Abstract
PDZ domains, which belong to protein–protein interaction networks, are critical for regulating important biological processes such as scaffolding, trafficking, and signaling cascades. Interfering with PDZ-mediated interactions could affect these numerous biological processes. Thus, PDZ domains have emerged as promising targets to decipher biological phenomena and potentially treat cancer and neurological diseases. In this minireview, we focus on the discovery and design of small molecule inhibitors to modulate PDZ domains. These compounds interfere with endogenous protein partners from the PDZ domain by binding at the protein–protein interface. While peptides or peptidomimetic ligands were described to modulate PDZ domains, the focus of this review is on small organic compounds.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Wang NX, Lee HJ, Zheng JJ (2008) Therapeutic use of PDZ protein-protein interaction antagonism. Drug News Perspect 21(3):137–141
Chi CN, Bach A, Strømgaard K, Gianni S, Jemth P (2012) Ligand binding by PDZ domains. Biofactors 38(5):338–348. https://doi.org/10.1002/biof.1031
Dev KK (2004) Making protein interactions druggable: targeting PDZ domains. Nat Rev Drug Discov 3(12):1047–1056. https://doi.org/10.1038/nrd1578
Grillo-Bosch D, Choquet D, Sainlos M (2013) Inhibition of PDZ domain-mediated interactions. Drug Discov Today Technol 10(4):e531–e540. https://doi.org/10.1016/j.ddtec.2012.10.003
Songyang Z, Fanning AS, Fu C, Xu J, Marfatia SM, Chishti AH, Crompton A, Chan AC, Anderson JM, Cantley LC (1997) Recognition of unique carboxyl-terminal motifs by distinct PDZ domains. Science 275(5296):73–77. https://doi.org/10.1126/science.275.5296.73
Wiedemann U, Boisguerin P, Leben R, Leitner D, Krause G, Moelling K, Volkmer-Engert R, Oschkinat H (2004) Quantification of PDZ domain specificity, prediction of ligand affinity and rational design of super-binding peptides. J Mol Biol 343(3):703–718. https://doi.org/10.1016/j.jmb.2004.08.064
Wawrzyniak AM, Vermeiren E, Zimmermann P, Ivarsson Y (2012) Extensions of PSD-95/discs large/ZO-1 (PDZ) domains influence lipid binding and membrane targeting of syntenin-1. FEBS Lett 586(10):1445–1451. https://doi.org/10.1016/j.febslet.2012.04.024
Aarts M, Liu Y, Liu L, Besshoh S, Arundine M, Gurd JW, Wang YT, Salter MW, Tymianski M (2002) Treatment of ischemic brain damage by perturbing NMDA receptor- PSD-95 protein interactions. Science 298(5594):846–850. https://doi.org/10.1126/science.1072873
Thorsen TS, Madsen KL, Rebola N, Rathje M, Anggono V, Bach A, Moreira IS, Stuhr-Hansen N, Dyhring T, Peters D, Beuming T, Huganir R, Weinstein H, Mulle C, Strømgaard K, Rønn LC, Gether U (2010) Identification of a small-molecule inhibitor of the PICK1 PDZ domain that inhibits hippocampal LTP and LTD. Proc Natl Acad Sci U S A 107(1):413–418. https://doi.org/10.1073/pnas.0902225107
Saupe J, Roske Y, Schillinger C, Kamdem N, Radetzki S, Diehl A, Oschkinat H, Krause G, Heinemann U, Rademann J (2011) Discovery, structure-activity relationship studies, and crystal structure of nonpeptide inhibitors bound to the Shank3 PDZ domain. ChemMedChem 6(8):1411–1422. https://doi.org/10.1002/cmdc.201100094
Grandy D, Shan J, Zhang X, Rao S, Akunuru S, Li H, Zhang Y, Alpatov I, Zhang XA, Lang RA, Shi DL, Zheng JJ (2009) Discovery and characterization of a small molecule inhibitor of the PDZ domain of dishevelled. J Biol Chem 284(24):16256–16263. https://doi.org/10.1074/jbc.M109.009647
Patra CR, Rupasinghe CN, Dutta SK, Bhattacharya S, Wang E, Spaller MR, Mukhopadhyay D (2012) Chemically modified peptides targeting the PDZ domain of GIPC as a therapeutic approach for cancer. ACS Chem Biol 7(4):770–779. https://doi.org/10.1021/cb200536r
