Unraveling structural mechanisms of allosteric drug action

How to improve R&D productivity: the pharmaceutical industry's grand challenge

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Mechanism of Activation of the RAF-ERK Signaling Pathway by Oncogenic Mutations of B-RAF

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The Conformational Plasticity of Protein Kinases

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An allosteric mechanism for activation of the kinase domain of epidermal growth factor receptor

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Mechanism of CDK activation revealed by the structure of a cyclinA-CDK2 complex

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Evolutionarily Conserved Pathways of Energetic Connectivity in Protein Families

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Evolutionarily conserved networks of residues mediate allosteric communication in proteins

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The Dynamic Process of β2-Adrenergic Receptor Activation

Nygaard, R., Zou, Y., Dror, R. O., Mildorf, T. J., Arlow, D. H., Manglik, A., Pan, A. C., Liu, C. W., Fung, J. J., Bokoch, M. P., et al. (2013) · Cell · doi:10.1016/j.cell.2013.01.008 · Cited by 797 · see citing works

Allostery in Disease and in Drug Discovery

Nussinov, R., & Tsai, C. (2013) · Cell · doi:10.1016/j.cell.2013.03.034 · Cited by 764 · see citing works

Allosteric Mechanisms of Signal Transduction

Changeux, J., & Edelstein, S. J. (2005) · Science · doi:10.1126/science.1108595 · Cited by 748 · see citing works

BAX activation is initiated at a novel interaction site

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Allosteric Modulation of G Protein–Coupled Receptors

May, L. T., Leach, K., Sexton, P. M., & Christopoulos, A. (2006) · The Annual Review of Pharmacology and Toxicology · doi:10.1146/annurev.pharmtox.47.120505.105159 · Cited by 698 · see citing works

Molecular Mechanism of β-Arrestin-Biased Agonism at Seven-Transmembrane Receptors

Reiter, É., Ahn, S., Shukla, A. K., & Lefkowitz, R. J. (2011) · The Annual Review of Pharmacology and Toxicology · doi:10.1146/annurev.pharmtox.010909.105800 · Cited by 582 · see citing works

Protein activity regulation by conformational entropy

Tzeng, S.-R., & Kalodimos, C. G. (2012) · Nature · doi:10.1038/nature11271 · Cited by 545 · see citing works

The two-state model of receptor activation

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Emerging paradigms in GPCR allostery: implications for drug discovery

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Allostery: Absence of a change in shape does not imply that allostery is not at play

Tsai, C.-J., del Sol, A., & Nussinov, R. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.02.034 · Cited by 453 · see citing works

A Unified View of “How Allostery Works”

Tsai, C.-J., & Nussinov, R. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003394 · Cited by 401 · see citing works

The Origin of Allosteric Functional Modulation: Multiple Pre-existing Pathways

del Sol, A., Tsai, C., Ma, B., & Nussinov, R. (2009) · Structure · doi:10.1016/j.str.2009.06.008 · Cited by 365 · see citing works

Ligand binding and micro-switches in 7TM receptor structures

Nygaard, R., Frimurer, T. M., Holst, B., ROSENKILDE, M. M., & Schwartz, T. W. (2009) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2009.02.006 · Cited by 347 · see citing works

Surface Sites for Engineering Allosteric Control in Proteins

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Searching for new allosteric sites in enzymes

Hardy, J. A., & Wells, J. A. (2004) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2004.10.009 · Cited by 330 · see citing works

Catalytic Control in the EGF Receptor and Its Connection to General Kinase Regulatory Mechanisms

Jura, N., Zhang, X., Endres, N. F., Seeliger, M. A., Schindler, T., & Kuriyan, J. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.03.004 · Cited by 310 · see citing works

Drugs for Allosteric Sites on Receptors

Wenthur, C. J., Gentry, P. R., Mathews, T. P., & Lindsley, C. W. (2011) · The Annual Review of Pharmacology and Toxicology · doi:10.1146/annurev-pharmtox-010611-134525 · Cited by 274 · see citing works

Energy Landscapes as a Tool to Integrate GPCR Structure, Dynamics, and Function

Deupí, X., & Kobilka, B. K. (2010) · Physiology · doi:10.1152/physiol.00002.2010 · Cited by 265 · see citing works

Mapping allostery through the covariance analysis of NMR chemical shifts

Selvaratnam, R., Chowdhury, S., VanSchouwen, B., & Melacini, G. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1017311108 · Cited by 228 · see citing works

Quantifying Correlations Between Allosteric Sites in Thermodynamic Ensembles

McClendon, C. L., Friedland, G. D., Mobley, D. L., Amirkhani, H., & Jacobson, M. P. (2009) · Journal of Chemical Theory and Computation · doi:10.1021/ct9001812 · Cited by 227 · see citing works

Structural basis for cAMP-mediated allosteric control of the catabolite activator protein

Popovych, N., Tzeng, S., Tonelli, M., Ebright, R. H., & Kalodimos, C. G. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0900595106 · Cited by 218 · see citing works

A new, structurally nonredundant, diverse data set of protein–protein interfaces and its implications

Keskin, Ö., Tsai, C., Wolfson, H. J., & Nussinov, R. (2004) · Protein Science · doi:10.1110/ps.03484604 · Cited by 198 · see citing works

Modeling the Functional Effects of Allosteric Modulators at Pharmacological Receptors: An Extension of the Two-State Model of Receptor Activation

Hall, D. A. (2000) · Molecular Pharmacology · doi:10.1124/mol.58.6.1412 · Cited by 185 · see citing works

