as the hydrolytic instability of these compounds could be reduced. RESULTS: This study presents a theoretical approach on the nanoencapsulation of a series of titanocenes with cytotoxic activity in alpha-, beta-, and gamma-cyclodextrin. The HyperChem 5.11 package was used for building and molecular modelling of titanocene and cyclodextrin structures, as well as for titanocene/cyclodextrin complex optimization. For titanocene/cyclodextrin complex optimization experiments, the titanocene and cyclodextrin structures in minimal energy conformations were set up at various distances and positions between molecules (molecular mechanics functionality, MM+). The best interaction between titanocene structures and cyclodextrins was obtained in the case of beta- and gamma-cyclodextrin, having the hydrophobic moieties oriented to the secondary face of cyclodextrin. The hydrophobicity of titanocenes (logP) correlate with the titanocene-cyclodextrin interaction parameters, especially with the titanocene-cyclodextrin interaction energy; the compatible geometry and the interaction energy denote that the titanocene/beta- and gamma-cyclodextrin complex can be achieved. Valuable quantitative structure-activity relationships (QSARs) were also obtained in the titanocene class by using the same logP as the main parameter for the in vitro cytotoxic activity against HeLa, K562, and Fem-x cell lines. CONCLUSIONS: According to our theoretical study, the titanocene/cyclodextrin inclusion compounds can be obtained (high interaction energy; the encapsulation is energetically favourable). Further, the most hydrophobic compounds are better encapsulated in beta- and gamma-cyclodextrin molecules and are more stable (from energetically point of view) in comparison with alpha-cyclodextrin case. This study suggests that the titanocene / beta- and gamma-cyclodextrin complexes (or synthetically modified cyclodextrins with higher water solubility) could be experimentally synthesized and could have enhanced cytotoxic activity and even lower toxicity.
Bcl-X is a member of Bcl-2 family of proteins involved in the regulation of intrinsic pathway of apoptosis. Its overexpression in many human cancers makes it an important target for anti-cancer drugs. Bcl-X interacts with the BH3 domain of several pro-apoptotic Bcl-2 partners. This helical bundle protein has a pronounced hydrophobic groove which acts as a binding region for the BH3 domains. Eight independent molecular dynamics simulations of the apo/holo forms of Bcl-X were carried out to investigate the behavior of solvent-exposed hydrophobic groove. The simulations used either a twin-range cut-off or particle mesh Ewald (PME) scheme to treat long-range interactions. Destabilization of the BH3 domain-containing helix H2 was observed in all four twin-range cut-off simulations. Most of the other major helices remained stable. The unwinding of H2 can be related to the ability of Bcl-X to bind diverse BH3 ligands. The loss of helical character can also be linked to the formation of homo- or hetero-dimers in Bcl-2 proteins. Several experimental studies have suggested that exposure of BH3 domain is a crucial event before they form dimers. Thus unwinding of H2 seems to be functionally very important. The four PME simulations, however, revealed a stable helix H2. It is possible that the H2 unfolding might occur in PME simulations at longer time scales. Hydrophobic residues in the hydrophobic groove are involved in stable interactions among themselves. The solvent accessible surface areas of bulky hydrophobic residues in the groove are significantly buried by the loop LB connecting the helix H2 and subsequent helix. These observations help to understand how the hydrophobic patch in Bcl-X remains stable in the solvent-exposed state. We suggest that both the destabilization of helix H2 and the conformational heterogeneity of loop LB are important factors for binding of diverse ligands in the hydrophobic groove of Bcl-X.
Explicit solvent molecular dynamics simulations have been used to complement preceding experimental and computational studies of folding of guanine quadruplexes (G-DNA). We initiate early stages of unfolding of several G-DNAs by simulating them under no-salt conditions and then try to fold them back using standard excess salt simulations. There is a significant difference between G-DNAs with all-anti parallel stranded stems and those with stems containing mixtures of syn and anti guanosines. The most natural rearrangement for all-anti stems is a vertical mutual slippage of the strands. This leads to stems with reduced numbers of tetrads during unfolding and a reduction of strand slippage during refolding. The presence of syn nucleotides prevents mutual strand slippage; therefore, the antiparallel and hybrid quadruplexes initiate unfolding via separation of the individual strands. The simulations confirm the capability of G-DNA molecules to adopt numerous stable locally and globally misfolded structures. The key point for a proper individual folding attempt appears to be correct prior distribution of syn and anti nucleotides in all four G-strands. The results suggest that at the level of individual molecules, G-DNA folding is an extremely multi-pathway process that is slowed by numerous misfolding arrangements stabilized on highly variable timescales.
