Publications

2020

57. Z Gao, J Bao, S Shi, X Zhang, Y Gao, Zhu T.*,Effect of Mutations on Drug Resistance of Smoothened Receptor Toward Inhibitors Probed by Molecular Modeling. Chem. Phys. Lett. 2020, 741, 137126.

56. Xianli Hu, Bo Hou, Zhiai Xu, Madiha Saeed, Fang Sun, Zhenmei Gao, Yi Lai, Zhu T, Fan Zhang, Wen Zhang, Haijun Yu*.Supramolecular Prodrug Nanovectors for Active Tumor Targeting and Combination Immunotherapy of Colorectal Cancer. Adv. Sci. 2020, 7, 1903332

55. Zeng, J. Z.; Cao, L. Q.; Xu, M. Y.; Zhu T.*; Zhang, J. Z. H.*, Neural Network Based in Silico Simulation of Combustion Reactions. arXiv:1911.12252.

54. Zeng, J. Z.,‡ Cao, L. Q., ‡ Chin, C. H.;* Ren, H. S.;* Zhang, J. Z. H.; Zhu T.*, ReacNetGenerator: an automatic reaction network generator for reactive molecular dynamics simulations. Phys. Chem. Chem. Phys., 2020, 22, 683-691.Graphical abstract: ReacNetGenerator: an automatic reaction network generator for reactive molecular dynamics simulations

2019

53. Chin, C. H.*; Zhu T.*; Zhang J. Z. H., Formation mechanism and spectroscopy of C6H radicals in extreme environments: a theoretical study. Phys. Chem. Chem. Phys., 2019, 21, 23044-23055

52. Tian, S. Z.; Zeng, J. Z.; Liu, X.*; Chen, J. Z.; Zhang, J. Z. H.; Zhu T.*, Understanding the selectivity of inhibitiors toward PI4KIIIa and PI4KIIIb based molecular modeling. Phys. Chem. Chem. Phys., 2019, 21, 22103-22112

51. Chen, J. Z.*; Pang, L. X.; Wang, W.; Wang, L. F.; Zhang, J. Z. H.; Zhu T.*, Binding modes and conformational changes of FK506-binding protein 51 induced by inhibitor bindings: insight into molecular mechanisms based on multiple simulation technologies.  J. Biomol. Struct. Dyn., 2019, 21, 22103-22112J. Biomol. Struct. Dyn., 2019, DOI: 10.1080/07391102.2019.1624616.

50. Xu, M.Y.; Zhu T.*; Zhang J.Z.H.*, Molecular Dynamics Simulation of Zinc Ion in Water with an Ab Initio Based Neural Network Potential. J. Phys. Chem. A. 2019, 123, 6587-6595.

49. Tang, Q.; Plank, T. N.; Zhu T.; Yu H. Z.; Ge Z. L.; Li Q.; Li L.; Davis J. T.*; Pei H.*, Self-Assembly of Metallo-Nucleoside Hydrogels for Injectable Materials That Promote Wound Closure. ACS Appl. Mater. Interfaces. 2019, 11, 19743−19750

48. Zhao, P.; Han, S.; Li, X. X.*; Zhu T.*; Tao, X. F.; Guo, L., Comparison of RP-3 Pyrolysis Reactions Between Surrogates and 45-component Model by ReaxFF MD Simulations. ACS Energy Fuels. 2019, 33, 7176-7187.

47. Sun, Z. X.*; Wang, X. H.; Zhao, Q. Q.; Zhu, T., Understanding Aldose Reductase-Inhibitors interactions with free energy simulation.  J. Mol. Graph. Model., 2019, 91, 10-21. 

46. Chen, J. Z.*; Wang, X. Y.; Pang, L. X.; Zhang, J. Z. H.; Zhu T.*, Effect of mutations on binding of ligands to guanine riboswitch probed by free energy perturbation and molecular dynamics simulations. Nucleic Acids Res. 2019, 47, 6618-6631.

45. Zhao, P.; Cao, H. L.; Chen, Y.; Zhu T.*, Insights into the binding mechanisms of inhibitors of MDM2 based on molecular dynamics simulations and binding free energy calculations. Chem. Phys. Lett., 2019, 728, 94-101.

44. Chen, J. Z.*; Pang, L. X.; Wang, W.; Wang, L. F.; Zhang, J. Z. H.; Zhu T.*, Decoding molecular mechanism of inhibitor bindings to CDK2 using molecular dynamics simulations and binding free energy calculations. J. Biomol. Struct. Dyn., 2019, 8, 1-12.