The Underappreciated Role of Allostery in the Cellular Network

Nussinov, R., Tsai, C., & Ma, B. (2013) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-083012-130257 · Cited by 174 · see citing works

Turning a protein kinase on or off from a single allosteric site via disulfide trapping

Sadowsky, J., Burlingame, M. A., Wolan, D. W., McClendon, C. L., Jacobson, M. P., & Wells, J. A. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1102376108 · Cited by 155 · see citing works

Allo-network drugs: harnessing allostery in cellular networks

Nussinov, R., Tsai, C., & Csermely, P. (2011) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2011.08.004 · Cited by 143 · see citing works

Structure and allosteric effects of low-molecular-weight activators on the protein kinase PDK1

Hindie, V., Stroba, A., Zhang, H., Lopez-Garcia, L. A., Idrissova, L., Zeuzem, S., Hirschberg, D., Schaeffer, F., Jørgensen, T. J. D., Engel, M., et al. (2009) · Nature Chemical Biology · doi:10.1038/nchembio.208 · Cited by 141 · see citing works

The Different Ways through Which Specificity Works in Orthosteric and Allosteric Drugs

Nussinov, R., & Tsai, C. (2012) · Current Pharmaceutical Design · doi:10.2174/138161212799436377 · Cited by 139 · see citing works

Raloxifene: A Selective Estrogen Receptor Modulator (SERM) with Multiple Target System Effects

Muchmore, D. B. (2000) · The Oncologist · doi:10.1634/theoncologist.5-5-388 · Cited by 133 · see citing works

‘7TM Receptor Allostery: Putting Numbers to Shapeshifting Proteins

Kenakin, T. (2009) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2009.06.007 · Cited by 126 · see citing works

Protein-Protein Interfaces: Architectures and Interactions in Protein-Protein Interfaces and in Protein Cores. Their Similarities and Differences

Tsai, C., Lin, S. L., Wolfson, H. J., & Nussinov, R. (1996) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.3109/10409239609106582 · Cited by 117 · see citing works

Allosteric Communication Occurs via Networks of Tertiary and Quaternary Motions in Proteins

Daily, M. D., & Gray, J. J. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000293 · Cited by 116 · see citing works

Novel Allosteric Agonists of M1 Muscarinic Acetylcholine Receptors Induce Brain Region-Specific Responses That Correspond with Behavioral Effects in Animal Models

Digby, G. J., Noetzel, M. J., Bubser, M., Utley, T. J., Walker, A. G., Byun, N. E., Lebois, E. P., Xiang, Z., Sheffler, D. J., Cho, H. P., et al. (2012) · Journal of Neuroscience · doi:10.1523/jneurosci.0337-12.2012 · Cited by 113 · see citing works

Allosteric activation of the protein kinase PDK1 with low molecular weight compounds

Engel, M., Hindie, V., Lopez-Garcia, L. A., Stroba, A., Schaeffer, F., Adrian, I., Imig, J., Idrissova, L., Nastainczyk, W., Zeuzem, S., et al. (2006) · The EMBO Journal · doi:10.1038/sj.emboj.7601416 · Cited by 110 · see citing works

Transient Non-native Hydrogen Bonds Promote Activation of a Signaling Protein

Gardino, A. K., Villali, J., Kivenson, A., Lei, M., Liu, C. F., Steindel, P. A., Eisenmesser, E. Z., Labeikovsky, W., Wolf‐Watz, M., Clarkson, M. W., et al. (2009) · Cell · doi:10.1016/j.cell.2009.11.022 · Cited by 107 · see citing works

Contact rearrangements form coupled networks from local motions in allosteric proteins

Daily, M. D., Upadhyaya, T. J., & Gray, J. J. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21800 · Cited by 103 · see citing works

Substrate-Selective Inhibition of Protein Kinase PDK1 by Small Compounds that Bind to the PIF-Pocket Allosteric Docking Site

Busschots, K., Lopez-Garcia, L. A., Lammi, C., Stroba, A., Zeuzem, S., Piiper, A., Alzari, P. M., Neimanis, S., Arencibia, J. M., Engel, M., et al. (2012) · Chemistry & Biology · doi:10.1016/j.chembiol.2012.07.017 · Cited by 83 · see citing works

Computational Modeling of Allosteric Communication Reveals Organizing Principles of Mutation-Induced Signaling in ABL and EGFR Kinases

Dixit, A., & Verkhivker, G. M. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002179 · Cited by 81 · see citing works

The Pharmacology of Imepitoin: The First Partial Benzodiazepine Receptor Agonist Developed for the Treatment of Epilepsy

Rundfeldt, C., & Löscher, W. (2013) · CNS Drugs · doi:10.1007/s40263-013-0129-z · Cited by 76 · see citing works

3,5-Diphenylpent-2-enoic Acids as Allosteric Activators of the Protein Kinase PDK1: Structure−Activity Relationships and Thermodynamic Characterization of Binding as Paradigms for PIF-Binding Pocket-Targeting Compounds†PDB code of 2Z with PDK1: 3HRF.

