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Chinese Chemical Letters 2024年第5期35卷 407-417页

作者： Hongmei Yu Baoxi Zhang Meiju Liu Cheng Xing Guorong He Li Zhang ningbo gong Yang Lu Guanhua Du Beijing Key Laboratory of Polymorphic Drugs Institute of Materia MedicaChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100050China Beijing City Key Laboratory of Drug Target Identification and Drug Screening Institute of Materia MedicaChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100050China

The virtual cocrystal screening approach based on molecular electrostatic potential surface(MEPS)maps is a fast and feasible computational method to estimate the probability of cocrystal formation by calculating the difference in the interaction site pairing energies of monomers and that of their assemblies prior to experimental screening.In this paper,we report 12 cocrystal forms of temozolomide with mono-,di-,and trihydroxy benzoic acids,namely,3-hydroxy-,2,4-dihydroxy-,2,5-dihydroxy-,2,6-dihydroxy-,3,4-dihydroxy-,and 3,4,5-trihydroxy-benzoic acids,as well as benzoic acid,as pharmaceutical coformers for the first time.10 single crystals out of the 12 cocrystal forms were obtained and unequivocally determined by single-crystal X-ray diffraction,which clarified spatial arrangements,molecular conformations,and supramolecular synthons.MEPS further gains some insights into the sites of hydrogen bonding interactions for exploring combination patterns in these assemblies.Modulated stability of TMZ was successfully achieved by cocrystallization with these acids.

关键词： Virtual Cocrystal Temozolomide Supramolecular synthon Phenolic acid Stability

Development of a new ferulic acid certified reference material for use in clinical chemistry and pharmaceutical analysis

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Acta Pharmaceutica Sinica B 2015年第3期5卷 231-237页

作者： Dezhi Yang Fengfeng Wang Li Zhang ningbo gong Yang Lv Beijing Key Laboratory of Polymorphic Drugs Institute of Materia MedicaChinese Academy of Medical Sciences and Peking Union Medical College

This study compares the results of three certified methods,namely differential scanning calorimetry(DSC),the mass balance(MB) method and coulometric titrimetry(CT),in the purity assessment of ferulic acid certified reference material(CRM).Purity and expanded uncertainty as determined by the three methods were respectively 99.81%,0.16%;99.79%,0.16%;and 99.81%,0.26%with,in all cases,a coverage factor(k) of 2(P ? 95%).The purity results are consistent indicating that the combination of DSC,the MB method and CT provides a confident assessment of the purity of suitable CRMs like ferulic acid.

关键词： Differential scanning calorimetry Mass balance Coulometric titrimetry Certified reference material Uncertainty Ferulic acid

Crystal Structures, Stability, and Solubility Evaluation of a 2:1 Diosgenin-Piperazine Cocrystal

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Natural Products and Bioprospecting 2020年第4期10卷 261-267页

作者： ningbo gong Hongmei Yu Ying Wang Cheng Xing Kun Hu Guanhua Du Yang Lu Beijing Key Laboratory of Polymorphic Drugs Institute of Materia MedicaChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100050China Beijing City Key Laboratory of Drug Target Identification and Drug Screening Institute of Materia MedicaChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100050China

A cocrystal of diosgenin with piperazine in 2:1 stoichiometry was successfully synthesized.The solid form was prepared by liquid assisted grinding,slurry and crystallization methods.The cocrystal was characterized by powder X-ray diffraction,differential scanning calorimetry,thermogravimetric analysis,Fourier transform infrared spectroscopy,and structure determined by single crystal X-ray diffraction,the hydrogen bonds formed into fish bone structure along the[010]direction and all the molecules packed into 3D layer structure along a axis.After formation of cocrystal,the solubility of diosgenin was improved,and the solubility value in 0.2%SDS solution was approximately 1.5 times as large as that of the parent material.

