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
- Influence of Cholesterol on the Orientation of the Farnesylated GTP-Bound KRas-4B Binding with Anionic Model MembranesHuixia Lu, Jordi Martı́ · 2020 · Membranes
- Discovery of ARS-1620 analogs as KRas G12C inhibitors with high in vivo antitumor activityHuiting Zhao, Ling Li, Jin Liu, Ruiyao Mai, Jingxuan Chen, Jianjun Chen · 2022 · Bioorganic Chemistry
- Pan-KRAS inhibitors suppress proliferation through feedback regulation in pancreatic ductal adenocarcinomaCheng-xiang Wang, Tingting Wang, Kun-Dong Zhang, Mingyu Li, Qiancheng Shen, Shaoyong Lu, Jian Zhang · 2022 · Acta Pharmacologica Sinica
- Identification of functional substates of KRas during GTP hydrolysis with enhanced sampling simulationsJuan Zeng, Jian Chen, Fei Xia, Qiang Cui, Xianming Deng, Xin Xu · 2022 · Physical Chemistry Chemical Physics
- Prochlorperazine enhances radiosensitivity of non-small cell lung carcinoma by stabilizing GDP-bound mutant KRAS conformationKirti Sad, Palak Parashar, Pragya Tripathi, Hungharla Hungyo, Ramesh K. Sistla, Ravi Soni, Vibha Tandon · 2021 · Free Radical Biology and Medicine
- Unveiling the State Transition Mechanisms of Ras Proteins through Enhanced Sampling and QM/MM SimulationsFangchen Hu, Yiqiu Wang, Juan Zeng, Xianming Deng, Fei Xia, Xin Xu · 2024 · The Journal of Physical Chemistry B
- Zoledronic acid enhances the efficacy of the MEK inhibitor trametinib in KRAS mutant cancersXinyu Dai, Hongwei Xia, Sheng Zhou, Qiulin Tang, Feng Bi · 2018 · Cancer Letters
- Impacts of Mutations in the P-Loop on Conformational Alterations of KRAS Investigated with Gaussian Accelerated Molecular Dynamics SimulationsShuhua Shi, Linqi Zheng, Yonglian Ren, Ziyu Wang · 2023 · Molecules
- Designing drugs and chemical probes with the dualsteric approachJinyin Zha, Jixiao He, Chengwei Wu, Mingyang Zhang, Xinyi Liu, Jian Zhang · 2023 · Chemical Society Reviews
- Understanding the influence of AMG 510 on the structure of KRAS G12C empowered by molecular dynamics simulationYu Li, Lei Han, Ziding Zhang · 2022 · Computational and Structural Biotechnology Journal
- Phosphorylation promotes binding affinity of Rap-Raf complex by allosteric modulation of switch loop dynamicsT Devanand, Prasanna Venkatraman, Satyavani Vemparala · 2018 · Scientific Reports
- Autopromotion of K-Ras4B Feedback Activation Through an SOS-Mediated Long-Range Allosteric EffectXuan He, Kui Du, Yuanhao Wang, Jigang Fan, Mingyu Li, Duan Ni, Shaoyong Lu, Xiaolan Bian, Yaqin Liu · 2022 · Frontiers in Molecular Biosciences
- Understanding the feasibility of chemotherapeutic and immunotherapeutic targets against non-small cell lung cancers: an update of resistant responses and recent combinatorial therapiesParth Malik, Ruma Rani, Raghu Solanki, Vishal Haribhai Patel, Tapan K. Mukherjee · 2023 · Exploration of Targeted Anti-tumor Therapy
- Scaffold repurposing of fendiline: Identification of potent KRAS plasma membrane localization inhibitorsPingyuan 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
- Robust Strategy for Hit-to-Lead Discovery: NMR for SARSacha 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
- Proximal Protein Interaction Landscape of RAS ParalogsBenoît Béganton, Étienne Coyaud, Estelle M. N. Laurent, Alain Mangé, Julien Jacquemetton, Muriel Le Romancer, Brian Raught, Jérôme Solassol · 2020 · Cancers
- Deoxypodophyllotoxin inhibits cell viability and invasion by blocking the PI3K/Akt signaling pathway in human glioblastoma cellsWei Wang, Wei Qiang Gao, Luyang Zhang, Dongyong Zhang, Zilong Zhao, Yijun Bao · 2019 · Oncology Reports · Retracted