Stroba, A., Schaeffer, F., Hindie, V., Lopez-Garcia, L. A., Adrian, I., Fröhner, W., Hartmann, R. W., Biondi, R. M., & Engel, M. (2009) · Journal of Medicinal Chemistry · doi:10.1021/jm9001499 · Cited by 75 · see citing works

MCPath: Monte Carlo path generation approach to predict likely allosteric pathways and functional residues

Kaya, C., Armutlulu, A., Ekesan, Ş., & Haliloǧlu, T. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt284 · Cited by 72 · see citing works

Ligand-binding dynamics rewire cellular signaling via estrogen receptor-α

Srinivasan, S., Nwachukwu, J. C., Parent, A. A., Cavett, V. J., Nowak, J., Hughes, T., Kojetin, D. J., Katzenellenbogen, J. A., & Nettles, K. W. (2013) · Nature Chemical Biology · doi:10.1038/nchembio.1214 · Cited by 70 · see citing works

Allosteric Communication across the Native and Mutated KIT Receptor Tyrosine Kinase

Laine, É., Auclair, C., & Tchertanov, L. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002661 · Cited by 65 · see citing works

Cyclic AMP Analog Blocks Kinase Activation by Stabilizing Inactive Conformation: Conformational Selection Highlights a New Concept in Allosteric Inhibitor Design

Badireddy, S., Yunfeng, G., Ritchie, M. A., Akamine, P., Wu, J., Kim, C., Taylor, S. S., Lin, Q., Swaminathan, K., & Anand, G. S. (2010) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m110.004390 · Cited by 65 · see citing works

Screened Nonbonded Interactions in Native Proteins Manipulate Optimal Paths for Robust Residue Communication

Atılgan, A. R., Turgut, D., & Atılgan, C. (2007) · Biophysical Journal · doi:10.1529/biophysj.106.099440 · Cited by 63 · see citing works

The allosteric communication pathways in KIX domain of CBP

Palazzesi, F., Barducci, A., Tollinger, M., & Parrinello, M. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1313548110 · Cited by 62 · see citing works

Allosteric Conformational Barcodes Direct Signaling in the Cell

Nussinov, R., Ma, B., Tsai, C.-J., & Csermely, P. (2013) · Structure · doi:10.1016/j.str.2013.06.002 · Cited by 55 · see citing works

The Arginine of the DRY Motif in Transmembrane Segment III Functions as a Balancing Micro-switch in the Activation of the β2-Adrenergic Receptor

Valentin-Hansen, L., Groenen, M., Nygaard, R., Frimurer, T. M., Holliday, N. D., & Schwartz, T. W. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.348565 · Cited by 45 · see citing works

Conformational Control of the Binding of the Transactivation Domain of the MLL Protein and c-Myb to the KIX Domain of CREB

Korkmaz, E. N., Nussinov, R., & Haliloǧlu, T. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002420 · Cited by 40 · see citing works

Three Sites and You Are Out: Ternary Synergistic Allostery Controls Aromatic Amino Acid Biosynthesis in Mycobacterium tuberculosis

Blackmore, N. J., Reichau, S., Jiao, W., Hutton, R. D., Baker, E. N., Jameson, G. B., & Parker, E. J. (2012) · Journal of Molecular Biology · doi:10.1016/j.jmb.2012.12.019 · Cited by 39 · see citing works

PheVI:09 (Phe6.44) as a Sliding Microswitch in Seven-transmembrane (7TM) G Protein-coupled Receptor Activation

Valentin-Hansen, L., Holst, B., Frimurer, T. M., & Schwartz, T. W. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.395137 · Cited by 37 · see citing works

The role of allostery in the ubiquitin–proteasome system

Liu, J., & Nussinov, R. (2012) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.3109/10409238.2012.742856 · Cited by 35 · see citing works

Dissecting the cAMP‐inducible allosteric switch in protein kinase A RIα

Sjoberg, T. J., Kornev, A. P., & Taylor, S. S. (2010) · Protein Science · doi:10.1002/pro.400 · Cited by 28 · see citing works

Allosteric inhibition via R-state destabilization in ATP sulfurylase from Penicillium chrysogenum

MacRae, I. J., Segel, I. H., & Fisher, A. J. (2002) · Nature Structural Biology · doi:10.1038/nsb868 · Cited by 24 · see citing works

cAMP-dependent allostery and dynamics in Epac: an NMR view

Selvaratnam, R., Akimoto, M., VanSchouwen, B., & Melacini, G. (2012) · Biochemical Society Transactions · doi:10.1042/bst20110628 · Cited by 23 · see citing works

Dynamic Fluctuations Provide the Basis of a Conformational Switch Mechanism in Apo Cyclic AMP Receptor Protein

Fas, B. A., Tutar, Y., & Haliloǧlu, T. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003141 · Cited by 12 · see citing works

Utilizing a Dynamical Description of IspH to Aid in the Development of Novel Antimicrobial Drugs

Blachly, P. G., de Oliveira, C. A. F., Williams, S., & McCammon, J. A. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003395 · Cited by 9 · see citing works

Cyclicamp Analog Blocks Kinase Activation by Stabilizing Inactive Conformation: Conformational Selection Highlights a New Concept in Allosteric Inhibitor Design

Badireddy, S., Yunfeng, G., Ritchie, M. A., et al. (2013) · OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) · Cited by 6 · see citing works

Small-Molecule Inhibitors of Protein-Protein Interactions: Progressing toward the Reality

Arkin, M. R., Tang, Y., & Wells, J. A. (2014) · Chemistry & Biology · doi:10.1016/j.chembiol.2014.09.001 · Cited by 1,065 · see citing works

G protein-coupled receptors (GPCRs): advances in structures, mechanisms and drug discovery

Zhang, M., Chen, T., Lu, X., Lan, X., Chen, K., & Lu, S. (2024) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-024-01803-6 · Cited by 520 · see citing works

Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell

Wei, G., Xi, W., Nussinov, R., & Ma, B. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00562 · Cited by 436 · see citing works

