2024

1. He J, Liu X, Zhu C, Zha J, Li Q, Zhao M, Wei J, Li M, Wu C, Wang J, Jiao Y, Ning S, Zhou J, Hong Y, Liu Y, He H, Zhang M, Chen F, Li Y, Song K, Lu X*, Zhang J*. ASD2023: towards the integrating landscapes of allosteric knowledgebase. Nucleic Acids Res. 2024, 52(D1):D376–D383.   [HTML][PDF]

2. Xu X, Zhang Q, Wang X, Jin J, Wu C, Feng L, Yang X, Zhao M, Chen Y, Lu S, Zheng Z, Lan X, Wang Y*, Zheng Y*, Lu X*, Zhang Q*, Zhang J*. Discovery of a potent and highly selective inhibitor of SIRT6 against pancreatic cancer metastasis in vivo. Acta Pharm Sin B. 2024, doi: 10.1016/j.apsb.2023.11.014.   [HTML][PDF]

3. Zhu C, Lan X, Wei Z, Yu J, Zhang J*. Allosteric modulation of G protein-coupled receptors as a novel therapeutic strategy in neuropathic pain. Acta Pharm Sin B. 2024, 14(1):67-86.   [HTML][PDF]

4. Xiao Z, Zha J, Yang X, Huang T, Huang S, Liu Q, Wang X, Zhong J, Zheng J, Liang R, Deng Z, Zhang J*, Dai S*, Lin S*. A three-level regulatory mechanism of a new AKR subfamily. Nat Commun. 2024, Accepted.

5. Sun F, Miao M, Li W, Lan X, Yu J, Zhang J*, An Z*. Electrochemical oxidative dehydrogenative annulation of 1-(2-aminophenyl)pyrroles with cleavage of ethers to synthesize pyrrolo[1,2-a]quinoxaline derivatives. Org Biomol Chem. 2024, 22(3): 472-476.   [HTML][PDF]

6. Miao M, Sun F, Lan X, Yu J, Guo X, Zhang J*, An Z*. Copper-catalyzed oxidative cyclization of 2-(1H-pyrrol-1-yl)aniline and alkylsilyl peroxides: a route to pyrrolo[1,2-a]quinoxalines. Org Biomol Chem. 2024, Accepted.

7. Li Q, Hu Z, He J, Liu X, Liu Y, Wei J, Wu B, Lu X, He H, Zhang Y, He J, Li M, Wu C, Lv L, Wang Y, Zhou L, Zhang Q, Zhang J*, Cheng X*, Shao H*, Lu X*. Deciphering the comprehensive knowledgebase landscape featuring infertility with IDDB Xtra. Comput Bio Med. 2024, 170: 108015.   [HTML][PDF]

8. Liu N, Zhang T, Chen Y, Tan J, Zhou J, Chen W, Jiang T, Zha J, Zeng X, Li B, Wei L, Zou Y, Zhang L, Hong Y, Wang X, Zhu R, Xu W, Xi J, Wang Q, Pan L, Zhang J, Luan Y, Zhu R, Chen C, Wang H. Global fungal-host interactome mapping identifies host targets of candidalysin. Nat Commun. 2024, Accepted.

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2023

1. Zha J, He J, Wu C, Zhang M, Liu X, Zhang J*. Designing drugs and chemical probes with the dualsteric approach. Chem Soc Rev. 2023, 52: 8651-8677.   [HTML][PDF]

2. Zha J, Li Q, Liu X, Lin W, Wang T, Wei J, Zhang Z, Lu X, Wu J, Ni D, Song K, Zhang L, Lu X*, Lu S*, Zhang J*. AlloReverse: multiscale understanding among hierarchical allosteric regulations. Nucleic Acids Res. 2023, 51(W1): 33-38.   [HTML][PDF]

3. Song Q, Li M, Li Q, Lu X, Song K, Zhang Z, Wei J, Zhang L, Wei J, Ye Y, Zha J, Zhang Q, Gao Q, Long J*, Liu X*, Lu X*, Zhang J*. DeepAlloDriver: a deep learning-based strategy to predict cancer driver mutations. Nucleic Acids Res. 2023, 51(W1): 129-133.   [HTML][PDF]

4. Li M, Zhang J*. A focus on harnessing big data and artificial intelligence: revolutionizing drug discovery from traditional Chinese medicine sources. Chem Sci. 2023, 14(39): 10628-10630.   [HTML][PDF]
(Invited Focus)

5. Zha J, Su J, Li T, Cao C, Ma Y, Wei H, Huang Z, Qian L, Wen K*, Zhang J*. Encoding molecular docking for quantum computers. J Chem Theory Comput. 2023, 19(24):9018-9024.   [HTML][PDF]
(This paper is highlighted with the cover )

6. Lu X, Lan X, Lu S, Zhang J*. Progressive computational approaches to facilitate decryption of allosteric mechanism and drug discovery. Curr Opin Struct Biol. 2023, 83: 102701.   [HTML][PDF]

7. Rehman AU, Khurshid B, Rasheed S, Wadood A, Ng HL, Wei Z*, Luo R*, Zhang J*. Computational approaches for the design of modulators targeting protein-protein interactions (PPIs). Expert Opin Drug Discov. 2023, 18(3): 315-333.   [HTML][PDF]
(ESI Top1% highly cited paper)

8. Shi X, Zhang J*. Using NanoB2 to gain insights into ligand pharmacology. Cell Rep Methods. 2023, 3(3): 100438.   [HTML][PDF]
(Invited Preview)

9. Li M, Lan X, Lu X, Zhang J*. A structure-based allosteric modulator design paradigm. Health Data Sci. 2023, 3: 0094.   [HTML][PDF]

10. Zhao N, Wu W, Wang Y, Song K, Chen G, Chen Y, Wang R, Xu J, Cui K, Zhang J*, Xiao Z*. DNA-modularized construction of bivalent ligands precisely regulates receptor binding and activation. Chem. 2023, 9(4): 901-923.   [HTML][PDF]

11. Hong X, Li N, Lv J, Zhang Y, Li J*, Zhang J*, Chen H*. PTMint Database of Experimentally Verified PTM Regulation on Protein-Protein Interaction. Bioinformatics.. 2023, 39(1): btac823.   [HTML][PDF]

12. Ji X, Cui X, Li Z, Choi T, Wang Y, Xiao W, Zhao Y, Zha J, Zhang J*, Chen HF*, Yu Z*. Research and evaluation of allosteric protein specific force field based on pre-training deep learning model. J Chem Inf Model. 2023, 63(8): 2456-2468.   [HTML][PDF]

13. Hong X, Lv J, Li Z, Xiong Y, Zhang J*, Chen HF*. Sequence-based machine learning method for predicting the effects of phosphorylation on protein-protein interactions. Int J Biol Macromol. 2023, 243: 125233.   [HTML][PDF]

14. Lan X, Ni Y, Liu N, Wei W, Liu Y, Yang J, Ma L, Bai R, Zhang J**, Yu J*. Neuroprotective effects of oxymatrine on hypoxic–ischemic brain damage in neonatal rats by activating the Wnt/β-catenin pathway. Biomed Pharmacother. 2023, 159: 11426.   [HTML][PDF]

15. Guo A, Yan K, Hu H, Zhai L, Hu T, Su H, Chi Y, Zha J, Xu Y, Zhao D, Lu X, Xu Y, Zhang J, Tan M, Chen X. Spatiotemporal and global profiling of DNA-protein interactions enables discovery of low-affinity transcription factors. Nat Chem. 2023, 15(6): 803-814.   [HTML][PDF]

16. Xiao X, Feng J, Ma J, Xia X, Liu X, Zhang J, Ding C, Pang X, Zhang A. Design, synthesis and pharmacological evaluation of multisubstituted pyrido[4,3-d]pyrimidine analogues bearing deuterated methylene linkers as potent KRAS-G12D inhibitors. J Med Chem. 2023, 66(22): 15524-15549.   [HTML][PDF]

17. Wang J, Zhou S, Cheng Y, Cheng L, Qin Y, Zhang Z, Bi A, Xiang H, He X, Tian X, Liu W, Zhang J, Peng C, Zhu Z, Huang M, Li Y, Zhuang G, Tan L. Selective covalent targeting of pyruvate kinase M2 using arsenous warheads. J Med Chem. 2023, 66(4): 2608-2621.   [HTML][PDF]

18. Zhang L, Song W, Li T, Mu Y, Zhang P, Hu J, Lin H, Zhang J, Gao H, Zhang L. Redox switching mechanism of the Adenosine 5'-phosphosulfate kinase domain (APSK2) of human PAPS synthase 2. Structure. 2023, 31(7): 826-835.   [HTML][PDF]

19. Guo X, Gao Y, Yang Y, Zhu Q, Guan H, He X, Zhang C, Wang Y, Xu G, Zou S, Wei M, Zhang J, Zhang J, Liao S. Amelioration effects of a-viniferin on hyperuricemia and hyperuricemia-induced kidney injury in mice. Phytomedicine. 2023, 116: 154868.   [HTML][PDF]

20. Liu G, Wang Y, Pan Y, Tian L, Choi MH, Wang L, Kim J, Zhang J, Cheng SH, Zhang L. Hypertonicity induces mitochondrial extracellular vesicles (MEVs) that activate TNF-α and β-catenin signaling to promote adipocyte dedifferentiation. Stem Cell Res Ther. 2023, 20;14(1):333.   [HTML][PDF]

