PubChemSR: A search and retrieval tool for PubChem

Background  

Recent years have seen an explosion in the amount of publicly available chemical and related biological information. A significant step has been the emergence of PubChem, which contains property information for millions of chemical structures, and acts as a repository of compounds and bioassay screening data for the NIH Roadmap. There is a strong need for tools designed for scientists that permit easy download and use of these data. We present one such tool, PubChemSR.     

NMR and quantum chemical studies on association of 2,6-bis(acylamino)pyridines with selected imides and 2,2′-dipyridylamine

Abstract  

Association constants of 2,6-bis(alkylcarbonylamino)pyridines (alkyl = methyl or ethyl) and their perfluoroalkyl analogues with succin- and maleimide as well as with 2,2′-dipyridylamine (complementary DAD and ADA hydrogen bonding motifs are responsible for formation of the associates) have been determined by NMR titrations and quantum chemical calculations. Interactions of 2,6-bis(alkylcarbonylamino)pyridines with imides differ by character from these of perfluoroalkyl analogues. Such large difference was not observed for the 2,2′-dipyridylamine associates. Since fluorine atoms cause carbonylamino groups to be stronger hydrogen bond donors, perfluorinated species of this type were found to be more stable. Single crystal X-ray structures of 2,6-bis(trifluoromethylcarbonylamino)pyridine and 2,6-bis(pentafluoroethylcarbonylamino)pyridine have been also determined.     

Theoretical conformational analysis of rutin

Abstract  

The structural properties of rutin were determined by using a computational multistep progression. In the first step a stochastic strategy based on a molecular mechanics calculation was adopted to obtain a preliminary screening of the low-energy rutin conformations. The most stable structures obtained by the random conformational search were used as a starting point for an Austin Model 1 (AM1) semiempirical optimization. After this treatment, 16 structures characterized by a more stable frontal in respect to back disposition of the glycosidic chain of rutin were identified. To validate the results found from the stochastic search a molecular dynamics simulation was carried out. The results evidenced the presence of a global minimum highly stabilized by a hydrogen bond between the hydroxyl in the 3′ position of the B ring and the endocyclic oxygen of the rhamnose unit followed by approximately 8 kJ mol⁻¹ less stable local minima with similar energy values. Finally, the reliability of the molecular model was confirmed by comparing the calculated electronic absorption spectrum with that measured on a methanolic rutin solution.     

Fusing C60 units without Stone–Wales bond rotations

Abstract  

Using ab-initio calculation, we have explored new chemical paths for the coalescence of C₆₀ units into higher fullerenes and novel structures. Besides the Stone–Wales paradigm used for rationalizing the fusion of fullerenes and nanotubes, we demonstrated that an alternative path exists for the fusion of two C₆₀ units. This path uses successive “π–π” additions and subsequent bond reorganizations to lead to a specific C₁₂₀ peanut-like structure. The energies of the chemical barriers, the intermediate structures, and the final product are markedly lower than their counterparts found in the chemical paths based on Stone–Wales bond rotations. The results rationalize the existence of a temperature range in which peanut-like structures are obtained during thermal treatment of peapod structures.     

Fast 3D shape screening of large chemical databases through alignment-recycling

Background  

Large chemical databases require fast, efficient, and simple ways of looking for similar structures. Although such tasks are now fairly well resolved for graph-based similarity queries, they remain an issue for 3D approaches, particularly for those based on 3D shape overlays. Inspired by a recent technique developed to compare molecular shapes, we designed a hybrid methodology, alignment-recycling, that enables efficient retrieval and alignment of structures with similar 3D shapes.     

Glycoproteomic characterization of carriers of the CD15/Lewis<Superscript>x</Superscript> epitope on Hodgkin's Reed-Sternberg cells

Background  

The Lewis^x trisaccharide, also referred to as the CD15 antigen, is a diagnostic marker used to distinguish Hodgkin's lymphoma from other lymphocytic cancers. However, the role of such fucosylated structures remains poorly understood, in part because carriers of Lewis^x structures on Hodgkin's Reed-Sternberg cells have not been identified.     

Pattern similarity study of functional sites in protein sequences: lysozymes and cystatins

Background  

Although it is generally agreed that topography is more conserved than sequences, proteins sharing the same fold can have different functions, while there are protein families with low sequence similarity. An alternative method for profile analysis of characteristic conserved positions of the motifs within the 3D structures may be needed for functional annotation of protein sequences. Using the approach of quantitative structure-activity relationships (QSAR), we have proposed a new algorithm for postulating functional mechanisms on the basis of pattern similarity and average of property values of side-chains in segments within sequences. This approach was used to search for functional sites of proteins belonging to the lysozyme and cystatin families.     

The effect of ultrasonic pre-treatment on the catalytic activity of lipases in aqueous and non-aqueous media

Background  

Ultrasound has been used to accelerate the rates of numerous chemical reactions, however its effects on enzymatic reactions have been less extensively studied. While known to result in the acceleration of enzyme-catalysed reactions, ultrasonication has also been shown to induce enzyme inactivation. In this study we investigated the effects of ultrasonic pretreatment on lipases in both aqueous and non-aqueous media.     

Charting calcium-regulated apoptosis pathways using chemical biology: role of calmodulin kinase II

Background  

Intracellular free calcium ([Ca²⁺]_i) is a key element in apoptotic signaling and a number of calcium-dependent apoptosis pathways have been described. We here used a chemical biology strategy to elucidate the relative importance of such different pathways.     