Anticancer drug resistance: An update and perspective

Nussinov, R., Tsai, C., & Jang, H. (2021) · Drug Resistance Updates · doi:10.1016/j.drup.2021.100796 · Cited by 395 · see citing works

Ras Conformational Ensembles, Allostery, and Signaling

Lu, S., Jang, H., Muratcioglu, S., Gursoy, A., Keskin, O., Nussinov, R., & Zhang, J. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00542 · Cited by 355 · see citing works

Allostery without a conformational change? Revisiting the paradigm

Nussinov, R., & Tsai, C.-J. (2015) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2014.11.005 · Cited by 202 · see citing works

AlphaFold, Artificial Intelligence (AI), and Allostery

Nussinov, R., Zhang, M., Liu, Y., & Jang, H. (2022) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.2c04346 · Cited by 190 · see citing works

PI3K inhibitors: review and new strategies

Zhang, M., Jang, H., & Nussinov, R. (2020) · Chemical Science · doi:10.1039/d0sc01676d · Cited by 182 · see citing works

Allosteric Methods and Their Applications: Facilitating the Discovery of Allosteric Drugs and the Investigation of Allosteric Mechanisms

Lu, S., Shen, Q., & Zhang, J. (2019) · Accounts of Chemical Research · doi:10.1021/acs.accounts.8b00570 · Cited by 166 · see citing works

Principles of Allosteric Interactions in Cell Signaling

Nussinov, R., Tsai, C.-J., & Liu, J. (2014) · Journal of the American Chemical Society · doi:10.1021/ja510028c · Cited by 154 · see citing works

Improved Method for the Identification and Validation of Allosteric Sites

Song, K., Liu, X., Huang, W., Lu, S., Shen, Q., Zhang, L., & Zhang, J. (2017) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.7b00014 · Cited by 152 · see citing works

Allosteric sites: remote control in regulation of protein activity

Guarnera, E., & Berezovsky, I. N. (2015) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2015.10.004 · Cited by 149 · see citing works

Rational design of selective allosteric inhibitors of PHGDH and serine synthesis with anti-tumor activity

Wang, Q., Liberti, M. V., Liu, P., Deng, X., Liu, Y., Locasale, J. W., & Lai, L. (2017) · Cell Chemical Biology · doi:10.1016/j.chembiol.2016.11.013 · Cited by 147 · see citing works

Structure-Based Statistical Mechanical Model Accounts for the Causality and Energetics of Allosteric Communication

Guarnera, E., & Berezovsky, I. N. (2016) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004678 · Cited by 141 · see citing works

Introduction to Protein Ensembles and Allostery

Nussinov, R. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.6b00283 · Cited by 135 · see citing works

AlloPred: prediction of allosteric pockets on proteins using normal mode perturbation analysis

Greener, J. G., & Sternberg, M. J. E. (2015) · BMC Bioinformatics · doi:10.1186/s12859-015-0771-1 · Cited by 134 · see citing works

Expanding the Paradigm: Intrinsically Disordered Proteins and Allosteric Regulation

Berlow, R. B., Dyson, H. J., & Wright, P. E. (2018) · Journal of Molecular Biology · doi:10.1016/j.jmb.2018.04.003 · Cited by 129 · see citing works

Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers

Nussinov, R., Jang, H., Tsai, C., & Cheng, F. (2019) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006658 · Cited by 129 · see citing works

ASD v3.0: unraveling allosteric regulation with structural mechanisms and biological networks

Shen, Q., Wang, G., Li, S., Liu, X., Lu, S., Chen, Z., Song, K., Yan, J., Geng, L., Huang, Z., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv902 · Cited by 122 · see citing works

The Design of Covalent Allosteric Drugs

Nussinov, R., & Tsai, C.-J. (2015) · Annual Review of Pharmacology and Toxicology · doi:10.1146/annurev-pharmtox-010814-124401 · Cited by 112 · see citing works

Hidden electrostatic basis of dynamic allostery in a PDZ domain

Kumawat, A., & Chakrabarty, S. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1705311114 · Cited by 97 · see citing works

AlphaFold, allosteric, and orthosteric drug discovery: Ways forward

Nussinov, R., Zhang, M., Liu, Y., & Jang, H. (2023) · Drug Discovery Today · doi:10.1016/j.drudis.2023.103551 · Cited by 96 · see citing works

Emergence of allosteric drug-resistance mutations: new challenges for allosteric drug discovery

Lu, S., Qiu, Y., Ni, D., He, X., Pu, J., & Zhang, J. (2019) · Drug Discovery Today · doi:10.1016/j.drudis.2019.10.006 · Cited by 94 · see citing works

Mechanism of allosteric activation of SIRT6 revealed by the action of rationally designed activators

Lu, S., Chen, Y.-Y., Wei, J., Zhao, M., Ni, D., He, X., & Zhang, J. (2020) · Acta Pharmaceutica Sinica B · doi:10.1016/j.apsb.2020.09.010 · Cited by 93 · see citing works

Structure-based prediction of protein allostery

Greener, J. G., & Sternberg, M. J. (2018) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2017.10.002 · Cited by 91 · see citing works

Toward Comprehensive Allosteric Control over Protein Activity

Guarnera, E., & Berezovsky, I. N. (2019) · Structure · doi:10.1016/j.str.2019.01.014 · Cited by 91 · see citing works

Advances in NMR Methods To Map Allosteric Sites: From Models to Translation

Boulton, S., & Melacini, G. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00718 · Cited by 89 · see citing works

