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Giugliano G, Gajo M, Marforio TD, Zerbetto F, Mattioli EJ, Calvaresi M. Identification of Potential Drug Targets of Calix[4]arene by Reverse Docking. Chemistry 2024:e202400871. [PMID: 38777795 DOI: 10.1002/chem.202400871] [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: 03/01/2024] [Revised: 05/20/2024] [Accepted: 05/22/2024] [Indexed: 05/25/2024]
Abstract
Calixarenes are displaying great potential for the development of new drug delivery systems, diagnostic imaging, biosensing devices and inhibitors of biological processes. In particular, calixarene derivatives are able to interact with many different enzymes and function as inhibitors. By screening of the potential drug target database (PDTD) with a reverse docking procedure, we identify and discuss a selection of 100 proteins that interact strongly with calix[4]arene. We also discover that leucine (23.5 %), isoleucine (11.3 %), phenylalanines (11.3 %) and valine (9.5 %) are the most frequent binding residues followed by hydrophobic cysteines and methionines and aromatic histidines, tyrosines and tryptophanes. Top binders are peroxisome proliferator-activated receptors that already are targeted by commercial drugs, demonstrating the practical interest in calix[4]arene. Nuclear receptors, potassium channel, several carrier proteins, a variety of cancer-related proteins and viral proteins are prominent in the list. It is concluded that calix[4]arene, which is characterized by facile access, well-defined conformational characteristics, and ease of functionalization at both the lower and higher rims, could be a potential lead compound for the development of enzyme inhibitors and theranostic platforms.
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Affiliation(s)
- Giulia Giugliano
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 2, 40126, Bologna, Italy E-Mail
| | - Margherita Gajo
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 2, 40126, Bologna, Italy E-Mail
| | - Tainah Dorina Marforio
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 2, 40126, Bologna, Italy E-Mail
| | - Francesco Zerbetto
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 2, 40126, Bologna, Italy E-Mail
| | - Edoardo Jun Mattioli
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 2, 40126, Bologna, Italy E-Mail
| | - Matteo Calvaresi
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 2, 40126, Bologna, Italy E-Mail
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Rogoża NH, Krupa MA, Krupa P, Sieradzan AK. Integrating Explicit and Implicit Fullerene Models into UNRES Force Field for Protein Interaction Studies. Molecules 2024; 29:1919. [PMID: 38731411 PMCID: PMC11085604 DOI: 10.3390/molecules29091919] [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: 03/26/2024] [Revised: 04/16/2024] [Accepted: 04/19/2024] [Indexed: 05/13/2024] Open
Abstract
Fullerenes, particularly C60, exhibit unique properties that make them promising candidates for various applications, including drug delivery and nanomedicine. However, their interactions with biomolecules, especially proteins, remain not fully understood. This study implements both explicit and implicit C60 models into the UNRES coarse-grained force field, enabling the investigation of fullerene-protein interactions without the need for restraints to stabilize protein structures. The UNRES force field offers computational efficiency, allowing for longer timescale simulations while maintaining accuracy. Five model proteins were studied: FK506 binding protein, HIV-1 protease, intestinal fatty acid binding protein, PCB-binding protein, and hen egg-white lysozyme. Molecular dynamics simulations were performed with and without C60 to assess protein stability and investigate the impact of fullerene interactions. Analysis of contact probabilities reveals distinct interaction patterns for each protein. FK506 binding protein (1FKF) shows specific binding sites, while intestinal fatty acid binding protein (1ICN) and uteroglobin (1UTR) exhibit more generalized interactions. The explicit C60 model shows good agreement with all-atom simulations in predicting protein flexibility, the position of C60 in the binding pocket, and the estimation of effective binding energies. The integration of explicit and implicit C60 models into the UNRES force field, coupled with recent advances in coarse-grained modeling and multiscale approaches, provides a powerful framework for investigating protein-nanoparticle interactions at biologically relevant scales without the need to use restraints stabilizing the protein, thus allowing for large conformational changes to occur. These computational tools, in synergy with experimental techniques, can aid in understanding the mechanisms and consequences of nanoparticle-biomolecule interactions, guiding the design of nanomaterials for biomedical applications.
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Affiliation(s)
- Natalia H. Rogoża
- Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities in Gdańsk, Bażyńskiego 8, 80-309 Gdańsk, Poland; (N.H.R.); (M.A.K.); (A.K.S.)
| | - Magdalena A. Krupa
- Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities in Gdańsk, Bażyńskiego 8, 80-309 Gdańsk, Poland; (N.H.R.); (M.A.K.); (A.K.S.)
| | - Pawel Krupa
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Adam K. Sieradzan
- Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities in Gdańsk, Bażyńskiego 8, 80-309 Gdańsk, Poland; (N.H.R.); (M.A.K.); (A.K.S.)
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3
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Beyerle ER, Tiwary P. Thermodynamically Optimized Machine-Learned Reaction Coordinates for Hydrophobic Ligand Dissociation. J Phys Chem B 2024; 128:755-767. [PMID: 38205806 DOI: 10.1021/acs.jpcb.3c08304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Ligand unbinding is mediated by its free energy change, which has intertwined contributions from both energy and entropy. It is important, but not easy, to quantify their individual contributions to the free energy profile. We model hydrophobic ligand unbinding for two systems, a methane particle and a C60 fullerene, both unbinding from hydrophobic pockets in all-atom water. Using a modified deep learning framework, we learn a thermodynamically optimized reaction coordinate to describe the hydrophobic ligand dissociation for both systems. Interpretation of these reaction coordinates reveals the roles of entropic and enthalpic forces as the ligand and pocket sizes change. In both cases, we observe that the free-energy barrier to unbinding is dominated by entropy considerations. Furthermore, the process of methane unbinding is driven by methane solvation, while fullerene unbinding is driven first by pocket wetting and then fullerene wetting. For both solutes, the direct importance of the distance from the binding pocket to the learned reaction coordinate is present, but low. Our framework and subsequent feature important analysis thus give useful thermodynamic insight into hydrophobic ligand dissociation problems that are otherwise difficult to glean.
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Affiliation(s)
- Eric R Beyerle
- Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, United States
| | - Pratyush Tiwary
- Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, United States
- Department of Chemistry, University of Maryland, College Park, Maryland 20742, United States
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Krupa MA, Krupa P. Free-Docking and Template-Based Docking: Physics Versus Knowledge-Based Docking. Methods Mol Biol 2024; 2780:27-41. [PMID: 38987462 DOI: 10.1007/978-1-0716-3985-6_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
Docking methods can be used to predict the orientations of two or more molecules with respect of each other using a plethora of various algorithms, which can be based on the physics of interactions or can use information from databases and templates. The usability of these approaches depends on the type and size of the molecules, whose relative orientation will be estimated. The two most important limitations are (i) the computational cost of the prediction and (ii) the availability of the structural information for similar complexes. In general, if there is enough information about similar systems, knowledge-based and template-based methods can significantly reduce the computational cost while providing high accuracy of the prediction. However, if the information about the system topology and interactions between its partners is scarce, physics-based methods are more reliable or even the only choice. In this chapter, knowledge-, template-, and physics-based methods will be compared and briefly discussed providing examples of their usability with a special emphasis on physics-based protein-protein, protein-peptide, and protein-fullerene docking in the UNRES coarse-grained model.
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Affiliation(s)
- Magdalena A Krupa
- Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland
| | - Paweł Krupa
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland.
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Serda M, Korzuch J, Dreszer D, Krzykawska-Serda M, Musioł R. Interactions between modified fullerenes and proteins in cancer nanotechnology. Drug Discov Today 2023; 28:103704. [PMID: 37453461 DOI: 10.1016/j.drudis.2023.103704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/30/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
Fullerenes have numerous properties that fill the gap between small molecules and nanomaterials. Several types of chemical reaction allow their surface to be ornamented with functional groups designed to change them into 'ideal' nanodelivery systems. Improved stability, and bioavailability are important, but chemical modifications can render them practically soluble in water. 'Buckyball' fullerene scaffolds can interact with many biological targets and inhibit several proteins essential for tumorigeneses. Herein, we focus on the inhibitory properties of fullerene nanomaterials against essential proteins in cancer nanotechnology, as well as the use of dedicated proteins to improve the bioavailability of these promising nanomaterials.
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Affiliation(s)
- Maciej Serda
- Institute of Chemistry, University of Silesia in Katowice, Katowice, Poland.
| | - Julia Korzuch
- Institute of Chemistry, University of Silesia in Katowice, Katowice, Poland
| | - Dominik Dreszer
- Institute of Chemistry, University of Silesia in Katowice, Katowice, Poland
| | | | - Robert Musioł
- Institute of Chemistry, University of Silesia in Katowice, Katowice, Poland
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Dreszer D, Szewczyk G, Szubka M, Maroń AM, Urbisz AZ, Małota K, Sznajder J, Rost-Roszkowska M, Musioł R, Serda M. Uncovering nanotoxicity of a water-soluble and red-fluorescent [70]fullerene nanomaterial. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 879:163052. [PMID: 36963679 DOI: 10.1016/j.scitotenv.2023.163052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/06/2023] [Accepted: 03/20/2023] [Indexed: 05/17/2023]
Abstract
Engineered fullerene materials have attracted the attention of researchers in the biomedical sciences, especially when their synthetic methodology is developed to endow them with significant levels of water-solubility and bioavailability. In this study, we synthesized and characterized a water-soluble and red-fluorescent [70]fullerene nanomaterial, which fluoresced at 693 nm with a quantum yield of 0.065 and a large Stokes shift (around 300 nm). The fullerene nanomaterial generated mainly singlet oxygen after illumination with blue LED light, while superoxide anion radical production was minimal. The transmission electron microscopy as well as fluorescent studies of Drosophila melanogaster revealed that prepared [70]fullerene nanoparticles had better bioavailability than pristine [70]fullerene nanoparticles. The designed nanomaterials were observed in the apical, perinuclear, and basal regions of digestive cells, as well as the basal lamina of the digestive system's epithelium, with no damage to cell organelles and no activation of degenerative processes and cell death. Our findings provide a new perspective for understanding the in vivo behavior of fullerene nanomaterials and their future application in bioimaging and light-activated nanotherapeutics.
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Affiliation(s)
- Dominik Dreszer
- Institute of Chemistry, University of Silesia in Katowice, Poland
| | - Grzegorz Szewczyk
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Poland
| | | | - Anna M Maroń
- Institute of Chemistry, University of Silesia in Katowice, Poland
| | - Anna Z Urbisz
- Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Poland
| | - Karol Małota
- Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Poland
| | - Justyna Sznajder
- Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Poland
| | - Magdalena Rost-Roszkowska
- Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Poland
| | - Robert Musioł
- Institute of Chemistry, University of Silesia in Katowice, Poland
| | - Maciej Serda
- Institute of Chemistry, University of Silesia in Katowice, Poland.