The Rosetta Molecular Modeling suite is a command-line-only collection of applications that enable high-resolution modeling and design of proteins and other molecules. Although extremely useful, Rosetta can be difficult to learn for scientists with little computational or programming experience. To that end, we have created a Graphical User Interface (GUI) for Rosetta, called the PyRosetta Toolkit, for creating and running protocols in Rosetta for common molecular modeling and protein design tasks and for analyzing the results of Rosetta calculations. The program is highly extensible so that developers can add new protocols and analysis tools to the PyRosetta Toolkit GUI.
Elucidating the druggable interface of protein-protein interactions using fragment docking and coevolutionary analysis
- Proceedings of the National Academy of Sciences of the United States of America
- Published almost 4 years ago
Protein-protein interactions play a central role in cellular function. Improving the understanding of complex formation has many practical applications, including the rational design of new therapeutic agents and the mechanisms governing signal transduction networks. The generally large, flat, and relatively featureless binding sites of protein complexes pose many challenges for drug design. Fragment docking and direct coupling analysis are used in an integrated computational method to estimate druggable protein-protein interfaces. (i) This method explores the binding of fragment-sized molecular probes on the protein surface using a molecular docking-based screen. (ii) The energetically favorable binding sites of the probes, called hot spots, are spatially clustered to map out candidate binding sites on the protein surface. (iii) A coevolution-based interface interaction score is used to discriminate between different candidate binding sites, yielding potential interfacial targets for therapeutic drug design. This approach is validated for important, well-studied disease-related proteins with known pharmaceutical targets, and also identifies targets that have yet to be studied. Moreover, therapeutic agents are proposed by chemically connecting the fragments that are strongly bound to the hot spots.
The Harvard Organic Photovoltaic Dataset (HOPV15) presented in this work is a collation of experimental photovoltaic data from the literature, and corresponding quantum-chemical calculations performed over a range of conformers, each with quantum chemical results using a variety of density functionals and basis sets. It is anticipated that this dataset will be of use in both relating electronic structure calculations to experimental observations through the generation of calibration schemes, as well as for the creation of new semi-empirical methods and the benchmarking of current and future model chemistries for organic electronic applications.
In this work, we report a combined time-resolved spectroscopic and density functional theory computational study on 2-(p-hydroxymethyl)phenylanthraquinone (PPAQ) in which the benzyl alcohol moiety is significantly farther away from the AQ ketone group compared to the compound 2-(1-hydroxyethyl) 9,10-anthraquinone (HEAQ) so as to investigate the photophysical and photochemical reactions of PPAQ in several solvents, especially for the photoredox reaction in a pH 2 aqueous solution. The results here indicate that PPAQ undergoes the photoredox reaction via a two-step pathway and that the low efficiency of the photoredox reaction of PPAQ compared to the related HEAQ molecule is caused by the longer distance between the benzyl alcohol moiety and the AQ ketone moieties.
We introduce a simple scheme to efficiently compute photon exchange-correlation contributions due to the coupling to transversal photons as formulated in the newly developed quantum-electrodynamical density-functional theory (QEDFT).1-5 Our construction employs the optimized-effective potential (OEP) approach by means of the Sternheimer equation to avoid the explicit calculation of unoccupied states. We demonstrate the efficiency of the scheme by applying it to an exactly solvable GaAs quantum ring model system, a single azulene molecule, and chains of sodium dimers, all located in optical cavities and described in full real space. While the first example is a two-dimensional system and allows to benchmark the employed approximations, the latter two examples demonstrate that the correlated electron-photon interaction appreciably distorts the ground-state electronic structure of a real molecule. By using this scheme, we not only construct typical electronic observables, such as the electronic ground-state density, but also illustrate how photon observables, such as the photon number, and mixed electron-photon observables, for example, electron-photon correlation functions, become accessible in a density-functional theory (DFT) framework. This work constitutes the first three-dimensional ab initio calculation within the new QEDFT formalism and thus opens up a new computational route for the ab initio study of correlated electron-photon systems in quantum cavities.
Observing the intricate chemical transformation of an individual molecule as it undergoes a complex reaction is a longstanding challenge in molecular imaging. Advances in scanning probe microscopy now provide the tools to visualize not only the frontier orbitals of chemical reaction partners and products, but their internal covalent bond configurations as well. Here, we demonstrate the use of noncontact atomic force microscopy to investigate reaction-induced changes in the detailed internal bond structure of individual oligo-(phenylene-1,2-ethynylenes) on Ag(100) as they undergo a series of cyclization processes. Our images reveal the complex surface reaction mechanisms underlying thermally induced cyclization cascades of enediynes. Additional evidence for the proposed reaction pathways is obtained using ab initio density functional theory.