The Structural Basis of ATP as an Allosteric Modulator

Lu, S., Huang, W., Wang, Q., Shen, Q., Li, S., Nussinov, R., & Zhang, J. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003831 · Cited by 86 · see citing works

Bidirectional Allosteric Communication between the ATP-Binding Site and the Regulatory PIF Pocket in PDK1 Protein Kinase

Schulze, J. O., Saladino, G., Busschots, K., Neimanis, S., Süß, E., Odadzic, D., Zeuzem, S., Hindie, V., Herbrand, A. K., Lisa, M., et al. (2016) · Cell chemical biology · doi:10.1016/j.chembiol.2016.06.017 · Cited by 84 · see citing works

2P2Idb v2: update of a structural database dedicated to orthosteric modulation of protein–protein interactions

Basse, M.-J., Betzi, S., Morelli, X., & Roche, P. (2016) · Database · doi:10.1093/database/baw007 · Cited by 83 · see citing works

Transient receptor potential vanilloid type 1 antagonists: a patent review (2011 – 2014)

Lee, Y., Hong, S., Cui, M., Sharma, P. K., Lee, J., & Choi, S. (2015) · Expert Opinion on Therapeutic Patents · doi:10.1517/13543776.2015.1008449 · Cited by 80 · see citing works

The Key Role of Calmodulin in KRAS-Driven Adenocarcinomas

Nussinov, R., Muratcioğlu, S., Tsai, C., Jang, H., Gürsoy, A., & Keskin, Ö. (2015) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-15-0165 · Cited by 77 · see citing works

Cell sensitivity, non-linearity and inverse effects

Bellavite, P., Signorini, A. M., Marzotto, M., Moratti, E., Bonafini, C., & Olioso, D. (2015) · Homeopathy · doi:10.1016/j.homp.2015.02.002 · Cited by 73 · see citing works

Computer-Aided Drug Discovery for Undruggable Targets

Sun, Q., Wang, H., Xie, J., Wang, L., Mu, J., Li, J., Ren, Y., & Lai, L. (2025) · Chemical Reviews · doi:10.1021/acs.chemrev.4c00969 · Cited by 69 · see citing works

Allostery: Allosteric Cancer Drivers and Innovative Allosteric Drugs

Nussinov, R., Zhang, M., Maloney, R., Liu, Y., Tsai, C.-J., & Jang, H. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2022.167569 · Cited by 66 · see citing works

Phosphorylated Calmodulin Promotes PI3K Activation by Binding to the SH2 Domains

Zhang, M., Jang, H., Gaponenko, V., & Nussinov, R. (2017) · Biophysical Journal · doi:10.1016/j.bpj.2017.09.008 · Cited by 64 · see citing works

Mechanism of cAMP Partial Agonism in Protein Kinase G (PKG)

VanSchouwen, B., Selvaratnam, R., Giri, R., Lorenz, R., Herberg, F. W., Kim, C., & Melacini, G. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m115.685305 · Cited by 55 · see citing works

Computational design of ligand-binding proteins

Yang, W., & Lai, L. (2016) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2016.11.021 · Cited by 52 · see citing works

Renaissance of Allostery to Disrupt Protein Kinase Interactions

Leroux, A. E., & Biondi, R. M. (2019) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2019.09.007 · Cited by 51 · see citing works

Conformational landscape of the epidermal growth factor receptor kinase reveals a mutant specific allosteric pocket

Kannan, S., Venkatachalam, G., Lim, H. H., Surana, U., & Verma, C. S. (2018) · Chemical Science · doi:10.1039/c8sc01262h · Cited by 48 · see citing works

Synergistic Allosteric Mechanism of Fructose-1,6-bisphosphate and Serine for Pyruvate Kinase M2 via Dynamics Fluctuation Network Analysis

Yang, J., Liu, H., Liu, X., Gu, C., Luo, R., & Chen, H. (2016) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.6b00115 · Cited by 46 · see citing works

Engineered control of enzyme structural dynamics and function

Boehr, D. D., D’Amico, R. N., & O’Rourke, K. F. (2018) · Protein Science · doi:10.1002/pro.3379 · Cited by 45 · see citing works

Emerging Allosteric Mechanism of EGFR Activation in Physiological and Pathological Contexts

Tsai, C., & Nussinov, R. (2019) · Biophysical Journal · doi:10.1016/j.bpj.2019.05.021 · Cited by 44 · see citing works

PI3K Driver Mutations: A Biophysical Membrane-Centric Perspective

Zhang, M., Jang, H., & Nussinov, R. (2020) · Cancer Research · doi:10.1158/0008-5472.can-20-0911 · Cited by 41 · see citing works

Harnessing Reversed Allosteric Communication: A Novel Strategy for Allosteric Drug Discovery

Fan, J., Liu, Y., Kong, R., Ni, D., Yu, Z., Lu, S., & Zhang, J. (2021) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.1c01695 · Cited by 41 · see citing works

Targeting allosteric regulation of cancer metabolism

Kremer, D. M., & Lyssiotis, C. A. (2022) · Nature Chemical Biology · doi:10.1038/s41589-022-00997-6 · Cited by 40 · see citing works

Bcr-Abl Allosteric Inhibitors: Where We Are and Where We Are Going to

Carofiglio, F., Trisciuzzi, D., Gambacorta, N., Leonetti, F., Stefanachi, A., & Nicolotti, O. (2020) · Molecules · doi:10.3390/molecules25184210 · Cited by 38 · see citing works

Coevolution-based prediction of key allosteric residues for protein function regulation