- GLOBAL AND TARGETED PROFILING OF GTP‐BINDING PROTEINS IN BIOLOGICAL SAMPLES BY MASS SPECTROMETRYMing Huang, Yinsheng Wang · 2020 · Mass Spectrometry Reviews
- Theoretical insights into mutation-mediated conformational changes of the GNP-bound H-RASJuan Zhao, Haibo Sun, Wei Wang, Lin Zhang, Jianzhong Chen · 2020 · Chemical Physics Letters
- m6A demethylase ALKBH5 attenuates doxorubicin-induced cardiotoxicity via posttranscriptional stabilization of Rasal3Rifeng Gao, Kun Yang, Yanan Qu, Xiang Wei, Jiaran Shi, Chunyu Lv, Yongchao Zhao, Xiaolei Sun, Ying‐Jia Xu, Yiqing Yang · 2023 · iScience
- Arl2-Mediated Allosteric Release of Farnesylated KRas4B from Shuttling Factor PDEδE. Sıla Özdemir, Hyunbum Jang, Attila Gürsoy, Özlem Keskin, Ruth Nussinov · 2018 · The Journal of Physical Chemistry B
- Exploring binding and allosteric energy landscapes for the KRAS interactions with effector proteins using Markov state modeling of conformational ensembles and allosteric network modelingSian Xiao, Mohammed Alshahrani, Guang Hu, Peng Tao, Gennady M. Verkhivker · 2025 · Protein Science
- Cluster analysis on conformational changes of the GDP/KRAS complex induced by A59G and D33EJuan Zhao, Lifei Wang, Huayin Bao, Jianzhong Chen · 2021 · Chemical Physics Letters
- The switch states of the GDP-bound HRAS affected by point mutations: a study from Gaussian accelerated molecular dynamics simulations and free energy landscapesHuayin Bao, Wei Wang, Haibo Sun, Jianzhong Chen · 2023 · Journal of Biomolecular Structure and Dynamics
- 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
- Design, synthesis and biological evaluation of phosphopeptides as Polo-like kinase 1 Polo-box domain inhibitorsTongyuan Lin, Hong-ping Min, Cheng Jiang, Miaomiao Niu, Yan Fang, Lili Xu, Bin Di · 2018 · Bioorganic & Medicinal Chemistry
- Pan‑RAF inhibitor LY3009120 is highly synergistic with low‑dose cytarabine, but not azacitidine, in acute myeloid leukemia withRASmutationsJihyun Park, Hyejoo Park, Ja Min Byun, Junshik Hong, Dong‐Yeop Shin, Youngil Koh, Sung‐Soo Yoon · 2021 · Oncology Letters
- Inhibition of K-Ras4B-plasma membrane association with a membrane microdomain-targeting peptideFang-Yi Li, Zhenfeng Zhang, Stephanie Voß, Yao‐Wen Wu, Yufen Zhao, Yanmei Li, Yong‐Xiang Chen · 2019 · Chemical Science
- 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 networkMohammed Alshahrani, Vedant Parikh, Brandon Foley, Guang Hu, Gennady M. Verkhivker · 2025 · Physical Chemistry Chemical Physics
- Discovery of Hit Compounds Targeting the P4 Allosteric Site of K-RAS, Identified through Ensemble-Based Virtual ScreeningPatricia Gómez‐Gutierrez, J. Rubio, Juan Jesús Pérez · 2023 · Journal of Chemical Information and Modeling
- Conformational States of the GDP- and GTP-Bound HRAS Affected by A59E and K117R: An Exploration from Gaussian Accelerated Molecular DynamicsZhiping Yu, Zhen Wang, Xiuzhen Cui, Zanxia Cao, Wanyunfei Zhang, Kunxiao Sun, Guodong Hu · 2024 · Molecules
- Multiscale calculations reveal new insights into the reaction mechanism between KRAS G12C and α, β-unsaturated carbonyl of covalent inhibitorsXiao 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
- Allosteric Activation of RhoA Complexed with p115-RhoGEF Deciphered by Conformational DynamicsNurit Haspel, Hyunbum Jang, Ruth Nussinov · 2024 · Journal of Chemical Information and Modeling
