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Duan M, Lv C, Zang J, Leng X, Zhao G, Zhang T. Metals at the Helm: Revolutionizing Protein Assembly and Applications. Macromol Biosci 2024:e2400126. [PMID: 39239781 DOI: 10.1002/mabi.202400126] [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: 03/20/2024] [Revised: 05/23/2024] [Indexed: 09/07/2024]
Abstract
Protein assembly is an essential process in biological systems, where proteins self-assemble into complex structures with diverse functions. Inspired by the exquisite control over protein assembly in nature, scientists have been exploring ways to design and assemble protein structures with precise control over their topologies and functions. One promising approach for achieving this goal is through metal coordination, which utilizes metal-binding motifs to mediate protein-protein interactions and assemble protein complexes with controlled stoichiometry and geometry. Metal coordination provides a modular and tunable approach for protein assembly and de novo structure design, where the metal ion acts as a molecular glue that holds the protein subunits together in a specific orientation. Metal-coordinated protein assemblies have shown great potential for developing functional metalloproteinase, novel biomaterials and integrated drug delivery systems. In this review, an overview of the recent advances in protein assemblies benefited from metal coordination is provided, focusing on various protein arrangements in different dimensions including protein oligomers, protein nanocage and higher-order protein architectures. Moreover, the key metal-binding motifs and strategies used to assemble protein structures with precise control over their properties are highlighted. The potential applications of metal-mediated protein assemblies in biotechnology and biomedicine are also discussed.
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Affiliation(s)
- Maoping Duan
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Chenyan Lv
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Jiachen Zang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Xiaojing Leng
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Guanghua Zhao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Tuo Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
- Center of Food Colloids and Delivery for Functionality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
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2
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Voltà-Durán E, Alba-Castellón L, Serna N, Casanova I, López-Laguna H, Gallardo A, Sánchez-Chardi A, Villaverde A, Unzueta U, Vázquez E, Mangues R. High-precision targeting and destruction of cancer-associated PDGFR-β + stromal fibroblasts through self-assembling, protein-only nanoparticles. Acta Biomater 2023; 170:543-555. [PMID: 37683965 DOI: 10.1016/j.actbio.2023.09.001] [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: 05/25/2023] [Revised: 08/30/2023] [Accepted: 09/01/2023] [Indexed: 09/10/2023]
Abstract
The need for more effective and precision medicines for cancer has pushed the exploration of new materials appropriate for drug delivery and imaging, and alternative receptors for targeting. Among the most promising strategies, finding suitable cell surface receptors and targeting agents for cancer-associated platelet derived growth factor receptor β (PDGFR-β)+ stromal fibroblasts is highly appealing. As a neglected target, this cell type mechanically and biologically supports the growth, progression, and infiltration of solid tumors in non-small cell lung, breast, pancreatic, and colorectal cancers. We have developed a family of PDGFR-β-targeted nanoparticles based on biofabricated, self-assembling proteins, upon hierarchical and iterative selective processes starting from four initial candidates. The modular protein PDGFD-GFP-H6 is well produced in recombinant bacteria, resulting in structurally robust oligomeric particles that selectively penetrates into PDGFR-β+ stromal fibroblasts in a dose-dependent manner, by means of the PDGFR-β ligand PDGFD. Upon in vivo administration, these GFP-carrying protein nanoparticles precisely accumulate in tumor tissues and enlighten them for IVIS observation. When GFP is replaced by a microbial toxin, selective tumor tissue destruction is observed associated with a significant reduction in tumor volume growth. The presented data validate the PDGFR-β/PDGFD pair as a promising toolbox for targeted drug delivery in the tumor microenvironment and oligomeric protein nanoparticles as a powerful instrument to mediate highly selective biosafe targeting in cancer through non-cancer cells. STATEMENT OF SIGNIFICANCE: We have developed a transversal platform for nanoparticle-based drug delivery into cancer-associated fibroblasts. This is based on the engineered modular protein PDGFD-GFP-H6 that spontaneously self-assemble and selectively penetrates into PDGFR-β+ stromal fibroblasts in a dose-dependent manner, by means of the PDGFR-β ligand PDGFD. In vivo, these protein nanoparticles accumulate in tumor and when incorporating a microbial toxin, they destroy tumor tissues with a significant reduction in tumor volume, in absence of side toxicities. The data presented here validate the PDGFR-β/PDGFD pair as a fully versatile toolbox for targeted drug delivery in the tumor microenvironment intended as a synergistic treatment.