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Marforio TD, Mattioli EJ, Zerbetto F, Calvaresi M. Exploiting Blood Transport Proteins as Carborane Supramolecular Vehicles for Boron Neutron Capture Therapy. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:nano13111770. [PMID: 37299673 DOI: 10.3390/nano13111770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/26/2023] [Accepted: 05/28/2023] [Indexed: 06/12/2023]
Abstract
Carboranes are promising agents for applications in boron neutron capture therapy (BNCT), but their hydrophobicity prevents their use in physiological environments. Here, by using reverse docking and molecular dynamics (MD) simulations, we identified blood transport proteins as candidate carriers of carboranes. Hemoglobin showed a higher binding affinity for carboranes than transthyretin and human serum albumin (HSA), which are well-known carborane-binding proteins. Myoglobin, ceruloplasmin, sex hormone-binding protein, lactoferrin, plasma retinol-binding protein, thyroxine-binding globulin, corticosteroid-binding globulin and afamin have a binding affinity comparable to transthyretin/HSA. The carborane@protein complexes are stable in water and characterized by favorable binding energy. The driving force in the carborane binding is represented by the formation of hydrophobic interactions with aliphatic amino acids and BH-π and CH-π interactions with aromatic amino acids. Dihydrogen bonds, classical hydrogen bonds and surfactant-like interactions also assist the binding. These results (i) identify the plasma proteins responsible for binding carborane upon their intravenous administration, and (ii) suggest an innovative formulation for carboranes based on the formation of a carborane@protein complex prior to the administration.
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Affiliation(s)
- Tainah Dorina Marforio
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum-Università di Bologna, Via Francesco Selmi 2, 40126 Bologna, Italy
| | - Edoardo Jun Mattioli
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum-Università di Bologna, Via Francesco Selmi 2, 40126 Bologna, Italy
| | - Francesco Zerbetto
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum-Università di Bologna, Via Francesco Selmi 2, 40126 Bologna, Italy
| | - Matteo Calvaresi
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum-Università di Bologna, Via Francesco Selmi 2, 40126 Bologna, Italy
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Dissecting the Interactions between Chlorin e6 and Human Serum Albumin. Molecules 2023; 28:molecules28052348. [PMID: 36903592 PMCID: PMC10005744 DOI: 10.3390/molecules28052348] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/28/2023] [Accepted: 02/28/2023] [Indexed: 03/08/2023] Open
Abstract
Chlorin e6 (Ce6) is among the most used sensitizers in photodynamic (PDT) and sonodynamic (SDT) therapy; its low solubility in water, however, hampers its clinical exploitation. Ce6 has a strong tendency to aggregate in physiological environments, reducing its performance as a photo/sono-sensitizer, as well as yielding poor pharmacokinetic and pharmacodynamic properties. The interaction of Ce6 with human serum albumin (HSA) (i) governs its biodistribution and (ii) can be used to improve its water solubility by encapsulation. Here, using ensemble docking and microsecond molecular dynamics simulations, we identified the two Ce6 binding pockets in HSA, i.e., the Sudlow I site and the heme binding pocket, providing an atomistic description of the binding. Comparing the photophysical and photosensitizing properties of Ce6@HSA with respect to the same properties regarding the free Ce6, it was observed that (i) a red-shift occurred in both the absorption and emission spectra, (ii) a maintaining of the fluorescence quantum yield and an increase of the excited state lifetime was detected, and (iii) a switch from the type II to the type I mechanism in a reactive oxygen species (ROS) production, upon irradiation, took place.
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Malarz K, Korzuch J, Marforio TD, Balin K, Calvaresi M, Mrozek-Wilczkiewicz A, Musiol R, Serda M. Identification and Biological Evaluation of a Water-Soluble Fullerene Nanomaterial as BTK Kinase Inhibitor. Int J Nanomedicine 2023; 18:1709-1724. [PMID: 37025922 PMCID: PMC10072273 DOI: 10.2147/ijn.s403058] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/14/2023] [Indexed: 04/03/2023] Open
Abstract
Introduction Thanks to recent advances in synthetic methodology, water-soluble fullerene nanomaterials that interfere with biomolecules, especially DNA/RNA and selected proteins, have been found with tremendous potential for applications in nanomedicine. Herein, we describe the synthesis and evaluation of a water-soluble glycine-derived [60]fullerene hexakisadduct (HDGF) with T h symmetry, which is a first-in-class BTK protein inhibitor. Methods We synthesized and characterized glycine derived [60]fullerene using NMR, ESI-MS, and ATR-FT-IR. DLS and zeta potential were measured and high-resolution transmission electron microscopy (HRTEM) observations were performed. The chemical composition of the water-soluble fullerene nanomaterial was examined by X-ray photoelectron spectrometry. To observe aggregate formation, the cryo-TEM analysis was carried out. The docking studies and molecular dynamic simulations were performed to determine interactions between HDGF and BTK. The in vitro cytotoxicity was evaluated on RAJI and K562 blood cancer cell lines. Subsequently, we examined the induction of cell death by autophagy and apoptosis by determining the expression levels of crucial genes and caspases. We investigated the direct association of HDGF on inhibition of the BTK signalling pathway by examining changes in the calcium levels in RAJI cells after treatment. The inhibitory potential of HDGF against non-receptor tyrosine kinases was evaluated. Finally, we assessed the effects of HDGF and ibrutinib on the expression of the BTK protein and downstream signal transduction in RAJI cells following anti-IgM stimulation. Results Computational studies revealed that the inhibitory activity of the obtained [60]fullerene derivative is multifaceted: it hampers the BTK active site, interacting directly with the catalytic residues, rendering it inaccessible to phosphorylation, and binds to residues that form the ATP binding pocket. The anticancer activity of produced carbon nanomaterial revealed that it inhibited the BTK protein and its downstream pathways, including PLC and Akt proteins, at the cellular level. The mechanistic studies suggested the formation of autophagosomes (increased gene expression of LC3 and p62) and two caspases (caspase-3 and -9) were responsible for the activation and progression of apoptosis. Conclusion These data illustrate the potential of fullerene-based BTK protein inhibitors as nanotherapeutics for blood cancer and provide helpful information to support the future development of fullerene nanomaterials as a novel class of enzyme inhibitors.
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Affiliation(s)
- Katarzyna Malarz
- A. Chełkowski Institute of Physics, University of Silesia in Katowice, Chorzów, Poland
| | - Julia Korzuch
- Institute of Chemistry, University of Silesia in Katowice, Katowice, Poland
| | | | - Katarzyna Balin
- A. Chełkowski Institute of Physics, University of Silesia in Katowice, Chorzów, Poland
| | - Matteo Calvaresi
- Department of Chemistry “Giacomo Ciamician”, University of Bologna, Bologna, Italy
| | | | - Robert Musiol
- Institute of Chemistry, University of Silesia in Katowice, Katowice, Poland
| | - Maciej Serda
- Institute of Chemistry, University of Silesia in Katowice, Katowice, Poland
- Correspondence: Maciej Serda; Katarzyna Malarz, Email ;
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Cantelli A, Malferrari M, Mattioli EJ, Marconi A, Mirra G, Soldà A, Marforio TD, Zerbetto F, Rapino S, Di Giosia M, Calvaresi M. Enhanced Uptake and Phototoxicity of C 60@albumin Hybrids by Folate Bioconjugation. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:nano12193501. [PMID: 36234629 PMCID: PMC9565331 DOI: 10.3390/nano12193501] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/23/2022] [Accepted: 09/28/2022] [Indexed: 06/12/2023]
Abstract
Fullerenes are considered excellent photosensitizers, being highly suitable for photodynamic therapy (PDT). A lack of water solubility and low biocompatibility are, in many instances, still hampering the full exploitation of their potential in nanomedicine. Here, we used human serum albumin (HSA) to disperse fullerenes by binding up to five fullerene cages inside the hydrophobic cavities. Albumin was bioconjugated with folic acid to specifically address the folate receptors that are usually overexpressed in several solid tumors. Concurrently, tetramethylrhodamine isothiocyanate, TRITC, a tag for imaging, was conjugated to C60@HSA in order to build an effective phototheranostic platform. The in vitro experiments demonstrated that: (i) HSA disperses C60 molecules in a physiological environment, (ii) HSA, upon C60 binding, maintains its biological identity and biocompatibility, (iii) the C60@HSA complex shows a significant visible-light-induced production of reactive oxygen species, and (iv) folate bioconjugation improves both the internalization and the PDT-induced phototoxicity of the C60@HSA complex in HeLa cells.
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Zadeh Mehrizi T, Shafiee Ardestani M. Application of non-metal nanoparticles, as a novel approach, for improving the stability of blood products: 2011-2021. Prog Biomater 2022; 11:137-161. [PMID: 35536502 PMCID: PMC9085557 DOI: 10.1007/s40204-022-00188-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/23/2022] [Indexed: 12/03/2022] Open
Abstract
Despite the importance of the proper quality of blood products for safe transfusion, conventional methods for preparation and their preservation, they lack significant stability. Non-metal nanoparticles with particular features may overcome these challenges. This review study for the first time provided a comprehensive vision of the interaction of non-metal nanoparticles with each blood product (red blood cells, platelets and plasma proteins). The findings of this review on the most effective nanoparticle for improving the stability of RBCs indicate that graphene quantum dots and nanodiamonds show compatibility with RBCs. For increasing the stability of platelet products, silica nanoparticles exhibited a suppressive impact on platelet aggregation. Pristine graphene also shows compatibility with platelets. For better stability of plasma products, graphene oxide was indicated to preserve free human serum albumin from thermal shocks at low ionic strength. For increased stability of Factor VIII, mesoporous silica nanoparticles with large pores exhibit the superb quality of recovered proteins. Furthermore, 3.2 nm quantum dots exhibited anticoagulant effects. As the best promising nanoparticles for immunoglobulin stability, graphene quantum dots showed compatibility with γ-globulins. Overall, this review recommends further research on the mentioned nanoparticles as the most potential candidates for enhancing the stability and storage of blood components.
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Affiliation(s)
- Tahereh Zadeh Mehrizi
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran.
| | - Mehdi Shafiee Ardestani
- Department of Radiopharmacy, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
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12
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Marforio TD, Mattioli EJ, Zerbetto F, Calvaresi M. Fullerenes against COVID-19: Repurposing C 60 and C 70 to Clog the Active Site of SARS-CoV-2 Protease. Molecules 2022; 27:molecules27061916. [PMID: 35335283 PMCID: PMC8955646 DOI: 10.3390/molecules27061916] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/11/2022] [Accepted: 03/13/2022] [Indexed: 11/28/2022] Open
Abstract
The persistency of COVID-19 in the world and the continuous rise of its variants demand new treatments to complement vaccines. Computational chemistry can assist in the identification of moieties able to lead to new drugs to fight the disease. Fullerenes and carbon nanomaterials can interact with proteins and are considered promising antiviral agents. Here, we propose the possibility to repurpose fullerenes to clog the active site of the SARS-CoV-2 protease, Mpro. Through the use of docking, molecular dynamics, and energy decomposition techniques, it is shown that C60 has a substantial binding energy to the main protease of the SARS-CoV-2 virus, Mpro, higher than masitinib, a known inhibitor of the protein. Furthermore, we suggest the use of C70 as an innovative scaffold for the inhibition of SARS-CoV-2 Mpro. At odds with masitinib, both C60 and C70 interact more strongly with SARS-CoV-2 Mpro when different protonation states of the catalytic dyad are considered. The binding of fullerenes to Mpro is due to shape complementarity, i.e., vdW interactions, and is aspecific. As such, it is not sensitive to mutations that can eliminate or invert the charges of the amino acids composing the binding pocket. Fullerenic cages should therefore be more effective against the SARS-CoV-2 virus than the available inhibitors such as masinitib, where the electrostatic term plays a crucial role in the binding.