- Inhibition of GTPase KRAS G12D : a review of patent literatureYuhang Li, Le Yang, Xiaoran Li, Xiaojin Zhang · 2024 · Expert Opinion on Therapeutic Patents
- Peptidomimetics designed to bind to RAS effector domain are promising cancer therapeutic compoundsChiara Pallara, Débora Cabot, Josep Rivas, Sònia Brun, Jesús Seco, Baraa Abuasaker, Teresa Tarragó, Montserrat Jaumot, Roger Prades, Neus Agell · 2022 · Scientific Reports
- Epigenomic tomography for probing spatially defined chromatin state in the brainZhengzhi 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
- GAP positions catalytic H-Ras residue Q61 for GTP hydrolysis in molecular dynamics simulations, complicating chemical rescue of Ras deactivationLara A. Patel, Timothy J. Waybright, Andrew G. Stephen, Chris Neale · 2023 · Computational Biology and Chemistry
- Precise diagnosis and treatment for peripheral T-cell lymphomas: From pathogenic mechanisms to innovative approachesYuran Qiu, Weili Zhao · 2024 · The Innovation Medicine
- RalA exerts an inhibitory effect on IL-1β/IL-18 secretion by blocking NLRP3 inflammasome activation in levornidazole-treated human THP-1 macrophagesXingqi Wang, Lingshan Gou, Yuzhi Gao, Yuqing Huang, Rui Kuai, Yu Li, Yujing Wang, Yanhong Chen, Jun Li, Chao Cheng et al. · 2020 · International Immunopharmacology
- The Chinese Herbal Formula Ruyan Neixiao Cream Inhibits Angiogenesis of Precancerous Breast Lesions via Regulation of Ras/Raf/MEK/ERK Signaling PathwayShujun Lin, Xuefeng Jiang, Guijuan Zhang, Xinqin Xiao, Xinyi Ma, Jieyan Wu, Dan Qiu, Xinyuan Li, Xianxin Yan, Min Ma · 2022 · Integrative Cancer Therapies
- Simulation toolkits at the molecular scale for trans-scale thermal signalingIkuo Kurisaki, Madoka Suzuki · 2023 · Computational and Structural Biotechnology Journal
- 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 ModelingSian Xiao, Mohammed Alshahrani, Guang Hu, Peng Tao, Gennady M. Verkhivker · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- Microsecond molecular dynamics simulations and dynamic network analysis provide understanding of the allosteric inactivation of GSK3β induced by the L343R mutationJun Li, Qiang Fu, Yang Yan Liang, Biao Cheng, Xiaolong Li · 2019 · Journal of Molecular Modeling
- Recent Advances in Developing K-Ras Plasma Membrane Localization InhibitorsNa Ye, Qingfeng Xu, Wanwan Li, Pingyuan Wang, Jia Zhou · 2019 · Current Topics in Medicinal Chemistry
- Clear Cell Renal Carcinoma: MicroRNAs With Efficacy in PreclinicalIn VivoModelsUlrich H. Weidle, Adam Nopora · 2021 · Cancer Genomics & Proteomics
- RAS: Circuitry and therapeutic targetingGagandeep Singh, Neelam Thakur, Umesh Kumar · 2022 · Cellular Signalling
- Protein–Protein Interface Topology as a Predictor of Secondary Structure and Molecular Function Using Convolutional Deep LearningBenjamin Bouvier · 2021 · Journal of Chemical Information and Modeling
- Effective drug design screening in bacterial glycolytic enzymes via targeting alternative allosteric sitesİpek 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
- In Silico Identification of Putative Allosteric Pockets and Inhibitors for the KRASG13D-SOS1 Complex in Cancer TherapyZehra Sarıca, Özge Kürkçüoğlu, Fethiye Aylin Sungur · 2025 · International Journal of Molecular Sciences
- Sequence‐Selective Covalent CaaX‐Box Receptors Prevent Farnesylation of Oncogenic Ras Proteins and Impact MAPK/PI3 K SignalingMatthias Franz, Britta Mörchen, Carsten Degenhart, Daniel Gülden, Oleksandr Shkura, Dirk Andreas Wolters, Uwe Koch, Bert Klebl, Raphael Stoll, Iris Helfrich et al. · 2021 · ChemMedChem
