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Park S, Fan J, Chamakuri S, Palaniappan M, Sharma K, Qin X, Wang J, Tan Z, Judge A, Hu L, Sankaran B, Li F, Prasad BVV, Matzuk MM, Palzkill T. Exploiting the Carboxylate-Binding Pocket of β-Lactamase Enzymes Using a Focused DNA-Encoded Chemical Library. J Med Chem 2024; 67:620-642. [PMID: 38117688 DOI: 10.1021/acs.jmedchem.3c01834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
β-Lactamase enzymes hydrolyze and thereby provide bacterial resistance to the important β-lactam class of antibiotics. The OXA-48 and NDM-1 β-lactamases cause resistance to the last-resort β-lactams, carbapenems, leading to a serious public health threat. Here, we utilized DNA-encoded chemical library (DECL) technology to discover novel β-lactamase inhibitors. We exploited the β-lactamase enzyme-substrate binding interactions and created a DECL targeting the carboxylate-binding pocket present in all β-lactamases. A library of 106 compounds, each containing a carboxylic acid or a tetrazole as an enzyme recognition element, was designed, constructed, and used to identify OXA-48 and NDM-1 inhibitors with micromolar to nanomolar potency. Further optimization led to NDM-1 inhibitors with increased potencies and biological activities. This work demonstrates that the carboxylate-binding pocket-targeting DECL, designed based on substrate binding information, aids in inhibitor identification and led to the discovery of novel non-β-lactam pharmacophores for the development of β-lactamase inhibitors for enzymes of different structural and mechanistic classes.
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Affiliation(s)
- Suhyeorn Park
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Jiayi Fan
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Srinivas Chamakuri
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Murugesan Palaniappan
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Kiran Sharma
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Xuan Qin
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Jian Wang
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Zhi Tan
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Allison Judge
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Advanced Light Source, Lawrence Berkeley National Lab, Berkeley, California 94720, United States
| | - Feng Li
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - B V Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Martin M Matzuk
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Timothy Palzkill
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
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2
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Stevens AO, Luo S, He Y. Three Binding Conformations of BIO124 in the Pocket of the PICK1 PDZ Domain. Cells 2022; 11:cells11152451. [PMID: 35954295 PMCID: PMC9368557 DOI: 10.3390/cells11152451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/29/2022] [Accepted: 08/04/2022] [Indexed: 11/30/2022] Open
Abstract
The PDZ family has drawn attention as possible drug targets because of the domains’ wide ranges of function and highly conserved binding pockets. The PICK1 PDZ domain has been proposed as a possible drug target because the interactions between the PICK1 PDZ domain and the GluA2 subunit of the AMPA receptor have been shown to progress neurodegenerative diseases. BIO124 has been identified as a sub µM inhibitor of the PICK1–GluA2 interaction. Here, we use all-atom molecular dynamics simulations to reveal the atomic-level interaction pattern between the PICK1 PDZ domain and BIO124. Our simulations reveal three unique binding conformations of BIO124 in the PICK1 PDZ binding pocket, referred to here as state 0, state 1, and state 2. Each conformation is defined by a unique hydrogen bonding network and a unique pattern of hydrophobic interactions between BIO124 and the PICK1 PDZ domain. Interestingly, each conformation of BIO124 results in different dynamic changes to the PICK1 PDZ domain. Unlike states 1 and 2, state 0 induces dynamic coupling between BIO124 and the αA helix. Notably, this dynamic coupling with the αA helix is similar to what has been observed in other PDZ–ligand complexes. Our analysis indicates that the interactions formed between BIO124 and I35 may be the key to inducing dynamic coupling with the αA helix. Lastly, we suspect that the conformational shifts observed in our simulations may affect the stability and thus the overall effectiveness of BIO124. We propose that a physically larger inhibitor may be necessary to ensure sufficient interactions that permit stable binding between a drug and the PICK1 PDZ domain.
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Affiliation(s)
- Amy O. Stevens
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Samuel Luo
- Albuquerque Academy, Albuquerque, NM 87131, USA
| | - Yi He
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131, USA
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87131, USA
- Correspondence:
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3
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Vincenzi M, Mercurio FA, Leone M. Protein Interaction Domains: Structural Features and Drug Discovery Applications (Part 2). Curr Med Chem 2021; 28:854-892. [PMID: 31942846 DOI: 10.2174/0929867327666200114114142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/28/2019] [Accepted: 11/04/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Proteins present a modular organization made up of several domains. Apart from the domains playing catalytic functions, many others are crucial to recruit interactors. The latter domains can be defined as "PIDs" (Protein Interaction Domains) and are responsible for pivotal outcomes in signal transduction and a certain array of normal physiological and disease-related pathways. Targeting such PIDs with small molecules and peptides able to modulate their interaction networks, may represent a valuable route to discover novel therapeutics. OBJECTIVE This work represents a continuation of a very recent review describing PIDs able to recognize post-translationally modified peptide segments. On the contrary, the second part concerns with PIDs that interact with simple peptide sequences provided with standard amino acids. METHODS Crucial structural information on different domain subfamilies and their interactomes was gained by a wide search in different online available databases (including the PDB (Protein Data Bank), the Pfam (Protein family), and the SMART (Simple Modular Architecture Research Tool)). Pubmed was also searched to explore the most recent literature related to the topic. RESULTS AND CONCLUSION PIDs are multifaceted: they have all diverse structural features and can recognize several consensus sequences. PIDs can be linked to different diseases onset and progression, like cancer or viral infections and find applications in the personalized medicine field. Many efforts have been centered on peptide/peptidomimetic inhibitors of PIDs mediated interactions but much more work needs to be conducted to improve drug-likeness and interaction affinities of identified compounds.