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Affiliation(s)
- Eric Voltà-Durán
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Spain
| | - Lorena Alba-Castellón
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Spain; Biomedical Research Institute Sant Pau (IIB Sant Pau), Barcelona 08041, Spain; Josep Carreras Leukaemia Research Institute, Barcelona 08025, Spain.
| | - Naroa Serna
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Spain
| | - Isolda Casanova
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Spain; Biomedical Research Institute Sant Pau (IIB Sant Pau), Barcelona 08041, Spain; Josep Carreras Leukaemia Research Institute, Barcelona 08025, Spain
| | - Hèctor López-Laguna
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Spain
| | - Alberto Gallardo
- Biomedical Research Institute Sant Pau (IIB Sant Pau), Barcelona 08041, Spain; Department of Pathology, Hospital de la Santa Creu i Sant Pau, Barcelona 08025, Spain
| | - Alejandro Sánchez-Chardi
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal 643, Barcelona 08028, Spain
| | - Antonio Villaverde
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Spain.
| | - Ugutz Unzueta
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Spain; Biomedical Research Institute Sant Pau (IIB Sant Pau), Barcelona 08041, Spain; Josep Carreras Leukaemia Research Institute, Barcelona 08025, Spain
| | - Esther Vázquez
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Spain
| | - Ramón Mangues
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Spain; Biomedical Research Institute Sant Pau (IIB Sant Pau), Barcelona 08041, Spain; Josep Carreras Leukaemia Research Institute, Barcelona 08025, Spain.
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Mikhaylina A, Lekontseva N, Marchenkov V, Kolesnikova V, Khairetdinova A, Nikonov O, Balobanov V. The New Functional Hybrid Chaperone Protein ADGroEL-SacSm. Molecules 2023; 28:6196. [PMID: 37687025 PMCID: PMC10488932 DOI: 10.3390/molecules28176196] [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: 07/14/2023] [Revised: 08/20/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023] Open
Abstract
The creation of new proteins by combining natural domains is a commonly used technique in protein engineering. In this work, we have tested the possibilities and limitations of using circular homo-oligomeric Sm-like proteins as a basis for attaching other domains. Attachment to such a stable base should bring target domains together and keep them in the correct mutual orientation. We chose a circular homoheptameric Sm-like protein from Sulfolobus acidocaldarius as a stable backbone and the apical domain of the GroEL chaperone protein as the domain of study. This domain by itself, separated from the rest of the GroEL molecule, does not form an oligomeric ring. In our design, the hyperstable SacSm held the seven ADGroELs together and forced them to oligomerize. The designed hybrid protein was obtained and studied with various physical and chemical methods. Stepwise assembly and self-organization of this protein have been shown. First, the SacSm base was assembled, and then ADGroEL was folded on it. Functional testing showed that the obtained fusion protein was able to bind the same non-native proteins as the full-length GroEL chaperone. It also reduced the aggregation of a number of proteins when they were heated, which confirms its chaperone activity. Thus, the engineering path we chose made it possible to create an efficient thermostable chaperone. The result obtained shows the productivity of the way we chose for the creation and stabilization of oligomeric proteins.