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2022

1. Zhong J, Guo Y, Lu S, Song K, Wang Y, Feng L, Zheng Z, Zhang Q, Wei J, Sang P, Shi Y, Cai J, Chen G, Liu C*, Yang X*, Zhang J*. Rational design of a sensitivity-enhanced tracer for discovering efficient APC–Asef inhibitors. Nat Commun. 2022, 13(1): 4961.   [HTML][PDF]

2. Ni D, Chai Z, Wang Y, Li M, Yu Z, Liu Y, Lu S*, Zhang J*. Along the allostery stream: Recent advances in computational methods for allosteric drug discovery. Wiley Interdiscip Rev Comput Mol Sci. 2022, 12(4): e1585.   [HTML][PDF]
(This paper is highlighted with the cover )

3. Zhang Q, Chen Y, Ni D, Huang Z, Wei J, Feng L, Su J, Wei Y, Ning S, Yang X, Zhao M, Qiu Y, Song K, Yu Z, Xu J, Li X, Lin H, Lu S*, Zhang J*. Targeting a cryptic allosteric site of SIRT6 with small-molecule inhibitors that inhibit the migration of pancreatic cancer cells. Acta Pharm Sin B. 2022, 12(2): 876-889.   [HTML][PDF]
(ESI Top1% highly cited paper and & APSB Outstanding Paper Award & This paper is highlighted with the cover )

4. Rehman AU, Lu S, Khan AZ, Khurshid B, Rasheed S, Wadood A, Zhang J*. Hidden allosteric sites and de-novo drug design. Expert Opin Drug Discov. 2022, 17(3): 283-295.   [HTML][PDF]
(ESI Top1% highly cited paper)

5. Ni D, Liu Y, Kong R, Yu Z, Lu S, Zhang J*. Computational elucidation of allosteric communication in proteins for allosteric drug design. Drug Discov Today.. 2022, 27(8): 2226-2234.   [HTML][PDF]

6. Zha J, Li M, Kong R, Lu S*, Zhang J*. Explaining and predicting allostery with allosteric database and modern analytical techniques. J Mol Biol.. 2022, 434(17): 167481.   [HTML][PDF]

7. Wang C, Wang T, Zhang K, Li M, Shen Q, Lu S* Zhang J*. Pan-KRAS inhibitors suppress proliferation through feedback regulation in pancreatic ductal adenocarcinoma. Acta Pharmacol Sin.. 2022, 43(10): 2696-2708.   [HTML][PDF]

8. Feng Y, Lu Y, Li J, Zhang H, Li Z, Feng H, Deng X, Liu D, Shi T, Jiang W, He Y*, Zhang J*, Wang Z*. Design, synthesis and biological evaluation of novel o-aminobenzamide derivatives as potential anti-gastric cancer agents in vitro and in vivo. Eur J Med Chem. 2022, 227: 113888.   [HTML][PDF]

9. Cheng C, Wang J, Xu P, Zhang K, Xin Z, Zhao H, Ji Z, Zhang M, Wang D, He Y, Jing N, Fan L, Liu K, Li F, Gong Y, Cui S, Sun Z, Sun D, Yao X, Li H, Zhang J, Zhang P, Dong B, Xue W, Qian X, Gao W, Zhu H. Gremlin1 is a therapeutically targetable FGFR1 ligand that regulates lineage plasticity and castration resistance in prostate cancer. Nat Cancer.. 2022, 3(5): 565-580.   [HTML][PDF]

10. Yan J, Zhang Y, Yu H, Zong Y, Wang D, Zheng J, Jin L, Yu X, Liu C, Zhang Y, Jiang F, Zhang R, Fang X, Xu T, Li M, Di J, Lu Y, Ma X, Zhang J, Jia W, Hu C. GPSM1 impairs metabolic homeostasis by controlling a pro2 inflammatory pathway in macrophages. Nat Commun.. 2022, 13: 7620.   [HTML][PDF]

11. Hao Y, Yang R, Li J, Zhou Z, Qian W, Zhang J, Wu Z, Jin L, Wu X, Zhang C, Zheng B, Tan J, Hao G, Li S, Li Q, Zheng D, Wang Y, Li R, Liu P, Qiao J. Age-specific random day serum anti-Mullerian hormone reference values for women of reproductive age in the general population: a large Chinese nationwide population-based survey. Am J Obstet Gynecol.. 2022, doi: 10.1016/j.ajog.2022.07.029.   [HTML][PDF]

12. Li Q, Zhou Z, Qian W, Zhang J, Wu Z, Jin L, Wu X, Zhang C, Zheng B, Tan J, Hao G, Li S, Tian T, Hao Y, Zheng D, Wang Y, Norman R, Li R, Liu P, Qiao J. Changes in the prevalence of polycystic ovary syndrome in China over the past decade. Lancet Reg Health West Pac.. 2022, 25: 100494.   [HTML][PDF]

13. Liu P, Cong X, Liao S, Jia X, Wang X, Dai W, Zhai L, Zhao L, Ji J, Ni D, Liu Z, Chen Y, Pan L, Liu W, Zhang J, Huang M, Liu B, Tan M. Global identification of phospho-dependent SCF substrates reveals a FBXO22 phosphodegron and an ERK-FBXO22-BAG3 axis in tumorigenesis. Cell Death Differ. 2022, 29(1):1-13.   [HTML][PDF]

14. Jia Y, Zhang L, Liu Z, Mao C, Ma Z, Li W, Yu F, Wang Y, Huang Y, Zheng J, Wang X, Xu Q, Zhang J, Feng W, Yun C, Liu C, Sun J, Fu Y, Cui Q, Zhang W, Kong W. Targeting Macrophage TFEB-14-3-3 Epsilon Interface by Naringenin Inhibits Abdominal Aortic Aneurysm. Cell Discov. 2022, 8(1): 21.   [HTML][PDF]

15. Zhang H, Ni D, Fan J, Li M, Zhang J, Hua C, Nussinov R, Lu S. Markov state models and molecular dynamics simulations reveal the conformational Transition of the intrinsically disordered hypervariable region of K-Ras4B to the ordered conformation. J Chem Inf Model.. 2022, 62(17): 4222-4231.   [HTML][PDF]

16. Cheng M, Cui X, Tang Y, Shao Z, Liu X, Su J, Zhang J, Wang Q, Li G. Total synthesis of leptochartamides A and B: two enantiomeric pairs of hydroxybenzyl dimers from a deep-Sea fungus leptosphaerulina chartarum. J Org Chem.. 2022, 87(16):11090-11096.   [HTML][PDF]

17. Wang Y, Li M, Liang W, Shi X, Fan J, Kong R, Liu Y, Zhang J, Chen T, Lu S. Delineating the activation mechanism and conformational landscape of a class B G protein-coupled receptor glucagon receptor. Comput Struct Biotechnol J.. 2022, 20: 628-639.   [HTML][PDF]

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2021

1. Lu S*, He X, Yang Z, Chai Z, Zhou S, Wang J, Rehman AU, Ni D, Pu J, Sun J*, Zhang J*. Activation pathway of a G protein-coupled receptor uncovers conformational intermediates as novel targets for allosteric drug design. Nat Commun. 2021, 12(1): 4721.   [HTML][PDF]
(ESI Top1% highly cited paper)

2. Ni D, Wei J, He X, Rehman AU, Li X, Qiu Y, Pu J, Lu S*, Zhang J*. Discovery of cryptic allosteric sites using reversed allosteric communication by a combined computational and experimental strategy. Chem Sci. 2021, 12: 464-476.   [HTML][PDF]
(Editor’s Choice & ESI Top1% highly cited paper)

3. Feng L, Lu S, Zheng Z, Chen Y, Zhao Y, Song K, Xue H, Jin L, Li Y, Li Y*, Zhang J*. Identification of an allosteric hotspot for additive activation on PPARγ in anti-diabetic effects. Sci Bull. 2021, 66(15): 1559-1570.   [HTML][PDF]

4. Wang Y, Yu Z, Xiao W, Lu S*, Zhang J*. Allosteric binding sites at the Receptor-Lipid bilayer interface: novel targets for GPCR drug discovery. Drug Discov Today. 2021, 26(3): 690-703.   [HTML][PDF]
(This paper was recommended by Faculty 1000

5. Lu S, Chen Y, Wei J, Zhao M, Ni D, He X, Zhang J*. Mechanism of allosteric activation of SIRT6 revealed by the action of rationally designed activators. Acta Pharm Sin B. . 2021, 11(5): 1355-1361.   [HTML][PDF]
(ESI Top1% highly cited paper and & APSB Outstanding Paper Award)

6. Fan J, Liu Y, Kong R, Ni D, Yu Z, Lu S, Zhang J*. Harnessing reversed allosteric communication: a novel strategy for allosteric drug discovery. J Med Chem. 2021, 64(24): 17728-17743.   [HTML][PDF]

7. Shang J, Ning S, Chen Y, Chen T*, Zhang J*. Pharmacological activation of SIRT6 suppresses proliferation and enhances EGFR therapy in non-small cell lung cancer. Acta Pharmacol Sin. . 2021, 42(1): 120-131.   [HTML][PDF]

