1
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Koldenhof P, Bemelmans MP, Ghosh B, Damm-Ganamet KL, van Vlijmen HWT, Pande V. Application of AlphaFold models in evaluating ligandable cysteines across E3 ligases. Proteins 2024; 92:819-829. [PMID: 38337153 DOI: 10.1002/prot.26675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/12/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024]
Abstract
Proteolysis Targeting Chimeras (PROTACs) are an emerging therapeutic modality and chemical biology tools for Targeted Protein Degradation (TPD). PROTACs contain a ligand targeting the protein of interest, a ligand recruiting an E3 ligase and a linker connecting these two ligands. There are over 600 E3 ligases known so far, but only a handful have been exploited for TPD applications. A key reason for this is the scarcity of ligands binding various E3 ligases and the paucity of structural data available, which complicates ligand design across the family. In this study, we aim to progress PROTAC discovery by proposing a shortlist of E3 ligases that can be prioritized for covalent targeting by performing systematic structural ligandability analysis on a chemoproteomic dataset of potentially reactive cysteines across hundreds of E3 ligases. One of the goals of this study is to apply AlphaFold (AF) models for ligandability evaluations, as for a vast majority of these ligases an experimental structure is not available in the protein data bank (PDB). Using a combination of pocket features, AF model quality and additional aspects, we propose a shortlist of E3 ligases and corresponding cysteines that can be prioritized to potentially discover covalent ligands and expand the PROTAC toolbox.
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Affiliation(s)
- Patrick Koldenhof
- Computer-Aided Drug Design, Janssen Pharmaceuticals, Beerse, Belgium
| | | | - Brahma Ghosh
- Discovery Chemistry, Janssen Pharmaceuticals, Spring House, Pennsylvania, USA
| | | | | | - Vineet Pande
- Computer-Aided Drug Design, Janssen Pharmaceuticals, Beerse, Belgium
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2
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Lu J, Feng Y, Yu D, Li H, Li W, Chen H, Chen L. A review of nuclear Dbf2-related kinase 1 (NDR1) protein interaction as promising new target for cancer therapy. Int J Biol Macromol 2024; 259:129188. [PMID: 38184050 DOI: 10.1016/j.ijbiomac.2023.129188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/19/2023] [Accepted: 12/31/2023] [Indexed: 01/08/2024]
Abstract
Nuclear Dbf2-related kinase 1 (NDR1) is a nuclear Dbf2-related (NDR) protein kinase family member, which regulates cell functions and participates in cell proliferation and differentiation through kinase activity. NDR1 regulates physiological functions by interacting with different proteins. Protein-protein interactions (PPIs) are crucial for regulating biological processes and controlling cell fate, and as a result, it is beneficial to study the actions of PPIs to elucidate the pathological mechanism of diseases. The previous studies also show that the expression of NDR1 is deregulated in numerous human cancer samples and it needs the context-specific targeting strategies for NDR1. Thus, a comprehensive understanding of the direct interaction between NDR1 and varieties of proteins may provide new insights into cancer therapies. In this review, we summarize recent studies of NDR1 in solid tumors, such as prostate cancer and breast cancer, and explore the mechanism of action of PPIs of NDR1 in tumors.
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Affiliation(s)
- Jiani Lu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yanjun Feng
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Danmei Yu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Hongtao Li
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Weihua Li
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Hongzhuan Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Lili Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
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3
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Jiang X, Xu Z, Jiang S, Wang H, Xiao M, Shi Y, Wang K. PDZ and LIM Domain-Encoding Genes: Their Role in Cancer Development. Cancers (Basel) 2023; 15:5042. [PMID: 37894409 PMCID: PMC10605254 DOI: 10.3390/cancers15205042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 10/13/2023] [Accepted: 10/15/2023] [Indexed: 10/29/2023] Open
Abstract
PDZ-LIM family proteins (PDLIMs) are a kind of scaffolding proteins that contain PDZ and LIM interaction domains. As protein-protein interacting molecules, PDZ and LIM domains function as scaffolds to bind to a variety of proteins. The PDLIMs are composed of evolutionarily conserved proteins found throughout different species. They can participate in cell signal transduction by mediating the interaction of signal molecules. They are involved in many important physiological processes, such as cell differentiation, proliferation, migration, and the maintenance of cellular structural integrity. Studies have shown that dysregulation of the PDLIMs leads to tumor formation and development. In this paper, we review and integrate the current knowledge on PDLIMs. The structure and function of the PDZ and LIM structural domains and the role of the PDLIMs in tumor development are described.
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Affiliation(s)
| | | | | | | | | | - Yueli Shi
- Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu 322000, China; (X.J.); (Z.X.); (S.J.); (H.W.); (M.X.)
| | - Kai Wang
- Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu 322000, China; (X.J.); (Z.X.); (S.J.); (H.W.); (M.X.)
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4
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Kosugi T, Ohue M. Design of Cyclic Peptides Targeting Protein-Protein Interactions Using AlphaFold. Int J Mol Sci 2023; 24:13257. [PMID: 37686057 PMCID: PMC10487914 DOI: 10.3390/ijms241713257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/18/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
More than 930,000 protein-protein interactions (PPIs) have been identified in recent years, but their physicochemical properties differ from conventional drug targets, complicating the use of conventional small molecules as modalities. Cyclic peptides are a promising modality for targeting PPIs, but it is difficult to predict the structure of a target protein-cyclic peptide complex or to design a cyclic peptide sequence that binds to the target protein using computational methods. Recently, AlphaFold with a cyclic offset has enabled predicting the structure of cyclic peptides, thereby enabling de novo cyclic peptide designs. We developed a cyclic peptide complex offset to enable the structural prediction of target proteins and cyclic peptide complexes and found AlphaFold2 with a cyclic peptide complex offset can predict structures with high accuracy. We also applied the cyclic peptide complex offset to the binder hallucination protocol of AfDesign, a de novo protein design method using AlphaFold, and we could design a high predicted local-distance difference test and lower separated binding energy per unit interface area than the native MDM2/p53 structure. Furthermore, the method was applied to 12 other protein-peptide complexes and one protein-protein complex. Our approach shows that it is possible to design putative cyclic peptide sequences targeting PPI.
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Affiliation(s)
| | - Masahito Ohue
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, G3-56-4259 Nagatsutacho, Midori-ku, Yokohama City 226-8501, Kanagawa, Japan;
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5
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Quagliano A, Gopalakrishnapillai A, Barwe SP. Tetraspanins set the stage for bone marrow microenvironment-induced chemoprotection in hematologic malignancies. Blood Adv 2023; 7:4403-4413. [PMID: 37561544 PMCID: PMC10432613 DOI: 10.1182/bloodadvances.2023010476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 06/06/2023] [Indexed: 08/11/2023] Open
Abstract
Despite recent advances in the treatment of hematologic malignancies, relapse still remains a consistent issue. One of the primary contributors to relapse is the bone marrow microenvironment providing a sanctuary to malignant cells. These cells interact with bone marrow components such as osteoblasts and stromal cells, extracellular matrix proteins, and soluble factors. These interactions, mediated by the cell surface proteins like cellular adhesion molecules (CAMs), induce intracellular signaling that leads to the development of bone marrow microenvironment-induced chemoprotection (BMC). Although extensive study has gone into these CAMs, including the development of targeted therapies, very little focus in hematologic malignancies has been put on a family of cell surface proteins that are just as important for mediating bone marrow interactions: the transmembrane 4 superfamily (tetraspanins; TSPANs). TSPANs are known to be important mediators of microenvironmental interactions and metastasis based on numerous studies in solid tumors. Recently, evidence of their possible role in hematologic malignancies, specifically in the regulation of cellular adhesion, bone marrow homing, intracellular signaling, and stem cell dynamics in malignant hematologic cells has come to light. Many of these effects are facilitated by associations with CAMs and other receptors on the cell surface in TSPAN-enriched microdomains. This could suggest that TSPANs play an important role in mediating BMC in hematologic malignancies and could be used as therapeutic targets. In this review, we discuss TSPAN structure and function in hematologic cells, their interactions with different cell surface and signaling proteins, and possible ways to target/inhibit their effects.
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Affiliation(s)
- Anthony Quagliano
- Lisa Dean Moseley Foundation Institute for Cancer and Blood Disorders, Nemours Children’s Hospital, Wilmington, DE
- Department of Biological Sciences, University of Delaware, Newark, DE
| | - Anilkumar Gopalakrishnapillai
- Lisa Dean Moseley Foundation Institute for Cancer and Blood Disorders, Nemours Children’s Hospital, Wilmington, DE
- Department of Biological Sciences, University of Delaware, Newark, DE
| | - Sonali P. Barwe
- Lisa Dean Moseley Foundation Institute for Cancer and Blood Disorders, Nemours Children’s Hospital, Wilmington, DE
- Department of Biological Sciences, University of Delaware, Newark, DE
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6
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Ohue M, Kojima Y, Kosugi T. Generating Potential Protein-Protein Interaction Inhibitor Molecules Based on Physicochemical Properties. Molecules 2023; 28:5652. [PMID: 37570623 PMCID: PMC10420264 DOI: 10.3390/molecules28155652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/06/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023] Open
Abstract
Protein-protein interactions (PPIs) are associated with various diseases; hence, they are important targets in drug discovery. However, the physicochemical empirical properties of PPI-targeted drugs are distinct from those of conventional small molecule oral pharmaceuticals, which adhere to the "rule of five (RO5)". Therefore, developing PPI-targeted drugs using conventional methods, such as molecular generation models, is challenging. In this study, we propose a molecular generation model based on deep reinforcement learning that is specialized for the production of PPI inhibitors. By introducing a scoring function that can represent the properties of PPI inhibitors, we successfully generated potential PPI inhibitor compounds. These newly constructed virtual compounds possess the desired properties for PPI inhibitors, and they show similarity to commercially available PPI libraries. The virtual compounds are freely available as a virtual library.
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Affiliation(s)
- Masahito Ohue
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, Kanagawa 226-8501, Japan (T.K.)
