Drugging Ras GTPase: a comprehensive mechanistic and signaling structural view

Lu, Shaoyong, Jang, Hyunbum, Gu, Shuo, Zhang, Jian, Nussinov, Ruth·2016·Chemical Society Reviews

Cited by (192)

Items 101–192 of 192

  1. Influence of Cholesterol on the Orientation of the Farnesylated GTP-Bound KRas-4B Binding with Anionic Model Membranes
    Huixia Lu, Jordi Martı́ · 2020 · Membranes
  2. Discovery of ARS-1620 analogs as KRas G12C inhibitors with high in vivo antitumor activity
    Huiting Zhao, Ling Li, Jin Liu, Ruiyao Mai, Jingxuan Chen, Jianjun Chen · 2022 · Bioorganic Chemistry
  3. Pan-KRAS inhibitors suppress proliferation through feedback regulation in pancreatic ductal adenocarcinoma
    Cheng-xiang Wang, Tingting Wang, Kun-Dong Zhang, Mingyu Li, Qiancheng Shen, Shaoyong Lu, Jian Zhang · 2022 · Acta Pharmacologica Sinica
  4. Identification of functional substates of KRas during GTP hydrolysis with enhanced sampling simulations
    Juan Zeng, Jian Chen, Fei Xia, Qiang Cui, Xianming Deng, Xin Xu · 2022 · Physical Chemistry Chemical Physics
  5. Prochlorperazine enhances radiosensitivity of non-small cell lung carcinoma by stabilizing GDP-bound mutant KRAS conformation
    Kirti Sad, Palak Parashar, Pragya Tripathi, Hungharla Hungyo, Ramesh K. Sistla, Ravi Soni, Vibha Tandon · 2021 · Free Radical Biology and Medicine
  6. Unveiling the State Transition Mechanisms of Ras Proteins through Enhanced Sampling and QM/MM Simulations
    Fangchen Hu, Yiqiu Wang, Juan Zeng, Xianming Deng, Fei Xia, Xin Xu · 2024 · The Journal of Physical Chemistry B
  7. Zoledronic acid enhances the efficacy of the MEK inhibitor trametinib in KRAS mutant cancers
    Xinyu Dai, Hongwei Xia, Sheng Zhou, Qiulin Tang, Feng Bi · 2018 · Cancer Letters
  8. Impacts of Mutations in the P-Loop on Conformational Alterations of KRAS Investigated with Gaussian Accelerated Molecular Dynamics Simulations
    Shuhua Shi, Linqi Zheng, Yonglian Ren, Ziyu Wang · 2023 · Molecules
  9. Designing drugs and chemical probes with the dualsteric approach
    Jinyin Zha, Jixiao He, Chengwei Wu, Mingyang Zhang, Xinyi Liu, Jian Zhang · 2023 · Chemical Society Reviews
  10. Understanding the influence of AMG 510 on the structure of KRAS G12C empowered by molecular dynamics simulation
    Yu Li, Lei Han, Ziding Zhang · 2022 · Computational and Structural Biotechnology Journal
  11. Phosphorylation promotes binding affinity of Rap-Raf complex by allosteric modulation of switch loop dynamics
    T Devanand, Prasanna Venkatraman, Satyavani Vemparala · 2018 · Scientific Reports
  12. Autopromotion of K-Ras4B Feedback Activation Through an SOS-Mediated Long-Range Allosteric Effect
    Xuan He, Kui Du, Yuanhao Wang, Jigang Fan, Mingyu Li, Duan Ni, Shaoyong Lu, Xiaolan Bian, Yaqin Liu · 2022 · Frontiers in Molecular Biosciences
  13. Understanding the feasibility of chemotherapeutic and immunotherapeutic targets against non-small cell lung cancers: an update of resistant responses and recent combinatorial therapies
    Parth Malik, Ruma Rani, Raghu Solanki, Vishal Haribhai Patel, Tapan K. Mukherjee · 2023 · Exploration of Targeted Anti-tumor Therapy
  14. Scaffold repurposing of fendiline: Identification of potent KRAS plasma membrane localization inhibitors