8. Wu J, Li D, Liu X, Li Q, He X, Wei J, Li X, Li M, Rehman AU, Xia Y, Wu C, Zhang J*, Lu X*. IDDB: a comprehensive resource featuring genes, variants, and characteristics associated with Infertility. Nucleic Acids Res. 2021, 49(D1): D1218-D1224.   [HTML][PDF]

9. Chen Z, Song K, Shang Y, Xiong Y, Lyu Z, Chen J, Zheng J, Li P, Wu Y, Gu C, Xie Y, Deng Q, Yu Z*, Zhang J*, Qi D*. Selection and identification of novel antibacterial agents against planktonic growth and biofilm formation of Enterococcus faecalis. J Med Chem. 2021, 64(20): 15037-15052.   [HTML][PDF]

10. Mu J, Liu H, Zhang J*, Luo R*, Chen H*. Recent Force field strategies for intrinsically disordered proteins. J Chem Inf Model. 2021, 61(3): 1037-1047.   [HTML][PDF]

11. He T, Shang J, Gao C, Guan X, Chen Y, Zhu L, Zhang L, Zhang C, Zhang J*, Pang T*. A novel SIRT6 activator ameliorates neuroinflammation and ischemic brain injury via EZH2/Foxc1 axis. Acta Pharm Sin B. . 2021, 11(3): 708-726.   [HTML][PDF]

12. Li Y, Song K, Zhang J*, Lu S*. A computational method to predict effects of residue mutations on catalytic efficiency of hydrolases. Catalysts. 2021, 11(2): 286.   [HTML][PDF]

13. Yang X, Zhong J, Zhang Q, Feng L, Zheng Z, Zhang J*, Lu S*. Advances and insights of APC-Asef inhibitors for metastatic colorectal cancer therapy. Front Mol Biosci. 2021, 8: 662579.   [HTML][PDF]

14. Yuan S, Liao G, Zhang M, Zhu Y, Xiao W, Wang K, Li C, Jia C, Sun N, Walch A, Gao D, Xu P*, Deng Q*, Zhang J*, Wang H*, Hui R*. Multiomics interrogation into HBV (Hepatitis B virus)-host interaction reveals novel coding potential in human genome, and identifies canonical and non-canonical proteins as host restriction factors against HBV. Cell Discov. 2021, 7(1): 105.   [HTML][PDF]

15. Qiu Y, Wang Y, Chai Z, Ni D, Li X, Pu J, Chen J, Zhang J*, Lu S*, Lv C*, Ji M*. Targeting Ras phosphorylation in cancer therapy: mechanisms and modulators. Acta Pharm Sin B. 2021, 11(11): 3433-3446.   [HTML][PDF]

16. Zhang J, Li Y, Liu Q, Huang Y, Li R, Wu T, Zhang Z, Zhou J, Huang H, Tang Q, Huang C, Zhao Y, Zhang G, Jiang W, Mo Li, Zhang J, Xie W, He J. SIRT6 alleviated liver fibrosis by deacetylating conserved lysine 54 on Smad2 in hepatic stellate cells. Hepatology. 2021, 73(3): 1140-1157.   [HTML][PDF]

17. Wang L, Shen Q, Liao H, Fu H, Wang Q, Yu J, Zhang W, Chen C, Dong Y, Yang X, Guo Q, Zhang J, Zhang J, Zhang W, Lin H, Duan Y. Multi-arm PEG/Peptidomimetic conjugate inhibitors of DR6/APP interaction block hematogenous tumor cell extravasation. Adv Sci. 2021, 8(11): e2003558.   [HTML][PDF]

18. Zhang H, Zhao B, Han W, Sun Y, Yang P, Chen Y, Ni D, Zhang J, Yin D. Acetylation of calmodulin regulates synaptic plasticity and fear learning. J Biol Chem. 2021, 297(3): 101034.   [HTML][PDF]

19. Lin Y, Lu S, Zhang J, Zheng Y. Structure of an inactive conformation of GTP-bound RhoA GTPase. Structure. 2021, 29(6): 553-563.   [HTML][PDF]

20. Pan G, Chang L, Zhang J, Liu Y, Hu L, Zhang S, Zhang J, Qiao J, Jakopin Z, Hu H, Dong J, Ding Z. GSK669, a NOD2 receptor antagonist, inhibits thrombosis and oxidative stress via targeting platelet GPVI. Biochem Pharmacol. 2021, 183: 114315.   [HTML][PDF]

21. Li X, Wang C, Peng T, Chai Z, Ni D, Liu Y, Zhang J, Chen T, Lu S. Atomic-scale insights into allosteric inhibition and evolutional rescue mechanism of Streptococcus thermophilus Cas9 by the anti-CRISPR protein AcrIIA6. Comput Struct Biotechnol J. 2021, 19: 6108-6124.   [HTML][PDF]

22. Wang Y, Ji D, Lei C, Chen Y, Qiu Y, Li X, Li M, Ni D, Pu J, Zhang J, Fu Q, Liu Y, Lu S. Mechanistic insights into the effect of phosphorylation on Ras conformational dynamics and its interactions with cell signaling proteins. Comput Struct Biotechnol J. 2021, 19: 1184-1199.   [HTML][PDF]

23. He X, Huang N, Qiu Y, Zhang J, Liu Y, Yin X, Lu S. Conformational selection mechanism provides structural insights into the optimization of APC-Asef inhibitors. Molecules. 2021, 26(4): 962.   [HTML][PDF]

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2020

1. Liu X, Lu S, Song K, Shen Q, Ni D, Li Q, He X, Zhang H, Wang Q, Chen Y, Li X, Wu J, Sheng C, Chen G, Liu Y, Lu X*, Zhang J*. Unraveling allosteric landscapes of allosterome with ASD. Nucleic Acids Res. 2020, 48(D1): D394 - D401.   [HTML][PDF]

2. Ni D, Li Y, Qiu Y, Lu S*, Zhang J*. Combining allosteric with orthosteric drugs to overcome drug-resistance. Trends Pharmacol Sci. 2020, 41(4): 336-348.   [HTML][PDF]

3. Shang J, Zhu Z, Chen Y, Song J, Huang Y, Song K, Zhong J, Xu X, Wei J, Wang C, Cong L, Liu C*, Zhang J*. Small-Molecule activating SIRT6 elicits therapeutic effects and synergistically promotes anti-tumor activity of vitamin D3 in colorectal cancer. Theranostics. 2020, 10(13): 5845 - 5864.   [HTML][PDF]

4. Lu S, Qiu Y, Ni D, He X, Pu J, Zhang J*. Emergence of allosteric drug-resistance mutations: new challenges for allosteric drug discovery. Drug Discov Today. 2020, 25(1): 177 - 184.   [HTML][PDF]

5. Chen Y, Chen J, Sun X, Yu J, Qian Z, Wu L, Xu X, Wan X, Jiang Y, Zhang J*, Gao S*, Mao Z*. The SIRT6 activator MDL-800 improves genomic stability and pluripotency of old murine-derived iPS cells. Aging Cell. 2020, 19(8): e13185.   [HTML][PDF]

6. Qiu Y, Li X, He X, Pu J, Zhang J*, Lu S*. Computational methods-guided design of modulators targeting protein-protein interactions (PPIs). Eur J Med Chem. 2020, 207: 112764.   [HTML][PDF]

7. Chen X, Jiang Y, Geng H, Liu X, Huang Y, Lu J, Guo C, Zhang S*, Zhang J*, Wang W*. Aldehydes switch regioselectivity: a novel prins cyclization strategy for the synthesis of indoline-fused THFs and indole-fused oxepanes. Adv Synth Catal. 2020, 362(13): 2620 - 2625.   [HTML][PDF]

8. Yuan H, Han Y, Wang X, Li N, Liu Q, Yin Y, Wang H, Pan L, Li L, Song K, Qiu T, Pan Q, Chen Q, Zhang G, Zang Y, Tan M, Zhang J, Li Q, Wang X, Jiang J, Qin J. SETD2 restricts prostate cancer metastasis by integrating EZH2 and AMPK signaling pathways. Cancer Cell. 2020, 38(3):350 - 365.e7.   [HTML][PDF]

9. Zeng J, Dong S, Luo Z, Xie X, Fu B, Li P, Liu C, Yang X, Chen Y, Wang X, Liu Z, Wu J, Yan Y, Wang F, Chen J, Zhang J, Long G, Goldman S, Li S, Zhao Z, Liang Q. The Zika virus capsid disrupts corticogenesis by suppressing Dicer activity and miRNA Biogenesis. Cell Stem Cell. 2020, 27(4): 618 - 632.e9.   [HTML][PDF]

10. Geng A, Tang H, Huang J, Qian Z, Qin N, Yao Y, Xu Z, Chen H, Lan L, Xie H, Zhang J, Jiang Y, Mao Z. The deacetylase SIRT6 promotes the repair of UV-induced DNA damage by targeting DDB2. Nucleic Acids Res. 2020, 48(16): 9181 - 9194.   [HTML][PDF]

11. Zhang X, Shi S, Su Y, Yang X, He S, Wu J, Zhang J, Rao F. Suramin and NF449 are IP5K inhibitors that disrupt IP6-mediated regulation of cullin RING ligase and sensitize cancer cells to MLN4924/pevonedistat. JBC. 2020, 295(30): 10281 - 10292.   [HTML][PDF]