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7
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Wang S, Zhao M, Zhang X, Su M, Tian Y, Qiu W. Birc3 and Tip1 are upregulated in renal ischemia reperfusion injury. Gene 2023:147492. [PMID: 37209886 DOI: 10.1016/j.gene.2023.147492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 05/10/2023] [Accepted: 05/15/2023] [Indexed: 05/22/2023]
Abstract
Identification of ischemia-reperfusion injury (I/R)-associated genes is essential for exploring I/R novel mechanisms. Previously, we screened differentially expressed genes in renal I/R mouse models and found that Tax1 binding protein 3 (Tip1) and baculoviral IAP repeat containing 3 (Birc3) are two upregulated genes in I/R. In the present study, we analyzed the expression of Tip1 and Birc3 in I/R models. We found that the expression of Tip1 and Birc3 was upregulated in I/R-treated mice, whereas Tip1 was downregulated and Birc3 was upregulated in oxygen-glucose deprivation/reoxygenation (OGD/R) in vitro models. By inhibiting Birc3 with AT-406 in I/R-treated mice, we observed that the serum creatinine or blood urea nitrogen did not vary. However, inhibition of Birc3 enhanced apoptosis of kidney tissues induced by I/R treatment. Consistently, we found that inhibition of Birc3 also increased the apoptosis rate in tubular epithelial cells induced by OGD/R. These data demonstrated that Tip1 and Birc3 were upregulated in I/R injury. The upregulation of Birc3 may protect against renal I/R injury.
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Affiliation(s)
- Sixu Wang
- Department of Urology, Beijing Friendship Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Meishan Zhao
- Department of Urology, Beijing Friendship Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Xiaofei Zhang
- Department of Urology, Beijing Friendship Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Ming Su
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, People's Republic of China
| | - Ye Tian
- Department of Urology, Beijing Friendship Hospital, Capital Medical University, Beijing, People's Republic of China.
| | - Wei Qiu
- Department of Urology, Beijing Friendship Hospital, Capital Medical University, Beijing, People's Republic of China.
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8
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Rathod SB, Prajapati PB, Pal R, Mansuri MF. AMPA GluA2 subunit competitive inhibitors for PICK1 PDZ domain: Pharmacophore-based virtual screening, molecular docking, molecular dynamics simulation, and ADME studies. J Biomol Struct Dyn 2023; 41:336-351. [PMID: 34809533 DOI: 10.1080/07391102.2021.2006086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
PICK1 (Protein interacting with C kinase-1) plays a key role in the regulation of intracellular trafficking of AMPA GluA2 subunit that is linked with synaptic plasticity. PICK1 is a scaffolding protein and binds numerous proteins through its PDZ domain. Research showed that synaptic plasticity is altered upon disrupting the GluA2-PDZ interactions. Inhibiting PDZ and GluA2 binding lead to beneficial effects in the cure of neurological diseases thus, targeting PDZ domain is proposed as a novel therapeutic target in such diseases. For this, various classes of synthetic peptides were tested. Though small organic molecules have been utilized to prevent these interactions, the number of such molecules is inadequate. Hence, in this study, ten molecular libraries containing large number of molecules were screened against the PDZ domain using pharmacophore-based virtual screening to find the best hits for the PDZ domain. Molecular docking and molecular dynamics simulation studies revealed that Hit_II is a potent inhibitor for the PDZ domain and confirm the allosteric nature of Hit_III. Additionally, ADME analysis suggests the drug-likeness of both Hit_II and Hit_III. This study suggests that tested hits may have potency against the PDZ domain and can be considered effective to treat neurological disorders.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shravan B Rathod
- Department of Chemistry, Smt. S. M. Panchal Science College, Talod, Gujarat, India
| | - Pravin B Prajapati
- Department of Chemistry, Sheth M. N. Science College, Patan, Gujarat, India
| | - Ranjan Pal
- Department of Medical Genetics, Sanjay Gandhi Post-Graduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Mohmedyasin F Mansuri
- Department of Microbiology, Smt. S. M. Panchal Science College, Talod, Gujarat, India
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9
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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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10
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Solubility-Aware Protein Binding Peptide Design Using AlphaFold. Biomedicines 2022; 10:biomedicines10071626. [PMID: 35884931 PMCID: PMC9312799 DOI: 10.3390/biomedicines10071626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 07/02/2022] [Accepted: 07/05/2022] [Indexed: 01/02/2023] Open
Abstract
New protein–protein interactions (PPIs) are identified, but PPIs have different physicochemical properties compared with conventional targets, making it difficult to use small molecules. Peptides offer a new modality to target PPIs, but designing appropriate peptide sequences by computation is challenging. Recently, AlphaFold and RoseTTAFold have made it possible to predict protein structures from amino acid sequences with ultra-high accuracy, enabling de novo protein design. We designed peptides likely to have PPI as the target protein using the “binder hallucination” protocol of AfDesign, a de novo protein design method using AlphaFold. However, the solubility of the peptides tended to be low. Therefore, we designed a solubility loss function using solubility indices for amino acids and developed a solubility-aware AfDesign binder hallucination protocol. The peptide solubility in sequences designed using the new protocol increased with the weight of the solubility loss function; moreover, they captured the characteristics of the solubility indices. Moreover, the new protocol sequences tended to have higher affinity than random or single residue substitution sequences when evaluated by docking binding affinity. Our approach shows that it is possible to design peptide sequences that can bind to the interface of PPI while controlling solubility.
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11
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Excoffon KJDA, Avila CL, Alghamri MS, Kolawole AO. The magic of MAGI-1: A scaffolding protein with multi signalosomes and functional plasticity. Biol Cell 2022; 114:185-198. [PMID: 35389514 DOI: 10.1111/boc.202200014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/01/2022] [Accepted: 04/04/2022] [Indexed: 11/29/2022]
Abstract
MAGI-1 is a critical cellular scaffolding protein with over 110 different cellular and microbial protein interactors. Since the discovery of MAGI-1 in 1997, MAGI-1 has been implicated in diverse cellular functions such as polarity, cell-cell communication, neurological processes, kidney function, and a host of diseases including cancer and microbial infection. Additionally, MAGI-1 has undergone nomenclature changes in response to the discovery of an additional PDZ domain, leading to lack of continuity in the literature. We address the nomenclature of MAGI-1 as well as summarize many of the critical functions of the known interactions. Given the importance of many of the interactors, such as human papillomavirus E6, the Coxsackievirus and adenovirus receptor (CAR), and PTEN, the enhancement or disruption of MAGI-based interactions has the potential to affect cellular functions that can potentially be harnessed as a therapeutic strategy for a variety of diseases.
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Affiliation(s)
| | - Christina L Avila
- Department of Biological Sciences, Wright State University, Dayton, Ohio, USA
| | - Mahmoud S Alghamri
- Department of Biological Sciences, Wright State University, Dayton, Ohio, USA
| | - Abimbola O Kolawole
- Department of Biological Sciences, Wright State University, Dayton, Ohio, USA
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12
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Binkle L, Klein M, Borgmeyer U, Kuhl D, Hermey G. The adaptor protein PICK1 targets the sorting receptor SorLA. Mol Brain 2022; 15:18. [PMID: 35183222 PMCID: PMC8858569 DOI: 10.1186/s13041-022-00903-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 02/07/2022] [Indexed: 11/26/2022] Open
Abstract
SorLA is a member of the Vps10p-domain (Vps10p-D) receptor family of type-I transmembrane proteins conveying neuronal endosomal sorting. The extracellular/luminal moiety of SorLA has a unique mosaic domain composition and interacts with a large number of different and partially unrelated ligands, including the amyloid precursor protein as well as amyloid-β. Several studies support a strong association of SorLA with sporadic and familial forms of Alzheimer’s disease (AD). Although SorLA seems to be an important factor in AD, the large number of different ligands suggests a role as a neuronal multifunctional receptor with additional intracellular sorting capacities. Therefore, understanding the determinants of SorLA’s subcellular targeting might be pertinent for understanding neuronal endosomal sorting mechanisms in general. A number of cytosolic adaptor proteins have already been demonstrated to determine intracellular trafficking of SorLA. Most of these adaptors and several ligands of the extracellular/luminal moiety are shared with the Vps10p-D receptor Sortilin. Although SorLA and Sortilin show both a predominant intracellular and endosomal localization, they are targeted to different endosomal compartments. Thus, independent adaptor proteins may convey their differential endosomal targeting. Here, we hypothesized that Sortilin and SorLA interact with the cytosolic adaptors PSD95 and PICK1 which have been shown to bind the Vps10p-D receptor SorCS3. We observed only an interaction for SorLA and PICK1 in mammalian-two-hybrid, pull-down and cellular recruitment experiments. We demonstrate by mutational analysis that the C-terminal minimal PDZ domain binding motif VIA of SorLA mediates the interaction. Moreover, we show co-localization of SorLA and PICK1 at vesicular structures in primary neurons. Although the physiological role of the interaction between PICK1 and SorLA remains unsolved, our study suggests that PICK1 partakes in regulating SorLA’s intracellular itinerary.
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13
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Nardella C, Visconti L, Malagrinò F, Pagano L, Bufano M, Nalli M, Coluccia A, La Regina G, Silvestri R, Gianni S, Toto A. Targeting PDZ domains as potential treatment for viral infections, neurodegeneration and cancer. Biol Direct 2021; 16:15. [PMID: 34641953 PMCID: PMC8506081 DOI: 10.1186/s13062-021-00303-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/24/2021] [Indexed: 02/08/2023] Open
Abstract
The interaction between proteins is a fundamental event for cellular life that is generally mediated by specialized protein domains or modules. PDZ domains are the largest class of protein-protein interaction modules, involved in several cellular pathways such as signal transduction, cell-cell junctions, cell polarity and adhesion, and protein trafficking. Because of that, dysregulation of PDZ domain function often causes the onset of pathologies, thus making this family of domains an interesting pharmaceutical target. In this review article we provide an overview of the structural and functional features of PDZ domains and their involvement in the cellular and molecular pathways at the basis of different human pathologies. We also discuss some of the strategies that have been developed with the final goal to hijack or inhibit the interaction of PDZ domains with their ligands. Because of the generally low binding selectivity of PDZ domain and the scarce efficiency of small molecules in inhibiting PDZ binding, this task resulted particularly difficult to pursue and still demands increasing experimental efforts in order to become completely feasible and successful in vivo.
