People_

Mr Duan Ni

Details

Member of The Centre for Drug Discovery Innovation

Member of the Charles Perkins Centre

Publications

By Type

Expand all

Journals

Taitz, J., Tan, J., Ni, D., Potier, C., Grau, G., Nanan, R., Macia, L. (2025). Antibiotic-mediated dysbiosis leads to activation of inflammatory pathways. Frontiers in Immunology, 15, 1493991. [More Information]
Ni, D., Senior, A., Raubenheimer, D., Simpson, S., Nanan, R. (2025). High-Fat and Low-Carbohydrate Dietary Environments Are Linked to Reduced Idiopathic Epilepsy Incidence and Prevalence. Annals of Clinical and Translational Neurology. [More Information]
Ni, D., Nanan, R. (2025). Multi-organ transcriptomic atlas reveals hallmarks of labour. Clinical and Translational Medicine, 15(2), e70208. [More Information]
Reyes, J., Ni, D., Santner-Nanan, B., Pinget, G., Kraftova, L., Ashhurst, T., Marsh-Wakefield, F., Wishart, C., Tan, J., Hsu, P., King, N., Macia, L., Nanan, R. (2024). A unique human cord blood CD8+CD45RA+CD27+CD161+ T-cell subset identified by flow cytometric data analysis using Seurat. Immunology, 173(1), 106-124. [More Information]
Ni, D., Reyes, J., Nanan, B., Pinget, G., Kraftova, L., Ashhurst, T., Marshwakefield, F., Wishart, C., Tan, J., Hsu, P., King, N., Macia, L., Nanan, R. (2024). A unique human cord blood CD8+CD45RA+CD27+CD161+T cell subset identified by flow cytometric data analysis using Seurat. European Journal of Immunology, 54(Suppl 1), 714-714. [More Information]
Ni, D., Tan, J., Macia, L., Nanan, R. (2024). Breastfeeding is associated with enhanced intestinal gluconeogenesis in infants. BMC Medicine, 22(1), 106. [More Information]
Ni, D., Senior, A., Raubenheimer, D., Simpson, S., Macia, L., Nanan, R. (2024). Global associations of macronutrient supply and asthma disease burden. European Journal of Immunology, 54(Suppl 1), 566-566. [More Information]
Ni, D., Senior, A., Raubenheimer, D., Simpson, S., Macia, L., Nanan, R. (2024). Global associations of macronutrient supply and asthma disease burden. Allergy, 79(7), 1989-1991. [More Information]
Ni, D., Nanan, R. (2024). Global Modelling Links Maternal Hypertensive Disorders to Early Childhood Allergic Disease Burden. Clinical and Experimental Allergy, 54(12), 1024-1026. [More Information]
Ni, D., Tan, J., Reyes, J., Senior, A., Andrews, C., Taitz, J., Potier, C., Wishart, C., Spiteri, A., Piccio, L., King, N., Simpson, S., Nanan, R., Macia, L. (2024). High fat low carbohydrate is linked to protection against the development of CNS autoimmunity. European Journal of Immunology, 54(1), 230-230. [More Information]
Ni, D., Senior, A., Tan, J., Macia, L., Nanan, R. (2024). How nutritional landscapes impact food allergy. European Journal of Immunology, 54(Suppl 1), 567-567. [More Information]
Ni, D., Senior, A., Tan, J., Macia, L., Nanan, R. (2024). Linking Macronutrient Composition of Common Allergenic Foods to European and North American Food Allergy Prevalence. Clinical and Experimental Allergy. [More Information]
Abeysekera, M., Ni, D., Gilbert, L., Hibbert, E., Nanan, R. (2024). Linking the reversal of gestational insulin resistance to postpartum depression. BMC Medicine, 22(1), 433. [More Information]
Tan, J., Potier-Villette, C., Ni, D., Hoeckh, M., Taitz, J., Simpson, S., Nanan, R., Macia, L. (2024). Succinate induces a Th2 environment in the small intestine but does not exacerbate food allergy. Allergy, 79(10), 2853-2855. [More Information]
Nanan, R., Ni, D. (2024). The maternal and fetal metabolic and immune landscape of gestational diabetes. Diabetologia, 67(Suppl 1), S218-S218. [More Information]
Zha, J., Li, Q., Liu, X., Lin, W., Wang, T., Wei, J., Zhang, Z., Lu, X., Wu, J., Ni, D., et al (2023). AlloReverse: Multiscale understanding among hierarchical allosteric regulations. Nucleic Acids Research, 51(W1), W33-W38. [More Information]