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Serda M, Gawecki R, Dulski M, Sajewicz M, Talik E, Szubka M, Zubko M, Malarz K, Mrozek-Wilczkiewicz A, Musioł R. Synthesis and applications of [60]fullerene nanoconjugate with 5-aminolevulinic acid and its glycoconjugate as drug delivery vehicles. RSC Adv 2022; 12:6377-6388. [PMID: 35424628 PMCID: PMC8981668 DOI: 10.1039/d1ra08499b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 02/17/2022] [Indexed: 01/18/2023] Open
Abstract
The 5-aminolevulinic acid (5-ALA) prodrug is widely used in clinical applications, primarily for skin cancer treatments and to visualize brain tumors in neurosurgery. Unfortunately, its applications are limited by unfavorable pharmacological properties, especially low lipophilicity; therefore, efficient nanovehicles are needed. For this purpose, we synthesized and characterized two novel water-soluble fullerene nanomaterials containing 5-ALA and d-glucuronic acid components. Their physicochemical properties were investigated using NMR, XPS, ESI mass spectrometry, as well as TEM and SEM techniques. In addition, HPLC and fluorescence measurements were performed to evaluate the biological activity of the fullerene nanomaterials in 5-ALA delivery and photodynamic therapy (PDT); additional detection of selected mRNA targets was carried out using the qRT-PCR methodology. The cellular response to the [60]fullerene conjugates resulted in increased levels of ABCG2 and PEPT-1 genes, as determined by qRT-PCR analysis. Therefore, we designed a combination PDT approach based on two fullerene materials, C60-ALA and C60-ALA-GA, along with the ABCG2 inhibitor Ko143.
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Affiliation(s)
- Maciej Serda
- Institute of Chemistry, University of Silesia in Katowice Szkolna 9 40-006 Katowice Poland +48322599978 +48323591545
| | - Robert Gawecki
- Silesian Center for Education and Interdisciplinary Research 75 Pulku Piechoty 1a 41-500 Chorzow Poland.,A. Chełkowski Institute of Physics, University of Silesia 75 Pulku Piechoty 1 41-500 Chorzow Poland
| | - Mateusz Dulski
- Institute of Materials Science, University of Silesia in Katowice 75 Pulku Piechoty, 1A Chorzow 41-500 Poland
| | - Mieczysław Sajewicz
- Institute of Chemistry, University of Silesia in Katowice Szkolna 9 40-006 Katowice Poland +48322599978 +48323591545
| | - Ewa Talik
- A. Chełkowski Institute of Physics, University of Silesia 75 Pulku Piechoty 1 41-500 Chorzow Poland
| | - Magdalena Szubka
- A. Chełkowski Institute of Physics, University of Silesia 75 Pulku Piechoty 1 41-500 Chorzow Poland
| | - Maciej Zubko
- Institute of Materials Science, University of Silesia in Katowice 75 Pulku Piechoty, 1A Chorzow 41-500 Poland.,Department of Physics, Faculty of Science, University of Hradec Králové Rokitanského 62 500 03 Hradec Králové Czech Republic
| | - Katarzyna Malarz
- Silesian Center for Education and Interdisciplinary Research 75 Pulku Piechoty 1a 41-500 Chorzow Poland.,A. Chełkowski Institute of Physics, University of Silesia 75 Pulku Piechoty 1 41-500 Chorzow Poland
| | - Anna Mrozek-Wilczkiewicz
- Silesian Center for Education and Interdisciplinary Research 75 Pulku Piechoty 1a 41-500 Chorzow Poland.,A. Chełkowski Institute of Physics, University of Silesia 75 Pulku Piechoty 1 41-500 Chorzow Poland
| | - Robert Musioł
- Institute of Chemistry, University of Silesia in Katowice Szkolna 9 40-006 Katowice Poland +48322599978 +48323591545
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14
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Interaction of fullerene C60 with bovine serum albumin at the water – air interface. Colloids Surf A Physicochem Eng Asp 2021. [DOI: 10.1016/j.colsurfa.2021.127702] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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15
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Recent advances in carbon nanotubes-based biocatalysts and their applications. Adv Colloid Interface Sci 2021; 297:102542. [PMID: 34655931 DOI: 10.1016/j.cis.2021.102542] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 10/04/2021] [Accepted: 10/06/2021] [Indexed: 12/23/2022]
Abstract
Enzymes have been incorporated into a wide variety of fields and industries as they catalyze many biochemical and chemical reactions. The immobilization of enzymes on carbon nanotubes (CNTs) for generating nano biocatalysts with high stability and reusability is gaining great attention among researchers. Functionalized CNTs act as excellent support for effective enzyme immobilization. Depending on the application, the enzymes can be tailored using the various surface functionalization techniques on the CNTs to extricate the desirable characteristics. Aiming at the preparation of efficient, stable, and recyclable nanobiocatalysts, this review provides an overview of the methods developed to immobilize the various enzymes. Various applications of carbon nanotube-based biocatalysts in water purification, bioremediation, biosensors, and biofuel cells have been comprehensively reviewed.
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16
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Marforio TD, Calza A, Mattioli EJ, Zerbetto F, Calvaresi M. Dissecting the Supramolecular Dispersion of Fullerenes by Proteins/Peptides: Amino Acid Ranking and Driving Forces for Binding to C 60. Int J Mol Sci 2021; 22:ijms222111567. [PMID: 34768997 PMCID: PMC8583719 DOI: 10.3390/ijms222111567] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 01/05/2023] Open
Abstract
Molecular dynamics simulations were used to quantitatively investigate the interactions between the twenty proteinogenic amino acids and C60. The conserved amino acid backbone gave a constant energetic interaction ~5.4 kcal mol−1, while the contribution to the binding due to the amino acid side chains was found to be up to ~5 kcal mol−1 for tryptophan but lower, to a point where it was slightly destabilizing, for glutamic acid. The effects of the interplay between van der Waals, hydrophobic, and polar solvation interactions on the various aspects of the binding of the amino acids, which were grouped as aromatic, charged, polar and hydrophobic, are discussed. Although π–π interactions were dominant, surfactant-like and hydrophobic effects were also observed. In the molecular dynamics simulations, the interacting residues displayed a tendency to visit configurations (i.e., regions of the Ramachandran plot) that were absent when C60 was not present. The amino acid backbone assumed a “tepee-like” geometrical structure to maximize interactions with the fullerene cage. Well-defined conformations of the most interactive amino acids (Trp, Arg, Met) side chains were identified upon C60 binding.
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17
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Korzuch J, Rak M, Balin K, Zubko M, Głowacka O, Dulski M, Musioł R, Madeja Z, Serda M. Towards water-soluble [60]fullerenes for the delivery of siRNA in a prostate cancer model. Sci Rep 2021; 11:10565. [PMID: 34012024 PMCID: PMC8134426 DOI: 10.1038/s41598-021-89943-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 05/04/2021] [Indexed: 02/05/2023] Open
Abstract
This paper presents two water-soluble fullerene nanomaterials (HexakisaminoC60 and monoglucosamineC60, which is called here JK39) that were developed and synthesized as non-viral siRNA transfection nanosystems. The developed two-step Bingel-Hirsch reaction enables the chemical modification of the fullerene scaffold with the desired bioactive fragments such as D-glucosamine while keeping the crucial positive charged ethylenediamine based malonate. The ESI-MS and 13C-NMR analyses of JK39 confirmed its high Th symmetry, while X-ray photoelectron spectroscopy revealed the presence of nitrogen and oxygen-containing C-O or C-N bonds. The efficiency of both fullerenes as siRNA vehicles was tested in vitro using the prostate cancer cell line DU145 expressing the GFP protein. The HexakisaminoC60 fullerene was an efficient siRNA transfection agent, and decreased the GFP fluorescence signal significantly in the DU145 cells. Surprisingly, the glycofullerene JK39 was inactive in the transfection experiments, probably due to its high zeta potential and the formation of an extremely stable complex with siRNA.
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Affiliation(s)
- Julia Korzuch
- Institute of Chemistry, University of Silesia in Katowice, 40-006, Katowice, Poland
| | - Monika Rak
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Kraków, Poland
| | - Katarzyna Balin
- Institute of Physics and Silesian Center for Education and Interdisciplinary Research, University of Silesia in Katowice, 41-500, Chorzów, Poland
| | - Maciej Zubko
- Institute of Materials Engineering, University of Silesia in Katowice, 41-500, Chorzów, Poland.,Department of Physics, Faculty of Science, University of Hradec Králové, 500-03, Hradec Králové, Czech Republic
| | - Olga Głowacka
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Kraków, Poland
| | - Mateusz Dulski
- Institute of Materials Engineering, University of Silesia in Katowice, 41-500, Chorzów, Poland
| | - Robert Musioł
- Institute of Chemistry, University of Silesia in Katowice, 40-006, Katowice, Poland
| | - Zbigniew Madeja
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Kraków, Poland
| | - Maciej Serda
- Institute of Chemistry, University of Silesia in Katowice, 40-006, Katowice, Poland.
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18
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Nisoh N, Jarerattanachat V, Karttunen M, Wong-Ekkabut J. Formation of aggregates, icosahedral structures and percolation clusters of fullerenes in lipids bilayers: The key role of lipid saturation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183328. [PMID: 32343957 DOI: 10.1016/j.bbamem.2020.183328] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/17/2020] [Accepted: 04/22/2020] [Indexed: 02/07/2023]
Abstract
Carbon nanoparticles (CNPs) are attractive materials for a great number of applications but there are serious concerns regarding their influence on health and environment. Here, our focus is on the behavior of fullerenes in lipid bilayers with varying lipid saturations, chain lengths and fullerene concentrations using coarse-grained molecular dynamics (CG-MD) simulations. Our findings show that the lipid saturation level is a key factor in determining how fullerenes behave and where the fullerenes are located inside a lipid bilayer. In saturated and monounsaturated bilayers fullerenes aggregated and formed clusters with some of them showing icosahedral structures. In polyunsaturated lipid bilayers, no such structures were observed: In polyunsaturated lipid bilayers at high fullerene concentrations, connected percolation-like networks of fullerenes spanning the whole lateral area emerged at the bilayer center. In other systems only separate isolated aggregates were observed. The effects of fullerenes on lipid bilayers depend strongly on fullerene aggregation. When fullerenes aggregate, their interactions with the lipid tails change.
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Affiliation(s)
- Nililla Nisoh
- Department of Physics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; Thailand Center of Excellence in Physics (ThEP Center), Ministry of Higher Education, Science, Research and Innovation, Bangkok 10400, Thailand
| | - Viwan Jarerattanachat
- Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; Specialized Center of Rubber and Polymer Materials for Agriculture and Industry (RPM), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; NSTDA Supercomputer Center (ThaiSC), National Electronics and Computer Technology Center (NECTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathumthani 12120, Thailand
| | - Mikko Karttunen
- Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 3K7, Canada; Department of Applied Mathematics, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada; The Centre for Advanced Materials Research (CAMBR), The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
| | - Jirasak Wong-Ekkabut
- Department of Physics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; Thailand Center of Excellence in Physics (ThEP Center), Ministry of Higher Education, Science, Research and Innovation, Bangkok 10400, Thailand; Specialized Center of Rubber and Polymer Materials for Agriculture and Industry (RPM), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.
