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Ray P, Sedigh A, Confeld M, Alhalhooly L, Iduoku K, Casanola-Martin GM, Pham-The H, Rasulev B, Choi Y, Yang Z, Mallik S, Quadir M. Design and Evaluation of Nanoscale Materials with Programmed Responsivity towards Epigenetic Enzymes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.26.585429. [PMID: 38586020 PMCID: PMC10996597 DOI: 10.1101/2024.03.26.585429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Self-assembled materials capable of modulating their assembly properties in response to specific enzymes play a pivotal role in advancing 'intelligent' encapsulation platforms for biotechnological applications. Here, we introduce a previously unreported class of synthetic nanomaterials that programmatically interact with histone deacetylase (HDAC) as the triggering stimulus for disassembly. These nanomaterials consist of co-polypeptides comprising poly (acetyl L-lysine) and poly(ethylene glycol) blocks. Under neutral pH conditions, they self-assemble into particles. However, their stability is compromised upon exposure to HDACs, depending on enzyme concentration and exposure time. Our investigation, utilizing HDAC8 as the model enzyme, revealed that the primary mechanism behind disassembly involves a decrease in amphiphilicity within the block copolymer due to the deacetylation of lysine residues within the particles' hydrophobic domains. To elucidate the response mechanism, we encapsulated a fluorescent dye within these nanoparticles. Upon incubation with HDAC, the nanoparticle structure collapsed, leading to controlled release of the dye over time. Notably, this release was not triggered by denatured HDAC8, other proteolytic enzymes like trypsin, or the co-presence of HDAC8 and its inhibitor. We further demonstrated the biocompatibility and cellular effects of these materials and conducted a comprehensive computational study to unveil the possible interaction mechanism between enzymes and particles. By drawing parallels to the mechanism of naturally occurring histone proteins, this research represents a pioneering step toward developing functional materials capable of harnessing the activity of epigenetic enzymes such as HDACs.
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Karuth A, Casanola-Martin GM, Lystrom L, Sun W, Kilin D, Kilina S, Rasulev B. Combined Machine Learning, Computational, and Experimental Analysis of the Iridium(III) Complexes with Red to Near-Infrared Emission. J Phys Chem Lett 2024; 15:471-480. [PMID: 38190332 DOI: 10.1021/acs.jpclett.3c02533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Various coordination complexes have been the subject of experimental and theoretical studies in recent decades because of their fascinating photophysical properties. In this work, a combined experimental and computational approach was applied to investigate the optical properties of monocationic Ir(III) complexes. An interpretative machine learning-based quantitative structure-property relationship (ML/QSPR) model was successfully developed that could reliably predict the emission wavelength of the Ir(III) complexes and provide a foundation for the theoretical evaluation of the optical properties of Ir(III) complexes. A hypothesis was proposed to explain the differences in the emission wavelengths between structurally different individual Ir(III) complexes. The efficacy of the developed model was demonstrated by high R2 values of 0.84 and 0.87 for the training and test sets, respectively. It is worth noting that a relationship between the N-N distance in the diimine ligands of the Ir(III) complexes and emission wavelengths is detected. This effect is most probably associated with a degree of distortion in the octahedral geometry of the complexes, resulting in a perturbed ligand field. This combined experimental and computational approach shows great potential for the rational design of new Ir(III) complexes with the desired optical properties. Moreover, the developed methodology could be extended to other transition-metal complexes.
