Fragment-Based Computational Method for Designing GPCR Ligands.

G protein-coupled receptors (GPCRs) are the largest family of cell surface receptors, which is arguably the most important family of drug target. With the technology breakthroughs in X-ray crystallography and cryo-electron microscopy, more than 300 GPCR-ligand complex structures have been publicly reported since 2007, covering about 60 unique GPCRs. Such abundant structural information certainly will facilitate the structure-based drug design by targeting GPCRs. In this study, we have developed a fragment-based computational method for designing novel GPCR ligands. We first extracted the characteristic interaction patterns (CIPs) on the binding interfaces between GPCRs and their ligands. The CIPs were used as queries to search the chemical fragments derived from GPCR ligands, which were required to form similar interaction patterns with GPCR. Then, the selected chemical fragments were assembled into complete molecules by using the AutoT&T2 software. In this work, we chose ß-adrenergic receptor (ß-AR) and muscarinic acetylcholine receptor (mAChR) as the targets to validate this method. Based on the designs suggested by our method, samples of 63 compounds were purchased and tested in a cell-based functional assay. A total of 15 and 22 compounds were identified as active antagonists for ß2-AR and mAChR M1, respectively. Molecular dynamics simulations and binding free energy analysis were performed to explore the key interactions (e.g., hydrogen bonds and π-π interactions) between those active compounds and their target GPCRs. In summary, our work presents a useful approach to the de novo design of GPCR ligands based on the relevant 3D structural information.

Combination of capillary electrophoresis and molecular modeling to study the enantiomer affinity pattern between ß-blockers and anionic cyclodextrin derivatives in a methanolic and water background electrolyte.

In order to have deep insights into the mechanisms of enantiomer affinity pattern in both aqueous and non-aqueous systems, an approach combining capillary electrophoresis and molecular modeling was undertaken. A chiral ß-blocker; acebutolol, was enantioseparated in aqueous capillary electrophoresis and non-aqueous capillary electrophoresis using two anionic ß-cyclodextrin derivatives. The enantiomer affinity pattern of acebutolol was found to be opposite when an aqueous background electrolyte was replaced with non-aqueous background electrolyte in the presence of heptakis(2,3-di-O-acetyl-6-sulfo)-ß-cyclodextrin but remained the same in the presence of heptakis(2,3-di-O-methyl-6-sulfo)-ß-cyclodextrin. Molecular docking of acebutolol into two ß-cyclodextrin derivatives indicated two distinct binding modes called 'up' and 'down' conformations. After structure optimization by molecular dynamics and energy minimization, both enantiomers of acebutolol were preferred to the 'up' conformation with heptakis(2,3-di-O-methyl-6-sulfo)-ß-cyclodextrin while 'down' conformation with heptakis(2,3-di-O-acetyl-6-sulfo)-ß-cyclodextrin. The further calculation of the complex energy with solvent effect indicated that heptakis(2,3-di-O-acetyl-6-sulfo)-ß-cyclodextrin had higher affinity to S-acebutolol than R-acebutolol in non-aqueous capillary electrophoresis while it showed better binding to R-acebutolol in aqueous capillary electrophoresis. However, the heptakis(2,3-di-O-methyl-6-sulfo)-ß-cyclodextrin bound better to R-acebutolol in both aqueous and non-aqueous capillary electrophoresis, implying that the binding mode played more important role in chiral separation of heptakis(2,3-di-O-methyl-6-sulfo)-ß-cyclodextrin while the solvent effect had prevailing impact on heptakis(2,3-di-O-acetyl-6-sulfo)-ß-cyclodextrin.

Structural Insights into a Flavin-Dependent [4 + 2] Cyclase that Catalyzes trans-Decalin Formation in Pyrroindomycin Biosynthesis.