Xie, J., Zhang, W., Zhu, X., Deng, M., & Lai, L. (2023) · eLife · doi:10.7554/elife.81850 · Cited by 38 · see citing works

Decrypting Allostery in Membrane-Bound K-Ras4B Using Complementary In Silico Approaches Based on Unbiased Molecular Dynamics Simulations

Castelli, M., Marchetti, F., Osuna, S., Oliveira, A. S. F., Mulholland, A. J., Serapian, S. A., & Colombo, G. (2023) · Journal of the American Chemical Society · doi:10.1021/jacs.3c11396 · Cited by 38 · see citing works

Efficient Nonequilibrium Method for Binding Free Energy Calculations in Molecular Dynamics Simulations

Sandberg, R. B., Banchelli, M., Guardiani, C., Menichetti, S., Caminati, G., & Procacci, P. (2015) · Journal of Chemical Theory and Computation · doi:10.1021/ct500964e · Cited by 36 · see citing works

Learning About Allosteric Drugs and Ways to Design Them

Tan, Z. W., Tee, W.-V., & Berezovsky, I. N. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2022.167692 · Cited by 36 · see citing works

Autoinhibition can identify rare driver mutations and advise pharmacology

Nussinov, R., Tsai, C., & Jang, H. (2019) · The FASEB Journal · doi:10.1096/fj.201901341r · Cited by 35 · see citing works

Pioneer in Molecular Biology: Conformational Ensembles in Molecular Recognition, Allostery, and Cell Function

Nussinov, R. (2025) · Journal of Molecular Biology · doi:10.1016/j.jmb.2025.169044 · Cited by 33 · see citing works

Engineering an Allosteric Control of Protein Function

Vishweshwaraiah, Y. L., Chen, J., & Dokholyan, N. V. (2021) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.0c11640 · Cited by 33 · see citing works

Alloscore: a method for predicting allosteric ligand–protein interactions

Li, S., Shen, Q., Su, M., Liu, X., Lu, S., Chen, Z., Wang, R., & Zhang, J. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw036 · Cited by 32 · see citing works

Computational Tools for Allosteric Drug Discovery: Site Identification and Focus Library Design

Huang, W., Nussinov, R., & Zhang, J. (2016) · Methods in molecular biology · doi:10.1007/978-1-4939-6637-0_23 · Cited by 31 · see citing works

Measurement of State-Specific Association Constants in Allosteric Sensors through Molecular Stapling and NMR

Moleschi, K., Akimoto, M., & Melacini, G. (2015) · Journal of the American Chemical Society · doi:10.1021/jacs.5b06557 · Cited by 30 · see citing works

K-Ras4B/calmodulin/PI3Kα: A promising new adenocarcinoma-specific drug target?

Nussinov, R., Muratcioğlu, S., Tsai, C., Jang, H., Gürsoy, A., & Keskin, Ö. (2015) · Expert Opinion on Therapeutic Targets · doi:10.1517/14728222.2016.1135131 · Cited by 30 · see citing works

Mechanism of activation and the rewired network: New drug design concepts

Nussinov, R., Zhang, M., Maloney, R., Tsai, C., Yavuz, B. R., Tunçbağ, N., & Jang, H. (2021) · Medicinal Research Reviews · doi:10.1002/med.21863 · Cited by 30 · see citing works

Predicting Allosteric Effects from Orthosteric Binding in Hsp90-Ligand Interactions: Implications for Fragment-Based Drug Design

Chandramohan, A., Krishnamurthy, S., Larsson, A., Nordlund, P., Jansson, A. E., & Anand, G. S. (2016) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004840 · Cited by 30 · see citing works

The value of protein allostery in rational anticancer drug design: an update

Nussinov, R., & Jang, H. (2024) · Expert Opinion on Drug Discovery · doi:10.1080/17460441.2024.2384467 · Cited by 29 · see citing works

Phosphorylation mediated structural and functional changes in pentameric ligand-gated ion channels: Implications for drug discovery

Talwar, S., & Lynch, J. W. (2014) · The International Journal of Biochemistry & Cell Biology · doi:10.1016/j.biocel.2014.05.028 · Cited by 28 · see citing works

Allosteric activation of RAF in the MAPK signaling pathway

Tsai, C., & Nussinov, R. (2018) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2018.07.007 · Cited by 27 · see citing works

Role of Dynamics in the Autoinhibition and Activation of the Hyperpolarization-activated Cyclic Nucleotide-modulated (HCN) Ion Channels

VanSchouwen, B., Akimoto, M., Sayadi, M., Fogolari, F., & Melacini, G. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m115.651877 · Cited by 25 · see citing works

Conservation and Diversity in Allosteric Fingerprints of Proteins for Evolutionary-inspired Engineering and Design

Tee, W.-V., Tan, Z. W., Guarnera, E., & Berezovsky, I. N. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2022.167577 · Cited by 25 · see citing works

Dynamics Correlation Network for Allosteric Switching of PreQ1 Riboswitch

Wang, W., Jiang, C., Zhang, J., Ye, W., Luo, R., & Chen, H. (2016) · Scientific Reports · doi:10.1038/srep31005 · Cited by 24 · see citing works

Allosteric Type and Pathways Are Governed by the Forces of Protein–Ligand Binding

Huang, Q., Song, P., Chen, Y., Liu, Z., & Lai, L. (2021) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.1c01253 · Cited by 24 · see citing works

Identification of an allosteric hotspot for additive activation of PPARγ in antidiabetic effects