    Pingyuan Wang, Dharini van der Hoeven, Na Ye, Haiying Chen, Zhiqing Liu, Xiaoping Ma, Dina Montufar‐Solis, Kristen M. Rehl, Kwang‐Jin Cho, Sabita Thapa et al. · 2021 · European Journal of Medicinal Chemistry
  15. Robust Strategy for Hit-to-Lead Discovery: NMR for SAR
    Sacha Thierry Larda, Yann Ayotte, Maria M. Denk, Paul W. Coote, Gregory J. Heffron, David Bendahan, Fatma Shahout, Nicolas Girard, Mustapha Iddir, Patricia Bouchard et al. · 2023 · Journal of Medicinal Chemistry
  16. Proximal Protein Interaction Landscape of RAS Paralogs
    Benoît Béganton, Étienne Coyaud, Estelle M. N. Laurent, Alain Mangé, Julien Jacquemetton, Muriel Le Romancer, Brian Raught, Jérôme Solassol · 2020 · Cancers
  17. Deoxypodophyllotoxin inhibits cell viability and invasion by blocking the PI3K/Akt signaling pathway in human glioblastoma cells
    Wei Wang, Wei Qiang Gao, Luyang Zhang, Dongyong Zhang, Zilong Zhao, Yijun Bao · 2019 · Oncology Reports · Retracted
  18. GLOBAL AND TARGETED PROFILING OF GTP‐BINDING PROTEINS IN BIOLOGICAL SAMPLES BY MASS SPECTROMETRY
    Ming Huang, Yinsheng Wang · 2020 · Mass Spectrometry Reviews
  19. Theoretical insights into mutation-mediated conformational changes of the GNP-bound H-RAS
    Juan Zhao, Haibo Sun, Wei Wang, Lin Zhang, Jianzhong Chen · 2020 · Chemical Physics Letters
  20. m6A demethylase ALKBH5 attenuates doxorubicin-induced cardiotoxicity via posttranscriptional stabilization of Rasal3
    Rifeng Gao, Kun Yang, Yanan Qu, Xiang Wei, Jiaran Shi, Chunyu Lv, Yongchao Zhao, Xiaolei Sun, Ying‐Jia Xu, Yiqing Yang · 2023 · iScience
  21. Arl2-Mediated Allosteric Release of Farnesylated KRas4B from Shuttling Factor PDEδ
    E. Sıla Özdemir, Hyunbum Jang, Attila Gürsoy, Özlem Keskin, Ruth Nussinov · 2018 · The Journal of Physical Chemistry B
  22. Exploring binding and allosteric energy landscapes for the KRAS interactions with effector proteins using Markov state modeling of conformational ensembles and allosteric network modeling
    Sian Xiao, Mohammed Alshahrani, Guang Hu, Peng Tao, Gennady M. Verkhivker · 2025 · Protein Science
  23. Cluster analysis on conformational changes of the GDP/KRAS complex induced by A59G and D33E
    Juan Zhao, Lifei Wang, Huayin Bao, Jianzhong Chen · 2021 · Chemical Physics Letters
  24. The switch states of the GDP-bound HRAS affected by point mutations: a study from Gaussian accelerated molecular dynamics simulations and free energy landscapes
    Huayin Bao, Wei Wang, Haibo Sun, Jianzhong Chen · 2023 · Journal of Biomolecular Structure and Dynamics
  25. Inhibitors of the GTPase KRASG12Cin cancer: a patent review (2019-2021)
    Qifu Xu, Guozhen Zhang, Qian Liu, Shunda Li, Yingjie Zhang · 2022 · Expert Opinion on Therapeutic Patents
  26. Design, synthesis and biological evaluation of phosphopeptides as Polo-like kinase 1 Polo-box domain inhibitors
    Tongyuan Lin, Hong-ping Min, Cheng Jiang, Miaomiao Niu, Yan Fang, Lili Xu, Bin Di · 2018 · Bioorganic & Medicinal Chemistry
  27. Pan‑RAF inhibitor LY3009120 is highly synergistic with low‑dose cytarabine, but not azacitidine, in acute myeloid leukemia withRASmutations