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19
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Di Giosia M, Marforio TD, Cantelli A, Valle F, Zerbetto F, Su Q, Wang H, Calvaresi M. Inhibition of α-chymotrypsin by pristine single-wall carbon nanotubes: Clogging up the active site. J Colloid Interface Sci 2020; 571:174-184. [DOI: 10.1016/j.jcis.2020.03.034] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 02/26/2020] [Accepted: 03/08/2020] [Indexed: 10/24/2022]
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20
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Di Giosia M, Genovese D, Cantelli A, Cingolani M, Rampazzo E, Strever G, Tavoni M, Zaccheroni N, Calvaresi M, Prodi L. Synthesis and characterization of a reconstituted myoglobin-chlorin e6 adduct for theranostic applications. J PORPHYR PHTHALOCYA 2020. [DOI: 10.1142/s108842461950202x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Chlorin e6 (Ce6) and its derivatives are among the most important photosensitizers in photodynamic therapy. Due to their intense fluorescence, chlorins may also be used for diagnostics. However, low solubility in water and high tendency to aggregation restrict their medical use. Here we demonstrate that apo-myoglobin, by reinserting Ce6 in its heme binding pocket, can be used to monomolecularly disperse it. The reconstructed myoglobin-Ce6 adduct presents noticeable changes in the photophysical properties of the chromophore. A red-shift, in particular in the transparency window, can be observed in the absorption and in the emission spectra of the adduct compared to the spectra of the free chlorin in PBS. The adduct presents a higher quantum yield and an increased excited-state lifetime with respect to the free Ce6. The binding of Ce6 to apo-myoglobin determines a decrease of the 1O2 generation but a three-fold increase of peroxides production, determining globally an increase in the performance of Ce6 as a photosensitizer and imaging agent.
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Affiliation(s)
- Matteo Di Giosia
- Dipartimento di Chimica “Giacomo Ciamician”, Alma Mater Studiorum — Università Degli Studi di Bologna, via Selmi 2, 40126 Bologna, Italy
| | - Damiano Genovese
- Dipartimento di Chimica “Giacomo Ciamician”, Alma Mater Studiorum — Università Degli Studi di Bologna, via Selmi 2, 40126 Bologna, Italy
| | - Andrea Cantelli
- Dipartimento di Chimica “Giacomo Ciamician”, Alma Mater Studiorum — Università Degli Studi di Bologna, via Selmi 2, 40126 Bologna, Italy
| | - Matteo Cingolani
- Dipartimento di Chimica “Giacomo Ciamician”, Alma Mater Studiorum — Università Degli Studi di Bologna, via Selmi 2, 40126 Bologna, Italy
| | - Enrico Rampazzo
- Dipartimento di Chimica “Giacomo Ciamician”, Alma Mater Studiorum — Università Degli Studi di Bologna, via Selmi 2, 40126 Bologna, Italy
| | - Giulia Strever
- Dipartimento di Chimica “Giacomo Ciamician”, Alma Mater Studiorum — Università Degli Studi di Bologna, via Selmi 2, 40126 Bologna, Italy
| | - Marta Tavoni
- Dipartimento di Chimica “Giacomo Ciamician”, Alma Mater Studiorum — Università Degli Studi di Bologna, via Selmi 2, 40126 Bologna, Italy
| | - Nelsi Zaccheroni
- Dipartimento di Chimica “Giacomo Ciamician”, Alma Mater Studiorum — Università Degli Studi di Bologna, via Selmi 2, 40126 Bologna, Italy
| | - Matteo Calvaresi
- Dipartimento di Chimica “Giacomo Ciamician”, Alma Mater Studiorum — Università Degli Studi di Bologna, via Selmi 2, 40126 Bologna, Italy
- CIRI Scienze Della Vita e Tecnologie per la Salute, Alma Mater Studiorum — Università Degli Studi di Bologna, via Selmi 2, 40126 Bologna, Italy
| | - Luca Prodi
- Dipartimento di Chimica “Giacomo Ciamician”, Alma Mater Studiorum — Università Degli Studi di Bologna, via Selmi 2, 40126 Bologna, Italy
- CIRI Scienze Della Vita e Tecnologie per la Salute, Alma Mater Studiorum — Università Degli Studi di Bologna, via Selmi 2, 40126 Bologna, Italy
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21
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Muraca F, Boselli L, Castagnola V, Dawson KA. Ultrasmall Gold Nanoparticle Cellular Uptake: Influence of Transient Bionano Interactions. ACS APPLIED BIO MATERIALS 2020; 3:3800-3808. [DOI: 10.1021/acsabm.0c00379] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Francesco Muraca
- Centre for BioNano Interactions, School of Chemistry, University College Dublin, Belfield Dublin 4, Ireland
| | - Luca Boselli
- Centre for BioNano Interactions, School of Chemistry, University College Dublin, Belfield Dublin 4, Ireland
| | - Valentina Castagnola
- Centre for BioNano Interactions, School of Chemistry, University College Dublin, Belfield Dublin 4, Ireland
| | - Kenneth A. Dawson
- Guangdong Provincial Education Department Key Laboratory of Nano-Immunoregulation Tumor Microenvironment, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, 510260, P.R. China
- Centre for BioNano Interactions, School of Chemistry, University College Dublin, Belfield Dublin 4, Ireland
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22
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Liutkus M, López-Andarias A, Mejías SH, López-Andarias J, Gil-Carton D, Feixas F, Osuna S, Matsuda W, Sakurai T, Seki S, Atienza C, Martín N, Cortajarena AL. Protein-directed crystalline 2D fullerene assemblies. NANOSCALE 2020; 12:3614-3622. [PMID: 31912074 DOI: 10.1039/c9nr07083d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Water soluble 2D crystalline monolayers of fullerenes grow on planar assemblies of engineered consensus tetratricopeptide repeat proteins. Designed fullerene-coordinating tyrosine clamps on the protein introduce specific fullerene binding sites, which facilitate fullerene nucleation. Through reciprocal interactions between the components, the hybrid material assembles into two-dimensional 2 nm thick structures with crystalline order, that conduct photo-generated charges. Thus, the protein-fullerene hybrid material is a demonstration of the developments toward functional materials with protein-based precision control of functional elements.
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Affiliation(s)
- Mantas Liutkus
- CIC biomaGUNE, Paseo de Miramón 182, E-20014 Donostia-San Sebastian, Spain.
| | - Alicia López-Andarias
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas. Universidad Complutense de Madrid, E-28040 Madrid, Spain.
| | - Sara H Mejías
- CIC biomaGUNE, Paseo de Miramón 182, E-20014 Donostia-San Sebastian, Spain.
| | - Javier López-Andarias
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas. Universidad Complutense de Madrid, E-28040 Madrid, Spain.
| | - David Gil-Carton
- CIC bioGUNE; Bizkaia Science and Technology Park, building 800, E-48160, Derio, Spain
| | - Ferran Feixas
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Spain
| | - Sílvia Osuna
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Spain and Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Wakana Matsuda
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Japan
| | - Tsuneaki Sakurai
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Japan
| | - Shu Seki
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Japan
| | - Carmen Atienza
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas. Universidad Complutense de Madrid, E-28040 Madrid, Spain.
| | - Nazario Martín
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas. Universidad Complutense de Madrid, E-28040 Madrid, Spain. and IMDEA-Nanoscience, Campus de Cantoblanco, E-28049 Madrid, Spain
| | - Aitziber L Cortajarena
- CIC biomaGUNE, Paseo de Miramón 182, E-20014 Donostia-San Sebastian, Spain. and Ikerbasque, Basque Foundation for Science, Mª Díaz de Haro 3, E-48013 Bilbao, Spain
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23
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Noor M, Goswami J, Davis VA. Comparison of Attachment and Antibacterial Activity of Covalent and Noncovalent Lysozyme-Functionalized Single-Walled Carbon Nanotubes. ACS OMEGA 2020; 5:2254-2259. [PMID: 32064386 PMCID: PMC7016910 DOI: 10.1021/acsomega.9b03387] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 01/14/2020] [Indexed: 06/10/2023]
Abstract
Carbon nanotube-lysozyme (LSZ) conjugates provide an attractive combination of high strength and antimicrobial activity. However, there has not been a direct comparison of the covalent and noncovalent methods for creating them. In this work, single-walled carbon nanotubes (SWNT) were functionalized with LSZ using both noncovalent adsorption and covalent attachment via N-ethyl-N-(3-dimethylamino-propyl) carbodiimide hydrochloride-N-hydroxysuccinimide (EDC-NHS) chemistry. The amount of attached lysozyme, dispersion stability, and antimicrobial activity was compared. In addition, the mechanical properties of LSZ-SWNT in poly(vinyl alcohol) (PVA) composite films were investigated. Dispersions of covalently bound LSZ-SWNT had better dispersion stability. This was attributed to covalent functionalization enabling sustained SWNT dispersion at a lower LSZ/SWNT ratio. The covalently bound LSZ-SWNT also exhibited a lower initial rate of antibacterial response but were active over a longer time scale. Composite films made from LSZ-SWNT maintained similar activity as the corresponding dispersions. However, the noncovalent LSZ-SWNT films were stronger and more hydrolytically stable than those made from covalent LSZ-SWNT.
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Affiliation(s)
- Matthew
M. Noor
- Department of Chemical Engineering, Auburn University, 212 Ross Hal, Auburn, Alabama 36849, United States
| | - Joyanta Goswami
- Department of Chemical Engineering, Auburn University, 212 Ross Hal, Auburn, Alabama 36849, United States
| | - Virginia A. Davis
- Department of Chemical Engineering, Auburn University, 212 Ross Hal, Auburn, Alabama 36849, United States
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24
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Glycofullerenes as non-receptor tyrosine kinase inhibitors- towards better nanotherapeutics for pancreatic cancer treatment. Sci Rep 2020; 10:260. [PMID: 31937861 PMCID: PMC6959220 DOI: 10.1038/s41598-019-57155-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 12/23/2019] [Indexed: 12/27/2022] Open
Abstract
The water-soluble glycofullerenes GF1 and GF2 were synthesized using two-step modified Bingel-Hirsch methodology. Interestingly, we identified buckyballs as a novel class of non-receptor Src kinases inhibitors. The evaluated compounds were found to inhibit Fyn A and BTK proteins with IC50 values in the low micromolar range, with the most active compound at 39 µM. Moreover, we have demonstrated that formation of protein corona on the surface of [60]fullerene derivatives is changing the landscape of their activity, tuning the selectivity of obtained carbon nanomaterials towards Fyn A and BTK kinases. The performed molecular biology studies revealed no cytotoxicity and no influence of engineered carbon nanomaterials on the cell cycle of PANC-1 and AsPC-1 cancer cell lines. Incubation with the tested compounds resulted in the cellular redox imbalance triggering the repair systems and influenced the changing of protein levels.