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Affiliation(s)
- Anas Karuth
- Coatings and Polymeric Materials, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Gerardo M Casanola-Martin
- Coatings and Polymeric Materials, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Levi Lystrom
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Wenfang Sun
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Dmitri Kilin
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Svetlana Kilina
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Bakhtiyor Rasulev
- Coatings and Polymeric Materials, North Dakota State University, Fargo, North Dakota 58108, United States
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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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A. A. Ibrahim M, S. M. Rady AS, A. M. Moussa N, Naeem Ahmed M, Sidhom PA, Shawky AM, Alqahtani AM, Mohamed LA. Investigation of Aluminum Nitride Nanocarrier for Drug Delivery Process of Favipiravir: A DFT Study. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Grasso G, Di Gregorio A, Mavkov B, Piga D, Labate GFD, Danani A, Deriu MA. Fragmented blind docking: a novel protein-ligand binding prediction protocol. J Biomol Struct Dyn 2022; 40:13472-13481. [PMID: 34641761 DOI: 10.1080/07391102.2021.1988709] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In the present paper we propose a novel blind docking protocol based on Autodock-Vina. The developed docking protocol can provide binding site identification and binding pose prediction at the same time, by a systematical exploration of the protein volume performed with several preliminary docking calculations. In our opinion, this protocol can be successfully applied during the first steps of the virtual screening pipeline, because it provides binding site identification and binding pose prediction at the same time without visual evaluation of the binding site. After the binding pose prediction, MM/GBSA re-scoring rescoring procedures has been applied to improve the accuracy of the protein-ligand bound state. The FRAD protocol has been tested on 116 protein-ligand complexes of the Heat Shock Protein 90 - alpha, on 176 of Human Immunodeficiency virus protease 1, and on more than 100 protein-ligand system taken from the PDBbind dataset. Overall, the FRAD approach combined to MM/GBSA re-scoring can be considered as a powerful tool to increase the accuracy and efficiency with respect to other standard docking approaches when the ligand-binding site is unknown.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gianvito Grasso
- Dalle Molle Institute for Artificial Intelligence, IDSIA - USI/SUPSI, Lugano-Viganello, Switzerland
| | - Arianna Di Gregorio
- Dalle Molle Institute for Artificial Intelligence, IDSIA - USI/SUPSI, Lugano-Viganello, Switzerland.,PolitoBIOMedLab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Italy
| | - Bojan Mavkov
- Dalle Molle Institute for Artificial Intelligence, IDSIA - USI/SUPSI, Lugano-Viganello, Switzerland
| | - Dario Piga
- Dalle Molle Institute for Artificial Intelligence, IDSIA - USI/SUPSI, Lugano-Viganello, Switzerland
| | | | - Andrea Danani
- Dalle Molle Institute for Artificial Intelligence, IDSIA - USI/SUPSI, Lugano-Viganello, Switzerland
| | - Marco A Deriu
- PolitoBIOMedLab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Italy
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Wang Q, Zhang P, Javed Ansari M, Aldawsari MF, Alalaiwe AS, Kaur J, Kumar R, Ng Kay Lup A, Enayati A, Mirzaei H, Soltani A, Su CH, Nguyen HC. Electrostatic interaction assisted Ca-decorated C20 fullerene loaded to anti-inflammatory drugs to manage cardiovascular disease risk in rheumatoid arthritis patients. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118564] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Patnode K, Rasulev B, Voronov A. Synergistic Behavior of Plant Proteins and Biobased Latexes in Bioplastic Food Packaging Materials: Experimental and Machine Learning Study. ACS APPLIED MATERIALS & INTERFACES 2022; 14:8384-8393. [PMID: 35119263 DOI: 10.1021/acsami.1c21650] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Plant-based proteins are attractive components which may serve as sustainable alternatives to current petrochemical products. Both soy protein and major corn protein, zein, are of interest in food packaging applications due to their sustainability, biodegradation properties, and inherent physicochemical properties. This study discusses the development of bioplastic materials, where it explores the effects of combining zein, soy protein, and plasticizing latexes derived from plant oil-based monomers (POBMs) on properties of resulting bioplastic films. By looking for synergistic effects of soy protein's inherent film formation ability and zein's higher strength, we prepare strong yet flexible soy-zein films as materials, called proteoposites. Incorporation of natural additive POBM-latexes helps to plasticize and hydrophobize the bioplastic films and thus to improve mechanical and barrier properties. Variation of the POBM-latexes' particle size further aims to enhance the performance of resulting bioplastic films. As a result, modified soy-zein proteoposite films with improved moisture resistance, enhanced mechanical behavior, and greater barrier properties were developed. Machine learning-based computational models were utilized in order to find main structural factors affecting the bioplastic's properties and develop a quantitative structure-property relationship model between the physicochemical properties of the film components and the resulted bioplastics' properties and performance. The developed model effectively predicts experimental outcomes with >85% (R2: 0.85) accuracy. The newly synthesized proteoposites confirmed the machine learning model predictions. As a result, proteoposite films made of two plant proteins and modified with POBM-latexes can be considered as an attractive and viable replacement for petrochemical food packaging products.