Wali, J., Ni, D., Facey, H., Dodgson, T., Pulpitel, T., Senior, A., Raubenheimer, D., Macia, L., Simpson, S. (2023). Determining the metabolic effects of dietary fat, sugars and fat-sugar interaction using nutritional geometry in a dietary challenge study with male mice. Nature Communications, 14(1). [More Information]
Spiteri, A., Wishart, C., Ni, D., Viengkhou, B., Macia, L., Hofer, M., King, N. (2023). Temporal tracking of microglial and monocyte single-cell transcriptomics in lethal favivirus infection. Springer Nature, 11(60). [More Information]
Ni, D., Chai, Z., Wang, Y., Li, M., Yu, Z., Liu, Y., Lu, S., Zhang, J. (2022). Along the allostery stream: Recent advances in computational methods for allosteric drug discovery. Computational Molecular Science, 12(4). [More Information]
He, X., Du, K., Wang, Y., Fan, J., Li, M., Ni, D., Lu, S., Bian, X., Liu, Y. (2022). Autopromotion of K-Ras4B Feedback Activation Through an SOS-Mediated Long-Range Allosteric Effect. Frontiers in Molecular Biosciences, 9. [More Information]
Ni, D., Liu, Y., Kong, R., Yu, Z., Lu, S., Zhang, J. (2022). Computational elucidation of allosteric communication in proteins for allosteric drug design. Drug Discovery Today, 27(8), 2226-2234. [More Information]
Tan, J., Ni, D., Taitz, J., Pinget, G., Read, M., Senior, A., Wali, J., Elnour, R., Shanahan, E., Wu, H., Chadban, S., Nanan, R., King, N., Grau, G., Simpson, S., Macia, L. (2022). Dietary protein increases T-cell-independent sIgA production through changes in gut microbiota-derived extracellular vesicles. Nature Communications, 13(1), 4336-1-4336-15. [More Information]
Pinget, G., Tan, J., Ni, D., Taitz, J., Daien, C., Mielle, J., Moore, R., Stanley, D., Simpson, S., King, N., Macia, L. (2022). Dysbiosis in imiquimod-induced psoriasis alters gut immunity and exacerbates colitis development. Cell Reports, 40(7). [More Information]
Zhuang, H., Fan, X., Ji, D., Wang, Y., Fan, J., Li, M., Ni, D., Lu, S., Li, X., Chai, Z. (2022). Elucidation of the conformational dynamics and assembly of Argonaute–RNA complexes by distinct yet coordinated actions of the supplementary microRNA. Computational and Structural Biotechnology Journal, 20, 1352-1365. [More Information]
Liu, P., Cong, X., Liao, S., Jia, X., Wang, X., Dai, W., Zhai, L., Zhao, L., Ji, J., Ni, D., et al (2022). Global identification of phospho-dependent SCF substrates reveals a FBXO22 phosphodegron and an ERK-FBXO22-BAG3 axis in tumorigenesis. Cell Death and Differentiation, 29(1). [More Information]
Ni, D., Tan, J., Niewold, P., Spiteri, A., Pinget, G., Stanley, D., King, N., Macia, L. (2022). Impact of Dietary Fiber on West Nile Virus Infection. Frontiers in Immunology, 13, 784486-1-784486-9. [More Information]
Zhang, H., Ni, D., Fan, J., Li, M., Zhang, J., Hua, C., Nussinov, R., Lu, S. (2022). Markov State Models and Molecular Dynamics Simulations Reveal the Conformational Transition of the Intrinsically Disordered Hypervariable Region of K-Ras4B to the Ordered Conformation. Journal of Chemical Information and Modeling, 62(17), 4222-4231. [More Information]
Zhang, H., Zhu, M., Li, M., Ni, D., Wang, Y., Deng, L., Du, K., Lu, S., Shi, H., Cai, C. (2022). Mechanistic Insights Into Co-Administration of Allosteric and Orthosteric Drugs to Overcome Drug-Resistance in T315I BCR-ABL1. Frontiers in Pharmacology, 13. [More Information]
Spiteri, A., Ni, D., Ling, Z., Macia, L., Campbell, I., Hofer, M., King, N. (2022). PLX5622 Reduces Disease Severity in Lethal CNS Infection by Off-Target Inhibition of Peripheral Inflammatory Monocyte Production. Frontiers in Immunology, 13, 851556. [More Information]
Zhang, Q., Chen, Y., Ni, D., Huang, Z., Wei, J., Feng, L., Su, J., Wei, Y., Ning, S., Yang, X., et al (2022). Targeting a cryptic allosteric site of SIRT6 with small-molecule inhibitors that inhibit the migration of pancreatic cancer cells. Acta Pharmaceutica Sinica B, 12(2), 876-889. [More Information]
Shi, Y., Cao, S., Ni, D., Fan, J., Lu, S., Xue, M. (2022). The Role of Conformational Dynamics and Allostery in the Control of Distinct Efficacies of Agonists to the Glucocorticoid Receptor. Frontiers in Molecular Biosciences, 9. [More Information]
