Chemomics and drug innovation

Chemomics is an interdisciplinary study using approaches from chemoinformatics,bioinformatics,synthetic chemistry,and other related disciplines.Biological systems make natural products from endogenous small molecules (natural product building blocks) through a sequence of enzyme catalytic reactions.For each reaction,the natural product building blocks may contribute a group of atoms to the target natural product.We describe this group of atoms as a chemoyl.A chemome is the complete set of chemoyls in an organism.Chemomics studies chemomes and the principles of natural product syntheses and evolutions.Driven by survival and reproductive demands,biological systems have developed effective protocols to synthesize natural products in order to respond to environmental changes;this results in biological and chemical diversity.In recent years,it has been realized that one of the bottlenecks in drug discovery is the lack of chemical resources for drug screening.Chemomics may solve this problem by revealing the rules governing the creation of chemical diversity in biological systems,and by developing biomimetic synthesis approaches to make quasi natural product libraries for drug screening.This treatise introduces chemomics and outlines its contents and potential applications in the fields of drug innovation.     

Preface

In life sciences,molecules are categorized into biological macromolecules(protein,DNA,RNA etc.)and small molecules(neurotransmitters,vitamins,drugs,natural products,water etc.).The main methodology of chemistry for life sciences is using chemical techniques and tools to explore and manipulate the functions of biological macromolecules.This methodology can be traced back to W hler’s synthesis of urea from"inorganic"compounds in 1828.Today,we realize that chemistry can advance a molecular understanding of biology,and the harnessing of biology can advance chemical knowledge as well[1–4].Chemicals are widely used as probes to investigate biological functions[5–7].     

Predicting hiCE inhibitors based upon pharmacophore models derived from the receptor and its ligands

Human intestinal carboxyl esterase (hiCE) is a drug target for ameliorating irinotecan-induced diarrhea. By reducing irinotecan-induced diarrhea, hiCE inhibitors can improve the anti-cancer efficacy of irinotecan. To find effective hiCE inhibitors, a new virtual screening protocol that combines pharmacophore models derived from the hiCE structure and its ligands has been proposed. The hiCE structure has been constructed through homology techniques using hCES1’s crystal structure. The hiCE structure was optimized via molecular dynamics simulations with the most known active hiCE inhibitors docked into the structure. An optimized pharmacophore, derived from the receptor, was then generated. A ligand-based pharmacophore was also generated from a larger set of known hiCE inhibitors. The final hiCE inhibitor predictions were based upon the virtual screening hits from both ligand-based and receptor-based pharmacophore models. The hit rates from the ligand-based and receptor-based pharmacophore models are 88% and 86%, respectively. The final hit rate is 94%. The two models are highly consistent with one another (85%). This proves that both models are reliable.     

Chemical Regulation of Carbon Quantum Dots from Synthesis to Photocatalytic Activity

Carbon quantum dots (CQDs) were synthesized by heating various carbon sources in HNO₃ solution at reflux, and the effects of HNO₃ concentration on the size of the CQDs were investigated. Furthermore, the oxygen‐containing surface groups of as‐prepared CQDs were selectively reduced by NaBH₄, leading to new surface states. The experimental results show that the sizes of CQDs can be tuned by HNO₃ concentration and then influence their photoluminescent behaviors; the photoluminescent properties are related to both the size and surface state of the CQDs, but the photocatalytic activities are determined by surface states alone. The different oxygen‐containing groups on the surface of the CQDs can induce different degrees of the band bending upward, which determine the separation and combination of the electron–hole pairs. The high upward band bending, which is induced by C?O and COOH groups, facilitates separation of the electron–hole pairs and then enhances high photocatalytic activity. In contrast, the low upward band bending induced by C? OH groups hardly prevents the electron–hole pairs from surface recombination and then exhibits strong photoluminescence. Therefore, both the photocatalytic activities and optical properties of CQDs can be tuned by their surface states.     

Transition Metal (Mn,Fe, Co,Ni)‐Doped Graphene Hybrids for Electrocatalysis

The development of electrocatalysts is crucial for renewable energy applications. Metal‐doped graphene hybrid materials have been explored for this purpose, however, with much focus on noble metals, which are limited by their low availability and high costs. Transition metals may serve as promising alternatives. Here, transition metal‐doped graphene hybrids were synthesized by a simple and scalable method. Metal‐doped graphite oxide precursors were thermally exfoliated in either hydrogen or nitrogen atmosphere; by changing exfoliation atmospheres from inert to reductive, we produced materials with different degrees of oxidation. Effects of the presence of metal nanoparticles and exfoliation atmosphere on the morphology and electrocatalytic activity of the hybrid materials were investigated using electron microscopy, energy‐dispersive X‐ray spectroscopy, X‐ray photoelectron spectroscopy, and cyclic voltammetry. Doping of graphene with transition metal nanoparticles of the 4th period significantly influenced the electrocatalysis of compounds important in energy production and storage applications, with hybrid materials exfoliated in nitrogen atmosphere displaying superior performance over those exfoliated in hydrogen atmosphere. Moreover, nickel‐doped graphene hybrids displayed outstanding electrocatalytic activities towards reduction of O₂ when compared to bare graphenes. These findings may be exploited in the research field of renewable energy.     

