Small‐molecule protein–protein interaction inhibitors: Therapeutic potential in light of molecular size, chemical space, and ligand binding efficiency considerations
Abstract
As the ultimate function of proteins depends to a great extent on their binding partners, protein–protein interactions (PPIs) represent a treasure trove of possible new therapeutic targets. Unfortunately, interfaces involved in PPIs are not well‐suited for effective small molecule binding. Nevertheless, successful examples of small‐molecule PPI inhibitors (PPIIs) are beginning to accumulate, and the sheer number of PPIs that form the human interactome implies that, despite the relative unsuitability of PPIs to serve as “druggable” targets, small‐molecule PPIIs can still provide novel pharmacological tools and new innovative drugs in at least some areas. Here, after some illustrative examples, accumulating information on the binding efficiency, molecular size, and chemical space requirements will be briefly reviewed. Therapeutic success can only be achieved if these considerations are incorporated into the search process and if careful medicinal chemistry approaches are used to address the absorption, distribution, metabolism, and excretion requirements of larger molecules that are often needed for this target class due to the lower efficiency of binding. © 2010 IUBMB IUBMB Life, 62(10): 724–731, 2010
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Undruggable proteins possess flat active sites, often act through PPI networks, which are characterized by large, flat, and undefined interfaces between proteins; these networks have been considered undruggable biological processes for decades.
“Undruggable proteins, which possess flat active sites, often act through PPI networks, which are characterized by large, flat, and undefined interfaces between proteins. These networks have been considered undruggable biological processes for decades.309–311”
From Recent advances in targeting the “undruggable” proteins: from drug discovery to clinical trials (2023) · cites this paper as [309]
Cites
Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (2001) · Advanced Drug Delivery Reviews · doi:10.1016/s0169-409x(00)00129-0 · Cited by 18,139 · see citing works
Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (1997) · Advanced Drug Delivery Reviews · doi:10.1016/s0169-409x(96)00423-1 · Cited by 11,484 · see citing works
How to improve R&D productivity: the pharmaceutical industry's grand challenge
Paul, S. M., Mytelka, D. S., Dunwiddie, C. T., Persinger, C. C., Munos, B. H., Lindborg, S. R., & Schacht, A. L. (2010) · Nature Reviews Drug Discovery · doi:10.1038/nrd3078 · Cited by 3,566 · see citing works
How many drug targets are there?
Overington, J. P., Al-Lazikani, B., & Hopkins, A. L. (2006) · Nature Reviews Drug Discovery · doi:10.1038/nrd2199 · Cited by 3,505 · see citing works
Cytokine Storm in a Phase 1 Trial of the Anti-CD28 Monoclonal Antibody TGN1412
Suntharalingam, G., Perry, M. R., Ward, S., Brett, S. J., Castello-Cortes, A., Brunner, M. D., & Panoskaltsis, N. (2006) · New England Journal of Medicine · doi:10.1056/nejmoa063842 · Cited by 2,164 · cited 2× · see citing works
“TGN1412, an anti-CD28 superagonist monoclonal antibody that induced a life-threatening cytokine storm in the first human clinical patients pointing to the importance of species relevance (4), is likely to make development of such biotechnology compounds even more complicated (5).”
BackgroundAnatomy of hot spots in protein interfaces
Bogan, A. A., & Thorn, K. S. (1998) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.1843 · Cited by 1,988 · see citing works
Reaching for high-hanging fruit in drug discovery at protein–protein interfaces
Wells, J. A., & McClendon, C. L. (2007) · Nature · doi:10.1038/nature06526 · Cited by 1,963 · see citing works
Protein Therapeutics: A Summary and Pharmacological Classification
Leader, B., Baca, Q. J., & Golan, D. E. (2008) · Nature Reviews Drug Discovery · doi:10.1038/nrd2399 · Cited by 1,913 · see citing works
Ligand efficiency: a useful metric for lead selection
Hopkins, A. L., Groom, C. R., & Alex, A. (2004) · Drug Discovery Today · doi:10.1016/s1359-6446(04)03069-7 · Cited by 1,895 · see citing works
Small-molecule inhibitors of protein–protein interactions: progressing towards the dream
Arkin, M. R., & Wells, J. A. (2004) · Nature Reviews Drug Discovery · doi:10.1038/nrd1343 · Cited by 1,705 · see citing works
Dorr, P. K., Westby, M., Dobbs, S., Griffin, P., Irvine, B., Macartney, M. J., Mori, J., Rickett, G., Smith‐Burchnell, C., Napier, C. M., et al. (2005) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.49.11.4721-4732.2005 · Cited by 1,154 · see citing works
Estimating the size of the human interactome
Stumpf, M. P. H., Thorne, T., de Silva, E., Stewart, R., An, H. J., Lappé, M., & Wiuf, C. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0708078105 · Cited by 827 · see citing works
Small-Molecule Inhibition of TNF-α
He, M. M., Stroustrup, A., Oslob, J. D., Flanagan, W. M., Braisted, A. C., Whitty, A., Cancilla, M. T., Wang, J., Lugovskoy, A. A., Yoburn, J. C., et al. (2005) · Science · doi:10.1126/science.1116304 · Cited by 626 · see citing works
Anti-TNF-α therapies: the next generation
Palladino, M. A., Bahjat, F. R., Theodorakis, E. A., & Moldawer, L. L. (2003) · Nature Reviews Drug Discovery · doi:10.1038/nrd1175 · Cited by 579 · see citing works
Privileged Molecules for Protein Binding Identified from NMR-Based Screening
Hajduk, P. J., Bures, M. G., Praestgaard, J., & Fesik, S. W. (2000) · Journal of Medicinal Chemistry · doi:10.1021/jm000164q · Cited by 353 · see citing works
Predicting druggable binding sites at the protein–protein interface
Fuller, J. C., Burgoyne, N. J., & Jackson, R. M. (2008) · Drug Discovery Today · doi:10.1016/j.drudis.2008.10.009 · Cited by 311 · see citing works
Park, C., Bruncko, M., Adickes, J., Bauch, J. L., Ding, H., Kunzer, A. R., Marsh, K. C., Nimmer, P. M., Shoemaker, A. R., Song, X., et al. (2008) · Journal of Medicinal Chemistry · doi:10.1021/jm800669s · Cited by 301 · see citing works
Modulation of Protein–Protein Interactions with Small Organic Molecules
Berg, T. (2003) · Angewandte Chemie International Edition · doi:10.1002/anie.200200558 · Cited by 292 · see citing works
Predicting protein druggability
Hajduk, P. J., Huth, J. R., & Tse, C. (2005) · Drug Discovery Today · doi:10.1016/s1359-6446(05)03624-x · Cited by 289 · see citing works
Fragment-Based Drug Design: How Big Is Too Big?
