Niu Huang, Ph.D. - Scientists&Research - 北京生命科学研究所

Niu Huang, Ph.D.

Associate Investigator, NIBS, Beijing, China

Phone：010-80726688-8570

Fax： 010-80726689

E-mail：huangniu@nibs.ac.cn

Education:

1994	Bachelor of Biophysics，Department of Physics University of Nankai, Tianjin,
2003	Ph.D.，Department of Pharmaceutical Sciences，University ofMaryland at Baltimore

Professional Experience:

2013	Associate Investigator, National Institute of Biological Sciences, Beijing, China
2007-2012	Assistant Investigator, National Institute of Biological Sciences, Beijing, China
2003-2007	Postdoctoral associate, Depts. of Pharmaceutical Chemistry and Biopharmaceutical Sciences, University of California at San Francisco
1994-1998	Research assistant, Institute of Materia Medica, Peking Union of Medical College & Chinese Academy of Medical Sciences

Research Description:

The opening of the 21st century has marked with the sequencing of the human genome. Today, the understanding of the sequence and structure of biologically relevant targets is growing rapidly and researchers from many disciplines, physics and computational science in particular, are making significant contributions to modern biology and drug discovery. State-of-the-art computational chemistry and molecular modeling techniques can be applied to study a wide range of chemical and biological systems of interest, which enable us to acquire information not obtainable by experimental techniques, to investigate structural phenomena at the atomic level and to identify novel compounds with desired biological characteristics. Our laboratory is interested in developing and applying computational techniques to study the structural and energetic basis of molecular recognition (i.e., protein-protein, protein-DNA and protein-ligand interactions). Aside from its fundamental biological interest, such theoretical studies have tremendous practical values of which one of the most important is structure-based drug design.

Publications

1. Li G, Zhang W, Xie Y, Li Y, Cao R, Zheng G, Huang N*, Zhou Y*. Structure-Based Optimization of 10-DEBC Derivatives as Potent and Selective Pim-1 Kinase Inhibitors. J Chem Inf Model. 2020 Jun 22;60(6):3287-3294.

2. Gao L, Su C, Du X, Wang R, Chen S, Zhou Y, Liu C, Liu X, Tian R, Zhang L, Xie K, Chen S, Guo Q, Guo L, Hano Y, Shimazaki M, Minami A, Oikawa H, Huang N, Houk KN, Huang L, Dai J, Lei X. FAD-dependent enzyme-catalysed intermolecular [4+2] cycloaddition in natural product biosynthesis. Nat Chem. 2020 Jul;12(7):620-628.

3. Ju D, Zhang W, Yan J, Zhao H, Li W, Wang J, Liao M, Xu Z, Wang Z, Zhou G, Mei L, Hou N, Ying S, Cai T, Chen S, Xie X, Lai L, Tang C, Park N, Takahashi JS, Huang N, Qi X, Zhang EE. Chemical perturbations reveal that RUVBL2 regulates the circadian phase in mammals. Sci Transl Med. 2020 May 6;12(542):eaba0769.

4. Yang J, Shen C, Huang N. Predicting or Pretending: Artificial Intelligence for Protein-Ligand Interactions Lack of Sufficiently Large and Unbiased Datasets. Front Pharmacol. 2020 Feb 25;11:69.

5. Lin H, Zhang X, Liu L, Fu Q, Zang C, Ding Y, Su Y, Xu Z, He S, Yang X, Wei X, Mao H, Cui Y, Wei Y, Zhou C, Du L, Huang N, Zheng N, Wang T, Rao F. Basis for metabolite-dependent Cullin-RING ligase deneddylation by the COP9 signalosome. Proc Natl Acad Sci U S A. 2020 Feb 25;117(8):4117-4124.

6. Peng S, Li W, Hou N, Huang N. A Review of FoxO1-Regulated Metabolic Diseases and Related Drug Discoveries. Cells. 2020 Jan 10;9(1). pii: E184.

7. Li G, Li W, Xie Y, Wan X, Zheng G, Huang N*, Zhou Y*. Discovery of Novel Pim-1 Kinase Inhibitors with a Flexible-Receptor Docking Protocol. J Chem Inf Model. 2019 Oct 28;59(10):4116-4119.

8. Jones AX, Cao Y, Tang YL, Wang JH, Ding YH, Tan H, Chen ZL, Fang RQ, Yin J, Chen RC, Zhu X, She Y, Huang N, Shao F, Ye K, Sun RX, He SM, Lei X, Dong MQ. Improving mass spectrometry analysis of protein structures with arginine-selective chemical cross-linkers. Nat Commun. 2019 Sep 2;10(1):3911.