43. Zhu, M. F.; Wang H.; Wang C. L.; Fang Y. F.; Zhu T.; Zhao W. L.; Dong X. C.*; Zhang X. W.*, L-4, a Well-Tolerated and Orally Active Inhibitor of Hedgehog Pathway, Exhibited Potent Anti-tumor Effects Against Medulloblastoma in vitro and in vivo. Front. Pharm. 2019, 10, 1-13.

42. Xu, M. Y.; Zhu T.*; Zhang, J. Z. H.*, A Fragment Quantum Mechanical Method for Metalloproteins. J. Chem. Theory Comput., 2019, 15, 1430–1439.

2018

41. Chen, J. Z.*; Wang, X. Y.; Zhang, J. Z. H.; Zhu T.*, Effect of Substituents in Different Positions of Aminothiazole Hinge-Binding Scaffolds on Inhibitor–CDK2 Association Probed by Interaction Entropy Method. ACS Omega, 2018, 3, 18052–18064.

40. Gao, Y.; Zhu T.*; Zhang, C. M.; Zhang, J. Z. H.; Mei, Y.*, Comparison of the Unfolding and Oligomerization of Human Prion Protein under acidic and neutral environments by Molecular Dynamics Simulations. Chem. Phys. Lett. 2018, 706, 594-600.

39. Gao, Y.; Zhu, T.*; Chen, J. Z.*, Exploring Drug-resistant Mechanisms of I84V Mutation in HIV-1 Protease toward Different Inhibitors by Thermodynamics Integration and Solvated Interaction Energy Method. Chem. Phys. Lett. 2018, 706, 400-408.

38. Yang, Q.; Hu, Z.; Zhu, S.; Ma, R.; Ma, H.; Ma, Z.; Wan, H.; Zhu, T.; Jiang, Z.; Liu, W.; Jiao, L.; Sun, H.; Liang, Y.; Dai, H., Donor Engineering for NIR-II Molecular Fluorophores with Enhanced Fluorescent Performance. J. Am. Chem. Soc. 2018, 140, 1715-1724.

37. Xu, M.; Zhu, T.*; Zhang, J. Z. H.*, A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein. Front. Chem. 2018, 6, 189.

36. Wang, X.*; Li, Y.; Gao, Y.; Yang, Z.; Lu, C.; Zhu, T.*, A quantum mechanical computational method for modeling electrostatic and solvation effects of protein. Sci. Rep. 2018, 8, 5475.

35. Jin, X.; Zhu, T.; Zhang, J. Z. H.; He, X., Automated Fragmentation QM/MM Calculation of NMR Chemical Shifts for Protein-Ligand Complexes. Front. Chem. 2018, 6, 150.

2017

34. Xi, J.-B.; Fang, Y.-F.; Frett, B.; Zhu, M.-L.; Zhu, T.; Kong, Y.-N.; Guan, F.-J.; Zhao, Y.; Zhang, X.-W.; Li, H.-Y.; Ma, M.-L.; Hu, W., Structure-based design and synthesis of imidazo 1,2-a pyridine derivatives as novel and potent Nek2 inhibitors with in vitro and in vivo antitumor activities. Eur. J. Med. Chem. 2017, 126, 1083-1106.

33. Sun, Z.; Zhu, T.; Wang, X.; Mei, Y.; Zhang, J. Z. H., Optimization of convergence criteria for fragmentation methods. Chem. Phys. Lett. 2017, 687, 163-170.

32. Luo, Z.; Gao, Y.; Zhu, T.*; Zhang, J. Z.; Xia, F.*, Origins of Protons in C-H Bond Insertion Products of Phenols: Proton-Self-Sufficient Function via Water Molecules. J. Phys. Chem. A 2017, 121, 6523-6529.

31. Liu, L.; Zhao, F.; Liu, W.; Zhu, T.; Zhang, J. Z. H.; Chen, C.; Dai, Z.; Peng, H.; Huang, J.-L.; Hu, Q.; Bu, W.; Tian, Y., An Electrochemical Biosensor with Dual Signal Outputs: Toward Simultaneous Quantification of pH and O-2 in the Brain upon Ischemia and in a Tumor during Cancer Starvation Therapy. Angew. Chem. Int. Edit. 2017, 56, 10471-10475.