Here, we provide structural insights into PyrE3, a flavin-dependent [4 + 2] cyclase that catalyzes trans-decalin formation in the biosynthesis of pyrroindomycins. PyrE3 shares an architecture/domain organization head-to-tail similarity with the members of the family of para-hydroxybenzoate hydroxylase (pHBH)-fold monooxygenases, and possesses a flavin adenine dinucleotide (FAD)-binding domain, a middle domain, and a C-terminal thioredoxin-like domain. The FAD-binding domain forms a central hub of the protein structure, and binds with FAD in a "closed" conformation of pHBH-fold family monooxygenases known for their highly dynamic catalytic processes. FAD plays an essential structural role in PyrE3, where it is amenable to redox change; however, redox change has little effect on [4 + 2] cyclization activity. PyrE3 appears to selectively accommodate a tetramate-containing, linear polyene intermediate in a highly positively charged pocket, which is located at the interface between the FAD-binding domain and the middle domain, and can accelerate trans-decalin formation likely through an endo-selective [4 + 2] transition state.

TopP-S: Persistent homology-based multi-task deep neural networks for simultaneous predictions of partition coefficient and aqueous solubility.

Aqueous solubility and partition coefficient are important physical properties of small molecules. Accurate theoretical prediction of aqueous solubility and partition coefficient plays an important role in drug design and discovery. The prediction accuracy depends crucially on molecular descriptors which are typically derived from a theoretical understanding of the chemistry and physics of small molecules. This work introduces an algebraic topology-based method, called element-specific persistent homology (ESPH), as a new representation of small molecules that is entirely different from conventional chemical and/or physical representations. ESPH describes molecular properties in terms of multiscale and multicomponent topological invariants. Such topological representation is systematical, comprehensive, and scalable with respect to molecular size and composition variations. However, it cannot be literally translated into a physical interpretation. Fortunately, it is readily suitable for machine learning methods, rendering topological learning algorithms. Due to the inherent correlation between solubility and partition coefficient, a uniform ESPH representation is developed for both properties, which facilitates multi-task deep neural networks for their simultaneous predictions. This strategy leads to a more accurate prediction of relatively small datasets. A total of six datasets is considered in this work to validate the proposed topological and multitask deep learning approaches. It is demonstrated that the proposed approaches achieve some of the most accurate predictions of aqueous solubility and partition coefficient. Our software is available online at http://weilab.math.msu.edu/TopP-S/. © 2018 Wiley Periodicals, Inc.

Reversible conversion between a pleated oligo-tetrathiafulvalene radical foldamer and folded donor-acceptor [3]pseudorotaxane under redox conditions.

Linear tetrathiafulvalene (TTF) oligomers were synthesized, which could not only form a pleated TTF˙+ radical cation foldamer under oxidation conditions, but also interlocked with CBPQT4+ to form folded donor-acceptor [3]pseudorotaxane in the neutral state of TTF. Moreover, switchable transformation between these two folded supramolecular structures was achieved under the alternative regulation of the redox states of TTF units.

Automatic parametrization of non-polar implicit solvent models for the blind prediction of solvation free energies.

In this work, a systematic protocol is proposed to automatically parametrize the non-polar part of implicit solvent models with polar and non-polar components. The proposed protocol utilizes either the classical Poisson model or the Kohn-Sham density functional theory based polarizable Poisson model for modeling polar solvation free energies. Four sets of radius parameters are combined with four sets of charge force fields to arrive at a total of 16 different parametrizations for the polar component. For the non-polar component, either the standard model of surface area, molecular volume, and van der Waals interactions or a model with atomic surface areas and molecular volume is employed. To automatically parametrize a non-polar model, we develop scoring and ranking algorithms to classify solute molecules. The their non-polar parametrization is obtained based on the assumption that similar molecules have similar parametrizations. A large database with 668 experimental data is collected and employed to validate the proposed protocol. The lowest leave-one-out root mean square (RMS) error for the database is 1.33 kcal/mol. Additionally, five subsets of the database, i.e., SAMPL0-SAMPL4, are employed to further demonstrate that the proposed protocol. The optimal RMS errors are 0.93, 2.82, 1.90, 0.78, and 1.03 kcal/mol, respectively, for SAMPL0, SAMPL1, SAMPL2, SAMPL3, and SAMPL4 test sets. The corresponding RMS errors for the polarizable Poisson model with the Amber Bondi radii are 0.93, 2.89, 1.90, 1.16, and 1.07 kcal/mol, respectively.

Enzyme-Dependent [4 + 2] Cycloaddition Depends on Lid-like Interaction of the N-Terminal Sequence with the Catalytic Core in PyrI4.