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Affiliation(s)
- Caterina Nardella
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185, Rome, Italy
| | - Lorenzo Visconti
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185, Rome, Italy
| | - Francesca Malagrinò
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185, Rome, Italy
| | - Livia Pagano
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185, Rome, Italy
| | - Marianna Bufano
- Laboratory Affiliated with the Institute Pasteur Italy - Cenci Bolognetti Foundation, Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Marianna Nalli
- Laboratory Affiliated with the Institute Pasteur Italy - Cenci Bolognetti Foundation, Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Antonio Coluccia
- Laboratory Affiliated with the Institute Pasteur Italy - Cenci Bolognetti Foundation, Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Giuseppe La Regina
- Laboratory Affiliated with the Institute Pasteur Italy - Cenci Bolognetti Foundation, Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Romano Silvestri
- Laboratory Affiliated with the Institute Pasteur Italy - Cenci Bolognetti Foundation, Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy.
| | - Stefano Gianni
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185, Rome, Italy.
| | - Angelo Toto
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185, Rome, Italy.
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14
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Kosugi T, Ohue M. Quantitative Estimate Index for Early-Stage Screening of Compounds Targeting Protein-Protein Interactions. Int J Mol Sci 2021; 22:10925. [PMID: 34681589 PMCID: PMC8539639 DOI: 10.3390/ijms222010925] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/02/2021] [Accepted: 10/07/2021] [Indexed: 12/13/2022] Open
Abstract
Drug-likeness quantification is useful for screening drug candidates. Quantitative estimates of drug-likeness (QED) are commonly used to assess quantitative drug efficacy but are not suitable for screening compounds targeting protein-protein interactions (PPIs), which have recently gained attention. Therefore, we developed a quantitative estimate index for compounds targeting PPIs (QEPPI), specifically for early-stage screening of PPI-targeting compounds. QEPPI is an extension of the QED method for PPI-targeting drugs that models physicochemical properties based on the information available for drugs/compounds, specifically those reported to act on PPIs. FDA-approved drugs and compounds in iPPI-DB, which comprise PPI inhibitors and stabilizers, were evaluated using QEPPI. The results showed that QEPPI is more suitable than QED for early screening of PPI-targeting compounds. QEPPI was also considered an extended concept of the "Rule-of-Four" (RO4), a PPI inhibitor index. We evaluated the discriminatory performance of QEPPI and RO4 for datasets of PPI-target compounds and FDA-approved drugs using F-score and other indices. The F-scores of RO4 and QEPPI were 0.451 and 0.501, respectively. QEPPI showed better performance and enabled quantification of drug-likeness for early-stage PPI drug discovery. Hence, it can be used as an initial filter to efficiently screen PPI-targeting compounds.
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Affiliation(s)
| | - Masahito Ohue
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, G3-56-4259 Nagatsutacho, Midori-ku, Yokohama 226-8501, Kanagawa, Japan;
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15
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NHERF4 hijacks Mas-mediated PLC/AKT signaling to suppress the invasive potential of clear cell renal cell carcinoma cells. Cancer Lett 2021; 519:130-140. [PMID: 34216689 DOI: 10.1016/j.canlet.2021.06.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 05/23/2021] [Accepted: 06/28/2021] [Indexed: 02/06/2023]
Abstract
The Mas receptor has been reported to promote migration and invasion of clear cell renal cell carcinoma (ccRCC) cells via Ang-(1-7)-dependent AKT signaling. However, the mechanism underlying the regulation of Mas function remains unknown. Here, eight PDZ domain-containing proteins were identified as Mas interactors using surface plasmon resonance (SPR) coupled to mass spectrometry (MS). NHERF4 was the only downregulated gene across multiple independent ccRCC datasets. GST pull-down and co-immunoprecipitation assays confirmed physical interaction between NHERF4 and Mas. Using NHERF4 overexpression and knockdown assays, we found that NHERF4 inhibited Mas-induced migration, invasion and in vivo metastasis of ccRCC cells. Mechanistically, NHERF4 suppressed Mas-stimulated AKT phosphorylation and the PLC/Ca2+ response. We further demonstrated that NHERF4 compromised Mas-mediated migration and invasion of ccRCC cells via regulation of the PLC/AKT signaling axis. Analysis of the ccRCC dataset revealed that low levels of NHERF4 expression were correlated with higher TNM stage, and independently predicted poor prognosis of ccRCC patients. Overall, our study identified NHERF4 as a novel regulator of ccRCC invasiveness, and a prognostic biomarker, which may be beneficial for determining optimal therapeutic strategies for ccRCC patients.
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16
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Ahmad H, Arifin N, Nolan TJ, Lok JB, Anuar NS, Noordin R. Strongyloides-Specific IgE Phage cDNA Clones and Development of a Novel ELISA for Strongyloidiasis. Diagnostics (Basel) 2021; 11:diagnostics11060985. [PMID: 34071716 PMCID: PMC8228214 DOI: 10.3390/diagnostics11060985] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 05/25/2021] [Indexed: 12/05/2022] Open
Abstract
Strongyloidiasis, caused mainly by the nematode Strongyloides stercoralis, is prevalent worldwide and potentially fatal in immunosuppressed patients. We report on a new IgE biomarker to diagnose Strongyloides infection. Sera from two groups infected with Strongyloides served as positive samples: Group 1A, in which infection was confirmed by stool-microscopy and/or stool-polymerase chain reaction (PCR) and was seropositive by an IgG-enzyme linked immunosorbent assay (ELISA) and an IgG4 rapid test, and Group 1B in which infection was confirmed by stool-PCR but was seronegative. Negative samples (controls) comprised infections with other parasites (Group II) and healthy donors (Group III). Immunoscreenings of an S. stercoralis complementary DNA (cDNA) library were performed, and the cDNA clone with the highest diagnostic potential (clone A133) was selected for recombinant protein production and then evaluated using IgE Western blot and ELISA. The Western blot showed that the recombinant protein (rA133) was 100% reactive with Group IA (n = 10) and Group IB (n = 5), and 96% non-reactive with Groups II and III (n = 25). Subsequently, the IgE-ELISA was developed and showed 100% diagnostic sensitivity in Groups IA (n = 32) and IB (n = 11); and 99.3% specificity in Groups II and III (n = 144). In conclusion, this study has identified rA133 as a novel recombinant protein with potential diagnostic value, and that the IgE-ELISA incorporating this protein may be useful for patient diagnosis and epidemiological studies.
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Affiliation(s)
- Hussain Ahmad
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor 11800, Malaysia; (H.A.); (N.A.); (N.S.A.)
- Department of Microbiology, Abdul Wali Khan University, Mardan 23200, Pakistan
| | - Norsyahida Arifin
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor 11800, Malaysia; (H.A.); (N.A.); (N.S.A.)
| | - Thomas J. Nolan
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (T.J.N.); (J.B.L.)
| | - James B. Lok
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (T.J.N.); (J.B.L.)
| | - Nor Suhada Anuar
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor 11800, Malaysia; (H.A.); (N.A.); (N.S.A.)
| | - Rahmah Noordin
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor 11800, Malaysia; (H.A.); (N.A.); (N.S.A.)
- Correspondence:
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17
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Haugaard-Kedström LM, Clemmensen LS, Sereikaite V, Jin Z, Fernandes EFA, Wind B, Abalde-Gil F, Daberger J, Vistrup-Parry M, Aguilar-Morante D, Leblanc R, Egea-Jimenez AL, Albrigtsen M, Jensen KE, Jensen TMT, Ivarsson Y, Vincentelli R, Hamerlik P, Andersen JH, Zimmermann P, Lee W, Strømgaard K. A High-Affinity Peptide Ligand Targeting Syntenin Inhibits Glioblastoma. J Med Chem 2021; 64:1423-1434. [PMID: 33502198 DOI: 10.1021/acs.jmedchem.0c00382] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Despite the recent advances in cancer therapeutics, highly aggressive cancer forms, such as glioblastoma (GBM), still have very low survival rates. The intracellular scaffold protein syntenin, comprising two postsynaptic density protein-95/discs-large/zona occludens-1 (PDZ) domains, has emerged as a novel therapeutic target in highly malignant phenotypes including GBM. Here, we report the development of a novel, highly potent, and metabolically stable peptide inhibitor of syntenin, KSL-128114, which binds the PDZ1 domain of syntenin with nanomolar affinity. KSL-128114 is resistant toward degradation in human plasma and mouse hepatic microsomes and displays a global PDZ domain selectivity for syntenin. An X-ray crystal structure reveals that KSL-128114 interacts with syntenin PDZ1 in an extended noncanonical binding mode. Treatment with KSL-128114 shows an inhibitory effect on primary GBM cell viability and significantly extends survival time in a patient-derived xenograft mouse model. Thus, KSL-128114 is a novel promising candidate with therapeutic potential for highly aggressive tumors, such as GBM.
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Affiliation(s)
- Linda M Haugaard-Kedström
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Louise S Clemmensen
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Vita Sereikaite
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Zeyu Jin
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, 120-749 Seoul, Korea
| | - Eduardo F A Fernandes
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Bianca Wind
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Flor Abalde-Gil
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Jan Daberger
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Maria Vistrup-Parry
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Diana Aguilar-Morante
- Brain Tumor Biology Group, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - Raphael Leblanc
- Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068-CNRS UMR7258, Aix-Marseille Université, Institut Paoli-Calmettes, 13009 Marseille, France
| | - Antonio L Egea-Jimenez
- Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068-CNRS UMR7258, Aix-Marseille Université, Institut Paoli-Calmettes, 13009 Marseille, France.,Department of Human Genetics, KU Leuven, ON1 Herestraat 49 Box 602, B-3000 Leuven, Belgium
| | - Marte Albrigtsen
- Marbio, UiT-The Artic University of Norway, N-9037 Tromsø, Norway
| | - Kamilla E Jensen
- Brain Tumor Biology Group, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - Thomas M T Jensen
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Ylva Ivarsson
- Department of Chemistry-BMC, Uppsala University, SE-751 23 Uppsala, Sweden
| | - Renaud Vincentelli
- Unité Mixte de Recherche (UMR) 7257, Centre National de la Recherche Scientifique (CNRS), Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques (AFMB), Campus de Luminy, 163 Avenue de Luminy, 13288 Marseille Cedex 09, France
| | - Petra Hamerlik
- Brain Tumor Biology Group, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | | | - Pascale Zimmermann
- Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068-CNRS UMR7258, Aix-Marseille Université, Institut Paoli-Calmettes, 13009 Marseille, France.,Department of Human Genetics, KU Leuven, ON1 Herestraat 49 Box 602, B-3000 Leuven, Belgium
| | - Weontae Lee
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, 120-749 Seoul, Korea
| | - Kristian Strømgaard
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
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18
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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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19
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Shin WH, Kumazawa K, Imai K, Hirokawa T, Kihara D. Current Challenges and Opportunities in Designing Protein-Protein Interaction Targeted Drugs. Adv Appl Bioinform Chem 2020; 13:11-25. [PMID: 33209039 PMCID: PMC7669531 DOI: 10.2147/aabc.s235542] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/22/2020] [Indexed: 12/24/2022] Open
Abstract
It has been noticed that the efficiency of drug development has been decreasing in the past few decades. To overcome the situation, protein-protein interactions (PPIs) have been identified as new drug targets as early as 2000. PPIs are more abundant in human cells than single proteins and play numerous important roles in cellular processes including diseases. However, PPIs have very different physicochemical features from the conventional drug targets, which make targeting PPIs challenging. Therefore, as of now, only a small number of PPI inhibitors have been approved or progressed to a stage of clinical trial. In this article, we first overview previous works that analyzed differences between PPIs with PPI targeting ligands and conventional drugs with their binding pockets. Then, we constructed an up-to-date list of PPI targeting drugs that have been approved or are currently under clinical trial and have bound drug-target structures available. Using the dataset, we analyzed the PPIs and their ligands using several scores of druggability. Druggability scores showed that PPI sites and their drugs targeting PPIs are less druggable than conventional binding pockets and drugs, which also indicates that PPI drugs do not follow the conventional rules for drug design, such as Lipinski's rule of five. Our analyses suggest that developing a new rule would be beneficial for guiding PPI-drug discovery.