Hajduk, P. J. (2006) · Journal of Medicinal Chemistry · doi:10.1021/jm060511h · Cited by 269 · see citing works
Drugs, leads, and drug-likeness: an analysis of some recently launched drugs
Proudfoot, J. (2002) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/s0960-894x(02)00244-5 · Cited by 252 · see citing works
Lehmann, D. M., Seneviratne, A. M. P. B., & Smrcka, A. V. (2007) · Molecular Pharmacology · doi:10.1124/mol.107.041780 · Cited by 234 · see citing works
Differential Targeting of Gßγ-Subunit Signaling with Small Molecules
Bonacci, T. M., Mathews, J. L., Yuan, C., Lehmann, D. M., Malik, S., Wu, D., Font, J. L., Bidlack, J. M., & Smrcka, A. V. (2006) · Science · doi:10.1126/science.1120378 · Cited by 231 · see citing works
Protein–protein interactions as targets for small molecule drug discovery
Fry, D. C. (2006) · Biopolymers · doi:10.1002/bip.20608 · Cited by 203 · see citing works
Rationalizing the chemical space of protein–protein interaction inhibitors
Spérandio, O., Reynès, C., Camproux, A., & Villoutreix, B. O. (2009) · Drug Discovery Today · doi:10.1016/j.drudis.2009.11.007 · Cited by 202 · see citing works
Blazer, L. L., & Neubig, R. R. (2009) · Neuropsychopharmacology · doi:10.1038/npp.2008.151 · Cited by 197 · see citing works
Arkin, M. R., & Whitty, A. (2009) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2009.05.125 · Cited by 190 · see citing works
Between a rock and a hard place?
Whitty, A., & Kumaravel, G. (2006) · Nature Chemical Biology · doi:10.1038/nchembio0306-112 · Cited by 170 · see citing works
The role of molecular size in ligand efficiency
Reynolds, C. H., Bembenek, S. D., & Tounge, B. A. (2007) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2007.05.038 · Cited by 168 · see citing works
Higueruelo, A. P., Schreyer, A. M., Bickerton, G. R., Pitt, W. R., Groom, C. R., & Blundell, T. L. (2009) · Chemical Biology & Drug Design · doi:10.1111/j.1747-0285.2009.00889.x · Cited by 155 · see citing works
KFC Server: interactive forecasting of protein interaction hot spots
Darnell, S. J., LeGault, L., & Mitchell, J. C. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn346 · Cited by 152 · see citing works
Carter, P. H., Scherle, P., Muckelbauer, J. A., Voss, M. E., Liu, R., Thompson, L. A., Tebben, A. J., Solomon, K. A., Lo, Y. C., Li, Z., et al. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.211178398 · Cited by 142 · see citing works
Roman, D. L., Talbot, J. N., Roof, R. A., Sunahara, R. K., Traynor, J. R., & Neubig, R. R. (2006) · Molecular Pharmacology · doi:10.1124/mol.106.028670 · Cited by 135 · see citing works
Small molecular weight protein–protein interaction antagonists—an insurmountable challenge?