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Affiliation(s)
| | | | | | | | | | | | - Vitalii Balobanov
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya Str. 4, 142290 Pushchino, Russia
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Martínez-Torró C, Alba-Castellón L, Carrasco-Díaz LM, Serna N, Imedio L, Gallardo A, Casanova I, Unzueta U, Vázquez E, Mangues R, Villaverde A. Lymphocyte infiltration and antitumoral effect promoted by cytotoxic inflammatory proteins formulated as self-assembling, protein-only nanoparticles. Biomed Pharmacother 2023; 164:114976. [PMID: 37276641 DOI: 10.1016/j.biopha.2023.114976] [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: 04/04/2023] [Revised: 05/24/2023] [Accepted: 05/30/2023] [Indexed: 06/07/2023] Open
Abstract
Two human proteins involved in the inflammatory cell death, namely Gasdermin D (GSDMD) and the Mixed Lineage Kinase Domain-Like (MLKL) protein have been engineered to accommodate an efficient ligand of the tumoral cell marker CXCR4, and a set of additional peptide agents that allow their spontaneous self-assembling. Upon production in bacterial cells and further purification, both proteins organized as stable nanoparticles of 46 and 54 nm respectively, that show, in this form, a moderate but dose-dependent cytotoxicity in cell culture. In vivo, and when administered in mouse models of colorectal cancer through repeated doses, the nanoscale forms of tumor-targeted GSDMD and, at a lesser extent, of MLKL promoted CD8+ and CD20+ lymphocyte infiltration in the tumor and an important reduction of tumor size, in absence of systemic toxicity. The potential of these novel pharmacological agents as anticancer drugs is discussed in the context of synergistic approaches to more effective cancer treatments.
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Affiliation(s)
- Carlos Martínez-Torró
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Lorena Alba-Castellón
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Institut d'Investigació Biomèdica Sant Pau (IIB SANT PAU), Barcelona, Spain; Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
| | - Luis Miguel Carrasco-Díaz
- Institut d'Investigació Biomèdica Sant Pau (IIB SANT PAU), Barcelona, Spain; Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
| | - Naroa Serna
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Laura Imedio
- Institut d'Investigació Biomèdica Sant Pau (IIB SANT PAU), Barcelona, Spain; Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
| | - Alberto Gallardo
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Department of Pathology, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Isolda Casanova
- Institut d'Investigació Biomèdica Sant Pau (IIB SANT PAU), Barcelona, Spain; Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
| | - Ugutz Unzueta
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Institut d'Investigació Biomèdica Sant Pau (IIB SANT PAU), Barcelona, Spain; Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
| | - Esther Vázquez
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Ramón Mangues
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Institut d'Investigació Biomèdica Sant Pau (IIB SANT PAU), Barcelona, Spain; Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain.
| | - Antonio Villaverde
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
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Becchi M, Capelli R, Perego C, Pavan GM, Micheletti C. Density-tunable pathway complexity in a minimalistic self-assembly model. SOFT MATTER 2022; 18:8106-8116. [PMID: 36239129 DOI: 10.1039/d2sm00968d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
An open challenge in self-assembly is learning how to design systems that can be conditionally guided towards different target structures depending on externally-controlled conditions. Using a theoretical and numerical approach, here we discuss a minimalistic self-assembly model that can be steered towards different types of ordered constructs at the equilibrium by solely tuning a facile selection parameter, namely the density of building blocks. Metadynamics and Langevin dynamics simulations allow us to explore the behavior of the system in and out of equilibrium conditions. We show that the density-driven tunability is encoded in the pathway complexity of the system, and specifically in the competition between two different main self-assembly routes. A comprehensive set of simulations provides insight into key factors allowing to make one self-assembling pathway prevailing on the other (or vice versa), determining the selection of the final self-assembled products. We formulate and validate a practical criterion for checking whether a specific molecular design is predisposed for such density-driven tunability of the products, thus offering a new, broader perspective to realize and harness this facile extrinsic control of conditional self-assembly.
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Affiliation(s)
- Matteo Becchi
- Scuola Internazionale Superiore di Studi Avanzati - SISSA, via Bonomea 265, 34136 Trieste, Italy.
| | - Riccardo Capelli
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy.
- Department of Biosciences, Università degli Studi di Milano, Via Giovanni Celoria 26, 20133 Milano, Italy
| | - Claudio Perego
- Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland, Polo Universitario Lugano, Campus Est, Via la Santa 1, 6962 Lugano-Viganello, Switzerland
| | - Giovanni M Pavan
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy.
- Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland, Polo Universitario Lugano, Campus Est, Via la Santa 1, 6962 Lugano-Viganello, Switzerland
| | - Cristian Micheletti
- Scuola Internazionale Superiore di Studi Avanzati - SISSA, via Bonomea 265, 34136 Trieste, Italy.