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Affiliation(s)
- Woong-Hee Shin
- Department of Chemical Science Education, Sunchon National University, Suncheon57922, Republic of Korea
| | - Keiko Kumazawa
- Pharmaceutical Discovery Research Laboratories, Teijin Pharma Limited, Tokyo191-8512, Japan
| | - Kenichiro Imai
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo135-0064, Japan
| | - Takatsugu Hirokawa
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo135-0064, Japan
| | - Daisuke Kihara
- Department of Biological Sciences, Purdue University, West Lafayette, IN47906, USA
- Department of Computer Science, Purdue University, West Lafayette, IN47906, USA
- Center for Cancer Research, Purdue University, West Lafayette, IN47906, USA
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Care, University of Cincinnati, Cincinnati, OH45229, USA
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20
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Bao Z, Zhou S, Zhou H. Sorting Nexin 27 as a potential target in G protein‑coupled receptor recycling for cancer therapy (Review). Oncol Rep 2020; 44:1779-1786. [PMID: 33000258 PMCID: PMC7551096 DOI: 10.3892/or.2020.7766] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 08/10/2020] [Indexed: 12/12/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are the largest family of membrane receptors and activate several downstream signaling pathways involved in numerous physiological cellular processes. GPCRs are usually internalized and desensitized by intracellular signals. Numerous studies have shown that several GPCRs interact with sorting nexin 27 (SNX27), a cargo selector of the retromer complex, and are recycled from endosomes to the plasma membrane. Recycled GPCRs usually contain specific C-terminal postsynaptic density protein 95/Discs large protein/Zonula occludens 1 (PDZ) binding motifs, which are specifically recognized by SNX27, and return to the cell surface as functionally naïve receptors. Aberrant endosome-to-membrane recycling of GPCRs mediated by SNX27 may serve a critical role in cancer growth and development. Therefore, SNX27 may be a novel target for cancer therapies.
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Affiliation(s)
- Zixu Bao
- Department of Biochemistry and Molecular Biology, Anhui Medical University, Hefei, Anhui 230032, P.R. China
| | - Shijun Zhou
- Department of Infectious Disease, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230601, P.R. China
| | - Haisheng Zhou
- Department of Biochemistry and Molecular Biology, Anhui Medical University, Hefei, Anhui 230032, P.R. China
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21
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Lei B, Wang D, Zhang M, Deng Y, Jiang H, Li Y. miR-615-3p promotes the epithelial-mesenchymal transition and metastasis of breast cancer by targeting PICK1/TGFBRI axis. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2020; 39:71. [PMID: 32336285 PMCID: PMC7183699 DOI: 10.1186/s13046-020-01571-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 04/14/2020] [Indexed: 02/22/2023]
Abstract
Background Increasing evidence indicates that epithelial-mesenchymal transition (EMT) can be regulated by microRNAs (miRNAs). miR-615-3p was shown to be involved in tumor development. However, the role of miR-615-3p in the metastasis of breast cancer remains largely unknown. Methods The expression of miR-615-3p in breast cancer cells and tissues was assessed by qRT-PCR and situ hybridization assays. Effects of miR-615-3p on tumor metastasis were evaluated with experiments in vitro and mouse model. EMT markers were detected by western blot and immunofluorescence assays. Molecular mechanism of miR-615-3p in the regulation of breast cancer cell metastasis was analyzed by Western Blot, Co-immunoprecipitation, and Luciferase assay. Results In the present study, we found that miR-615-3p was significantly elevated in breast cancer cells and tissues, especially in those with metastasis. In breast cancer cell lines, stable overexpression of miR-615-3p was sufficient to promote cell motility in vitro, and pulmonary metastasis in vivo, accompanied by the reduced expression of epithelial markers and the increased levels of mesenchymal markers. Further studies revealed that the reintroduction of miR-615-3p increased the downstream signaling of TGF-β, the type I receptor (TGFBRI) by targeting the 3′-untranslated regions (3′-UTR) of PICK1. PICK1 inhibits the binding of DICER1 to Smad2/3 and the processing of pre-miR-615-3p to mature miR-615-3p in breast cancer cells, thus exerting a negative feedback loop. Conclusions Our data highlight an important role of miR-615-3p in the molecular etiology of breast cancer, and implicate the potential application of miR-615-3p in cancer therapy.
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Affiliation(s)
- Bo Lei
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150086, China
| | - Dandan Wang
- Department of Radiology, The Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Harbin, 150086, China
| | - Ming Zhang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150086, China
| | - Yuwei Deng
- Department of Oncology, The Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Harbin, 150086, China
| | - Huijie Jiang
- Department of Radiology, The Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Harbin, 150086, China.
| | - Yiwen Li
- Department of Oncology, The Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Harbin, 150086, China.
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22
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Martin ER, Barbieri A, Ford RC, Robinson RC. In vivo crystals reveal critical features of the interaction between cystic fibrosis transmembrane conductance regulator (CFTR) and the PDZ2 domain of Na +/H + exchange cofactor NHERF1. J Biol Chem 2020; 295:4464-4476. [PMID: 32014995 DOI: 10.1074/jbc.ra119.012015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/17/2020] [Indexed: 12/23/2022] Open
Abstract
Crystallization of recombinant proteins has been fundamental to our understanding of protein function, dysfunction, and molecular recognition. However, this information has often been gleaned under extremely nonphysiological protein, salt, and H+ concentrations. Here, we describe the development of a robust Inka1-Box (iBox)-PAK4cat system that spontaneously crystallizes in several mammalian cell types. The semi-quantitative assay described here allows the measurement of in vivo protein-protein interactions using a novel GFP-linked reporter system that produces fluorescent readouts from protein crystals. We combined this assay with in vitro X-ray crystallography and molecular dynamics studies to characterize the molecular determinants of the interaction between the PDZ2 domain of Na+/H+ exchange regulatory cofactor NHE-RF1 (NHERF1) and cystic fibrosis transmembrane conductance regulator (CFTR), a protein complex pertinent to the genetic disease cystic fibrosis. These experiments revealed the crystal structure of the extended PDZ domain of NHERF1 and indicated, contrary to what has been previously reported, that residue selection at positions -1 and -3 of the PDZ-binding motif influences the affinity and specificity of the NHERF1 PDZ2-CFTR interaction. Our results suggest that this system could be utilized to screen additional protein-protein interactions, provided they can be accommodated within the spacious iBox-PAK4cat lattice.
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Affiliation(s)
- Eleanor R Martin
- School of Biological Sciences, Faculty of Biology Medicine and Health, Michael Smith Building, The University of Manchester, Manchester, M13 9PL, United Kingdom.,Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis 138673, Singapore
| | - Alessandro Barbieri
- School of Biological Sciences, Faculty of Biology Medicine and Health, Michael Smith Building, The University of Manchester, Manchester, M13 9PL, United Kingdom.,Bioinformatics Institute (BII), A*STAR (Agency for Science, Technology and Research), Biopolis 138671, Singapore
| | - Robert C Ford
- School of Biological Sciences, Faculty of Biology Medicine and Health, Michael Smith Building, The University of Manchester, Manchester, M13 9PL, United Kingdom
| | - Robert C Robinson
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis 138673, Singapore .,School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand.,Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
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23
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Translating preclinical findings in clinically relevant new antipsychotic targets: focus on the glutamatergic postsynaptic density. Implications for treatment resistant schizophrenia. Neurosci Biobehav Rev 2019; 107:795-827. [DOI: 10.1016/j.neubiorev.2019.08.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 07/20/2019] [Accepted: 08/22/2019] [Indexed: 02/07/2023]
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24
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Heinemann U, Schuetz A. Structural Features of Tight-Junction Proteins. Int J Mol Sci 2019; 20:E6020. [PMID: 31795346 PMCID: PMC6928914 DOI: 10.3390/ijms20236020] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/25/2019] [Accepted: 11/26/2019] [Indexed: 12/14/2022] Open
Abstract
Tight junctions are complex supramolecular entities composed of integral membrane proteins, membrane-associated and soluble cytoplasmic proteins engaging in an intricate and dynamic system of protein-protein interactions. Three-dimensional structures of several tight-junction proteins or their isolated domains have been determined by X-ray crystallography, nuclear magnetic resonance spectroscopy, and cryo-electron microscopy. These structures provide direct insight into molecular interactions that contribute to the formation, integrity, or function of tight junctions. In addition, the known experimental structures have allowed the modeling of ligand-binding events involving tight-junction proteins. Here, we review the published structures of tight-junction proteins. We show that these proteins are composed of a limited set of structural motifs and highlight common types of interactions between tight-junction proteins and their ligands involving these motifs.