Li, F., Lu, S., Zheng, Z., Chen, Y., Zhao, Y., Song, K., Xue, H., Jin, L., Li, Y., Huang, C., et al. (2021) · 中国科学通报：英文版 · doi:10.1016/j.scib.2021.01.023 · Cited by 24 · see citing works

A novel allosteric site in casein kinase 2α discovered using combining bioinformatics and biochemistry methods

Jiang, H., Dong, J.-K., Song, K., Wang, T., Huang, W., Zhang, J.-M., Yang, X.-Y., Shen, Y. H., & Zhang, J. (2017) · Acta Pharmacologica Sinica · doi:10.1038/aps.2017.55 · Cited by 23 · see citing works

Dynamics Govern Specificity of a Protein-Protein Interface: Substrate Recognition by Thrombin

Fuchs, J. E., Huber, R. G., Waldner, B. J., Kahler, U., von Grafenstein, S., Krämer, C., & Liedl, K. R. (2015) · PLoS ONE · doi:10.1371/journal.pone.0140713 · Cited by 23 · see citing works

Molecular dynamics simulations reveal the allosteric effect of F1174C resistance mutation to ceritinib in ALK-associated lung cancer

Ni, Z., Wang, X., Zhang, T., & Jin, R. (2016) · Computational Biology and Chemistry · doi:10.1016/j.compbiolchem.2016.10.005 · Cited by 23 · see citing works

Characteristics of Allosteric Proteins, Sites, and Modulators

He, X., Ni, D., Lu, S., & Zhang, J. (2019) · Advances in experimental medicine and biology · doi:10.1007/978-981-13-8719-7_6 · Cited by 22 · see citing works

Role of Protein Dimeric Interface in Allosteric Inhibition of N-Acetyl-Aspartate Hydrolysis by Human Aspartoacylase

Kots, E. D., Lushchekina, S. V., Varfolomeev, S. D., & Nemukhin, A. V. (2017) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.7b00133 · Cited by 22 · see citing works

Probing the Activity Modification Space of the Cysteine Peptidase Cathepsin K with Novel Allosteric Modifiers

Novinec, M., Lenar≷cic̆, B., & Baici, A. (2014) · PLoS ONE · doi:10.1371/journal.pone.0106642 · Cited by 22 · see citing works

Parallel Allostery by cAMP and PDE Coordinates Activation and Termination Phases in cAMP Signaling

Krishnamurthy, S., Tulsian, N. K., Chandramohan, A., & Anand, G. S. (2015) · Biophysical Journal · doi:10.1016/j.bpj.2015.06.067 · Cited by 22 · see citing works

Calcium-Mediated Control of S100 Proteins: Allosteric Communication via an Agitator/Signal Blocking Mechanism

Xiao, Y., Shaw, G. S., & Konermann, L. (2017) · Journal of the American Chemical Society · doi:10.1021/jacs.7b04380 · Cited by 22 · see citing works

Self-organization, entropy and allostery

Kornev, A. P. (2018) · Biochemical Society Transactions · doi:10.1042/bst20160144 · Cited by 22 · see citing works

A journey from molecule to physiology and in silico tools for drug discovery targeting the transient receptor potential vanilloid type 1 (TRPV1) channel

Amaya-Rodriguez, C. A., Carvajal-Zamorano, K., Bustos, D., Alegría‐Arcos, M., & Castillo, K. (2024) · Frontiers in Pharmacology · doi:10.3389/fphar.2023.1251061 · Cited by 21 · see citing works

Calmodulin and IQGAP1 activation of PI3Kα and Akt in KRAS, HRAS and NRAS-driven cancers

Nussinov, R., Zhang, M., Tsai, C., & Jang, H. (2017) · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease · doi:10.1016/j.bbadis.2017.10.032 · Cited by 20 · see citing works

Allostery in Disease: Anticancer Drugs, Pockets, and the Tumor Heterogeneity Challenge

Nussinov, R., Yavuz, B. R., & Jang, H. (2025) · Journal of Molecular Biology · doi:10.1016/j.jmb.2025.169050 · Cited by 19 · see citing works

Allosteric mechanism of cyclopropylindolobenzazepine inhibitors for HCV NS5B RdRp via dynamic correlation network analysis

Rahman, M. U., Liu, H., Wadood, A., & Chen, H. (2016) · Molecular BioSystems · doi:10.1039/c6mb00521g · Cited by 19 · see citing works

Dynamic Protein Allosteric Regulation and Disease

Nussinov, R., Tsai, C.-J., & Jang, H. (2019) · Advances in Experimental Medicine and Biology · doi:10.1007/978-981-13-8719-7_2 · Cited by 18 · see citing works

Identification of an in vivo orally active dual-binding protein-protein interaction inhibitor targeting TNFα through combined in silico/in vitro/in vivo screening

Mouhsine, H., Guillemain, H., Moreau, G., Fourati, N., Zerrouki, C., Baron, B., Desallais, L., Gizzi, P., Nasr, N. B., Perrier, J., et al. (2017) · Scientific Reports · doi:10.1038/s41598-017-03427-z · Cited by 18 · see citing works

Emerging chemical scaffolds with potential SHP2 phosphatase inhibitory capabilities – A comprehensive review

Tripathi, R. K. P., & Ayyannan, S. R. (2020) · Chemical Biology & Drug Design · doi:10.1111/cbdd.13807 · Cited by 18 · see citing works

Evidence of Allosteric Enzyme Regulation via Changes in Conformational Dynamics: A Hydrogen/Deuterium Exchange Investigation of Dihydrodipicolinate Synthase

