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NMR Studies on the Interaction between Oncogene RET G-Quadruplex and Berberine

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Chinese Journal of Chemistry 2020年第12期38卷 1656-1662页

作者： Fei wang Chunxi wang Yaping Liu Wenxian Lan renxiao wang Shaohua Huang Chunyang Cao State Key Laboratory of Bioorganic and Natural Product Chemistry Center for Excellence in Molecular Synthesisshonghailmsitute of Organic ChemistryChinese Academy of Sciences345 Lingling RoadShanghai 200032China University of Chinese Academy of Science No.19AYuquan RoadShijingshan DistrictBeijing 100049China Institute of Drug Discovery Technology Ningbo UniversityNo 818 Fenghua RoadNingboZhejiang 315211Ching

of main observation and conclusion RET G-quadruplex DNA(G4-DNA)is formed in the promoter region of RET protein,which is involved in the initiation and progression of human *** inhibits cancer cell growth through interactions with RET G4-DNA,but how it binds to RET G4-DNA remains ***,we reported that colchicine selectively bound to RET G4-DNA,but the structural basis of its binding selectivity is still ***,mainly by NMR,we demonstrated how berberine bound to RET G4-DNA in a means different from colchicine,and implied several key determinants for small molecules specifically binding to one G4-DNA.

关键词： Berberine RET berberine

Quantitative Analysis of Cytokinins in Plants by High Performance Liquid Chromatography:Electronspray Ionization Ion Trap Mass Spectrometry

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Journal of Integrative Plant Biology 2010年第10期52卷 925-932页

作者： Weiqi Chen Ying Gai Shichang Liu renxiao wang Xiangning Jiang College of Life Sciencesand Biotechnology Bering Forestry University The Tree and Ornamental Plant Bree~ng and BiotechnologyLaboratory of Chinese Forestry Administration National Engineering Laboratory for Tree Breeding Beijing 100083 China Institute of Genetics and Developmental Biology Chinese Academy of Sciences Beijing 100101 China

The present paper introduces a highly sensitive and selective method for simultaneous quantification of 12 cytokinins （free form and their conjugates）. The method includes a protocol of extraction with methanol/water/formic acid （15/4/1, v/v/v） to the micro-scale samples, pre-purification with solid phase extraction （SPE） cartridges of the extracts, separation with a high performance liquid chromatography （HPLC） and detection by an electrospray ionization ion trap mass spectrometry （ESl-lon trap-MS） system in a consecutive ion monitoring （CRM） mode at the three stage fragmentation of mass spectrometry （MS3）. The lowest detection level of the cytokinins of the method reaches 0.1-2.0 pg with a very wide range of linear regression from 1-512 pg, at the coefficient factors of 0.98-0.99. The feasibility of this method has been proven in the application of the method to the analysis of the trace-amount contents of cytokinins in the micro-scale samples of various types of plant materials, such as aerial parts of rice and poplar leaves etc. 12 endogenous cytokinins had been identified and quantified in the plant tissues, with an acceptable relatively higher recovery rate from 40% to 70%.

关键词： Methanol Cytokinins Extraction Extracts Methods Mass spectrometry Weight Traps Trapping Ions

An unusual UMP C-5 methylase in nucleoside antibiotic polyoxin biosynthesis

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Protein & Cell 2016年第9期7卷 673-683页

作者： Wenqing Chen Yan Li Jie Li Lian Wu renxiao wang Zixin Deng Jiahai Zhou Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education and School of Pharmaceutical Sciences Wuhan University Wuhan 430071 China State Key Laboratory of Bioorganic and Natural Products Chemistry Shanghai Institute of Organic Chemistry Chinese Academy of Sciences Shanghai 200032 China State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology Shanghai Jiao Tong University Shanghai 200030 China