关键词： Diosgenin Piperazine Cocrystal Characterization Solubility

An innovative rhein-matrine cocrystal: Synthesis, characterization,formation mechanism and pharmacokinetic study

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Chinese Chemical Letters 2023年第2期34卷 546-549页

作者： Hongjuan Wang Dezhi Yang Wen Zhang Junke Song ningbo gong Mingchao Yu Shiying Yang Baoxi Zhang Qiwen Liu Guanhua Du Yang Lu Beijing Key Laboratory of Polymorphic Drugs Center of Pharmaceutical PolymorphsInstitute of Materia MedicaChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100050China Beijing Key Laboratory of Drug Targets Identification and Drug Screening National Center for Pharmaceutical ScreeningInstitute of Materia MedicaChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100050China

Rhein(Rhe), an anthraquinone derivative, exhibits excellent anti-inflammatory effects and other pharmacological activities, but its clinical application remains limited due to poor solubility. The present work aims at the improvement of solubility and oral bioavailability of Rhe through cocrystal formation. For this purpose, Rhe and matrine(Mat) were selected as pharmaceutical ingredient(API) and cocrystal former(CCF), respectively, and the Rhe-Mat cocrystal was synthesized and characterized by single crystal X-ray diffraction(SXRD), powder X-ray diffraction(PXRD), thermogravimetric analysis(TGA), differential scanning calorimetry(DSC). The formation mechanism of Rhe-Mat cocrystal was elucidated by molecular surface electrostatic potential(MSEP). It is worth mentioning that the 50-fold increment of dissolution in vitro was observed in pure water in the form of Rhe-Mat cocrystal. Furthermore, the in vivo studies revealed that Rhe-Mat cocrystal indicated the faster absorption rate and the higher peak blood concentration than the pure Rhe. Hence, it can be concluded that current study successfully improved the solubility and oral bioavailability of Rhe.

关键词： Rhein Matrine Cocrystal Poor solubility Molecular surface electrostatic potential

Single small molecule-assembled nanoparticles mediate efficient oral drug delivery

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Nano Research 2019年第10期12卷 2468-2476页

作者： Xin Yang Chao Ma Zeming Chen Jun Liu Fuyao Liu Rongbin Xie Haitian Zhao Gang Deng Ann TChen ningbo gong Lei Yao Pengjian Zuo Kangkang Zhi Jiacheng Wang Xiaobin Gao Jing Wang Louzhen Fan Jiangbing Zhou School of Chemistry and Chemical Engineering Harbin Institute of TechnologyHarbin 150090China College of Biological Sciences and Biotechnology Beijing Forestry UniversityBeijing 100083China Department of Neurosurgery Yale UniversityNew HavenCT 06510USA Department of Chemistry Beijing Normal UniversityBeijing 100875China Department of Biomedical Engineering Yale UniversityNew HavenCT 06510USA Beijing Key Laboratory of Polymorphic Drugs Institute of Materia MedicoChinese Academy cf Medical Sciences and Peking Union Medical CollegeBeijing 100050China Department of Pathology Yale UniversityNew HavenCT 06510USA

Oral drug delivery,which requires surviving the harsh environment in the gastrointestinal(Gl)tract and penetrating the intestinal epithelium,has not bee n achieved using simple formulatio n nan oparticles(NPs).Medici nal natural products(MNPs)have bee n widely used in traditi onal medicine for disease management through oral consumption.However,most pharmacologically active compounds within MNPs do not have the properties suitable for oral applicatio ns.We hypothesize that some MNPs contain n atural nano materials that can convert those compounds into oral formulations by forming NPs.After screening 66 MNPs,we identified five classes of small molecules that form NPs,many of which are capable of efficient drug encapsulation and Gl penetration.We show that one of them,dehydrotrametenolic acid(DTA),is capable of mediating oral delivery for effective disease treatment.We determined that DTA NPs assemble through hydrogen bonding and penetra怕the Gl tract via apical sodium-depe ndent bile acid tran sporter.Our study reveals a no vel class of single comp orient,small molecule-assembled NPs for oral drug delivery,and suggests a n ovel approach to modernizi ng MNPs through nano material discovery.