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Affiliation(s)
- Marian Vincenzi
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy
| | - Flavia Anna Mercurio
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy
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4
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Hoffer L, Roche P, Morelli X. Rational Design of PDZ Domain Inhibitors: Discovery of Small Organic Compounds Targeting PDZ Domains. Methods Mol Biol 2021; 2256:277-289. [PMID: 34014528 DOI: 10.1007/978-1-0716-1166-1_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
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.
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Affiliation(s)
- Laurent Hoffer
- Centre de Recherche en Cancérologie de Marseille (CRCM), Aix-Marseille Université, Inserm, CNRS and Institut Paoli-Calmettes, Marseille, France.
| | - Philippe Roche
- Centre de Recherche en Cancérologie de Marseille (CRCM), Aix-Marseille Université, Inserm, CNRS and Institut Paoli-Calmettes, Marseille, France
| | - Xavier Morelli
- Centre de Recherche en Cancérologie de Marseille (CRCM), Aix-Marseille Université, Inserm, CNRS and Institut Paoli-Calmettes, Marseille, France.
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5
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Rosenbaum MI, Clemmensen LS, Bredt DS, Bettler B, Strømgaard K. Targeting receptor complexes: a new dimension in drug discovery. Nat Rev Drug Discov 2020; 19:884-901. [PMID: 33177699 DOI: 10.1038/s41573-020-0086-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2020] [Indexed: 12/11/2022]
Abstract
Targeting receptor proteins, such as ligand-gated ion channels and G protein-coupled receptors, has directly enabled the discovery of most drugs developed to modulate receptor signalling. However, as the search for novel and improved drugs continues, an innovative approach - targeting receptor complexes - is emerging. Receptor complexes are composed of core receptor proteins and receptor-associated proteins, which have profound effects on the overall receptor structure, function and localization. Hence, targeting key protein-protein interactions within receptor complexes provides an opportunity to develop more selective drugs with fewer side effects. In this Review, we discuss our current understanding of ligand-gated ion channel and G protein-coupled receptor complexes and discuss strategies for their pharmacological modulation. Although such strategies are still in preclinical development for most receptor complexes, they exemplify how receptor complexes can be drugged, and lay the groundwork for this nascent area of research.
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Affiliation(s)
- Mette Ishøy Rosenbaum
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Louise S Clemmensen
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - David S Bredt
- Neuroscience Discovery, Janssen Pharmaceutical Companies of Johnson & Johnson, San Diego, CA, USA
| | - Bernhard Bettler
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Kristian Strømgaard
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark.
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6
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Capdevielle C, Desplat A, Charpentier J, Sagliocco F, Thiebaud P, Thézé N, Fédou S, Hooks KB, Silvestri R, Guyonnet-Duperat V, Petrel M, Raymond AA, Dupuy JW, Grosset CF, Hagedorn M. HDAC inhibition induces expression of scaffolding proteins critical for tumor progression in pediatric glioma: focus on EBP50 and IRSp53. Neuro Oncol 2020; 22:550-562. [PMID: 31711240 DOI: 10.1093/neuonc/noz215] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Diffuse midline glioma (DMG) is a pediatric malignancy with poor prognosis. Most children die less than one year after diagnosis. Recently, mutations in histone H3 have been identified and are believed to be oncogenic drivers. Targeting this epigenetic abnormality using histone deacetylase (HDAC) inhibitors such as panobinostat (PS) is therefore a novel therapeutic option currently evaluated in clinical trials. METHODS BH3 profiling revealed engagement in an irreversible apoptotic process of glioma cells exposed to PS confirmed by annexin-V/propidium iodide staining. Using proteomic analysis of 3 DMG cell lines, we identified 2 proteins deregulated after PS treatment. We investigated biological effects of their downregulation by silencing RNA but also combinatory effects with PS treatment in vitro and in vivo using a chick embryo DMG model. Electron microscopy was used to validate protein localization. RESULTS Scaffolding proteins EBP50 and IRSp53 were upregulated by PS treatment. Reduction of these proteins in DMG cell lines leads to blockade of proliferation and migration, invasion, and an increase of apoptosis. EBP50 was found to be expressed in cytoplasm and nucleus in DMG cells, confirming known oncogenic locations of the protein. Treatment of glioma cells with PS together with genetic or chemical inhibition of EBP50 leads to more effective reduction of cell growth in vitro and in vivo. CONCLUSION Our data reveal a specific relation between HDAC inhibitors and scaffolding protein deregulation which might have a potential for therapeutic intervention for cancer treatment.