Kegelman TP, Wu B, Das SK, Talukdar S, Beckta JM, Hu B, Emdad L, Valerie K, Sarkar D, Furnari FB, Cavenee WK, Wei J, Purves A, De SK, Pellecchia M, Fisher PB (2017) Inhibition of radiation-induced glioblastoma invasion by genetic and pharmacological targeting of MDA-9/Syntenin. Proc Natl Acad Sci U S A 114(2):370–375. https://doi.org/10.1073/pnas.1616100114
Bach A, Chi CN, Olsen TB, Pedersen SW, Røder MU, Pang GF, Clausen RP, Jemth P, Strømgaard K (2008) Modified peptides as potent inhibitors of the postsynaptic density-95/N-methyl-D-aspartate receptor interaction. J Med Chem 51(20):6450–6459. https://doi.org/10.1021/jm800836w
Bach A, Eildal JN, Stuhr-Hansen N, Deeskamp R, Gottschalk M, Pedersen SW, Kristensen AS, Strømgaard K (2011) Cell-permeable and plasma-stable peptidomimetic inhibitors of the postsynaptic density-95/N-methyl-D-aspartate receptor interaction. J Med Chem 54(5):1333–1346. https://doi.org/10.1021/jm1013924
Bach A, Clausen BH, Møller M, Vestergaard B, Chi CN, Round A, Sørensen PL, Nissen KB, Kastrup JS, Gajhede M, Jemth P, Kristensen AS, Lundström P, Lambertsen KL, Strømgaard K (2012) A high-affinity, dimeric inhibitor of PSD-95 bivalently interacts with PDZ1-2 and protects against ischemic brain damage. Proc Natl Acad Sci U S A 109(9):3317–3322. https://doi.org/10.1073/pnas.1113761109
Wells JA, McClendon CL (2007) Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature 450(7172):1001–1009. https://doi.org/10.1038/nature06526
Morelli X, Bourgeas R, Roche P (2011) Chemical and structural lessons from recent successes in protein-protein interaction inhibition (2P2I). Curr Opin Chem Biol 15(4):475–481. https://doi.org/10.1016/j.cbpa.2011.1005.1024
Bourgeas R, Basse MJ, Morelli X, Roche P (2010) Atomic analysis of protein-protein interfaces with known inhibitors: the 2P2I database. PLoS One 5(3):e9598. https://doi.org/10.1371/journal.pone.0009598
Chen X, Longgood JC, Michnoff C, Wei S, Frantz DE, Bezprozvanny L (2007) High-throughput screen for small molecule inhibitors of Mint1-PDZ domains. Assay Drug Dev Technol 5(6):769–783. https://doi.org/10.1089/adt.2007.092
Hajduk P, Huth J, Fesik S (2005) Druggability indices for protein targets derived from NMR-based screening data. J Med Chem 48(7):2518–2525. https://doi.org/10.1021/jm049131r
Fujii N, Haresco JJ, Novak KA, Stokoe D, Kuntz ID, Guy RK (2003) A selective irreversible inhibitor targeting a PDZ protein interaction domain. J Am Chem Soc 125(40):12074–12075. https://doi.org/10.1021/ja035540l
Ewing TJ, Makino S, Skillman GA, Kuntz ID (2001) DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. J Comput Aided Mol Des 15(5):411–428
Fujii N, Haresco JJ, Novak KA, Gage RM, Pedemonte N, Stokoe D, Kuntz ID, Guy RK (2007) Rational design of a nonpeptide general chemical scaffold for reversible inhibition of PDZ domain interactions. Bioorg Med Chem Lett 17(2):549–552. https://doi.org/10.1016/j.bmcl.2006.10.006
Fujii N, You L, Xu Z, Uematsu K, Shan J, He B, Mikami I, Edmondson LR, Neale G, Zheng J, Guy RK, Jablons DM (2007) An antagonist of dishevelled protein-protein interaction suppresses beta-catenin-dependent tumor cell growth. Cancer Res 67(2):573–579. https://doi.org/10.1158/0008-5472.CAN-06-2726
Mayasundari A, Ferreira AM, He L, Mahindroo N, Bashford D, Fujii N (2008) Rational design of the first small-molecule antagonists of NHERF1/EBP50 PDZ domains. Bioorg Med Chem Lett 18(3):942–945. https://doi.org/10.1016/j.bmcl.2007.12.038