关键词： natural material oral drug delivery nano particle dehydrotrametenolic acid(DTA)

Sparse Reconstructive Evidential Clustering for Multi-View Data

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IEEE/CAA Journal of Automatica Sinica 2024年第2期11卷 459-473页

作者： Chaoyu gong Yang You School of Computing National University of SingaporeSingapore

Although many multi-view clustering(MVC) algorithms with acceptable performances have been presented, to the best of our knowledge, nearly all of them need to be fed with the correct number of clusters. In addition, these existing algorithms create only the hard and fuzzy partitions for multi-view objects,which are often located in highly-overlapping areas of multi-view feature space. The adoption of hard and fuzzy partition ignores the ambiguity and uncertainty in the assignment of objects, likely leading to performance degradation. To address these issues, we propose a novel sparse reconstructive multi-view evidential clustering algorithm(SRMVEC). Based on a sparse reconstructive procedure, SRMVEC learns a shared affinity matrix across views, and maps multi-view objects to a 2-dimensional humanreadable chart by calculating 2 newly defined mathematical metrics for each object. From this chart, users can detect the number of clusters and select several objects existing in the dataset as cluster centers. Then, SRMVEC derives a credal partition under the framework of evidence theory, improving the fault tolerance of clustering. Ablation studies show the benefits of adopting the sparse reconstructive procedure and evidence theory. Besides,SRMVEC delivers effectiveness on benchmark datasets by outperforming some state-of-the-art methods.

关键词： Evidence theory multi-view clustering(MVC) optimization sparse reconstruction

Exploring a Promising Region and Enhancing Decision Space Diversity for Multimodal Multi-Objective Optimization

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Tsinghua Science and Technology 2024年第2期29卷 325-342页

作者： Fei Ming Wenyin gong School of Computer Science China University of GeosciencesWuhan 430074China

During the past decade,research efforts have been gradually directed to the widely existing yet less noticed multimodal multi-objective optimization problems(MMOPs)in the multi-objective optimization community.Recently,researchers have begun to investigate enhancing the decision space diversity and preserving valuable dominated solutions to overcome the shortage caused by a preference for objective space convergence.However,many existing methods still have limitations,such as giving unduly high priorities to convergence and insufficient ability to enhance decision space diversity.To overcome these shortcomings,this article aims to explore a promising region(PR)and enhance the decision space diversity for handling MMOPs.Unlike traditional methods,we propose the use of non-dominated solutions to determine a limited region in the PR in the decision space,where the Pareto sets(PSs)are included,and explore this region to assist in solving MMOPs.Furthermore,we develop a novel neighbor distance measure that is more suitable for the complex geometry of PSs in the decision space than the crowding distance.Based on the above methods,we propose a novel dual-population-based coevolutionary algorithm.Experimental studies on three benchmark test suites demonstrates that our proposed methods can achieve promising performance and versatility on different MMOPs.The effectiveness of the proposed neighbor distance has also been justified through comparisons with crowding distance methods.

关键词： multimodal multi-objective optimization evolutionary algorithms promising region neighbor distance decision space coevolution

Metagenomics reveals the microbial community and functional metabolism variation in the partial nitritation-anammox process:From collapse to recovery

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Journal of Environmental Sciences 2024年第1期135卷 210-221页

作者： Hong Wang Hui gong Xiaohu Dai Min Yang State Key Laboratory of Pollution Control and Resource Reuse College of Environmental Science and EngineeringTongji UniversityShanghai 200092China BIOMATH Department of Data Analysis and Mathematical ModellingGhent UniversityGhent 9000Belgium