Dömling, A. S. S. (2008) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2008.04.603 · Cited by 128 · see citing works
Atomic Analysis of Protein-Protein Interfaces with Known Inhibitors: The 2P2I Database
Bourgeas, R., Basse, M.-J., Morelli, X., & Roche, P. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009598 · Cited by 126 · see citing works
Reynès, C., Host, H., Camproux, A., Laconde, G., Leroux, F., Mazars, A., Deprez, B. P., Fåhræus, R., Villoutreix, B. O., & Spérandio, O. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000695 · Cited by 119 · see citing works
Raimundo, B. C., Oslob, J. D., Braisted, A. C., Hyde, J., McDowell, R. S., Randal, M., Waal, N. D., Wilkinson, J., Yu, C. H., & Arkin, M. R. (2004) · Journal of Medicinal Chemistry · doi:10.1021/jm049967u · Cited by 86 · see citing works
Discovery of a novel small molecule binding site of human survivin
Wendt, M. D., Sun, C. C., Kunzer, A. R., Sauer, D. R., Sarris, K., Hoff, E. D., Yu, L. P., Nettesheim, D. G., Chen, J., Jin, S. S., et al. (2007) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2007.03.042 · Cited by 82 · see citing works
Kojima, K., Burks, J. K., Arts, J., & Andreeff, M. (2010) · Molecular Cancer Therapeutics · doi:10.1158/1535-7163.mct-10-0337 · Cited by 78 · see citing works
Fry, D. C. (2008) · Current Protein and Peptide Science · doi:10.2174/138920308784533989 · Cited by 76 · see citing works
Neugebauer, A., Hartmann, R. W., & Klein, C. D. P. (2007) · Journal of Medicinal Chemistry · doi:10.1021/jm070533j · Cited by 75 · see citing works
Fischer, P. M., & Lane, D. P. (2004) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2004.04.011 · Cited by 70 · see citing works
London's disastrous drug trial has serious side effects for research
Wadman, M. (2006) · Nature · doi:10.1038/440388a · Cited by 60 · see citing works
Identification of small-molecule inhibitors of the JIP–JNK interaction
Chen, T. X., Kablaoui, N. M., Little, J., Timofeevski, S. L., Tschantz, W. R., Chen, P., Feng, J., Charlton, M. E., Stanton, R. V., & Bauer, P. H. (2009) · Biochemical Journal · doi:10.1042/bj20081899 · Cited by 55 · see citing works
The RGS protein inhibitor CCG-4986 is a covalent modifier of the RGS4 Gα-interaction face
Kimple, A. J., Willard, F. S., Giguère, P. M., Johnston, C. A., Mocanu, V., & Siderovski, D. P. (2007) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2007.06.002 · Cited by 50 · see citing works
Buchwald, P. (2007) · Steroids · doi:10.1016/j.steroids.2007.10.001 · Cited by 40 · see citing works
Self-citationSmall-molecule costimulatory blockade: organic dye inhibitors of the CD40–CD154 interaction
Margolles‐Clark, E., Umland, O., Kenyon, N. S., Ricordi, C., & Buchwald, P. (2009) · Journal of Molecular Medicine · doi:10.1007/s00109-009-0519-3 · Cited by 35 · see citing works
Self-citationSandiford, S. L., Wang, Q., Levay, K., Buchwald, P., & Slepak, V. Z. (2010) · Biochemistry · doi:10.1021/bi100080p · Cited by 21 · see citing works
Self-citationMargolles‐Clark, E., Kenyon, N. S., Ricordi, C., & Buchwald, P. (2010) · Chemical Biology & Drug Design · doi:10.1111/j.1747-0285.2010.01014.x · Cited by 17 · see citing works
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
Lu, H., Zhou, Q., He, J., Jiang, Z., Peng, C., Tong, R., & Shi, J. (2020) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-020-00315-3 · Cited by 891 · see citing works
“Besides, compared to traditional small molecule drugs (200–500 Da), drugs acting on PPIs have a higher molecular weight (>400 Da), which makes it challenging to meet the criteria like Lipinski’s “rule of 5”.(23,27)”
BackgroundTargeting protein–protein interactions as an anticancer strategy
Ivanov, A. A., Khuri, F. R., & Fu, H. (2013) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2013.04.007 · Cited by 401 · see citing works
“Recent studies have addressed some of these concerns as detailed in several publications [1, 9, 10].”
BackgroundVillar, E. A., Beglov, D., Chennamadhavuni, S., Porco, J. A. J., Kozakov, D., Vajda, S., & Whitty, A. (2014) · Nature Chemical Biology · doi:10.1038/nchembio.1584 · Cited by 401 · see citing works
Recent advances in targeting the “undruggable” proteins: from drug discovery to clinical trials
Xie, X., Yu, T., Li, X., Zhang, N., Foster, L. J., Peng, C., Huang, W., & He, G. (2023) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-023-01589-z · Cited by 396 · see citing works
Peptide therapeutics: Targeting the undruggable space
Tsomaia, N. (2015) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2015.01.014 · Cited by 348 · see citing works
Getting pharmaceutical R&D back on target
Bunnage, M. E. (2011) · Nature Chemical Biology · doi:10.1038/nchembio.581 · Cited by 258 · see citing works
Morelli, X., Bourgeas, R., & Roche, P. (2011) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2011.05.024 · Cited by 223 · see citing works
Buckton, L. K., Rahimi, M. N., & McAlpine, S. R. (2020) · Chemistry - A European Journal · doi:10.1002/chem.201905385 · Cited by 194 · see citing works
Wehbi, V. L., & Taskén, K. (2016) · Frontiers in Immunology · doi:10.3389/fimmu.2016.00222 · Cited by 182 · see citing works
State-of-the-art strategies for targeting protein–protein interactions by small-molecule inhibitors
Sheng, C., Dong, G., Miao, Z., Zhang, W., & Wang, W. (2015) · Chemical Society Reviews · doi:10.1039/c5cs00252d · Cited by 165 · see citing works
Bojadzic, D., Alcazar, O., Chen, J., Chuang, S.-T., Capcha, J. M. C., Shehadeh, L. A., & Buchwald, P. (2021) · ACS Infectious Diseases · doi:10.1021/acsinfecdis.1c00070 · Cited by 143 · see citing works
Self-citationDiscovery of low-molecular weight anti-PD-L1 peptides for cancer immunotherapy
Liu, H., Zhao, Z., Zhang, L., Li, Y., Jain, A., Barve, A. J., Jin, W., Liu, Y., Fetse, J., & Cheng, K. (2019) · Journal for ImmunoTherapy of Cancer · doi:10.1186/s40425-019-0705-y · Cited by 133 · see citing works