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Affiliation(s)
- Udo Heinemann
- Macromolecular Structure and Interaction Laboratory, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Anja Schuetz
- Protein Production & Characterization Platform, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
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25
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V K MA, Chandrasekaran VM, Pandurangan S. Protein Domain Level Cancer Drug Targets in the Network of MAPK Pathways. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019; 16:2057-2065. [PMID: 29993692 DOI: 10.1109/tcbb.2018.2829507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Proteins in the MAPK pathways considered as potential drug targets for cancer treatment. Pathways along with the cross-talks increase their scope to view them as a network of MAPK pathways. Side effect causing targeted domains act as a proxy for drug targets due to its structural similarity and frequent reuse of their variants. We proposed to identify non-repeatable protein domains as the drug targets to disrupt the signal transduction than targeting the whole protein. Network based approach is used to understand the contribution of 52 domains in non-hub, non-essential, and intra-pathway cancerous nodes and to identify potential drug target domains. 34 distinct domains in the cancerous proteins are playing vital roles in making cancer as a complex disease and pose challenges to identify potential drug targets. Distribution of domain families follows the power law in the network. Single promiscuous domains are contributing to the formation of hubs like Pkinease, Pkinease Tyr, and Ras. Hub nodes are positively correlated with the domain coverage and targeting them would disrupt functional properties of the proteins. EIF 4EBP, alpha Kinase, Sel1, ROKNT, and KH 1 are the domains identified as potential domain targets for the disruption of the signaling mechanism involved in cancer.
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26
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Borah S, Vasudevan D, Swain RK. C-type lectin family XIV members and angiogenesis. Oncol Lett 2019; 18:3954-3962. [PMID: 31579078 DOI: 10.3892/ol.2019.10760] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 05/29/2019] [Indexed: 12/21/2022] Open
Abstract
The growth and metastasis of tumors is dependent on angiogenesis. C-type lectins are carbohydrate-binding proteins with a diverse range of functions. The C-type lectin family XIV members are transmembrane glycoproteins, and all four members of this family have been reported to regulate angiogenesis, although the detailed mechanism of action has yet to be completely elucidated. They interact with extracellular matrix proteins and mediate cell-cell adhesion by their lectin-like domain. The aim of the present study was to summarize the available information on the function and mechanism of C-type lectin family XIV in angiogenesis and discuss their potential as targets for cancer therapy.
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Affiliation(s)
- Supriya Borah
- Institute of Life Sciences, Bhubaneswar, Odisha 751023, India.,Department of Biotechnology, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | | | - Rajeeb K Swain
- Institute of Life Sciences, Bhubaneswar, Odisha 751023, India
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27
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Shabanzadeh AP, D'Onofrio PM, Magharious M, Choi KAB, Monnier PP, Koeberle PD. Modifying PTEN recruitment promotes neuron survival, regeneration, and functional recovery after CNS injury. Cell Death Dis 2019; 10:567. [PMID: 31358730 PMCID: PMC6662832 DOI: 10.1038/s41419-019-1802-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/07/2019] [Accepted: 06/28/2019] [Indexed: 12/13/2022]
Abstract
Phosphatase and tensin homolog (PTEN) regulates apoptosis and axonal growth in the developing and adult central nervous system (CNS). Here, we show that human PTEN C-terminal PDZ interactions play a critical role in neuronal apoptosis and axon regeneration after traumatic CNS injury and stroke, highlighted by the findings that antagonizing the PDZ-motif interactions of PTEN has therapeutic applicability for these indications. Interestingly, the death-inducing function of PTEN following ischemic insult depends on a PDZ-domain interaction with MAGI-2 and MAST205, PDZ proteins that are known to recruit PTEN to the plasma membrane and stabilize its interaction with PIP3. Treatments with a human peptide that prevents PTEN association with MAGI-2 or MAST205 increased neuronal survival in multiple stroke models, in vitro. A pro-survival effect was also observed in models of retinal ischemia, optic nerve transection, and after middle cerebral artery occlusion (MCAO) in adult rats. The human PTEN peptide also improved axonal regeneration in the crushed optic nerve. Furthermore, human PTEN peptide therapy promoted functional improvement after MCAO or retinal ischemia induced via ophthalmic artery ligation. These findings show that the human peptide-based targeting of C-terminal PTEN PDZ interactions has therapeutic potential for insults of the CNS, including trauma and stroke.
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Affiliation(s)
- Alireza Pirsaraei Shabanzadeh
- Division of Anatomy, Department of Surgery, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Krembil Research Institute, University Health Network, Toronto, ON, M5T 2S8, Canada
| | - Philippe Matteo D'Onofrio
- Division of Anatomy, Department of Surgery, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Rehabilitation Science Institute, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Mark Magharious
- Division of Anatomy, Department of Surgery, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Rehabilitation Science Institute, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Kyung An Brian Choi
- Division of Anatomy, Department of Surgery, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Philippe Patrick Monnier
- Departments of Physiology, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Krembil Research Institute, University Health Network, Toronto, ON, M5T 2S8, Canada
| | - Paulo Dieter Koeberle
- Division of Anatomy, Department of Surgery, University of Toronto, Toronto, ON, M5S 1A8, Canada. .,Rehabilitation Science Institute, University of Toronto, Toronto, ON, M5S 1A8, Canada.
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28
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Harish M, Kannan S, Puttagunta S, Pradhan MR, Verma CS, Venkatraman P. A Novel Determinant of PSMD9 PDZ Binding Guides the Evolution of the First Generation of Super Binding Peptides. Biochemistry 2019; 58:3422-3433. [DOI: 10.1021/acs.biochem.9b00308] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Mahalakshmi Harish
- Protein Interactome Lab for Structural and Functional Biology, Advanced Centre for Treatment, Research and Education in Cancer, Sector 22, Kharghar, Navi Mumbai, Maharashtra, India 410210
- Homi Bhabha National Institute, 2nd floor, BARC Training School Complex, Anushaktinagar, Mumbai, Maharashtra, India 400094
| | | | - Srivalli Puttagunta
- Protein Interactome Lab for Structural and Functional Biology, Advanced Centre for Treatment, Research and Education in Cancer, Sector 22, Kharghar, Navi Mumbai, Maharashtra, India 410210
| | - Mohan R. Pradhan
- Bioinformatics Institute (BII), A*STAR, 30 Biopolis Street, 07-01 Matrix, Singapore 138671
| | - Chandra S. Verma
- Bioinformatics Institute (BII), A*STAR, 30 Biopolis Street, 07-01 Matrix, Singapore 138671
- Department of Biological Sciences, National University of Singapore, 16 Science Drive, Singapore 117558
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Prasanna Venkatraman
- Protein Interactome Lab for Structural and Functional Biology, Advanced Centre for Treatment, Research and Education in Cancer, Sector 22, Kharghar, Navi Mumbai, Maharashtra, India 410210
- Homi Bhabha National Institute, 2nd floor, BARC Training School Complex, Anushaktinagar, Mumbai, Maharashtra, India 400094
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29
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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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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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31
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Sharma S, Young RJ, Chen J, Chen X, Oh EC, Schiller MR. Minimotifs dysfunction is pervasive in neurodegenerative disorders. ALZHEIMER'S & DEMENTIA (NEW YORK, N. Y.) 2018; 4:414-432. [PMID: 30225339 PMCID: PMC6139474 DOI: 10.1016/j.trci.2018.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Minimotifs are modular contiguous peptide sequences in proteins that are important for posttranslational modifications, binding to other molecules, and trafficking to specific subcellular compartments. Some molecular functions of proteins in cellular pathways can be predicted from minimotif consensus sequences identified through experimentation. While a role for minimotifs in regulating signal transduction and gene regulation during disease pathogenesis (such as infectious diseases and cancer) is established, the therapeutic use of minimotif mimetic drugs is limited. In this review, we discuss a general theme identifying a pervasive role of minimotifs in the pathomechanism of neurodegenerative diseases. Beyond their longstanding history in the genetics of familial neurodegeneration, minimotifs are also major players in neurotoxic protein aggregation, aberrant protein trafficking, and epigenetic regulation. Generalizing the importance of minimotifs in neurodegenerative diseases offers a new perspective for the future study of neurodegenerative mechanisms and the investigation of new therapeutics.
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Affiliation(s)
- Surbhi Sharma
- Nevada Institute of Personalized Medicine, Las Vegas, NV, USA
- School of Life Sciences, Las Vegas, NV, USA
| | - Richard J. Young
- Nevada Institute of Personalized Medicine, Las Vegas, NV, USA
- School of Life Sciences, Las Vegas, NV, USA
| | - Jingchun Chen
- Nevada Institute of Personalized Medicine, Las Vegas, NV, USA
| | - Xiangning Chen
- Nevada Institute of Personalized Medicine, Las Vegas, NV, USA
- Department of Psychology, Las Vegas, NV, USA
| | - Edwin C. Oh
- Nevada Institute of Personalized Medicine, Las Vegas, NV, USA
- School of Medicine, Las Vegas, NV, USA
| | - Martin R. Schiller
- Nevada Institute of Personalized Medicine, Las Vegas, NV, USA
- School of Life Sciences, Las Vegas, NV, USA
- School of Medicine, Las Vegas, NV, USA
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32
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Targeting PTEN in Colorectal Cancers. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1110:55-73. [DOI: 10.1007/978-3-030-02771-1_5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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33
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Structure function relations in PDZ-domain-containing proteins: Implications for protein networks in cellular signalling. J Biosci 2017. [DOI: 10.1007/s12038-017-9727-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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34
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de Bartolomeis A, Buonaguro EF, Latte G, Rossi R, Marmo F, Iasevoli F, Tomasetti C. Immediate-Early Genes Modulation by Antipsychotics: Translational Implications for a Putative Gateway to Drug-Induced Long-Term Brain Changes. Front Behav Neurosci 2017; 11:240. [PMID: 29321734 PMCID: PMC5732183 DOI: 10.3389/fnbeh.2017.00240] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 11/22/2017] [Indexed: 12/12/2022] Open
Abstract
An increasing amount of research aims at recognizing the molecular mechanisms involved in long-lasting brain architectural changes induced by antipsychotic treatments. Although both structural and functional modifications have been identified following acute antipsychotic administration in humans, currently there is scarce knowledge on the enduring consequences of these acute changes. New insights in immediate-early genes (IEGs) modulation following acute or chronic antipsychotic administration may help to fill the gap between primary molecular response and putative long-term changes. Moreover, a critical appraisal of the spatial and temporal patterns of IEGs expression may shed light on the functional "signature" of antipsychotics, such as the propensity to induce motor side effects, the potential neurobiological mechanisms underlying the differences between antipsychotics beyond D2 dopamine receptor affinity, as well as the relevant effects of brain region-specificity in their mechanisms of action. The interest for brain IEGs modulation after antipsychotic treatments has been revitalized by breakthrough findings such as the role of early genes in schizophrenia pathophysiology, the involvement of IEGs in epigenetic mechanisms relevant for cognition, and in neuronal mapping by means of IEGs expression profiling. Here we critically review the evidence on the differential modulation of IEGs by antipsychotics, highlighting the association between IEGs expression and neuroplasticity changes in brain regions impacted by antipsychotics, trying to elucidate the molecular mechanisms underpinning the effects of this class of drugs on psychotic, cognitive and behavioral symptoms.