12. Qin J, Shen X, Zhang J, Jia D. Allosteric inhibitors of the STAT3 signaling pathway. Eur J Med Chem. 2020, doi: 10.1016/j.ejmech.2020.112122.   [HTML][PDF]

13. Li X, Ye M, Wang Y, Qiu M, Fu T, Zhang J, Zhou B, Lu S. How Parkinson's disease-related mutations disrupt the dimerization of WD40 domain in LRRK2: a comparative molecular dynamics simulation study. Phys Chem Chem Phys. 2020, 22(36): 20421-20433.   [HTML][PDF]

14. McClory J, Hui C, Zhang J, Huang M. The Phosphorylation Mechanism of Mevalonate Diphosphate Decarboxylase, a QM/MM Study. Org Biomol Chem. 2020, 18(3): 518 - 529.   [HTML][PDF]

15. Li X, Dai J, Ni D, He X, Zhang H, Zhang J, Fu Q, Liu Y, Lu S. Insight into the mechanism of allosteric activation of PI3Kα by oncoprotein K-Ras4B. Int J Biol Macromol. 2020, 144: 643 - 655.   [HTML][PDF]

16. He X, Ni D, Zhang H, Li X, Zhang J, Fu Q, Liu Y, Lu S. Zinc-mediated conformational preselection mechanism in the allosteric control of DNA binding to the zinc transcriptional regulator (ZitR). Sci Rep. 2020, 10(1): 13276.   [HTML][PDF]

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2019

1. Lu S, Shen Q, Zhang J*. Allosteric methods and their Applications: Facilitating the Discovery of Allosteric Drugs and the Investigation of Allosteric Mechanisms. Acc Chem Res. 2019, 52(2): 492 - 500.   [HTML][PDF]
(This paper is an ESI highly cited paper)

2. Song K, Li Q, Gao W, Lu S, Shen Q, Liu X, Wu Y, Wang B, Lin H, Chen G, Zhang J*. AlloDriver: a method for the identification and analysis of cancer driver targets. Nucleic Acids Res. 2019, 47(W1): W315-W321.   [HTML][PDF]

3. Lu S*, Ni D, Wang C, He X, Lin H, Wang Z*, Zhang J*. Deactivation pathway of Ras GTPase underlies conformational substates as targets for drug design. ACS Catalysis. 2019, 9(8): 7188-7196.   [HTML][PDF]

4. Lu S, He X, Ni D, Zhang J*. Allosteric modulator discovery: from serendipity to structure-based design. J Med Chem. 2019, 62(14): 6405-6421.   [HTML][PDF]
(This paper is an ESI highly cited paper, and was recommended by Faculty 1000 for 4 times.)

5. Lu S, Zhang J*. Small Molecule Allosteric Modulators of G-Protein-Coupled Receptors: Drug-Target Interactions. J Med Chem. 2019, 62(1): 24-45.   [HTML][PDF]

6. Ni D, Lu S*, Zhang J*. Emerging roles of allosteric modulators in regulation of Protein-Protein Interactions (PPIs): new paradigm for PPI drug discovery. Med Res Rev. 2019, 39(6): 2314 - 2342.   [HTML][PDF]

7. An X, Lu S, Song K, Shen Q, Huang M, Yao X, Liu H*, Zhang J*. Are the Apo Proteins Suitable for the Rational Discovery of Allosteric Drugs? J Chem Inf Model. 2019, 59(1): 597 - 604.   [HTML][PDF]

8. Yang X, Deng M, Zhang X, Song K, Ruan C, Meng L*, Zhang J*. Design, synthesis, and biological evaluation of thieno[3,2-d]pyrimidine derivatives as potential simplified phosphatidylinositol 3-kinase alpha (PI3Kα) inhibitors. Chem Biol Drug Des. 2019, 94: 2013 – 2022.   [HTML][PDF]

9. He X, Ni D, Lu S, Zhang J*. Characteristics of Allosteric Proteins, Sites, and Modulators. Adv Exp Med Biol. 2019, 1163: 107-139.   [HTML][PDF]

10. Wang L, Zhang L, Li L, Jiang J, Zheng Z, Shang J, Wang C, Chen W, Bao Q, Xu X, Jiang Z*, Zhang J*, You Q*. Small-molecule inhibitor targeting the Hsp90-Cdc37 protein-protein interaction in colorectal cancer. Sci Adv. 2019, 5(9): eaax2277.   [HTML][PDF]

11. Tang Y, Wu J, Fan T, Zhang H, Gong X, Cao Z, Zhang J*, Lin H*, Han B*. Chemical and biological study of aplysiatoxin derivatives showing inhibition of potassium channel Kv1.5. RSC Adv. 2019, 9: 7594 - 7600.   [HTML][PDF]

12. Huang K, Liang Q, Zhou Y, Jiang L, Gu W, Luo M, Tang Y, Wang Y, Lu W, Huang M, Zhang S, Zhuang G, Dai Q, Shen Q, Zhang J, Lei H, Zhu L, Ye D, Chen H, Zhou L, Shen Y*. A novel allosteric inhibitor of phosphorglycerate mutase 1 suppresses growth and metastasis of non-small-cell lung cancer. Cell Metabolism. 2019, 30(6): 1107 - 1119.   [HTML][PDF]

13. Chen G, Xu Y, Shen S, Zhang J. Phenotypes and targets-based chemical biology investigations in cancers. Natl Sci Rev. 2019, 6(6): 1111 - 1127.   [HTML][PDF]

14. Lei H, Zhang K, Wang C, Wang Y, Zhuang G, Lu L, Zhang J, Shen Y, Chen H, Zhu L. Aldehyde dehydrogenase 1A1 confers erlotinib resistance via facilitating the reactive oxygen species–reactive carbonyl species metabolic pathway in lung adenocarcinomas. Theranostics. 2019, 9(24): 7122 - 7139.   [HTML][PDF]

15. Kong R, Wang F, Zhang J, Wang FF, Chang S. CoDockPP: a Multistage Approach for Global and Site-specific Protein-protein Docking. J Chem Inf Model. 2019, 59(8): 3556 - 3564.   [HTML][PDF]

16. Ni D, Li X, He X, Zhang H, Zhang J, Lu S. Drugging K-RasG12C through covalent inhibitors: Mission possible? Pharmacol Ther. 2019, 202: 1 - 17.   [HTML][PDF]

17. McClory J, Lin JT, Timson DJ, Zhang J, Huang M*. Catalytic mechanism of mevalonate kinase revisited, a QM/MM study. Org Biomol Chem. 2019, 17(9): 2423-2431.   [HTML][PDF]

18. Xu X, Chen Y, Fu Q, Ni D, Zhang J, Li X, Lu S. The chemical diversity and structure-based discovery of allosteric modulators for the PIF-pocket of protein kinase PDK1. J Enzyme Inhib Med Chem. 2019, 34: 361 - 374.   [HTML][PDF]

19. Ren J, Sang Y, Qin R, Su Y, Cui Z, Mang Z, Li H, Lu S, Zhang J, Cheng S, Liu X, Li J, Lu J, Wu W, Zhao G, Shao F, Yao Y. Metabolic intermediate acetyl phosphate modulates bacterial virulence via acetylation. Emerg Microbes Infect. 2019, 8(1): 55 - 69.   [HTML][PDF]

20. Song K, Zhang J, Lu S. Progress in Allosteric Database. Adv Exp Med Biol. 2019, 1163: 65 - 87.   [HTML][PDF]

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2018

1. Huang Z, Zhao J, Deng W, Chen Y, Shang J, Song K, Zhang L, Wang C, Lu S, Yang X, He B, Min J, Hu H, Tan M, Xu J, Zhang Q, Zhong J, Sun X, Mao Z, Lin H, Xiao M, Chin YE, Jiang H, Xu Y*, Chen G*, Zhang J*. Identification of a cellularly active SIRT6 allosteric activator. Nat Chem Biol. 2018, 14(12): 1118 - 1126.   [HTML][PDF]
(This paper was recommended by BioCentury )

2. Huang M, Song K, Liu X, Lu S, Shen Q, Wang R, Gao J, Hong Y, Li Q, Ni D, Xu J, Chen G, Zhang J*. AlloFinder: a strategy for allosteric modulator discovery and allosterome analyses. Nucleic Acids Res. 2018, 46(W1): W451 - W458.   [HTML][PDF]

3. Yang X, Zhong J, Zhang Q, Qian J, Song K, Ruan C, Xu J, Ding K, Zhang J*. Rational Design and Structure Validation of a Novel peptide Inhibitor of the Adenomatous Polyposis Coli (APC)-Rho Guanine Nucleotide Exchange Factor 4 (Asef) Interaction. J Med Chem. 2018, 61(17): 8017 - 8028.   [HTML][PDF]

4. Lu S, Ji M, Ni D, Zhang J*. Discovery of hidden allosteric sites as novel targets for allosteric drug design. Drug Discov Today. 2018, 23(2): 359 - 365.   [HTML][PDF]
(This paper was an ESI highly cited paper, and recommended by Drug Discovery Today News )

5. Wang G, Zhang M, Jang H, Lu S, Lin S, Chen G, Nussinov R*, Zhang J*, Gaponenko V*. Interaction of Calmodulin with the cSH2 Domain of the p85 Regulatory Subunit. Biochemistry. 2018, 57(12): 1917 - 1928.   [HTML][PDF]