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Affiliation(s)
- Caroline Capdevielle
- National Institute of Health and Medical Research (INSERM) Unit 1035, MicroRNAs in Cancer and Development (miRCADE) team, Bordeaux, France.,University of Bordeaux, Bordeaux, France
| | - Angélique Desplat
- National Institute of Health and Medical Research (INSERM) Unit 1035, MicroRNAs in Cancer and Development (miRCADE) team, Bordeaux, France
| | - Justine Charpentier
- National Institute of Health and Medical Research (INSERM) Unit 1035, MicroRNAs in Cancer and Development (miRCADE) team, Bordeaux, France.,University of Bordeaux, Bordeaux, France
| | - Francis Sagliocco
- National Institute of Health and Medical Research (INSERM) Unit 1035, MicroRNAs in Cancer and Development (miRCADE) team, Bordeaux, France.,University of Bordeaux, Bordeaux, France
| | - Pierre Thiebaud
- INSERM Unit 1035 Dermatology team, Bordeaux, France.,XenoFish Platform, University of Bordeaux, Bordeaux, France.,University of Bordeaux, Bordeaux, France
| | - Nadine Thézé
- INSERM Unit 1035 Dermatology team, Bordeaux, France.,XenoFish Platform, University of Bordeaux, Bordeaux, France.,University of Bordeaux, Bordeaux, France
| | - Sandrine Fédou
- INSERM Unit 1035 Dermatology team, Bordeaux, France.,XenoFish Platform, University of Bordeaux, Bordeaux, France.,University of Bordeaux, Bordeaux, France
| | - Katarzyna B Hooks
- National Institute of Health and Medical Research (INSERM) Unit 1035, MicroRNAs in Cancer and Development (miRCADE) team, Bordeaux, France.,University of Bordeaux, Bordeaux, France
| | - Romano Silvestri
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
| | | | - Melina Petrel
- Bordeaux Imaging Center, University of Bordeaux, Bordeaux, France
| | - Anne-Aurélie Raymond
- National Institute of Health and Medical Research (INSERM) Unit 1035, MicroRNAs in Cancer and Development (miRCADE) team, Bordeaux, France.,University of Bordeaux, Bordeaux, France.,Oncoprot, Bordeaux, France
| | - Jean-William Dupuy
- University of Bordeaux, Bordeaux, France.,Proteomics Platform, Bordeaux Functional Genomics Center, University of Bordeaux, Bordeaux, France
| | - Christophe F Grosset
- National Institute of Health and Medical Research (INSERM) Unit 1035, MicroRNAs in Cancer and Development (miRCADE) team, Bordeaux, France.,University of Bordeaux, Bordeaux, France
| | - Martin Hagedorn
- National Institute of Health and Medical Research (INSERM) Unit 1035, MicroRNAs in Cancer and Development (miRCADE) team, Bordeaux, France.,University of Bordeaux, Bordeaux, France
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7
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Baliova M, Jursky F. Comparison of SynCAM1/CADM1 PDZ interactions with MUPP1 using mammalian and bacterial pull-down systems. Brain Behav 2020; 10:e01587. [PMID: 32108449 PMCID: PMC7177587 DOI: 10.1002/brb3.1587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 01/20/2020] [Accepted: 02/15/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Synaptic cell adhesion molecule 1 (SynCAM1) also known as cell adhesion molecule 1 (CADM1) is a transmembrane cell adhesion protein that operates in a variety of physiological and pathological cellular contexts, and its interaction with the PDZ signalling protein MUPP1 have been previously implicated in autism spectrum disorder (ASD). METHODS We used in vitro pull-down systems based on the bacterial and mammalian extracts to study SynCAM1/CADM1 PDZ interactions with MUPP1 at various conditions. RESULTS So far, the investigated interaction of SynCAM1/CADM1 with MUPP1 has been mostly attributed to an unspecified region of MUPP1 PDZ domains 1-5 or exclusively to domain 2, using a yeast two-hybrid system. We also confirmed the single interaction of native synaptosomal CADM1 with PDZ domain 2. However, in this work, using recombinant proteins overexpressed in bacteria, we found an in vitro pull-down conditions in which all first five domains and, to a much lesser extent, MUPP1 domains 7 and 11 significantly interacted with the whole C-terminal domain of SynCAM1/CADM1. These PDZ interactions were confirmed by a pull-down assay using the last seven amino acids of the SynCAM1/CADM1 PDZ motif and using two fusion partners. Multiple interactions were additionally replicated using the continuous N-terminal MUPP1 protein fragment, which included first five PDZ domains, containing either intact or mutated domain 2. CONCLUSIONS We hypothesize that multiple interactions might exist in vivo, representing transient low-affinity interactions or alternative binding sites on MUPP1 when domain 2 is occupied or occluded by the interaction with other ligands. This newly identified interactions extend the potential genetic mutations, possibly affecting SynCAM1/CADM1/MUPP1 function. Possible reasons for the absence of some of the identified CADM1 PDZ interactions in mammalian extracts are discussed.
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Affiliation(s)
- Martina Baliova
- Laboratory of Neurobiology, Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Frantisek Jursky
- Laboratory of Neurobiology, Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
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8
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Valgardson J, Cosbey R, Houser P, Rupp M, Van Bronkhorst R, Lee M, Jagodzinski F, Amacher JF. MotifAnalyzer-PDZ: A computational program to investigate the evolution of PDZ-binding target specificity. Protein Sci 2019; 28:2127-2143. [PMID: 31599029 DOI: 10.1002/pro.3741] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 09/27/2019] [Accepted: 09/30/2019] [Indexed: 12/15/2022]
Abstract
Recognition of short linear motifs (SLiMs) or peptides by proteins is an important component of many cellular processes. However, due to limited and degenerate binding motifs, prediction of cellular targets is challenging. In addition, many of these interactions are transient and of relatively low affinity. Here, we focus on one of the largest families of SLiM-binding domains in the human proteome, the PDZ domain. These domains bind the extreme C-terminus of target proteins, and are involved in many signaling and trafficking pathways. To predict endogenous targets of PDZ domains, we developed MotifAnalyzer-PDZ, a program that filters and compares all motif-satisfying sequences in any publicly available proteome. This approach enables us to determine possible PDZ binding targets in humans and other organisms. Using this program, we predicted and biochemically tested novel human PDZ targets by looking for strong sequence conservation in evolution. We also identified three C-terminal sequences in choanoflagellates that bind a choanoflagellate PDZ domain, the Monsiga brevicollis SHANK1 PDZ domain (mbSHANK1), with endogenously-relevant affinities, despite a lack of conservation with the targets of a homologous human PDZ domain, SHANK1. All three are predicted to be signaling proteins, with strong sequence homology to cytosolic and receptor tyrosine kinases. Finally, we analyzed and compared the positional amino acid enrichments in PDZ motif-satisfying sequences from over a dozen organisms. Overall, MotifAnalyzer-PDZ is a versatile program to investigate potential PDZ interactions. This proof-of-concept work is poised to enable similar types of analyses for other SLiM-binding domains (e.g., MotifAnalyzer-Kinase). MotifAnalyzer-PDZ is available at http://motifAnalyzerPDZ.cs.wwu.edu.
