Niu Huang Ph.D.

The opening of the 21st century has marked with the sequencing of the human genome. Today, the understanding of the sequence, structure and function of biologically relevant targets is growing rapidly and researchers from multi-disciplines, physics and computational science in particular, are making significant contributions to modern biology and drug discovery.

We are interested in developing and applying computational chemistry approaches to study the structural and energetic basis of molecular recognition (i.e. protein-ligand, protein-DNA and protein-protein 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.

Our lab has successfully applied computational approaches to discover first-in-class drug lead compounds against novel drug targets in the fields of obesity, cancer and fibrosis. Currently, we are actively pursuing experimental collaborations in developing these novel drug candidates.

Sep, 90 – July, 94

University of Nankai, Tianjin, Bachelor of Biophysics
Department of Physics

Sep, 98 – Oct, 2003

University of Maryland at Baltimore, Ph.D. candidate
Department of Pharmaceutical Sciences
Specialization: Computational Chemistry
Advisor: Prof. Alexander D. MacKerell, Jr.

Sep, 94 – Aug, 98

Institute of Materia Medica, Research Assistant
Department of Medicinal Synthetic ChemistryPeking Union of Medical College & Chinese Academy of Medical Sciences
Specialization: Computer-aided Drug Design
Advisor: Prof. Zongru Guo

Oct, 03 – Sep, 07

University of California at San Francisco, Postdoctoral associate
Depts. of Pharmaceutical Chemistry and Biopharmaceutical Sciences
Specialization: Molecular docking methods and scoring functions
Advisors: Profs. Brian Shoichet and Matt Jacobson

Oct, 07 -Aug 2013

National Institute of Biological Sciences, Beijing
Assistant Investigator

Aug,2013 – Present

National Institute of Biological Sciences, Beijing
Associate Investigator

WuXi PharmaTech Life Science and Chemistry Award, 2013.

Science and Technology Progress 2nd Award from Department of Health, China. “Drug design, synthesis and evaluation based on retinoid nuclear receptors” by Zongru Guo, Rui Han, Fengmin Chu, Minmin Wang, Niu Huang, et al. 1999. Award Number-99201304.

Dr. Frank Slama Endowed Fellowship & Merit Award, 2001-2002, Department of Pharmaceutical Sciences, University of Maryland, Baltimore.

H.A.B Dunning Fellowship & Merit Award, 2002-2003, Department of Pharmaceutical Sciences, University of Maryland, Baltimore.

Reviewers for Proteins, PLoS. Comp. Biol., J. Med. Chem., J. Phys. Chem., JACS, BMC Bioinformatics, Chem. Med. Chem., Chem. Bio. & Drug Design, Bioorg. Med. Chem., J. Comp. Aided Mol. Des., Acta Pharmaceutica Sinica. and Science China Chemistry.

BIAMIDO HETEROCYCLIC DERIVATIVE WITH ANTITUMOR ACTIVITY AND ITS PREPARATION METHOD AND USE by Chunzheng Yang, Hui Peng, Jin Qi, Niu Huang, Jianxiang Wang, Ping Xie, Caiyun Wang and Yuan Zhou. (Pub. No.: CN1597668)

SUBSTITUTED AROMATIC RADICAL BIGUANIDE COMPOUNDS AND THE APPLICATION OF THEIR MEDICINE COMPOSITION IN PREPARING MEDICINE FOR RESISTING MALIGNANT TUMORS by Hui Peng, Yuan Zhou, Niu Huang, Qin Ji, Jin Qi, Ying Xiao and Chunzheng Yang. (Pub. No.: CN1846694)

IMMUNOMODULATORY COMPOUNDS THAT TARGET AND INHIBIT THE pY+3 BINDING SITE OF TYROSENE KINASE p56 LCK SH2 DOMAIN by Alex MacKerell, Jun Hayashi, Ashish Nagarsekar, Niu Huang and Alba Macias. (Pub. No.: PCT/US03/39501) Licensed to A&G Pharmaceutical. INC..

