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Niu Huang's Lab


Niu Huang Ph.D.

Niu Huang Ph.D. (黄牛博士)
Niu Huang, Ph. D.
Associate Investigator
National Institute of Biological Sciences (NIBS), Beijing
No. 7 Science Park Road, Zhongguancun Life Science Park
Changping District, Beijing 102206, P. R. China
Fax:    86-010-80720813










  • Consultant, BeiGene LTD (2011.3 to 2016.3)





  1. Niu Huang, Minmin Wang, Fengmin Chu and Zongru Guo. Studies on the Structure-Activity Relationship of Retinoids: I. 3D-QSAR of Retinoidal Anti-Carcinogenic Activities. Acta Pharmaceutica Sinica. 1996, 31(12): 932-939
  2. Minmin Wang, Niu Huang, Guangzhong Yang and Zongru Guo. Studies on the Structure-Activity Relationship of Retinoids: II. 3D-QSAR of Retinoids and Receptor Interaction. Acta Pharmaceutical Sinica. 1997, 32(1): 43-48
  3. Qiqin Zhu, Zongru Guo, Niu Huang, Minmin Wang, and Fengming Chu. Comparative Molecular Field Analysis of a Series of Taxol Analogues. J. Med. Chem, 1997, 40: 4319-4328
  4. Niu Huang, Fengmin Chu and Zongru Guo. Studies on the Structure-Activity Relationship of Retinoids: Hansch Analysis and 3D-QSAR Studies on Specific Ligands of Retinoid X Receptor. Acta Pharmaceutica Sinica. 1998, 33: 442-448
  5. Niu Huang, Linbo Qu, Qiqing Zhu, Fengming Chu, Guangzhong Yang and Zongru Guo. Studies on the Structure-Activity Relationship of Retinoids: Molecular Modeling of Interaction between Selective Retinoids Nuclear Receptors. Acta Pharmaceutica Sinica.1999, 34: 358-362
  6. Niu Huang and Alexander D. MacKerell, Jr. An Ab Initio Quantum Mechanical Study of Hydrogen-Bonded Complexes of Biological Interest. J. Phys. Chem  A, 2002, 106: 7820-7827.
  7. Yongping Pan, Niu Huang, Sam Cho and Alexander D. MacKerell, Jr. Consideration of Molecular Weight During Compound Selection in Virtual Target-Based Database Screening.  J. Chem. Inf. Comput. Sci. 2003;43(1); 267-272
  8. Niu Huang, Nilesh K. Banavali and Alexander D. MacKerell, Jr. Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase. Proc. Natl. Acad. Sci. U S A, 2003, 100: 68-73.
  9. Hui Peng#, Niu Huang#, Jing Qi, Ping Xie, Chen Xu, Jianxiang Wang and Chunzheng Yang. Identification of novel inhibitors of BCR-ABL tyrosine kinase via virtual screening. Bioorg. Med. Chem. Lett. 2003, 13(21):3693-3699.  # equal contribution
  10. Niu Huang and Alexander D. MacKerell, Jr. Atomistic view of Base flipping in DNA. Phil. Trans. Roy. Soc. Lond. Series A. 2004, 362: 1-22.
  11. Niu Huang, Ashish Nagarsekar, Guanjun Xia, Jun Hayashi and Alexander D. MacKerell, Jr. Identification of Non-Phosphate-Containing Small Molecular Weight Inhibitors of the Tyrosine Kinase p56 Lck SH2 Domain via in Silico Screening against the pY+3 Binding Site. J. Med. Chem. 2004, 47 (14):3502-3511.
  12. John R. Horton, Gary Ratner, Nilesh K. Banavali, Niu Huang, Yongseok Choi, Martin A. Maier, Victor E. Marquez, Alexander D. MacKerell, Jr., Xiaodong Cheng. Caught in the Middle of the Act: Visualization of a Putative Transition State During DNA Base Flipping. Nucl. Acids. Res. 2004, 32: 3877-3886.
  13. Niu Huang and Alexander D. MacKerell, Jr. Specificity in protein-DNA interactions: Energetic recognition by the (cytosine-C5)-methyltransferase from HhaI. J. Mol. Biol. 2005, 345:265-274.
  14. Victor M. Anisimov, Guillaume Lamoureux, Igor V. Vorobyov, Niu Huang, Benoit Roux, Alexander D. MacKerell, Jr. Determination of Electrostatic Parameters for a polarizable Force Field Based on the Classical Drude Oscillator. J. Chem. Theory. Comp. 2005, 1: 153-168.
  15. Niu Huang, Chakrapani Kalyanaraman, John Irwin, Matthew P. Jacobson. Physics-based Scoring of Protein-ligand Complexes: Enrichment of known inhibitors in Large-Scale Virtual Screening. J. Chem. Inf. Model. 2006, 46:243-253.