30. Li, S.; Zhu, A.; Zhu, T.; Zhang, J. Z. H.; Tian, Y., Single Biosensor for Simultaneous Quantification of Glucose and pH in a Rat Brain of Diabetic Model Using Both Current and Potential Outputs. Anal. Chem. 2017, 89, 6656-6662.

29. Jing, C.; Li, Z.; Jia, K.; Chen, C.; Liu, X.; Wang, B.; Hu, W.; Li, J.; Zhu, T*.; Dong, S.*, Discovery of Bisindole as a Novel Scaffold for Protein Tyrosine Phosphatase 1B Inhibitors. Arch. Pharm. 2017, 350, e1600173.

28. Huang, M.; Luo, Z.; Zhu, T.; Chen, J.; Zhang, J. Z.; Xia, F., A theoretical study of the substituent effect on reactions of amines, carbon dioxide and ethylene oxide catalyzed by binary ionic liquids. RSC Adv. 2017, 7, 51521-51527.

27. Gao, Y.; Zhang, C.; Wang, X.; Zhu, T.*, A test of AMBER force fields in predicting the secondary structure of alpha-helical and beta-hairpin peptides. Chem. Phys. Lett. 2017, 679, 112-118.

26. Duan, L. L.; Zhu, T.; Li, Y. C.; Zhang, Q. G.; Zhang, J. Z. H., Effect of polarization on HIV-1protease and fluoro-substituted inhibitors binding energies by large scale molecular dynamics simulations. Sci. Rep. 2017, 7, 42223.

25. Duan, L.; Zhu, T.; Ji, C.; Zhang, Q.; Zhang, J. Z. H., Direct folding simulation of helical proteins using an effective polarizable bond force field. Phys. Chem. Chem. Phys. 2017, 19, 15273-15284.

24. Dong, S.; Lei, Y.; Jia, S.; Gao, L.; Li, J.; Zhu, T.; Liu, S.; Hu, W., Discovery of core-structurally novel PTP1B inhibitors with specific selectivity containing oxindole-fused spirotetrahydrofurochroman by one-pot reaction. Bioorg. Med. Chem. Lett. 2017, 27, 1105-1108.

2016

23. Wang, Y.; Liu, J. F.; Zhu, T.; Zhang, L. J.; He, X.; Zhang, J. Z. H., Predicted PAR1 inhibitors from multiple computational methods. Chem. Phys. Lett. 2016, 659, 295-303.

22. Lv, F.; Chen, C.; Tang, Y.; Wei, J.; Zhu, T.*; Hu, W*., New peptide deformylase inhibitors design, synthesis and pharmacokinetic assessment. Bioorg. Med. Chem. Lett.  2016, 26, 3714-3718.

21. Liu, X.; Liu, J. F.; Zhu, T.; Zhang, L. J.; He, X.; Zhang, J. Z. H., PBSA_E: A PBSA-Based Free Energy Estimator for Protein-Ligand Binding Affinity. J. Chem. Inf. Model. 2016, 56, 854-861.

20. Liu, W.; Lu, Y.; Chai, X.; Liu, X.; Zhu, T.; Wu, X.; Fang, Y.; Liu, X.; Zhang, X.*, Antitumor activity of TY-011 against gastric cancer by inhibiting Aurora A, Aurora B and VEGFR2 kinases. J. Exp. Clin. Canc. Res. 2016, 35, 183.

19. Jin, X.; Zhu, T.; Zhang, J. Z. H.; He, X.*, A systematic study on RNA NMR chemical shift calculation based on the automated fragmentation QM/MM approach. RSC Adv. 2016, 6, 108590-108602.

18. Fang, Y.; Kong, Y.; Xi, J.; Zhu, M.; Zhu, T.; Jiang, T.; Hu, W.; Ma, M.*; Zhang, X.*, Preclinical activity of MBM-5 in gastrointestinal cancer by inhibiting NEK2 kinase activity. Oncotarget 2016, 7, 79313-79327.

2015

17. Zhu, T.; Zhang, J. Z. H.*; He, X.*, Quantum Calculation of Protein NMR Chemical Shifts Based on the Automated Fragmentation Method. In Advance in Structural Bioinformatics, Wei, D.; Xu, Q.; Zhao, T.; Dai, H., Eds. 2015; Vol. 827, pp 49-70.

