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Cano-Garrido O, Álamo P, Sánchez-García L, Falgàs A, Sánchez-Chardi A, Serna N, Parladé E, Unzueta U, Roldán M, Voltà-Durán E, Casanova I, Villaverde A, Mangues R, Vázquez E. Biparatopic Protein Nanoparticles for the Precision Therapy of CXCR4 + Cancers. Cancers (Basel) 2021; 13:cancers13122929. [PMID: 34208189 PMCID: PMC8230831 DOI: 10.3390/cancers13122929] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/28/2021] [Accepted: 06/07/2021] [Indexed: 01/05/2023] Open
Abstract
Simple Summary Aimed at minimizing side toxicities cancer therapies require appropriate functional vehicles at the nanoscale, for receptor-mediated tumor-targeted drug delivery. The aim of the present study was to explore the human peptide EPI-X4 as a CXCR4-targeting agent in self-assembled, protein-only nanoparticles. While the systemic tumor biodistribution of EPI-X4-based materials is modest, this peptide shows potent proapoptotic effects on CXCR4+ cancer cells. Interestingly, the in vivo selectivity of EPI-X4 was dramatically improved, once combined into biparatopic nanoparticles, with a second CXCR4 ligand, the peptide T22. Biparatopic nanoparticles promote a highly selective tumor destruction in a mouse model of human colorectal cancer, probably associated to the CXCR4 antagonist role of EPI-X4. This study not only validates a new human ligand of the tumoral marker CXCR4, but it also offers a novel strategy for the combination, in protein nanoparticles, of dual acting ligands of tumoral markers for highly selective drug delivery. Abstract The accumulated molecular knowledge about human cancer enables the identification of multiple cell surface markers as highly specific therapeutic targets. A proper tumor targeting could significantly avoid drug exposure of healthy cells, minimizing side effects, but it is also expected to increase the therapeutic index. Specifically, colorectal cancer has a particularly poor prognosis in late stages, being drug targeting an appropriate strategy to substantially improve the therapeutic efficacy. In this study, we have explored the potential of the human albumin-derived peptide, EPI-X4, as a suitable ligand to target colorectal cancer via the cell surface protein CXCR4, a chemokine receptor overexpressed in cancer stem cells. To explore the potential use of this ligand, self-assembling protein nanoparticles have been generated displaying an engineered EPI-X4 version, which conferred a modest CXCR4 targeting and fast and high level of cell apoptosis in tumor CXCR4+ cells, in vitro and in vivo. In addition, when EPI-X4-based building blocks are combined with biologically inert polypeptides containing the CXCR4 ligand T22, the resulting biparatopic nanoparticles show a dramatically improved biodistribution in mouse models of CXCR4+ human cancer, faster cell internalization and enhanced target cell death when compared to the version based on a single ligand. The generation of biparatopic materials opens exciting possibilities in oncotherapies based on high precision drug delivery based on the receptor CXCR4.
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Affiliation(s)
- Olivia Cano-Garrido
- Nanoligent SL, Edifici EUREKA, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain; (O.C.-G.); (N.S.)
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain; (L.S.-G.); (E.P.); (E.V.-D.)
| | - Patricia Álamo
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, 28029 Madrid, Spain; (P.Á.); (A.F.); (U.U.); (I.C.)
- Instituto de Investigación Biomédica Sant Pau (IIB Sant Pau), Sant Antoni Ma Claret 167, 08025 Barcelona, Spain
- Instituto de Investigación Contra la Leucemia Josep Carreras, 08025 Barcelona, Spain
| | - Laura Sánchez-García
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain; (L.S.-G.); (E.P.); (E.V.-D.)
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, 28029 Madrid, Spain; (P.Á.); (A.F.); (U.U.); (I.C.)
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Aïda Falgàs
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, 28029 Madrid, Spain; (P.Á.); (A.F.); (U.U.); (I.C.)
- Instituto de Investigación Biomédica Sant Pau (IIB Sant Pau), Sant Antoni Ma Claret 167, 08025 Barcelona, Spain
- Instituto de Investigación Contra la Leucemia Josep Carreras, 08025 Barcelona, Spain
| | - Alejandro Sánchez-Chardi
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain;
- Servei de Microscòpia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Naroa Serna
- Nanoligent SL, Edifici EUREKA, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain; (O.C.-G.); (N.S.)
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain; (L.S.-G.); (E.P.); (E.V.-D.)
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, 28029 Madrid, Spain; (P.Á.); (A.F.); (U.U.); (I.C.)
| | - Eloi Parladé
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain; (L.S.-G.); (E.P.); (E.V.-D.)
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, 28029 Madrid, Spain; (P.Á.); (A.F.); (U.U.); (I.C.)
| | - Ugutz Unzueta
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, 28029 Madrid, Spain; (P.Á.); (A.F.); (U.U.); (I.C.)