- Analysis of Pan-Specific Inhibitors of Oncogenic Mutant Forms of KRAS GTPaseIlya A. Eliseev, Dmitrii O. Shkil, Valentina S. Shumakova, Vladimir V. Chernyshov, Konstantin V. Balakin, Roman A. Ivanov · 2025 · Current Medicinal Chemistry
- Phosphorylation induces altered protonation states and allosterically regulates Rac1– RhoGDI complexKrishnendu Sinha, Amit Kumawat, Hyunbum Jang, Ruth Nussinov, Suman Chakrabarty · 2025 · Protein Science
- 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
- Hepatocyte Growth Factor Overexpression Slows the Progression of 4NQO-Induced Oral TumorigenesisXiaoxi He, Si Chen, Yinghua Tang, Xiaomin Zhao, Liting Yan, Lihong Wu, Zhicong Wu, Weijia Liu, Xinming Chen, Xinhong Wang · 2021 · Frontiers in Oncology
- 143D, a novel selective KRASG12C inhibitor exhibits potent antitumor activity in preclinical modelsLansong 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
- The structural basis of the autoinhibition mechanism of glycogen synthase kinase 3β (GSK3β): molecular modeling and molecular dynamics simulation studiesLinkai Mou, Wenwen Dou, Gang Meng, Ke Sun, Xiangyu Chen · 2019 · Journal of Biomolecular Structure and Dynamics
- Methods Applied for the Allosteric Site RevelationDuan Ni, Shaoyong Lu, Jian Zhang · 2018 · Encyclopedia of Analytical Chemistry
- Development of potent inhibitors against KRAS, its mutant G12R, allosteric and Switch-I/Switch-II siteVikas Yadav, Mohammad Kashif, Swati Sharma, Naidu Subbarao · 2025 · In Silico Pharmacology
- Targeting KRAS for cancer therapyJianlong Jia, Ruonan Liu, Tonia A. Adamide, Isis E. Fernandez, Georgios T. Stathopoulos · 2026 · British Journal of Pharmacology
- Computational dissection of allosteric inhibition of the SH2 domain of Bcr-Abl kinase by the monobody inhibitor AS25Mingfei Ji, Guodong Zheng, Xiaolong Li, Zhongqin Zhang, Guanqun Jv, Xiaowei Wang, Jialin Wang · 2017 · Journal of Molecular Modeling
- LUMAKRAS® (sotorasib)Nuria A. Tamayo, Ryan P. Wurz, Brian A. Lanman · 2024 · Elsevier eBooks
- 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 BindingMohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady M. Verkhivker · 2025 · Biomolecules
- Structural mechanism of mRNA decoding by mammalian GTPase GTPBP1Susorov, Denis, Miścicka, Anna, Golovenko, Dmitrij, Loveland, Anna B., Zinoviev, Alexandra, Pestova, Tatyana V., Korostelev, Andrei A. · 2025 · Nature Communications
- 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 pathwayCuiyu Lai, Dandan Tan, Xu Han, Yu Fu, Jinlin Chen, Xiaofan Yang, Xuesong Shan, Yang Chen, Huaizhi Jiang · 2025 · Genetics Selection Evolution
- Rosmarinic acid inhibits non-small cell lung cancer progression by directly targeting KRASG12C and modulating the KRAS/AKT/ERK signaling axisWentong Zhao, Qian Zhang, Yujing He, Xuefeng Xing, Yehai An, Ying Zhang, Wenhui Li, Shiguang Yang, Xuan Xiong, Weiyi He et al. · 2026 · Phytomedicine
- Integrated Structural and Dynamic Analysis Reveals Destabilizing Effects of KRAS Missense Variants Associated with Lung CancerMd. Sohel Mia, Bimal Kumar Datta, Khadija Akter, Tomal Krishno Das Topu, Jamima Mahzabin Shawon, Faisul Hossen, Abdur Rahman Pranto, Md. Saklain Tanver Shadhin, Nowmee Tahsin, Safa H. Qahl et al. · 2026 · The Protein Journal
- Vaccine Therapy in Pancreatic CancerBenjamin Adam Weinberg, Michael J. Pishvaian · 2017 · Springer eBooks
- Oncogenic G12D mutation alters local conformations and dynamics of K-RasSezen Vatansever, Burak Erman, Zeynep Hulya Gumus · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
