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Fjodorova N, Novič M, Venko K, Rasulev B, Türker Saçan M, Tugcu G, Sağ Erdem S, Toropova AP, Toropov AA. Cheminformatics and Machine Learning Approaches to Assess Aquatic Toxicity Profiles of Fullerene Derivatives. Int J Mol Sci 2023; 24:14160. [PMID: 37762462 PMCID: PMC10531479 DOI: 10.3390/ijms241814160] [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: 08/21/2023] [Revised: 09/05/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
Fullerene derivatives (FDs) are widely used in nanomaterials production, the pharmaceutical industry and biomedicine. In the present study, we focused on the potential toxic effects of FDs on the aquatic environment. First, we analyzed the binding affinity of 169 FDs to 10 human proteins (1D6U, 1E3K, 1GOS, 1GS4, 1H82, 1OG5, 1UOM, 2F9Q, 2J0D, 3ERT) obtained from the Protein Data Bank (PDB) and showing high similarity to proteins from aquatic species. Then, the binding activity of 169 FDs to the enzyme acetylcholinesterase (AChE)-as a known target of toxins in fathead minnows and Daphnia magna, causing the inhibition of AChE-was analyzed. Finally, the structural aquatic toxicity alerts obtained from ToxAlert were used to confirm the possible mechanism of action. Machine learning and cheminformatics tools were used to analyze the data. Counter-propagation artificial neural network (CPANN) models were used to determine key binding properties of FDs to proteins associated with aquatic toxicity. Predicting the binding affinity of unknown FDs using quantitative structure-activity relationship (QSAR) models eliminates the need for complex and time-consuming calculations. The results of the study show which structural features of FDs have the greatest impact on aquatic organisms and help prioritize FDs and make manufacturing decisions.
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Affiliation(s)
- Natalja Fjodorova
- Laboratory for Chemoinformatics, Theory Department, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia; (M.N.); (K.V.)
| | - Marjana Novič
- Laboratory for Chemoinformatics, Theory Department, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia; (M.N.); (K.V.)
| | - Katja Venko
- Laboratory for Chemoinformatics, Theory Department, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia; (M.N.); (K.V.)
| | - Bakhtiyor Rasulev
- Department of Coatings and Polymeric Materials, North Dakota State University, NDSU Dept 2510, P.O. Box 6050, Fargo, ND 58108, USA;
| | - Melek Türker Saçan
- Ecotoxicology and Chemometrics Lab, Institute of Environmental Sciences, Bogazici University, Hisar Campus, 34342 Istanbul, Turkey;
| | - Gulcin Tugcu
- Department of Toxicology, Faculty of Pharmacy, Yeditepe University, Atasehir, 34755 Istanbul, Turkey;
| | - Safiye Sağ Erdem
- Department of Chemistry, Marmara University, 34722 Istanbul, Turkey;
| | - Alla P. Toropova
- Laboratory of Environmental Chemistry and Toxicology, Istituto di Ricerche Farmacologiche Mario Negri, Via Mario Negri 2, 20156 Milano, Italy; (A.P.T.); (A.A.T.)
| | - Andrey A. Toropov
- Laboratory of Environmental Chemistry and Toxicology, Istituto di Ricerche Farmacologiche Mario Negri, Via Mario Negri 2, 20156 Milano, Italy; (A.P.T.); (A.A.T.)
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How fullerene derivatives (FDs) act on therapeutically important targets associated with diabetic diseases. Comput Struct Biotechnol J 2022; 20:913-924. [PMID: 35242284 PMCID: PMC8861571 DOI: 10.1016/j.csbj.2022.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 02/09/2022] [Accepted: 02/09/2022] [Indexed: 12/12/2022] Open
Abstract
Five proteins related to diabetic disease were selected from Protein Data Bank. Binding scores were calculated for five proteins with 169 fullerene derivatives. Correlation between drug-like descriptors and binding scores activity was examined. The contribution of descriptors to protein-ligand binding was demonstrated. The QSARs models for prediction of binding scores activity were built.