Drugging the undruggable: Transcription therapy for cancer
Yan, C., & Higgins, P. J. (2012) · Biochimica et Biophysica Acta (BBA) - Reviews on Cancer · doi:10.1016/j.bbcan.2012.11.002 · Cited by 121 · see citing works
Progress and Developments in Tau Aggregation Inhibitors for Alzheimer Disease
Bulic, B., Pickhardt, M., & Mandelkow�, E. (2013) · Journal of Medicinal Chemistry · doi:10.1021/jm3017317 · Cited by 116 · see citing works
Villoutreix, B. O., Kuenemann, M. A., Poyet, J., Bruzzoni‐Giovanelli, H., Labbé, C. M., Lagorce, D., Spérandio, O., & Miteva, M. A. (2014) · Molecular Informatics · doi:10.1002/minf.201400040 · Cited by 114 · see citing works
Targeting Protein–Protein Interactions and Fragment-Based Drug Discovery
Valkov, E., Sharpe, T., Marsh, M., Greive, S., & Hyvönen, M. (2011) · Topics in Current Chemistry · doi:10.1007/128_2011_265 · Cited by 107 · see citing works
Frank, C., Szaszák, M., Friedl, S., Drewianka, S., Lorenz, D., Gonçalves, A. C. D. C., Furkert, J., Vargas, C., Schmieder, P., Götz, F. M., et al. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.160614 · Cited by 107 · see citing works
He, S., Senter, T. J., Pollock, J., Han, C., Upadhyay, S. K., Purohit, T., Gogliotti, R. D., Lindsley, C. W., Cierpicki, T., Stauffer, S. R., et al. (2014) · Journal of Medicinal Chemistry · doi:10.1021/jm401868d · Cited by 99 · see citing works
Emerging Importance of Survivin in Stem Cells and Cancer: the Development of New Cancer Therapeutics
Warrier, N. M., Agarwal, P., & Kumar, P. (2020) · Stem Cell Reviews and Reports · doi:10.1007/s12015-020-09995-4 · Cited by 92 · see citing works
Sable, R. V., & Jois, S. D. S. (2015) · Molecules · doi:10.3390/molecules200611569 · Cited by 90 · see citing works
Basse, M.-J., Betzi, S., Morelli, X., & Roche, P. (2016) · Database · doi:10.1093/database/baw007 · Cited by 83 · see citing works
HIV-1 capsid inhibitors as antiretroviral agents
Thenin-Houssier, S., & Valente, S. (2016) · Current HIV Research · doi:10.2174/1570162x14999160224103555 · Cited by 75 · see citing works
“The development of inhibitors of protein-protein interactions in drug discovery was traditionally thought to be complicated, because the interactions involved large protein surfaces with less defined binding pockets than those present in tradition targets of most current drugs (G-protein coupled receptors, ion channel…”
BackgroundBojadzic, D., & Buchwald, P. (2018) · Current Topics in Medicinal Chemistry · doi:10.2174/1568026618666180531092503 · Cited by 81 · see citing works
“5 kJ/atom means that the addition of one non-hydrogen atom has to be accompanied by an approximately two-fold increase in affinity to maintain the same LE [42, 90].”
BackgroundSelf-citationBorkin, D., Pollock, J., Kempińska, K., Purohit, T., Li, X., Wen, B., Zhao, T., Miao, H., Shukla, S., He, M., et al. (2016) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.5b01305 · Cited by 61 · see citing works
“6-Methoxy-5-((4-((6-(2,2,2-trifluoroethyl)thieno[2,3-d]-pyrimidin-4yl)amino)piperidin-1-yl)methyl)-1H-indole-2-carbonitrile (18)—Similar procedure was used as for 1 but starting with 116 mg (0.”
MethodThe food colorant erythrosine is a promiscuous protein–protein interaction inhibitor
Ganesan, L., Margolles‐Clark, E., Song, Y., & Buchwald, P. (2011) · Biochemical Pharmacology · doi:10.1016/j.bcp.2010.12.020 · Cited by 74 · see citing works
Self-citationMelagraki, G., Ntougkos, E., Rinotas, V. E., Papaneophytou, C. P., Leonis, G., Mavromoustakos, T., Kontopidis, G. A., Douni, E. K., Afantitis, A., & Kollias, G. A. (2017) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005372 · Cited by 69 · see citing works
Borkin, D., Kłossowski, S., Pollock, J., Miao, H. Z., Linhares, B. M., Kempińska, K., Jin, Z., Purohit, T., Wen, B., He, M., et al. (2018) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.8b00071 · Cited by 65 · see citing works
“4-methyl-1-(2-(4-(methylsulfonyl)piperazin-1-yl)ethyl)-5-((4-((6-(2,2,2trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl)amino)piperidin-1-yl)methyl)-1Hindole-2-carbonitrile (19)—The reaction was performed with the methanesulfonyl chloride.”
MethodSeifert, L. L., Si, C., Saha, D., Sadic, M., de Vries, M., Ballentine, S., Briley, A., Wang, G., Valero-Jimenez, A. M., Mohamed, A., et al. (2019) · PLoS Pathogens · doi:10.1371/journal.ppat.1007634 · Cited by 56 · see citing works
Translational aspect in peptide drug discovery and development: An emerging therapeutic candidate
Anand, U., Bandyopadhyay, A., Jha, N. K., de la Lastra, J. M. P., & Dey, A. (2022) · BioFactors · doi:10.1002/biof.1913 · Cited by 62 · see citing works
“However, there are exceptions where antagonists have been developed for targets that required large surface area and complex structures to achieve subtype selectivity and minimize off-target effects.(47,48) A class of peptide superagonists of GnRH targeting receptor inactivation by receptor desensitization successfull…”
BackgroundKuenemann, M. A., Spérandio, O., Labbé, C. M., Lagorce, D., Miteva, M. A., & Villoutreix, B. O. (2015) · Progress in Biophysics and Molecular Biology · doi:10.1016/j.pbiomolbio.2015.02.006 · Cited by 61 · see citing works
Computational approaches for the design of modulators targeting protein-protein interactions
Rehman, A. U., Khurshid, B., Ali, Y., Rasheed, S., Wadood, A., Ng, H. L., Chen, H., Wei, Z., Luo, R., & Zhang, J. (2023) · Expert Opinion on Drug Discovery · doi:10.1080/17460441.2023.2171396 · Cited by 62 · see citing works
“( 3 ) PPI-targeting drugs have a relatively higher molecular weight (>400 Dalton) as compared to the typical ligands (200– 500 Dalton), making it hard to meet Lipinski’s rule of 5 criteria [17,18].”