The Diels-Alder [4 + 2] cycloaddition reaction is one of the most powerful and elegant organic synthesis methods for forming 6-membered molecules and has been known for nearly a century. However, whether and how enzymes catalyze this type of reaction is still not completely clear. Here we focus on PyrI4, an enzyme found in the biosynthetic pathway of pyrroindomycins where it catalyzes the formation of a spiro-conjugate via an enzyme-dependent exo-selective [4 + 2] cycloaddition reaction. We report the crystal structures of PyrI4 alone and in complex with its product. Comparative analysis of these structures, combined with biochemical analysis, lead us to propose a unique trapping mechanism whereby the lid-like action of the N-terminal tail imposes conformational constraints on the ß barrel catalytic core, which enhances the proximity and polarization effects of reactive groups (1,3-diene and alkene) to drive cyclization in a regio- and stereo-specific manner. This work represents an important step toward the wider application of enzyme-catalyzed [4 + 2] cyclization for synthetic purposes.

AutoT&T v.2: An Efficient and Versatile Tool for Lead Structure Generation and Optimization.

UNLABELLED: In structure-based drug design, automated de novo design methods are helpful tools for lead discovery as well as lead optimization. In a previous study ( J. Chem. Inf. MODEL: 2011 , 51 , 1474 - 1491 ) we reported a new de novo design method, namely, Automatic Tailoring and Transplanting (AutoT&T). It overcomes some intrinsic problems in conventional fragment-based buildup methods. In this study, we describe an upgraded version, namely, AutoT&T2. Structural operations conducted by AutoT&T2 have been largely optimized by introducing several new algorithms. As a result, its overall speed in multiround optimization jobs has been improved by a few thousand fold. With this improvement, it is now practical to conduct structural crossover among multiple lead molecules using AutoT&T2. Three different test cases are described in this study that demonstrate the new features and versatile applications of AutoT&T2. The AutoT&T2 software suite is available to the public. Besides, a Web portal for running AutoT&T2 online is provided at http://www.sioc-ccbg.ac.cn/software/att2 for testing.

Temperature-Responsive Chiral (A)6B Supramolecular Cages Based on Conformational Preferences.

Two chiral (A)6B-typed supramolecular cages were constructed from hydrogen-bonded C6 -symmetric zinc porphyrin hexamers and chiral C3-symmetric pyridyl hexadentates with a core of 1,3,5-triphenylbenzene. Circular dichroism and molecular simulations revealed that the symmetry of the supramolecular cages switched from pseudo-C3v to C3 with the rotational confinement of the biphenyl backbones at low temperatures, which generated conformationally chiral transfer and amplification. This unique phenomenon suggests a new strategy to develop smart materials with high sensitivity and excellent reversibility.

Multiresolution persistent homology for excessively large biomolecular datasets.

Although persistent homology has emerged as a promising tool for the topological simplification of complex data, it is computationally intractable for large datasets. We introduce multiresolution persistent homology to handle excessively large datasets. We match the resolution with the scale of interest so as to represent large scale datasets with appropriate resolution. We utilize flexibility-rigidity index to access the topological connectivity of the data set and define a rigidity density for the filtration analysis. By appropriately tuning the resolution of the rigidity density, we are able to focus the topological lens on the scale of interest. The proposed multiresolution topological analysis is validated by a hexagonal fractal image which has three distinct scales. We further demonstrate the proposed method for extracting topological fingerprints from DNA molecules. In particular, the topological persistence of a virus capsid with 273 780 atoms is successfully analyzed which would otherwise be inaccessible to the normal point cloud method and unreliable by using coarse-grained multiscale persistent homology. The proposed method has also been successfully applied to the protein domain classification, which is the first time that persistent homology is used for practical protein domain analysis, to our knowledge. The proposed multiresolution topological method has potential applications in arbitrary data sets, such as social networks, biological networks, and graphs.

Multiresolution Topological Simplification.