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25
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Yu CH, Qin Z, Martin-Martinez FJ, Buehler MJ. A Self-Consistent Sonification Method to Translate Amino Acid Sequences into Musical Compositions and Application in Protein Design Using Artificial Intelligence. ACS NANO 2019; 13:7471-7482. [PMID: 31240912 DOI: 10.1021/acsnano.9b02180] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We report a self-consistent method to translate amino acid sequences into audible sound, use the representation in the musical space to train a neural network, and then apply it to generate protein designs using artificial intelligence (AI). The sonification method proposed here uses the normal mode vibrations of the amino acid building blocks of proteins to compute an audible representation of each of the 20 natural amino acids, which is fully defined by the overlay of its respective natural vibrations. The vibrational frequencies are transposed to the audible spectrum following the musical concept of transpositional equivalence, playing or writing music in a way that makes it sound higher or lower in pitch while retaining the relationships between tones or chords played. This transposition method ensures that the relative values of the vibrational frequencies within each amino acid and among different amino acids are retained. The characteristic frequency spectrum and sound associated with each of the amino acids represents a type of musical scale that consists of 20 tones, the "amino acid scale". To create a playable instrument, each tone associated with the amino acids is assigned to a specific key on a piano roll, which allows us to map the sequence of amino acids in proteins into a musical score. To reflect higher-order structural details of proteins, the volume and duration of the notes associated with each amino acid are defined by the secondary structure of proteins, computed using DSSP and thereby introducing musical rhythm. We then train a recurrent neural network based on a large set of musical scores generated by this sonification method and use AI to generate musical compositions, capturing the innate relationships between amino acid sequence and protein structure. We then translate the de novo musical data generated by AI into protein sequences, thereby obtaining de novo protein designs that feature specific design characteristics. We illustrate the approach in several examples that reflect the sonification of protein sequences, including multihour audible representations of natural proteins and protein-based musical compositions solely generated by AI. The approach proposed here may provide an avenue for understanding sequence patterns, variations, and mutations and offers an outreach mechanism to explain the significance of protein sequences. The method may also offer insight into protein folding and understanding the context of the amino acid sequence in defining the secondary and higher-order folded structure of proteins and could hence be used to detect the effects of mutations through sound.
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Affiliation(s)
- Chi-Hua Yu
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Department of Civil and Environmental Engineering , Massachusetts Institute of Technology , 77 Massachusetts Avenue 1-290 , Cambridge , Massachusetts 02139 , United States
| | - Zhao Qin
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Department of Civil and Environmental Engineering , Massachusetts Institute of Technology , 77 Massachusetts Avenue 1-290 , Cambridge , Massachusetts 02139 , United States
| | - Francisco J Martin-Martinez
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Department of Civil and Environmental Engineering , Massachusetts Institute of Technology , 77 Massachusetts Avenue 1-290 , Cambridge , Massachusetts 02139 , United States
| | - Markus J Buehler
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Department of Civil and Environmental Engineering , Massachusetts Institute of Technology , 77 Massachusetts Avenue 1-290 , Cambridge , Massachusetts 02139 , United States
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26
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Panwar N, Soehartono AM, Chan KK, Zeng S, Xu G, Qu J, Coquet P, Yong KT, Chen X. Nanocarbons for Biology and Medicine: Sensing, Imaging, and Drug Delivery. Chem Rev 2019; 119:9559-9656. [DOI: 10.1021/acs.chemrev.9b00099] [Citation(s) in RCA: 238] [Impact Index Per Article: 47.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Nishtha Panwar
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Alana Mauluidy Soehartono
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Kok Ken Chan
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Shuwen Zeng
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore
- CINTRA CNRS/NTU/THALES, UMI 3288, Research Techno Plaza, 50 Nanyang Drive, Border X Block, Singapore 637553, Singapore
| | - Gaixia Xu
- Key Laboratory of Optoelectronics Devices and Systems of Ministry of Education/Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, P. R. China
| | - Junle Qu
- Key Laboratory of Optoelectronics Devices and Systems of Ministry of Education/Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, P. R. China
| | - Philippe Coquet
- CINTRA CNRS/NTU/THALES, UMI 3288, Research Techno Plaza, 50 Nanyang Drive, Border X Block, Singapore 637553, Singapore
- Institut d’Electronique, de Microélectronique et de Nanotechnologie (IEMN), CNRS UMR 8520—Université de Lille, 59650 Villeneuve d’Ascq, France
| | - Ken-Tye Yong
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Xiaoyuan Chen
- Laboratory of Molecular Imaging and Nanomedicine, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892, United States
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27
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Ganazzoli F, Raffaini G. Classical atomistic simulations of protein adsorption on carbon nanomaterials. Curr Opin Colloid Interface Sci 2019. [DOI: 10.1016/j.cocis.2018.11.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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28
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Wan Y, Guan S, Qian M, Huang H, Han F, Wang S, Zhang H. Structural basis of fullerene derivatives as novel potent inhibitors of protein acetylcholinesterase without catalytic active site interaction: insight into the inhibitory mechanism through molecular modeling studies. J Biomol Struct Dyn 2019; 38:410-425. [DOI: 10.1080/07391102.2019.1576543] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yongfeng Wan
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, People’s Republic of China
| | - Shanshan Guan
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, People’s Republic of China
- College of Biology and Food Engineering, Jilin Engineering Normal University, Changchun, Jilin, China
| | - Mengdan Qian
- State Key Laboratory on Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University, Changchun, China
| | - Houhou Huang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, People’s Republic of China
| | - Fei Han
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, People’s Republic of China
| | - Song Wang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, People’s Republic of China
| | - Hao Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, People’s Republic of China
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29
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Di Giosia M, Nicolini F, Ferrazzano L, Soldà A, Valle F, Cantelli A, Marforio TD, Bottoni A, Zerbetto F, Montalti M, Rapino S, Tolomelli A, Calvaresi M. Stable and Biocompatible Monodispersion of C 60 in Water by Peptides. Bioconjug Chem 2019; 30:808-814. [PMID: 30616344 DOI: 10.1021/acs.bioconjchem.8b00916] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The lack of solubility in water and the formation of aggregates hamper many opportunities for technological exploitation of C60. Here, different peptides were designed and synthesized with the aim of monomolecular dispersion of C60 in water. Phenylalanines were used as recognizing moieties, able to interact with C60 through π-π stacking, while a varying number of glycines were used as spacers, to connect the two terminal phenylalanines. The best performance in the dispersion of C60 was obtained with the FGGGF peptidic nanotweezer at a pH of 12. A full characterization of this adduct was carried out. The peptides disperse C60 in water with high efficiency, and the solutions are stable for months both in pure water and in physiological environments. NMR measurements demonstrated the ability of the peptides to interact with C60. AFM measurements showed that C60 is monodispersed. Electrospray ionization mass spectrometry determined a stoichiometry of C60@(FGGGF)4. Molecular dynamics simulations showed that the peptides assemble around the C60 cage, like a candy in its paper wrapper, creating a supramolecular host able to accept C60 in the cavity. The peptide-wrapped C60 is fully biocompatible and the C60 "dark toxicity" is eliminated. C60@(FGGGF)4 shows visible light-induced reactive oxygen species (ROS) generation at physiological saline concentrations and reduction of the HeLa cell viability in response to visible light irradiation.
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Affiliation(s)
- Matteo Di Giosia
- Dipartimento di Chimica "Giacomo Ciamician" , Alma Mater Studiorum - Università di Bologna , Via Francesco Selmi, 2 - 40126 Bologna , Italy
| | - Federica Nicolini
- Dipartimento di Chimica "Giacomo Ciamician" , Alma Mater Studiorum - Università di Bologna , Via Francesco Selmi, 2 - 40126 Bologna , Italy
| | - Lucia Ferrazzano
- Dipartimento di Chimica "Giacomo Ciamician" , Alma Mater Studiorum - Università di Bologna , Via Francesco Selmi, 2 - 40126 Bologna , Italy
| | - Alice Soldà
- Dipartimento di Chimica "Giacomo Ciamician" , Alma Mater Studiorum - Università di Bologna , Via Francesco Selmi, 2 - 40126 Bologna , Italy
| | - Francesco Valle
- Istituto per lo Studio dei Materiali Nanostrutturati, ISMN-CNR , via Gobetti 101 , 40129 Bologna , Italy
| | - Andrea Cantelli
- Dipartimento di Chimica "Giacomo Ciamician" , Alma Mater Studiorum - Università di Bologna , Via Francesco Selmi, 2 - 40126 Bologna , Italy
| | - Tainah Dorina Marforio
- Dipartimento di Chimica "Giacomo Ciamician" , Alma Mater Studiorum - Università di Bologna , Via Francesco Selmi, 2 - 40126 Bologna , Italy
| | - Andrea Bottoni
- Dipartimento di Chimica "Giacomo Ciamician" , Alma Mater Studiorum - Università di Bologna , Via Francesco Selmi, 2 - 40126 Bologna , Italy
| | - Francesco Zerbetto
- Dipartimento di Chimica "Giacomo Ciamician" , Alma Mater Studiorum - Università di Bologna , Via Francesco Selmi, 2 - 40126 Bologna , Italy
| | - Marco Montalti
- Dipartimento di Chimica "Giacomo Ciamician" , Alma Mater Studiorum - Università di Bologna , Via Francesco Selmi, 2 - 40126 Bologna , Italy
| | - Stefania Rapino
- Dipartimento di Chimica "Giacomo Ciamician" , Alma Mater Studiorum - Università di Bologna , Via Francesco Selmi, 2 - 40126 Bologna , Italy
| | - Alessandra Tolomelli
- Dipartimento di Chimica "Giacomo Ciamician" , Alma Mater Studiorum - Università di Bologna , Via Francesco Selmi, 2 - 40126 Bologna , Italy
| | - Matteo Calvaresi
- Dipartimento di Chimica "Giacomo Ciamician" , Alma Mater Studiorum - Università di Bologna , Via Francesco Selmi, 2 - 40126 Bologna , Italy
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30
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Yin X, Li B, Liu S, Gu Z, Zhou B, Yang Z. Effect of the surface curvature on amyloid-β peptide adsorption for graphene. RSC Adv 2019; 9:10094-10099. [PMID: 35520900 PMCID: PMC9062381 DOI: 10.1039/c8ra10015b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 03/12/2019] [Indexed: 11/21/2022] Open
Abstract
The adsorption of amyloid-β peptide (Aβ) onto graphene nanosheets with curvature at a neutral pH has been studied by using molecular dynamics simulations in combination with umbrella sampling. We found that Aβ adsorbed onto graphene with distinct characteristics, causing the breakage of hydrogen bonds which leads to its conformational change. Interestingly, the adsorption capacity of graphene's surface varies significantly depending on its curvature, namely, the surface with negative curvature has a higher probability to adsorb the Aβ than the one with positive curvature. This phenomenon is further evidenced by the binding energy between the complex of graphene and Aβ derived from the potential of mean force (PMF). The hydrophobic interactions and the direct dispersion interactions between the graphene nanosheet and the Aβ play a dominant role in the adsorption process. These findings indicate that not only is the chemical composition an important factor but also the shape of the nanoparticle is important in determining its interaction with proteins: the contacting surface curvature can lead to different adsorption capability. The adsorbing capacity of graphene's surface varies significantly depending on its curvature, namely, the surface with negative curvature has a higher probability to adsorb the Aβ than the one with positive curvature.![]()
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Affiliation(s)
- Xiuhua Yin
- Institute of Quantitative Biology and Medicine
- State Key Laboratory of Radiation Medicine and Protection
- School of Radiation Medicine and Protection
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions
- Soochow University
| | - Baoyu Li
- Institute of Quantitative Biology and Medicine
- State Key Laboratory of Radiation Medicine and Protection
- School of Radiation Medicine and Protection
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions
- Soochow University
| | - Shengtang Liu
- Institute of Quantitative Biology and Medicine
- State Key Laboratory of Radiation Medicine and Protection
- School of Radiation Medicine and Protection
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions
- Soochow University
| | - Zonglin Gu
- Institute of Quantitative Biology and Medicine
- State Key Laboratory of Radiation Medicine and Protection
- School of Radiation Medicine and Protection
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions
- Soochow University
| | - Bo Zhou
- School of Electronic Engineering
- Chengdu Technological University
- Chengdu 611730
- China
| | - Zaixing Yang
- Institute of Quantitative Biology and Medicine
- State Key Laboratory of Radiation Medicine and Protection
- School of Radiation Medicine and Protection
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions
- Soochow University
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31
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Bologna F, Mattioli EJ, Bottoni A, Zerbetto F, Calvaresi M. Interactions between Endohedral Metallofullerenes and Proteins: The Gd@C 60-Lysozyme Model. ACS OMEGA 2018; 3:13782-13789. [PMID: 31458078 PMCID: PMC6644377 DOI: 10.1021/acsomega.8b01888] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 10/09/2018] [Indexed: 06/10/2023]
Abstract
Endohedral metallofullerenes (EMFs) have great potential as radioisotope carriers for nuclear medicine and as contrast agents for X-ray and magnetic resonance imaging. EMFs have still important restrictions for their use due to low solubility in physiological environments, low biocompatibility, nonspecific cellular uptake, and a strong dependence of their peculiar properties on physiological parameters, such as pH and salt content. Conjugation of the EMFs with proteins can overcome many of these limitations. Here we investigated the thermodynamics of binding of a model EMF (Gd@C60) with a protein (lysozyme) that is known to act as a host for the empty fullerene. As a rule, even if the shape of an EMF is exactly the same as that of the related fullerene, the interactions with a protein are significantly different. The estimated interaction energy (ΔG binding) between Gd@C60 and lysozyme is -18.7 kcal mol-1, suggesting the possibility of using proteins as supramolecular carriers for EMFs. π-π stacking, hydrophobic interactions, surfactant-like interactions, and electrostatic interactions govern the formation of the hybrid between Gd@C60 and lysozyme. The comparison of the energy contributions to the binding between C60 or Gd@C60 and lysozyme suggests that, although shape complementarity remains the driving force of the binding, the presence of electron transfer from the gadolinium atom to the carbon cage induces a charge distribution on the fullerene cage that strongly affects its interaction with the protein.