Tan, J., Taitz, J., Sun, S., Langford, L., Ni, D., Macia, L. (2022). Your Regulatory T Cells Are What You Eat: How Diet and Gut Microbiota Affect Regulatory T Cell Development. Frontiers in Nutrition, 9. [More Information]
Zhang, H., Zhao, B., Han, W., Sun, Y., Yang, P., Chen, Y., Ni, D., Zhang, J., Yin, D. (2021). Acetylation of calmodulin regulates synaptic plasticity and fear learning. Journal of Biological Chemistry, 297(3). [More Information]
Lu, S., He, X., Yang, Z., Chai, Z., Zhou, S., Wang, J., Rehman, A., Ni, D., Pu, J., Sun, J., et al (2021). Activation pathway of a G protein-coupled receptor uncovers conformational intermediates as targets for allosteric drug design. Nature Communications, 12(1). [More Information]
Li, X., Wang, C., Peng, T., Chai, Z., Ni, D., Liu, Y., Zhang, J., Chen, T., Lu, S. (2021). Atomic-scale insights into allosteric inhibition and evolutional rescue mechanism of Streptococcus thermophilus Cas9 by the anti-CRISPR protein AcrIIA6. Computational and Structural Biotechnology Journal, 19, 6108-6124. [More Information]
Chen, H., Yao, J., Bao, R., Dong, Y., Zhang, T., Du, Y., Wang, G., Ni, D., Xun, Z., Niu, X., et al (2021). Cross-talk of four types of RNA modification writers defines tumor microenvironment and pharmacogenomic landscape in colorectal cancer. Molecular Cancer, 20(1), 29. [More Information]
Tan, J., Ni, D., Wali, J., Cox, D., Pinget, G., Taitz, J., Daien, C., Senior, A., Read, M., Simpson, S., King, N., Macia, L. (2021). Dietary carbohydrate, particularly glucose, drives B cell lymphopoiesis and function. iScience, 24(8), 102835. [More Information]
Ni, D., Wei, J., He, X., Rehman, A., Li, X., Qiu, Y., Pu, J., Lu, S., Zhang, J. (2021). Discovery of cryptic allosteric sites using reversed allosteric communication by a combined computational and experimental strategy. Chemical Science, 12(1), 464-476. [More Information]
Daien, C., Tan, J., Audo, R., Mielle, J., Quek, L., Krycer, J., Angelatos, A., Duraes, M., Pinget, G., Ni, D., Amian, M., Sierro, F., Parmar, A., Hoque, S., Gosby, A., Simpson, S., Ribeiro, R., Macia, L., et al (2021). Gut-derived acetate promotes B10 cells with antiinflammatory effects. JCI Insight, 6(7), e144156. [More Information]
Fan, J., Liu, Y., Kong, R., Ni, D., Yu, Z., Lu, S., Zhang, J. (2021). Harnessing Reversed Allosteric Communication: A Novel Strategy for Allosteric Drug Discovery. Journal of Medicinal Chemistry, 64(24), 17728-17743. [More Information]
Tan, J., Ni, D., Ribeiro, R., Pinget, G., Macia, L. (2021). How changes in the nutritional landscape shape gut immunometabolism. Nutrients, 13(3), 1-36. [More Information]
Li, X., Qi, Z., Ni, D., Lu, S., Chen, L., Chen, X. (2021). Markov state models and molecular dynamics simulations provide understanding of the nucleotide-dependent dimerization-based activation of lrrk2 roc domain. Molecules, 26(18). [More Information]
Lu, S., Chen, Y., Wei, J., Zhao, M., Ni, D., He, X., Zhang, J. (2021). Mechanism of allosteric activation of SIRT6 revealed by the action of rationally designed activators. Acta Pharmaceutica Sinica B, 11(5), 1355-1361. [More Information]
Rehman, A., Zhen, G., Zhong, B., Ni, D., Li, J., Nasir, A., Gabr, M., Rafiq, H., Wadood, A., Lu, S., et al (2021). Mechanism of zinc ejection by disulfiram in nonstructural protein 5A. Physical Chemistry Chemical Physics, 23(21), 12204-12215. [More Information]
Wang, Y., Ji, D., Lei, C., Chen, Y., Qiu, Y., Li, X., Li, M., Ni, D., Pu, J., Zhang, J., et al (2021). Mechanistic insights into the effect of phosphorylation on Ras conformational dynamics and its interactions with cell signaling proteins. Computational and Structural Biotechnology Journal, 19, 1184-1199. [More Information]
Wang, X., Ni, D., Liu, Y., Lu, S. (2021). Rational Design of Peptide-Based Inhibitors Disrupting Protein-Protein Interactions. Frontiers in Chemistry, 9, 682675. [More Information]