BackgroundColeman, N., & Rodon, J. A. (2021) · American Society of Clinical Oncology Educational Book · doi:10.1200/edbk_325885 · Cited by 58 · see citing works
Vukićević, T., Schulz, M., Faust, D., & Klußmann, E. (2016) · Frontiers in Pharmacology · doi:10.3389/fphar.2016.00023 · Cited by 59 · see citing works
Metz, A., Ciglia, E., & Gohlke, H. (2012) · Current Pharmaceutical Design · doi:10.2174/138161212802651553 · Cited by 57 · see citing works
“As related studies and discovered PPIMs have been the subject of many detailed reviews already [3, 11, 87, 107, 229-234], we solely give a survey of the so far identified PPIMs with their reported potency (Fig.”
BackgroundTakahashi, H., Takahashi, C., Moreland, N. J., Chang, Y., Sawasaki, T., Ryo, A., Vasudevan, S. G., Suzuki, Y., & Yamamoto, N. (2012) · Antiviral Research · doi:10.1016/j.antiviral.2012.09.023 · Cited by 55 · see citing works
“Hence, it is becoming evident that the hot-spots of protein–protein interfaces are suitable targets for novel therapeutic drugs (Arkin and Wells, 2004; Buchwald, 2010; Pagliaro et al., 2004; Ryan and Matthews, 2005) Although the X-ray structure of NS3 complexed with NS5 is not available, previous studies with truncate…”
BackgroundLi, Y., Li, W., & Xu, Z. (2021) · Marine Drugs · doi:10.3390/md19060311 · Cited by 57 · see citing works
“The development of drugs against protein-protein interactions (PPIs) is challenging for small molecules [1,2].”
BackgroundProtein–Peptide Binding Site Detection Using 3D Convolutional Neural Networks
Kozlovskii, I., & Popov, P. A. (2021) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.1c00475 · Cited by 51 · see citing works
Hamon, V., Bourgeas, R., Ducrot, P., Théret, I., Xuereb, L., Basse, M. J., Brunel, J. M., Combes, S., Morelli, X., & Roche, P. (2013) · Journal of The Royal Society Interface · doi:10.1098/rsif.2013.0860 · Cited by 46 · see citing works
“Small molecule PPI inhibitors can be classified as orthosteric or allosteric modulators, depending upon their modes of interaction [50].”
BackgroundGul, S., & Hadian, K. (2014) · Expert Opinion on Drug Discovery · doi:10.1517/17460441.2014.954544 · Cited by 46 · see citing works
“MDM2--p53 Cancer [10-13] Bcl2/Bcl-XL--Bax/Bak Cancer [14-16] CCR5--gp120 (approved drug: Maraviroc) Virology (HIV-1) [17] Fibrinogen--GpIIb/IIIa (approved drug: Tirofiban) Cardiovascular [18] b-catenin--TCF4 Cancer [31] CD80--CD28 Immunology [36] RhoA--LARG Cancer [43] Rac1--p67 Inflammation [44] b-catenin–BCL9 Cancer…”
BackgroundNetwork-Based Strategies Can Help Mono- and Poly-pharmacology Drug Discovery: A Systems Biology View
Engin, H., Gürsoy, A., Nussinov, R., & Keskin, Ö. (2014) · Current Pharmaceutical Design · doi:10.2174/13816128113199990066 · Cited by 45 · see citing works
“There are a number of reviews [13, 15, 25, 31-35], which investigate PPI inhib-”
BackgroundDruggability Assessment of Protein–Protein Interfaces
Wanner, J., Fry, D. C., Peng, Z., & Roberts, J. (2011) · Future Medicinal Chemistry · doi:10.4155/fmc.11.156 · Cited by 44 · see citing works
Eftekhari, Z., Zohrabi, H., Oghalaie, A., Ebrahimi, T., Shariati, F. S., Behdani, M., & Kazemi‐Lomedasht, F. (2024) · Molecular Therapy — Nucleic Acids · doi:10.1016/j.omtn.2024.102313 · Cited by 43 · see citing works
Fiorentini, C., Savoia, P., Savoldi, D., Barbon, A., & Missale, C. (2013) · Neurobiology of Disease · doi:10.1016/j.nbd.2013.01.005 · Cited by 41 · see citing works
“Despite their molecular complexity, it has become increasingly clear that, for protein partners characterized by small interface for their high-affinity binding, including those involving a SH2 domain (Buchwald, 2010), small molecules can act as effective protein-protein interaction antagonists.”
