(67) X Zhang#, D Lyu#, S Li#, H Xiao, Y Qiu, K Xu, N Chen, L Deng*, H Huang*, R Wu*. Discovery of a SUCNR1 antagonist for potential treatment of diabetic nephropathy: In silico and in vitro studies. Int J Biol Macromol, 2024, 268, 131898.
(66) X Shen, T Zeng, N Chen, J Li*, R Wu*. NIMO: A Natural Product-Inspired Molecular Generative Model Based on Conditional Transformer. Molecules, 2024, 29, 1867.
(65) B Jin#, K Xu#, J Guo#, Y Ma, J Yang, N Chen, T Zeng, J Wang, J Liu, M Tian, Q Ma, H Zhang, R Peters, G Cui*, R Wu*, L Huang*. From Functional Plasticity of Two Diterpene Synthases (IrTPS2/IrKSL3a) to Enzyme Evolution. ACS Catal, 2024, 14, 2959-2970.
(64) F Zhang#, S Wang#, W Xiao#, M Yu, F Sha, R Wu*, Z Xiang*. Harnessing the catalytic plasticity of the ent-kaurene synthase from Bradyrhizobium japonicum to produce the ent-rosane and ent-pimarane scaffolds. Catal Sci Technol, 2024,14, 306-314.
(63) Y Luo#, X Ma#, Y Qiu#, Y Lu, S Shen, Y Li, H Gao, K Chen, J Zhou, T Hu, L Tu, H Zhao, D Li, F Leng, W Gao, T Jiang, C Liu*, L Huang*, R Wu*, Y Tong*. Structural and Catalytic Insight into the Unique Pentacyclic Triterpene Synthase TwOSC. Angew Chem Int Ed, 2023, 62, e202313429.
(61) Z Li#, L Zhang#, K Xu#, Y Jiang, J Du, X Zhang, L Meng, Q Wu, L Du, X Li, Y Hu, Z Xie, X Jiang, Y Tang, R Wu*, R Guo*, S Li*. Molecular insights into the catalytic promiscuity of a bacterial diterpene synthase. Nat Commun, 2023, 14, 4001.
(60) F Zhang#, Y Wang#, J Yue, R Zhang, Y Hu, R Huang, A Ji, B. Hess Jr., Z Liu*, L Duan*, R Wu*. Discovering a uniform functional trade-off of the CBC-type 2,3-oxidosqualene cyclases and deciphering its chemical logic. Sci Adv, 2023, 9, eadh1418.
(59) T Lou#, A Li#, H Xu#, J Pan#, B Xing, R Wu*, J Dickschat*, D Yang*, M Ma*. Structural Insights into Three Sesquiterpene Synthases for the Biosynthesis of Tricyclic Sesquiterpenes and Chemical Space Expansion by Structure-Based Mutagenesis. J Am Chem Soc, 2023, 145, 8474–8485.
(58) N Chen#, R Zhang#, T Zeng#, X Zhang, R Wu*. Developing TeroENZ and TeroMAP modules for the terpenome research platform TeroKit. Database, 2023, 2023, baad020.
(57) Y Li, R Zhang, Y Song, H Xie*, R Wu*. A DFT study of the endo-selectivity mechanism of the Diels–Alder reaction in lindenane dimeric sesquiterpene synthesis promoted by pyridines. Phys Chem Chem Phys, 2023, 25, 3772-3779.
(55) S Zheng#, T Zeng#, C Li, B Chen, Connor W. Coley, Y Yang*, R Wu*. Deep learning driven biosynthetic pathways navigation for natural products with BioNavi-NP. Nat Commun, 2022, 13, 3342.
(53) W Zha#, F Zhang#, J Shao, X Ma, J Zhu, P Sun, R Wu*, J Zi*. Rationally engineering santalene synthase to readjust the component ratio of sandalwood oil. Nat Commun, 2022, 13, 2508.
(52) T Zeng#, Y Chen#, Y Jian, F Zhang, R Wu*. Chemotaxonomic Investigation of Plant Terpenoids with an Established Database (TeroMOL). New Phytol, 2022, 235, 662-673.