Qiu, Y., Wang, Y., Chai, Z., Ni, D., Li, X., Pu, J., Chen, J., Zhang, J., Lu, S., Lv, C., et al (2021). Targeting RAS phosphorylation in cancer therapy: Mechanisms and modulators. Acta Pharmaceutica Sinica B, 11(11), 3433-3446. [More Information]
Ni, D., Li, Y., Qiu, Y., Pu, J., Lu, S., Zhang, J. (2020). Combining Allosteric and Orthosteric Drugs to Overcome Drug Resistance. Trends In Pharmacological Sciences, 41(5), 336-348. [More Information]
Lu, S., Qiu, Y., Ni, D., He, X., Pu, J., Zhang, J. (2020). Emergence of allosteric drug-resistance mutations: new challenges for allosteric drug discovery. Drug Discovery Today, 25(1), 177-184. [More Information]
Zhang, H., He, X., Ni, D., Mou, L., Chen, X., Lu, S. (2020). How does the novel T315L mutation of breakpoint cluster region-abelson (BCR-ABL) kinase confer resistance to ponatinib: a comparative molecular dynamics simulation study. Journal of Biomolecular Structure and Dynamics, 38(1), 89-100. [More Information]
Li, X., Dai, J., Ni, D., He, X., Zhang, H., Zhang, J., Fu, Q., Liu, Y., Lu, S. (2020). Insight into the mechanism of allosteric activation of PI3Kα by oncoprotein K-Ras4B. International Journal of Biological Macromolecules, 144, 643-655. [More Information]
Liu, X., Lu, S., Song, K., Shen, Q., Ni, D., Li, Q., He, X., Zhang, H., Wang, Q., Chen, Y., et al (2020). Unraveling allosteric landscapes of allosterome with ASD. Nucleic Acids Research, 48(D1), D394-D401. [More Information]
He, X., Ni, D., Zhang, H., Li, X., Zhang, J., Fu, Q., Liu, Y., Lu, S. (2020). Zinc-mediated conformational preselection mechanism in the allosteric control of DNA binding to the zinc transcriptional regulator (ZitR). Scientific Reports, 10(1). [More Information]
Lu, S., He, X., Ni, D., Zhang, J. (2019). Allosteric Modulator Discovery: From Serendipity to Structure-Based Design. Journal of Medicinal Chemistry, 62(14), 6405-6421. [More Information]
Lu, S., Ni, D., Wang, C., He, X., Lin, H., Wang, Z., Zhang, J. (2019). Deactivation Pathway of Ras GTPase Underlies Conformational Substates as Targets for Drug Design. ACS Catalysis, 9(8), 7188-7196. [More Information]
Ni, D., Li, X., He, X., Zhang, H., Zhang, J., Lu, S. (2019). Drugging K-RasG12C through covalent inhibitors: Mission possible? Pharmacology and Therapeutics, 202, 1-17. [More Information]
Ni, D., Lu, S., Zhang, J. (2019). Emerging roles of allosteric modulators in the regulation of protein-protein interactions (PPIs): A new paradigm for PPI drug discovery. Medicinal Research Reviews, 39(6), 2314-2342. [More Information]
Wang, L., Zheng, G., Liu, X., Ni, D., He, X., Cheng, J., Lu, S. (2019). Molecular dynamics simulations provide insights into the origin of gleevec’s selectivity toward human tyrosine kinases. Journal of Biomolecular Structure and Dynamics, 37(10), 2733-2744. [More Information]
Xu, X., Chen, Y., Fu, Q., Ni, D., Zhang, J., Li, X., Lu, S. (2019). The chemical diversity and structure-based discovery of allosteric modulators for the PIF-pocket of protein kinase PDK1. Journal of Enzyme Inhibition and Medicinal Chemistry, 34(1), 361-374. [More Information]
Huang, M., Song, K., Liu, X., Lu, S., Shen, Q., Wang, R., Gao, J., Hong, Y., Li, Q., Ni, D., et al (2018). AlloFinder: A strategy for allosteric modulator discovery and allosterome analyses. Nucleic Acids Research, 46(W1), W451-W458. [More Information]
Ni, D., Liu, D., Zhang, J., Lu, S. (2018). Computational insights into the interactions between calmodulin and the c/nSH2 domains of p85α regulatory subunit of PI3Kα: Implication for PI3Kα activation by calmodulin. International Journal of Molecular Sciences, 19(1). [More Information]
Lu, S., Ji, M., Ni, D., Zhang, J. (2018). Discovery of hidden allosteric sites as novel targets for allosteric drug design. Drug Discovery Today, 23(2), 359-365. [More Information]
Ni, D., Song, K., Zhang, J., Lu, S. (2017). Molecular dynamics simulations and dynamic network analysis reveal the allosteric unbinding of monobody to H-Ras triggered by R135K mutation. International Journal of Molecular Sciences, 18(11). [More Information]