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Affiliation(s)
- Kristen Patnode
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, North Dakota 58102-6050, United States
| | - Bakhtiyor Rasulev
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, North Dakota 58102-6050, United States
| | - Andriy Voronov
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, North Dakota 58102-6050, United States
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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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A partial least squares and artificial neural network study for a series of arylpiperazines as antidepressant agents. J Mol Model 2021; 27:297. [PMID: 34558019 DOI: 10.1007/s00894-021-04906-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/08/2021] [Indexed: 10/20/2022]
Abstract
Depression affects more than 300 million people around the world and can lead to suicide. About 30% of patients on treatment for depression drop out of therapy due to side effects or to latency time associated to therapeutic effects. 5-HT receptor, known as serotonin, is considered the key in depression treatment. Arylpiperazine compounds are responsible for several pharmacological effects and are considered as ligands in serotonin receptors, such as the subtype 5-HT2a. Here, in silico studies were developed using partial least squares (PLSs) and artificial neural networks (ANNs) to design new arylpiperazine compounds that could interact with the 5-HT2a receptor. First, molecular and electronic descriptors were calculated and posteriorly selected from correlation matrixes and genetic algorithm (GA). Then, the selected descriptors were used to construct PLS and ANN models that showed to be robust and predictive. Lastly, new arylpiperazine compounds were designed and their biological activity values were predicted by both PLS and ANN models. It is worth to highlight compounds G5 and G7 (predicted by the PLS model) and G3 and G15 (predicted by the ANN model), whose predicted pIC50 values were as high as the three highest values from the arylpiperazine original set studied here. Therefore, it can be asserted that the two models (PLS and ANN) proposed in this work are promising for the prediction of the biological activity of new arylpiperazine compounds and may significantly contribute to the design of new drugs for the treatment of depression.
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Karuth A, Alesadi A, Xia W, Rasulev B. Predicting glass transition of amorphous polymers by application of cheminformatics and molecular dynamics simulations. POLYMER 2021. [DOI: 10.1016/j.polymer.2021.123495] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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11
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Noureddine O, Issaoui N, Al-Dossary O. DFT and molecular docking study of chloroquine derivatives as antiviral to coronavirus COVID-19. JOURNAL OF KING SAUD UNIVERSITY SCIENCE 2020; 33:101248. [PMID: 33250604 PMCID: PMC7687412 DOI: 10.1016/j.jksus.2020.101248] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/02/2020] [Accepted: 11/18/2020] [Indexed: 01/18/2023]
Abstract
The recently emerged COVID-19 virus caused hundreds of thousands of deaths and instigated a widespread fear, threatening the world’s most advanced health security. In 2020, chloroquine derivatives are among the drugs tested against the coronavirus pandemic and showed an apparent efficacy. In the present work, the chloroquine and the chloroquine phosphate molecules have been proposed as potential antiviral for the treatment of COVID-19 diseases combining DFT and molecular docking calculations. Molecular geometries, electronic properties and molecular electrostatic potential were investigated using density functional theory (DFT) at the B3LYP/6-31G* method. As results, we found a good agreement between the theoretical and the experimental geometrical parameters (bond lengths and bond angles). The frontier orbitals analysis has been calculated at the same level of theory to determine the charge transfer within the molecule. In order to perform a better description of the FMOs, the density of states was determined. The molecular electrostatic potential maps were calculated to provide information on the chemical reactivity of molecule and also to describe the intermolecular interactions. All these studies help us a lot in determining the reactivity of the mentioned compounds. Finally, docking calculations were carried out to determine the pharmaceutical activities of the chloroquine derivatives against coronavirus diseases. The choice of these ligands was based on their antiviral activities.