Fullerene derivatives (FDs) belong to a relatively new family of nano-sized organic compounds. They are widely applied in materials science, pharmaceutical industry, and (bio) medicine. This research focused on the study of FDs in terms of their potential inhibitory effect on therapeutic targets associated with diabetic disease, as well as analysis of protein–ligand binding in order to identify the key binding characteristics of FDs. Therapeutic drug compounds when entering the biological system usually inevitably encounter and interact with a vast variety of biomolecules that are responsible for many different functions in organisms. Protein biomolecules are the most important functional components and used in this study as target structures. The structures of proteins [(PDB ID: 1BMQ, 1FM6, 1GPB, 1H5U, 1US0)] belonging to the class of anti-diabetes targets were obtained from the Protein Data Bank (PDB). Protein binding activity data (binding scores) were calculated for the dataset of 169 FDs related to these five proteins. Subsequently, the resulting data were analyzed using various machine learning and cheminformatics methods, including artificial neural network algorithms for variable selection and property prediction. The Quantitative Structure-Activity Relationship (QSAR) models for prediction of binding scores activity were built up according to five Organization for Economic Co-operation and Development (OECD) principles. All the data obtained can provide important information for further potential use of FDs with different functional groups as promising medical antidiabetic agents. Binding scores activity can be used for ranking of FDs in terms of their inhibitory activity (pharmacological properties) and potential toxicity.
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Rahman MM, Junaid M, Hosen SMZ, Mostafa M, Liu L, Benkendorff K. Mollusc-Derived Brominated Indoles for the Selective Inhibition of Cyclooxygenase: A Computational Expedition. Molecules 2021; 26:molecules26216538. [PMID: 34770946 PMCID: PMC8587571 DOI: 10.3390/molecules26216538] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/25/2021] [Accepted: 10/25/2021] [Indexed: 11/16/2022] Open
Abstract
Inflammation plays an important role in different chronic diseases. Brominated indoles derived from the Australian marine mollusk Dicathais orbita (D. orbita) are of interest for their anti-inflammatory properties. This study evaluates the binding mechanism and potentiality of several brominated indoles (tyrindoxyl sulfate, tyrindoleninone, 6-bromoisatin, and 6,6′-dibromoindirubin) against inflammatory mediators cyclooxygenases-1/2 (COX-1/2) using molecular docking, followed by molecular dynamics simulation, along with physicochemical, drug-likeness, pharmacokinetic (pk), and toxicokinetic (tk) properties. Molecular docking identified that these indole compounds are anchored, with the main amino acid residues, positioned in the binding pocket of the COX-1/2, required for selective inhibition. Moreover, the molecular dynamics simulation based on root mean square deviation (RMSD), radius of gyration (Rg), solvent accessible surface area (SASA), and root mean square fluctuation (RMSF) analyses showed that these natural brominated molecules transit rapidly to a progressive constant configuration during binding with COX-1/2 and seem to accomplish a consistent dynamic behavior by maintaining conformational stability and compactness. The results were comparable to the Food and Drug Administration (FDA)-approved selective COX inhibitor, aspirin. Furthermore, the free energy of binding for the compounds assessed by molecular mechanics–Poisson–Boltzmann surface area (MM–PBSA) confirmed the binding capacity of indoles towards COX-1/2, with suitable binding energy values except for the polar precursor tyrindoxyl sulfate (with COX-1). The physicochemical and drug-likeness analysis showed zero violations of Lipinski’s rule, and the compounds are predicted to have excellent pharmacokinetic profiles. These indoles are projected to be non-mutagenic and free from hepatotoxicity, with no inhibition of human ether-a-go–go gene (hERG) I inhibitors, and the oral acute toxicity LD50 in rats is predicted to be similar or lower than aspirin. Overall, this work has identified a plausible mechanism for selective COX inhibition by natural marine indoles as potential therapeutic candidates for the mitigation of inflammation.
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Affiliation(s)
- Md. Mominur Rahman
- Marine Ecology Research Centre, Faculty of Science and Engineering, Southern Cross University, Lismore, NSW 2480, Australia;
| | - Md. Junaid
- Molecular Modeling Drug-design and Discovery Laboratory, Pharmacology Research Division, BCSIR Laboratories Chattogram, Bangladesh Council of Scientific and Industrial Research, Chattogram 4217, Bangladesh; (M.J.); (S.M.Z.H.); (M.M.)
| | - S. M. Zahid Hosen
- Molecular Modeling Drug-design and Discovery Laboratory, Pharmacology Research Division, BCSIR Laboratories Chattogram, Bangladesh Council of Scientific and Industrial Research, Chattogram 4217, Bangladesh; (M.J.); (S.M.Z.H.); (M.M.)