    Jihyun Park, Hyejoo Park, Ja Min Byun, Junshik Hong, Dong‐Yeop Shin, Youngil Koh, Sung‐Soo Yoon · 2021 · Oncology Letters
  28. Inhibition of K-Ras4B-plasma membrane association with a membrane microdomain-targeting peptide
    Fang-Yi Li, Zhenfeng Zhang, Stephanie Voß, Yao‐Wen Wu, Yufen Zhao, Yanmei Li, Yong‐Xiang Chen · 2019 · Chemical Science
  29. Probing binding and allosteric mechanisms of the KRAS interactions with monobodies and affimer proteins: ensemble-based mutational profiling and thermodynamic analysis of binding energetics and allostery reveal diversity of functional hotspots and cryptic pockets linked by conserved communication network
    Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Guang Hu, Gennady M. Verkhivker · 2025 · Physical Chemistry Chemical Physics
  30. Discovery of Hit Compounds Targeting the P4 Allosteric Site of K-RAS, Identified through Ensemble-Based Virtual Screening
    Patricia Gómez‐Gutierrez, J. Rubio, Juan Jesús Pérez · 2023 · Journal of Chemical Information and Modeling
  31. Conformational States of the GDP- and GTP-Bound HRAS Affected by A59E and K117R: An Exploration from Gaussian Accelerated Molecular Dynamics
    Zhiping Yu, Zhen Wang, Xiuzhen Cui, Zanxia Cao, Wanyunfei Zhang, Kunxiao Sun, Guodong Hu · 2024 · Molecules
  32. Multiscale calculations reveal new insights into the reaction mechanism between KRAS G12C and α, β-unsaturated carbonyl of covalent inhibitors
    Xiao Hong Yan, Chuan‐Hua Qu, Qin Li, Lei Zhu, Henry H. Y. Tong, Huanxiang Liu, Qin Ouyang, Xiaojun Yao · 2024 · Computational and Structural Biotechnology Journal
  33. Allosteric Activation of RhoA Complexed with p115-RhoGEF Deciphered by Conformational Dynamics
    Nurit Haspel, Hyunbum Jang, Ruth Nussinov · 2024 · Journal of Chemical Information and Modeling
  34. Inhibition of GTPase KRAS G12D : a review of patent literature
    Yuhang Li, Le Yang, Xiaoran Li, Xiaojin Zhang · 2024 · Expert Opinion on Therapeutic Patents
  35. Peptidomimetics designed to bind to RAS effector domain are promising cancer therapeutic compounds
    Chiara Pallara, Débora Cabot, Josep Rivas, Sònia Brun, Jesús Seco, Baraa Abuasaker, Teresa Tarragó, Montserrat Jaumot, Roger Prades, Neus Agell · 2022 · Scientific Reports
  36. Epigenomic tomography for probing spatially defined chromatin state in the brain
    Zhengzhi Liu, Chengyu Deng, Zirui Zhou, Ya Xiao, Shan Jiang, Bohan Zhu, Lynette B. Naler, Xiaoting Jia, Danfeng Daphne Yao, Chang Lu · 2024 · Cell Reports Methods
  37. GAP positions catalytic H-Ras residue Q61 for GTP hydrolysis in molecular dynamics simulations, complicating chemical rescue of Ras deactivation
    Lara A. Patel, Timothy J. Waybright, Andrew G. Stephen, Chris Neale · 2023 · Computational Biology and Chemistry
  38. Precise diagnosis and treatment for peripheral T-cell lymphomas: From pathogenic mechanisms to innovative approaches
    Yuran Qiu, Weili Zhao · 2024 · The Innovation Medicine
  39. RalA exerts an inhibitory effect on IL-1β/IL-18 secretion by blocking NLRP3 inflammasome activation in levornidazole-treated human THP-1 macrophages
    Xingqi Wang, Lingshan Gou, Yuzhi Gao, Yuqing Huang, Rui Kuai, Yu Li, Yujing Wang, Yanhong Chen, Jun Li, Chao Cheng et al. · 2020 · International Immunopharmacology