show 60 more

By Year

Expand all

2025

Taitz, J., Tan, J., Ni, D., Potier, C., Grau, G., Nanan, R., Macia, L. (2025). Antibiotic-mediated dysbiosis leads to activation of inflammatory pathways. Frontiers in Immunology, 15, 1493991. [More Information]
Ni, D., Senior, A., Raubenheimer, D., Simpson, S., Nanan, R. (2025). High-Fat and Low-Carbohydrate Dietary Environments Are Linked to Reduced Idiopathic Epilepsy Incidence and Prevalence. Annals of Clinical and Translational Neurology. [More Information]
Ni, D., Nanan, R. (2025). Multi-organ transcriptomic atlas reveals hallmarks of labour. Clinical and Translational Medicine, 15(2), e70208. [More Information]

2024

Reyes, J., Ni, D., Santner-Nanan, B., Pinget, G., Kraftova, L., Ashhurst, T., Marsh-Wakefield, F., Wishart, C., Tan, J., Hsu, P., King, N., Macia, L., Nanan, R. (2024). A unique human cord blood CD8+CD45RA+CD27+CD161+ T-cell subset identified by flow cytometric data analysis using Seurat. Immunology, 173(1), 106-124. [More Information]
Ni, D., Reyes, J., Nanan, B., Pinget, G., Kraftova, L., Ashhurst, T., Marshwakefield, F., Wishart, C., Tan, J., Hsu, P., King, N., Macia, L., Nanan, R. (2024). A unique human cord blood CD8+CD45RA+CD27+CD161+T cell subset identified by flow cytometric data analysis using Seurat. European Journal of Immunology, 54(Suppl 1), 714-714. [More Information]
Ni, D., Tan, J., Macia, L., Nanan, R. (2024). Breastfeeding is associated with enhanced intestinal gluconeogenesis in infants. BMC Medicine, 22(1), 106. [More Information]
Ni, D., Senior, A., Raubenheimer, D., Simpson, S., Macia, L., Nanan, R. (2024). Global associations of macronutrient supply and asthma disease burden. European Journal of Immunology, 54(Suppl 1), 566-566. [More Information]
Ni, D., Senior, A., Raubenheimer, D., Simpson, S., Macia, L., Nanan, R. (2024). Global associations of macronutrient supply and asthma disease burden. Allergy, 79(7), 1989-1991. [More Information]
Ni, D., Nanan, R. (2024). Global Modelling Links Maternal Hypertensive Disorders to Early Childhood Allergic Disease Burden. Clinical and Experimental Allergy, 54(12), 1024-1026. [More Information]
Ni, D., Tan, J., Reyes, J., Senior, A., Andrews, C., Taitz, J., Potier, C., Wishart, C., Spiteri, A., Piccio, L., King, N., Simpson, S., Nanan, R., Macia, L. (2024). High fat low carbohydrate is linked to protection against the development of CNS autoimmunity. European Journal of Immunology, 54(1), 230-230. [More Information]
Ni, D., Senior, A., Tan, J., Macia, L., Nanan, R. (2024). How nutritional landscapes impact food allergy. European Journal of Immunology, 54(Suppl 1), 567-567. [More Information]
Ni, D., Senior, A., Tan, J., Macia, L., Nanan, R. (2024). Linking Macronutrient Composition of Common Allergenic Foods to European and North American Food Allergy Prevalence. Clinical and Experimental Allergy. [More Information]
Abeysekera, M., Ni, D., Gilbert, L., Hibbert, E., Nanan, R. (2024). Linking the reversal of gestational insulin resistance to postpartum depression. BMC Medicine, 22(1), 433. [More Information]
Tan, J., Potier-Villette, C., Ni, D., Hoeckh, M., Taitz, J., Simpson, S., Nanan, R., Macia, L. (2024). Succinate induces a Th2 environment in the small intestine but does not exacerbate food allergy. Allergy, 79(10), 2853-2855. [More Information]
Nanan, R., Ni, D. (2024). The maternal and fetal metabolic and immune landscape of gestational diabetes. Diabetologia, 67(Suppl 1), S218-S218. [More Information]

show 9 more

2023

Zha, J., Li, Q., Liu, X., Lin, W., Wang, T., Wei, J., Zhang, Z., Lu, X., Wu, J., Ni, D., et al (2023). AlloReverse: Multiscale understanding among hierarchical allosteric regulations. Nucleic Acids Research, 51(W1), W33-W38. [More Information]
Wali, J., Ni, D., Facey, H., Dodgson, T., Pulpitel, T., Senior, A., Raubenheimer, D., Macia, L., Simpson, S. (2023). Determining the metabolic effects of dietary fat, sugars and fat-sugar interaction using nutritional geometry in a dietary challenge study with male mice. Nature Communications, 14(1). [More Information]
Spiteri, A., Wishart, C., Ni, D., Viengkhou, B., Macia, L., Hofer, M., King, N. (2023). Temporal tracking of microglial and monocyte single-cell transcriptomics in lethal favivirus infection. Springer Nature, 11(60). [More Information]