- Pancreatic Research Group, South Western Sydney Clinical School, and Ingham Institute for AppliedMedical Research, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia
| | - Mohammad Mostafa
- Molecular Modeling Drug-design and Discovery Laboratory, Pharmacology Research Division, BCSIR Laboratories Chattogram, Bangladesh Council of Scientific and Industrial Research, Chattogram 4217, Bangladesh; (M.J.); (S.M.Z.H.); (M.M.)
| | - Lei Liu
- Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, Lismore, NSW 2480, Australia;
| | - Kirsten Benkendorff
- Marine Ecology Research Centre, Faculty of Science and Engineering, Southern Cross University, Lismore, NSW 2480, Australia;
- National Marine Science Centre, Faculty of Science and Engineering, Southern Cross University, Coffs Harbour, NSW 2450, Australia
- Correspondence:
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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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Marcoulaki E, López de Ipiña JM, Vercauteren S, Bouillard J, Himly M, Lynch I, Witters H, Shandilya N, van Duuren-Stuurman B, Kunz V, Unger WES, Hodoroaba VD, Bard D, Evans G, Jensen KA, Pilou M, Viitanen AK, Bochon A, Duschl A, Geppert M, Persson K, Cotgreave I, Niga P, Gini M, Eleftheriadis K, Scalbi S, Caillard B, Arevalillo A, Frejafon E, Aguerre-Chariol O, Dulio V. Blueprint for a self-sustained European Centre for service provision in safe and sustainable innovation for nanotechnology. NANOIMPACT 2021; 23:100337. [PMID: 35559838 DOI: 10.1016/j.impact.2021.100337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/05/2021] [Accepted: 06/17/2021] [Indexed: 06/15/2023]
Abstract
The coming years are expected to bring rapid changes in the nanotechnology regulatory landscape, with the establishment of a new framework for nano-risk governance, in silico approaches for characterisation and risk assessment of nanomaterials, and novel procedures for the early identification and management of nanomaterial risks. In this context, Safe(r)-by-Design (SbD) emerges as a powerful preventive approach to support the development of safe and sustainable (SSbD) nanotechnology-based products and processes throughout the life cycle. This paper summarises the work undertaken to develop a blueprint for the deployment and operation of a permanent European Centre of collaborating laboratories and research organisations supporting safe innovation in nanotechnologies. The proposed entity, referred to as "the Centre", will establish a 'one-stop shop' for nanosafety-related services and a central contact point for addressing stakeholder questions about nanosafety. Its operation will rely on significant business, legal and market knowledge, as well as other tools developed and acquired through the EU-funded EC4SafeNano project and subsequent ongoing activities. The proposed blueprint adopts a demand-driven service update scheme to allow the necessary vigilance and flexibility to identify opportunities and adjust its activities and services in the rapidly evolving regulatory and nano risk governance landscape. The proposed Centre will play a major role as a conduit to transfer scientific knowledge between the research and commercial laboratories or consultants able to provide high quality nanosafety services, and the end-users of such services (e.g., industry, SMEs, consultancy firms, and regulatory authorities). The Centre will harmonise service provision, and bring novel risk assessment and management approaches, e.g. in silico methodologies, closer to practice, notably through SbD/SSbD, and decisively support safe and sustainable innovation of industrial production in the nanotechnology industry according to the European Chemicals Strategy for Sustainability.
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Affiliation(s)
- Effie Marcoulaki
- National Centre for Scientific Research "Demokritos", PO Box 60037, 15310 Agia Paraskevi, Greece.
| | - Jesús M López de Ipiña
- TECNALIA, Basque Research and Technology Alliance (BRTA), Parque Tecnológico de Alava, 01510 Miñano, Spain.
| | | | - Jacques Bouillard
- Institut national de l'environnement industriel et des risques (INERIS), Rue Jacques Taffanel, Parc technologique ALATA, Verneuil-en-Halatte, 60550, France.
| | - Martin Himly
- Paris Lodron University of Salzburg, Kapitelgasse 4/6, 5020 Salzburg, Austria.
| | - Iseult Lynch
- School of Geography, Earth & Environmental Sciences, University of Birmingham, Edgbaston, B15 2TT Birmingham, UK.
| | - Hilda Witters
- VITO NV, Health Unit, Boeretang 200, 2400 Mol, Belgium.
| | - Neeraj Shandilya
- TNO, Research group Risk Analysis for Products in Development (RAPID), Princetonlaan 6, 3584 CB Utrecht, Netherlands.
| | - Birgit van Duuren-Stuurman
- TNO, Research group Risk Analysis for Products in Development (RAPID), Princetonlaan 6, 3584 CB Utrecht, Netherlands.