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de Pinho Favaro MT, Atienza-Garriga J, Martínez-Torró C, Parladé E, Vázquez E, Corchero JL, Ferrer-Miralles N, Villaverde A. Recombinant vaccines in 2022: a perspective from the cell factory. Microb Cell Fact 2022; 21:203. [PMID: 36199085 PMCID: PMC9532831 DOI: 10.1186/s12934-022-01929-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/30/2022] [Indexed: 12/02/2022] Open
Abstract
The last big outbreaks of Ebola fever in Africa, the thousands of avian influenza outbreaks across Europe, Asia, North America and Africa, the emergence of monkeypox virus in Europe and specially the COVID-19 pandemics have globally stressed the need for efficient, cost-effective vaccines against infectious diseases. Ideally, they should be based on transversal technologies of wide applicability. In this context, and pushed by the above-mentioned epidemiological needs, new and highly sophisticated DNA-or RNA-based vaccination strategies have been recently developed and applied at large-scale. Being very promising and effective, they still need to be assessed regarding the level of conferred long-term protection. Despite these fast-developing approaches, subunit vaccines, based on recombinant proteins obtained by conventional genetic engineering, still show a wide spectrum of interesting potentialities and an important margin for further development. In the 80's, the first vaccination attempts with recombinant vaccines consisted in single structural proteins from viral pathogens, administered as soluble plain versions. In contrast, more complex formulations of recombinant antigens with particular geometries are progressively generated and explored in an attempt to mimic the multifaceted set of stimuli offered to the immune system by replicating pathogens. The diversity of recombinant antimicrobial vaccines and vaccine prototypes is revised here considering the cell factory types, through relevant examples of prototypes under development as well as already approved products.
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Affiliation(s)
- Marianna Teixeira de Pinho Favaro
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, 08193, Barcelona, Spain
- Laboratory of Vaccine Development, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Jan Atienza-Garriga
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, 08193, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Cerdanyola del Vallès, 08193, Barcelona, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, 08193, Barcelona, Spain
| | - Carlos Martínez-Torró
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, 08193, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Cerdanyola del Vallès, 08193, Barcelona, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, 08193, Barcelona, Spain
| | - Eloi Parladé
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, 08193, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Cerdanyola del Vallès, 08193, Barcelona, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, 08193, Barcelona, Spain
| | - Esther Vázquez
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, 08193, Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Cerdanyola del Vallès, 08193, Barcelona, Spain.
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, 08193, Barcelona, Spain.
| | - José Luis Corchero
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, 08193, Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Cerdanyola del Vallès, 08193, Barcelona, Spain.
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, 08193, Barcelona, Spain.
| | - Neus Ferrer-Miralles
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, 08193, Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Cerdanyola del Vallès, 08193, Barcelona, Spain.
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, 08193, Barcelona, Spain.
| | - Antonio Villaverde
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, 08193, Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Cerdanyola del Vallès, 08193, Barcelona, Spain.
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, 08193, Barcelona, Spain.
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7
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Cano-Garrido O, Serna N, Unzueta U, Parladé E, Mangues R, Villaverde A, Vázquez E. Protein scaffolds in human clinics. Biotechnol Adv 2022; 61:108032. [PMID: 36089254 DOI: 10.1016/j.biotechadv.2022.108032] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 07/30/2022] [Accepted: 09/03/2022] [Indexed: 11/02/2022]
Abstract
Fundamental clinical areas such as drug delivery and regenerative medicine require biocompatible materials as mechanically stable scaffolds or as nanoscale drug carriers. Among the wide set of emerging biomaterials, polypeptides offer enticing properties over alternative polymers, including full biocompatibility, biodegradability, precise interactivity, structural stability and conformational and functional versatility, all of them tunable by conventional protein engineering. However, proteins from non-human sources elicit immunotoxicities that might bottleneck further development and narrow their clinical applicability. In this context, selecting human proteins or developing humanized protein versions as building blocks is a strict demand to design non-immunogenic protein materials. We review here the expanding catalogue of human or humanized proteins tailored to execute different levels of scaffolding functions and how they can be engineered as self-assembling materials in form of oligomers, polymers or complex networks. In particular, we emphasize those that are under clinical development, revising their fields of applicability and how they have been adapted to offer, apart from mere mechanical support, highly refined functions and precise molecular interactions.