2022

Ni, D., Chai, Z., Wang, Y., Li, M., Yu, Z., Liu, Y., Lu, S., Zhang, J. (2022). Along the allostery stream: Recent advances in computational methods for allosteric drug discovery. Computational Molecular Science, 12(4). [More Information]
He, X., Du, K., Wang, Y., Fan, J., Li, M., Ni, D., Lu, S., Bian, X., Liu, Y. (2022). Autopromotion of K-Ras4B Feedback Activation Through an SOS-Mediated Long-Range Allosteric Effect. Frontiers in Molecular Biosciences, 9. [More Information]
Ni, D., Liu, Y., Kong, R., Yu, Z., Lu, S., Zhang, J. (2022). Computational elucidation of allosteric communication in proteins for allosteric drug design. Drug Discovery Today, 27(8), 2226-2234. [More Information]
Tan, J., Ni, D., Taitz, J., Pinget, G., Read, M., Senior, A., Wali, J., Elnour, R., Shanahan, E., Wu, H., Chadban, S., Nanan, R., King, N., Grau, G., Simpson, S., Macia, L. (2022). Dietary protein increases T-cell-independent sIgA production through changes in gut microbiota-derived extracellular vesicles. Nature Communications, 13(1), 4336-1-4336-15. [More Information]
Pinget, G., Tan, J., Ni, D., Taitz, J., Daien, C., Mielle, J., Moore, R., Stanley, D., Simpson, S., King, N., Macia, L. (2022). Dysbiosis in imiquimod-induced psoriasis alters gut immunity and exacerbates colitis development. Cell Reports, 40(7). [More Information]
Zhuang, H., Fan, X., Ji, D., Wang, Y., Fan, J., Li, M., Ni, D., Lu, S., Li, X., Chai, Z. (2022). Elucidation of the conformational dynamics and assembly of Argonaute–RNA complexes by distinct yet coordinated actions of the supplementary microRNA. Computational and Structural Biotechnology Journal, 20, 1352-1365. [More Information]
Liu, P., Cong, X., Liao, S., Jia, X., Wang, X., Dai, W., Zhai, L., Zhao, L., Ji, J., Ni, D., et al (2022). Global identification of phospho-dependent SCF substrates reveals a FBXO22 phosphodegron and an ERK-FBXO22-BAG3 axis in tumorigenesis. Cell Death and Differentiation, 29(1). [More Information]
Ni, D., Tan, J., Niewold, P., Spiteri, A., Pinget, G., Stanley, D., King, N., Macia, L. (2022). Impact of Dietary Fiber on West Nile Virus Infection. Frontiers in Immunology, 13, 784486-1-784486-9. [More Information]
Zhang, H., Ni, D., Fan, J., Li, M., Zhang, J., Hua, C., Nussinov, R., Lu, S. (2022). Markov State Models and Molecular Dynamics Simulations Reveal the Conformational Transition of the Intrinsically Disordered Hypervariable Region of K-Ras4B to the Ordered Conformation. Journal of Chemical Information and Modeling, 62(17), 4222-4231. [More Information]
Zhang, H., Zhu, M., Li, M., Ni, D., Wang, Y., Deng, L., Du, K., Lu, S., Shi, H., Cai, C. (2022). Mechanistic Insights Into Co-Administration of Allosteric and Orthosteric Drugs to Overcome Drug-Resistance in T315I BCR-ABL1. Frontiers in Pharmacology, 13. [More Information]
Spiteri, A., Ni, D., Ling, Z., Macia, L., Campbell, I., Hofer, M., King, N. (2022). PLX5622 Reduces Disease Severity in Lethal CNS Infection by Off-Target Inhibition of Peripheral Inflammatory Monocyte Production. Frontiers in Immunology, 13, 851556. [More Information]
Zhang, Q., Chen, Y., Ni, D., Huang, Z., Wei, J., Feng, L., Su, J., Wei, Y., Ning, S., Yang, X., et al (2022). Targeting a cryptic allosteric site of SIRT6 with small-molecule inhibitors that inhibit the migration of pancreatic cancer cells. Acta Pharmaceutica Sinica B, 12(2), 876-889. [More Information]
Shi, Y., Cao, S., Ni, D., Fan, J., Lu, S., Xue, M. (2022). The Role of Conformational Dynamics and Allostery in the Control of Distinct Efficacies of Agonists to the Glucocorticoid Receptor. Frontiers in Molecular Biosciences, 9. [More Information]
Tan, J., Taitz, J., Sun, S., Langford, L., Ni, D., Macia, L. (2022). Your Regulatory T Cells Are What You Eat: How Diet and Gut Microbiota Affect Regulatory T Cell Development. Frontiers in Nutrition, 9. [More Information]

