基本信息
郑明月  男  博导  中国科学院上海药物研究所
电子邮件: myzheng@simm.ac.cn
通信地址: 上海市浦东新区祖冲之路555号1105室
邮政编码:

招生信息

   
招生专业
1007Z1-药物设计学
100800-中药学
招生方向
药物设计学
中药药理学

教育背景

2001-09--2006-07   中科院上海药物研究所   博士学位
1997-09--2001-07   中国海洋大学   学士学位

工作经历

   
工作简历
2015-10~现在, 中国科学院上海药物研究所, 研究员
2008-10~2015-09,中国科学院上海药物研究所, 副研究员
2006-07~2008-09,中科院上海药物研究所, 助理研究员
2001-09~2006-07,中科院上海药物研究所, 博士学位
1997-09~2001-07,中国海洋大学, 学士学位
社会兼职
2022-01-01-今,中国生物信息学会药物发现专业委员会, 委员
2019-01-01-今,中国化学会计算机化学专业委员会, 委员
2009-11-01-2016-06-16,J MED CHEM编辑助理,

教授课程

药物设计学

专利与奖励

   
奖励信息
(1) 药明康德生命化学研究奖, 部委级, 2021
(2) 赛诺菲-中科院上海生科院优秀青年人才奖, 一等奖, 院级, 2015
(3) 第17届中国药学会-施维雅青年药物化学奖, 一等奖, 专项, 2014
(4) 上海药物研究所“优秀青年科技工作者”, 一等奖, 研究所(学校), 2013
专利成果
( 1 ) 8-羟基喹啉类药物或其盐在制备用于治疗与BRD4相关的疾病的药物中的应用, 2017, 第 2 作者, 专利号: 2017104864336