(51) M Liang#, F Zhang#, J Xu, X Wang, R Wu*, Z Xue*. A conserved mechanism affecting hydride shifting and deprotonation in the synthesis of hopane triterpenes as compositions of wax in oat. Proc Natl Acad Sci, 2022, 119, e2118709119.
(50) J Zhuang#, F Zhang#, X Tang, C Liu, M Huang, H Xie*, R Wu*. Insights into the Enzymatic Catalytic Mechanism of bCinS: The Importance of Protein Conformational Change. Catal Sci Technol, 2022, 12, 1651-1662.
(49) Y Wang#, H Xu#, J Zhou#, X Chen, Y Zhuang, W Liu, Celik E, G Chen, D Hu, H Gao, R Wu*, P Sun*, J Dickschat*. Catalytic Role of Carbonyl Oxygens and Water in Selinadiene Synthase. Nat Catal, 2022, 5, 128-135.
(48) W He#, D Liang#, K Wang, N Lv, H Diao, R Wu*. AromTool: Predicting Aromatic Stacking Energy Using an Atomic Neural Network Model. Phys Chem Chem Phys, 2021, 23, 16044-16052.
(47) Y Qiu, H Diao, Y Zheng, R Wu*. Multiscale Simulations on the Catalytic Plasticity of CYP76AH1. Front Chem, 2021, 9, 689731.
(46) X Tang, F Zhang, T Zeng, W Li, S Yin*, R Wu*. Enzymatic Plasticity Inspired by the Diterpene Cyclase CotB2. ACS Chem Biol, 2020, 15, 2820-2832.
(45) S Wu#, F Zhang#, W Xiong, Molnár I, J Liang, A Ji, Y Li, C Wang, S Wang, Z Liu*, R Wu*, L Duan*. An Unexpected Oxidosqualene Cyclase Active Site Architecture in the Iris tectorum Multifunctional α-Amyrin Synthase. ACS Catal, 2020, 10, 9515-9520.
(44) K Wang#, N Lyu#, H Diao, S Jin, T Zeng, Y Zhou*, R Wu*. GM-DockZn: A Geometry Matching based Docking Algorithm for Zinc Proteins. Bioinformatics, 2020, 36, 4004-4011.
(43) T Zeng#, Z Liu#, J Zhuang, Y Jiang, W He, H Diao, N Lv, Y Jian, D Liang, Y Qiu, R Zhang, F Zhang, X Tang, R Wu*. TeroKit: A Database-Driven Web Server for Terpenome Research. J Chem Inf Model, 2020, 60, 2082-2090.
(42) J Liang#, Y Huang#, Q Zhou#, Y Gao, Z Li, D Wu, S Yu, L Guo, Z Chen, L Huang, S Liang, X He*, R Wu*, H Luo*. Discovery and Optimization of α-Mangostin Derivatives as Novel PDE4 Inhibitors for the Treatment of Vascular Dementia. J Med Chem, 2020, 63, 3370−3380.
(41) H Diao#, N Chen#, K Wang, F Zhang, Y Wang*, R Wu*. Biosynthetic Mechanism of Lanosterol: A Completed Story. ACS Catal, 2020, 10, 2157-2168.
(40) F Zhang#, T An#, X Tang, J Zi*, H Luo*, R Wu*. Enzyme Promiscuity versus Fidelity in Two Sesquiterpene Cyclases (TEAS versus ATAS). ACS Catal, 2020, 10, 1470-1484.
(38) H Liu#, F Zhang#, K Wang, X Tang, R Wu*. Conformational dynamics and allosteric effect modulated by the unique zinc-binding motif in class IIa HDACs.Phys Chem Chem Phys, 2019, 21, 12173-12183.
(37) Y Wang, F Zhang, H Diao, R Wu*. The Covalent Inhibition Mechanism of Antidiabetic Drugs--Vildagliptin vs Saxagliptin. ACS Catal, 2019, 9, 2292-2302.
(36) M Hu#, J Zhou#, W Luo, S Chen, Z Huang, R Wu*, J Tan*. Development of a Smart Fluorescent Sensor That Specifically Recognizes the c-MYC G-Quadruplex. Anal Chem, 2019, 91, 2480-2487.