| | - Valentin Kunz
- Bundesanstalt für Materialforschung und -prüfung (BAM), Unter den Eichen 44-46, 12203 Berlin, Germany
| | - Wolfgang E S Unger
- Bundesanstalt für Materialforschung und -prüfung (BAM), Unter den Eichen 44-46, 12203 Berlin, Germany
| | - Vasile-Dan Hodoroaba
- Bundesanstalt für Materialforschung und -prüfung (BAM), Unter den Eichen 44-46, 12203 Berlin, Germany.
| | - Delphine Bard
- Health & Safety Executive Science and Research Centre, Harpur Hill, Buxton, Derbyshire SK17 9JN, UK.
| | - Gareth Evans
- Health & Safety Executive Science and Research Centre, Harpur Hill, Buxton, Derbyshire SK17 9JN, UK.
| | - Keld Alstrup Jensen
- National Research Center for the Work Environment (NRCWE), Lersø Parkallé 105, 2100 København, Denmark.
| | - Marika Pilou
- National Centre for Scientific Research "Demokritos", PO Box 60037, 15310 Agia Paraskevi, Greece.
| | - Anna-Kaisa Viitanen
- Finnish Institute of Occupational Health (FIOH), P.O. Box 40, FI-00032 Työterveyslaitos, Finland.
| | - Anthony Bochon
- JurisLab, Centre de droit privé, Université Libre de Bruxelles, Avenue F. Roosevelt 50, CP 137, 1050 Bruxelles, Belgium.
| | - Albert Duschl
- Paris Lodron University of Salzburg, Kapitelgasse 4/6, 5020 Salzburg, Austria.
| | - Mark Geppert
- Paris Lodron University of Salzburg, Kapitelgasse 4/6, 5020 Salzburg, Austria.
| | - Karin Persson
- RISE Surface, Process and Formulation, Box 5607, SE-114 86 Stockholm, Sweden.
| | - Ian Cotgreave
- RISE Surface, Process and Formulation, Box 5607, SE-114 86 Stockholm, Sweden.
| | - Petru Niga
- RISE Surface, Process and Formulation, Box 5607, SE-114 86 Stockholm, Sweden.
| | - Maria Gini
- National Centre for Scientific Research "Demokritos", PO Box 60037, 15310 Agia Paraskevi, Greece.
| | | | - Simona Scalbi
- ENEA, Agenzia Nazionale per le nuove tecnologie, l'energia e lo sviluppo sostenibile, SSPT-USER-RISE, Via martiri di monte sole 4, 40129 Bologna, Italy.
| | - Bastien Caillard
- European Risk Management Institute (EU-VRi), Fangelsbachstr. 14, 70178 Stuttgart, Germany.
| | - Alfonso Arevalillo
- TECNALIA, Basque Research and Technology Alliance (BRTA), Area Anardi 5, 20730 Azpeitia, Spain.
| | - Emeric Frejafon
- BRGM, 3 av. Claude-Guillemin, BP 36009, 45100 Orléans Cedex 2, France.
| | - Olivier Aguerre-Chariol
- Institut national de l'environnement industriel et des risques (INERIS), Rue Jacques Taffanel, Parc technologique ALATA, Verneuil-en-Halatte, 60550, France.
| | - Valeria Dulio
- Institut national de l'environnement industriel et des risques (INERIS), Rue Jacques Taffanel, Parc technologique ALATA, Verneuil-en-Halatte, 60550, France.
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Zhang S, Xiao J, Chen X, Li Y. Insulation and Flame Retardancy Improvement of PBDEs Using 3D-QSAR Model Combined with a Fuzzy Membership Function Method. Chem Res Chin Univ 2021. [DOI: 10.1007/s40242-021-0358-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Chauhan PS, Yadav D, Koul B, Mohanta YK, Jin JO. Recent Advances in Nanotechnology: A Novel Therapeutic System for the Treatment of Alzheimer's Disease. Curr Drug Metab 2020; 21:1144-1151. [PMID: 33234100 DOI: 10.2174/1389200221666201124140518] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 07/14/2020] [Accepted: 10/15/2020] [Indexed: 11/22/2022]
Abstract
A amyloid-β (Aβ) plaque formation in the brain is known to be the root cause of Alzheimer's disease (AD), which affects the behavior, memory, and cognitive ability in humans. The brain starts undergoing changes several years before the actual appearance of the symptoms. Nanotechnology could prove to be an alternative strategy for treating the disease effectively. It encompasses the diagnosis as well as the therapeutic aspect using validated biomarkers and nano-based drug delivery systems, respectively. A nano-based therapy may provide an alternate strategy, wherein one targets the protofibrillar amyloid-β (Aβ) structures, and this is followed by their disaggregation as random coils. Conventional/routine drug therapies are inefficient in crossing the blood-brain barrier; however, this hurdle can be overcome with the aid of nanoparticles. The present review highlights the various challenges in the diagnosis and treatment of AD. Meticulous and collaborative research using nanotherapeutic systems could provide remarkable breakthroughs in the early-stage diagnosis and therapy of AD.