6. Bai J, Gao Y, Chen L, Yin Q, Lou F, Wang Z, Xu Z, Zhou H, Li Q, Cai W, Sun Y, Niu L, Wang H, Wei Z, Lu S, Zhou A, Zhang J, Wang H. Identification of a natural inhibitor of methionine adenosyltransferase 2A regulating one-carbon metabolism in keratinocytes. EBioMedicine. 2018, pii: S2352-3964(18)30613-3.   [HTML][PDF]

7. Chen Y, Li Z, Xu Z, Tang H, Guo W, Sun X, Zhang W, Zhang J, Wan X, Jiang Y, Mao Z. Use of the XRCC2 promoter for in vivo cancer diagnosis and therapy. Cell Death Dis. 2018, 9(4): 420.   [HTML][PDF]

8. Li S, Jang H, Zhang J, Nussinov R. Raf-1 Cysteine-Rich Domain Increases the Affinity of K-Ras/Raf at the Membrane, Promoting MAPK Signaling. Structure. 2018, 26(3): 513 - 525.   [HTML][PDF]

9. Zhang M, Li Z, Wang G, Jang H, Sacks DB, Zhang J, Gaponenko V, Nussinov R. Calmodulin (CaM) Activates PI3Kα by Targeting the "Soft" CaM-Binding Motifs in Both the nSH2 and cSH2 Domains of p85α. J Phys Chem B. 2018, 122(49): 11137-11146.   [HTML][PDF]

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2017

1. Jiang H, Deng R, Yang X, Shang J, Lu S, Zhao Y, Song K, Liu X, Zhang Q, Chen Y, Chinn YE, Wu G, Li J, Chen G, Yu J*, Zhang J*. Peptidomimetic inhibitors of APC-Asef interaction block colorectal cancer migration. Nat Chem Biol. 2017, 13: 994 - 1001.   [HTML][PDF]
(Recommended by "Research Watch" in , 2017)

2. Shen Q, Cheng F, Song H, Lu W, Zhao J, An X, Liu M, Chen G, Zhao Z*, Zhang J*. Proteome-scale investigation of protein allosteric regulation perturbed by somatic mutations in 7,000 cancer genomes. Am J Hum Genet. 2017, 100: 5 - 20.   [HTML][PDF]

3. Lu S, Zhang J*. Designed covalent allosteric modulators: An emerging paradigm in drug discovery. Drug Discov Today. 2017, 22, 447 - 453.   [HTML][PDF]
(This paper was recommended by Drug Discovery Today News )

4. Song K, Liu X, Huang W, Lu S, Shen Q, Zhang L, Zhang J*. Improved method for the identification and validation of allosteric sites. J Chem Inf Model. 2017, 57(9): 2358 - 2363.   [HTML][PDF]

5. Luo Y, Chen Y, Ma H*, Tian Z, Zhang Y, Zhang J*. Enhancing the biocatalytic manufacture of the key intermediate of atorvastatin by focused directed evolution of halohydrin dehalogenase. Sci Rep. 2017, 7: 42064.   [HTML][PDF]

6. Jiang H, Dong J, Song K, Wang T, Huang W, Zhang J, Yang X*, Shen Y*, Zhang J*. Discovery of an allosteric site in casein kinase 2α by combining computational and experimental methods. Acta Pharmacol Sin. 2017, 38(12):1691 -1 698.   [HTML][PDF]

7. Nussinov R, Jang H, Tsai CJ, Liao T, Li S, Zhang J. Intrinsic protein disorder in oncogenic KRAS signaling. Cell Mol Life Sci. 2017, 74(17): 3245 - 3261.   [HTML][PDF]

8. Zhang Q, Peng C, Song J, Zhang Y, Chen J, Song Z, Shou X, Ma Z, Peng H, Jian X, He W, Ye Z, Li Z, Wang Y, Ye H, Zhang Z, Shen M, Tang F, Chen H, Shi Z, Chen C, Chen Z, Shen Y, Wang Y, Lu S, Zhang J, Li Y, Li S, Mao Y, Zhou L, Yan H, Shi Y, Huang C, Zhao Y. Germline Mutations in CDH23, Encoding Cadherin-Related 23, Are Associated with Both Familial and Sporadic Pituitary Adenomas. Am J Hum Genet. 2017, 100, 817 - 823.   [HTML][PDF]

9. McClory J, Timson DJ, Singh W, Zhang J, Huang M. Reaction Mechanism of Isopentenyl Phosphate Kinase: A QM/MM Study. J Phys Chem B. 2017, 121(49): 11062 - 11071.   [HTML][PDF]

10. Nussinov R, Wang G, Tsai CJ, Jang H, Lu S, Banerjee A, Zhang J, Gaponenko V. Calmodulin and PI3K Signaling in KRAS Cancers. Trends Cancer. 2017, 3, 214 - 224.   [HTML][PDF]

11. Wang Y, Jiang L, Mo X, Lan Y, Yang X, Liu X, Zhang J, Zhu L, Liu J, Wu X. Megakaryocytic Smad4 Regulates Platelet Function Through Syk and ROCK2 Expression. Mol Pharmacol. 2017, 92(3): 285 - 296.   [HTML][PDF]

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2016

1. Lu S, Jang H, Muratcioglu S, Gursoy A, Keskin O, Nussinov R*, Zhang J*. Ras conformational ensembles, allostery and signaling. Chem Rev. 2016, 116, 6607 - 6665.   [HTML][PDF]
(This paper is highlighted with the cover )

2. Shen Q, Wang G, Li S, Liu X, Lu S, Chen Z, Song K, Yan J, Geng L, Huang Z, Huang W, Cheng G, Zhang J*. ASD v3.0: unraveling allosteric regulation with structural mechanisms and biological networks. Nucleic Acids Res. 2016, 44, D527 - D535.   [HTML][PDF]

3. Li S, Shen Q, Su M, Liu X, Lu S, Chen Z, Wang R, Zhang J*. Alloscore: a method for predicting allosteric ligand-protein interactions. Bioinformatics. 2016, 32, 1574 - 1576.   [HTML][PDF]

4. Huang W, Shen Q, Su X, Ji M, Liu X, Chen Y, Lu S, Zhuang H, Zhang J*. BitterX: a tool for deciphering bitter taste in humans. Sci Rep. 2016, 6, 23450.   [HTML][PDF]

5. Lu S, Jane H, Nussinov R*, Zhang J*. The Structural Basis of Oncogenic Mutations G12, G13 and Q61 in Small GTPase K-Ras4B. Sci Rep. 2016, 6, 21949.   [HTML][PDF]

6. Shang J, Lu S, Jiang Y, Zhang J*. Allosteric modulators of MEK1: drug design and discovery. Chem Biol Drug Des. 2016, 88, 485 - 497.   [HTML][PDF]

7. Lu S, Jang H, Gu S, Zhang J*, Nussinov R*. Drugging Ras GTPase: a comprehensive mechanistic and signaling structural view. Chem Soc Rev. 2016, 45, 4929 - 4952.   [HTML]
(This paper is highlighted with the cover )

8. Wei W, Ma C, Cao Y, Yang L, Huang Z, Qin D, Chen Y, Liu C, Wang T, Lei H, Yu Y, Huang M, Tong Y, Xu H, Gao F, Zhang J*, Wu Y*. Identification of H7 as a novel peroxiredoxin I inhibitor to induce differentiation of leukemia cells. Oncotarget. 2016, 7, 3873 - 3883.   [HTML][PDF]

9. Lu S, Jang H, Zhang J*, Nussinov R*. Inhibitors of Ras-SOS interactions. ChemMedChem. 2016, 11, 814 - 821.   [HTML][PDF]

10. Huang M, Chen Z, Zhang L, Huang Z, Chen Y, Xu J, Zhang J*, Shu X*. Screening and Biological Evaluation of a Novel STAT3 Signaling Pathway Inhibitor against Cancer. Bioorg Med Chem Lett. 2016, 26(21): 5172-5176.

11. Li Y, Han J, Zhang Y, Cao F, Liu Z, Li S, Wu J, Hu C, Wang Y, Shuai J, Chen J, Cao L, Li D, Shi P, Tian C, Zhang J, Dou Y, Li G, Chen Y, Lei M. Structural basis for activity regulation of MLL family methyltransferases. Nature. 2016, 530, 447 - 452.   [HTML][PDF]

12. Jang H, Banerjee A, Chavan T, Lu S, Zhang J, Gaponenko V, Nussinov R. The higher level of complexity of K-Ras4B activation at the membrane. FASEB J. 2016, 30, 1643 - 1655.   [HTML][PDF]

13. Marenco L, Wang R, McDougal R, Olender T, Twik M, Bruford E, Liu X, Zhang J, Lancet D, Shepherd G, Crasto C. ORDB, HORDE, ODORactor and other on-line knowledge resources of olfactory receptor-odorant interactions. Database. 2016, pii: baw132.