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Affiliation(s)
- Jordan Valgardson
- Department of Computer Science, Western Washington University, Bellingham, Washington.,Department of Chemistry, Western Washington University, Bellingham, Washington
| | - Robin Cosbey
- Department of Computer Science, Western Washington University, Bellingham, Washington
| | - Paul Houser
- Department of Computer Science, Western Washington University, Bellingham, Washington
| | - Milo Rupp
- Department of Computer Science, Western Washington University, Bellingham, Washington
| | - Raiden Van Bronkhorst
- Department of Computer Science, Western Washington University, Bellingham, Washington
| | - Michael Lee
- Department of Computer Science, Western Washington University, Bellingham, Washington
| | - Filip Jagodzinski
- Department of Computer Science, Western Washington University, Bellingham, Washington
| | - Jeanine F Amacher
- Department of Chemistry, Western Washington University, Bellingham, Washington
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9
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Engineering selective competitors for the discrimination of highly conserved protein-protein interaction modules. Nat Commun 2019; 10:4521. [PMID: 31586061 PMCID: PMC6778148 DOI: 10.1038/s41467-019-12528-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 09/14/2019] [Indexed: 12/13/2022] Open
Abstract
Designing highly specific modulators of protein-protein interactions (PPIs) is especially challenging in the context of multiple paralogs and conserved interaction surfaces. In this case, direct generation of selective and competitive inhibitors is hindered by high similarity within the evolutionary-related protein interfaces. We report here a strategy that uses a semi-rational approach to separate the modulator design into two functional parts. We first achieve specificity toward a region outside of the interface by using phage display selection coupled with molecular and cellular validation. Highly selective competition is then generated by appending the more degenerate interaction peptide to contact the target interface. We apply this approach to specifically bind a single PDZ domain within the postsynaptic protein PSD-95 over highly similar PDZ domains in PSD-93, SAP-97 and SAP-102. Our work provides a paralog-selective and domain specific inhibitor of PSD-95, and describes a method to efficiently target other conserved PPI modules. Developing inhibitors that target specific protein-protein interactions (PPIs) is challenging. Here, the authors show that target selectivity and PPI blocking can be achieved simultaneously with PPI inhibitors that contain two functional modules, and create a paralog-selective PSD-95 inhibitor as proof-of-concept.
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10
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Christensen NR, Čalyševa J, Fernandes EFA, Lüchow S, Clemmensen LS, Haugaard‐Kedström LM, Strømgaard K. PDZ Domains as Drug Targets. ADVANCED THERAPEUTICS 2019; 2:1800143. [PMID: 32313833 PMCID: PMC7161847 DOI: 10.1002/adtp.201800143] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 03/25/2019] [Indexed: 12/14/2022]
Abstract
Protein-protein interactions within protein networks shape the human interactome, which often is promoted by specialized protein interaction modules, such as the postsynaptic density-95 (PSD-95), discs-large, zona occludens 1 (ZO-1) (PDZ) domains. PDZ domains play a role in several cellular functions, from cell-cell communication and polarization, to regulation of protein transport and protein metabolism. PDZ domain proteins are also crucial in the formation and stability of protein complexes, establishing an important bridge between extracellular stimuli detected by transmembrane receptors and intracellular responses. PDZ domains have been suggested as promising drug targets in several diseases, ranging from neurological and oncological disorders to viral infections. In this review, the authors describe structural and genetic aspects of PDZ-containing proteins and discuss the current status of the development of small-molecule and peptide modulators of PDZ domains. An overview of potential new therapeutic interventions in PDZ-mediated protein networks is also provided.