SUBSTITUTED HYDROXY ACETOPHENONE AGENTS USED FOR METABOLIC DISEASES by Jijie Chai, Niu Huang, Zhifu Han, Shiming Peng and Tianhui Niu. (Pub. No.: CN 102652749 A)

Entacapone for prevention and treatment of obesity and related metabolic diseases by Niu Huang, Gang Zhi, Jijie Chai, Shiming Peng and Nannan Hou (CN201210497436.7, PCT/CN2013/087581, this application has been granted in AU, CA, CN, EP and NZ)

5HT-2B ANTAGONISTS by Niu Huang, Yu Zhou and Xingyu Lin (WO/2015/158214, granted in US, Japan, EP and AU)

FTO Inhibitors by Niu Huang and Shiming Peng (PCT/CN2015/082052)

Kinase Inhibitors by Niu Huang, Xiangbing Qi, Yanli Wang and Yuze Sun (PCT/CN2016/076045)

Solvent Property Analysis program (SPA 1.0) by Hanzi Sun, Lifeng Zhao and Niu Huang. (Reg. No.: 2013SR008306)

Cross-link Molecular Dynamics program (XLMD 1.0) by Lifeng Zhao, Yao Wu and Niu Huang. (Reg. No.: 2013SR008308)

American Chemical Society (ACS)

Biophysical Society

Lecturing at “Modern Biological Techniques” 2008

Lecturing at “Modern Biology” 2011 and 2013

PREDOCTRORAL MENTORING:

⊕

Current graduate students:

Yulin Zhang
Yuchan Pei
Yizhen Wang
Qiancheng Xia
Zhao Chen
Yujie Cheng
Lejia Zeng
Xuelian Li
Hui zhu
Jie Feng
Cheng Shen
Min Xu
Qing Wang

Past graduate students:

Wei Li (Peking Union Medical College, 2007-2012); Director at Rpxds Ltd.
Xingyu Lin (Beijing Normal University, 2008-2013); Research scientist at Pharmaron Inc.
Fanqi Zeng (Chongqing University of Technology, 2011-2013); Research staff at NIBS.
Ran Cao (Tianjin University, 2010-2013); Assistant Researcher at Institute of Materia Medica, PUMC&CAMS.
Xiaobo Wan (Peking Union Medical College, 2008-2013); Postdoc fellow at UCSF.
Shiming Peng (Chinese Agriculture University, 2008-2013); Postdoc at NIBS
Yao Wu (Peking Union Medical College, 2008-2013); Research scientist at Pharmaron Inc
Hanzi Sun (Beijing Normal University, 2009-2014); Research scientist at Beigene Ltd.
Yu Zhou (Beijing Normal University, 2009-2014); Postdoc at NIBS

Current Postdoctoral Fellows:

Yuanxun Wang
Jincai Yang
Yang Li

Past Postdoctoral Fellows:

Hui Zhang (2008-2009), Professor at Harbin University of Science and Technology
Qiang Pei (2008-2011), Director at Honest Medical Inc.
Yun He (2008-2009), Senior research scientist at Novartis, Shanghai
Jing Dong (2008-2010), Postdoctoral fellow at University of Zurich
Andrew Christofferson (2009-2011), Postdoctoral fellow at RMIT university
Wei Zhang (2012-2013), Research Scientist at RPXD.com at Suzhou.
Lifeng Zhao (2008-2014), Research Scientist at P&G in Beijing.
Lan Hua (2015-2017), Research Scientist at GHDDI
Shanshan Qin (2015-2017), Postdoc at PKU
Yanli Wang (2008-2017).