14. Wang M, Sang J, Ren Y, Liu K, Liu X, Zhang J, Wang H, Wang J, Orian A, Yang J, Yi J. SENP3 regulates the global protein turnover and the Sp1 level via antagonizing SUMO2/3-targeted ubiquitination and degradation. Protein Cell. 2016, 7, 63 - 77.   [HTML][PDF]

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2015

1. Lu S, Banerjee A, Jang H, Zhang J*, Gaponenko V*, Nussinov R*. GTP binding and oncogenic mutations may attenuate hypervariable region (HVR)-catalytic domain interactions in small GTPase KRAS4B, exposing the effector binding site. J Biol Chem. 2015, 290, 28887 - 28900.   [HTML][PDF]

2. Lu S, Deng R, Jiang H, Song H, Li S, Shen Q, Huang W, Nussinov R, Yu J*, Zhang J*. The mechanism of ATP-dependent allosteric protection of Akt kinase phosphorylation. Structure. 2015, 23, 1725 - 1734.   [HTML][PDF]

3. Huang W, Wang G, Shen Q, Liu X, Lu S, Geng Lv, Huang Z, Zhang J*. ASBench: benchmarking sets for allosteric discovery. Bioinformatics. 2015, 31, 2598 - 2600.   [HTML][PDF]

4. Hu Y, Li S, Liu F, Geng L, Shu X*, Zhang J*. Discovery of novel nonpeptide allosteric inhibitors interrupting the interaction of CDK2/cyclin A3 by virtual screening and bioassays. Bioorg Med Chem Lett. 2015, 25, 4069 - 4073.   [HTML][PDF]

5. Guan B, Siampour H, Fan Z, Wang S, Kong X, Mesli A, Zhang J*, Dan Y*. Nanoscale nitrogen doping in silicon by self-assembled monolayers. Sci Rep. 2015, 5, 12641.   [HTML][PDF]

6. Guo S, Huang W, Zhang J*, Wang Y*. Novel inhibitor against Malassezia globosa LIP1 (SMG1), a potential anti-dandruff target. Bioorg Med Chem Lett. 2015, 25, 3464 - 3467.   [HTML][PDF]

7. Liang Y, Fu Y, Qi R, Wang M, Yang N, He L, Yu F, Zhang J, Yun C, Wang X, Liu J, Kong W. Cartilage oligomeric matrix protein is a natural inhibitor of thrombin. Blood. 2015, 126, 905 - 914.   [HTML][PDF]

8. Song F, Xia L, Ji P, Tang Y, Huang Z, Zhu L, Zhang J, Wang J, Zhao G, Ge H, Zhang Y, Wang Y. Human dCTP Pyrophosphatase 1 promotes breast cancer cell growth and stemness through modulation on 5-methyl-dCTP metabolism and global hypomethylation. Oncogenesis. 2015, 4, e159.   [HTML][PDF]

9. Zhang D, Wang Y, Shi Z, Liu J, Sun P, Hou X, Zhang J, Zhao S, Zhou B, Mi J. Metabolic Reprogramming of Cancer-Associated Fibroblasts by IDH3α Downregulation. Cell Rep. 2015, 10, 1335 - 1348.   [HTML][PDF]

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2014

1. Lu S, Huang W, Wang Q, Shen Q, Li S, Nussinov R*, Zhang J*. The Structural Basis of ATP as an Allosteric Modulator. PLoS Comput Biol. 2014, 10, e1003831.   [HTML][PDF]

2. Huang Z, Mou L, Shen Q, Lu S, Li C, Liu X, Wang G, Li S, Geng L, Liu Y, Wu J, Chen G, Zhang J*. ASD v2.0: updated content and novel features focusing on allosteric regulation. Nucleic Acids Res. 2014, 42(1), D510 - D516.   [HTML][PDF]

3. Zhao Y, Zhang X, Chen Y, Lu S, Peng Y, Wang X, Guo C, Zhou A, Zhang J, Luo Y, Shen Q, Ding J, Meng L*, Zhang J*. Crystal Structures of PI3Kα Complexed with PI103 and Its Derivatives: New Directions for Inhibitors Design. ACS Med. Chem. Lett. 2014, 5, 138 - 142.   [HTML][PDF]
(This paper was recommended by Faculty 1000 and ACS )

4. Lu S, Li S, Zhang J*. Harnessing allostery: a novel approach to drug discovery. Med Res Rev. 2014, 34, 1242 - 1285.   [HTML][PDF]

5. Lu S, Huang W, Zhang J*. Recent computational advances in the identification of allosteric sites in proteins. Drug Discov Today. 2014, 19, 1595 - 1600.   [HTML][PDF]
(This paper was recommended by Drug Discovery Today News )

6. Shi T, Luo Y, Wang X, Zhao Y, Lu S, Zhang J*. Theoretical studies on the mechanism, enantioselectivity and axial ligand effect of Ru(salen)-catalyzed asymmetric cyclopropanation reaction. Organometallics. 2014, 33, 3673 - 3682.   [HTML][PDF]

7. Li S, Zhang J, Lu S, Huang W, Geng L, Shen Q, Zhang J*. Mechanism of allosteric inhibition of protein tyrosine phosphatase 1B. PLoS ONE. 2014, 9, e97668.   [HTML][PDF]

8. Xu Y, Chen S, Zhang J, Fang S, Guo Q, Wang J, Fu Q, Xu R, Sun K. Novel TBX1 loss-of-function mutation causes isolated conotruncal heart defects in Chinese patients without 22q11.2 deletion. BMC Med Genet. 2014, 15, 78.   [HTML][PDF]

9. Zhang Q, Zhang W, Li Y, Wang J, Zhang J, Hou T. MORT: a powerful foundational library for computational biology and CADD. J Cheminformatics. 2014, 6, 36.   [HTML][PDF]

10. Wei Z, Sun M, Liu X, Zhang J, Jin Y. Rufy3, a protein specifically expressed in neurons, interacts with actin-bundling protein Fascin to control the growth of axons. J Neurochem. 2014, 130, 678 - 692.   [HTML][PDF]

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2013

1. Huang W, Lu S, Huang Z, Liu X, Mou L, Luo Y, Zhao Y, Liu Y, Chen Z, Hou T, Zhang J*. Allosite: a method for predicting allosteric sites. Bioinformatics. 2013, 29, 2357 - 2359.   [HTML][PDF]

2. Shi T, Han Y, Li W, Zhao Y, Liu Y, Huang Z, Lu S, Zhang J*. Exploring the Desumoylation Process of SENP1: A Study Combined MD Simulations with QM/MM Calculations on SENP1-SUMO1-RanGAP1. J Chem Inf Model. 2013, 53, 2360 - 2368.   [HTML][PDF]

3. Lu S, Huang Z, Huang W, Liu X, Chen Y, Shi T, Zhang J*. How calcium inhibits the magnesium-dependent kinase GSK3β: A molecular simulation study. PROTEINS: Structure, Function, and Bioinformatics. 2013, 81, 740 - 753.   [HTML][PDF]

4. Huang M, Lu S, Shi T, Zhao Y, Chen Y, Li X, Liu X, Huang Z, Zhang J*. Conformational transition pathway in the activation process of allosteric glucokinase. PLOS ONE. 2013, 8, e55857.   [HTML][PDF]

5. Li X, Chen Y, Lu S, Huang Z, Liu X, Wang Q, Shi T, Zhang J*. Towards an understanding of the sequence and structural basis of allosteric proteins. J Mol Graph Model. 2013, 40, 30 - 39.   [HTML][PDF]

6. Wang W, Ye W, Yu Q, Jiang C, Zhang J*, Luo R*, Chen HF*. Conformation Selection and Induced Fit in Specific Antibody and Antigen Recognition: SPE7 as a Case Study. J Phys Chem B. 2013, 117, 4912 - 23.   [HTML][PDF]

7. Hou X, Du J, Zhang J, Du L, Fang H, Li M. How to improve docking accuracy of AutoDock4.2: A case study using different electrostatic potentials. J Chem Inf Model. 2013, 53, 188 - 200.   [HTML][PDF]

8. Tang J, Zhang ZH, Huang M, Heise T, Zhang J, Liu GL. Phosphorylation of human La protein at Ser366 by casein kinase II contributes to hepatitis B virus replication and expression in vitro. J Viral Hepatitis. 2013, 20, 24 - 33.   [HTML][PDF]

9. Uckun F, Ma H, Qazi S, Ozer Z, Zhang J, Ishkhanian R. Regulatory phosphorylation of Ikaros by Bruton's tyrosine kinase. PLOS ONE. 2013, 8, e71302.   [HTML][PDF]

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2012

1. Lu S, Huang W, Li X, Huang Z, Liu X, Chen Y, Shi T, Zhang J*. Insights into the Role of Magnesium Triad in myo-Inositol Monophosphatase: Metal Mechanism, Substrate Binding and Lithium Therapy. J Chem Inf Model. 2012, 52, 2398 - 2409.   [HTML][PDF]

2. Chen Y, Wen D, Huang Z, Huang M, Luo Y, Liu B, Lu H, WuY, Peng Y*, Zhang J*. 2-(4-chlorophenyl)-2-oxoethyl-4-benzamidobenzoate derivatives, a novel class of SENP1 Inhibitors: Virtual screening, synthesis and biological evaluation. Bioorg Med Chem Lett. 2012, 22, 6867 - 6870.   [HTML][PDF]

3. Wang Q, Zheng M, Huang Z, Liu X, Zhou H, Chen Y, Shi T, Zhang J*. Toward understanding the molecular basis for chemical allosteric modulator design. J Mol Graph Model. 2012, 38, 324 - 333.   [HTML][PDF]