Sowole, M. A., Simpson, S., Skovpen, Y. V., Palmer, D. R. J., & Konermann, L. (2016) · Biochemistry · doi:10.1021/acs.biochem.6b00764 · Cited by 17 · see citing works

Sequence-dependent model of allosteric communication

Guarnera, E., & Berezovsky, I. N. (2023) · The Journal of Chemical Physics · doi:10.1063/5.0139848 · Cited by 17 · see citing works

Calmodulin (CaM) Activates PI3Kα by Targeting the “Soft” CaM-Binding Motifs in Both the nSH2 and cSH2 Domains of p85α

Zhang, M., Li, Z., Wang, G., Jang, H., Sacks, D. B., Zhang, J., Gaponenko, V., & Nussinov, R. (2018) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.8b05982 · Cited by 17 · see citing works

How does the novel T315L mutation of breakpoint cluster region-abelson (BCR-ABL) kinase confer resistance to ponatinib: a comparative molecular dynamics simulation study

Zhang, H., He, X., Ni, D., Mou, L., Chen, X., & Lu, S. (2019) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2019.1567390 · Cited by 16 · see citing works

Noncognate DNA damage prevents the formation of the active conformation of the Y‐family DNA polymerases DinB and DNA polymerase κ

Nevin, P., Lu, X., Zhang, K., Engen, J. R., & Beuning, P. J. (2015) · FEBS Journal · doi:10.1111/febs.13304 · Cited by 16 · see citing works

Probe into the Molecular Mechanism of Ibuprofen Interaction with Warfarin Bound to Human Serum Albumin in Comparison to Ascorbic and Salicylic Acids: Allosteric Inhibition of Anticoagulant Release

Kalhor, H. R., & Taghikhani, E. (2021) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.1c00352 · Cited by 15 · see citing works

Allosteric regulation of substrate channeling: Salmonella typhimurium tryptophan synthase

Ghosh, R. K., Hilario, E., Chang, C. A., Mueller, L. J., & Dunn, M. F. (2022) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2022.923042 · Cited by 14 · see citing works

Phosphorylation of the Hsp90 Co-Chaperone Hop Changes its Conformational Dynamics and Biological Function

Castelli, M., Bhattacharya, K., Abboud, E., Serapian, S. A., Picard, D., & Colombo, G. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2022.167931 · Cited by 14 · see citing works

Information flow and protein dynamics: the interplay between nuclear magnetic resonance spectroscopy and molecular dynamics simulations

Pastor, N., & Amero, C. (2015) · Frontiers in Plant Science · doi:10.3389/fpls.2015.00306 · Cited by 14 · see citing works

Leveraging conformational ensembles in allosteric drug discovery

Nussinov, R., Regev, C., & Jang, H. (2026) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2026.01.006 · Cited by 13 · see citing works

Conformational dynamics and kinetics of protein interactions by nuclear magnetic resonance

Moraes, A. H., & Valente, A. P. (2023) · Journal of Magnetic Resonance Open · doi:10.1016/j.jmro.2023.100093 · Cited by 13 · see citing works

Allosteric Inhibition of Bacterial Targets: An Opportunity for Discovery of Novel Antibacterial Classes

Meisel, J. E., Fisher, J. F., Chang, M., & Mobashery, S. (2017) · Topics in medicinal chemistry · doi:10.1007/7355_2017_21 · Cited by 13 · see citing works

Directed Evolution of the Escherichia coli cAMP Receptor Protein at the cAMP Pocket

Gunasekara, S. M., Hicks, M. N., Park, J., Brooks, C. L., Serate, J., Saunders, C. V., Grover, S. K., Goto, J. J., Lee, J., & Youn, H. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m115.678474 · Cited by 13 · see citing works

Mechanistic Insights into the Allosteric Inhibition of Androgen Receptors by Binding Function 3 Antagonists from an Integrated Molecular Modeling Study

Kong, X., Xing, E., Zhuang, T., Li, P., & Cheng, X. (2021) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.1c00124 · Cited by 12 · see citing works

Allosteric Regulation of the Soluble Epoxide Hydrolase by Nitro Fatty Acids: a Combined Experimental and Computational Approach

Qiu, Q., Abis, G., Mattingly-Peck, F., Lynham, S., Fraternali, F., & Conte, M. R. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2022.167600 · Cited by 11 · see citing works

Deciphering the T790M/L858R-Selective Inhibition Mechanism of an Allosteric Inhibitor of EGFR: Insights from Molecular Simulations

Li, M., & Guo, J. (2021) · ACS Chemical Neuroscience · doi:10.1021/acschemneuro.0c00633 · Cited by 11 · see citing works

Identifying and Quantifying Allosteric Drug Function

Kenakin, T. (2016) · Royal Society of Chemistry eBooks · doi:10.1039/9781782629276-00024 · Cited by 3 · see citing works

The Different Ways through Which Specificity Works in Orthosteric and Allosteric Drugs

Nussinov, R., & Tsai, C. (2012) · Current Pharmaceutical Design · doi:10.2174/138161212799436377 · Cited by 139 · see citing works

Allosteric Modulators

Lu, S., & Zhang, J. (2016) · Elsevier eBooks · doi:10.1016/b978-0-12-409547-2.12324-8 · Cited by 9 · see citing works

Allosteric sites: remote control in regulation of protein activity

Guarnera, E., & Berezovsky, I. N. (2015) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2015.10.004 · Cited by 149 · see citing works

Structural insights into allosteric GPCR drugs

Harrison, C. (2013) · Nature Reviews Drug Discovery · doi:10.1038/nrd4188 · Cited by 1 · see citing works