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Walther D. Specifics of Metabolite-Protein Interactions and Their Computational Analysis and Prediction. Methods Mol Biol 2023; 2554:179-197. [PMID: 36178627 DOI: 10.1007/978-1-0716-2624-5_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Computational approaches to the characterization and prediction of compound-protein interactions have a long research history and are well established, driven primarily by the needs of drug development. While, in principle, many of the computational methods developed in the context of drug development can also be applied directly to the investigation of metabolite-protein interactions, the interactions of metabolites with proteins (enzymes) are characterized by a number of particularities that result from their natural evolutionary origin and their biological and biochemical roles, as well as from a different problem setting when investigating them. In this review, these special aspects will be highlighted and recent research on them and developed computational approaches presented, along with available resources. They concern, among others, binding promiscuity, allostery, the role of posttranslational modifications, molecular steering and crowding effects, and metabolic conversion rate predictions. Recent breakthroughs in the field of protein structure prediction and newly developed machine learning techniques are being discussed as a tremendous opportunity for developing a more detailed molecular understanding of metabolism.
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Affiliation(s)
- Dirk Walther
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany.
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Chen J, Liu X, Chen J. Targeting Intrinsically Disordered Proteins through Dynamic Interactions. Biomolecules 2020; 10:E743. [PMID: 32403216 PMCID: PMC7277182 DOI: 10.3390/biom10050743] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/04/2020] [Accepted: 05/09/2020] [Indexed: 12/18/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are over-represented in major disease pathways and have attracted significant interest in understanding if and how they may be targeted using small molecules for therapeutic purposes. While most existing studies have focused on extending the traditional structure-centric drug design strategies and emphasized exploring pre-existing structure features of IDPs for specific binding, several examples have also emerged to suggest that small molecules could achieve specificity in binding IDPs and affect their function through dynamic and transient interactions. These dynamic interactions can modulate the disordered conformational ensemble and often lead to modest compaction to shield functionally important interaction sites. Much work remains to be done on further elucidation of the molecular basis of the dynamic small molecule-IDP interaction and determining how it can be exploited for targeting IDPs in practice. These efforts will rely critically on an integrated experimental and computational framework for disordered protein ensemble characterization. In particular, exciting advances have been made in recent years in enhanced sampling techniques, Graphic Processing Unit (GPU)-computing, and protein force field optimization, which have now allowed rigorous physics-based atomistic simulations to generate reliable structure ensembles for nontrivial IDPs of modest sizes. Such de novo atomistic simulations will play crucial roles in exploring the exciting opportunity of targeting IDPs through dynamic interactions.
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Affiliation(s)
- Jianlin Chen
- Department of Hematology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou 318000, Zhejiang, China;
| | - Xiaorong Liu
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA;
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA;
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
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Santofimia-Castaño P, Xia Y, Peng L, Velázquez-Campoy A, Abián O, Lan W, Lomberk G, Urrutia R, Rizzuti B, Soubeyran P, Neira JL, Iovanna J. Targeting the Stress-Induced Protein NUPR1 to Treat Pancreatic Adenocarcinoma. Cells 2019; 8:E1453. [PMID: 31744261 PMCID: PMC6912534 DOI: 10.3390/cells8111453] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 11/13/2019] [Accepted: 11/15/2019] [Indexed: 12/17/2022] Open
Abstract
Cancer cells activate stress-response mechanisms to adapt themselves to a variety of stressful conditions. Among these protective mechanisms, those controlled by the stress-induced nuclear protein 1 (NUPR1 ) belong to the most conserved ones. NUPR1 is an 82-residue-long, monomeric, basic and intrinsically disordered protein (IDP), which was found to be invariably overexpressed in some, if not all, cancer tissues. Remarkably, we and others have previously showed that genetic inactivation of the Nupr1 gene antagonizes the growth of pancreatic cancer as well as several other tumors. With the use of a multidisciplinary strategy by combining biophysical, biochemical, bioinformatic, and biological approaches, a trifluoperazine-derived compound, named ZZW-115, has been identified as an inhibitor of the NUPR1 functions. The anticancer activity of the ZZW-115 was first validated on a large panel of cancer cells. Furthermore, ZZW-115 produced a dose-dependent tumor regression of the tumor size in xenografted mice. Mechanistically, we have demonstrated that NUPR1 binds to several importins. Because ZZW-115 binds NUPR1 through the region around the amino acid Thr68, which is located into the nuclear location signal (NLS) region of the protein, we demonstrated that treatment with ZZW-115 inhibits completely the translocation of NUPR1 from the cytoplasm to the nucleus by competing with importins.