16. Swails, J.; Zhu, T.; He, X.*; Case, D. A.*, AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules. J. Biomol. NMR  2015, 63, 125-139.

15. Liu, J.; Zhu, T*.; Wang, X.; He, X.*; Zhang, J. Z. H*., Quantum Fragment Based ab Initio Molecular Dynamics for Proteins. J. Chem. Theory Comput. 2015, 11, 5897-5905.

14. Chen, J.; Wang, X.; Zhu, T.*; Zhang, Q.; Zhang, J. Z. H., A Comparative Insight into Amprenavir Resistance of Mutations V32I, G48V, I50V, I54V, and I84V in HIV-1 Protease Based on Thermodynamic Integration and MM-PBSA Methods. J. Chem. Inf. Model. 2015, 55, 1903-1913.

2010-2014

13. Zhu, T.; Zhang, J. Z. H.; He, X.*, Correction of erroneously packed protein’s side chains in the NMR structure based on ab initio chemical shift calculations. Phys. Chem. Chem. Phys. 2014, 16, 18163-18169.

12. He, X.*; Zhu, T.; Wang, X.; Liu, J.; Zhang, J. Z. H.*, Fragment Quantum Mechanical Calculation of Proteins and Its Applications. Accounts Chem. Res. 2014, 47, 2748-2757.

11. Duan, L. L.; Zhu, T.; Zhang, Q. G.; Tang, B.*; Zhang, J. Z. H.*, Electronic polarization stabilizes tertiary structure prediction of HP-36. J. Mol. Model. 2014, 20.

10. Chen, J.; Chen, H.; Zhu, T.; Zhou, D.; Zhang, F.; Lao, X.*; Zheng, H.*, Asp120Asn mutation impairs the catalytic activity of NDM-1 metallo-beta-lactamase: experimental and computational study. Phys. Chem. Chem. Phys. 2014, 16, 6709-6716.

9. Zhu, T.; Zhang, J. Z. H.; He, X.*, Automated Fragmentation QM/MM Calculation of Amide Proton Chemical Shifts in Proteins with Explicit Solvent Model.  J. Chem. Theory Comput. 2013, 9, 2104-2114.

8. Zhu, T.; Xiao, X.; Ji, C.*; Zhang, J. Z. H.*, A New Quantum Calibrated Force Field for Zinc-Protein Complex.  J. Chem. Theory Comput. 2013, 9, 1788-1798.

7. Duan, L. L.; Zhu, T.; Mei, Y.*; Zhang, Q. G.; Tang, B.; Zhang, J. Z. H.*, An implementation of hydrophobic force in implicit solvent molecular dynamics simulation for packed proteins. J. Mol. Model. 2013, 19, 2605-2612.

6. Zhu, T.; He, X.*; Zhang, J. Z. H., Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation. Phys. Chem. Chem. Phys. 2012, 14, 7837-7845.

5. Zhu, T.; Hu, G. D.; Zhang, Q. G.*, Quasi-classical Trajectory Study of Reaction O (P-3) plus HCl (v=2; j=1, 6, 9) -> OH plus Cl. Chinese Phys. Lett. 2010, 27.

4. Zhu, T.; Hu, G.-D.; Chen, J. Z.; Liu, X. G.; Zhang, Q. G., Theoretical study of stereodynamics for reaction O(P-3)+HCl. Chinese Phys. B 2010, 19.

3. Zhu, T.; Hu, G.; Zhang, Q.*, Quasi-classical trajectory study of the reaction O(P-3) plus HCl -> OH + Cl and O(P-3) plus DCl -> OD plus Cl: Vector and scalar properties. J. Mol. Struc-Theochem 2010, 948, 36-42.

2. Liu, H.; Liu, X.; Zhu, T.; Sun, H.; Zhang, Q.*, THE EFFECT OF VIBRATIONAL EXCITATION OF THE REACTION O(P-3)+HCl -> OH plus Cl FOR THE (3)A ” ELECTRONIC STATES. J. Theor. Comput. Chem. 2010, 9, 1033-1042.

1. Hu, G.-D.; Zhu, T.; Zhang, S.-L.; Wang, D.; Zhang, Q.-G.*, Some insights into mechanism for binding and drug resistance of wild type and I50V V82A and I84V mutations in HIV-1 protease with GRL-98065 inhibitor from molecular dynamic simulations. Eur. J. Med. Chem. 2010, 45, 227-235.50