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Affiliation(s)
- Andrea de Bartolomeis
- Laboratory of Molecular and Translational Psychiatry and Unit of Treatment Resistant Psychosis, Section of Psychiatry, Department of Neuroscience, Reproductive Sciences and Odontostomatology, University School of Medicine "Federico II", Naples, Italy
| | - Elisabetta F Buonaguro
- Laboratory of Molecular and Translational Psychiatry and Unit of Treatment Resistant Psychosis, Section of Psychiatry, Department of Neuroscience, Reproductive Sciences and Odontostomatology, University School of Medicine "Federico II", Naples, Italy
| | - Gianmarco Latte
- Laboratory of Molecular and Translational Psychiatry and Unit of Treatment Resistant Psychosis, Section of Psychiatry, Department of Neuroscience, Reproductive Sciences and Odontostomatology, University School of Medicine "Federico II", Naples, Italy
| | - Rodolfo Rossi
- Laboratory of Molecular and Translational Psychiatry and Unit of Treatment Resistant Psychosis, Section of Psychiatry, Department of Neuroscience, Reproductive Sciences and Odontostomatology, University School of Medicine "Federico II", Naples, Italy
| | - Federica Marmo
- Laboratory of Molecular and Translational Psychiatry and Unit of Treatment Resistant Psychosis, Section of Psychiatry, Department of Neuroscience, Reproductive Sciences and Odontostomatology, University School of Medicine "Federico II", Naples, Italy
| | - Felice Iasevoli
- Laboratory of Molecular and Translational Psychiatry and Unit of Treatment Resistant Psychosis, Section of Psychiatry, Department of Neuroscience, Reproductive Sciences and Odontostomatology, University School of Medicine "Federico II", Naples, Italy
| | - Carmine Tomasetti
- Laboratory of Molecular and Translational Psychiatry and Unit of Treatment Resistant Psychosis, Section of Psychiatry, Department of Neuroscience, Reproductive Sciences and Odontostomatology, University School of Medicine "Federico II", Naples, Italy
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35
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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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Pedersen SW, Moran GE, Sereikaitė V, Haugaard-Kedström LM, Strømgaard K. Importance of a Conserved Lys/Arg Residue for Ligand/PDZ Domain Interactions as Examined by Protein Semisynthesis. Chembiochem 2016; 17:1936-1944. [DOI: 10.1002/cbic.201600322] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Søren W. Pedersen
- Center for Biopharmaceuticals; Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Griffin E. Moran
- Center for Biopharmaceuticals; Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Vita Sereikaitė
- Center for Biopharmaceuticals; Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Linda M. Haugaard-Kedström
- Center for Biopharmaceuticals; Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Kristian Strømgaard
- Center for Biopharmaceuticals; Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
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The role of claudins in cancer metastasis. Oncogene 2016; 36:1176-1190. [PMID: 27524421 DOI: 10.1038/onc.2016.289] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Revised: 07/11/2016] [Accepted: 07/11/2016] [Indexed: 01/24/2023]
Abstract
TJs are large intercellular adhesion complexes that maintain cell polarity in normal epithelia and endothelia. During the metastatic process, TJs must be 'loosened' or dismantled in cancer cells to enable migration and dissemination. Diminished TJ integrity must also occur within endothelial cells to allow intravasation and extravasation of cancer cells across endothelial barriers. Claudins are critical components of TJs, forming homo- and heteromeric interactions between the adjacent cells, which have been implicated as key modulators of carcinogenesis and metastasis. Numerous epithelial-derived cancers display altered claudin expression patterns and certain claudins can now be used as biomarkers to predict patient prognosis. Moreover, claudins have been functionally implicated in numerous steps of the metastatic cascade. The distinct roles played by claudins during the cancer progression to metastatic disease are just starting to be elucidated. A more complete understanding of the mechanisms through which claudins augment cancer metastasis is required to develop new therapeutic agents against this family of proteins. In this review, we will summarize the relationship between the claudin expression and clinical outcomes in diverse cancers, discuss tumor intrinisic roles through which claudins regulate metastasis and explore claudin-mediated functions within stromal cells that influence the metastatic process. Finally, we will consider possible strategies for targeting claudins that have the potential to improve the management of metastatic cancer.
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38
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Xie J, Wu X, Zhou Q, Yang Y, Tian Y, Huang C, Meng X, Li J. PICK1 confers anti-inflammatory effects in acute liver injury via suppressing M1 macrophage polarization. Biochimie 2016; 127:121-32. [PMID: 27157267 DOI: 10.1016/j.biochi.2016.05.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 05/02/2016] [Indexed: 12/11/2022]
Abstract
Protein interacting with C kinase 1 (PICK1) is a scaffolding protein mainly implicated in neurological diseases, however, the function of PICK1 in acute liver injury (ALI) remains unknown. Our study found a dramatical decrease in mRNA and protein levels of PICK1 in liver tissues and isolated Kupffer cells (KCs) from the liver in mice with ALI. Furthermore, pretreatment the mice with ALI with FSC-231, a pharmacological inhibitor of PICK1, could significantly augment inflammatory response. Furthermore, in vitro studies showed that both lipopolysaccharide (LPS) and interferon gamma (IFN-γ) significantly reduced the expression of PICK1, while IL-4 elevated its expression in RAW 264.7 cells. Additionally, over-expression of PICK1 inhibited the expression of M1 biomarkers by suppressing NF-κB activity, and enhanced the expression of M2 biomarkers by promoting STAT6 activity. In contrast, knockdown of PICK1 or FSC-231 pretreatment promoted M1 polarization and suppressed M2 polarization. Besides, caveolin-1 was identified as a potential target gene controlled by PICK1 in RAW 264.7 cells. Mechanistic investigation revealed a dual role of PICK1 in regulating macrophage polarization and implied PICK1 as a potential therapeutic target in ALI.
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Affiliation(s)
- Juan Xie
- School of Pharmacy, Anhui Medical University, Meishan Road, Hefei, 230032, China; Institute for Liver Diseases of Anhui Medical University (AMU), China; Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, 230032, China
| | - Xiaoqin Wu
- School of Pharmacy, Anhui Medical University, Meishan Road, Hefei, 230032, China; Institute for Liver Diseases of Anhui Medical University (AMU), China; Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, 230032, China
| | - Qun Zhou
- School of Pharmacy, Anhui Medical University, Meishan Road, Hefei, 230032, China; Institute for Liver Diseases of Anhui Medical University (AMU), China; Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, 230032, China
| | - Yang Yang
- School of Pharmacy, Anhui Medical University, Meishan Road, Hefei, 230032, China; Institute for Liver Diseases of Anhui Medical University (AMU), China; Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, 230032, China
| | - Yuanyao Tian
- School of Pharmacy, Anhui Medical University, Meishan Road, Hefei, 230032, China; Institute for Liver Diseases of Anhui Medical University (AMU), China; Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, 230032, China
| | - Cheng Huang
- School of Pharmacy, Anhui Medical University, Meishan Road, Hefei, 230032, China; Institute for Liver Diseases of Anhui Medical University (AMU), China; Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, 230032, China
| | - Xiaoming Meng
- School of Pharmacy, Anhui Medical University, Meishan Road, Hefei, 230032, China; Institute for Liver Diseases of Anhui Medical University (AMU), China; Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, 230032, China
| | - Jun Li
- School of Pharmacy, Anhui Medical University, Meishan Road, Hefei, 230032, China; Institute for Liver Diseases of Anhui Medical University (AMU), China; Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, 230032, China.
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39
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Liu J, Liu M, Zheng B, Yao Z, Xia J. Affinity Enhancement by Ligand Clustering Effect Inspired by Peptide Dendrimers-Shank PDZ Proteins Interactions. PLoS One 2016; 11:e0149580. [PMID: 26918521 PMCID: PMC4769301 DOI: 10.1371/journal.pone.0149580] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 02/01/2016] [Indexed: 01/28/2023] Open
Abstract
High-affinity binders are desirable tools to probe the function that specific protein−protein interactions play in cell. In the process of seeking a general strategy to design high-affinity binders, we found a clue from the βPIX (p21-activated kinase interacting exchange factor)−Shank PDZ interaction in synaptic assembly: three PDZ-binding sites are clustered by a parallel coiled-coil trimer but bind to Shank PDZ protein with 1:1 stoichiometry (1 trimer/1 PDZ). Inspired by this architecture, we proposed that peptide dendrimer, mimicking the ligand clustering in βPIX, will also show enhanced binding affinity, yet with 1:1 stoichiometry. This postulation has been proven here, as we synthesized a set of monomeric, dimeric and trimeric peptides and measured their binding affinity and stoichiometry with Shank PDZ domains by isothermal titration calorimetry, native mass spectrometry and surface plasmon resonance. This affinity enhancement, best explained by proximity effect, will be useful to guide the design of high-affinity blockers for protein−protein interactions.