( 2 ) 一类稠合双环杂芳基或芳基化合物,及其用途, 2017, 第 3 作者, 专利号: 2017104864393

( 3 ) 五元杂环并[3,4-d]哒嗪酮类化合物、其制备方法、药物组合物及其应用, 2016, 第 4 作者, 专利号: 2016103530352

( 4 ) 基于分层原子加和模型的分子酸碱解离常数的预测方法, 2012, 第 5 作者, 专利号: 200710047343.3

( 5 ) 新颖的吡唑类5-脂氧酶小分子抑制剂及制备方法、药物组合物和应用, 2008, 第 4 作者, 专利号: ZL2008100351896.9

( 6 ) D3Pharma分子模拟与药物设计软件, 2008, 第 3 作者, 专利号: ZL2008SR13316

( 7 ) 基于分子亲电矢量(MEV)和扩展支持向量机(SVM)的基因毒性概率预测方法, 2007, 第 5 作者, 专利号: ZL200710047343.3

( 8 ) 取代-1H-吲哚类化合物、其制备方法、其应用及其药物组合物, 2006, 第 5 作者, 专利号: ZL200610030357.X

出版信息

   
发表论文
(1) Structural Optimization of Fibroblast Growth Factor Receptor Inhibitors for Treating Solid Tumors, JOURNAL OF MEDICINAL CHEMISTRY, 2023, 通讯作者
(2) Graph neural network approaches for drug-target interactions, CURRENT OPINION IN STRUCTURAL BIOLOGY, 2022, 通讯作者
(3) An inductive graph neural network model for compound-protein interaction prediction based on a homogeneous graph, BRIEFINGS IN BIOINFORMATICS, 2022, 通讯作者
(4) 人工智能技术在化学反应预测中的应用, Application of Artificial Intelligence in Chemical Reaction Prediction, 中国现代应用药学, 2022, 第 5 作者
(5) Discovery of the First-in-Class Agonist-Based SOS1 PROTACs Effective in Human Cancer Cells Harboring Various KRAS Mutations, JOURNAL OF MEDICINAL CHEMISTRY, 2022, 通讯作者
(6) Discovery and identification of a novel small molecule BCL-2 inhibitor that binds to the BH4 domain, ACTA PHARMACOLOGICA SINICA, 2022, 通讯作者
(7) Blood–brain barrier penetration prediction enhanced by uncertainty estimation, JOURNAL OF CHEMINFORMATICS, 2022, 通讯作者
(8) 药物-靶点相互作用预测中的方法、数据及软件的发展现状, Development of Methods, Data and Software for Drug Target Interaction Prediction, 中国现代应用药学, 2022, 第 4 作者
(9) Discovery of Pyrazolo3,4-dpyridazinone Derivatives as Selective DDR1 Inhibitors via Deep Learning Based Design, Synthesis, and Biological Evaluation, JOURNAL OF MEDICINAL CHEMISTRY, 2022, 通讯作者
(10) Drug target inference by mining transcriptional data using a novel graph convolutional network framework, Drug target inference by mining transcriptional data using a novel graph convolutional network framework, PROTEIN & CELL, 2022, 通讯作者
(11) Discovery of ARF1-targeting inhibitor demethylzeylasteral as a potential agent against breast cancer, ACTA PHARMACEUTICA SINICA B, 2022, 通讯作者
(12) Design, synthesis and biological evaluation of pyrazolo3,4-dpyridazinone derivatives as covalent FGFR inhibitors, Design, synthesis and biological evaluation of pyrazolo3,4-dpyridazinone derivatives as covalent FGFR inhibitors, ACTA PHARMACEUTICA SINICA B, 2021, 通讯作者
(13) 高价值数据挖掘与人工智能技术加速创新药物研发, Accelerating R&D of Innovative Drugs through High-value Data Mining and Artificial Intelligence, 药学进展, 2021, 第 1 作者
(14) DrugSpaceX: a large screenable and synthetically tractable database extending drug space, NUCLEIC ACIDS RESEARCH, 2021, 通讯作者
(15) Drug target inference by mining transcriptional data using a novel graph convolutional network framework, PROTEIN & CELL, 2021, 通讯作者
(16) Ligand-Promoted Alkynylation of Aryl Ketones: A Practical Tool for Structural Diversity in Drugs and Natural Products, ACS CATALYSIS, 2021, 通讯作者
(17) Graph neural networks for automated de novo drug design, DRUG DISCOVERY TODAY, 2021, 通讯作者
(18) 中药在新冠肺炎防治中的应用和研究进展, Application and research progress of traditional Chinese medicine in prevention and treatment of corona virus disease 2019, 上海中医药大学学报, 2020, 第 5 作者
(19) Optimizing chemical reaction conditions using deep learning: a case study for the Suzuki-Miyaura cross-coupling reaction, ORGANIC CHEMISTRY FRONTIERS, 2020, 通讯作者
(20) Discovery of novel glyceraldehyde-3-phosphate dehydrogenase inhibitor via docking-based virtual screening, BIOORGANIC CHEMISTRY, 2020, 通讯作者
(21) Deep Learning Enhancing Kinome-Wide Polypharmacology Profiling: Model Construction and Experiment Validation, JOURNAL OF MEDICINAL CHEMISTRY, 2020, 通讯作者
(22) Bioactivity Prediction Based on Matched Molecular Pair and Matched Molecular Series Methods, CURRENT PHARMACEUTICAL DESIGN, 2020, 通讯作者
(23) Revisiting Aldehyde Oxidase Mediated Metabolism in Drug-like Molecules: An Improved Computational Model, JOURNAL OF MEDICINAL CHEMISTRY, 2020, 通讯作者
(24) Solution-Phase DNA-Compatible Pictet-Spengler Reaction Aided by Machine Learning Building Block Filtering, ISCIENCE, 2020, 通讯作者
(25) Discovery of triazoloquinoxaline as novel STING agonists via structure-based virtual screening, BIOORGANIC CHEMISTRY, 2020, 通讯作者
(26) Pushing the Boundaries of Molecular Representation for Drug Discovery with the Graph Attention Mechanism, JOURNAL OF MEDICINAL CHEMISTRY, 2020, 通讯作者
(27) 人工智能算法在药物细胞敏感性预测中的应用, The application of artificial intelligence to drug sensitivity prediction, 科学通报, 2020, 第 10 作者
(28) TransformerCPI: improving compound-protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments, BIOINFORMATICS, 2020, 通讯作者
(29) Discovery and characterization of natural products as novel indoleamine 2,3-dioxygenase 1 inhibitors through high-throughput screening, Discovery and characterization of natural products as novel indoleamine 2,3-dioxygenase 1 inhibitors through high-throughput screening, ACTA PHARMACOLOGICA SINICA, 2020, 第 6 作者
(30) Characterization of covalent binding of tyrosine kinase inhibitors to plasma proteins, DRUG METABOLISM AND PHARMACOKINETICS, 2020, 第 3 作者
(31) Automated design and optimization of multitarget schizophrenia drug candidates by deep learning, EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 2020, 通讯作者
(32) Discovery of Highly Potent, Selective, and Orally Efficacious p300/CBP Histone Acetyltransferases Inhibitors, JOURNAL OF MEDICINAL CHEMISTRY, 2020, 通讯作者