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Affiliation(s)
- Patricia Santofimia-Castaño
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université, CEDEX, 13288 Marseille, France; (P.S.-C.); (W.L.); (P.S.)
- Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, CEDEX, 13288 Marseille, France
| | - Yi Xia
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China;
| | - Ling Peng
- Aix-Marseille Université, CNRS, Centre Interdisciplinaire de Nanoscience de Marseille, UMR 7325, «Equipe Labellisée Ligue Contre le Cancer», Parc Scientifique et Technologique de Luminy, CEDEX, 13288 Marseille, France;
| | - Adrián Velázquez-Campoy
- Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, 50009 Universidad de Zaragoza, Spain; (A.V.-C.); (O.A.); (J.L.N.)
- Aragon Institute for Health Research (IIS Aragon), Universidad de Zaragoza, 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
- Fundacion ARAID, Government of Aragon, Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Olga Abián
- Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, 50009 Universidad de Zaragoza, Spain; (A.V.-C.); (O.A.); (J.L.N.)
- Aragon Institute for Health Research (IIS Aragon), Universidad de Zaragoza, 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
- Instituto Aragonés de Ciencias de la Salud (IACS), Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Wenjun Lan
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université, CEDEX, 13288 Marseille, France; (P.S.-C.); (W.L.); (P.S.)
- Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, CEDEX, 13288 Marseille, France
| | - Gwen Lomberk
- Division of Research, Department of Surgery and the Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI 53226, USA; (G.L.); (R.U.)
| | - Raul Urrutia
- Division of Research, Department of Surgery and the Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI 53226, USA; (G.L.); (R.U.)
| | - Bruno Rizzuti
- CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics, University of Calabria, 87036 Cosenza, Italy;
| | - Philippe Soubeyran
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université, CEDEX, 13288 Marseille, France; (P.S.-C.); (W.L.); (P.S.)
- Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, CEDEX, 13288 Marseille, France
| | - José Luis Neira
- Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, 50009 Universidad de Zaragoza, Spain; (A.V.-C.); (O.A.); (J.L.N.)
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Edificio Torregaitán, 03202 Elche, Alicante, Spain
| | - Juan Iovanna
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université, CEDEX, 13288 Marseille, France; (P.S.-C.); (W.L.); (P.S.)
- Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, CEDEX, 13288 Marseille, France
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Marciel MP, Hoffmann PR. Molecular Mechanisms by Which Selenoprotein K Regulates Immunity and Cancer. Biol Trace Elem Res 2019; 192:60-68. [PMID: 31187393 PMCID: PMC6801056 DOI: 10.1007/s12011-019-01774-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 06/05/2019] [Indexed: 02/07/2023]
Abstract
Many of the 25 members of the selenoprotein family function as enzymes that utilize their selenocysteine (Sec) residues to catalyze redox-based reactions. However, some selenoproteins likely do not exert enzymatic activity by themselves and selenoprotein K (SELENOK) is one such selenoprotein family member that uses its Sec residue in an alternative manner. SELENOK is an endoplasmic reticulum (ER) transmembrane protein that has been shown to be important for ER stress and for calcium-dependent signaling. Molecular mechanisms for the latter have recently been elucidated using knockout mice and genetically manipulated cell lines. These studies have shown that SELENOK interacts with an enzyme in the ER membrane, DHHC6 (letters represent the amino acids aspartic acid, histidine, histidine, and cysteine in the catalytic domain), and the SELENOK/DHHC6 complex catalyzes the transfer of acyl groups such as palmitate to cysteine residues in target proteins, i.e., palmitoylation. One protein palmitoylated by SELENOK/DHHC6 is the calcium channel protein, the inositol 1,4,5-trisphosphate receptor (IP3R), which is acylated as a means for stabilizing the tetrameric calcium channel in the ER membrane. Factors that lower SELENOK levels or function impair IP3R-driven calcium flux. This role for SELENOK is important for the activation and proliferation of immune cells, and recently, a critical role for SELENOK in promoting calcium flux for the progression of melanoma has been demonstrated. This review provides a summary of these findings and their implications in terms of designing new therapeutic interventions that target SELENOK for treating cancers like melanoma.
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Affiliation(s)
- Michael P Marciel
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, USA
| | - Peter R Hoffmann
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, USA.
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