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Holtzman R, Giulini M, Potestio R. Making sense of complex systems through resolution, relevance, and mapping entropy. Phys Rev E 2022; 106:044101. [PMID: 36397524 DOI: 10.1103/physreve.106.044101] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/16/2022] [Indexed: 06/16/2023]
Abstract
Complex systems are characterized by a tight, nontrivial interplay of their constituents, which gives rise to a multiscale spectrum of emergent properties. In this scenario, it is practically and conceptually difficult to identify those degrees of freedom that mostly determine the behavior of the system and separate them from less prominent players. Here, we tackle this problem making use of three measures of statistical information: Resolution, relevance, and mapping entropy. We address the links existing among them, taking the moves from the established relation between resolution and relevance and further developing novel connections between resolution and mapping entropy; by these means we can identify, in a quantitative manner, the number and selection of degrees of freedom of the system that preserve the largest information content about the generative process that underlies an empirical dataset. The method, which is implemented in a freely available software, is fully general, as it is shown through the application to three very diverse systems, namely, a toy model of independent binary spins, a coarse-grained representation of the financial stock market, and a fully atomistic simulation of a protein.
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Affiliation(s)
- Roi Holtzman
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Marco Giulini
- Physics Department, University of Trento, via Sommarive, 14 I-38123 Trento, Italy
- INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, I-38123 Trento, Italy
| | - Raffaello Potestio
- Physics Department, University of Trento, via Sommarive, 14 I-38123 Trento, Italy
- INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, I-38123 Trento, Italy
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2
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Choromańska A, Chwiłkowska A, Kulbacka J, Baczyńska D, Rembiałkowska N, Szewczyk A, Michel O, Gajewska-Naryniecka A, Przystupski D, Saczko J. Modifications of Plasma Membrane Organization in Cancer Cells for Targeted Therapy. Molecules 2021; 26:1850. [PMID: 33806009 PMCID: PMC8037978 DOI: 10.3390/molecules26071850] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/18/2021] [Accepted: 03/23/2021] [Indexed: 12/11/2022] Open
Abstract
Modifications of the composition or organization of the cancer cell membrane seem to be a promising targeted therapy. This approach can significantly enhance drug uptake or intensify the response of cancer cells to chemotherapeutics. There are several methods enabling lipid bilayer modifications, e.g., pharmacological, physical, and mechanical. It is crucial to keep in mind the significance of drug resistance phenomenon, ion channel and specific receptor impact, and lipid bilayer organization in planning the cell membrane-targeted treatment. In this review, strategies based on cell membrane modulation or reorganization are presented as an alternative tool for future therapeutic protocols.
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Affiliation(s)
- Anna Choromańska
- Department of Molecular and Cellular Biology, Wroclaw Medical University, Borowska 211A, 50-556 Wroclaw, Poland; (J.K.); (D.B.); (N.R.); (A.S.); (O.M.); (A.G.-N.); (J.S.)
| | - Agnieszka Chwiłkowska
- Department of Molecular and Cellular Biology, Wroclaw Medical University, Borowska 211A, 50-556 Wroclaw, Poland; (J.K.); (D.B.); (N.R.); (A.S.); (O.M.); (A.G.-N.); (J.S.)
| | - Julita Kulbacka
- Department of Molecular and Cellular Biology, Wroclaw Medical University, Borowska 211A, 50-556 Wroclaw, Poland; (J.K.); (D.B.); (N.R.); (A.S.); (O.M.); (A.G.-N.); (J.S.)
| | - Dagmara Baczyńska
- Department of Molecular and Cellular Biology, Wroclaw Medical University, Borowska 211A, 50-556 Wroclaw, Poland; (J.K.); (D.B.); (N.R.); (A.S.); (O.M.); (A.G.-N.); (J.S.)
| | - Nina Rembiałkowska
- Department of Molecular and Cellular Biology, Wroclaw Medical University, Borowska 211A, 50-556 Wroclaw, Poland; (J.K.); (D.B.); (N.R.); (A.S.); (O.M.); (A.G.-N.); (J.S.)
| | - Anna Szewczyk
- Department of Molecular and Cellular Biology, Wroclaw Medical University, Borowska 211A, 50-556 Wroclaw, Poland; (J.K.); (D.B.); (N.R.); (A.S.); (O.M.); (A.G.-N.); (J.S.)
| | - Olga Michel
- Department of Molecular and Cellular Biology, Wroclaw Medical University, Borowska 211A, 50-556 Wroclaw, Poland; (J.K.); (D.B.); (N.R.); (A.S.); (O.M.); (A.G.-N.); (J.S.)