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Affiliation(s)
- Fabio Bologna
- Dipartimento di Chimica “Giacomo
Ciamician”, Alma Mater Studiorum—Università
di Bologna, via F. Selmi 2, 40126 Bologna, Italy
| | - Edoardo Jun Mattioli
- Dipartimento di Chimica “Giacomo
Ciamician”, Alma Mater Studiorum—Università
di Bologna, via F. Selmi 2, 40126 Bologna, Italy
| | - Andrea Bottoni
- Dipartimento di Chimica “Giacomo
Ciamician”, Alma Mater Studiorum—Università
di Bologna, via F. Selmi 2, 40126 Bologna, Italy
| | - Francesco Zerbetto
- Dipartimento di Chimica “Giacomo
Ciamician”, Alma Mater Studiorum—Università
di Bologna, via F. Selmi 2, 40126 Bologna, Italy
| | - Matteo Calvaresi
- Dipartimento di Chimica “Giacomo
Ciamician”, Alma Mater Studiorum—Università
di Bologna, via F. Selmi 2, 40126 Bologna, Italy
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32
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Fullerene Derivatives of Nucleoside HIV Reverse Transcriptase Inhibitors-In Silico Activity Prediction. Int J Mol Sci 2018; 19:ijms19103231. [PMID: 30347655 PMCID: PMC6214040 DOI: 10.3390/ijms19103231] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/09/2018] [Accepted: 10/17/2018] [Indexed: 11/17/2022] Open
Abstract
Here we present new derivatives of nucleoside reverse transcriptase inhibitors with a C20 fullerene. The computational chemistry methods used in this study evaluate affinity of designed compounds towards the HIV-1 reverse transcriptase (RT) binding site and select the most active ones. The best of the designed compounds have superior or similar affinity to RT active site in comparison to most active test compounds, including drugs used in anti-HIV therapy.
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33
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Silva RAL, de Brito SF, Machado DFS, Carvalho-Silva VH, de Oliveira HCB, Ribeiro L. The influence of the configuration of the (C 70) 2 dimer on its rovibrational spectroscopic properties: a theoretical survey. J Mol Model 2018; 24:235. [PMID: 30112677 DOI: 10.1007/s00894-018-3780-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 08/01/2018] [Indexed: 12/01/2022]
Abstract
A study of the spectroscopic properties of the buckyball dimer (C70)2 was performed, which involved mapping the potential energy curve of this system. The spectroscopic constants of the system were obtained using theoretical Dunham and discrete variable representation methods, as well as the Rydberg analytical function expanded to the sixth degree. Because the fullerenes in the dimer have both hexagonal and pentagonal faces, the properties of (C70)2 were examined for different system configurations. The fullerene dimerization process involves a weak interaction, possibly mediated by short-range components such as van der Waals forces. The differences between the spectroscopic constants of the various (C70)2 configurations and between their dissociation energies De were found to be rather small, which can be attributed to the dominant influence of the hexagonal faces of the fullerenes on the interaction between the fullerenes. These results should aid our understanding of the process of fullerene dimer formation and hopefully facilitate the development and application of new materials based on these dimers. Graphical Abstract Comparison of the potential energy curve and a schematic representation for the all (C70)2 fullerenes dimers configurations.
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Affiliation(s)
- Rodrigo A L Silva
- Grupo de Química Teórica e Estrutural de Anápolis (GQTEA), Câmpus Anápolis de Ciências Exatas e Tecnológicas Henrique Santillo, Universidade Estadual de Goiás, CP 459, Anápolis, GO, Brazil
| | - Sandro F de Brito
- Laboratório de Estrutura Eletrônica e Dinâmica Molecular I (LEEDMOL I), Instituto de Química, Universidade de Brasília, CP 4478, Brasília, DF, 70919-970, Brazil
| | - Daniel F S Machado
- Laboratório de Estrutura Eletrônica e Dinâmica Molecular I (LEEDMOL I), Instituto de Química, Universidade de Brasília, CP 4478, Brasília, DF, 70919-970, Brazil
| | - Valter H Carvalho-Silva
- Grupo de Química Teórica e Estrutural de Anápolis (GQTEA), Câmpus Anápolis de Ciências Exatas e Tecnológicas Henrique Santillo, Universidade Estadual de Goiás, CP 459, Anápolis, GO, Brazil
| | - Heibbe C B de Oliveira
- Laboratório de Estrutura Eletrônica e Dinâmica Molecular I (LEEDMOL I), Instituto de Química, Universidade de Brasília, CP 4478, Brasília, DF, 70919-970, Brazil.,Laboratório de Estrutura Eletrônica e Dinâmica Molecular II (LEEDMOL II), Instituto de Química, Universidade Federal de Goiás, CP 131, Goiânia, GO, 74001-970, Brazil
| | - Luciano Ribeiro
- Grupo de Química Teórica e Estrutural de Anápolis (GQTEA), Câmpus Anápolis de Ciências Exatas e Tecnológicas Henrique Santillo, Universidade Estadual de Goiás, CP 459, Anápolis, GO, Brazil.
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34
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Di Giosia M, Bomans PHH, Bottoni A, Cantelli A, Falini G, Franchi P, Guarracino G, Friedrich H, Lucarini M, Paolucci F, Rapino S, Sommerdijk NAJM, Soldà A, Valle F, Zerbetto F, Calvaresi M. Proteins as supramolecular hosts for C 60: a true solution of C 60 in water. NANOSCALE 2018; 10:9908-9916. [PMID: 29790558 DOI: 10.1039/c8nr02220h] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Hybrid systems have great potential for a wide range of applications in chemistry, physics and materials science. Conjugation of a biosystem to a molecular material can tune the properties of the components or give rise to new properties. As a workhorse, here we take a C60@lysozyme hybrid. We show that lysozyme recognizes and disperses fullerene in water. AFM, cryo-TEM and high resolution X-ray powder diffraction show that the C60 dispersion is monomolecular. The adduct is biocompatible, stable in physiological and technologically-relevant environments, and easy to store. Hybridization with lysozyme preserves the electrochemical properties of C60. EPR spin-trapping experiments show that the C60@lysozyme hybrid produces ROS following both type I and type II mechanisms. Due to the shielding effect of proteins, the adduct generates significant amounts of 1O2 also in aqueous solution. In the case of type I mechanism, the protein residues provide electrons and the hybrid does not require addition of external electron donors. The preparation process and the properties of C60@lysozyme are general and can be expected to be similar to other C60@protein systems. It is envisaged that the properties of the C60@protein hybrids will pave the way for a host of applications in nanomedicine, nanotechnology, and photocatalysis.
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Affiliation(s)
- Matteo Di Giosia
- Dipartimento di Chimica "G. Ciamician", Alma Mater Studiorum - Università di Bologna, via F. Selmi 2, 40126 Bologna, Italy.
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35
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Di Giosia M, Valle F, Cantelli A, Bottoni A, Zerbetto F, Calvaresi M. C 60 Bioconjugation with Proteins: Towards a Palette of Carriers for All pH Ranges. MATERIALS (BASEL, SWITZERLAND) 2018; 11:E691. [PMID: 29702620 PMCID: PMC5978068 DOI: 10.3390/ma11050691] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 04/20/2018] [Accepted: 04/23/2018] [Indexed: 12/28/2022]
Abstract
The high hydrophobicity of fullerenes and the resulting formation of aggregates in aqueous solutions hamper the possibility of their exploitation in many technological applications. Noncovalent bioconjugation of fullerenes with proteins is an emerging approach for their dispersion in aqueous media. Contrary to covalent functionalization, bioconjugation preserves the physicochemical properties of the carbon nanostructure. The unique photophysical and photochemical properties of fullerenes are then fully accessible for applications in nanomedicine, sensoristic, biocatalysis and materials science fields. However, proteins are not universal carriers. Their stability depends on the biological conditions for which they have evolved. Here we present two model systems based on pepsin and trypsin. These proteins have opposite net charge at physiological pH. They recognize and disperse C60 in water. UV-Vis spectroscopy, zeta-potential and atomic force microscopy analysis demonstrates that the hybrids are well dispersed and stable in a wide range of pH’s and ionic strengths. A previously validated modelling approach identifies the protein-binding pocket involved in the interaction with C60. Computational predictions, combined with experimental investigations, provide powerful tools to design tailor-made C60@proteins bioconjugates for specific applications.
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Affiliation(s)
- Matteo Di Giosia
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, via F. Selmi 2, 40126 Bologna, Italy.
| | - Francesco Valle
- Istituto per lo Studio dei Materiali Nanostrutturati (CNR-ISMN), Consiglio Nazionale delle Ricerche, via P. Gobetti 101, 40129 Bologna, Italy.
| | - Andrea Cantelli
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, via F. Selmi 2, 40126 Bologna, Italy.
| | - Andrea Bottoni
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, via F. Selmi 2, 40126 Bologna, Italy.
| | - Francesco Zerbetto
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, via F. Selmi 2, 40126 Bologna, Italy.
| | - Matteo Calvaresi
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, via F. Selmi 2, 40126 Bologna, Italy.