Mainstream partial nitritation-anammox(PNA)process easily suffers from performance instability and even reactor collapse in application.Thus,it is of great significance to unveil the characteristic of performance recovery,understand the intrinsic mechanism and then propose operational strategy.In this study,we combined long-term reactor operation,batch tests,and metagenomics to reveal the succession of microbial community and functional metabolism variation from system collapse to recovery.Proper aeration control(0.10-0.25mg O_(2)/L)was critical for performance recovery.It was also found that Candidatus Brocadia became the dominant flora and its abundance increased from 3.5%to 11.0%.Significant enhancements in carbon metabolism and phospholipid biosynthesis were observed during system recovery,and the genes abundance related to signal transduction was dramatically increased.The up-regulation of sdh and suc genes showed the processes of succinate dehydrogenation and succinyl-CoA synthesis might stimulate the production of amino acids and the synthesis of proteins,thereby possibly improving the activity and abundance of AnAOB,which was conducive to the performance recovery.Moreover,the increase in abundance of hzs and hdh genes suggested the enhancement of the anammox process.Changes in the abundance of key genes involved in nitrogen metabolism indicated that nitrogen removal pathway was more diverse after system recovery.The achievement of performance recovery was driven by anammox,nitrification and denitrification coupled with dissimilatory nitrate reduction to ammonium.These results provide deeper insights into the recovery mechanism of PNA system and also provide a potential regulation strategy for the stable operation of the mainstream PNA process.

关键词： Partial nitritation-anammox Metagenomics Microbial community Functional metabolism Recovery

Predictive model using four ferroptosis-related genes accurately predicts gastric cancer prognosis

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World Journal of Gastrointestinal Oncology 2024年第5期16卷 2018-2037页

作者： Li Wang Wei-Hua gong Department of Emergency The Second Affiliated Hospital of Zhejiang University School of MedicineHangzhou 310000Zhejiang ProvinceChina Department of Surgery The Second Affiliated Hospital Zhejiang University School of MedicineHangzhou 310052Zhejiang ProvinceChina

BACKGROUND Gastric cancer(GC)is a common malignancy of the digestive system.According to global 2018 cancer data,GC has the fifth-highest incidence and the thirdhighest fatality rate among malignant tumors.More than 60%of GC are linked to infection with Helicobacter pylori(H.pylori),a gram-negative,active,microaerophilic,and helical bacterium.This parasite induces GC by producing toxic factors,such as cytotoxin-related gene A,vacuolar cytotoxin A,and outer membrane proteins.Ferroptosis,or iron-dependent programmed cell death,has been linked to GC,although there has been little research on the link between H.pylori infection-related GC and ferroptosis.AIM To identify coregulated differentially expressed genes among ferroptosis-related genes(FRGs)in GC patients and develop a ferroptosis-related prognostic model with discrimination ability.METHODS Gene expression profiles of GC patients and those with H.pylori-associated GC were obtained from The Cancer Genome Atlas and Gene Expression Omnibus(GEO)databases.The FRGs were acquired from the FerrDb database.A ferroptosis-related gene prognostic index(FRGPI)was created using least absolute shrinkage and selection operator–Cox regression.The predictive ability of the FRGPI was validated in the GEO cohort.Finally,we verified the expression of the hub genes and the activity of the ferroptosis inducer FIN56 in GC cell lines and tissues.RESULTS Four hub genes were identified(NOX4,MTCH1,GABARAPL2,and SLC2A3)and shown to accurately predict GC and H.pylori-associated GC.The FRGPI based on the hub genes could independently predict GC patient survival;GC patients in the high-risk group had considerably worse overall survival than did those in the low-risk group.The FRGPI was a significant predictor of GC prognosis and was strongly correlated with disease progression.Moreover,the gene expression levels of common immune checkpoint proteins dramatically increased in the highrisk subgroup of the FRGPI cohort.The hub genes were also confirmed to be highly overexpressed in GC cell line

关键词： Ferroptosis Gastric cancer Helicobacter pylori infection Immune checkpoint protein Prognostic model Ferroptosis-related gene prognostic index

Interplant communication:an emerging battlefield in plant-aphid-virus interactions

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Science China(Life Sciences) 2024年第5期67卷 1069-1071页

作者： Yunjing Wang Qian gong Yule Liu MOE Key Laboratory of Bioinformatics and Center for Plant Biology School of Life SciencesTsinghua UniversityBeijing 100084China Tsinghua-Peking Center for Life Sciences Beijing 100084China

Plants constantly face threats from various organisms,including pathogens and herbivores.Among the pathogens,plant viruses are obligate intracellular parasites that infect plants and cause serious crop yield losses.

关键词： plant Plants communication