  16. Nilesh K. Banavali, Niu Huang and Alexander D. MacKerell, Jr. Conserved Patterns in Backbone Torsion Changes Allow For Single Base Flipping from Duplex DNA with Minimal Distortion of the Double Helix. J. Phys. Chem. B. 2006, 110:10997-11004.
  17. Niu Huang, Chakrapani Kalyanaraman, Katarzyna Bernacki and Matthew P. Jacobson. Ligand Binding Free-energy Calculations via Physics-based Scoring Methods. Phys. Chem. Chem. Phys. 2006, 8:5166-5177.
  18. Niu Huang, John Irwin and Brian Shoichet. Benchmarking Sets for Molecular Docking. J. Med. Chem. 2006, 49:6789-6801.
  19. Niu Huang and Matthew P. Jacobson. Physics-based Methods for Studying Protein-Ligand Interactions. Curr. Opin. Drug Discov. Devel. 2007, 10:325-331.
  20. Linjie Chen, Huayi Wang, Jie Zhang, Lichuan Gu, Niu Huang, Jian-Min Zhou and Jijie Chai. Structural basis for the catalytic mechanism of phosphothreonine lyase. Nat. Struct. Mol. Biol. 2008, 15:101-102
  21. Niu Huang and Brian Shoichet. Exploring Ordered Waters in Molecular Docking. J. Med. Chem. 2008, 51:4862-4865
  22. Zhiwei Huang, Yingcai Feng, Xiaojing Wu, Xiaojun Wang, Xingguo Xiao, Wenhui Li, Niu Huang, Lichuan Gu, Guangming Zhong and Jijie Chai. Structural and biochemical mechanisms of the catalysis, activation and inhibition of CPAF (Chlamydial Protease/Proteasome-like Activity Factor). Cell Host & Microbe. 2008, 4: 529-542
  23. Qing Yao, Jixin Cui, Yongqun Zhu, Guolun Wang, Liyan Hu, Chengzu Long, Ran Cao, Xinqi Liu, Niu Huang, She Chen, Liping Liu and Feng Shao. A bacterial type III effector family uses the papain-like hydrolytic activity to arrest the host cell cycle. Proc. Natl. Acad. Sci. U S A. 2009, 106:3716-3721
  24. Chaya S. Rapp, Cheryl Schonbrun, Matthew P. Jacobson, Chakrapani Kalyanaraman and Niu Huang. Automated Site Preparation in Rescoring of Receptor Ligand Complexes. Proteins. 2009, 77:52-61
  25. John Irwin, Brian Shoichet, Michael Mysinger, Niu Huang, Francesco Colizzi, Pascal Wassam and Yiqun Cao. Automated docking screens: a feasibility study. J. Med. Chem. 2009, 52:5712-20
  26. Niu Huang and Matthew P. Jacobson. Binding-Site Assessment by Virtual Fragment Screening. PLoS ONE. 2010, 5: e10109
  27. Qiang Pei, Andrew Christofferson, Hui Zhang, Jijie Chai and Niu Huang. Computational Investigation of the Enzymatic Mechanisms of Phosphothreonine Lyase. Biophys. Chem. 2011, 157:16-23.
  28. Andrew Christofferson, Lifeng Zhao, Hanzi Sun, Zhen Huang and Niu Huang. Theoretical Studies of the Base Pair Fidelity of Selenium-modified DNA. J. Phys. Chem B. 2011, 115:10041-8.
  29. Lifeng Zhao, Chuanjie Wu and Niu Huang. Mutual Solubilities Study for Binary Mixtures of Dipropylene Glycol Dimethyl Ether and Water via Molecular Dynamics Simulation and AMOEBA Polarizable Force Field. Fluid. Phase. Equilib. 2011, 310: 32-8.
  30. Andrew Christofferson and Niu Huang. How to Benchmark Methods for Structure-Based Virtual Screening of Large Compound Libraries. Methods in Molecular Biology. 2012. 819:187-95.
  31. Chen P, Song Z, Qi Y, Feng X, Xu N, Sun Y, Wu X, Yao X, Mao Q, Li X, Dong W, Wan X, Huang N, Shen X, Liang Z, Li W. Molecular determinants of enterovirus 71 viral entry: cleft around GLN-172 on VP1 protein interacts with variable region on scavenge receptor B 2. J. Biol. Chem. 2012, 287:6406-20.