Vogrig A, Dorr L, Bouzidi N, Boucherle B, Wattiez AS, Cassier E, Vallon G, Ripoche I, Abrunhosa-Thomas I, Marin P, Nauton L, Thery V, Courteix C, Lian LY, Ducki S (2013) Structure-based design of PDZ ligands as inhibitors of 5-HT(2A) receptor/PSD-95 PDZ1 domain interaction possessing anti-hyperalgesic activity. ACS Chem Biol 8(10):2209–2216. https://doi.org/10.1021/cb400308u
Trott O, Olson AJ (2010) AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 31(2):455–461. https://doi.org/10.1002/jcc.21334
Bach A, Pedersen TB, Strømgaard K (2016) Design and synthesis of triazole-based peptidomimetics of a PSD-95 PDZ domain inhibitor. MedChemComm 7(3):531–536. https://doi.org/10.1039/C5MD00445D
Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP, Knoll EH, Shelley M, Perry JK, Shaw DE, Francis P, Shenkin PS (2004) Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 47(7):1739–1749. https://doi.org/10.1021/jm0306430
Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 19(14):1639–1662
Goodsell DS, Morris GM, Olson AJ (1996) Automated docking of flexible ligands: applications of AutoDock. J Mol Recognit 9(1):1–5
Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ (2009) AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem 30(16):2785–2791. https://doi.org/10.1002/jcc.21256
Case DA, Cheatham TE, Darden T, Gohlke H, Luo R, Merz KM, Onufriev A, Simmerling C, Wang B, Woods RJ (2005) The Amber biomolecular simulation programs. J Comput Chem 26(16):1668–1688. https://doi.org/10.1002/jcc.20290
Bach A, Stuhr-Hansen N, Thorsen TS, Bork N, Moreira IS, Frydenvang K, Padrah S, Christensen SB, Madsen KL, Weinstein H, Gether U, Strømgaard K (2010) Structure-activity relationships of a small-molecule inhibitor of the PDZ domain of PICK1. Org Biomol Chem 8(19):4281–4288. https://doi.org/10.1039/c0ob00025f
Lin EYS, Silvian LF, Marcotte DJ, Banos CC, Jow F, Chan TR, Arduini RM, Qian F, Baker DP, Bergeron C, Hession CA, Huganir RL, Borenstein CF, Enyedy I, Zou J, Rohde E, Wittmann M, Kumaravel G, Rhodes KJ, Scannevin RH, Dunah AW, Guckian KM (2018) Potent PDZ-domain PICK1 inhibitors that modulate amyloid beta-mediated synaptic dysfunction. Sci Rep 8(1):13438. https://doi.org/10.1038/s41598-018-31680-3
Marcotte DJ, Hus JC, Banos CC, Wildes C, Arduini R, Bergeron C, Hession CA, Baker DP, Lin E, Guckian KM, Dunah AW, Silvian LF (2018) Lock and chop: a novel method for the generation of a PICK1 PDZ domain and piperidine-based inhibitor co-crystal structure. Protein Sci 27(3):672–680. https://doi.org/10.1002/pro.3361
Joshi M, Vargas C, Boisguerin P, Diehl A, Krause G, Schmieder P, Moelling K, Hagen V, Schade M, Oschkinat H (2006) Discovery of low-molecular-weight ligands for the AF6 PDZ domain. Angew Chem Int Ed Engl 45(23):3790–3795. https://doi.org/10.1002/anie.200503965
Vargas C, Radziwill G, Krause G, Diehl A, Keller S, Kamdem N, Czekelius C, Kreuchwig A, Schmieder P, Doyle D, Moelling K, Hagen V, Schade M, Oschkinat H (2014) Small-molecule inhibitors of AF6 PDZ-mediated protein-protein interactions. ChemMedChem 9(7):1458–1462. https://doi.org/10.1002/cmdc.201300553
Lee HJ, Wang NX, Shi DL, Zheng JJ (2009) Sulindac inhibits canonical Wnt signaling by blocking the PDZ domain of the protein Dishevelled. Angew Chem Int Ed Engl 48(35):6448–6452. https://doi.org/10.1002/anie.200902981
Tripos Sybyl. St. Louis, MO
Kramer B, Rarey M, Lengauer T (1999) Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking. Proteins 37(2):228–241. https://doi.org/10.1002/(SICI)1097-0134(19991101)37:2<228::AID-PROT8>3.0.CO;2-8
Bouzidi N, Deokar H, Vogrig A, Boucherle B, Ripoche I, Abrunhosa-Thomas I, Dorr L, Wattiez AS, Lian LY, Marin P, Courteix C, Ducki S (2013) Identification of PDZ ligands by docking-based virtual screening for the development of novel analgesic agents. Bioorg Med Chem Lett 23(9):2624–2627. https://doi.org/10.1016/j.bmcl.2013.02.100