show 11 more

2021

Zhang, H., Zhao, B., Han, W., Sun, Y., Yang, P., Chen, Y., Ni, D., Zhang, J., Yin, D. (2021). Acetylation of calmodulin regulates synaptic plasticity and fear learning. Journal of Biological Chemistry, 297(3). [More Information]
Lu, S., He, X., Yang, Z., Chai, Z., Zhou, S., Wang, J., Rehman, A., Ni, D., Pu, J., Sun, J., et al (2021). Activation pathway of a G protein-coupled receptor uncovers conformational intermediates as targets for allosteric drug design. Nature Communications, 12(1). [More Information]
Li, X., Wang, C., Peng, T., Chai, Z., Ni, D., Liu, Y., Zhang, J., Chen, T., Lu, S. (2021). Atomic-scale insights into allosteric inhibition and evolutional rescue mechanism of Streptococcus thermophilus Cas9 by the anti-CRISPR protein AcrIIA6. Computational and Structural Biotechnology Journal, 19, 6108-6124. [More Information]
Chen, H., Yao, J., Bao, R., Dong, Y., Zhang, T., Du, Y., Wang, G., Ni, D., Xun, Z., Niu, X., et al (2021). Cross-talk of four types of RNA modification writers defines tumor microenvironment and pharmacogenomic landscape in colorectal cancer. Molecular Cancer, 20(1), 29. [More Information]
Tan, J., Ni, D., Wali, J., Cox, D., Pinget, G., Taitz, J., Daien, C., Senior, A., Read, M., Simpson, S., King, N., Macia, L. (2021). Dietary carbohydrate, particularly glucose, drives B cell lymphopoiesis and function. iScience, 24(8), 102835. [More Information]
Ni, D., Wei, J., He, X., Rehman, A., Li, X., Qiu, Y., Pu, J., Lu, S., Zhang, J. (2021). Discovery of cryptic allosteric sites using reversed allosteric communication by a combined computational and experimental strategy. Chemical Science, 12(1), 464-476. [More Information]
Daien, C., Tan, J., Audo, R., Mielle, J., Quek, L., Krycer, J., Angelatos, A., Duraes, M., Pinget, G., Ni, D., Amian, M., Sierro, F., Parmar, A., Hoque, S., Gosby, A., Simpson, S., Ribeiro, R., Macia, L., et al (2021). Gut-derived acetate promotes B10 cells with antiinflammatory effects. JCI Insight, 6(7), e144156. [More Information]
Fan, J., Liu, Y., Kong, R., Ni, D., Yu, Z., Lu, S., Zhang, J. (2021). Harnessing Reversed Allosteric Communication: A Novel Strategy for Allosteric Drug Discovery. Journal of Medicinal Chemistry, 64(24), 17728-17743. [More Information]
Tan, J., Ni, D., Ribeiro, R., Pinget, G., Macia, L. (2021). How changes in the nutritional landscape shape gut immunometabolism. Nutrients, 13(3), 1-36. [More Information]
Li, X., Qi, Z., Ni, D., Lu, S., Chen, L., Chen, X. (2021). Markov state models and molecular dynamics simulations provide understanding of the nucleotide-dependent dimerization-based activation of lrrk2 roc domain. Molecules, 26(18). [More Information]
Lu, S., Chen, Y., Wei, J., Zhao, M., Ni, D., He, X., Zhang, J. (2021). Mechanism of allosteric activation of SIRT6 revealed by the action of rationally designed activators. Acta Pharmaceutica Sinica B, 11(5), 1355-1361. [More Information]
Rehman, A., Zhen, G., Zhong, B., Ni, D., Li, J., Nasir, A., Gabr, M., Rafiq, H., Wadood, A., Lu, S., et al (2021). Mechanism of zinc ejection by disulfiram in nonstructural protein 5A. Physical Chemistry Chemical Physics, 23(21), 12204-12215. [More Information]
Wang, Y., Ji, D., Lei, C., Chen, Y., Qiu, Y., Li, X., Li, M., Ni, D., Pu, J., Zhang, J., et al (2021). Mechanistic insights into the effect of phosphorylation on Ras conformational dynamics and its interactions with cell signaling proteins. Computational and Structural Biotechnology Journal, 19, 1184-1199. [More Information]
Wang, X., Ni, D., Liu, Y., Lu, S. (2021). Rational Design of Peptide-Based Inhibitors Disrupting Protein-Protein Interactions. Frontiers in Chemistry, 9, 682675. [More Information]
Qiu, Y., Wang, Y., Chai, Z., Ni, D., Li, X., Pu, J., Chen, J., Zhang, J., Lu, S., Lv, C., et al (2021). Targeting RAS phosphorylation in cancer therapy: Mechanisms and modulators. Acta Pharmaceutica Sinica B, 11(11), 3433-3446. [More Information]