Niu Huang, Nilesh K. Banavali and Alexander D. MacKerell, Jr. Probing the Mechanism of Base Flipping in DNA via Potential of Mean Force Calculations. 34^th Middle Atlantic Regional Meeting, American Chemical Society, 2001
Niu Huang, Jun Hayashi and Alexander D. MacKerell, Jr. Application of Computer Screening Tools to Investigate Protein-Protein Interaction: Database Mining Studies on the Tyrosine Kinase p56-Lck SH2 Domain. 220^th ACS National Meeting, Aug 2000, Washington D, C
Niu Huang, Nilesh K. Banavali and Alexander D. MacKerell, Jr. Probing the Mechanism of Protein-facilitated Base Flipping via Potential of Mean Force Calculations. 224^th ACS National Meeting, Aug 2002, Boston; Gordon Research Conference in Computational Chemistry, New London, 2002
Niu Huang (invited talks), Computational Chemistry in Structural Biology and Pharmaceutical Sciences. National Cancer Institute, July, 08^th, 2003,Frederick , MD University of California San Francisco, Sept, 15^th, 2003, San Francisco, CA
Niu Huang (invited talk and poster section), Automating and Improving Virtual Screening of Large Compound Databases. 226^th ACS National Meeting, Aug 2004, Philly, PA
Niu Huang (invited talk), In-Silico Biology. South Illinois University, Medical School, Sept, 24^th, 2004, Springfield, IL
Niu Huang (invited talk), The cycle of life – probing the DNA base flipping mechanism via molecular dynamics based free energy calculations. Mini-Symposium on Molecular Dynamics, Oct, 26^th, 2004, UCSF
Niu Huang, CK Kalyanaraman and Matthew P. Jacobson. Developing and Applying a Physics-based Scoring Method to Improve Large Scale Virtual Screening against HIV/AIDS Related Molecular Targets. The Nineteenth Meeting of Groups Studying the Structures of AIDS-related Systems and their Application to Targeted Drug Design, June, 23-24^th, 2005, NIH, Bethesda, MD
Niu Huang (invited talk), Computational Chemistry in Structure Biology and Drug Design. The Fourth Sino-US Symposium on Medicine in the 21 Century. Aug, 19-21^st, 2005, San Francisco, CA
Niu Huang (invited talk), Automating, Benchmarking and Improving Small Molecule Docking. University of Maryland, Baltimore, School of Pharmacy, July, 2007, Baltimore, MD
Niu Huang (poster sections), Physics-based Scoring of Protein-ligand Complexes. Investigating Bias in Docking Screens with Target, Ligand and Decoy Benchmarking Sets. 232^th ACS National Meeting, Sep 2006, San Francisco, CA
Niu Huang (invited talk), Virtual Screening Studies Targeting the Tyrosine Kinase p56 Lck SH2 Domain. Zhengzhou University, Jan 2008, Henan Province, China
Niu Huang (poster section), Tying Protein Druggability Prediction with Fragment-based Virtual Screening. Computational Protein Structure and Mechanics (PSAM) 2008, Sept 12^th, Shanghai, China
Niu Huang (invited talks), Physics-based Scoring Method in Drug Discovery. Institute of Materia Medica, CAMS&PUMC, Feb 2009, Beijing, China; Shanghai JiaoTong University, Dept. Chemistry, Dec 2008, Shanghai, China; Beijing University, Center for Theoretical Biology, Nov 2008, Beijing, China; Shandong University, Nov 2008, Jinan, China
Niu Huang (invited talk), Free-energy Guided Ligand Discovery. Symposium on Drug Molecule Design, CNCBD, May 2009, Shengzhen, China
Niu Huang (talk and poster section), Identifying novel CPAF inhibitors via physics-based binding energy calculation methods. Anticancer Mechanism of a Novel Bis-chelated Gold Diphosphine Compound. 239^th ACS National Meeting, Mar 2010, San Francisco, CA