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Affiliation(s)
- Olfa Noureddine
- University of Monastir, Laboratory of Quantum and Statistical Physics (LR18ES18), Faculty of Sciences, Monastir 5079, Tunisia
| | - Noureddine Issaoui
- University of Monastir, Laboratory of Quantum and Statistical Physics (LR18ES18), Faculty of Sciences, Monastir 5079, Tunisia
| | - Omar Al-Dossary
- Department of Physics and Astronomy, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
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Almagro L, Lemos R, Makowski K, Rodríguez H, Ortiz O, Cáceres W, Herranz MÁ, Molero D, Martínez‐Álvarez R, Suárez M, Martín N. [60]Fullerene Hybrids Bearing “Steroid Wings”: A Joined Experimental and Theoretical Investigation. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000989] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Luis Almagro
- Laboratorio de Síntesis Orgánica Facultad de Química Universidad de la Habana 10400 La Habana Cuba
| | - Reinier Lemos
- Laboratorio de Síntesis Orgánica Facultad de Química Universidad de la Habana 10400 La Habana Cuba
| | - Kamil Makowski
- School of Chemical Sciences and Engineering Yachay Tech University 100119 Urququi Ecuador
| | - Hortensia Rodríguez
- School of Chemical Sciences and Engineering Yachay Tech University 100119 Urququi Ecuador
| | - Orlando Ortiz
- Laboratorio de Síntesis Orgánica Facultad de Química Universidad de la Habana 10400 La Habana Cuba
| | - William Cáceres
- Laboratorio de Síntesis Orgánica Facultad de Química Universidad de la Habana 10400 La Habana Cuba
| | - M. Ángeles Herranz
- Departamento de Química Orgánica Facultad de Ciencias Químicas Universidad Complutense de Madrid 28040 Madrid Spain
| | - Dolores Molero
- CAI RMN Universidad Complutense de Madrid 28040 Madrid Spain
| | - Roberto Martínez‐Álvarez
- Departamento de Química Orgánica Facultad de Ciencias Químicas Universidad Complutense de Madrid 28040 Madrid Spain
| | - Margarita Suárez
- Laboratorio de Síntesis Orgánica Facultad de Química Universidad de la Habana 10400 La Habana Cuba
| | - Nazario Martín
- Departamento de Química Orgánica Facultad de Ciencias Químicas Universidad Complutense de Madrid 28040 Madrid Spain
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Alonso D, Hernández-Castillo D, Almagro L, González-Alemán R, Molero D, Herranz MÁ, Medina-Páez E, Coro J, Martínez-Álvarez R, Suárez M, Martín N. Diastereoselective Synthesis of Steroid–[60]Fullerene Hybrids and Theoretical Underpinning. J Org Chem 2020; 85:2426-2437. [DOI: 10.1021/acs.joc.9b03121] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Dayana Alonso
- Laboratorio de Sı́ntesis Orgánica, Facultad de Quı́mica, Universidad de la Habana, 10400 La Habana, Cuba
| | - David Hernández-Castillo
- Laboratorio de Quı́mica Computacional y Teórica, Facultad de Quı́mica, Universidad de la Habana, 10400 La Habana, Cuba
| | - Luis Almagro
- Laboratorio de Sı́ntesis Orgánica, Facultad de Quı́mica, Universidad de la Habana, 10400 La Habana, Cuba
| | - Roy González-Alemán
- Laboratorio de Quı́mica Computacional y Teórica, Facultad de Quı́mica, Universidad de la Habana, 10400 La Habana, Cuba
| | - Dolores Molero
- CAI RMN, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - M. Ángeles Herranz
- Departamento de Quı́mica Orgánica, Facultad de Ciencias Quı́micas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Erick Medina-Páez
- Laboratorio de Quı́mica Computacional y Teórica, Facultad de Quı́mica, Universidad de la Habana, 10400 La Habana, Cuba
| | - Julieta Coro
- Laboratorio de Sı́ntesis Orgánica, Facultad de Quı́mica, Universidad de la Habana, 10400 La Habana, Cuba