  32. Xingyu Lin, Xiping Huang, Gang Chen, Ryan Whaley, Shiming Peng, Yanli Wang, Guoliang Zhang, Shaohui Wang, Xiang Wang, Brian Roth and Niu Huang. Life Beyond Kinases: Structure-Based Discovery of Sorafenib as Nanomolar Antagonist of 5-HT Receptors. J. Med. Chem. 2012, 55:5749-59. (Selected by F1000 Pharmacology & Drug Discovery, Congreve M: 2012. )
  33. Shiming Peng, Xingyu Lin, Zongru Guo and Niu Huang. Identifying Multiple-Target Ligands via Computational Chemogenomics Approaches.  Curr. Top. Med. Chem. 2012, 12:1363-1375.
  34. Ran Cao, Minyu Liu, Min Yin, Quanhai Liu, Yanli Wang and Niu Huang. Discovery of Novel Tubulin Inhibitors via Structure-Based Hierarchical Virtual Screening. J. Chem. Inf. Model. 2012, 52:2730-40.
  35. Qing Yao, Jixin Cui, Jiayi Wang, Ting Li, Xiaobo Wan, Tianming Luo, Yi-Nan Gong, Ying Xu, Niu Huang and Feng Shao. Structural mechanism of ubiquitin and NEDD8 deamidation catalyzed by bacterial effectors that induce macrophage-specific apoptosis. Proc. Natl. Acad. Sci. U S A. 2012,109:20395-400.
  36. Yanli Wang, Minyu Liu, Ran Cao, Ming Yin, Riuhua Xiao, Quanhai Liu and Niu Huang. A Soluble Bis-chelated Gold(I) Diphosphine Compound with Strong Anticancer Activity and Low Toxicity. J. Med. Chem., 2013, 56 (4), pp 1455–1466
  37. Yao Wu, Xiaodong Dai, Niu Huang* and Lifeng Zhao*. A partition function-based weighting scheme in force field parameter development using ab initio calculation results in global configurational space. Journal of Computational Chemistry. Volume 34, Issue 15, pages 1271–1282, 5 June 2013
  38. Xiaobo Wan, Wei Zhang, Li Li, Yuting Xie, Wei Li and Niu Huang. A New Target for An Old Drug: Identifying Mitoxantrone as a Nanomolar Inhibitor of PIM1 Kinase via Kinome-wide Selectivity Modeling. J. Med. Chem., 2013, 56 (6), pp 2619–2629
  39. Xiaobo Wan, Yue Ma, Christopher L. McClendon, Lily Jun-shen Huang and Niu Huang. Ab Initio Modeling and Experimental Assessment of Janus Kinase 2 (JAK2) Kinase-Pseudokinase Complex Structure. PLoS Comp. Biol. 2013.
  40. Fanqi Zeng, Shiming Peng, Li Li, Libing Mu, Zhenghua Zhang, Zhiyuan Zhang and Niu Huang. HAT off: structure-based identification of drug-like inhibitors of p300 histone acetyltransferase. Acta Pharmaceutica Sinica. 2013, 48:700-708.
  41. Shiming Peng, Yu Zhou and Niu Huang. Improving the accuracy of pose prediction in molecular docking via structural filtering and conformational clustering. Chinese Chem. Lett. 2013, 24:1001-1004.
  42. Ran Cao, Wei Li, Hanzi Sun, Yu Zhou and Niu Huang. Computational chemistry in structure-based drug design. Acta Pharmaceutica Sinica. 2013, 48:1041-1052.
  43. Hanzi Sun, Lifeng Zhao, Shiming Peng and Niu Huang. Incorporating Replacement Free Energy of Binding-site Waters in Molecular Docking. Proteins. 2014, 82:1765-76.
  44. Wei Li, Xiaobo Wan, Wei Zhang, Fanqi Zeng, Yanli Wang, Yuting Xie, Li Li and Niu Huang. More than just GPCR Ligand: Structure-based Discovery of Thioridazine Derivatives as Pim-1 Kinase Inhibitors. Med. Chem.Commun. 2014, 5:507-511.
  45. Yu Zhou, Chao Wu, Lifeng Zhao and Niu Huang. Exploring the early stages of the pH-induced conformational change of influenza hemagglutinin. Proteins. 2014, 82:2412-28.
  46. Deng M, Lu Z, Zheng J, Wan X, Chen X, Hirayasu K, Sun H, Lam Y, Chen L, Wang Q, Song C, Huang N, Gao GF, Jiang Y, Arase H, Zhang CC. A motif in LILRB2 critical for Angptl2 binding and activation. Blood. 2014, 124:924-35.
  47. Ran Cao, Niu Huang and Yanli Wang. Evaluation and application of MD-PB/SA in structure-based hierarchical virtual screening. J Chem Inf Model. 2014, 54:1987-96.
  48. Yao Q, Lu Q, Wan X, Song F, Xu Y, Hu M, Zamyatina A, Liu X, Huang N, Zhu P, Shao F. A structural mechanism for bacterial autotransporter glycosylation by a dodecameric heptosyltransferase family. Elife. 2014, Oct 13;3. doi: 10.7554/eLife.03714.