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Affiliation(s)
- Nikolaj R. Christensen
- Center for BiopharmaceuticalsDepartment of Drug Design and PharmacologyUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
| | - Jelena Čalyševa
- European Molecular Biology Laboratory (EMBL)Structural and Computational Biology UnitMeyerhofstraße 169117HeidelbergGermany
- EMBL International PhD ProgrammeFaculty of BiosciencesEMBL–Heidelberg UniversityGermany
| | - Eduardo F. A. Fernandes
- Center for BiopharmaceuticalsDepartment of Drug Design and PharmacologyUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
| | - Susanne Lüchow
- Department of Chemistry – BMCUppsala UniversityBox 576SE75123UppsalaSweden
| | - Louise S. Clemmensen
- Center for BiopharmaceuticalsDepartment of Drug Design and PharmacologyUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
| | - Linda M. Haugaard‐Kedström
- Center for BiopharmaceuticalsDepartment of Drug Design and PharmacologyUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
| | - Kristian Strømgaard
- Center for BiopharmaceuticalsDepartment of Drug Design and PharmacologyUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
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11
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Liu X, Fuentes EJ. Emerging Themes in PDZ Domain Signaling: Structure, Function, and Inhibition. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2019; 343:129-218. [PMID: 30712672 PMCID: PMC7185565 DOI: 10.1016/bs.ircmb.2018.05.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Post-synaptic density-95, disks-large and zonula occludens-1 (PDZ) domains are small globular protein-protein interaction domains widely conserved from yeast to humans. They are composed of ∼90 amino acids and form a classical two α-helical/six β-strand structure. The prototypical ligand is the C-terminus of partner proteins; however, they also bind internal peptide sequences. Recent findings indicate that PDZ domains also bind phosphatidylinositides and cholesterol. Through their ligand interactions, PDZ domain proteins are critical for cellular trafficking and the surface retention of various ion channels. In addition, PDZ proteins are essential for neuronal signaling, memory, and learning. PDZ proteins also contribute to cytoskeletal dynamics by mediating interactions critical for maintaining cell-cell junctions, cell polarity, and cell migration. Given their important biological roles, it is not surprising that their dysfunction can lead to multiple disease states. As such, PDZ domain-containing proteins have emerged as potential targets for the development of small molecular inhibitors as therapeutic agents. Recent data suggest that the critical binding function of PDZ domains in cell signaling is more than just glue, and their binding function can be regulated by phosphorylation or allosterically by other binding partners. These studies also provide a wealth of structural and biophysical data that are beginning to reveal the physical features that endow this small modular domain with a central role in cell signaling.
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Affiliation(s)
- Xu Liu
- Department of Biochemistry, University of Iowa, Iowa City, IA, United States
| | - Ernesto J. Fuentes
- Department of Biochemistry, University of Iowa, Iowa City, IA, United States
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, United States
- Corresponding author: E-mail:
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12
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Caron A, Briscoe DM, Richard D, Laplante M. DEPTOR at the Nexus of Cancer, Metabolism, and Immunity. Physiol Rev 2018; 98:1765-1803. [PMID: 29897294 DOI: 10.1152/physrev.00064.2017] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
DEP domain-containing mechanistic target of rapamycin (mTOR)-interacting protein (DEPTOR) is an important modulator of mTOR, a kinase at the center of two important protein complexes named mTORC1 and mTORC2. These highly studied complexes play essential roles in regulating growth, metabolism, and immunity in response to mitogens, nutrients, and cytokines. Defects in mTOR signaling have been associated with the development of many diseases, including cancer and diabetes, and approaches aiming at modulating mTOR activity are envisioned as an attractive strategy to improve human health. DEPTOR interaction with mTOR represses its kinase activity and rewires the mTOR signaling pathway. Over the last years, several studies have revealed key roles for DEPTOR in numerous biological and pathological processes. Here, we provide the current state of the knowledge regarding the cellular and physiological functions of DEPTOR by focusing on its impact on the mTOR pathway and its role in promoting health and disease.
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Affiliation(s)
- Alexandre Caron
- Department of Internal Medicine, Division of Hypothalamic Research, The University of Texas Southwestern Medical Center , Dallas, Texas ; Transplant Research Program, Boston Children's Hospital , Boston, Massachusetts ; Department of Pediatrics, Harvard Medical School , Boston, Massachusetts ; Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec (CRIUCPQ), Faculté de Médecine, Université Laval , Québec , Canada ; and Centre de Recherche sur le Cancer de l'Université Laval, Université Laval , Québec , Canada
| | - David M Briscoe
- Department of Internal Medicine, Division of Hypothalamic Research, The University of Texas Southwestern Medical Center , Dallas, Texas ; Transplant Research Program, Boston Children's Hospital , Boston, Massachusetts ; Department of Pediatrics, Harvard Medical School , Boston, Massachusetts ; Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec (CRIUCPQ), Faculté de Médecine, Université Laval , Québec , Canada ; and Centre de Recherche sur le Cancer de l'Université Laval, Université Laval , Québec , Canada
| | - Denis Richard
- Department of Internal Medicine, Division of Hypothalamic Research, The University of Texas Southwestern Medical Center , Dallas, Texas ; Transplant Research Program, Boston Children's Hospital , Boston, Massachusetts ; Department of Pediatrics, Harvard Medical School , Boston, Massachusetts ; Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec (CRIUCPQ), Faculté de Médecine, Université Laval , Québec , Canada ; and Centre de Recherche sur le Cancer de l'Université Laval, Université Laval , Québec , Canada
| | - Mathieu Laplante
- Department of Internal Medicine, Division of Hypothalamic Research, The University of Texas Southwestern Medical Center , Dallas, Texas ; Transplant Research Program, Boston Children's Hospital , Boston, Massachusetts ; Department of Pediatrics, Harvard Medical School , Boston, Massachusetts ; Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec (CRIUCPQ), Faculté de Médecine, Université Laval , Québec , Canada ; and Centre de Recherche sur le Cancer de l'Université Laval, Université Laval , Québec , Canada
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13
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Cysteine modifiers suggest an allosteric inhibitory site on the CAL PDZ domain. Biosci Rep 2018; 38:BSR20180231. [PMID: 29472314 PMCID: PMC6435542 DOI: 10.1042/bsr20180231] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 02/17/2018] [Accepted: 02/22/2018] [Indexed: 01/28/2023] Open
Abstract
Protein-protein interactions have become attractive targets for both experimental and therapeutic interventions. The PSD-95/Dlg1/ZO-1 (PDZ) domain is found in a large family of eukaryotic scaffold proteins that plays important roles in intracellular trafficking and localization of many target proteins. Here, we seek inhibitors of the PDZ protein that facilitates post-endocytic degradation of the cystic fibrosis (CF) transmembrane conductance regulator (CFTR): the CFTR-associated ligand (CAL). We develop and validate biochemical screens and identify methyl-3,4-dephostatin (MD) and its analog ethyl-3,4-dephostatin (ED) as CAL PDZ inhibitors. Depending on conditions, MD can bind either covalently or non-covalently. Crystallographic and NMR data confirm that MD attacks a pocket at a site distinct from the canonical peptide-binding groove, and suggests an allosteric connection between target residue Cys319 and the conserved Leu291 in the GLGI motif. MD and ED thus appear to represent the first examples of small-molecule allosteric regulation of PDZ:peptide affinity. Their mechanism of action may exploit the known conformational plasticity of the PDZ domains and suggests that allosteric modulation may represent a strategy for targeting of this family of protein-protein binding modules.