(35) F Zhang, Y Wang, X Tang, R Wu*. Catalytic promiscuity of the non-native FPP substrate in the TEAS enzyme: non-negligible flexibility of the carbocation intermediate. Phys Chem Chem Phys, 2018, 20, 15061-15073.
(34) N Chen, F Zhang, R Wu*, B. Hess Jr.*. Biosynthesis of Spinosyn A: a [4+2] or [6+4] Cycloaddition? ACS Catal, 2018, 8, 2353-2358.
(33) Y Wang, F Zhang, J Zhou, H Xie, R Wu*. Reply to Comment on "Substrate Folding Modes in Trichodiene Synthase: A Determinant of Chemo- and Stereoselectivity". ACS Catal, 2018, ACS Catal. 2018, 8, 1363−1370.
(32) C Cheng, H Diao, F Zhang, Y Wang, K Wang*, R Wu*. Deciphering the Mechanisms of Selective inhibition for the tandem BD1/BD2 in the BET-bromodomain family. Phys Chem Chem Phys, 2017, 19, 23934-23941.
(31) J Zhou#, Y Huang#, C Cheng, K Wang, R Wu*. Intrinsic Dynamics of the Binding Rail and Its Allosteric Effect in the Class I Histone Deacetylases.J Chem Inf Model, 2017, 57, 2309-2320.
(30) Y Wang, H Xie, J Zhou, F Zhang, R Wu*. Substrate Folding Modes in Trichodiene Synthase: A Determinant of Chemo- and Stereoselectivity. ACS Catal, 2017, 7, 5841-5846.
(29) F Zhang#, N Chen#, J Zhou, R Wu*. Protonation-Dependent Diphosphate Cleavage in FPP Cyclases and Synthases.ACS Catal, 2016, 6, 6918-6929.
(27) F Zhang, N Chen, R Wu*. Molecular Dynamics Simulations Elucidate Conformational Dynamics Responsible for the Cyclization Reaction in TEAS. J Chem Inf Model, 2016, 56, 877-885.
(25) W Gong, R Wu*, Y Zhang*. Thiol versus Hydroxamate as Zinc Binding Group in HDAC Inhibition: An ab initio QM/MM Molecular Dynamics Study. J Comput Chem, 2015, 36, 2228-2235.
(22) N Chen#, Y Zhao#, J Lu, R Wu*, Z Cao*. Mechanistic Insights into the Rate-Limiting Step in Purine-Specific Nucleoside Hydrolase. J Chem Theory Comput, 2015, 11, 3180-3188.
(21) X Li, G Luo*, K Fang, J Zhou, Q Zhao, R Wu*. Photocatalytic hydrogen generation based on noble-metal-free BODIPY or Aza-BODIPY organic dyes as photosensitizers. Scientia Sinica Chimica, 2015, 45, 843-854.
(20) J Zhou, X Wang, M Kuang, L Wang, H Luo, Y Mo*,R Wu*. Protonation-Triggered Carbon-Chain Elongation in Geranyl Pyrophosphate Synthase (GPPS).ACS Catal, 2015, 5, 4466-4478.
(19) J Zhou, R Wu*, B Wang, Z Cao*, H Yan, Y Mo*. Proton-Shuttle-Assisted Heterolytic Carbon–Carbon Bond Cleavage and Formation. ACS Catal, 2015, 5, 2805-2813.
(18) J Zhou, M Li, N Chen, S Wang, H Luo, Y Zhang*, R Wu*. Computational Design of a Time-Dependent Histone Deacetylase 2 Selective Inhibitor. ACS Chem Biol, 2015, 10, 687-692.
(17) J Zhou, H Xie, Z Liu, H Luo, R Wu*. Structure−Function Analysis of the Conserved Tyrosine and Diverse π-Stacking among Class I Histone Deacetylases: A QM (DFT)/MM MD Study. J Chem Inf Model, 2014, 54, 3162-3171.
(16) Y Zhao#, N Chen#, R Wu*, Z Cao*. A QM/MM MD study of the pH-dependent ring-opening catalysis and lid motif flexibility in glucosamine 6-phosphate deaminase. Phys Chem Chem Phys, 2014, 16, 18406-18417.