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Affiliation(s)
- Pallavi Singh Chauhan
- Amity Institute of Biotechnology, Amity University Madhya Pradesh, Gwalior, 474005, India
| | - Dhananjay Yadav
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, South Korea
| | - Bhupendra Koul
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara-144411, Punjab, India
| | - Yugal Kishore Mohanta
- Biochemistry Laboratory, Department of Botany, North Orissa University Baripada- 757003, India
| | - Jun-O Jin
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, South Korea
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Serdiuk V, Shogren KL, Kovalenko T, Rasulev B, Yaszemski M, Maran A, Voronov A. Detection of macromolecular inversion-induced structural changes in osteosarcoma cells by FTIR microspectroscopy. Anal Bioanal Chem 2020; 412:7253-7262. [PMID: 32879994 DOI: 10.1007/s00216-020-02858-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/01/2020] [Accepted: 08/03/2020] [Indexed: 11/29/2022]
Abstract
Fourier transform infrared (FTIR) microspectroscopy provides a biochemical fingerprint of the cells. In this study, chemical changes in 143B osteosarcoma cells were investigated using FTIR analysis of cancer cells after their treatment with polymeric invertible micellar assemblies (IMAs) and curcumin-loaded IMAs and compared with untreated osteosarcoma cells. A comprehensive principal component analysis (PCA) was applied to analyze the FTIR results and confirm noticeable changes in cell surface chemical structures in the fingerprint regions of 1480-900 cm-1. The performed clustering shows visible differences for all investigated groups of cancer cells. It is demonstrated that a combination of FTIR microspectroscopy with PCA can be an efficient approach in determining interactions of osteosarcoma cells and drug-loaded polymer micellar assemblies. Graphical abstract.
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Affiliation(s)
- Vitalii Serdiuk
- Department of Orthopedics, Mayo Clinic, Rochester, MN, 55905, USA.,Department of Coatings & Polymeric Materials, North Dakota State University, Fargo, ND, 58105, USA.,Department of Organic Chemistry, Lviv Polytechnic National University, Lviv, 79013, Ukraine
| | | | - Tetiana Kovalenko
- Department of Organic Chemistry, Lviv Polytechnic National University, Lviv, 79013, Ukraine
| | - Bakhtiyor Rasulev
- Department of Coatings & Polymeric Materials, North Dakota State University, Fargo, ND, 58105, USA
| | | | | | - Andriy Voronov
- Department of Coatings & Polymeric Materials, North Dakota State University, Fargo, ND, 58105, USA.
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Di Costanzo L, Geremia S. Atomic Details of Carbon-Based Nanomolecules Interacting with Proteins. Molecules 2020; 25:E3555. [PMID: 32759758 PMCID: PMC7435792 DOI: 10.3390/molecules25153555] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 07/30/2020] [Accepted: 07/31/2020] [Indexed: 12/21/2022] Open
Abstract
Since the discovery of fullerene, carbon-based nanomolecules sparked a wealth of research across biological, medical and material sciences. Understanding the interactions of these materials with biological samples at the atomic level is crucial for improving the applications of nanomolecules and address safety aspects concerning their use in medicine. Protein crystallography provides the interface view between proteins and carbon-based nanomolecules. We review forefront structural studies of nanomolecules interacting with proteins and the mechanism underlying these interactions. We provide a systematic analysis of approaches used to select proteins interacting with carbon-based nanomolecules explored from the worldwide Protein Data Bank (wwPDB) and scientific literature. The analysis of van der Waals interactions from available data provides important aspects of interactions between proteins and nanomolecules with implications on functional consequences. Carbon-based nanomolecules modulate protein surface electrostatic and, by forming ordered clusters, could modify protein quaternary structures. Lessons learned from structural studies are exemplary and will guide new projects for bioimaging tools, tuning of intrinsically disordered proteins, and design assembly of precise hybrid materials.
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Affiliation(s)
- Luigi Di Costanzo
- Department of Agricultural Sciences, University of Naples Federico II, 100, 80055 Portici, Italy
| | - Silvano Geremia
- Centre of Excellence in Biocrystallography, Department of Chemical and Pharmaceutical Sciences, University of Trieste, 34127 Trieste, Italy;
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