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14
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Seisel Q, Rädisch M, Gill NP, Madden DR, Boisguerin P. Optimization of the process of inverted peptides (PIPE PLUS) to screen PDZ domain ligands. Bioorg Med Chem Lett 2017; 27:3111-3116. [PMID: 28549735 PMCID: PMC5523833 DOI: 10.1016/j.bmcl.2017.05.045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 05/12/2017] [Accepted: 05/13/2017] [Indexed: 11/21/2022]
Abstract
PDZ domains play crucial roles in cell signaling processes and are therefore attractive targets for the development of therapeutic inhibitors. In many cases, C-terminal peptides are the physiological binding partners of PDZ domains. To identify both native ligands and potential inhibitors we have screened arrays synthesized by the process of inverted peptides (PIPE), a variant of SPOT synthesis that generates peptides with free C-termini. Here, we present the development of a new functionalized cellulose membrane as solid support along with the optimized PIPEPLUS technology. Improved resolution and accuracy of the synthesis were shown with peptide arrays containing both natural and non-natural amino acids. These new screening possibilities will advance the development of active, selective and metabolically stable PDZ interactors.
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Affiliation(s)
- Quentin Seisel
- Centre de Recherche de Biologie cellulaire de Montpellier, CNRS UMR 5237, Université de Montpellier, 1919 Route de Mende, 34293 Montpellier Cedex 5, France
| | - Marisa Rädisch
- Bioorganische Chemie, Universität Bayreuth, Gebäude NW I, 95440 Bayreuth, Germany
| | - Nicholas P Gill
- Department of Biochemistry & Cell Biology, Geisel School of Medicine at Dartmouth, 7200 Vail Building, Hanover, NH 03755-3844, United States
| | - Dean R Madden
- Department of Biochemistry & Cell Biology, Geisel School of Medicine at Dartmouth, 7200 Vail Building, Hanover, NH 03755-3844, United States
| | - Prisca Boisguerin
- Centre de Recherche de Biologie cellulaire de Montpellier, CNRS UMR 5237, Université de Montpellier, 1919 Route de Mende, 34293 Montpellier Cedex 5, France.
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15
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Yang Y, Ren Y, Shi Y. Intermolecular disulfide bond in the dimerization of S-periaxin mediated by Cys88 and Cys139. Acta Biochim Biophys Sin (Shanghai) 2016; 48:326-33. [PMID: 26940996 DOI: 10.1093/abbs/gmw008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 11/30/2015] [Indexed: 12/13/2022] Open
Abstract
Periaxin is expressed in mammalian Schwann cells and lens fiber cells, and has been identified in a screen for cytoskeleton-associated proteins. Charcot-Marie-Tooth 4F is caused by losses or mutations of theperiaxingene. Theperiaxingene encodes two protein isoforms, namely, L-periaxin and S-periaxin.S-periaxin contains 147 amino acid residues and has an N-terminal PDZ domain. In this paper, S-periaxin was reported to be homodimerized through the formation of intermolecular disulfide bonds with its Cys88 and Cys139 residues under mild oxidation conditions. The covalent dimer of S-periaxin was also observed by western blot analysis and bimolecular fluorescence complementation analyses. S-periaxin dimerization formation could be regulated by cellular redox fluctuations. These results offer a possible mechanism to the formation of periaxin complexes, improvement of complex stability, and establishment of a link between the extracellular matrix and the cytoskeleton.
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Affiliation(s)
- Yan Yang
- Key Laboratory of Chemical Biology and Molecular Engineering of the Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China Chemical and Biological Engineering College, Taiyuan University of Science and Technology, Taiyuan 030006, China
| | - Yemei Ren
- Key Laboratory of Chemical Biology and Molecular Engineering of the Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
| | - Yawei Shi
- Key Laboratory of Chemical Biology and Molecular Engineering of the Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
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16
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Corbi-Verge C, Kim PM. Motif mediated protein-protein interactions as drug targets. Cell Commun Signal 2016; 14:8. [PMID: 26936767 PMCID: PMC4776425 DOI: 10.1186/s12964-016-0131-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 02/25/2016] [Indexed: 12/17/2022] Open
Abstract
Protein-protein interactions (PPI) are involved in virtually every cellular process and thus represent an attractive target for therapeutic interventions. A significant number of protein interactions are frequently formed between globular domains and short linear peptide motifs (DMI). Targeting these DMIs has proven challenging and classical approaches to inhibiting such interactions with small molecules have had limited success. However, recent new approaches have led to the discovery of potent inhibitors, some of them, such as Obatoclax, ABT-199, AEG-40826 and SAH-p53-8 are likely to become approved drugs. These novel inhibitors belong to a wide range of different molecule classes, ranging from small molecules to peptidomimetics and biologicals. This article reviews the main reasons for limited success in targeting PPIs, discusses how successful approaches overcome these obstacles to discovery promising inhibitors for human protein double minute 2 (HDM2), B-cell lymphoma 2 (Bcl-2), X-linked inhibitor of apoptosis protein (XIAP), and provides a summary of the promising approaches currently in development that indicate the future potential of PPI inhibitors in drug discovery.