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Affiliation(s)
- Olivia Cano-Garrido
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès (Barcelona), Spain
| | - Naroa Serna
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès (Barcelona), Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Instituto de Salud Carlos III, 08193 Cerdanyola del Vallès (Barcelona), Spain
| | - Ugutz Unzueta
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Instituto de Salud Carlos III, 08193 Cerdanyola del Vallès (Barcelona), Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès (Barcelona), Spain; Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025 Barcelona, Spain; Josep Carreras Leukaemia Research Institute, 08916 Badalona (Barcelona), Spain
| | - Eloi Parladé
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès (Barcelona), Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Instituto de Salud Carlos III, 08193 Cerdanyola del Vallès (Barcelona), Spain
| | - Ramón Mangues
- Biomedical Research Institute Sant Pau (IIB Sant Pau), 08025 Barcelona, Spain; Josep Carreras Leukaemia Research Institute, 08916 Badalona (Barcelona), Spain
| | - Antonio Villaverde
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès (Barcelona), Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Instituto de Salud Carlos III, 08193 Cerdanyola del Vallès (Barcelona), Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès (Barcelona), Spain.
| | - Esther Vázquez
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès (Barcelona), Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Instituto de Salud Carlos III, 08193 Cerdanyola del Vallès (Barcelona), Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès (Barcelona), Spain.
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8
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Self-Assembling Lectin Nano-Block Oligomers Enhance Binding Avidity to Glycans. Int J Mol Sci 2022; 23:ijms23020676. [PMID: 35054861 PMCID: PMC8775495 DOI: 10.3390/ijms23020676] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 12/29/2021] [Accepted: 12/31/2021] [Indexed: 02/01/2023] Open
Abstract
Lectins, carbohydrate-binding proteins, are attractive biomolecules for medical and biotechnological applications. Many lectins have multiple carbohydrate recognition domains (CRDs) and strongly bind to specific glycans through multivalent binding effect. In our previous study, protein nano-building blocks (PN-blocks) were developed to construct self-assembling supramolecular nanostructures by linking two oligomeric proteins. A PN-block, WA20-foldon, constructed by fusing a dimeric four-helix bundle de novo protein WA20 to a trimeric foldon domain of T4 phage fibritin, self-assembled into several types of polyhedral nanoarchitectures in multiples of 6-mer. Another PN-block, the extender PN-block (ePN-block), constructed by tandemly joining two copies of WA20, self-assembled into cyclized and extended chain-type nanostructures. This study developed novel functional protein nano-building blocks (lectin nano-blocks) by fusing WA20 to a dimeric lectin, Agrocybe cylindracea galectin (ACG). The lectin nano-blocks self-assembled into various oligomers in multiples of 2-mer (dimer, tetramer, hexamer, octamer, etc.). The mass fractions of each oligomer were changed by the length of the linkers between WA20 and ACG. The binding avidity of the lectin nano-block oligomers to glycans was significantly increased through multivalent effects compared with that of the original ACG dimer. Lectin nano-blocks with high avidity will be useful for various applications, such as specific cell labeling.
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Artificial protein assemblies with well-defined supramolecular protein nanostructures. Biochem Soc Trans 2021; 49:2821-2830. [PMID: 34812854 DOI: 10.1042/bst20210808] [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: 10/08/2021] [Revised: 10/28/2021] [Accepted: 11/02/2021] [Indexed: 12/13/2022]
Abstract
Nature uses a wide range of well-defined biomolecular assemblies in diverse cellular processes, where proteins are major building blocks for these supramolecular assemblies. Inspired by their natural counterparts, artificial protein-based assemblies have attracted strong interest as new bio-nanostructures, and strategies to construct ordered protein assemblies have been rapidly expanding. In this review, we provide an overview of very recent studies in the field of artificial protein assemblies, with the particular aim of introducing major assembly methods and unique features of these assemblies. Computational de novo designs were used to build various assemblies with artificial protein building blocks, which are unrelated to natural proteins. Small chemical ligands and metal ions have also been extensively used for strong and bio-orthogonal protein linking. Here, in addition to protein assemblies with well-defined sizes, protein oligomeric and array structures with rather undefined sizes (but with definite repeat protein assembly units) also will be discussed in the context of well-defined protein nanostructures. Lastly, we will introduce multiple examples showing how protein assemblies can be effectively used in various fields such as therapeutics and vaccine development. We believe that structures and functions of artificial protein assemblies will be continuously evolved, particularly according to specific application goals.