Persistent homology has been advocated as a new strategy for the topological simplification of complex data. However, it is computationally intractable for large data sets. In this work, we introduce multiresolution persistent homology for tackling large datasets. Our basic idea is to match the resolution with the scale of interest so as to create a topological microscopy for the underlying data. We adjust the resolution via a rigidity density-based filtration. The proposed multiresolution topological analysis is validated by the study of a complex RNA molecule.

PDB-wide collection of binding data: current status of the PDBbind database.

MOTIVATION: Molecular recognition between biological macromolecules and organic small molecules plays an important role in various life processes. Both structural information and binding data of biomolecular complexes are indispensable for depicting the underlying mechanism in such an event. The PDBbind database was created to collect experimentally measured binding data for the biomolecular complexes throughout the Protein Data Bank (PDB). It thus provides the linkage between structural information and energetic properties of biomolecular complexes, which is especially desirable for computational studies or statistical analyses. RESULTS: Since its first public release in 2004, the PDBbind database has been updated on an annual basis. The latest release (version 2013) provides experimental binding affinity data for 10,776 biomolecular complexes in PDB, including 8302 protein-ligand complexes and 2474 other types of complexes. In this article, we will describe the current methods used for compiling PDBbind and the updated status of this database. We will also review some typical applications of PDBbind published in the scientific literature. AVAILABILITY AND IMPLEMENTATION: All contents of this database are freely accessible at the PDBbind-CN Web server at http://www.pdbbind-cn.org/. CONTACT: wangrx@mail.sioc.ac.cn. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Comparative assessment of scoring functions on an updated benchmark: 1. Compilation of the test set.

Scoring functions are often applied in combination with molecular docking methods to predict ligand binding poses and ligand binding affinities or to identify active compounds through virtual screening. An objective benchmark for assessing the performance of current scoring functions is expected to provide practical guidance for the users to make smart choices among available methods. It can also elucidate the common weakness in current methods for future improvements. The primary goal of our comparative assessment of scoring functions (CASF) project is to provide a high-standard, publicly accessible benchmark of this type. Our latest study, i.e., CASF-2013, evaluated 20 popular scoring functions on an updated set of protein-ligand complexes. This data set was selected out of 8302 protein-ligand complexes recorded in the PDBbind database (version 2013) through a fairly complicated process. Sample selection was made by considering the quality of complex structures as well as binding data. Finally, qualified complexes were clustered by 90% similarity in protein sequences. Three representative complexes were chosen from each cluster to control sample redundancy. The final outcome, namely, the PDBbind core set (version 2013), consists of 195 protein-ligand complexes in 65 clusters with binding constants spanning nearly 10 orders of magnitude. In this data set, 82% of the ligand molecules are "druglike" and 78% of the protein molecules are validated or potential drug targets. Correlation between binding constants and several key properties of ligands are discussed. Methods and results of the scoring function evaluation will be described in a companion work in this issue (doi: 10.1021/ci500081m ).

Folding-induced folding: the assembly of aromatic amide and 1,2,3-triazole hybrid helices.

Folding-induced folding for the construction of artificial hybrid helices from two different kinds of aromatic sequences is described. Linear compounds 1 a, 1 b, and 2, containing one aromatic amide trimer or pentamer and one or two aromatic 1,2,3-triazole tetramers, have been designed and synthesized. The trimeric and pentameric amide segments are driven by intramolecluar N-H⋅⋅⋅F hydrogen bonding to adopt a folded or helical conformation, whereas the triazole segment is intrinsically disordered. In organic solvents of low polarity, the amide foldamer segment induces the attached triazole segment(s) to fold through intramolecular stacking, leading to the formation of hybrid helices. The helical conformation of these hybrid sequences has been confirmed by (1)H and (19)F NMR spectroscopy, UV/Vis spectroscopy, circular dichroism (CD) experiments, and theoretical calculations. It was found that the amide pentamer exhibits a stronger ability to induce the folding of the attached triazole segment(s) compared with that of the shorter trimer. Enantiomers (R)-3 and (S)-3, which contain an R- or S-(1-naphthyl)ethylamino group at the end of a tetraamide segment, have also been synthesized. CD experiments showed that introduction of a chiral group caused the whole framework to produce a strong helicity bias. Density-functional-theory calculations on (S)-3 suggested that this compound exists as a right-handed (P) helix.