(33) 中国药物分子设计40年发展成就, Development of drug design in China:40 years of achievements, 中国科学:生命科学, 2019, 第 6 作者
(34) Improving the Virtual Screening Ability of Target-Specific Scoring Functions Using Deep Learning Methods, FRONTIERS IN PHARMACOLOGY, 2019, 通讯作者
(35) Discovery and Development of a Series of Pyrazolo3,4-dpyridazinone Compounds as the Novel Covalent Fibroblast Growth Factor Receptor Inhibitors by the Rational Drug Design, JOURNAL OF MEDICINAL CHEMISTRY, 2019, 通讯作者
(36) Deep Neural Network Classifier for Virtual Screening Inhibitors of (S)-Adenosyl-L-Methionine (SAM)-Dependent Methyltransferase Family, FRONTIERS IN CHEMISTRY, 2019, 通讯作者
(37) Rational design of 5-((1H-imidazol-1-yl)methyl)quinolin-8-ol derivatives as novel bromodomain-containing protein 4 inhibitors, EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 2019, 通讯作者
(38) Hydrolytic Metabolism of Cyanopyrrolidine DPP-4 Inhibitors Mediated by Dipeptidyl Peptidases, DRUGMETABOLISMANDDISPOSITION, 2019, 第 5 作者
(39) KinomeX: a web application for predicting kinome-wide polypharmacology effect of small molecules, BIOINFORMATICS, 2019, 通讯作者
(40) Artificial intelligence in drug design, Artificial intelligence in drug design, 中国科学:生命科学英文版, 2018, 第 15 作者
(41) Computational chemical biology and drug design: facilitating protein structure, function, and modulation studies, MEDICINAL RESEARCH REVIEWS, 2018, 第 1 作者
(42) Discovery of Novel Inhibitors of Indoleamine 2,3-Dioxygenase 1 Through Structure-Based Virtual Screening, FRONTIERS IN PHARMACOLOGY, 2018, 通讯作者
(43) Development and evaluation of a novel series of Nitroxoline-derived BET inhibitors with antitumor activity in renal cell carcinoma, ONCOGENESIS, 2018, 通讯作者
(44) Artificial intelligence in drug design, SCIENCE CHINA-LIFE SCIENCES, 2018, 通讯作者
(45) Discovery and optimization of selective inhibitors of protein arginine methyltransferase 5 by docking-based virtual screening, ORGANIC & BIOMOLECULAR CHEMISTRY, 2017, 通讯作者
(46) 青蒿素及其衍生物的抗疟构效关系研究和治疗新适应症衍生物的发现, Structure-activity relationships of the antimalarial agent artemisinin and the research progress on the artemisinin analogues with novel pharmacological actions, 科学通报, 2017, 第 1 作者
(47) Design, Synthesis, and Pharmacological Evaluation of Novel Multisubstituted Pyridin-3-amine Derivatives as Multitargeted Protein Kinase Inhibitors for the Treatment of Non-Small Cell Lung Cancer, JOURNAL OF MEDICINAL CHEMISTRY, 2017, 通讯作者
(48) A Machine-learning-assisted Approach for Discovering Novel Inhibitors Targeting Bromodomain-containing Protein 4, Journal of Chemical Information Modeling, 2017, 通讯作者
(49) Machine-Learning-Assisted Approach for Discovering Novel Inhibitors Targeting Bromodomain-Containing Protein 4, JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2017, 通讯作者
(50) Aspirin Inhibits Cancer Metastasis and Angiogenesis via Targeting Heparanase, CLINICAL CANCER RESEARCH, 2017, 第11作者
(51) Discovery of Novel Disruptor of Silencing Telomeric 1-Like (DOT1L) Inhibitors using a Target-Specific Scoring Function for the (S)-Adenosyl-l-methionine (SAM)-Dependent Methyltransferase Family., JOURNAL OF MEDICINAL CHEMISTRY, 2017, 通讯作者
(52) Conformation and dynamics of the C-terminal region in human phosphoglycerate mutase 1, ACTA PHARMACOLOGICA SINICA, 2017, 第 6 作者
(53) Aldehyde Oxidase Mediated Metabolism in Drug-like Molecules: A Combined Computational and Experimental Study, JOURNAL OF MEDICINAL CHEMISTRY, 2017, 通讯作者
(54) Discovery of novel BET inhibitors by drug repurposing of nitroxoline and its analogues., ORGANIC & BIOMOLECULAR CHEMISTRY, 2017, 通讯作者
(55) Discovery of novel BRD4 inhibitors by high-throughput screening, crystallography, and cell-based assays, BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, 2017, 第 10 作者
(56) Predicting hepatotoxicity of drug metabolites via an ensemble approach based on support vector machine, COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING, 2017, 通讯作者
(57) Discovery of Novel Disruptor of Silencing Telomeric 1-Like (DOTI L) Inhibitors using a Target-Specific Scoring Function for the (S)-Adenosyl-L-methionine (SAM)-Dependent Methyltransferase Family, JOURNAL OF MEDICINAL CHEMISTRY, 2017, 通讯作者
(58) Discovery of novel trimethoxy-ring BRD4 bromodomain inhibitors: AlphaScreen assay, crystallography and cell-based assay, MEDCHEMCOMM, 2017, 第11作者
(59) 药源性急性肾损伤的关联靶标预测, 2016, 第 2 作者
(60) Estimation of elimination half-lives of organic chemicals in humans using gradient boosting machine, BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 2016, 通讯作者
(61) Estimation of elimination half-lives of organic chemicals in humans using gradient boosting machine., BIOCHIMICA ET BIOPHYSICA ACTA, 2016, 第 6 作者
(62) 科研信息化助力合理药物设计新发展, 中国科学院院刊, 2016, 第 10 作者
(63) Discovery of novel inhibitors targeting the menin-mixed lineage leukemia interface using pharmacophore- and docking-based virtual screening, JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2016, 通讯作者
(64) In silico ADME/T modelling for rational drug design, QUARTERLY REVIEWS OF BIOPHYSICS, 2015, 通讯作者
(65) TarPred: a web application for predicting therapeutic and side effect targets of chemical compounds, BIOINFORMATICS, 2015, 第 10 作者
(66) 多样性合成及其在药物发现中的应用, Diversity-oriented synthesis and its application in drug discovery, 药学学报, 2015, 第 2 作者
(67) Combinatorial Pharmacophore Modeling of Multidrug and Toxin Extrusion Transporter 1 Inhibitors: a Theoretical Perspective for Understanding Multiple Inhibitory Mechanisms., SCIENTIFIC REPORTS, 2015, 其他(合作组作者)