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Zhu J, Avakyan N, Kakkis AA, Hoffnagle AM, Han K, Li Y, Zhang Z, Choi TS, Na Y, Yu CJ, Tezcan FA. Protein Assembly by Design. Chem Rev 2021; 121:13701-13796. [PMID: 34405992 PMCID: PMC9148388 DOI: 10.1021/acs.chemrev.1c00308] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteins are nature's primary building blocks for the construction of sophisticated molecular machines and dynamic materials, ranging from protein complexes such as photosystem II and nitrogenase that drive biogeochemical cycles to cytoskeletal assemblies and muscle fibers for motion. Such natural systems have inspired extensive efforts in the rational design of artificial protein assemblies in the last two decades. As molecular building blocks, proteins are highly complex, in terms of both their three-dimensional structures and chemical compositions. To enable control over the self-assembly of such complex molecules, scientists have devised many creative strategies by combining tools and principles of experimental and computational biophysics, supramolecular chemistry, inorganic chemistry, materials science, and polymer chemistry, among others. Owing to these innovative strategies, what started as a purely structure-building exercise two decades ago has, in short order, led to artificial protein assemblies with unprecedented structures and functions and protein-based materials with unusual properties. Our goal in this review is to give an overview of this exciting and highly interdisciplinary area of research, first outlining the design strategies and tools that have been devised for controlling protein self-assembly, then describing the diverse structures of artificial protein assemblies, and finally highlighting the emergent properties and functions of these assemblies.
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Affiliation(s)
| | | | - Albert A. Kakkis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Alexander M. Hoffnagle
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Kenneth Han
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Yiying Li
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Zhiyin Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Tae Su Choi
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Youjeong Na
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Chung-Jui Yu
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
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Pujari I, Sengupta R, Babu VS. Docking and ADMET studies for investigating the anticancer potency of Moscatilin on APC10/DOC1 and PKM2 against five clinical drugs. J Genet Eng Biotechnol 2021; 19:161. [PMID: 34665359 PMCID: PMC8526629 DOI: 10.1186/s43141-021-00256-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 09/26/2021] [Indexed: 12/17/2022]
Abstract
BACKGROUND Moscatilin is a bibenzyl derivative (stilbenoid), mainly found in Dendrobium species. This plant-derived chemical is a potential cytotoxic anticancer drug that acts against different cancer types. The present study compared the structural interactions of Moscatilin along with five clinically relevant drugs against two target proteins, viz., Anaphase-Promoting Complex subunit 10/Death of Cyclase 1 and Pyruvate Kinase Muscle isozyme M2 in silico. Out of five clinical ligands, four were plant-derived compounds, viz., Resveratrol, Paclitaxel, Shikonin, and Colchicine. The synthetic chemotherapeutic agent, Mitomycin-C, was used as a ligand to compare the mechanistic insights. The objective of the study was to determine the anticancer potency of Moscatilin in silico. RESULTS Moscatilin was found to have an advantage over other drugs of interest due to its structural simplicity and folding bridge connecting the bibenzyl structures. Moscatilin exhibited dual function by exclusively affecting the cancer cells, creating instabilities in biochemical and molecular cascades. CONCLUSIONS The study demonstrates that Moscatilin is has a multi-antimetastatic function. Moscatilin interaction with APC10/DOC1 indicated that the drug is involved with post-replicative inhibition, and with PKM2 showed glycolytic pathway inhibition in cancer cells. Moscatilin can function as an effective cell cycle inhibitor.
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Affiliation(s)
- Ipsita Pujari
- Department of Plant Sciences, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Udupi, Karnataka, 576104, India
| | - Ritobrata Sengupta
- Department of Plant Sciences, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Udupi, Karnataka, 576104, India
| | - Vidhu Sankar Babu
- Department of Plant Sciences, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Udupi, Karnataka, 576104, India.