Surface‐Passivated SBA‐15‐Supported Gold Nanoparticles: Highly Improved Catalytic Activity and Selectivity toward Hydrophobic Substrates

Silanol groups on a silica surface affect the activity of immobilized catalysts because they can influence the hydrophilicity/hydrophobicity, matter transfer, or even transition state in a catalytic reaction. Previously, these silanol groups have usually been passivated by using surface‐passivation reagents, such as alkoxysilanes, bis‐silylamine reagents, chlorosilanes, etc., and surface passivation has typically been found in mesoporous‐silicas‐supported molecular catalysts and heteroatomic catalysts. However, this property has rarely been reported in mesoporous‐silicas‐supported metal‐nanoparticle catalysts. Herein, we prepared an almost‐superhydrophobic SBA‐15‐supported gold‐nanoparticle catalyst by using surface passivation, in which the catalytic activity increased more than 14 times for the reduction of nitrobenzene compared with non‐passivated SBA‐15. In addition, this catalyst can selectively catalyze hydrophobic molecules under our experimental conditions, owing to its high (almost superhydrophobic) hydrophobic properties.     

Zinc Porphyrins with a Pyridine‐Ring‐Anchoring Group for Dye‐Sensitized Solar Cells

Anchoring groups are extremely important in controlling the performance of dye‐sensitized solar cells (DSCs). The design and characterization of sensitizers with new anchoring groups, in particular non‐carboxylic acid groups, has become a recent focus of DSC research. Herein, new donor? π? acceptor zinc? porphyrin dyes with a pyridine ring as an anchoring group have been designed and synthesized for applications in DSCs. Photophysical and electrochemical investigations demonstrated that the pyridine ring worked effectively as an anchoring group for the porphyrin sensitizers. DSCs that were based on these new porphyrins showed an overall power‐conversion efficiency of about 4.0 % under full sunlight (AM 1.5G, 100 mW cm^?2).     

A new three‐dimensional silver(I) coordination framework with a diamondoid topology constructed from 2‐(pyridin‐4‐yl)‐1H‐imidazole‐4,5‐dicarboxylic acid

The title compound, poly[[μ₄‐5‐carboxy‐4‐carboxylato‐2‐(pyridin‐4‐yl)‐1H‐imidazol‐1‐ido]disilver(I)], [Ag₂(C₁₀H₅N₃O₄)]_n, was synthesized by reacting silver nitrate with 2‐(pyridin‐4‐yl)‐1H‐imidazole‐4,5‐dicarboxylic acid (H₃PyIDC) under hydrothermal conditions. The asymmetric unit contains two crystallographically independent Ag^I cations and one unique HPyIDC²⁻ anion. Both Ag^I cations are three‐coordinated in distorted T‐shaped coordination geometries. One Ag^I cation is coordinated by one N and two O atoms from two HPyIDC²⁻ anions, while the other is bonded to one O and two N atoms from two HPyIDC²⁻ anions. It is interesting to note that the HPyIDC²⁻ group acts as a μ₄‐bridging ligand to link the Ag^I cations into a three‐dimensional framework, which can be simplified as a diamondoid topology. The thermal stability and photoluminescent properties of the title compound have also been studied.     

Development of a rapid method for the simultaneous separation and determination of 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol and its N- and O-glucuronides in human urine by liquid chromatography–tandem mass spectrometry

Determination of the tobacco-specific nitrosamine metabolite 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol (NNAL) and its N- and O-glucuronides (NNAL-N-Gluc and NNAL-O-Gluc) is important for toxicology analysis of tobacco smoke induced carcinogenicity and the understanding of detoxification mechanisms of the carcinogenic nitrosamine in humans. But previously reported indirect measurement methods involving enzymolysis and base treatment steps were tedious and time-consuming. In this work, a direct measurement method for simultaneous determination of urinary NNAL, NNAL-N-Gluc and NNAL-O-Gluc by liquid chromatography–tandem mass spectrometry (LC–MS/MS) in a single run was developed for the first time without the need to perform enzymatic or base hydrolysis. Urine samples were purified using dichloromethane and further extracted by solid-phase extraction. Then they were analyzed by LC–MS/MS operated in electrospray positive ionization mode. Chromatographic separation was achieved on a Phenomenex Kinetex PFP column within 6 min. The proposed method was validated and the results demonstrated that the method can produce satisfactory recoveries and reproducibility for the analytes. The applicability of this newly developed method was investigated for the simultaneous analysis of the three metabolites in smokers’ urine and the obtained results were comparable to those detected using the conventional enzymolysis method.     

Construction of microscale structures in enclosed microfluidic networks by using a magnetic beads based method

A large number of microscale structures have been used to elaborate flowing control or complex biological and chemical reaction on microfluidic chips. However, it is still inconvenient to fabricate microstructures with different heights (or depths) on the same substrate. These kinds of microstructures can be fabricated by using the photolithography and wet-etching method step by step, but involves time-consuming design and fabrication process, as well as complicated alignment of different masters. In addition, few existing methods can be used to perform fabrication within enclosed microfluidic networks. It is also difficult to change or remove existing microstructures within these networks. In this study, a magnetic-beads-based approach is presented to build microstructures in enclosed microfluidic networks. Electromagnetic field generated by microfabricated conducting wires (coils) is used to manipulate and trap magnetic beads on the bottom surface of a microchannel. These trapped beads are accumulated to form a microscale pile with desired shape, which can adjust liquid flow, dock cells, modify surface, and do some other things as those fabricated microstructures. Once the electromagnetic field is changed, trapped beads may form new shapes or be removed by a liquid flow. Besides being used in microfabrication, this magnetic-beads-based method can be used for novel microfluidic manipulation. It has been validated by forming microscale dam structure for cell docking and modified surface for cell patterning, as well as guiding the growth of neurons.