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36
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Xia S, Li J, Zu M, Li J, Liu J, Bai X, Chang Y, Chen K, Gu W, Zeng L, Zhao L, Xing G, Xing G. Small size fullerenol nanoparticles inhibit thrombosis and blood coagulation through inhibiting activities of thrombin and FXa. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2018; 14:929-939. [DOI: 10.1016/j.nano.2017.12.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 12/16/2017] [Accepted: 12/16/2017] [Indexed: 12/13/2022]
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37
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Pandya V, Baweja L, Dhawan A. Preferential binding of fullerene and fullerenol with the N-terminal and middle regions of amyloid beta peptide: an in silico investigation. Int J Nanomedicine 2018; 13:71-73. [PMID: 29593399 PMCID: PMC5863620 DOI: 10.2147/ijn.s125011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Amyloid beta (Aβ) deposits are implicated in the pathogenesis of debilitating neurodegenerative disorders such as Alzheimer’s disease. In the present study, the interactions of carbon-based nanoparticles (NPs) such as fullerene and fullerenol having different surface chemistry with Aβ were investigated using molecular dynamics simulations and docking studies. A detailed analysis of docking results showed that in 68% of the Aβ conformations, fullerene and fullerenol showed interactions with the N-terminal region of the peptide. However, the high-affinity binding site (E=−48.31 kJ/mol) of fullerene resides in the hydrophobic middle region of the peptide, whereas fullerenol interacts favorably with the charged N-terminal region with a binding energy of −50.42 kJ/mol. The above differences in binding could be attributed to the surface chemistry of fullerene and fullerenol. Moreover, the N-terminal and middle regions of Aβ play an important role in Aβ aggregation. Therefore, the binding of fullerene and fullerenol could inhibit amyloid aggregation. This information will be helpful in designing NPs for targeting amyloid-related disorders.
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Affiliation(s)
- Vishal Pandya
- Division of Biological & Life Sciences, School of Arts & Sciences, (Formerly, Institute of Life Sciences), Ahmedabad University, Ahmedabad, Gujarat
| | - Lokesh Baweja
- Division of Biological & Life Sciences, School of Arts & Sciences, (Formerly, Institute of Life Sciences), Ahmedabad University, Ahmedabad, Gujarat.,Nanotherapeutics & Nanomaterial Toxicology Group, CSIR-Indian Institute of Toxicology Research, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh, India
| | - Alok Dhawan
- Division of Biological & Life Sciences, School of Arts & Sciences, (Formerly, Institute of Life Sciences), Ahmedabad University, Ahmedabad, Gujarat.,Nanotherapeutics & Nanomaterial Toxicology Group, CSIR-Indian Institute of Toxicology Research, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh, India
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38
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Xu X, Huang M, Zou X. Docking-based inverse virtual screening: methods, applications, and challenges. BIOPHYSICS REPORTS 2018; 4:1-16. [PMID: 29577065 PMCID: PMC5860130 DOI: 10.1007/s41048-017-0045-8] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 09/08/2017] [Indexed: 01/09/2023] Open
Abstract
Identifying potential protein targets for a small-compound ligand query is crucial to the process of drug development. However, there are tens of thousands of proteins in human alone, and it is almost impossible to scan all the existing proteins for a query ligand using current experimental methods. Recently, a computational technology called docking-based inverse virtual screening (IVS) has attracted much attention. In docking-based IVS, a panel of proteins is screened by a molecular docking program to identify potential targets for a query ligand. Ever since the first paper describing a docking-based IVS program was published about a decade ago, the approach has been gradually improved and utilized for a variety of purposes in the field of drug discovery. In this article, the methods employed in docking-based IVS are reviewed in detail, including target databases, docking engines, and scoring function methodologies. Several web servers developed for non-expert users are also reviewed. Then, a number of applications are presented according to different research purposes, such as target identification, side effects/toxicity, drug repositioning, drug-target network development, and receptor design. The review concludes by discussing the challenges that docking-based IVS needs to overcome to become a robust tool for pharmaceutical engineering.
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Affiliation(s)
- Xianjin Xu
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO 65211 USA
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211 USA
- Informatics Institute, University of Missouri, Columbia, MO 65211 USA
- Department of Biochemistry, University of Missouri, Columbia, MO 65211 USA
| | - Marshal Huang
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO 65211 USA
- Informatics Institute, University of Missouri, Columbia, MO 65211 USA
| | - Xiaoqin Zou
- Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO 65211 USA
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211 USA
- Informatics Institute, University of Missouri, Columbia, MO 65211 USA
- Department of Biochemistry, University of Missouri, Columbia, MO 65211 USA
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39
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Liu Y, Fu J, Pan W, Xue Q, Liu X, Zhang A. Inhibition of thrombin by functionalized C 60 nanoparticles revealed via in vitro assays and in silico studies. J Environ Sci (China) 2018; 63:285-295. [PMID: 29406112 DOI: 10.1016/j.jes.2017.08.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 08/09/2017] [Accepted: 08/21/2017] [Indexed: 06/07/2023]
Abstract
The studies on the human toxicity of nanoparticles (NPs) are far behind the rapid development of engineered functionalized NPs. Fullerene has been widely used as drug carrier skeleton due to its reported low risk. However, different from other kinds of NPs, fullerene-based NPs (C60 NPs) have been found to have an anticoagulation effect, although the potential target is still unknown. In the study, both experimental and computational methods were adopted to gain mechanistic insight into the modulation of thrombin activity by nine kinds of C60 NPs with diverse surface chemistry properties. In vitro enzyme activity assays showed that all tested surface-modified C60 NPs exhibited thrombin inhibition ability. Kinetic studies coupled with competitive testing using 3 known inhibitors indicated that six of the C60 NPs, of greater hydrophobicity and hydrogen bond (HB) donor acidity or acceptor basicity, acted as competitive inhibitors of thrombin by directly interacting with the active site of thrombin. A simple quantitative nanostructure-activity relationship model relating the surface substituent properties to the inhibition potential was then established for the six competitive inhibitors. Molecular docking analysis revealed that the intermolecular HB interactions were important for the specific binding of C60 NPs to the active site canyon, while the additional stability provided by the surface groups through van der Waals interaction also play a key role in the thrombin binding affinity of the NPs. Our results suggest that thrombin is a possible target of the surface-functionalized C60 NPs relevant to their anticoagulation effect.
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Affiliation(s)
- Yanyan Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China.
| | - Jianjie Fu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Wenxiao Pan
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Qiao Xue
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Xian Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Aiqian Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China; Institute of Environment and Health, Jianghan University, Wuhan 430056, China.
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40
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Yu Y, Sun H, Hou T, Wang S, Li Y. Fullerene derivatives act as inhibitors of leukocyte common antigen based on molecular dynamics simulations. RSC Adv 2018; 8:13997-14008. [PMID: 35539330 PMCID: PMC9079904 DOI: 10.1039/c7ra13543b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 04/10/2018] [Indexed: 11/21/2022] Open
Abstract
Fullerene-based molecules are being studied as potential inhibitors of protein tyrosine phosphatases due to their unique properties and low toxicity. However, the underlying molecular mechanism remains elusive. In this study, molecular dynamics (MD) simulations in conjunction with molecular docking calculations were utilized to investigate the binding effects of C60, C60(NH2)30, and C60(OH)30 on the enzymatic activity of CD45 (a receptor-like protein tyrosine phosphatase). Our results show that all the investigated molecules can be docked into the region between D1 and D2 domains of CD45, and stabilize the protein structure. The average number of residues that directly interact with the C60(NH2)30 is two more than that of C60(OH)30, F819 and F820 (located in the loop connects α3 and β12), resulting in different effects of C60(NH2)30 and C60(OH)30 on protein activity. Detailed MD simulation analyses show that transformation of the interaction network caused by C60(NH2)30 is completely different from that of the control simulation due to the misfolding of α3. Furthermore, the movement of D1 active pocket and KNRY motif are most severely impaired by docking with C60(NH2)30. Our simulation results illustrate that fullerene derivatives modified with amino groups exhibit conspicuous tumor inhibition to protein tyrosine phosphatases, and can act as effective inhibitors. Our results give insight into the inhibitory effects of fullerene-based molecules on protein tyrosine phosphatases and providing a theoretical basis for the design of effective inhibitors. Fullerene-based molecules are being studied as potential inhibitors of protein tyrosine phosphatases due to their unique properties and low toxicity.![]()
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Affiliation(s)
- Yi Yu
- Institute of Functional Nano & Soft Materials (FUNSOM)
- Soochow University
- Suzhou 215123
- China
| | - Huiyong Sun
- Institute of Functional Nano & Soft Materials (FUNSOM)
- Soochow University
- Suzhou 215123
- China
| | - Tingjun Hou
- Institute of Functional Nano & Soft Materials (FUNSOM)
- Soochow University
- Suzhou 215123
- China
| | - Suidong Wang
- Institute of Functional Nano & Soft Materials (FUNSOM)
- Soochow University
- Suzhou 215123
- China
| | - Youyong Li
- Institute of Functional Nano & Soft Materials (FUNSOM)
- Soochow University
- Suzhou 215123
- China
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41
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Minois P, Bayardon J, Meunier-Prest R, Jugé S. [60]Fullerene l-Amino Acids and Peptides: Synthesis under Phase-Transfer Catalysis Using a Phosphine–Borane Linker. Electrochemical Behavior. J Org Chem 2017; 82:11358-11369. [DOI: 10.1021/acs.joc.7b01737] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pauline Minois
- Institut de Chimie Moléculaire de l’Université de Bourgogne (ICMUB-UMR 6302), BP 47870, Université de Bourgogne-Franche-Comté, 9 avenue A. Savary, Dijon 21078 Cedex, France
| | - Jérôme Bayardon
- Institut de Chimie Moléculaire de l’Université de Bourgogne (ICMUB-UMR 6302), BP 47870, Université de Bourgogne-Franche-Comté, 9 avenue A. Savary, Dijon 21078 Cedex, France
| | - Rita Meunier-Prest
- Institut de Chimie Moléculaire de l’Université de Bourgogne (ICMUB-UMR 6302), BP 47870, Université de Bourgogne-Franche-Comté, 9 avenue A. Savary, Dijon 21078 Cedex, France
| | - Sylvain Jugé
- Institut de Chimie Moléculaire de l’Université de Bourgogne (ICMUB-UMR 6302), BP 47870, Université de Bourgogne-Franche-Comté, 9 avenue A. Savary, Dijon 21078 Cedex, France
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42
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Ahmed L, Rasulev B, Kar S, Krupa P, Mozolewska MA, Leszczynski J. Inhibitors or toxins? Large library target-specific screening of fullerene-based nanoparticles for drug design purpose. NANOSCALE 2017; 9:10263-10276. [PMID: 28696446 DOI: 10.1039/c7nr00770a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Fullerene-based nanoparticles have been the subject of vital interest due to their unique properties and potential application in many areas, including medicine. Here we explore their characteristics that could make them prospective leads for known disease-related proteins. High-throughput virtual screening supported by comprehensive multi-software protein-ligand docking simulation and cheminformatics approaches has been applied in investigation of interactions of 1117 proteins with a 169 fullerene nanoparticles decorated with different small molecules. Moreover, obtained docking results were confirmed by the series of unrestricted all-atom molecular dynamics (MD) simulations. Hydrophobicity of fullerene core along with hydrophilic interaction of side chains plays a key role in binding with the studied proteins. We identified a series of nanoparticles that can lead to development of robust drugs for target proteins and another series that can behave as a highly toxic agent. The structure-activity relationship analysis revealed two significant molecular properties responsible for the binding score values. The application of carefully selected computational techniques and described outcome of the study facilitate development of functional fullerene nanoparticles for drug-like and drug delivery applications.