- Instituto de Investigación Biomédica Sant Pau (IIB Sant Pau), Sant Antoni Ma Claret 167, 08025 Barcelona, Spain
- Instituto de Investigación Contra la Leucemia Josep Carreras, 08025 Barcelona, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Mònica Roldán
- Unitat de Microscòpia Confocal i Imatge Cel·lular, Servei de Medicina Genètica i Molecular, Institut Pediàtric de Malalties Rares (IPER), Hospital Sant Joan de Déu, Esplugues de Llobregat, 08950 Barcelona, Spain;
- Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, 08950 Barcelona, Spain
| | - Eric Voltà-Durán
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain; (L.S.-G.); (E.P.); (E.V.-D.)
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, 28029 Madrid, Spain; (P.Á.); (A.F.); (U.U.); (I.C.)
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Isolda Casanova
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, 28029 Madrid, Spain; (P.Á.); (A.F.); (U.U.); (I.C.)
- Instituto de Investigación Biomédica Sant Pau (IIB Sant Pau), Sant Antoni Ma Claret 167, 08025 Barcelona, Spain
- Instituto de Investigación Contra la Leucemia Josep Carreras, 08025 Barcelona, Spain
| | - Antonio Villaverde
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain; (L.S.-G.); (E.P.); (E.V.-D.)
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, 28029 Madrid, Spain; (P.Á.); (A.F.); (U.U.); (I.C.)
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- Correspondence: (A.V.); (R.M.); (E.V.)
| | - Ramón Mangues
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, 28029 Madrid, Spain; (P.Á.); (A.F.); (U.U.); (I.C.)
- Instituto de Investigación Biomédica Sant Pau (IIB Sant Pau), Sant Antoni Ma Claret 167, 08025 Barcelona, Spain
- Instituto de Investigación Contra la Leucemia Josep Carreras, 08025 Barcelona, Spain
- Correspondence: (A.V.); (R.M.); (E.V.)
| | - Esther Vázquez
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain; (L.S.-G.); (E.P.); (E.V.-D.)
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, 28029 Madrid, Spain; (P.Á.); (A.F.); (U.U.); (I.C.)
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- Correspondence: (A.V.); (R.M.); (E.V.)
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Sahin K, Orhan MD, Avsar T, Durdagi S. Hybrid In Silico and TR-FRET-Guided Discovery of Novel BCL-2 Inhibitors. ACS Pharmacol Transl Sci 2021; 4:1111-1123. [PMID: 34151203 DOI: 10.1021/acsptsci.0c00210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Indexed: 12/31/2022]
Abstract
B-Cell lymphoma 2 (BCL-2) regulates cell death in humans. In this study, combined multiscale in silico approaches and in vitro studies were employed. A small-molecule library that includes more than 210 000 compounds was used. The predicted therapeutic activity value (TAV) of the compounds in this library was computed with the binary cancer quantitative structure-activity relationships (QSAR) model. The molecules with a high calculated TAV were used in 26 individual toxicity QSAR models. As a result of this screening protocol, 288 nontoxic molecules with high predicted TAV were identified. These selected hits were then screened against the BCL-2 target protein using hybrid docking and molecular dynamics (MD) simulations. The interaction energies of identified compounds were compared with two known BCL-2 inhibitors. Then, the short MD simulations were carried out by initiating the best docking poses of 288 molecules. Average MM/GBSA energies were computed, and long MD simulations were employed to selected hits. The same calculations were also applied for two known BCL-2 inhibitors. Moreover, a five-site (AHRRR) structure-based pharmacophore model was constructed, and this model was used in the screening of the same database. On the basis of hybrid data-driven ligand identification study, final hits were selected and used in in vitro studies. Based on results of the time-resolved fluorescence resonance energy transfer (TR-FRET) analysis, further filtration was carried out for the U87-MG cell line tests. MTT cell proliferation assay analysis results showed that selected three potent compounds were significantly effective on glioma cells.
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Affiliation(s)
- Kader Sahin
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul 34353, Turkey
| | - Muge Didem Orhan
- Neuroscience Program, Health Sciences Institute, Bahcesehir University, Istanbul 34353, Turkey.,Neuroscience Laboratory, Health Sciences Institute, Bahcesehir University, Istanbul 34353, Turkey
| | - Timucin Avsar
- Neuroscience Program, Health Sciences Institute, Bahcesehir University, Istanbul 34353, Turkey.,Neuroscience Laboratory, Health Sciences Institute, Bahcesehir University, Istanbul 34353, Turkey.,Department of Medical Biology, School of Medicine, Bahcesehir University, Istanbul 34353, Turkey
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul 34353, Turkey.,Neuroscience Program, Health Sciences Institute, Bahcesehir University, Istanbul 34353, Turkey.,Neuroscience Laboratory, Health Sciences Institute, Bahcesehir University, Istanbul 34353, Turkey.,Virtual Drug Screening and Development Laboratory, School of Medicine, Bahcesehir University, Istanbul 34353, Turkey
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Şahİn K, DurdaĞi S. Combined ligand and structure-based virtual screening approaches for identification of novel AChE inhibitors. Turk J Chem 2020; 44:574-588. [PMID: 33488178 PMCID: PMC7671205 DOI: 10.3906/kim-1911-57] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/03/2020] [Indexed: 11/26/2022] Open
Abstract
The excessive activity of acetylcholinesterase enzyme (AChE) causes different neuronal problems, especially dementia and neuronal cell deaths. Food and Drug Administration (FDA) approved drugs donepezil, rivastigmine, tacrine and galantamine are AChE inhibitors and in the treatment of Alzheimer’s disease (AD) these drugs are currently prescribed. However, these inhibitors have various adverse side effects. Therefore, there is a great need for the novel selective AChE inhibitors with fewer adverse side effects for the effective treatment. In this study, combined ligand-based and structure-based virtual screening approaches were used to identify new hit compounds from small molecules library of National Cancer Institute (NCI) containing approximately 265,000 small molecules. In the present study, we developed a computational pipeline method to predict the binding affinities of the studied compounds at the specific target sites. For this purpose, a text mining study was carried out initially and compounds containing the keyword “indol” were considered. The therapeutic activity values against AD were screened using the binary quantitative structure activity relationship (QSAR) models. We then performed docking, molecular dynamics (MD) simulations and free energy analysis to clarify the interactions between selected ligands and enzyme. Thus, in this study we identified new promising hit compounds from a large database that may be used to inhibit the enzyme activity of AChE.