  40. The Chinese Herbal Formula Ruyan Neixiao Cream Inhibits Angiogenesis of Precancerous Breast Lesions via Regulation of Ras/Raf/MEK/ERK Signaling Pathway
    Shujun Lin, Xuefeng Jiang, Guijuan Zhang, Xinqin Xiao, Xinyi Ma, Jieyan Wu, Dan Qiu, Xinyuan Li, Xianxin Yan, Min Ma · 2022 · Integrative Cancer Therapies
  41. Simulation toolkits at the molecular scale for trans-scale thermal signaling
    Ikuo Kurisaki, Madoka Suzuki · 2023 · Computational and Structural Biotechnology Journal
  42. Accurate Characterization of the Allosteric Energy Landscapes, Binding Hotspots and Long-Range Communications for KRAS Complexes with Effector Proteins : Integrative Approach Using Microsecond Molecular Dynamics, Deep Mutational Scanning of Binding Energetics and Allosteric Network Modeling
    Sian Xiao, Mohammed Alshahrani, Guang Hu, Peng Tao, Gennady M. Verkhivker · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  43. Microsecond molecular dynamics simulations and dynamic network analysis provide understanding of the allosteric inactivation of GSK3β induced by the L343R mutation
    Jun Li, Qiang Fu, Yang Yan Liang, Biao Cheng, Xiaolong Li · 2019 · Journal of Molecular Modeling
  44. Recent Advances in Developing K-Ras Plasma Membrane Localization Inhibitors
    Na Ye, Qingfeng Xu, Wanwan Li, Pingyuan Wang, Jia Zhou · 2019 · Current Topics in Medicinal Chemistry
  45. Clear Cell Renal Carcinoma: MicroRNAs With Efficacy in PreclinicalIn VivoModels
    Ulrich H. Weidle, Adam Nopora · 2021 · Cancer Genomics & Proteomics
  46. RAS: Circuitry and therapeutic targeting
    Gagandeep Singh, Neelam Thakur, Umesh Kumar · 2022 · Cellular Signalling
  47. Protein–Protein Interface Topology as a Predictor of Secondary Structure and Molecular Function Using Convolutional Deep Learning
    Benjamin Bouvier · 2021 · Journal of Chemical Information and Modeling
  48. Effective drug design screening in bacterial glycolytic enzymes via targeting alternative allosteric sites
    İpek Türkmenoğlu, Gamze Kurtuluş, Cenk Sesal, Özge Kürkçüoğlu, Merve Ayyildiz, Serkan Çeliker, Fatih Ozhelvaci, Xin Du, George Y. Liu, Moshe Arditi et al. · 2024 · Archives of Biochemistry and Biophysics
  49. In Silico Identification of Putative Allosteric Pockets and Inhibitors for the KRASG13D-SOS1 Complex in Cancer Therapy
    Zehra Sarıca, Özge Kürkçüoğlu, Fethiye Aylin Sungur · 2025 · International Journal of Molecular Sciences
  50. Sequence‐Selective Covalent CaaX‐Box Receptors Prevent Farnesylation of Oncogenic Ras Proteins and Impact MAPK/PI3 K Signaling
    Matthias Franz, Britta Mörchen, Carsten Degenhart, Daniel Gülden, Oleksandr Shkura, Dirk Andreas Wolters, Uwe Koch, Bert Klebl, Raphael Stoll, Iris Helfrich et al. · 2021 · ChemMedChem
  51. Analysis of Pan-Specific Inhibitors of Oncogenic Mutant Forms of KRAS GTPase
    Ilya A. Eliseev, Dmitrii O. Shkil, Valentina S. Shumakova, Vladimir V. Chernyshov, Konstantin V. Balakin, Roman A. Ivanov · 2025 · Current Medicinal Chemistry
  52. Phosphorylation induces altered protonation states and allosterically regulates Rac1– RhoGDI complex
    Krishnendu Sinha, Amit Kumawat, Hyunbum Jang, Ruth Nussinov, Suman Chakrabarty · 2025 · Protein Science
