Scientists&Research
Niu Huang, Ph.D.
- Information
- Education
- Experience
- Research
- Publication

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 of |
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:
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
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
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