  49. Yao Q, Zhang L, Wan X, Chen J, Hu L, Ding X, Li L, Karar J, Peng H, Chen S, Huang N, Rauscher FJ, Shao F. (2014) Structure and Specificity of the Bacterial Cysteine Methyltransferase Effector NleE Suggests a Novel Substrate in Human DNA Repair Pathway. PLoS Pathog. 2014, 10(11): e1004522.
  50. Yu zhou and Niu Huang. Binding site druggability assessment in fragment-based drug design.. Methods Mol. Biol. 2015, 1289:13-21.
  51. Dong T, Li C, Wang X, Dian L, Zhang X, Li L, Chen S, Cao R, Li L, Huang N, He S, Lei X. Ainsliadimer A selectively inhibits IKKα/β by covalently binding a conserved cysteine. Nat Commun. 2015, 6:6522.
  52. Hu Z, Wan X, Hao R, Zhang H, Li L, Li L, Xie Q, Wang P, Gao Y, Chen S, Wei M, Luan Z, Zhang A, Huang N, Chen L. Phosphorylation of mutationally introduced tyrosine in the activation loop of HER2 confers gain-of-function activity. PLoS One. 2015,10(4):e0123623.
  53. Ran Cao, Yanli Wang and Niu Huang. Discovery of 2-Acylaminothiophene-3-Carboxamides as Multitarget Inhibitors for BCR-ABL Kinase and Microtubules. J Chem Inf Model. 2015, 55(11):2435-42.
  54. Yu Zhou, Jing Ma, Xinyu Lin, Xiping Huang, Kaichun Wu and Niu Huang. Structure-Based Discovery of Novel and Selective 5-Hydroxytryptamine 2B Receptor Antagonists for the Treatment of Irritable Bowel Syndrome. J. Med. Chem. 2016, 59(2):707-20.
  55. Xiao W, Adhikari S, Dahal U, Chen YS, Hao YJ, Sun BF, Sun HY, Li A, Ping XL, Lai WY, Wang X, Ma HL, Huang CM, Yang Y, Huang N, Jiang GB, Wang HL, Zhou Q, Wang XJ, Zhao YL, Yang YG. Nuclear m(6)A Reader YTHDC1 Regulates mRNA Splicing. Mol Cell. 2016, 61(4):507-19.
  56. Liu JJ, Niu CY, Wu Y, Tan D, Wang Y, Ye MD, Liu Y, Zhao W, Zhou K, Liu QS, Dai J, Yang X, Dong MQ, Huang N, Wang HW. CryoEM structure of yeast cytoplasmic exosome complex. Cell Res. 2016, 26(7):822-37.
  57. Liu X, Dong T, Zhou Y, Huang N, Lei X. Exploring the Binding Proteins of Glycolipids with Bifunctional Chemical Probes. Angew Chem Int Ed Engl. 2016, 55(46):14330-14334.
  58. Zhu Q, Venzke D, Walimbe AS, Anderson ME, Fu Q, Kinch LN, Wang W, Chen X, Grishin NV, Huang N, Yu L, Dixon JE, Campbell KP, Xiao J. Structure of protein O-mannose kinase reveals a unique active site architecture. Elife. 2016, 5. pii: e22238.
  59. Yang X, Yang Y, Sun BF, Chen YS, Xu JW, Lai WY, Li A, Wang X, Bhattarai DP, Xiao W, Sun HY, Zhu Q, Ma HL, Adhikari S, Sun M, Hao YJ, Zhang B, Huang CM, Huang N, Jiang GB, Zhao YL, Wang HL, Sun YP, Yang YG. 5-methylcytosine promotes mRNA export – NSUN2 as the methyltransferase and ALYREF as an m5C reader. Cell Res. 2017, 27(5):606-625
  60. Zhang L, Sun H, Chen Z, Liu Z, Huang N*, Qian F*. Intermolecular Interactions between Coencapsulated Drugs Inhibit Drug Crystallization and Enhance Colloidal Stability of Polymeric Micelles. Mol Pharm. 2017 Oct 2;14(10):3568-3576
  61. Wang Y, Sun Y, Cao R, Liu D, Xie Y, Li L, Qi X*, Huang N*. In Silico Identification of a Novel Hinge-Binding Scaffold for Kinase Inhibitor Discovery. J Med Chem. 2017 Oct 26;60(20):8552-8564.
  62. Ren S, Caforio A, Yang Q, Sun B, Yu F, Zhu X, Wang J, Dou C, Fu Q, Huang N, Sun Q, Nie C, Qi S, Gong X, He J, Wei Y, Driessen AJ, Cheng W. Structural and mechanistic insights into the biosynthesis of CDP-archaeol in membranes. Cell Res. 2017 Nov;27(11):1378-1391