  53. Revealing conformational changes of GTP-bound NRAS mutants probed by GaMD and Markov state models.
    Lu Zhao, Jian Wang, Hai-Peng Ping, Wanchun Yang, Haijun Cao, Jian-Zhong Chen · 2026 · Physical Chemistry, Chemical Physics - PCCP
  54. Hepatocyte Growth Factor Overexpression Slows the Progression of 4NQO-Induced Oral Tumorigenesis
    Xiaoxi He, Si Chen, Yinghua Tang, Xiaomin Zhao, Liting Yan, Lihong Wu, Zhicong Wu, Weijia Liu, Xinming Chen, Xinhong Wang · 2021 · Frontiers in Oncology
  55. 143D, a novel selective KRASG12C inhibitor exhibits potent antitumor activity in preclinical models
    Lansong Xu, Su-xin Zheng, Lianghe Mei, Kexin Yang, Ya‐Fang Wang, Qiang Zhou, Xiangtai Kong, Ming-yue Zheng, Hualiang Jiang, Chengying Xie · 2023 · Acta Pharmacologica Sinica
  56. The structural basis of the autoinhibition mechanism of glycogen synthase kinase 3β (GSK3β): molecular modeling and molecular dynamics simulation studies
    Linkai Mou, Wenwen Dou, Gang Meng, Ke Sun, Xiangyu Chen · 2019 · Journal of Biomolecular Structure and Dynamics
  57. Methods Applied for the Allosteric Site Revelation
    Duan Ni, Shaoyong Lu, Jian Zhang · 2018 · Encyclopedia of Analytical Chemistry
  58. Development of potent inhibitors against KRAS, its mutant G12R, allosteric and Switch-I/Switch-II site
    Vikas Yadav, Mohammad Kashif, Swati Sharma, Naidu Subbarao · 2025 · In Silico Pharmacology
  59. Targeting KRAS for cancer therapy
    Jianlong Jia, Ruonan Liu, Tonia A. Adamide, Isis E. Fernandez, Georgios T. Stathopoulos · 2026 · British Journal of Pharmacology
  60. Computational dissection of allosteric inhibition of the SH2 domain of Bcr-Abl kinase by the monobody inhibitor AS25
    Mingfei Ji, Guodong Zheng, Xiaolong Li, Zhongqin Zhang, Guanqun Jv, Xiaowei Wang, Jialin Wang · 2017 · Journal of Molecular Modeling
  61. LUMAKRAS® (sotorasib)
    Nuria A. Tamayo, Ryan P. Wurz, Brian A. Lanman · 2024 · Elsevier eBooks
  62. Ensemble-Based Binding Free Energy Profiling and Network Analysis of the KRAS Interactions with DARPin Proteins Targeting Distinct Binding Sites: Revealing Molecular Determinants and Universal Architecture of Regulatory Hotspots and Allosteric Binding
    Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady M. Verkhivker · 2025 · Biomolecules
  63. Structural mechanism of mRNA decoding by mammalian GTPase GTPBP1
    Susorov, Denis, Miścicka, Anna, Golovenko, Dmitrij, Loveland, Anna B., Zinoviev, Alexandra, Pestova, Tatyana V., Korostelev, Andrei A. · 2025 · Nature Communications
  64. A 3′ UTR polymorphism g.1618 G > A in the MAFA gene modulates miR-3678-3p binding and enhances meat production in sheep via the MAFA/GHR/JAK2 pathway
    Cuiyu Lai, Dandan Tan, Xu Han, Yu Fu, Jinlin Chen, Xiaofan Yang, Xuesong Shan, Yang Chen, Huaizhi Jiang · 2025 · Genetics Selection Evolution
  65. Rosmarinic acid inhibits non-small cell lung cancer progression by directly targeting KRASG12C and modulating the KRAS/AKT/ERK signaling axis
    Wentong Zhao, Qian Zhang, Yujing He, Xuefeng Xing, Yehai An, Ying Zhang, Wenhui Li, Shiguang Yang, Xuan Xiong, Weiyi He et al. · 2026 · Phytomedicine
  66. Integrated Structural and Dynamic Analysis Reveals Destabilizing Effects of KRAS Missense Variants Associated with Lung Cancer
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  67. Vaccine Therapy in Pancreatic Cancer
    Benjamin Adam Weinberg, Michael J. Pishvaian · 2017 · Springer eBooks
  68. Oncogenic G12D mutation alters local conformations and dynamics of K-Ras
    Sezen Vatansever, Burak Erman, Zeynep Hulya Gumus · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
  69. Combined computational and solution scattering methods to study the dynamical properties of Ras