Kim HY, Choi S, Yoon JH, Lim HJ, Lee H, Choi J, Ro EJ, Heo JN, Lee W, No KT, Choi KY (2016) Small molecule inhibitors of the Dishevelled-CXXC5 interaction are new drug candidates for bone anabolic osteoporosis therapy. EMBO Mol Med 8(4):375–387. https://doi.org/10.15252/emmm.201505714
AccelrysSoftware Discovery Studio. San Diego, CA
Choi J, Ma S, Kim HY, Yun JH, Heo JN, Lee W, Choi KY, No KT (2016) Identification of small-molecule compounds targeting the dishevelled PDZ domain by virtual screening and binding studies. Bioorg Med Chem 24(15):3259–3266. https://doi.org/10.1016/j.bmc.2016.03.026
Ma S, Choi J, Jin X, Kim HY, Yun JH, Lee W, Choi KY, No KT (2018) Discovery of a small-molecule inhibitor of Dvl-CXXC5 interaction by computational approaches. J Comput Aided Mol Des 32(5):643–655. https://doi.org/10.1007/s10822-018-0118-x
Shan J, Zhang X, Bao J, Cassell R, Zheng JJ (2012) Synthesis of potent dishevelled PDZ domain inhibitors guided by virtual screening and NMR studies. Chem Biol Drug Des 79(4):376–383. https://doi.org/10.1111/j.1747-0285.2011.01295.x
Hori K, Ajioka K, Goda N, Shindo A, Takagishi M, Tenno T, Hiroaki H (2018) Discovery of potent disheveled/Dvl inhibitors using virtual screening optimized with NMR-based docking performance index. Front Pharmacol 9:983. https://doi.org/10.3389/fphar.2018.00983
Jones G, Willett P, Glen R, Leach A, Taylor R (1997) Development and validation of a genetic algorithm for flexible docking. J Mol Biol 267(3):727–748. https://doi.org/10.1006/jmbi.1996.0897
Verdonk ML, Cole JC, Hartshorn MJ, Murray CW, Taylor RD (2003) Improved protein-ligand docking using GOLD. Proteins 52(4):609–623. https://doi.org/10.1002/prot.10465
Cartier-Michaud A, Bailly AL, Betzi S, Shi X, Lissitzky JC, Zarubica A, Sergé A, Roche P, Lugari A, Hamon V, Bardin F, Derviaux C, Lembo F, Audebert S, Marchetto S, Durand B, Borg JP, Shi N, Morelli X, Aurrand-Lions M (2017) Genetic, structural, and chemical insights into the dual function of GRASP55 in germ cell Golgi remodeling and JAM-C polarized localization during spermatogenesis. PLoS Genet 13(6):e1006803. https://doi.org/10.1371/journal.pgen.1006803
Jain AN (2003) Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine. J Med Chem 46(4):499–511. https://doi.org/10.1021/jm.020406h
Petta I, Lievens S, Libert C, Tavernier J, De Bosscher K (2016) Modulation of protein-protein interactions for the development of novel therapeutics. Mol Ther 24(4):707–718. https://doi.org/10.1038/mt.2015.214
Ivanov AA, Revennaugh B, Rusnak L, Gonzalez-Pecchi V, Mo X, Johns MA, Du Y, Cooper LAD, Moreno CS, Khuri FR, Fu H (2018) The OncoPPi portal: an integrative resource to explore and prioritize protein-protein interactions for cancer target discovery. Bioinformatics 34(7):1183–1191. https://doi.org/10.1093/bioinformatics/btx743
Author information
Authors and Affiliations
Corresponding authors
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2021 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Hoffer, L., Roche, P., Morelli, X. (2021). Rational Design of PDZ Domain Inhibitors: Discovery of Small Organic Compounds Targeting PDZ Domains. In: Borg, JP. (eds) PDZ Mediated Interactions. Methods in Molecular Biology, vol 2256. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1166-1_16
Download citation
DOI: https://doi.org/10.1007/978-1-0716-1166-1_16
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-1165-4
Online ISBN: 978-1-0716-1166-1
eBook Packages: Springer Protocols