Niu Huang (invited talk), Anticancer Mechanism of a Novel Bis-chelated Gold Diphosphine Compound. 10^th Beijing Life Science Annual Conference, April 2010, Beijing
Niu Huang (invited talk), Physics-based Scoring Method in Early Stages of Drug Discovery BIT’s 1^st Annual International Conference of Medichem, May 2010, Beijing. PKU-Pfizer Symposium on Drug Discovery and Chemical Biology, May 2010, PKU, Beijing
Niu Huang (invited talk), Treating Explicit Water in Docking and Scoring. 240^th ACS National Meeting, Aug 2010, Boston, MA
Niu Huang (talk), HATs off: Identification of Novel Inhibitors of the Histone Acetyltransferases via Structure-based Virtual Screening Methods. 241^th ACS National Meeting, Mar 2011, Anaheim, CA
Niu Huang (talk), Molecular Modeling of Janus Kinase 2 (JAK2) Pseudokinase-Kinase Complex Structure. 11^th Computational Chemistry Conference, July 2011, Lanzhou, Gansu Province, China
Niu Huang (talk), Life Beyond Kinases: Structure-based Discovery of Sorafenib as Nanomolar Antagonist of 5-HT Receptors. Protein Structure-based Drug Design, CSHA, Sep 2011, Su Zhou, Jiangsu Province, China
Niu Huang (invited talks), Marrying Physics to Biology. Peking University Shengzhen Graduate School, Nov 2011, Shengzhen, China 1^st Multidisplinary Biology Conference, Nov 2011, Beijing, China
Niu Huang (invited talks), Physics-based Scoring Method in Early Stages of Drug Discovery. Merck Research Laboratory, March 2012, NJ, USA; D. E. Shaw Res., Dec 2011, NYC, USA;
Niu Huang (talk), Life Beyond Kinases: Structure-based Discovery of Sorafenib as Nanomolar Antagonist of 5-HT Receptors. 243^th ACS National Meeting, March 2012, San Diego, CA, USA
Niu Huang (invited talk), Marrying Physics to Biology. Beijing Computational Science Research Center, Aug 2012, Beijing, China
Niu Huang (invited talks),Physics-based Scoring Method in Early Stages of Drug Discovery
Institute of Material Medica, PUMC&CAMS, March 2013, Beijing, China Tianjin University, June 2013, Tianjin, China
The Fourth Military Medical University, July 2013, XiAn, China
Niu Huang (invited talks), Discovering new uses for old drugs via physics-based approaches
12th National Symposium of Computational Chemistry, Oct 2013, Suzhou, China
Pharmaron. Ltd. Oct 2013, Beijing, China
Sun Yat-sen University, Nov 2013, Guangzhou, China
Niu Huang (invited talk), Supercomputing in Chemistry and Biology
5th SCA, Oct 2015, Guangzhou, China
Niu Huang (invited talk), Molecular Docking in Structure-based Lead Discovery
1th Acta Pharmaceutica Sinica Symposium, Oct 2015, Tianjin, China
Niu Huang (invited talk), Developing a Novel Quantum Mechanics-based Scoring Function for Molecular Docking.
14th International and Chinese Biophysics Meeting, Nov 2015, Kunmin, China
Niu Huang (invited talk),In silico Discovery of Novel 5-HT2B Receptor Antagonists for the Treatment of Irritable Bowel Syndrome.
The 12th SINO-US Chemistry Professors Conference, Jun 2016, Guangzhou, China
Niu Huang (invited talk), Discovering New Uses for Old Drugs via Physics-based Approaches
2th Acta Pharmaceutica Sinica Symposium, Oct 2015, Lanzhou, China
Niu Huang (invited talk), Developing a Novel Quantum Mechanics-based Scoring Function for Molecular Docking
The 13th SINO-US Chemistry Professors Conference, Jun 2016, Nantong, China