- Combined computational and solution scattering methods to study the dynamical properties of RasGuterres · 2018
- Redesigned GAP to activate oncogenic GAPDénes Berta, Sascha Gehrke, Kinga Nyíri, Beáta G. Vértessy, Edina Rosta · 2023 · ChemRxiv
- 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 AllosteryMohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady M. Verkhivker · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- Evaluación de potenciales propiedades antiaterogénicas y antitumorales del aceite de la cáscara de Citrus reticulataMaría Agustina Castro · 2019
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- Epigenomic tomography for probing spatially-defined molecular state in the brainZhengzhi 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)
- Discovery of a novel drug using lipid-based formulation targeting G12D-mutated KRAS4B through non-covalent bondsHuixia Lu, Zheyao Hu, Jordi Faraudo, Jordi Martı́ · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
- Pharmaceutical Research Based on the Structure of KRAS Protein—Research and Practice on Teaching Reform of Biochemistry Course修恩 曹 · 2023 · Hans Journal of Biomedicine
- Distinct association of HRAS and KRAS with Mn2+ ion illustrated by paramagnetic NMRJialiang Chen, Xun‐Cheng Su · 2024 · Magnetic Resonance Letters
- 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 AllosteryMohammed Alshahrani, Vedant Parikh, Brandon Foley, Guang Hu, Gennady M. Verkhivker · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- Elucidating conformational dynamics of GDP/GTP-KRAS complexes caused by mutations from the switch domain I through Gaussian accelerated molecular dynamics simulationsShuhua Shi, Aijia Liu, Yutian Guo · 2026 · Journal of Biomolecular Structure and Dynamics
- Cell penetrating and interfering peptides as new cancer therapyXiguang Zhang · 2017 · theses.fr (ABES)
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- Discovery and Characterization of RP04340 : A Highly Potent and Orally Active Pan-KRAS PROTAC DegraderXiang Ling Ji, Yuening Du, Qiguo Zhang, Bin Zong, Kang Du, Xiaolin He, Gang Wu, Chao Liang, 胡磬遥, Yuwei Zhang et al. · 2026 · Journal of Medicinal Chemistry
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- Binding mechanism of the molecular glue inhibitor in overcoming the “undruggable” Kirsten rat sarcoma viral oncogene homolog through conformational remodelingHoude Liang, Xiaole Xu, Enhao Zhang, Jinxin Liu, Yihan Wang, Xinguo Liu, Song Luo, Lili Duan · 2026 · Spectrochimica Acta Part A Molecular and Biomolecular Spectroscopy
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- Recent advances in scaffold-based KRAS G12C inhibitors: SAR and biological evaluation insightsTomojit Bhattacharjee, Ankush Kumar, Thakur Gurjeet Singh, Rohit Bhatia · 2026 · RSC Medicinal Chemistry
- BindingDB Entry 50013756: Scaffold repurposing of fendiline: Identification of potent KRAS plasma membrane localization inhibitors.BindingDB · 2022 · UC San Diego
- BindingDB Entry 50001273: Design, synthesis and biological evaluation of phosphopeptides as Polo-like kinase 1 Polo-box domain inhibitors.BindingDB · 2020 · UC San Diego
- BindingDB Entry 50009378: Allosteric Modulator Discovery: From Serendipity to Structure-Based Design.BindingDB · 2021 · UC San Diego
- BindingDB Entry 50006764: Small Molecule Allosteric Modulators of G-Protein-Coupled Receptors: Drug-Target Interactions.BindingDB · 2021 · UC San Diego