Generating 3D molecules conditional on receptor binding sites with deep generative models

The goal of structure-based drug discovery is to find small molecules that bind to a given target protein. Deep learning has been used to generate drug-like molecules with certain cheminformatic properties, but has not yet been applied to generating 3D molecules predicted to bind to proteins by sampling the conditional distribution of protein–ligand binding interactions. In this work, we describe for the first time a deep learning system for generating 3D molecular structures conditioned on a receptor binding site. We approach the problem using a conditional variational autoencoder trained on an atomic density grid representation of cross-docked protein–ligand structures. We apply atom fitting and bond inference procedures to construct valid molecular conformations from generated atomic densities. We evaluate the properties of the generated molecules and demonstrate that they change significantly when conditioned on mutated receptors. We also explore the latent space learned by our generative model using sampling and interpolation techniques. This work opens the door for end-to-end prediction of stable bioactive molecules from protein structures with deep learning.

We generate 3D molecules conditioned on receptor binding sites by training a deep generative model on protein–ligand complexes. Our model uses the conditional receptor information to make chemically relevant changes to the generated molecules.     

Antibacterial mono- and sesquiterpene esters of benzoic acids from Iranian propolis

Background  

Propolis (bee glue) has been used as a remedy since ancient times. Propolis from unexplored regions attracts the attention of scientists in the search for new bioactive molecules.     

Synthesis and pharmacological activity of some synthesized polyazacyclopenta[a]naphthalenes and pyrazolo[3,4-b]pyridines using 2-amino-6-methyl-4-phenylnicotinonitrile as synthon

Abstract  

A series of pyridines, pyrimidines, and their derivatives were synthesized using 2-amino-6-methyl-4-phenylnicotinonitrile as starting material. Thirteen new heterocyclics containing a pyridine ring were thus prepared. Pharmacological screening showed that many of these compounds have good anti-inflammatory and analgesic activity comparable with those of diclofenac potassium and valdecoxib as reference drugs. Assignment of the structures of the new compounds was based on chemical and spectroscopic evidence. Synthesis, spectroscopic data, and pharmacological properties of the compounds are reported in detail.     

Calculated conformer energies for organic molecules with multiple polar functionalities are method dependent: Taxol (case study)

Background  

Molecular mechanics (MM) and quantum chemical (QM) calculations are widely applied and powerful tools for the stereochemical and conformational investigations of molecules. The same methods have been extensively used to probe the conformational profile of Taxol (Figure 1) both in solution and at the β-tubulin protein binding site.     

Biochemical characterization of bovine plasma thrombin-activatable fibrinolysis inhibitor (TAFI)

Background  

TAFI is a plasma protein assumed to be an important link between coagulation and fibrinolysis. The three-dimensional crystal structures of authentic mature bovine TAFI (TAFIa) in complex with tick carboxypeptidase inhibitor, authentic full lenght bovine plasma thrombin-activatable fibrinolysis inhibitor (TAFI), and recombinant human TAFI have recently been solved. In light of these recent advances, we have characterized authentic bovine TAFI biochemically and compared it to human TAFI.     

Predicting olfactory receptor neuron responses from odorant structure

Background  

Olfactory receptors work at the interface between the chemical world of volatile molecules and the perception of scent in the brain. Their main purpose is to translate chemical space into information that can be processed by neural circuits. Assuming that these receptors have evolved to cope with this task, the analysis of their coding strategy promises to yield valuable insight in how to encode chemical information in an efficient way.     

Characterization of a core fragment of the rhesus monkey TRIM5α protein

Background  

Like all tripartite motif (TRIM) proteins, the retroviral restriction factor TRIM5α consists of RING, B-box 2 and coiled-coil domains, with a C-terminal B30.2(SPRY) domain. Although structures have been determined for some individual TRIM domains, the structure of an intact TRIM protein is unknown.     

Structure and chromotropic properties of mono- and binuclear mixed-ligand nickel(II) complexes containing 1,3-diketonate and polyamine ligands

Abstract  

Mixed-ligand Ni^II complexes have been synthesized with 1,3-diketonate and bulky tri- or tetra-amine ligands. Their structures were determined by X-ray crystallography, and solvatochromic behavior was examined by UV–vis–NIR spectroscopy. Steric effects of the bulky ligands on the coordination distances and spectral properties are discussed.     

Chemogenetic fingerprinting by analysis of cellular growth dynamics

Background  

A fundamental goal in chemical biology is the elucidation of on- and off-target effects of drugs and biocides. To this aim chemogenetic screens that quantify drug induced changes in cellular fitness, typically taken as changes in composite growth, is commonly applied.     

Evolutionary algorithms in computer-aided molecular design

Summary In recent years, search and optimisation algorithms inspired by evolutionary processes have been applied with marked success to a wide variety of problems in diverse fields of study. In this review, we survey the growing application of these evolutionary algorithms in one such area: computer-aided molecular design. In the course of the review, we seek to summarise the work to date and to indicate where evolutionary algorithms have met with success and where they have not fared so well. In addition to this, we also attempt to discern some future trends in both the basic research concerning these algorithms and their application to the elucidation, design and modelling of chemical and biochemical structures.