Polyoxin is a group of structurally-related peptidyl nucleoside antibiotics bearing C-5 modifications on the nucleoside skeleton. Although the structural diversity and bioactivity preference of polyoxin are, to some extent, affected by such modifications, the biosynthetic logic for their occurence remains obscure. Here we report the identification of PolB in polyoxin pathway as an unusual UMP C-5 methylase with thymidylate syn- thase activity which is responsible for the C-5 methyla- tion of the nucleoside skeleton. To probe its molecular mechanism, we determined the crystal structures of PolB alone and in complexes with 5-Br UMP and 5-Br dUMP at 2.15 A, 1.76 A and 2.28 A resolutions, respec- tively. Loop 1 （residues 117-131）, Loop 2 （residues 192- 201） and the substrate recognition peptide （residues 94- 102） of PolB exhibit considerable conformational flexi-bility and adopt distinct structures upon binding to different substrate analogs. Consistent with the structural findings, a PolB homolog that harbors an identical function from Streptomyces viridochromogenes DSM 40736 was identified. The discovery of UMP C5-methy-lase opens the way to rational pathway engineering for polyoxin component optimization, and will also enrich the toolbox for natural nucleotide chemistry.

关键词： polyoxin nucleoside antibiotics,biosynthesis UMP C5-methylase thymidylate synthase

Synthesis of 4-（2-Phenylhydrazono）-l-（4-phenylthiazol-2-yl）- 1H-pyrazol-5（4H）-one Compounds and Characterization of Their Affinities to Anti-apoptotic Bcl-2 Family Proteins

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Chinese Journal of Chemistry 2013年第9期31卷 1133-1138页

作者： Shicheng Shi Li Han Mi Zhou Yangfeng Li Zhen Li Biao Yu renxiao wang State Key Laboratory of Bioorganic and Natural Products Chemistry Shanghai Institute of Organic Chemistry Chinese Academy of Sciences Shanghai 200032 China

Organic compounds containing the thiazol-2-yl-lH-pyrazol-5（4H）-one moiety are known to be associated with versatile pharmacological applications. In this study, we describe the methods for preparing 4-（2-phenylhydrazono）- l-（4-phenylthiazol-2-yl）-1H-pyrazol-5（4H）-one compounds. A set of 26 compounds were synthesized with overall yields ranging between 37%-92%. They were tested in a fluorescence polarization-based binding assay against three anti-apoptotic Bcl-2 family proteins, including Bcl-xL, Bcl-2, and Mcl-1. Our results indicate that this class of compounds are not effective inhibitors of these anti-apoptotic Bcl-2 family proteins. Their apoptosis-inducing ef- fects are possibly due to BAX activation as suggested by Gavathiotis et al. in their recent study. However, other possibilities should not be ignored. In addition, a crystal structure obtained by us reveals that the exocyclic double bond in the molecular structure of this class of compounds is in the （Z）-configuration.

关键词： apoptosis inducer BAX activation Bcl-2 inhibition protein-protein interaction small-molecule in-hibitor

Special Issue of ＂Medicinal Chemistry＂

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Chinese Journal of Chemistry 2013年第9期31卷 1115-1115页

作者： renxiao wang State Key Laboratory of Bioorganic and Natural Products Chemistry Shanghai Institute of Organic Chemistry Chinese Academy of Sciences Shanghai 200032 China

Medicinal chemistry is the application of chemical techniques to the discovery and development of bio-active molecules with pharrnaceutical potentials. Chemical research in China has progressed greatly in the past ten years or so. As a major branch of chemistry, no wonder medicinal chemistry research is also very active in China. This special issue of ＂Medicinal Chem- istry＂ of Chinese Journal o[＂ Chemistl3, presents 11 lull papers, two communications, and one review. These studies describe molecular design, synthesis, and bio- logical testing of various compounds with anti-virus, anti-cancer, anti-fungal and other activities, which are contributed by researchers from a range of top universi- ties and institutes across China. We hope that these studies help the readers establish an understanding of the current state of medicinal chemistry research in China.

关键词： MOLECULES PHARMACEUTICAL chemistry PERIODICAL articles DESIGN & construction

High-performance simulation and prediction of the protein-ligand unbinding process and kinetics

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High-performance simulation and prediction of the protein-li...