9. Wang Y, Fu Q, Zhou Y, Du Y, Huang N. Replacement of Protein Binding-Site Waters Contributes to Favorable Halogen Bond Interactions. J Chem Inf Model. 2019 Jul 22;59(7):3136-3143

10. Peng S, Xiao W, Ju D, Sun B, Hou N, Liu Q, Wang Y, Zhao H, Gao C, Zhang S, Cao R, Li P, Huang H, Ma Y, Wang Y, Lai W, Ma Z, Zhang W, Huang S, Wang H, Zhang Z, Zhao L, Cai T, Zhao Y, Wang F, Nie Y, Zhi G, Yang YG*, Zhang EE*, Huang N*. Identification of Entacapone as a Chemical Inhibitor of FTO Mediating Metabolic Regulation through FOXO1. Sci. Transl. Med., 2019, 11(488) :eaau7116.

11. Zhang C, Qin S, Hu B, Lv J, Yang Z, Yan W, Wang J, Huang N, Huang Z. Disruption of nucleobase stacking to restore reactivity. Nucleosides Nucleotides Nucleic Acids. 2019 Mar 28:1-11.

12. Sun L, Ma L, Zhang H, Cao Y, Wang C, Hou N, Huang N, von Deneen KM, Zhao C, Shi Y, Pan Y, Wang M, Ji G, Nie Y. Fto Deficiency Reduces Anxiety- and Depression-Like Behaviors in Mice via Alterations in Gut Microbiota. Theranostics. 2019 Jan 24;9(3):721-733.

13. Wang Y, Du Y, Huang N. A survey of the role of nitrile groups in protein-ligand interactions. Future Med Chem. 2018 Dec;10(23):2713-2728.

14. Zhou Y, Wang Y, Li P, Huang XP, Qi X, Du Y*, Huang N*. Exploring Halogen Bonds in 5-Hydroxytryptamine 2B Receptor-Ligand Interactions. ACS Med Chem Lett. 2018 Oct 1;9(10):1019-1024.

15. Lei Z, Chai N, Tian M, Zhang Y, Wang G, Liu J, Tian Z, Yi X, Chen D, Li X, Yu P, Hu H, Xu B, Jian C, Bian Z, Guo H, Wang J, Peng S, Nie Y, Huang N, Hu S, Wu K. Novel peptide GX1 inhibits angiogenesis by specifically binding to transglutaminase-2 in the tumorous endothelial cells of gastric cancer. Cell Death Dis. 2018 May 21;9(6):579.

16. 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.

17. 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.

18. 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.

19. 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.

20. 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.

21. 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.

22. 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.

23. 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.

24. 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.

25. 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.

26. 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.

27. 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.

28. Yu Zhou and Niu Huang. Binding site druggability assessment in fragment-based drug design. Methods Mol. Biol. 2015, 1289:13-21.

29. 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.

30. 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, 3: 03714.

31. 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.

32. 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.

33. 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.

34. 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.

35. 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.

36. 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.

37. 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.

38. 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.

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, 9: e1003022.

40. 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, 56:2619-29.

41. 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. J. Comp. Chem. 2013, 34:1271-82.

42. 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: 1455-66.

43. 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.

44. 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.

45. 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.

46. 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. http://f1000.com/717951322)

47. 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.

48. 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.

49. 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.

50. 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.

51. 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.

52. Niu Huang* and Matthew P. Jacobson. Binding-Site Assessment by Virtual Fragment Screening. PLoS ONE. 2010, 5: e10109

53. 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

54. 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

55. 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

56. 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

57. Niu Huang and Brian Shoichet. Exploring Ordered Waters in Molecular Docking. J. Med. Chem. 2008, 51:4862-4865

58. 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

59. Niu Huang and Matthew P. Jacobson. Physics-based Methods for Studying Protein-Ligand Interactions. Curr. Opin. Drug Discov. Devel. 2007, 10:325-331.

60. Niu Huang, John Irwin and Brian Shoichet. Benchmarking Sets for Molecular Docking. J. Med. Chem. 2006, 49:6789-6801.

61. 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.

62. 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.

63. 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.

64. 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.

65. 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.

66. 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.

67. 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.

68. 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.

69. 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.

70. 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.

71. 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

72. 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.

73. 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

74. 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

75. 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

76. 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

77. 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

Scientists&Research

Niu Huang,Ph.D.