(15) Z Li, Y Wu, L Feng, R Wu*, H Luo*. Ab Initio QM/MM Study Shows a Highly Dissociated SN2 Hydrolysis Mechanism for the cGMP-Specific Phosphodiesterase-5. J Chem Theory Comput, 2014, 10, 5448-5457.
(14) Z Liu#, J Zhou#, R Wu*, J Xu*. Mechanism of Assembling Isoprenoid Building Blocks 1. Elucidation of the Structural Motifs for Substrate Binding in Geranyl Pyrophosphate Synthase. J Chem Theory Comput, 2014, 10, 5057-5067.
(13) N Chen, J Zhou, J Li, J Xu*, R Wu*. Concerted Cyclization of Lanosterol C-Ring and D-Ring Under Human Oxidosqualene Cyclase Catalysis: An ab Initio QM/MM MD Study.J Chem Theory Comput, 2014, 10, 1109-1120.
(12) R Wu#, Z Chen#, Q Han, T Lin, J Zhou, G Tang, S Yin*. Determination of the Absolute Stereochemistry of Two New Aristophyllene Sesquiterpenes: A Combined Theoretical and Experimental Investigation. Chirality, 2014, 26, 189-193.
(11) J Zhang#, H Tian#, N Chen, X Bai, J Li, R Zhang, R Wu*, R Jiang*. Caesalpinimin A, a novel rearranged furanoditerpene with an unprecedented carbon skeleton from the seeds of Caesalpinia minax Hance. RSC Adv, 2014, 4, 7440-7443.
(9) R Wu, W Gong, T Liu, Y Zhang, Z Cao*. A QM/MM Molecular Dynamics Study of Purine-Specific Nucleoside Hydrolase. J Phys Chem B, 2012, 116, 1984-1991.
(8) R Wu, Z Cao*, Y Zhang*. Computational Simulations of Zinc Enzyme: Challenges and Recent Advances. (Review) Progress in Chemistry, 2012, 24, 1175-1184.
(7) R Wu, Z Lu, Z Cao*, Y Zhang*. Zinc Chelation with Hydroxamate in Histone Deacetylases Modulated by Water Access to the Linker Binding Channel. J Am Chem Soc, 2011, 133, 6110-6113.
(6) R Wu, Z Lu, Z Cao, Y Zhang*. A Transferable Non-bonded Pairwise Force Field to Model Zinc Interactions in Metalloproteins. J Chem Theory Comput, 2011, 7, 433-443.
(5) R Wu, S Wang, N Zhou, Z Cao, Y Zhang*. A Proton-Shuttle Reaction Mechanism for Histone Deacetylase 8 and the Catalytic Role of Metal Ions. J Am Chem Soc, 2010, 132, 9471-9479.
(4) R Wu, P Hu, S Wang, Z Cao, Y Zhang*. Flexibility of Catalytic Zinc Coordination in Thermolysin and HDAC8: A Born-Oppenheimer ab initio QM/MM Molecular Dynamics Study. J Chem Theory Comput, 2010, 6, 337-343.
(3) R Wu, H Xie, Y Mo, Z Cao*. Broad Substrate Specificity and Catalytic Mechanism of Pseudomonas stutzeri L-Rhamnose Isomerase: Insights from QM/MM Molecular Dynamics Simulations. J Phys Chem A, 2009, 113, 11595-11603.
(2) R Wu, H Xie, Z Cao*, Y Mo. Combined Quantum Mechanics/Molecular Mechanics Study on the Reversible Isomerization of Glucose and Fructose Catalyzed by Pyrococcus furiosus Phosphoglucose Isomerase.J Am Chem Soc, 2008, 130, 7022-7031.
(1) Wu, R. Z Cao*. QM/MM study of catalytic methyl transfer by the N5-glutamine SAM-dependent methyltransferase and its inhibition by the nitrogen analogue of coenzyme. J Comput Chem, 2008, 29, 350-357.