2019中国化学会第十五届全国计算（机）化学学术会议

作者：杜宇 renxiao wang 中科院上海有机化学所 Shanghai Institute of Organic Chemistry Chinese Academy of Sciences

In target-based drug design, a small molecule is designed to bind selected target（s） and makes a strong and enduring effect safely in vivo. Although researchers are split over the kinetic rate constant being a good indicator for lead optimization in non-equilibrium system like human body, with more crystal structures and the advance of computational capability and enhanced sampling methods, they don’t satisfy with the study of stable binding states and are further interested in the process and kinetics of（un）binding. There have been several methods for studying the dynamic processes before and after stable binding states, but it is still a challenge to fully understand the molecular mechanism of（un）binding kinetics. In this MD simulation work, we specifically and smoothly scaled down the non-bonding interaction between protein and ligand to speed up the dissociation process. Our approach showed reasonable unbinding dynamics of ligand, protein and water. The binding free energy sum correlated well with the dissociation rate constant. Therefore, we believe our approach can be a great tool for small molecules design from the viewpoint of dynamics and kinetics.

关键词： Drug design Binding kinetics Molecular dynamics

Dynamic Network Modelling of Bcl-2 Family Proteins

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Dynamic Network Modelling of Bcl-2 Family Proteins

2019中国化学会第十五届全国计算（机）化学学术会议

作者：杨启帆 renxiao wang 上海有机化学研究所 State Key Laboratory of Bioorganic and Natural Products Chemistry Shanghai Institute of Organic Chemistry Chinese Academy of Sciences Department of Medicinal Chemistry School of Pharmacy Fudan University

The Bcl-2 family consists of several proteins that share Bcl-2 homology（BH） domain and control apoptosis by governing mitochondrial outer membrane permeabilization（MOMP）, which is a key step in the intrinsic pathway of apoptosis. However, the dynamic mechanism of action between the Bcl-2 family proteins is not clear. In addition, it remains an unknown issue that how small molecules induce apoptosis by regulating the protein-protein interaction network. Herein, we attempt to build a dynamic network model, which describes the interactions between the Bcl-2 family proteins by a set of ordinary differential equations. Two special nodes representing small molecules were added to our network model to investigate the induction of apoptosis by anti-apoptotic protein inhibitors. To fit the parameters of the model and verify its rationality, the Bcl-2 family proteins concentration was measured by quantitative western blotting assay. Interestingly, we have found some nonlinear dynamic properties in the dynamic network. When the concentration of the inhibitor is at a low level, the apoptosis signal（MOMP） value is nearly 0. Only the concentration exceeds a certain threshold, the apoptosis signal jump to a high level and the cell apoptosis is activated. This study has deepened our understanding on the Bcl-2 family protein interactions. By utilizing such a dynamic network model, it helps researchers to design the multi-target drugs or combination therapies.

关键词： Bcl-2 Family Proteins Dynamic Network Inhibitors Multi-Target Drug

A Computational Study on Binding Hot Spots Prediction and Agonist Binding Patterns of Bax Protein

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A Computational Study on Binding Hot Spots Prediction and Ag...

2019中国化学会第十五届全国计算（机）化学学术会议

作者：冯国勤 renxiao wang State Key Laboratory of Bio-Organic and Natural Products Chemistry Shanghai Institute of Organic Chemistry Chinese Academy of Sciences

＜正＞Pro-apoptotic protein Bax is the executor of mitochondrial membrane permeabilization and mitochondrial dysfunction, and direct targeting of Bax has great potential to become a new cancer therapy in the future. However, the crystal complex structure of the Bax has not been reported yet, which delays the functional research and the discovery of active small molecule regulators for Bax protein.

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Conformational Analysis of Cyclopeptide:Evidence from DFT Calculations and Molecular Dynamics Simulations

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Conformational Analysis of Cyclopeptide:Evidence from DFT Ca...

第八届全国化学生物学学术会议

作者： Han Li Min Chiju wang renxiao State Key Laboratory of Bioorganic Chemistry Shanghai Institute of Organic ChemistryChinese Academy of Sciences

＜正＞Polypeptide drugs cause increasing attention due to their application in clinical *** the one hand,many linear peptides have good stability and biological activity in vitro,they degradate rapidly in *** the othe... 详细信息

关键词： Cyclopeptide Molecular Dynamics Simulation Clustering Analysis Potential energy surface