Chemical and biochemical applications of MALDI TOF-MS based on analyzing the small organic compounds.

This review focuses on the recent applications of matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI TOF-MS) technologies for analysis of small molecular compounds (SMCs) on qualitative and quantitative levels to provide valuable information for the relative chemical and biochemical researches. We summarized the approaches to minimize the interference in low m/z range and ion suppression effects by adding chemical reagents, sample cleaning and preparation, matrix selection and performing chromatographic separation before MALDI TOF-MS analysis. Meanwhile, we discussed the strategies to enhance the MALDI TOF-MS detection sensitivity and selectivity by derivatization to attach the "charge tags" to SMCs. In addition, the mass spectrometric imaging (MSI) methods for locating the target SMCs in bio-tissues by MALDI TOF-MS were reviewed. Furthermore, the applications of MALDI TOF-MS for monitoring enzyme reactions and the screening of their inhibitors were also presented. Finally, the chemical applications of MALDI TOF-MS on characterization of small molecular transition-metal complexes and monitoring the organic reactions, especially the polymerization reactions, were discussed.

Self-resistance to an antitumor antibiotic: a DNA glycosylase triggers the base-excision repair system in yatakemycin biosynthesis.

Resistance is (not) futile: The yatakemycin biosynthetic gene cluster involves the ytkR2 gene, which encodes a protein with homology to a recently discovered bacterial DNA glycosylase. Genetic validation in vivo, biochemical assays, and in vitro mutagenesis studies revealed that YtkR2 confers resistance for the bacteria by specifically recognizing and cleaving the YTM-modified base (see scheme).

Studies on CH3CN-assisted decomposition of 1st Grubbs catalyst by electrospray ionization tandem mass spectrometry.

The CH(3)CN-assisted decomposition reaction of the 1(st) Grubbs catalyst (1) was studied using electrospray ionization tandem mass spectrometry (ESI-MS/MS). We detected a series of Ru-intermediates and decomposition products by off-line and on-line ESI-MS(/MS) monitoring of the decomposition process. In particular, an on-line microreactor method was applied with ESI-MS/MS to profile the change and relationship of various Ru-intermediates by controlling the reaction within the first 30 s of its time scale. The main fast decomposition mechanism of Ru-catalyst 1 in the presence of CH(3)CN was similar to that proposed by Grubbs, and this was confirmed by detecting the (PhCH(2)PCy(3))(+) ion at m/z 371 as the major decomposition products with ESI-MS. We also studied the time evolution of the transient reactive Ru-intermediate ions step by step with ESI-MS/MS and detected the C-H bond activation products of toluene--dehydrogenated PCy(3), such as P(Cy)(2)(C(6)H(9)), P(Cy)(2)Ph--by analyzing the decomposition reaction solution by gas chromatography (GC)/MS. The mechanism of another minor decomposition pathway involving the phosphine activation of catalyst 1 was proposed on the basis of the ESI-MS(/MS) interception and characterization of the transient reactive Ru-species in the decomposition reaction solution. Finally the coordination effect of the CH(3)CN in assisting the decomposition and stabilizing the transient Ru-complexes is discussed.

Analysis of low molecular weight compounds by MALDI-FTICR-MS.

This review focuses on recent applications of matrix-assisted laser desorption ionization-Fourier-transform ion cyclotron resonance mass spectrometry (MALDI-FTICR-MS) in qualitative and quantitative analysis of low molecular weight compounds. The scope of the work includes amino acids, small peptides, mono and oligosaccharides, lipids, metabolic compounds, small molecule phytochemicals from medicinal herbs and even the volatile organic compounds from tobacco. We discuss both direct analysis and analysis following derivatization. In addition we review sample preparation strategies to reduce interferences in the low m/z range and to improve sensitivities by derivatization with charge tags. We also present coupling of head space techniques with MALDI-FTICR-MS. Furthermore, omics analyses based on MALDI-FTICR-MS were also discussed, including proteomics, metabolomics and lipidomics, as well as the relative MS imaging for bio-active low molecular weight compounds. Finally, we discussed the investigations on dissociation/rearrangement processes of low molecular weight compounds by MALDI-FTICR-MS.