BackgroundCooper, C. D. O., Newman, J. A., & Gileadi, O. (2014) · Biochemical Society Transactions · doi:10.1042/bst20130227 · Cited by 42 · see citing works
Chen, S., & Zacharias, M. (2023) · ACS Central Science · doi:10.1021/acscentsci.3c00003 · Cited by 40 · see citing works
Yasui, T., Yamamoto, T., Sakai, N., Asano, K., Takai, T., Yoshitomi, Y., Davis, M., Takagi, T., Sakamoto, K., Sogabe, S., et al. (2017) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2017.07.037 · Cited by 39 · see citing works
New insights into KLFs and SOXs in cancer pathogenesis, stemness, and therapy
Zeng, L., Zhu, Y., Moreno, C. S., & Wan, Y. (2023) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2023.02.003 · Cited by 37 · see citing works
The phytotoxin fusicoccin differently regulates 14-3-3 proteins association to mode III targets
Paiardini, A., Aducci, P., Cervoni, L., Cutruzzolà, F., Lucente, C. D., Janson, G., Pascarella, S., Rinaldo, S., Visconti, S., & Camoni, L. (2014) · IUBMB Life · doi:10.1002/iub.1239 · Cited by 38 · see citing works
“As their dysregulation can contribute to human disease, modulation of these binding events by small molecules represents a promising strategy in drug discovery (1).”
BackgroundFeldman, P., & Khanna, R. (2013) · Neuroscience Letters · doi:10.1016/j.neulet.2013.06.057 · Cited by 37 · see citing works
“In addition to direct block of calcium channels, targeting of protein-protein interaction (PPI) interfaces within a PPI complex is gaining momentum as a potentially new manner of drug development [27].”
BackgroundThe present and the future of motif-mediated protein–protein interactions
Seo, M., & Kim, P. M. (2018) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2018.04.005 · Cited by 37 · see citing works
New Approaches to Difficult Drug Targets: The Phosphatase Story
Lazo, J. S., McQueeney, K. E., & Sharlow, E. R. (2017) · SLAS DISCOVERY · doi:10.1177/2472555217721142 · Cited by 36 · see citing works
Recent Advances on Small-Molecule Survivin Inhibitors
Xiao, M., & Li, W. (2015) · Current Medicinal Chemistry · doi:10.2174/0929867322666150114102146 · Cited by 36 · see citing works
“Small-molecule survivin inhibitors have to disrupt the protein-protein interaction between survivin and other proteins, which could be difficult because most interfaces in protein-protein interactions (PPIs) are not well suitable for effective small molecule binding [48].”
BackgroundSmall-Molecule Inhibitors of the Interaction Between TNF and TNFR
Davis, J. M., & Colangelo, J. (2012) · Future Medicinal Chemistry · doi:10.4155/fmc.12.192 · Cited by 35 · see citing works
Camps-Fajol, C., Cavero, D., Minguillón, J., & Surrallés, J. (2024) · Pharmacological Research · doi:10.1016/j.phrs.2024.107544 · Cited by 35 · see citing works
Protein–Protein Interaction Modulators for Epigenetic Therapies
(2018) · Advances in Protein Chemistry and Structural Biology · doi:10.1016/bs.apcsb.2017.06.002 · Cited by 31 · see citing works
Zheng, G.-H., Shen, J., Zhan, Y.-C., Hong, Y., Xue, S.-T., Wang, Z., Ji, X., & Li, Z. (2014) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2014.05.027 · Cited by 32 · see citing works
Pellegrino, S., Contini, A., Gelmi, M. L., Presti, L. L., Soave, R., & Erba, E. (2014) · The Journal of Organic Chemistry · doi:10.1021/jo500237j · Cited by 32 · see citing works
TNF Superfamily Protein-Protein Interactions: Feasibility of Small- Molecule Modulation
Song, Y., & Buchwald, P. (2015) · Current Drug Targets · doi:10.2174/1389450116666150223115628 · Cited by 31 · see citing works
“Accordingly, as we noted [6], they also “tend to have a larger molecular size, a more hydrophobic nature, and structures with more rigid, aromatic scaffolds in combination with charged or polar functionalities.”
BackgroundInfluentialSelf-citationHamon, V., Brunel, J. M., Combes, S., Basse, M. J., Roche, P., & Morelli, X. (2013) · MedChemComm · doi:10.1039/c3md00018d · Cited by 31 · see citing works
Discovery of Novel Small Molecule Inhibitors Disrupting the PCSK9-LDLR Interaction
Sun, H., Wang, J., Liu, S., Zhou, X., Dai, L. X., Chen, C., Xu, Q., Wen, X., Cheng, K., Sun, H., et al. (2021) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.1c00521 · Cited by 31 · see citing works
Elwakeel, A. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.879632 · Cited by 32 · see citing works
“Secondly, the interface of protein-protein interaction is large, flat, and hydrophobic with few grooves or pockets with which an inhibitor could bind (Buchwald, 2010).”
BackgroundDrug discovery by targeting the protein–protein interactions involved in autophagy
Xiang, H., Zhou, M., Li, Y., Zhou, L., & Wang, R. (2023) · Acta Pharmaceutica Sinica B · doi:10.1016/j.apsb.2023.07.016 · Cited by 31 · see citing works
Small-Molecule Inhibitors of the CD40–CD40L Costimulatory Protein–Protein Interaction
Chen, J., Song, Y. G., Bojadzic, D., Tamayo, A., Landin, A. M., Blomberg, B. B., & Buchwald, P. (2017) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.7b01154 · Cited by 31 · see citing works
Self-citationAi, Y., Hwang, L., MacKerell, A. D., Melnick, A. M., & Xue, F. (2021) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.0c01686 · Cited by 29 · see citing works
Li, Q., Zeng, C., Liu, H., Yung, K. W. Y., Chen, C., Xie, Q., Zhang, Y., Wan, S. W. C., Mak, B. S. W., Xia, J., et al. (2021) · iScience · doi:10.1016/j.isci.2021.102423 · Cited by 28 · see citing works
“effectively enough to block the PPI (Buchwald, 2010; Sperandio et al., 2010).”