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Affiliation(s)
- Carles Corbi-Verge
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada.
| | - Philip M Kim
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 3E1, Canada.
- Department of Computer Science, University of Toronto, Toronto, ON, M5S 3E1, Canada.
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17
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Nevola L, Giralt E. Modulating protein-protein interactions: the potential of peptides. Chem Commun (Camb) 2015; 51:3302-15. [PMID: 25578807 DOI: 10.1039/c4cc08565e] [Citation(s) in RCA: 187] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Protein-protein interactions (PPIs) have emerged as important and challenging targets in chemical biology and medicinal chemistry. The main difficulty encountered in the discovery of small molecule modulators derives from the large contact surfaces involved in PPIs when compared with those that participate in protein-small molecule interactions. Because of their intrinsic features, peptides can explore larger surfaces and therefore represent a useful alternative to modulate PPIs. The use of peptides as therapeutics has been held back by their instability in vivo and poor cell internalization. However, more than 200 peptide drugs and homologous compounds (proteins or antibodies) containing peptide bonds are (or have been) on the market, and many alternatives are now available to tackle these limitations. This review will focus on the latest progress in the field, spanning from "lead" identification methods to binding evaluation techniques, through an update of the most successful examples described in the literature.
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Affiliation(s)
- Laura Nevola
- Institute for Research in Biomedicine (IRB Barcelona), C/Baldiri Reixac 10, 08028 Barcelona, Spain.
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18
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Wu J, Peng D, Zhang Y, Lu Z, Voehler M, Sanders CR, Li J. Biophysical characterization of interactions between the C-termini of peripheral nerve claudins and the PDZ₁ domain of zonula occludens. Biochem Biophys Res Commun 2015; 459:87-93. [PMID: 25712527 DOI: 10.1016/j.bbrc.2015.02.075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 02/14/2015] [Indexed: 11/30/2022]
Abstract
Our recent study has shown that cellular junctions in myelin and in the epi-/perineruium that encase nerve fibers regulate the permeability of the peripheral nerves. This permeability may affect propagation of the action potential. Direct interactions between the PDZ₁ domain of zonula occludens (ZO₁ or ZO₂) and the C-termini of claudins are known to be crucial for the formation of tight junctions. Using the purified PDZ₁ domain of ZO₂ and a variety of C-terminal mutants of peripheral nerve claudins (claudin-1, claudin-2, claudin-3, claudin-5 in epi-/perineurium; claudin-19 in myelin), we have utilized NMR spectroscopy to determine specific roles of the 3 C-terminal claudin residues (position -2, -1, 0) for their interactions with PDZ₁ of ZO₂. In contrast to the canonical model that emphasizes the importance of residues at the -2 and 0 positions, our results demonstrate that, for peripheral nerve claudins, the residue at position -1 plays a critical role in association with PDZ₁, while the side-chain of residue 0 plays a significant but lesser role. Surprisingly, claudin-19, the most abundant claudin in myelin, exhibited no binding to ZO₂. These findings reveal that the binding mechanism of claudin/ZO in epi-/perineurium is distinct from the canonical interactions between non-ZO PDZ-containing proteins with their ligands. This observation provides the molecular basis for a strategy to develop drugs that target tight junctions in the epi-/perineurium of peripheral nerves.
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Affiliation(s)
- Jiawen Wu
- Department of Neurology, Vanderbilt University School of Medicine, USA; Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Dungeng Peng
- Department of Neurology, Vanderbilt University School of Medicine, USA
| | - Yang Zhang
- Department of Neurology, Vanderbilt University School of Medicine, USA
| | - Zhenwei Lu
- Department of Biochemistry, Vanderbilt University School of Medicine, USA
| | - Markus Voehler
- Center for Structural Biology, Vanderbilt University, USA
| | - Charles R Sanders
- Department of Biochemistry, Vanderbilt University School of Medicine, USA; Center for Structural Biology, Vanderbilt University, USA
| | - Jun Li
- Department of Neurology, Vanderbilt University School of Medicine, USA; Tennessee Valley Healthcare System (TVHS), Nashville, VA, USA; Center for Human Genetics Research, Vanderbilt University School of Medicine, USA.
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19
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Zheng F, Jewell H, Fitzpatrick J, Zhang J, Mierke DF, Grigoryan G. Computational design of selective peptides to discriminate between similar PDZ domains in an oncogenic pathway. J Mol Biol 2014; 427:491-510. [PMID: 25451599 DOI: 10.1016/j.jmb.2014.10.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 10/21/2014] [Accepted: 10/23/2014] [Indexed: 11/25/2022]
Abstract
Reagents that target protein-protein interactions to rewire signaling are of great relevance in biological research. Computational protein design may offer a means of creating such reagents on demand, but methods for encoding targeting selectivity are sorely needed. This is especially challenging when targeting interactions with ubiquitous recognition modules--for example, PDZ domains, which bind C-terminal sequences of partner proteins. Here we consider the problem of designing selective PDZ inhibitor peptides in the context of an oncogenic signaling pathway, in which two PDZ domains (NHERF-2 PDZ2-N2P2 and MAGI-3 PDZ6-M3P6) compete for a receptor C-terminus to differentially modulate oncogenic activities. Because N2P2 has been shown to increase tumorigenicity and M3P6 to decreases it, we sought to design peptides that inhibit N2P2 without affecting M3P6. We developed a structure-based computational design framework that models peptide flexibility in binding yet is efficient enough to rapidly analyze tradeoffs between affinity and selectivity. Designed peptides showed low-micromolar inhibition constants for N2P2 and no detectable M3P6 binding. Peptides designed for reverse discrimination bound M3P6 tighter than N2P2, further testing our technology. Experimental and computational analysis of selectivity determinants revealed significant indirect energetic coupling in the binding site. Successful discrimination between N2P2 and M3P6, despite their overlapping binding preferences, is highly encouraging for computational approaches to selective PDZ targeting, especially because design relied on a homology model of M3P6. Still, we demonstrate specific deficiencies of structural modeling that must be addressed to enable truly robust design. The presented framework is general and can be applied in many scenarios to engineer selective targeting.