(68) In Silico target fishing: addressing a "Big Data" problem by ligand-based similarity rankings with data fusion, JOURNAL OF CHEMINFORMATICS, 2014, 第 8 作者
(69) Mechanism of the All‑α to All‑β Conformational Transition of RfaH-CTD: Molecular Dynamics Simulation and Markov State Model., J. Chem. Theory Comput., 2014, 通讯作者
(70) In Silico Site of Metabolism (SOM) Prediction for Human UGT-Catalyzed Reactions., Bioinformatics, 2014, 通讯作者
(71) Identifying novel selective non-nucleoside DNA methyltransferase 1 inhibitors through docking-based virtual screening., JOURNAL OF MEDICINAL CHEMISTRY, 2014, 第 17 作者
(72) Prediction of Cancer Drugs by Chemical-Chemical Interactions, PLOS ONE, 2014, 第 6 作者
(73) Predicting Drugs Side Effects Based on Chemical-Chemical Interactions and Protein-Chemical Interactions, BIOMED RESEARCH INTERNATIONAL, 2013, 第 4 作者
(74) Combinatorial pharmacophore modeling of organic cation transporter 2 (OCT2) inhibitors: insights into multiple inhibitory mechanisms., MOLECULAR PHARMACEUTICS, 2013, 第 8 作者
(75) Prediction of Effective Drug Combinations by Chemical Interaction, Protein Interaction and Target Enrichment of KEGG Pathways, BIOMED RESEARCH INTERNATIONAL, 2013, 第 3 作者
(76) Computational methods for drug design and discovery: focus on China, TRENDS IN PHARMACOLOGICAL SCIENCES, 2013, 第 1 作者
(77) Water PMF for predicting the properties of water molecules in protein binding site, JOURNAL OF COMPUTATIONAL CHEMISTRY, 2013, 通讯作者
(78) 核受体FXR的配体及复合物结构研究进展, Progress in the ligands and their complex structures of farnesoid X receptor, 药学学报, 2012, 第 3 作者
(79) SOMEViz: A Web Service for Site of Metabolism Estimating and Visualizing, PROTEIN AND PEPTIDE LETTERS, 2012, 通讯作者
(80) Progress in the ligands and crystal structures of Farnesoid X Receptor., 2012, 通讯作者
(81) Computational screening for active compounds targeting protein sequences: methodology and experimental validation., JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2011, 第 5 作者
(82) An integrated drug-likeness study for bicyclic privileged structures: from physicochemical properties to in vitro ADME propertie., MOLDIVERS, 2011, 第 1 作者
(83) AST1306, A Novel Irreversible Inhibitor of the Epidermal Growth Factor Receptor 1 and 2, Exhibits Antitumor Activity Both In Vitro and In Vivo, PLOS ONE, 2011, 第 5 作者
(84) Knowledge-based scoring functions in drug design: 3. A two-dimensional knowledge-based hydrogen-bonding potential for the prediction of protein-ligand interactions., JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2011, 通讯作者
(85) Knowledge-based scoring functions in drug design: 2. Can the knowledge base be enriched?, JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2011, 第 3 作者
(86) Fragment-based prediction of skin sensitization using recursive partitioning., JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 2011, 第 2 作者
(87) Knowledge-based scoring functions in drug design. 1. Developing a target-specific method for kinase-ligand interactions., JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2010, 第 2 作者
(88) Using support vector regression coupled with the genetic algorithm for predicting acute toxicity to the fathead minnow, SAR QSAR Environ Res 2010, QSAR Environ Res, 2010, 第 1 作者
(89) SOMEViz—预测小分子CYP450酶代谢位点的Web服务, 2010, 第 2 作者
(90) Discovering Potent Inhibitors Against the _-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) of Helicobacter pylori: Structure-Based Design, Synthesis, Bioassay, and Crystal Structure Determination, J. Med. Chem, 2009, 
(91) Site of Metabolism (SOM) Prediction for Six Cytochromes P450-mediated Reactions, Bioinformatics, 2009, 
(92) An effective docking strategy for virtual screening based on multi-objective optimization algorithm, 2009, 第 6 作者
(93) A Triad of Lys12, Lys41, Arg78 Spatial Domain, a Novel Identified Heparin Binding Site on Tat Protein, Facilitates Tat-Driven Cell Adhesion, PLOS ONE, 2008, 第 3 作者
(94) Dynamic Mechanism of Fatty Acid Transport across Cellular Membranes through FadL: Molecular Dynamics Simulations, JOURNAL OF PHYSICAL CHEMISTRY B, 2008, 第 2 作者
(95) Dynamic Mechanism of Fatty Acids Transporting across Cellular Membrane through FadL: Molecular Dynamics Simulations, J Phys Chem B, 2008, 第 1 作者
(96) Indole derivatives as potent inhibitors of 5-lipoxygenase: design, synthesis, biological evaluation, and molecular modeling., BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, 2007, 第 2 作者
(97) 3D-QSAR study of 20 (S)-camptothecin analogs, 3D-QSAR study of 20 (S)-camptothecin analogs, 中国药理学报:英文版, 2007, 第 3 作者
(98) Towards discovering dual functional inhibitors against both wide type and K103N mutant HIV-1 reverse transcriptases: molecular docking and QSAR studies on 4,1-benzoxazepinone analogues., 2006, 第 1 作者
(99) Mutagenic probability estimation of chemical compounds by a novel molecular electrophilicity vector and support vector machine, BIOINFORMATICS, 2006, 第 1 作者
(100) Syntheses of triazole-modified zanamivir analogues via click chemistry and anti-AIV activities, BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, 2006, 第 2 作者
(101) Essential structural profile of a dual functional inhibitor against cyclooxygenase-2 (COX-2) and 5-lipoxygenase (5-LOX): Molecular docking and 3D-QSAR analyses on DHDMBF analogues, BIOORGANIC & MEDICINAL CHEMISTRY, 2006, 
(102) QSAR analyses on avian influenza virus neuraminidase inhibitors using CoMFA, CoMSIA, and HQSAR, JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 2006, 第 1 作者