BackgroundSmall‐molecule modulators of the OX 40– OX40 ligand co‐stimulatory protein–protein interaction
Song, Y. G., Margolles‐Clark, E., Bayer, A. L., & Buchwald, P. (2014) · British Journal of Pharmacology · doi:10.1111/bph.12819 · Cited by 28 · see citing works
“Nevertheless, within the last few years, several sufficiently effective and even clinically promising small-molecule PPI inhibitors (PPIIs) have been identified for a number of different targets (Cochran, 2000; Arkin and Wells, 2004; Whitty and Kumaravel, 2006; Wells and McClendon, 2007; Buchwald, 2010).”
BackgroundInfluentialSelf-citationFloris, M., & Moro, S. (2011) · Molecular Informatics · doi:10.1002/minf.201100093 · Cited by 25 · see citing works
Zaka, M., Abbasi, B. H., & Durdağı, S. (2018) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2018.1491423 · Cited by 26 · see citing works
“It is also very difficult to identify the unique binding pocket that helps in direct interaction of small molecules with protein to inhibit its function (Buchwald, 2010; Haraguchi et al., 2006).”
BackgroundTargeting platelet inhibition receptors for novel therapies: PECAM-1 and G6b-B
Jerez, E. M. S., Gibbins, J. M., & Hughes, C. E. (2021) · Platelets · doi:10.1080/09537104.2021.1882668 · Cited by 23 · see citing works
Pallai, R., Bhaskar, A., Barnett-Bernodat, N., Ebert, C., Pusey, M., Nickels, J. T., & Rice, L. M. (2015) · Tumor Biology · doi:10.1007/s13277-015-3326-1 · Cited by 23 · see citing works
“While PPI inhibition presents challenges, there have been advances in the successful targeting of PPI for therapeutic purposes [50, 51].”
BackgroundAfonso, A. L., Cavaleiro, C. T., Castanho, M. A. R. B., Neves, V., & Cavaco, M. C. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26073117 · Cited by 23 · see citing works
Papadopoulou, D., Drakopoulos, A., Lagarias, P. I., Melagraki, G., Kollias, G. A., & Afantitis, A. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms221910220 · Cited by 20 · see citing works
Buchwald, P. (2022) · Frontiers in Drug Discovery · doi:10.3389/fddsv.2022.898035 · Cited by 20 · see citing works
“Tens of PPI-targeting SMIs have reached preclinical development (Arkin and Wells, 2004; Wells and McClendon, 2007; Wilson, 2009; Buchwald, 2010; Arkin et al., 2014; Milroy et al., 2014; Song and Buchwald, 2015; Scott et al., 2016), and three are approved by the FDA for clinical use: lifitegrast…”
BackgroundSelf-citationInhibition of FOXP3 by stapled alpha-helical peptides dampens regulatory T cell function
Hawley, K. M., Eclov, R. J., Schnorenberg, M. R., Tian, Y. P., Shah, R. N., Thomas-Toth, A. T., Fefferman, M. L., Bird, G. H., Walensky, L. D., Tirrell, M., et al. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2209044119 · Cited by 19 · see citing works
Yefidoff‐Freedman, R., Chen, T., Sahoo, R., Chen, L., Wagner, G., Halperin, J. A., Aktas, B. H., & Chorev, M. (2014) · ChemBioChem · doi:10.1002/cbic.201300723 · Cited by 19 · see citing works
Brueckner, A. C., Deng, Q., Cleves, A. E., Lesburg, C. A., Alvarez, J. C., Reibarkh, M., Sherer, E. C., & Jain, A. N. (2021) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.0c02159 · Cited by 18 · see citing works
Advances in the synthesis of glycosidic macrolides: clavosolides A–D and cyanolide A
Lee, K., Lanier, M. L., Kwak, J., Kim, H., & Hong, J. (2016) · Natural Product Reports · doi:10.1039/c6np00073h · Cited by 18 · see citing works
Salgania, H. K., Metz, J., & Jeske, M. (2024) · Nature Communications · doi:10.1038/s41467-024-47233-4 · Cited by 17 · see citing works
Application of Nanopore Sensors for Biomolecular Interactions and Drug Discovery
Jeong, K., Kim, J., Dhanasekar, N. N., Lee, M., & Chi, S. (2022) · Chemistry - An Asian Journal · doi:10.1002/asia.202200679 · Cited by 17 · see citing works
The promiscuous protein binding ability of erythrosine B studied by metachromasy (metachromasia)
Ganesan, L., & Buchwald, P. (2013) · Journal of Molecular Recognition · doi:10.1002/jmr.2263 · Cited by 17 · see citing works
“Furthermore, small-molecule inhibition of PPIs is being increasingly pursued (Arkin and Wells, 2004; Wells and McClendon, 2007; Buchwald, 2010; Mullard, 2012), and being able to avoid promiscuous inhibitors is an important goal, just as it is in high-throughput screening strategies that are often”
BackgroundSelf-citationQaiser, H., Saeed, M., Nerukh, D., & Ul‐Haq, Z. (2020) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2020.1796794 · Cited by 16 · see citing works
“It is very challenging to find a low molecular weight compound that interacts directly with protein to block its function (Buchwald, 2010).”
BackgroundSelected Approaches to Disrupting Protein–Protein Interactions within the MAPK/RAS Pathway
Harwood, S. J., Smith, C. R., Lawson, J. D., & Ketcham, J. M. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24087373 · Cited by 16 · see citing works
“PPI inhibitors routinely fall outside of Lipinski physiochemical property space [15] by having higher molecular weights and LogP values than the average approved small molecule drug [16,17].”
BackgroundBojadzic, D., Chen, J., Alcazar, O., & Buchwald, P. (2018) · Molecules · doi:10.3390/molecules23051153 · Cited by 15 · see citing works
Self-citationKumar, S., Ali, I. F. M., Abbas, F., Rana, A., Pandey, S., Garg, M., & Kumar, D. (2023) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2023.2252496 · Cited by 14 · see citing works
“Ligands with higher LE achieve better binding activity per unit of molecular weight (Buchwald, 2010).”