Others：
(16) P Xiong, R Wu, J Zhan*, Y Zhou*. Pairing a high-resolution statistical potential with a nucleobase-centric sampling algorithm for improving RNA model refinement. Nat Commun, 2021, 12, 2777.
(15) Q Huang, Y Zhong, B Li, S Ouyang, L Deng, J Mo, S Shi, N Lv, R Wu, P Liu, W Hu, X Zhang*, Y Wang*. Structure-based discovery of potent and selective small-molecule inhibitors targeting signal transducer and activator of transcription 3 (STAT3). Eur J Med Chem, 2021, 221, 113525.
(14) J Zhuang, F Zhang, J Zhou*, W Deng*, R Wu. Residue-Orientation-Dependent Dynamics and Selectivity of Active Pocket in Microbe Class I Terpene Cyclases. J Chem Inf Model, 2020, 60, 4985-4994.
(13) J Shen, T Zhang, S Zhu, J. M Sun, L Tong, M Lai, R Zhang, W Xu, R Wu, J Ding, Yun C. H.*, H Xie*, X Lu*, K Ding*. Structure-Based Design of 5-Methylpyrimidopyridone Derivatives as New Wild-Type Sparing Inhibitors of the Epidermal Growth Factor Receptor Triple Mutant (EGFR(L858R/T790M/C797S)). J Med Chem, 2019, 62, 7302-7308.
(12) Z Kang, Y Wang, D Zhang, R Wu, X Xu*, W Hu*. Asymmetric Counter-Anion-Directed Aminomethylation: Synthesis of Chiral β-Amino Acids via Trapping of an Enol Intermediate. J Am Chem Soc, 2019, 141, 1473-1478.
(11) H Tian, L Ruan, T Yu, N Chen, R Wu, L Wang*, R Jiang*, W Ye*. Bufospirostenin A and Bufogargarizin C, Steroids with Rearranged Skeletons from the Toad Bufo bufo gargarizans. J Nat Prod, 2017, 80, 1182–1186.
(10) J Li, Y Wang, Y Yu, R Wu,. J Wang*, G Lu*. Copper-Catalyzed Remote C–H Functionalizations of Naphthylamides through a Coordinating Activation Strategy and Single-Electron-Transfer (SET) Mechanism. ACS Catal, 2017, 7, 2661-2667.
(9) Y Lu, M Kuang, G Hu, R Wu,. J Wang*, L Liu, Y Lin. Loddigesiinols G-J: α-glucosidase inhibitors from Dendrobium loddigesii. Molecules, 2014, 19, 8544-8555.
(8) Z Pan, J Zhou, J Xia, K Fang, R Wu, G Luo*. A simple BODIPY-aniline-based fluorescent chemosensor as multiple logic operations for the detection of pH and CO2 gas. Dalton Transactions, 2014, 43, 8499-8507.
(7) H Ge, J Liu, W Zhao, Y Wang, Q He, R Wu, J Xu*, D Li*. Mechanistic studies for tri-targeted inhibition of enzymes involved in cholesterol biosynthesis by green tea polyphenols. Org Biomol Chem, 2014, 12, 4941-4951.
(6) H Ge, Y Wang, C Li, N Chen, Y Xie, M Xu, Y He, X Gu, R Wu, Q Gu, L Zeng, J Xu*. Molecular Dynamics-Based Virtual Screening: Accelerating the Drug Discovery Process by High-Performance Computing J Chem Inf
Model, 2013, 53, 2757-2764.
(5) F Lu, Q Gu, R Wu, J Xu*. A Structure-Similarity-Based Software for the Cardiovascular Toxicity Prediction of Traditional Chinese Medicine. Bioinformation, 2012, 8, 110-113.
(4) G Luo, R Wu, D Sun, J Chen, N Zhang, R Huang*, L Lin, L Zheng. J Mol Struc, 2009, 930, 9.
(3) X Zhang, R Wu, L Song, M Lin, Z Cao, W Wu, Y Mo*. J Comput Chem, 2009, 30, 2388.
(2) H Xie, R Wu, Z Zhou, Z Cao*. J Phys Chem B, 2008, 112, 11435.
(1) H Xie, R Wu, F Xia, Z Cao*. J Comput Chem, 2008, 29, 2025.