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Affiliation(s)
- Kader Şahİn
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahçeşehir University, Istanbul Turkey
| | - Serdar DurdaĞi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahçeşehir University, Istanbul Turkey
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Sahin K, Zengin Kurt B, Sonmez F, Durdagi S. Novel AChE and BChE inhibitors using combined virtual screening, text mining and in vitro binding assays. J Biomol Struct Dyn 2019; 38:3342-3358. [PMID: 31462153 DOI: 10.1080/07391102.2019.1660218] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In the current work, we developed a computational pipeline method for predicting the binding affinities of studied compounds at the specific target sites. Since many approved therapeutic compounds involve indole or indole-derivative rings, in the current study we focused compounds including these fingerprints. Initially, 212520 compounds were retrieved from Specs-SC library and after the conversion of IUPAC text file format, compounds that include 'indol' keyword (5194 compounds) were used in binary QSAR-based models to screen against a defined therapeutic activity "Alzheimer's disease" (AD). The molecules that have higher AD therapeutic activity values (>0.5) were then used in the 26 different toxicity-QSAR models. Binary QSAR models resulted 89 hits that have high AD therapeutic activity and no toxicity. Selected 89 molecules were then screened against acetylcholinesterase (AChE) targets using molecular docking and top-docking poses of compounds were used in initially short (10 ns) molecular dynamics (MD) simulations. Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) binding free energy calculations were performed for 89 ligands and tightly bound 17 ligands based on average MM/GBSA scores were selected for long (100 ns) MD simulations. The same protocol was also applied for the known 4 AChE inhibitors. Selected hits were also docked to the binding pocket of butyrylcholinesterase (BChE). Finally, based on MM/GBSA scores, as well as their corresponding docking scores and metabolite production profiles, 7 compounds were selected and their in vitro tests were performed. Out of 7 compounds, 6 of them showed μM-level inhibition for both AChE and BChE targets.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kader Sahin
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Belma Zengin Kurt
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Bezmialem Vakif University, Istanbul, Turkey
| | - Fatih Sonmez
- Pamukova Vocational High School, Sakarya University of Applied Sciences, Sakarya, Turkey
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
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Wong AG, Raleigh DP. The dye SYPRO orange binds to amylin amyloid fibrils but not pre-fibrillar intermediates. Protein Sci 2016; 25:1834-40. [PMID: 27479186 DOI: 10.1002/pro.2992] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 07/27/2016] [Indexed: 01/11/2023]
Abstract
Amyloid deposition underlies a broad range of diseases including multiple neurodegenerative diseases, systemic amyloidosis and type-2 diabetes. Amyloid sensitive dyes, particularly thioflavin-T, are widely used to detect ex-vivo amyloid deposits, to monitor amyloid formation in vitro and to follow the kinetics of amyloid self-assembly. We show that the dye SYPRO-orange binds to amyloid fibrils formed by human amylin, the polypeptide responsible for islet amyloid formation in type-2 diabetes. No fluorescence enhancement is observed in the presence of pre-fibrillar species or in the presence of non-amyloidogenic rat amylin. The kinetics of human amylin amyloid formation can be monitored by SYPRO-orange fluorescence and match the time course determined with thioflavin-T assays. Thus, SYPRO-orange offers an alternative to thioflavin-T assays of amylin amyloid formation. The implications for the interpretation of SYPRO-orange-based assays of protein stability and protein-ligand interactions are discussed.
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Affiliation(s)
- Amy G Wong
- Department of Chemistry, Stony Brook University, Stony Brook, New York, 11794-3400
| | - Daniel P Raleigh
- Department of Chemistry, Stony Brook University, Stony Brook, New York, 11794-3400. .,Graduate Program in Biochemistry and Structural Biology, Stony Brook University, Stony Brook, New York, 11794.
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