Naveed, M., Hussain, M., Aziz, T. A., Hanif, N., Kanwal, N., Arshad, A., Khan, A. A., Alshammari, A., & Alharbi, M. (2024) · Scientific Reports · doi:10.1038/s41598-024-81037-2 · Cited by 13 · see citing works
Development of Small Molecules to Target the Ige:FcεRi Protein–Protein Interaction in Allergies
Smith, L. D., Leatherbarrow, R. J., & Spivey, A. C. (2013) · Future Medicinal Chemistry · doi:10.4155/fmc.13.112 · Cited by 13 · see citing works
Kim, C., Jung, J., Tùng, T. T., & Park, S. B. (2015) · Chemical Science · doi:10.1039/c5sc03493k · Cited by 13 · see citing works
Split-Luciferase Complementation Assay to Detect Channel–Protein Interactions in Live Cells
Shavkunov, A. S., Ali, S. R., Panova, N. I., & Laezza, F. (2015) · Methods in molecular biology · doi:10.1007/978-1-4939-2425-7_33 · Cited by 12 · see citing works
Virtual screening for inhibitors of the human TSLP:TSLPR interaction
Rompaey, D. V., Verstraete, K., Peelman, F., Savvides, S. N., Augustyns, K., der Veken, P. V., & Winter, H. L. D. (2017) · Scientific Reports · doi:10.1038/s41598-017-17620-7 · Cited by 11 · see citing works
Hakmi, M., Bouricha, E. M., Akachar, J., Lmimouni, B., Harti, J. E., Belyamani, L., & Ibrahimi, A. (2020) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2020.1830175 · Cited by 10 · see citing works
“The discovery of PPI-modulating small molecules is a huge challenge due to relatively large protein interfaces which makes them generally regarded as undruggable [22, 25].”
BackgroundTooyserkani, R., Rasaee, M. J., Bandehpour, M., & Löwik, D. W. P. M. (2021) · Journal of drug targeting · doi:10.1080/1061186x.2021.1879087 · Cited by 9 · see citing works
Computational methods for binding site prediction on macromolecules
Kozlovskii, I., & Popov, P. A. (2025) · Quarterly Reviews of Biophysics · doi:10.1017/s003358352500006x · Cited by 8 · see citing works
Bergman, D. R., Sweis, R. F., Pearson, A. T., Nazari, F., & Jackson, T. L. (2022) · iScience · doi:10.1016/j.isci.2022.104387 · Cited by 8 · see citing works
Choi, H. Y., Iatan, I., Ruel, I. L., Brown, L., Hales, L., Choi, S., & Genest, J. J. (2023) · Arteriosclerosis Thrombosis and Vascular Biology · doi:10.1161/atvbaha.122.318275 · Cited by 8 · see citing works
Zhang, Z., Zhao, L., Gao, M., Chen, Y., Wang, J., & Wang, C. (2024) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2024.108287 · Cited by 7 · see citing works
Chuang, S.-T., Alcazar, O., Watts, B. M., Abdulreda, M. H., & Buchwald, P. (2024) · Frontiers in Immunology · doi:10.3389/fimmu.2024.1484425 · Cited by 7 · see citing works
Self-citationTorielli, L., Serapian, S. A., Mussolin, L., Moroni, E., & Colombo, G. (2022) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.2c01408 · Cited by 7 · see citing works
Alam, A. (2014) · Malaria Research and Treatment · doi:10.1155/2014/642391 · Cited by 7 · see citing works
“…it is not always possible to target the protein interfaces because of the involvement of large surface area, it has been recognized that in many cases protein interfaces could be targeted because of the presence of hot spots composed of crucial binding residues (reviewed by Buchwald 2010) [38].”
BackgroundA general model for predicting the binding affinity of reversibly and irreversibly dimerized ligands
Foreman, K. W. (2017) · PLoS ONE · doi:10.1371/journal.pone.0188134 · Cited by 7 · see citing works
Ferková, S., Froehlich, U., Nepveu-Traversy, M.-É., Murza, A., Azad, T., Grandbois, M., Sarret, P., Lavigne, P., & Boudreault, P. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms25010166 · Cited by 6 · see citing works
“Such surfaces are not convenient for traditional small-molecule drugs (200–500 Da) [6,7].”
Background
- Authors
- Buchwald, P.
- Venue
- IUBMB Life
- Publisher
- Wiley
- Published
- 2010-10
- Volume
- 62
- Issue
- 10
- Pages
- 724-731
- ISSN
- 1521-6543 (ISSN-L)
- 1521-6551
- OpenAlex
- W2059388258
- Cited by
- 133
- References
- 49
- Citations by year
- 2026: 2 · 2025: 8 · 2024: 7 · 2023: 13 · 2022: 8 · 2021: 15 · 2020: 6 · 2019: 2 · 2018: 6 · 2017: 7 · 2016: 8 · 2015: 13 · 2014: 13 · 2013: 10 · 2012: 7
- FWCI
- 0.68
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- IUBMB Life (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Diabetes Research Institute Foundation
- Topics
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chemical Synthesis and Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Degradation and Inhibitors
- Keywords
- protein-protein interaction inhibitors, small molecule inhibitors, molecular size, chemical space, druggability, human interactome, medicinal chemistry, drug discovery
- MeSH terms
- Humans, Ligands, Protein Binding, Proteins, Drug Design, Signal Transduction, Protein Interaction Mapping, Small Molecule Libraries
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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