| | - Agnieszka Gajewska-Naryniecka
- Department of Molecular and Cellular Biology, Wroclaw Medical University, Borowska 211A, 50-556 Wroclaw, Poland; (J.K.); (D.B.); (N.R.); (A.S.); (O.M.); (A.G.-N.); (J.S.)
| | - Dawid Przystupski
- Department of Paediatric Bone Marrow Transplantation, Oncology and Haematology, Wroclaw Medical University, Borowska 213, 50-556 Wroclaw, Poland;
| | - Jolanta Saczko
- Department of Molecular and Cellular Biology, Wroclaw Medical University, Borowska 211A, 50-556 Wroclaw, Poland; (J.K.); (D.B.); (N.R.); (A.S.); (O.M.); (A.G.-N.); (J.S.)
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Giulini M, Menichetti R, Shell MS, Potestio R. An Information-Theory-Based Approach for Optimal Model Reduction of Biomolecules. J Chem Theory Comput 2020; 16:6795-6813. [PMID: 33108737 PMCID: PMC7659038 DOI: 10.1021/acs.jctc.0c00676] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Indexed: 02/06/2023]
Abstract
In theoretical modeling of a physical system, a crucial step consists of the identification of those degrees of freedom that enable a synthetic yet informative representation of it. While in some cases this selection can be carried out on the basis of intuition and experience, straightforward discrimination of the important features from the negligible ones is difficult for many complex systems, most notably heteropolymers and large biomolecules. We here present a thermodynamics-based theoretical framework to gauge the effectiveness of a given simplified representation by measuring its information content. We employ this method to identify those reduced descriptions of proteins, in terms of a subset of their atoms, that retain the largest amount of information from the original model; we show that these highly informative representations share common features that are intrinsically related to the biological properties of the proteins under examination, thereby establishing a bridge between protein structure, energetics, and function.
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Affiliation(s)
- Marco Giulini
- Physics
Department, University of Trento, via Sommarive 14, I-38123 Trento, Italy
- INFN-TIFPA, Trento
Institute for Fundamental Physics and Applications, I-38123 Trento, Italy
| | - Roberto Menichetti
- Physics
Department, University of Trento, via Sommarive 14, I-38123 Trento, Italy
- INFN-TIFPA, Trento
Institute for Fundamental Physics and Applications, I-38123 Trento, Italy
| | - M. Scott Shell
- Department
of Chemical Engineering, University of California
Santa Barbara, Santa
Barbara, California 93106, United States
| | - Raffaello Potestio
- Physics
Department, University of Trento, via Sommarive 14, I-38123 Trento, Italy
- INFN-TIFPA, Trento
Institute for Fundamental Physics and Applications, I-38123 Trento, Italy
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Mayorga-Flores M, Chantôme A, Melchor-Meneses CM, Domingo I, Titaux-Delgado GA, Galindo-Murillo R, Vandier C, del Río-Portilla F. Novel Blocker of Onco SK3 Channels Derived from Scorpion Toxin Tamapin and Active against Migration of Cancer Cells. ACS Med Chem Lett 2020; 11:1627-1633. [PMID: 32832033 DOI: 10.1021/acsmedchemlett.0c00300] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 07/10/2020] [Indexed: 11/28/2022] Open
Abstract
Peptide-based therapy against cancer is a field of great interest for biomedical developments. Since it was shown that SK3 channels promote cancer cell migration and metastatic development, we started using these channels as targets for the development of antimetastatic drugs. Particularly, tamapin (a peptide found in the venom of the scorpion Mesobuthus tamulus) is the most specific toxin against the SK2 channel currently known. Considering this fact, we designed diverse tamapin mutants based on three different hypotheses to discover a new potent molecule to block SK3 channels. We performed in vitro studies to evaluate this new toxin derivative inhibitor of cancer cell migration. Our results can be used to generate a new tamapin-based therapy against cancer cells that express SK3 channels.