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Affiliation(s)
- Lucky Ahmed
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry and Biochemistry, Jackson State University, 1400 J.R. Lynch Street, P.O. Box 17910, Jackson, MS 39217, USA.
| | - Bakhtiyor Rasulev
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry and Biochemistry, Jackson State University, 1400 J.R. Lynch Street, P.O. Box 17910, Jackson, MS 39217, USA. and Center for Computationally Assisted Science and Technology (CCAST), North Dakota State University, 1805 NDSU Research Park Dr, PO Box 6050, Fargo, ND 58108, USA and Department of Coatings and Polymer Materials, North Dakota State University, NDSU Dept. 2760, PO Box 6050, Fargo, ND 58108, USA
| | - Supratik Kar
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry and Biochemistry, Jackson State University, 1400 J.R. Lynch Street, P.O. Box 17910, Jackson, MS 39217, USA.
| | - Paweł Krupa
- Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668 Warsaw, Poland
| | - Magdalena A Mozolewska
- Institute of Computer Science, Polish Academy of Sciences, ul. Jana Kazimierza 5, Warszaw, 01-248, Poland
| | - Jerzy Leszczynski
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry and Biochemistry, Jackson State University, 1400 J.R. Lynch Street, P.O. Box 17910, Jackson, MS 39217, USA.
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43
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Liu Y, Yan B, Winkler DA, Fu J, Zhang A. Competitive Inhibition Mechanism of Acetylcholinesterase without Catalytic Active Site Interaction: Study on Functionalized C 60 Nanoparticles via in Vitro and in Silico Assays. ACS APPLIED MATERIALS & INTERFACES 2017; 9:18626-18638. [PMID: 28492309 DOI: 10.1021/acsami.7b05459] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Acetylcholinesterase (AChE) activity regulation by chemical agents or, potentially, nanomaterials is important for both toxicology and pharmacology. Competitive inhibition via direct catalytic active sites (CAS) binding or noncompetitive inhibition through interference with substrate and product entering and exiting has been recognized previously as an AChE-inhibition mechanism for bespoke nanomaterials. The competitive inhibition by peripheral anionic site (PAS) interaction without CAS binding remains unexplored. Here, we proposed and verified the occurrence of a presumed competitive inhibition of AChE without CAS binding for hydrophobically functionalized C60 nanoparticles (NPs) by employing both experimental and computational methods. The kinetic inhibition analysis distinguished six competitive inhibitors, probably targeting the PAS, from the pristine and hydrophilically modified C60 NPs. A simple quantitative nanostructure-activity relationship (QNAR) model relating the pocket accessible length of substituent to inhibition capacity was then established to reveal how the geometry of the surface group decides the NP difference in AChE inhibition. Molecular docking identified the PAS as the potential binding site interacting with the NPs via a T-shaped plug-in mode. Specifically, the fullerene core covered the enzyme gorge as a lid through π-π stacking with Tyr72 and Trp286 in the PAS, while the hydrophobic ligands on the fullerene surface inserted into the AChE active site to provide further stability for the complexes. The modeling predicted that inhibition would be severely compromised by Tyr72 and Trp286 deletions, and the subsequent site-directed mutagenesis experiments proved this prediction. Our results demonstrate AChE competitive inhibition of NPs without CAS participation to gain further understanding of both the neurotoxicity and the curative effect of NPs.
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Affiliation(s)
- Yanyan Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences , Beijing 100190, China
| | - Bing Yan
- School of Chemistry and Chemical Engineering, Shandong University , Jinan 250100, China
- School of Environment, Guangzhou Key Laboratory of Environmental Exposure and Health and Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University , Guangzhou 510632, China
| | - David A Winkler
- CSIRO Manufacturing , Clayton 3168, Australia
- Monash Institute of Pharmaceutical Sciences , Parkville 3052, Australia
- Latrobe Institute for Molecular Science , Bundoora, 3046, Australia
- School of Chemical and Physical Science, Flinders University , Bedford Park 5042, Australia
| | - Jianjie Fu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences , Beijing 100190, China
| | - Aiqian Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences , Beijing 100190, China
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44
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Giełdoń A, Witt MM, Gajewicz A, Puzyn T. Rapid insight into C60 influence on biological functions of proteins. Struct Chem 2017. [DOI: 10.1007/s11224-017-0957-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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45
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Recent Developments in 3D QSAR and Molecular Docking Studies of Organic and Nanostructures. HANDBOOK OF COMPUTATIONAL CHEMISTRY 2017. [PMCID: PMC7123761 DOI: 10.1007/978-3-319-27282-5_54] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
The development of quantitative structure–activity relationship (QSAR) methods is going very fast for the last decades. OSAR approach already plays an important role in lead structure optimization, and nowadays, with development of big data approaches and computer power, it can even handle a huge amount of data associated with combinatorial chemistry. One of the recent developments is a three-dimensional QSAR, i.e., 3D QSAR. For the last two decades, 3D-OSAR has already been successfully applied to many datasets, especially of enzyme and receptor ligands. Moreover, quite often 3D QSAR investigations are going together with protein–ligand docking studies and this combination works synergistically. In this review, we outline recent advances in development and applications of 3D QSAR and protein–ligand docking approaches, as well as combined approaches for conventional organic compounds and for nanostructured materials, such as fullerenes and carbon nanotubes.
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46
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Trozzi F, Marforio TD, Bottoni A, Zerbetto F, Calvaresi M. Engineering the Fullerene-protein Interface by Computational Design: The Sum is More than its Parts. Isr J Chem 2016. [DOI: 10.1002/ijch.201600127] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Francesco Trozzi
- Dipartimento di Chimica “G. Ciamician”; Alma Mater Studiorum; Università di Bologna; via F. Selmi 2 40126 Bologna Italy
| | - Tainah Dorina Marforio
- Dipartimento di Chimica “G. Ciamician”; Alma Mater Studiorum; Università di Bologna; via F. Selmi 2 40126 Bologna Italy
| | - Andrea Bottoni
- Dipartimento di Chimica “G. Ciamician”; Alma Mater Studiorum; Università di Bologna; via F. Selmi 2 40126 Bologna Italy
| | - Francesco Zerbetto
- Dipartimento di Chimica “G. Ciamician”; Alma Mater Studiorum; Università di Bologna; via F. Selmi 2 40126 Bologna Italy
| | - Matteo Calvaresi
- Dipartimento di Chimica “G. Ciamician”; Alma Mater Studiorum; Università di Bologna; via F. Selmi 2 40126 Bologna Italy
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47
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Calvaresi M, Eckhart L, Alibardi L. The molecular organization of the beta-sheet region in Corneous beta-proteins (beta-keratins) of sauropsids explains its stability and polymerization into filaments. J Struct Biol 2016; 194:282-91. [DOI: 10.1016/j.jsb.2016.03.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 02/29/2016] [Accepted: 03/05/2016] [Indexed: 11/17/2022]
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48
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Chen Q, Hu X, Wang R, Yuan J, Yin D. Fullerene inhibits benzo(a)pyrene Efflux from Cyprinus carpio hepatocytes by affecting cell membrane fluidity and P-glycoprotein expression. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2016; 174:36-45. [PMID: 26918948 DOI: 10.1016/j.aquatox.2016.02.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Revised: 02/14/2016] [Accepted: 02/15/2016] [Indexed: 06/05/2023]
Abstract
P-Glycoprotein (P-gp) can protect cells by pumping out toxic compounds, and has been found widely expressed in fish tissues. Here, we illustrate the P-gp efflux ability for benzo(a)pyrene (BaP) in the hepatocytes of common carp (Cyprinus carpio) after exposing to fullerene aqueous suspension (nC60). The results revealed that nC60 increased the membrane fluidity by decreasing the ratio of saturated to unsaturated fatty acids, and increased the cholesterol contents. These findings, combined with 10-38% and 70-75% down-regulation of P-gp mRNA and protein respectively, suggested that nC60 caused inhibition on P-gp efflux transport system. Therefore, we further investigated the cellular efflux ability for BaP. Results showed unequivocally that nC60 is a potent P-gp inhibitor. The retaining BaP amounts after efflux were elevated by 1.7-2.8 fold during the 10 day exposure. Meanwhile, 5mg/L humic acid (one of the important fractions of natural organic matter, which is ubiquitous in aquatic environment) alleviated the nC60 damage to hepatocytes in terms of oxidative damage, cholesterol increment, and P-gp content reduction; and finally attenuated the suppressed P-gp efflux ability. Collectively, this study provides the first evidence of nC60 toxicity to P-gp functionality in fish and illustrates the possible mechanism of the suppressed P-gp efflux ability for BaP.
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Affiliation(s)
- Qiqing Chen
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Xialin Hu
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Rui Wang
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Jin Yuan
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Daqiang Yin
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China.
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Protein-directed self-assembly of a fullerene crystal. Nat Commun 2016; 7:11429. [PMID: 27113637 PMCID: PMC4853425 DOI: 10.1038/ncomms11429] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 03/23/2016] [Indexed: 01/03/2023] Open
Abstract
Learning to engineer self-assembly would enable the precise organization of molecules by design to create matter with tailored properties. Here we demonstrate that proteins can direct the self-assembly of buckminsterfullerene (C60) into ordered superstructures. A previously engineered tetrameric helical bundle binds C60 in solution, rendering it water soluble. Two tetramers associate with one C60, promoting further organization revealed in a 1.67-Å crystal structure. Fullerene groups occupy periodic lattice sites, sandwiched between two Tyr residues from adjacent tetramers. Strikingly, the assembly exhibits high charge conductance, whereas both the protein-alone crystal and amorphous C60 are electrically insulating. The affinity of C60 for its crystal-binding site is estimated to be in the nanomolar range, with lattices of known protein crystals geometrically compatible with incorporating the motif. Taken together, these findings suggest a new means of organizing fullerene molecules into a rich variety of lattices to generate new properties by design. Self-assembly enables complex structures to be fabricated from a few relatively simple components, but requires a detailed understanding of how the constituents may interact. Here, the authors report the rational assembly and crystallographic characterization of a fullerene-protein superstructure.
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50
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Analyses of the Binding between Water Soluble C60 Derivatives and Potential Drug Targets through a Molecular Docking Approach. PLoS One 2016; 11:e0147761. [PMID: 26829126 PMCID: PMC4735121 DOI: 10.1371/journal.pone.0147761] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 01/07/2016] [Indexed: 11/19/2022] Open
Abstract
Fullerene C60, a unique sphere-shaped molecule consisting of carbon, has been proved to have inhibitory effects on many diseases. However, the applications of C60 in medicine have been severely hindered by its complete insolubility in water and low solubility in almost all organic solvents. In this study, the water-soluble C60 derivatives and the C60 binding protein’s structures were collected from the literature. The selected proteins fall into several groups, including acetylcholinesterase, glutamate racemase, inosine monophosphate dehydrogenase, lumazine synthase, human estrogen receptor alpha, dihydrofolate reductase and N-myristoyltransferase. The C60 derivatives were docked into the binding sites in the proteins. The binding affinities of the C60 derivatives were calculated. The bindings between proteins and their known inhibitors or native ligands were also characterized in the same way. The results show that C60 derivatives form good interactions with the binding sites of different protein targets. In many cases, the binding affinities of C60 derivatives are better than those of known inhibitors and native ligands. This study demonstrates the interaction patterns of C60 derivatives and their binding partners, which will have good impact on the fullerene-based drug discovery.
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