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Affiliation(s)
- Jiahui Liu
- Department of Chemistry, Centre of Novel Biomaterials, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Miao Liu
- Department of Chemistry, Centre of Novel Biomaterials, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Bo Zheng
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
| | - Zhongping Yao
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
| | - Jiang Xia
- Department of Chemistry, Centre of Novel Biomaterials, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- * E-mail:
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Zhang W, Coba MP, Sun F. Inference of domain-disease associations from domain-protein, protein-disease and disease-disease relationships. BMC SYSTEMS BIOLOGY 2016; 10 Suppl 1:4. [PMID: 26818594 PMCID: PMC4895779 DOI: 10.1186/s12918-015-0247-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Background Protein domains can be viewed as portable units of biological function that defines the functional properties of proteins. Therefore, if a protein is associated with a disease, protein domains might also be associated and define disease endophenotypes. However, knowledge about such domain-disease relationships is rarely available. Thus, identification of domains associated with human diseases would greatly improve our understandingof the mechanism of human complex diseases and further improve the prevention, diagnosis and treatment of these diseases. Methods Based on phenotypic similarities among diseases, we first group diseases into overlapping modules. We then develop a framework to infer associations between domains and diseases through known relationships between diseases and modules, domains and proteins, as well as proteins and disease modules. Different methods including Association, Maximum likelihood estimation (MLE), Domain-disease pair exclusion analysis (DPEA), Bayesian, and Parsimonious explanation (PE) approaches are developed to predict domain-disease associations. Results We demonstrate the effectiveness of all the five approaches via a series of validation experiments, and show the robustness of the MLE, Bayesian and PE approaches to the involved parameters. We also study the effects of disease modularization in inferring novel domain-disease associations. Through validation, the AUC (Area Under the operating characteristic Curve) scores for Bayesian, MLE, DPEA, PE, and Association approaches are 0.86, 0.84, 0.83, 0.83 and 0.79, respectively, indicating the usefulness of these approaches for predicting domain-disease relationships. Finally, we choose the Bayesian approach to infer domains associated with two common diseases, Crohn’s disease and type 2 diabetes. Conclusions The Bayesian approach has the best performance for the inference of domain-disease relationships. The predicted landscape between domains and diseases provides a more detailed view about the disease mechanisms. Electronic supplementary material The online version of this article (doi:10.1186/s12918-015-0247-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wangshu Zhang
- Molecular and Computational Biology Program, University of Southern California, 1050 Childs Way, Los Angeles, USA.
| | - Marcelo P Coba
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA. .,Department of Psychiatry and Behavioral Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| | - Fengzhu Sun
- Molecular and Computational Biology Program, University of Southern California, 1050 Childs Way, Los Angeles, USA. .,Centre for Computational Systems Biology, School of Mathematical Sciences, Fudan University, Shanghai, China.
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Pedersen SW, Pedersen SB, Anker L, Hultqvist G, Kristensen AS, Jemth P, Strømgaard K. Probing backbone hydrogen bonding in PDZ/ligand interactions by protein amide-to-ester mutations. Nat Commun 2015; 5:3215. [PMID: 24477114 DOI: 10.1038/ncomms4215] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 01/07/2014] [Indexed: 01/30/2023] Open
Abstract
PDZ domains are scaffolding modules in protein-protein interactions that mediate numerous physiological functions by interacting canonically with the C-terminus or non-canonically with an internal motif of protein ligands. A conserved carboxylate-binding site in the PDZ domain facilitates binding via backbone hydrogen bonds; however, little is known about the role of these hydrogen bonds due to experimental challenges with backbone mutations. Here we address this interaction by generating semisynthetic PDZ domains containing backbone amide-to-ester mutations and evaluating the importance of individual hydrogen bonds for ligand binding. We observe substantial and differential effects upon amide-to-ester mutation in PDZ2 of postsynaptic density protein 95 and other PDZ domains, suggesting that hydrogen bonding at the carboxylate-binding site contributes to both affinity and selectivity. In particular, the hydrogen-bonding pattern is surprisingly different between the non-canonical and canonical interaction. Our data provide a detailed understanding of the role of hydrogen bonds in protein-protein interactions.
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Affiliation(s)
- Søren W Pedersen
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Stine B Pedersen
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Louise Anker
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Greta Hultqvist
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden
| | - Anders S Kristensen
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden
| | - Kristian Strømgaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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Arora K, Sinha C, Zhang W, Moon CS, Ren A, Yarlagadda S, Dostmann WR, Adebiyi A, Haberman Y, Denson LA, Wang X, Naren AP. Altered cGMP dynamics at the plasma membrane contribute to diarrhea in ulcerative colitis. THE AMERICAN JOURNAL OF PATHOLOGY 2015; 185:2790-804. [PMID: 26261085 DOI: 10.1016/j.ajpath.2015.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 05/31/2015] [Accepted: 06/29/2015] [Indexed: 12/19/2022]
Abstract
Ulcerative colitis (UC) belongs to inflammatory bowel disorders, a group of gastrointestinal disorders that can produce serious recurring diarrhea in affected patients. The mechanism for UC- and inflammatory bowel disorder-associated diarrhea is not well understood. The cystic fibrosis transmembrane-conductance regulator (CFTR) chloride channel plays an important role in fluid and water transport across the intestinal mucosa. CFTR channel function is regulated in a compartmentalized manner through the formation of CFTR-containing macromolecular complexes at the plasma membrane. In this study, we demonstrate the involvement of a novel macromolecular signaling pathway that causes diarrhea in UC. We found that a nitric oxide-producing enzyme, inducible nitric oxide synthase (iNOS), is overexpressed under the plasma membrane and generates compartmentalized cGMP in gut epithelia in UC. The scaffolding protein Na(+)/H(+) exchanger regulatory factor 2 (NHERF2) bridges iNOS with CFTR, forming CFTR-NHERF2-iNOS macromolecular complexes that potentiate CFTR channel function via the nitric oxide-cGMP pathway under inflammatory conditions both in vitro and in vivo. Potential disruption of these complexes in Nherf2(-/-) mice may render them more resistant to CFTR-mediated secretory diarrhea than Nherf2(+/+) mice in murine colitis models. Our study provides insight into the mechanism of pathophysiologic occurrence of diarrhea in UC and suggests that targeting CFTR and CFTR-containing macromolecular complexes will ameliorate diarrheal symptoms and improve conditions associated with inflammatory bowel disorders.
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Affiliation(s)
- Kavisha Arora
- Division of Pulmonary Medicine, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Physiology, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Chandrima Sinha
- Department of Physiology, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Weiqiang Zhang
- Department of Physiology, University of Tennessee Health Science Center, Memphis, Tennessee; Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Chang Suk Moon
- Division of Pulmonary Medicine, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Physiology, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Aixia Ren
- Department of Physiology, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Sunitha Yarlagadda
- Division of Pulmonary Medicine, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Physiology, University of Tennessee Health Science Center, Memphis, Tennessee
| | | | - Adebowale Adebiyi
- Department of Physiology, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Yael Haberman
- Division of Gastroenterology, Hepatology, and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Lee A Denson
- Division of Gastroenterology, Hepatology, and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Xusheng Wang
- Department of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Anjaparavanda P Naren
- Division of Pulmonary Medicine, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Physiology, University of Tennessee Health Science Center, Memphis, Tennessee.
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Cheng MH, Block E, Hu F, Cobanoglu MC, Sorkin A, Bahar I. Insights into the Modulation of Dopamine Transporter Function by Amphetamine, Orphenadrine, and Cocaine Binding. Front Neurol 2015; 6:134. [PMID: 26106364 PMCID: PMC4460958 DOI: 10.3389/fneur.2015.00134] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 05/26/2015] [Indexed: 12/29/2022] Open
Abstract
Human dopamine (DA) transporter (hDAT) regulates dopaminergic signaling in the central nervous system by maintaining the synaptic concentration of DA at physiological levels, upon reuptake of DA into presynaptic terminals. DA translocation involves the co-transport of two sodium ions and the channeling of a chloride ion, and it is achieved via alternating access between outward-facing (OF) and inward-facing states of DAT. hDAT is a target for addictive drugs, such as cocaine, amphetamine (AMPH), and therapeutic antidepressants. Our recent quantitative systems pharmacology study suggested that orphenadrine (ORPH), an anticholinergic agent and anti-Parkinson drug, might be repurposable as a DAT drug. Previous studies have shown that DAT-substrates like AMPH or -blockers like cocaine modulate the function of DAT in different ways. However, the molecular mechanisms of modulation remained elusive due to the lack of structural data on DAT. The newly resolved DAT structure from Drosophila melanogaster opens the way to a deeper understanding of the mechanism and time evolution of DAT–drug/ligand interactions. Using a combination of homology modeling, docking analysis, molecular dynamics simulations, and molecular biology experiments, we performed a comparative study of the binding properties of DA, AMPH, ORPH, and cocaine and their modulation of hDAT function. Simulations demonstrate that binding DA or AMPH drives a structural transition toward a functional form predisposed to translocate the ligand. In contrast, ORPH appears to inhibit DAT function by arresting it in the OF open conformation. The analysis shows that cocaine and ORPH competitively bind DAT, with the binding pose and affinity dependent on the conformational state of DAT. Further assays show that the effect of ORPH on DAT uptake and endocytosis is comparable to that of cocaine.
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Affiliation(s)
- Mary Hongying Cheng
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh , Pittsburgh, PA , USA
| | - Ethan Block
- Department of Cell Biology, School of Medicine, University of Pittsburgh , Pittsburgh, PA , USA
| | - Feizhuo Hu
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh , Pittsburgh, PA , USA ; Department of Pharmacology and Pharmaceutical Sciences, School of Medicine, Tsinghua University , Beijing , China
| | - Murat Can Cobanoglu
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh , Pittsburgh, PA , USA
| | - Alexander Sorkin
- Department of Cell Biology, School of Medicine, University of Pittsburgh , Pittsburgh, PA , USA
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh , Pittsburgh, PA , USA
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Zhang R, Yang J, Chu TW, Hartley JM, Kopeček J. Multimodality imaging of coiled-coil mediated self-assembly in a "drug-free" therapeutic system. Adv Healthc Mater 2015; 4:1054-65. [PMID: 25612325 DOI: 10.1002/adhm.201400679] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 12/15/2014] [Indexed: 01/23/2023]
Abstract
Two complementary coiled-coil peptides CCE/CCK are used to develop a "drug free" therapeutic system, which can specifically kill cancer cells without a drug. CCE is attached to the Fab' fragment of anti-CD20 1F5 antibody (Fab'-CCE), and CCK is conjugated in multiple grafts to poly[N-(2-hydroxypropyl)methacrylamide] (P-(CCK)x ). Two conjugates are consecutively administered: First, Fab'-CCE coats peptide CCE at CD20 antigen of lymphoma cell surface; second, CCE/CCK biorecognition between Fab'-CCE and P-(CCK)x leads to coiled-coil formation, CD20 crosslinking, membrane reorganization, and ultimately cell apoptosis. To prove that two conjugates can assemble at cell surface, multiple fluorescence imaging studies are performed, including 2-channel FMT, 3D confocal microscopy, and 4-color FACS. Confocal microscopy shows colocalization of two fluorescently labeled conjugates on non-Hodgkin's lymphoma (NHL) Raji cell surface, indicating "two-step" targeting specificity. The fluorescent images also reveal that these two conjugates can disrupt normal membrane lipid distribution and form lipid raft clusters, leading to cancer cell apoptosis. This "two-step" biorecognition capacity is further demonstrated in a NHL xenograft model, using fluorescent images at whole-body, tissue and cell levels. It is also found that delaying injection of P-(CCK)x can significantly enhance targeting efficacy. This high-specificity therapeutics provide a safe option to treat NHL and other B cell malignancies.