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
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
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
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
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
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.
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
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.
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
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.
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.
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.
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.
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.
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.
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.
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.
Niu Huang, John Irwin and Brian Shoichet. Benchmarking Sets for Molecular Docking. J. Med. Chem. 2006, 49:6789-6801.
Niu Huang and Matthew P. Jacobson. Physics-based Methods for Studying Protein-Ligand Interactions. Curr. Opin. Drug Discov. Devel. 2007, 10:325-331.
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
Niu Huang and Brian Shoichet. Exploring Ordered Waters in Molecular Docking. J. Med. Chem. 2008, 51:4862-4865
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
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
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
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
Niu Huang and Matthew P. Jacobson. Binding-Site Assessment by Virtual Fragment Screening. PLoS ONE. 2010, 5: e10109
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.
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.
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.
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.
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.
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. )
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.
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.
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.
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
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
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
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.
Fanqi Zeng, Shiming Peng, Li Li, Libing Mu, Zhenghua Zhang, Zhiyuan Zhang and Niu Huang. structure-based identification of drug-like inhibitors of p300 histone acetyltransferase. Acta Pharmaceutica Sinica. 2013, 48:700-708.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Yu zhou and Niu Huang. Binding site druggability assessment in fragment-based drug design.. Methods Mol. Biol. 2015, 1289:13-21.
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.
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.
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.
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.
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.
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.
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.
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.
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
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
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.
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
Yu Zhou, Yuanxun Wang, Pengfei Li, Xi-Ping Huang, Xiangbin Qi, Yunfei Du, and Niu Huang, Exploring Halogen Bonds in 5-Hydroxytryptamine 2B Receptor–Ligand Interactions. ACS Med. Chem. Lett. 2018, 9(10), 1019-1024.
Yuanxun Wang, Yunfei Du, Niu Huang. A survey of the role of nitrile groups in protein–ligand interactions. Future Med. Chem. 2018, 10(23), 2713-2728.
Shiming Peng, Wen Xiao, Dapeng Ju1, Baofa Sun, Nannan Hou, Qianlan Liu, Yanli Wang, Haijiao Zhao, Chunchun Gao, Song Zhang, Ran Cao, Pengfei Li, Huanwei Huang, Yongfen Ma, Yankai Wang, Weiyi Lai, Zhixiong Ma, Wei Zhang, Song Huang, Hailin Wang, Zhiyuan Zhang, Liping Zhao, Tao Cai, Yong-Liang Zhao, Fengchao Wang, Yongzhan Nie, Gang Zhi, Yun-Gui Yang, Eric Erquan Zhang, and Niu Huang, Identification of entacapone as a chemical inhibitor of FTO mediating metabolic regulation through FOXO1. Sci. Transl. Med. 2019, 11: eaau7116.
Wei Li, Jincai Yang, Niu Huang. Deep learning in drug design and discovery. Acta Pharmaceutica Sinica, 2019, 54: 761-767.
Yuanxun Wang, Qiuyu Fu, Yu Zhou, Yunfei Du, Niu Huang. Replacement of Protein Binding-Site Waters Contributes to Favorable Halogen Bond Interactions. J. Chem. Inf. Model. 2019, 59 (7), 3136-3143.
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 17. doi: 10.1021/acs.jcim.9b00494.
Shiming Peng, Wei Li, Nannan Hou and Niu Huang, A Review of FoxO1-Regulated Metabolic Diseases and Related Drug Discoveries. Cells 2020, 9(1), 184; https://doi.org/10.3390/cells9010184
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. doi: 10.3389/fphar.2020.00069
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, 117(8):4117-4124
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, 12(542):eaba0769
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, 12(7):620-628
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, 22;60(6):3287-3294
Wang Q, Zhou Y, Huang J, Huang N. Structure, Function, and Pharmaceutical Ligands of 5-Hydroxytryptamine 2B Receptor. Pharmaceuticals (Basel). 2021 Jan 20;14(2):76
Han P, Su C, Zhang Y, Bai C, Zheng A, Qiao C, Wang Q, Niu S, Chen Q, Zhang Y, Li W, Liao H, Li J, Zhang Z, Cho H, Yang M, Rong X, Hu Y, Huang N, Yan J, Wang Q, Zhao X, Gao GF, Qi J. Molecular insights into receptor binding of recent emerging SARS-CoV-2 variants. Nat Commun. 2021 Oct 20;12(1):6103
Chen J, Liu N, Huang Y, Wang Y, Sun Y, Wu Q, Li D, Gao S, Wang HW*, Huang N*, Qi X*, Wang X*. Structure of PDE3A-SLFN12 complex and structure-based design for a potent apoptosis inducer of tumor cells. Nat Commun. 2021 Oct 27;12(1):6204
Wang JH, Tang YL, Gong Z, Jain R, Xiao F, Zhou Y, Tan D, Li Q, Huang N, Liu SQ, Ye K, Tang C, Dong MQ, Lei X. Characterization of protein unfolding by fast cross-linking mass spectrometry using di-ortho-phthalaldehyde cross-linkers. Nat Commun. 2022 Mar 18;13(1):1468

Teng X, Chen S, Wang Q, Chen Z, Wang X, Huang N, Zheng S. Structural insights into G protein activation by D1 dopamine receptor. Sci Adv. 2022 Jun 10;8(23):eabo4158
Li L, Liao H, Meng Y, Li W, Han P, Liu K, Wang Q, Li D, Zhang Y, Wang L, Fan Z, Zhang Y, Wang Q, Zhao X*, Sun Y*, Huang N*, Qi J, Gao GF*. Structural basis of human ACE2 higher binding affinity to currently circulating Omicron SARS-CoV-2 sub-variants BA.2 and BA.1.1. Cell. 2022 Jun 16:S0092-8674(22)00728-0
Xu J, Shen C, Xie Y, Qiu B, Ren X, Zhou Y, Li G*, Zheng G*, Huang N*. Design, synthesis, and bioactivity evaluation of macrocyclic benzo[b]pyrido[4,3-e][1,4]oxazine derivatives as novel Pim-1 kinase inhibitors. Bioorg Med Chem Lett. 2022 Jun 30;72:128874

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