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  70. Redesigned GAP to activate oncogenic GAP
    Dénes Berta, Sascha Gehrke, Kinga Nyíri, Beáta G. Vértessy, Edina Rosta · 2023 · ChemRxiv
  71. A Conserved Architecture of Allosteric Communications and Regulatory Hotspots in the KRAS Complexes with Diverse Binding Proteins Controls Mechanisms of Effector Mimicry and Allosteric Modulation : Atomistic Revelations from Molecular Simulations and Mutational Scanning of Binding Energetics and Allostery
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  72. Evaluación de potenciales propiedades antiaterogénicas y antitumorales del aceite de la cáscara de Citrus reticulata
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  73. Modeling and Simulation of Lipid Membranes
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  74. Epigenomic tomography for probing spatially-defined molecular state in the brain
    Zhengzhi Liu, Chengyu Deng, Zirui Zhou, Ya Xiao, Shan Jiang, Bohan Zhu, Lynette B. Naler, Xiaoting Jia, Danfeng Daphne Yao, Chang Lu · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  75. Discovery of a novel drug using lipid-based formulation targeting G12D-mutated KRAS4B through non-covalent bonds
    Huixia Lu, Zheyao Hu, Jordi Faraudo, Jordi Martı́ · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  76. Pharmaceutical Research Based on the Structure of KRAS Protein—Research and Practice on Teaching Reform of Biochemistry Course
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  77. Distinct association of HRAS and KRAS with Mn2+ ion illustrated by paramagnetic NMR
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  78. Atomistic Profiling of KRAS Interactions with Monobodies and Affimer Proteins Through Ensemble-Based Mutational Scanning Unveils Conserved Residue Networks Linking Cryptic Pockets and Regulating Mechanisms of Binding, Specificity and Allostery
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  79. Elucidating conformational dynamics of GDP/GTP-KRAS complexes caused by mutations from the switch domain I through Gaussian accelerated molecular dynamics simulations
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  80. Cell penetrating and interfering peptides as new cancer therapy
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  83. Targeted analysis of KRAS and CREBBP mutations uncovers a potential population-specific signature in thai patients with liver fluke-associated cholangiocarcinoma
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  84. Discovery and Characterization of RP04340 : A Highly Potent and Orally Active Pan-KRAS PROTAC Degrader
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  86. Binding mechanism of the molecular glue inhibitor in overcoming the “undruggable” Kirsten rat sarcoma viral oncogene homolog through conformational remodeling
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  88. Recent advances in scaffold-based KRAS G12C inhibitors: SAR and biological evaluation insights
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  89. BindingDB Entry 50013756: Scaffold repurposing of fendiline: Identification of potent KRAS plasma membrane localization inhibitors.
    BindingDB · 2022 · UC San Diego
  90. BindingDB Entry 50001273: Design, synthesis and biological evaluation of phosphopeptides as Polo-like kinase 1 Polo-box domain inhibitors.
    BindingDB · 2020 · UC San Diego
  91. BindingDB Entry 50009378: Allosteric Modulator Discovery: From Serendipity to Structure-Based Design.
    BindingDB · 2021 · UC San Diego
  92. BindingDB Entry 50006764: Small Molecule Allosteric Modulators of G-Protein-Coupled Receptors: Drug-Target Interactions.
    BindingDB · 2021 · UC San Diego