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Affiliation(s)
- Marlen Mayorga-Flores
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, 04510 Ciudad de México, Mexico
| | - Aurélie Chantôme
- N2C UMR 1069, University of Tours, INSERM, Faculté de Pharmacie, Calciscreen Platform, 37032 Tours, France
| | - Carolina Monserrath Melchor-Meneses
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, 04510 Ciudad de México, Mexico
| | - Isabelle Domingo
- N2C UMR 1069, University of Tours, INSERM, Calciscreen Platform, 37032 Tours, France
| | - Gustavo Alfredo Titaux-Delgado
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, 04510 Ciudad de México, Mexico
| | - Rodrigo Galindo-Murillo
- Department of Medicinal Chemistry, L. S. Skaggs Pharmacy Institute, University of Utah, Salt Lake City, Utah 84112, United States
| | - Christophe Vandier
- N2C UMR 1069, University of Tours, INSERM, Calciscreen Platform, 37032 Tours, France
| | - Federico del Río-Portilla
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, 04510 Ciudad de México, Mexico
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Díaz-García A, Varela D. Voltage-Gated K +/Na + Channels and Scorpion Venom Toxins in Cancer. Front Pharmacol 2020; 11:913. [PMID: 32655396 PMCID: PMC7325878 DOI: 10.3389/fphar.2020.00913] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 06/04/2020] [Indexed: 12/25/2022] Open
Abstract
Ion channels have recently been recognized as novel therapeutic targets in cancer research since they are overexpressed in different histological tissues, and their activity is linked to proliferation, tumor progression, angiogenesis, metastasis, and apoptosis. Voltage gated-potassium channels (VGKC) are involved in cell proliferation, cancer progression, cell cycle transition, and apoptosis. Moreover, voltage-dependent sodium channels (VGSC) contribute to decreases in extracellular pH, which, in turn, promotes cancer cell migration and invasion. Furthermore, VGSC and VGKC modulate voltage-sensitive Ca2+ channel activity by controlling the membrane potential and regulating Ca2+ influx, which functions as a second messenger in processes related to proliferation, invasion, migration, and metastasis. The subgroup of these types of channels that have shown a high oncogenic potential have become known as "oncochannels", and the evidence has highlighted them as key potential therapeutic targets. Scorpion venoms contain a high proportion of peptide toxins that act by modulating voltage-gated Na+/K+ channel activity. Increasing scientific data have pointed out that scorpion venoms and their toxins can affect the activity of oncochannels, thus showing their potential for anticancer therapy. In this review, we provide an update of the most relevant voltage-gated Na+\K+ ion channels as cellular targets and discuss the possibility of using scorpion venom and toxins for anticancer therapy.
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Affiliation(s)
- Alexis Díaz-García
- LifEscozul Chile SpA, Santiago, Chile
- Millennium Nucleus of Ion Channel-Associated Diseases (MiNICAD), Universidad de Chile, Santiago, Chile
| | - Diego Varela
- Millennium Nucleus of Ion Channel-Associated Diseases (MiNICAD), Universidad de Chile, Santiago, Chile
- Program of Physiology and Biophysics, Faculty of Medicine, Institute of Biomedical Sciences (ICBM), Universidad de Chile, Santiago, Chile
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Scorpion Toxins and Ion Channels: Potential Applications in Cancer Therapy. Toxins (Basel) 2020; 12:toxins12050326. [PMID: 32429050 PMCID: PMC7290751 DOI: 10.3390/toxins12050326] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 12/24/2022] Open
Abstract
Apoptosis, a genetically directed process of cell death, has been studied for many years, and the biochemical mechanisms that surround it are well known and described. There are at least three pathways by which apoptosis occurs, and each pathway depends on extra or intracellular processes for activation. Apoptosis is a vital process, but disturbances in proliferation and cell death rates can lead to the development of diseases like cancer. Several compounds, isolated from scorpion venoms, exhibit inhibitory effects on different cancer cells. Indeed, some of these compounds can differentiate between healthy and cancer cells within the same tissue. During the carcinogenic process, morphological, biochemical, and biological changes occur that enable these compounds to modulate cancer but not healthy cells. This review highlights cancer cell features that enable modulation by scorpion neurotoxins. The properties of the isolated scorpion neurotoxins in cancer cells and the potential uses of these compounds as alternative treatments for cancer are discussed.
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Leyva E, Medrano-Cerano JL, Cano-Sánchez P, López-González I, Gómez-Velasco H, del Río-Portilla F, García-Hernández E. Bacterial expression, purification and biophysical characterization of wheat germ agglutinin and its four hevein-like domains. Biopolymers 2018; 110:e23242. [DOI: 10.1002/bip.23242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 10/25/2018] [Accepted: 11/07/2018] [Indexed: 12/27/2022]
Affiliation(s)
- Eduardo Leyva
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria; México Mexico
| | - Jorge L. Medrano-Cerano
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria; México Mexico
| | - Patricia Cano-Sánchez
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria; México Mexico
| | - Itzel López-González
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria; México Mexico
| | - Homero Gómez-Velasco
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria; México Mexico
| | - Federico del Río-Portilla
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria; México Mexico
| | - Enrique García-Hernández
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria; México Mexico
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