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Kumar G, Sinha S. Biophysical approaches to understand and re-purpose bacterial microcompartments. Curr Opin Microbiol 2021; 63:43-51. [PMID: 34166983 DOI: 10.1016/j.mib.2021.05.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 04/15/2021] [Accepted: 05/17/2021] [Indexed: 11/30/2022]
Abstract
Bacterial microcompartments represent a modular class of prokaryotic organelles associated with metabolic processes. They harbor a congregation of enzymes that work in cascade within a small, confined volume. These sophisticated nano-engineered crafts of nature offer a tempting paradigm for the fabrication of biosynthetic nanoreactors. Repurposing bacterial microcompartments to develop nanostructures with desired functions requires a careful manipulation in their structural makeup and composition. This calls for a comprehensive understanding of all the interactions of the physical components which frame such molecular architectures. Over recent years, several biophysical techniques have been essential in illuminating the role played by bacterial microcompartments within cells, and have revealed crucial details regarding the morphology, physical properties and functions of their constituent proteins. This has promoted contemplation of ideas for engineering microcompartments inspired biomaterials with novel features and functions.
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Affiliation(s)
- Gaurav Kumar
- Chemical Biology Unit, Institute of Nano Science and Technology, Sector-81, Mohali (SAS Nagar), Knowledge City, Punjab 140306, India
| | - Sharmistha Sinha
- Chemical Biology Unit, Institute of Nano Science and Technology, Sector-81, Mohali (SAS Nagar), Knowledge City, Punjab 140306, India.
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Serna N, Carratalá JV, Parladé E, Sánchez-Chardi A, Aviñó A, Unzueta U, Mangues R, Eritja R, Ferrer-Miralles N, Vazquez E, Villaverde A. Developing Protein-Antitumoral Drug Nanoconjugates as Bifunctional Antimicrobial Agents. ACS APPLIED MATERIALS & INTERFACES 2020; 12:57746-57756. [PMID: 33325705 DOI: 10.1021/acsami.0c18317] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
A novel concept about bifunctional antimicrobial drugs, based on self-assembling protein nanoparticles, has been evaluated here over two biofilm-forming pathogens, namely Pseudomonas aeruginosa and Staphylococcus aureus. Two structurally different antimicrobial peptides (GWH1 and PaDBS1R1) were engineered to form regular nanoparticles of around 35 nm, to which the small molecular weight drug Floxuridine was covalently conjugated. Both the assembled peptides and the chemical, a conventional cytotoxic drug used in oncotherapy, showed potent antimicrobial activities that were enhanced by the combination of both molecules in single pharmacological entities. Therefore, the resulting prototypes show promises as innovative nanomedicines, being potential alternatives to conventional antibiotics. The biological performance and easy fabrication of these materials fully support the design of protein-based hybrid constructs for combined molecular therapies, expected to have broad applicability beyond antimicrobial medicines. In addition, the approach taken here validates the functional exploration and repurposing of antitumoral drugs, which at low concentrations perform well as unexpected biofilm-inhibiting agents.
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Affiliation(s)
- Naroa Serna
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, 28029 Madrid, Spain
| | - Jose Vicente Carratalá
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, 28029 Madrid, Spain
| | - Eloi Parladé
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, 28029 Madrid, Spain
| | - Alejandro Sánchez-Chardi
- Servei de Microscòpia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain
| | - Anna Aviñó
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, 28029 Madrid, Spain
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, 08034 Barcelona, Spain
| | - Ugutz Unzueta
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, 28029 Madrid, Spain
- Biomedical Research Institute Sant Pau (IIB Sant Pau), Sant Antoni Maria Claret 167, 08025 Barcelona, Spain
| | - Ramón Mangues
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, 28029 Madrid, Spain
- Biomedical Research Institute Sant Pau (IIB Sant Pau), Sant Antoni Maria Claret 167, 08025 Barcelona, Spain
| | - Ramón Eritja
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, 28029 Madrid, Spain
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, 08034 Barcelona, Spain
| | - Neus Ferrer-Miralles
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, 28029 Madrid, Spain
| | - Esther Vazquez
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, 28029 Madrid, Spain
| | - Antonio Villaverde
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), C/Monforte de Lemos 3-5, 28029 Madrid, Spain
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