科研活动

   
科研项目
( 1 ) 靶向NS3/4A蛋白酶的抗丙肝病毒药物先导物发现和优化研究, 负责人, 国家任务, 2011-01--2013-12
( 2 ) 高性能计算环境应用服务优化关键技术研究, 参与, 国家任务, 2014-07--2016-12
( 3 ) 个性化药物研究数据共享系统的集成研究, 负责人, 中国科学院计划, 2016-01--2018-12
( 4 ) 针对 EBOV,MERS-CoV,ZIKV,DENV,CHIKV 的药物研发及相关技术平台的建立, 负责人, 国家任务, 2016-07--2018-12
( 5 ) 甲氨蝶呤靶甲氨蝶呤靶向ENPP1发挥抗肿瘤免疫作用机制及结构改造研究, 负责人, 国家任务, 2023-01--2026-12
( 6 ) 人工智能药物设计, 负责人, 国家任务, 2023-01--2027-12
( 7 ) 人工智能预测蛋白质动力学新技术开发及其在新药研发中的应用, 参与, 国家任务, 2022-11--2027-10
( 8 ) 糖类药物研究关键技术发展及原创品种研发, 参与, 地方任务, 2021-01--2022-07
参与会议
(1)Data-driven drug design in the era of "big data"   2016年UNMC-中国合作研究论坛   2016-05-04