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Affiliation(s)
- Fan Zheng
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Heather Jewell
- Department of Computer Science, Dartmouth College, Hanover, NH 03755, USA
| | | | - Jian Zhang
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Dale F Mierke
- Department of Chemistry, Dartmouth College, Hanover, NH 03755, USA
| | - Gevorg Grigoryan
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA; Department of Computer Science, Dartmouth College, Hanover, NH 03755, USA.
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20
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Pal K, Pletnev AA, Dutta SK, Wang E, Zhao R, Baral A, Yadav VK, Aggarwal S, Krishnaswamy S, Alkharfy KM, Chowdhury S, Spaller MR, Mukhopadhyay D. Inhibition of endoglin-GIPC interaction inhibits pancreatic cancer cell growth. Mol Cancer Ther 2014; 13:2264-75. [PMID: 25125675 PMCID: PMC4229952 DOI: 10.1158/1535-7163.mct-14-0291] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Endoglin, a 180-kDa disulfide-linked homodimeric transmembrane receptor protein mostly expressed in tumor-associated endothelial cells, is an endogenous binding partner of GAIP-interacting protein, C terminus (GIPC). Endoglin functions as a coreceptor of TβRII that binds TGFβ and is important for vascular development, and consequently has become a compelling target for antiangiogenic therapies. A few recent studies in gastrointestinal stromal tumor (GIST), breast cancer, and ovarian cancer, however, suggest that endoglin is upregulated in tumor cells and is associated with poor prognosis. These findings indicate a broader role of endoglin in tumor biology, beyond angiogenic effects. The goal of our current study is to evaluate the effects of targeting endoglin in pancreatic cancer both in vitro and in vivo. We analyzed the antiproliferative effect of both RNAi-based and peptide ligand-based inhibition of endoglin in pancreatic cancer cell lines, the latter yielding a GIPC PDZ domain-targeting lipopeptide with notable antiproliferative activity. We further demonstrated that endoglin inhibition induced a differentiation phenotype in the pancreatic cancer cells and sensitized them against conventional chemotherapeutic drug gemcitabine. Most importantly, we have demonstrated the antitumor effect of both RNAi-based and competitive inhibitor-based blocking of endoglin in pancreatic cancer xenograft models in vivo. To our knowledge, this is the first report exploring the effect of targeting endoglin in pancreatic cancer cells.
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Affiliation(s)
- Krishnendu Pal
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Alexandre A Pletnev
- Department of Pharmacology and Toxicology, Geisel School of Medicine at Dartmouth and Norris Cotton Cancer Center, Lebanon, New Hampshire
| | - Shamit K Dutta
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Enfeng Wang
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Ruizhi Zhao
- Department of Pharmacology and Toxicology, Geisel School of Medicine at Dartmouth and Norris Cotton Cancer Center, Lebanon, New Hampshire
| | - Aradhita Baral
- Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, Council for Scientific and Industrial Research, New Delhi, India
| | - Vinod Kumar Yadav
- G.N.R. Knowledge Center for Genome Informatics, Institute of Genomics and Integrative Biology, Council for Scientific and Industrial Research, New Delhi, India
| | - Suruchi Aggarwal
- G.N.R. Knowledge Center for Genome Informatics, Institute of Genomics and Integrative Biology, Council for Scientific and Industrial Research, New Delhi, India
| | | | - Khalid M Alkharfy
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota. Department of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Shantanu Chowdhury
- Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, Council for Scientific and Industrial Research, New Delhi, India. G.N.R. Knowledge Center for Genome Informatics, Institute of Genomics and Integrative Biology, Council for Scientific and Industrial Research, New Delhi, India
| | - Mark R Spaller
- Department of Pharmacology and Toxicology, Geisel School of Medicine at Dartmouth and Norris Cotton Cancer Center, Lebanon, New Hampshire
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21
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Focused chemical libraries--design and enrichment: an example of protein-protein interaction chemical space. Future Med Chem 2014; 6:1291-307. [PMID: 24773599 DOI: 10.4155/fmc.14.57] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
One of the many obstacles in the development of new drugs lies in the limited number of therapeutic targets and in the quality of screening collections of compounds. In this review, we present general strategies for building target-focused chemical libraries with a particular emphasis on protein-protein interactions (PPIs). We describe the chemical spaces spanned by nine commercially available PPI-focused libraries and compare them to our 2P2I3D academic library, dedicated to orthosteric PPI modulators. We show that although PPI-focused libraries have been designed using different strategies, they share common subspaces. PPI inhibitors are larger and more hydrophobic than standard drugs; however, an effort has been made to improve the drug-likeness of focused chemical libraries dedicated to this challenging class of targets.
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