show 12 more

2020

Ni, D., Li, Y., Qiu, Y., Pu, J., Lu, S., Zhang, J. (2020). Combining Allosteric and Orthosteric Drugs to Overcome Drug Resistance. Trends In Pharmacological Sciences, 41(5), 336-348. [More Information]
Lu, S., Qiu, Y., Ni, D., He, X., Pu, J., Zhang, J. (2020). Emergence of allosteric drug-resistance mutations: new challenges for allosteric drug discovery. Drug Discovery Today, 25(1), 177-184. [More Information]
Zhang, H., He, X., Ni, D., Mou, L., Chen, X., Lu, S. (2020). How does the novel T315L mutation of breakpoint cluster region-abelson (BCR-ABL) kinase confer resistance to ponatinib: a comparative molecular dynamics simulation study. Journal of Biomolecular Structure and Dynamics, 38(1), 89-100. [More Information]
Li, X., Dai, J., Ni, D., He, X., Zhang, H., Zhang, J., Fu, Q., Liu, Y., Lu, S. (2020). Insight into the mechanism of allosteric activation of PI3Kα by oncoprotein K-Ras4B. International Journal of Biological Macromolecules, 144, 643-655. [More Information]
Liu, X., Lu, S., Song, K., Shen, Q., Ni, D., Li, Q., He, X., Zhang, H., Wang, Q., Chen, Y., et al (2020). Unraveling allosteric landscapes of allosterome with ASD. Nucleic Acids Research, 48(D1), D394-D401. [More Information]
He, X., Ni, D., Zhang, H., Li, X., Zhang, J., Fu, Q., Liu, Y., Lu, S. (2020). Zinc-mediated conformational preselection mechanism in the allosteric control of DNA binding to the zinc transcriptional regulator (ZitR). Scientific Reports, 10(1). [More Information]

show 3 more

2019

Lu, S., He, X., Ni, D., Zhang, J. (2019). Allosteric Modulator Discovery: From Serendipity to Structure-Based Design. Journal of Medicinal Chemistry, 62(14), 6405-6421. [More Information]
Lu, S., Ni, D., Wang, C., He, X., Lin, H., Wang, Z., Zhang, J. (2019). Deactivation Pathway of Ras GTPase Underlies Conformational Substates as Targets for Drug Design. ACS Catalysis, 9(8), 7188-7196. [More Information]
Ni, D., Li, X., He, X., Zhang, H., Zhang, J., Lu, S. (2019). Drugging K-RasG12C through covalent inhibitors: Mission possible? Pharmacology and Therapeutics, 202, 1-17. [More Information]
Ni, D., Lu, S., Zhang, J. (2019). Emerging roles of allosteric modulators in the regulation of protein-protein interactions (PPIs): A new paradigm for PPI drug discovery. Medicinal Research Reviews, 39(6), 2314-2342. [More Information]
Wang, L., Zheng, G., Liu, X., Ni, D., He, X., Cheng, J., Lu, S. (2019). Molecular dynamics simulations provide insights into the origin of gleevec’s selectivity toward human tyrosine kinases. Journal of Biomolecular Structure and Dynamics, 37(10), 2733-2744. [More Information]
Xu, X., Chen, Y., Fu, Q., Ni, D., Zhang, J., Li, X., Lu, S. (2019). The chemical diversity and structure-based discovery of allosteric modulators for the PIF-pocket of protein kinase PDK1. Journal of Enzyme Inhibition and Medicinal Chemistry, 34(1), 361-374. [More Information]

show 3 more

2018

Huang, M., Song, K., Liu, X., Lu, S., Shen, Q., Wang, R., Gao, J., Hong, Y., Li, Q., Ni, D., et al (2018). AlloFinder: A strategy for allosteric modulator discovery and allosterome analyses. Nucleic Acids Research, 46(W1), W451-W458. [More Information]
Ni, D., Liu, D., Zhang, J., Lu, S. (2018). Computational insights into the interactions between calmodulin and the c/nSH2 domains of p85α regulatory subunit of PI3Kα: Implication for PI3Kα activation by calmodulin. International Journal of Molecular Sciences, 19(1). [More Information]
Lu, S., Ji, M., Ni, D., Zhang, J. (2018). Discovery of hidden allosteric sites as novel targets for allosteric drug design. Drug Discovery Today, 23(2), 359-365. [More Information]

2017

Ni, D., Song, K., Zhang, J., Lu, S. (2017). Molecular dynamics simulations and dynamic network analysis reveal the allosteric unbinding of monobody to H-Ras triggered by R135K mutation. International Journal of Molecular Sciences, 18(11). [More Information]

Faculty of Medicine and Health

Page not found

Mr Duan Ni

Publications

By Type

By Year