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Affiliation(s)
- Rui Zhang
- Department of Pharmaceutics and Pharmaceutical Chemistry/CCCD; University of Utah; Salt Lake City UT 84112 USA
| | - Jiyuan Yang
- Department of Pharmaceutics and Pharmaceutical Chemistry/CCCD; University of Utah; Salt Lake City UT 84112 USA
| | - Te-Wei Chu
- Department of Pharmaceutics and Pharmaceutical Chemistry/CCCD; University of Utah; Salt Lake City UT 84112 USA
| | - Jonathan M. Hartley
- Department of Bioengineering; University of Utah; Salt Lake City UT 84112 USA
| | - Jindřich Kopeček
- Department of Pharmaceutics and Pharmaceutical Chemistry/CCCD; University of Utah; Salt Lake City UT 84112 USA
- Department of Bioengineering; University of Utah; Salt Lake City UT 84112 USA
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Xia W, Liu Y, Jiao J. GRM7 regulates embryonic neurogenesis via CREB and YAP. Stem Cell Reports 2015; 4:795-810. [PMID: 25921811 PMCID: PMC4437472 DOI: 10.1016/j.stemcr.2015.03.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 03/19/2015] [Accepted: 03/20/2015] [Indexed: 01/15/2023] Open
Abstract
Metabotropic glutamate receptor 7 (GRM7) has recently been identified to be associated with brain developmental defects, such as attention deficit hyperactivity disorder (ADHD) and autism. However, the function of GRM7 during brain development remains largely unknown. Here, we used gain- and loss-of-function strategies to investigate the role of GRM7 in early cortical development. We demonstrate that Grm7 knockdown increases neural progenitor cell (NPC) proliferation, decreases terminal mitosis and neuronal differentiation, and leads to abnormal neuronal morphology. GRM7 regulates the phosphorylation of cyclic AMP response element-binding protein (CREB) and the expression of Yes-associated protein (YAP) by directly interacting with CaM, which subsequently regulates the expression of CyclinD1 and ultimately affects early cortical development. These defects in neurogenesis are ameliorated by Grm7 overexpression, Creb knockdown, or Yap knockdown. Thus, our findings indicate that GRM7 signaling via CREB and YAP is necessary for neurogenesis in the brain. GRM7 is essential for brain development and neuron production GRM7 acts through CREB and YAP to regulate neurogenesis Grm7 knockdown causes neuronal development defects
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MESH Headings
- Adaptor Proteins, Signal Transducing/antagonists & inhibitors
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/metabolism
- Animals
- Cell Cycle Proteins
- Cell Proliferation
- Cells, Cultured
- Cyclic AMP Response Element-Binding Protein/metabolism
- Female
- Immunoprecipitation
- Mice
- Mice, Inbred ICR
- Microscopy, Confocal
- Mitosis
- Neural Stem Cells/cytology
- Neural Stem Cells/metabolism
- Neurogenesis
- Phosphoproteins/antagonists & inhibitors
- Phosphoproteins/genetics
- Phosphoproteins/metabolism
- Phosphorylation
- RNA Interference
- RNA, Small Interfering/metabolism
- Receptors, Metabotropic Glutamate/antagonists & inhibitors
- Receptors, Metabotropic Glutamate/genetics
- Receptors, Metabotropic Glutamate/metabolism
- Signal Transduction
- YAP-Signaling Proteins
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Affiliation(s)
- Wenlong Xia
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - YanLi Liu
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianwei Jiao
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
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Daqrouq K, Alhmouz R, Balamesh A, Memic A. Application of wavelet transform for PDZ domain classification. PLoS One 2015; 10:e0122873. [PMID: 25860375 PMCID: PMC4393179 DOI: 10.1371/journal.pone.0122873] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Accepted: 02/24/2015] [Indexed: 11/18/2022] Open
Abstract
PDZ domains have been identified as part of an array of signaling proteins that are often unrelated, except for the well-conserved structural PDZ domain they contain. These domains have been linked to many disease processes including common Avian influenza, as well as very rare conditions such as Fraser and Usher syndromes. Historically, based on the interactions and the nature of bonds they form, PDZ domains have most often been classified into one of three classes (class I, class II and others - class III), that is directly dependent on their binding partner. In this study, we report on three unique feature extraction approaches based on the bigram and trigram occurrence and existence rearrangements within the domain's primary amino acid sequences in assisting PDZ domain classification. Wavelet packet transform (WPT) and Shannon entropy denoted by wavelet entropy (WE) feature extraction methods were proposed. Using 115 unique human and mouse PDZ domains, the existence rearrangement approach yielded a high recognition rate (78.34%), which outperformed our occurrence rearrangements based method. The recognition rate was (81.41%) with validation technique. The method reported for PDZ domain classification from primary sequences proved to be an encouraging approach for obtaining consistent classification results. We anticipate that by increasing the database size, we can further improve feature extraction and correct classification.
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Affiliation(s)
- Khaled Daqrouq
- Electrical and Computer Engineering Department, Faculty of Engineering, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Rami Alhmouz
- Electrical and Computer Engineering Department, Faculty of Engineering, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Ahmed Balamesh
- Electrical and Computer Engineering Department, Faculty of Engineering, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Adnan Memic
- Center of Nanotechnology, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
- * E-mail:
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Freudenberg F, Celikel T, Reif A. The role of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors in depression: central mediators of pathophysiology and antidepressant activity? Neurosci Biobehav Rev 2015; 52:193-206. [PMID: 25783220 DOI: 10.1016/j.neubiorev.2015.03.005] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 02/23/2015] [Accepted: 03/06/2015] [Indexed: 12/27/2022]
Abstract
Depression is a major psychiatric disorder affecting more than 120 million people worldwide every year. Changes in monoaminergic transmitter release are suggested to take part in the pathophysiology of depression. However, more recent experimental evidence suggests that glutamatergic mechanisms might play a more central role in the development of this disorder. The importance of the glutamatergic system in depression was particularly highlighted by the discovery that N-methyl-D-aspartate (NMDA) receptor antagonists (particularly ketamine) exert relatively long-lasting antidepressant like effects with rapid onset. Importantly, the antidepressant-like effects of NMDA receptor antagonists, but also other antidepressants (both classical and novel), require activation of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors. Additionally, expression of AMPA receptors is altered in patients with depression. Moreover, preclinical evidence supports an important involvement of AMPA receptor-dependent signaling and plasticity in the pathophysiology and treatment of depression. Here we summarize work published on the involvement of AMPA receptors in depression and discuss a possible central role for AMPA receptors in the pathophysiology, course and treatment of depression.
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Affiliation(s)
- Florian Freudenberg
- Department of Psychiatry, Psychosomatics and Psychotherapy, University Hospital of Frankfurt, Heinrich-Hoffmann-Straße 10, 60528 Frankfurt am Main, Germany.
| | - Tansu Celikel
- Department of Neurophysiology, Donders Center for Neuroscience, Radboud University Nijmegen, 6500 AA Nijmegen, The Netherlands
| | - Andreas Reif
- Department of Psychiatry, Psychosomatics and Psychotherapy, University Hospital of Frankfurt, Heinrich-Hoffmann-Straße 10, 60528 Frankfurt am Main, Germany
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48
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Eildal JNN, Bach A, Dogan J, Ye F, Zhang M, Jemth P, Strømgaard K. Rigidified Clicked Dimeric Ligands for Studying the Dynamics of the PDZ1-2 Supramodule of PSD-95. Chembiochem 2014; 16:64-9. [DOI: 10.1002/cbic.201402547] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Indexed: 11/06/2022]
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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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50
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Hijacking Dlg1 for oncogenic phosphatidylinositol 3-kinase activation in human epithelial cells is a conserved mechanism of human adenovirus E4-ORF1 proteins. J Virol 2014; 88:14268-77. [PMID: 25253337 DOI: 10.1128/jvi.02324-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
UNLABELLED The E4-ORF1 gene of human adenoviruses encodes a 14-kDa protein that promotes viral replication as well as cellular metabolic reprogramming, survival, and transformation by constitutively activating cellular phosphatidylinositol 3-kinase (PI3K). We recently reported that the E4-ORF1 protein from subgroup D human adenovirus type 9 upregulates and oncogenically activates PI3K by a novel mechanism involving separate interactions of E4-ORF1 with cellular discs large 1 (Dlg1) and PI3K to form a ternary complex that translocates to the plasma membrane (K. Kong, M. Kumar, M. Taruishi, and R. T. Javier, PLoS Pathog. 10:e1004102, 2014, doi:10.1371/journal.ppat.1004102). The current study was carried out to investigate whether other human adenovirus E4-ORF1 proteins share this mechanism of action. The results showed that in human MCF10A epithelial cells, stable expression of E4-ORF1 proteins encoded by representative human adenovirus serotypes from subgroups A to D induce ternary complex formation, Dlg1-dependent PI3K activation, PI3K protein elevation, Dlg1 and PI3K membrane recruitment, and PI3K-dependent cellular transformation. The first three of these E4-ORF1 activities were also observed in MCF10A cells infected with each wild-type human adenovirus from subgroups A to D. Our findings indicate that most, if not all, human adenovirus E4-ORF1 proteins share a conserved molecular mechanism of PI3K activation, which confers a common capacity to promote oncogenic transformation in human epithelial cells. IMPORTANCE PI3K activation by the adenovirus E4-ORF1 protein mediates oncogenic cellular transformation by human adenovirus type 9, augments viral protein expression and replication by human adenovirus type 5, and dysregulates cellular glucose and lipid metabolism by human adenovirus type 36. For the first time, we report that E4-ORF1 proteins from human adenoviruses in subgroups A to D evolved a conserved molecular mechanism to mediate constitutive PI3K activation that can provoke oncogenic transformation in human epithelial cells. The results raise potential safety concerns about the use of vectors encoding the E4-ORF1 gene in human gene therapy and vaccination. Our findings further suggest that the conserved mechanism revealed here may be targeted for development of therapeutic drugs to treat and prevent adenovirus-associated human diseases.
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