4. Huang Z, Jiang H, Liu X, Chen Y, Wang Q, Huang W, Shi T, Zhang J*. HEMD: an integrated tool of human epigenetic enzymes and chemical modulators for therapeutics. PLOS ONE. 2012, 7, e39917.   [HTML][PDF]

5. Tang J, Huang Z, Chen Y, Zhang Z, Liu G*, Zhang J*. A novel inhibitor of human La protein with anti-HBV activity discovered by structure-based virtual screening and in vitro evaluation. PLOS ONE. 2012, 7, e36363.   [HTML][PDF]

6. Liu X, Liu B, Huang Z, Shi T, Chen Y, Zhang J*. SPPS: a sequence-based method for predicting probability of protein-protein interaction partners. PLOS ONE. 2012, 7, e30938.   [HTML][PDF]

7. Ye W, Chen Y, Wang W, Yu QF, Li Y, Zhang J*, Chen HF*. Insight into the Stability of Cross-b Amyloid Fibril from VEALYL Short Peptide with Molecular Dynamics Simulation. PLOS ONE. 2012, 7, e36382.   [HTML][PDF]

8. Qin F, Ye W, Chen Y, Chen X, Li Y, Zhang J*, Chen HF*. Atomistic Mechanism of microRNA Translation Upregulation via Molecular Dynamics Simulations. PLOS ONE. 2012, 7, e43788.   [HTML][PDF]

9. Qin F, Ye W, Chen Y, Chen X, Li Y, Zhang J*, Chen HF*. Specific recognition between intrinsically disordered LEF and DNA. Phys Chem Chem Phys. 2012, 14, 538 - 545.   [HTML]

10. Zhang Z, Chen L, Gao L, Lin K, Zhu L, Lu Y, Shi X, Gao Y, Zhou J, Xu P, Zhang J*, Wu G*. Structural basis for the recognition of Asef by Adenomatous Polyposis Coli. Cell Res. 2012, 22, 372 - 386.   [HTML][PDF]
(This paper was recommended by Faculty 1000 )

11. Lv M, Shi T, Mao X, Li X, Chen Y, Zhu J, Ni S, Shen X, Jiang H, Li J*, Zhang J*, Huang J*. 1-(2,6-Dibenzyloxybenzoyl)-3-(9H-fluoren-9-yl)-urea: a novel Cyclophilin A allosteric activator. Biochem Biophys Res Commun. 2012, 425, 938 - 943.   [HTML][PDF]

12. Huang J#, Yan J#, Zhang J# (co-first), Zhu SG, Wang YL, Shi T, Zhu CH, Chen C, Liu X, Cheng JK, Mustelin T, Feng GS, Chen GQ, Yu J. SUMO1 modification of PTEN regulates tumorigenesis by controlling its association with plasma membrane. Nat Commun. 2012, 3, 911.   [HTML][PDF]
(This paper was recommended by Faculty 1000 )

13. Duan XF, Eric B, Li Z, Timothy C, Zhang J, Huang Z, Su X, Pan Y, Wu L, Chi Q, Thomas S, Zhang S, Ma M, Hiroaki M, Chen GQ, Zhuang H. Crucial role of copper in detection of metal-coordinating odorants. Proc Natl Acad Sci USA. 2012, 109, 3492 - 3497.   [HTML][PDF]

14. Uckun F, Ma H, Zhang J, Ozer Z, Dovat S, Mao C, Ishkhanian R, Goodman P, Qazi S. Serine phosphorylation by SYK is critical for nuclear localization and transcription factor function of IKAROS. Proc Natl Acad Sci USA. 2012, 109, 18072 - 18077.   [HTML][PDF]

15. Li W, Fu J, Cheng F, Zheng M, Zhang J, Liu G, Tang Y. Unbinding pathways of GW4064 from human farnesoid X receptor as revealed by molecular dynamics simulations. J Chem Inf Model. 2012, 52, 3043 - 3052.   [HTML][PDF]

16. Liu B, Zheng Y, Wang TD, Xu HZ, Xia L, Zhang J, Wu YL, Chen GQ, Wang LS. Proteomic Identification of Common SCF Ubiquitin Ligase FBXO6-Interacting Glycoproteins in Three kinds of Cells. J Proteome Res. 2012, 11, 1773 - 1781.   [HTML][PDF]

17. Zhou Z, Lin J, Huo R, Huang W, Zhang J, Wang L, Sun Y, Shen B, Li N. Total glucosides of paeony attenuated functional maturation of dendritic cells via blocking TLR4/5 signaling in vivo. Int Immunopharmacol. 2012, 14, 275 - 282.   [HTML][PDF]

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2011

1. Huang Z, Zhu L, Cao Y, Wu G, Liu X, Chen Y, Wang Q, Shi T, Zhao Y, Wang Y, Li W, Li Y, Chen H*, Chen G, Zhang J*. ASD: a comprehensive database of allosteric proteins and modulators. Nucleic Acids Res. 2011, 39, D663 - D669.

2. Liu X, Su X, Wang F, Huang Z, Wang Q, Li Z, Zhang R, Wu L, Pan Y, Chen Y, Zhuang H, Chen G, Shi T, Zhang J*. ODORactor: a web server for deciphering olfactory coding. Bioinformatics. 2011, 27, 2302 - 2303.

3. Shi T, Lu Y, Liu X, Chen Y, Jiang H*, Zhang J*. Mechanism for the Autophosphorylation of CheA Histidine Kinase: QM/MM Calculations. J Phys Chem B. 2011, 115, 11895 - 11901.

4. Wang F, Liu D, Wang H, Luo C, Zheng M, Liu H, Zhu W, Luo X, Zhang J*, Jiang H*. Computational screening for active compounds targeting protein sequences: methodology and experimental validation. J Chem Inf Model. 2011, 51, 2821 - 2828.

5. Zhang H, Qin F, Ye W, Li Z, Ma S, Xia Y, Jiang Y, Zhu J, Li Y, Zhang J*, Chen HF*. Revealing the Drug-Resistant Mechanism for Diarylpyrimidine Analogue Inhibitors of HIV-1 Reverse Transcriptase. Chem Biol Drug Des. 2011, 78, 427 - 437.

6. Tian S, Li Y, Wang J, Zhang J*, Hou T*. ADME Evaluation in Drug Discovery. 9. Prediction of Oral Bioavailability in Humans Based on Molecular Properties and Structural Fingerprints. Mol Pharm. 2011, 8, 841 - 851.

7. Li Z, Zhang H, Li Y, Zhang J*, Chen HF*. Drug Resistant Mechanism of Diaryltriazine Analog Inhibitors of HIV-1 Reverse Transcriptase Using Molecular Dynamics Simulation and 3D-QSAR. Chem Biol Drug Des. 2011, 77, 63 - 74.

8. Qin F, Jiang Y, Chen Y, Wu M, Yan G, Ye W, Li Y, Zhang J*, Chen HF*. Conformational Selection or Induced Fit for Brinker and DNA Recognition. Phys Chem Chem Phys. 2011, 13, 1407 - 1412.

9. Zhou C, Mo J, Wang X, Zhang J*, Gan LS*. Theoretical study on flueggenines A and B: A comparison of calculated spectroscopic properties with IR, UV and ECD experimental data. J Mol Struct. 2011, 989, 131 - 135.

10. Zhou C, Wang X, Mo J, Zhang J*, Gan LS*. Optical Resolution and Structure Determination of New Indolizidine Alkaloids from Elaeocarpus sphaericus. Helv Chim Acta. 2011, 94, 347 - 354.

11. Cai X, Zhang J, Chen M, Wu Y, Wang X, Chen J, Zhang J, Shen X, Qu D, Jiang H. The effect of the potential PhoQ histidine kinase inhibitors on Shigella flexneri virulence. PLOS ONE. 2011, 6, e23100.

12. Zhang Z, Li H, Chen L, Lu X, Zhang J, Xu P, Lin K, Wu G. Molecular basis for the recognition of adenomatous polyposis coli by the discs large 1 protein. PLOS ONE. 2011, 6, e23507.

13. Pang X, Zhang L, Lai L, Chen J, Wu Y, Yi Z, Zhang J, Qu W, Aggarwal BB, Liu M. 1'-Acetoxychavicol acetate suppresses angiogenesis-mediated human prostate tumor growth by targeting VEGF-mediated Src-FAK-Rho GTPase-signaling pathway. Carcinogenesis. 2011, 32, 904 - 912.

14. Wu Y, He L, Zhang L, Chen J, Yi Z, Zhang J, Liu M, Pang X. Anacardic acid (6-pentadecylsalicylic acid) inhibits tumor angiogenesis by targeting Src/FAK/Rho GTPases signaling pathway. J Pharmacol Exp Ther. 2011, 39, 403 - 411.

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2010

1. Zhao Y, Lu X, Yang CY, Huang Z, Fu W, Hou T, Zhang J*. Computational Modeling Toward Understanding Agonist Binding on Dopamine 3. J. Chem. Inf. Model. 2010, 50, 1633 - 1643.

2. Liu H, Shen Q, Zhang J*, Fu W*. Evaluation of various inverse docking schemes in multiple targets identification. J. Mol. Graph. Model. 2010, 29, 326 - 330.

3. Qin F, Chen Y, Wu M, Li Y, Zhang J*, Chen HF*. Induced Fit or Conformational Selection for RNA/U1A folding. RNA 2010, 16, 1053 - 1061.

4. Chen Y, He YJ, Wu M, Yan G, Li Y, Zhang J*, Chen HF*. Insight into the Stability of Cross-β Amyloid Fibril from Molecular Dynamics Simulation. Biopolymers 2010, 93, 578 - 586.

5. Zhang S, Hu L, Du H, Guo Y, Zhang Y, Niu H, Jin J, Zhang J, Liu J, Zhang X, Kunapuli SP, Ding Z. BF0801, a novel adenine derivative, inhibits platelet activation via PDE inhibition and P2Y12 antagonism. Thromb Haemost. 2010, 104, 845 - 857.

6. Lin P, Hu T, Hu J, Yu W, Han C, Zhang J, Qin G, Yu K, G?tz F, Shen X, Jiang H, Qu D. Characterization of peptide deformylase homologues from Staphylococcus epidermidis. Microbiology. 2010, 156, 3194 - 3202.

7. Dong MX, Zhang J, Peng XQ, Lu H, Yun LH, Jiang S, Dai QY. Tricyclononene carboxamide derivatives as novel anti-HIV-1 agents. Eur.J.Med.Chem. 2010, 45, 4096 - 4103.

8. Chen J, Bai L, Bernard D, Nikolovska-Coleska Z, Gomez C, Zhang J, Yi H, Wang S. Structure-Based Design of Conformationally Constrained, Cell-Permeable STAT3 Inhibitors. ACS Med. Chem. Lett. 2010, 1, 85 - 89.

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2003-2009

1. Zhang J, Li C, Shi T, Chen K, Shen X, Jiang H. Lys169 of Human Glucokinase Is a Determinant for Glucose Phosphorylation: Implication for the Atomic Mechanism of Glucokinase Catalysis. PLOS ONE 2009, 4, e6304.

2. Gomez C, Bai L, Zhang J, Nikolovska-Coleska Z, Chen J, Yi H, Wang S. Design, Synthesis and Evaluation of Peptidomimetics Containing Freidinger Lactams as STAT3 Inhibitors. Bioorg. Med. Chem. Lett. 2009, 19, 1733 - 1736.

3. Shangary S, Qin D, McEachern D, Liu M, Miller RS, Qiu S, Nikolovska-Coleska Z, Ding K, Wang G, Chen J, Bernard D, Zhang J, Lu Y, Gu Q, Shah RB, Pienta KJ, Ling X, Kang S, Guo M, Sun Y, Yang D, Wang S. Temporal activation of p53 by a specific MDM2 inhibitor is selectively toxic to tumors and leads to complete tumor growth inhibition. Proc. Natl. Acad. Sci. USA. 2008, 105, 3933 - 3938.

4. Chen S¹, Hu T¹, Zhang J¹(1 are contributed equally to this work), Chen J, Chen K, Ding J, Jiang H, Shen X. Mutation of Gly11 on the Dimer Interface Results in the Complete Crystallographic Dimer Dissociation of SARS-CoV 3CLpro: Crystal Structure in Conjunction with Molecular Dynamics Simulations. J. Biol. Chem. 2008, 283, 554 - 564.

5. Yu XL, Hu T, Du JM, Yang XM, Zhang J, Yang B, Shen X, Zhang Z, Zhong WD, Wen N, Ding JP, Jiang H, Zhu P, Chen ZN. Crystal structure of HAb18G/CD147: implications for immunoglobulin superfamily homophilic adhesion. J. Biol. Chem. 2008, 283, 18056 - 18065.

6. Chen S, Zhang J, Hu T, Chen K, Jiang H, Shen X. Residues on the Dimer Interface of SARS Coronavirus 3C-like Protease: Dimer Stability Characterization and Enzyme Catalytic Activity Analysis. J. Biochem. 2008, 143, 552 - 536.

7. Chen J, Collins GT, Zhang J, Yang CY, Levant B, Woods J, Wang S. Design, Synthesis and Evaluation of a Potent and Selective Ligand for the Dopamine 3 (D3) Receptor with a Novel In vivo Behavioral Profile. J. Med. Chem. 2008, 51, 5905 - 5908.

8. Shen J¹, Zhang J¹(1 are contributed equally to this work), Luo X, Zhu W, Yu K, Chen K, Li Y, Jiang H. Predicting protein-protein interactions based only on sequences information. Proc. Natl. Acad. Sci. USA. 2007, 104, 4337 - 4341

9. Han C¹, Zhang J¹(1 are contributed equally to this work), Chen L, Chen K, Shen X, Jiang H. Discovery of Helicobacter pylori shikimate kinase inhibitors: bioassay and molecular modeling. Bioorg. Med. Chem. 2007, 15, 656 - 662.

10. Ye D, Li J, Zhang J, Liu H, Jiang H. Simultaneous stereoselective 4-amination with cyclic secondary amines and 2-O-deacetylation of peracetylated sialic acid derivatives. Tetrahedron Lett. 2007, 48, 4023 - 4027.

11. Lu A, Zhang J, Yin X, Luo X, Jiang H. Farnesyltransferase pharmacophore model derived from diverse classes of inhibitors. Bioorg. Med. Chem. Lett. 2007, 15, 243 - 249.

12. Huang M, Gao H, Chen Y, Zhu H, Cai Y, Zhang X, Miao Z, Jiang H, Zhang J, Shen H, Lin L, Lu W, Ding J. Chimmitecan, a novel 9-substituted camptothecin, with improved anticancer pharmacologic profiles in vitro and in vivo. Clin. Cancer Res. 2007, 6, 484 - 495.

13. Qin Z, Lee B, Yang L, Zhang J, Yang X, Qu D, Jiang H, Molin S. Antimicrobial activities of YycG histidine kinase inhibitors against Staphylococcus epidermidis biofilms. FEMS Microbiol. Lett. 2007, 273, 149 - 156.

14. Zhang J, Li C, Chen K, Zhu W, Shen X, Jiang H. Conformational transition pathway in the allosteric process of human glucokinase. Proc. Natl. Acad. Sci. USA. 2006, 103, 13368 - 13373.

15. Li J¹, Zhang J¹(1 are contributed equally to this work), Chen J, Luo X, Zhu W, Shen J, Liu H, Shen X, Jiang H. An effective strategy for discovering novel chemical inhibitors of human cyclophilin A: focused library design, virtual screening, chemical synthesis and bioassay. J. Comb. Chem. 2006, 8, 326 - 337.

16. Qin Z¹, Zhang J¹(1 are contributed equally to this work), Xu B, Chen L, Wu Y, Ou Y, Yang X, Shen X, Jiang H, Qu D. Structure-based discovery of inhibitors of the YycG histidine kinase: New chemical leads to combat Staphylococcus epidermidis infections. BMC Microbiol. 2006, 6, 96 - 114.

17. Zhang J, Yu K, Zhu W, Jiang H. Neuraminidase pharmacophore model derived from diverse classes of inhibitors. Bioorg. Med. Chem. Lett. 2006, 16, 3009 - 3014.

18. Cai J, Han C, Hu T, Zhang J, Wu D, Wang F, Liu Y, Ding J, Chen K, Yue J, Shen X, Jiang H. PDF enzyme is a potential target for anti-helicobacter pylori drugs: reverse docking, enzymatic assay and X-ray crystallography validation. Protein Sci. 2006, 15, 2071 - 2081.

19. Li J, Chen J, Gui C, Zhang L, Qin Y, Xu Q, Zhang J, Liu H, Shen X, Jiang H. Discovering novel chemical inhibitors of human cyclophilin A: virtual screening, synthesis, and bioassay. Bioorg. Med. Chem. 2006, 14, 2209 - 2224.

20. Li J, Tan J, Chen L, Zhang J, Shen X, Mei C, Fu L, Lin L, Ding J, Xiong B, Xiong X, Liu H, Luo X, Jiang H. Design, synthesis and antitumor evaluation of a new series of N-substituted-thiourea derivatives. Acta Pharmacol. Sin. 2006, 27, 1259 - 1271.

21. Zhang J, Xu Y, Shen J, Luo X, Chen J, Chen K, Zhu W, Jiang H. Dynamic mechanism for the autophosphorylation of CheA histidine kinase: molecular dynamics simulations. J. Am. Chem. Soc. 2005, 127, 11709 - 11719.

22. Chen G, Zheng S, Luo X, Shen J, Zhu W, Liu H, Gui C, Zhang J, Zheng M, Puah CM, Chen K, Jiang H. Focused combinatorial library design based on structural diversity, druglikeness and binding affinity score. J. Comb. Chem. 2005, 7, 398 - 406.

23. Zhang J, Zhu X, Hao P, Mao Y, Sun X, Wu L, Li G, Qiu X. Immunoglobulin G expression in lung cancer cells. Acta Bioch. Bioph. Sin. 2003, 35, 197 - 214.

24. Qiu X, Zhu X, Zhang L, Mao Y, Zhang J, Hao P, Li G, Lv P, Li Z, Sun X, Wu L, Zheng J, Deng Y, Hou C, Tang P, Zhang S, Zhang Y. Human epithelial cancers secrete immunoglobulin G with unidentified specificity to promote growth and survival of tumor cells. Cancer Res. 2003, 63, 6488 - 6495.