| | - Roberto Martínez-Álvarez
- Departamento de Quı́mica Orgánica, Facultad de Ciencias Quı́micas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Margarita Suárez
- Laboratorio de Sı́ntesis Orgánica, Facultad de Quı́mica, Universidad de la Habana, 10400 La Habana, Cuba
| | - Nazario Martín
- Departamento de Quı́mica Orgánica, Facultad de Ciencias Quı́micas, Universidad Complutense de Madrid, 28040 Madrid, Spain
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Fullerene C60 containing porphyrin-like metal center as drug delivery system for ibuprofen drug. J Mol Model 2019; 26:7. [PMID: 31834504 DOI: 10.1007/s00894-019-4267-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 11/25/2019] [Indexed: 10/25/2022]
Abstract
Today, drug delivery systems based on nanostructures have become the most efficient to be studied. Recent studies revealed that the fullerenes can be used as drug carriers and transport drugs in a target cell. The aim of the present work is to study the interaction of C60 fullerene containing porphyrin-like transition metal-N4 clusters (TMN4C55, TM = Fe, Co, and Ni) with a non-steroidal anti-inflammatory drug (ibuprofen (Ibp)) by employing the method of the density functional theory. Results showed that the C60 fullerene with TMN4 clusters could significantly enhance the tendency of C60 for adsorption of ibuprofen drug. Also, our ultraviolet-visible results show that the electronic spectra of Ibp/TMN4C55 complexes exhibit a blue shift toward lower wavelengths (higher energies). It was found that the NiN4C55 fullerene had high chemical reactivity, which was important for binding of the drug onto the carrier surface. In order to gain insight into the binding features of Ibp/TMN4C55 complexes, the atoms in molecules analysis was also performed. Our results exhibit the electrostatic features of the Ibp/TMN4C55 bonding. Consequently, this study demonstrated that the TMN4C55 fullerenes could be used as potential carriers for delivery of Ibp drug in the nanomedicine domain. Graphical Abstract The TMN4C55 (TM=Fe, Co, and Ni) fullerenes could be used as potential carriers for delivery of ibuprofen drug in the nanomedicine domain.
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Buglak AA, Zherdev AV, Dzantiev BB. Nano-(Q)SAR for Cytotoxicity Prediction of Engineered Nanomaterials. Molecules 2019; 24:molecules24244537. [PMID: 31835808 PMCID: PMC6943593 DOI: 10.3390/molecules24244537] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 11/24/2019] [Accepted: 12/10/2019] [Indexed: 12/12/2022] Open
Abstract
Although nanotechnology is a new and rapidly growing area of science, the impact of nanomaterials on living organisms is unknown in many aspects. In this regard, it is extremely important to perform toxicological tests, but complete characterization of all varying preparations is extremely laborious. The computational technique called quantitative structure–activity relationship, or QSAR, allows reducing the cost of time- and resource-consuming nanotoxicity tests. In this review, (Q)SAR cytotoxicity studies of the past decade are systematically considered. We regard here five classes of engineered nanomaterials (ENMs): Metal oxides, metal-containing nanoparticles, multi-walled carbon nanotubes, fullerenes, and silica nanoparticles. Some studies reveal that QSAR models are better than classification SAR models, while other reports conclude that SAR is more precise than QSAR. The quasi-QSAR method appears to be the most promising tool, as it allows accurately taking experimental conditions into account. However, experimental artifacts are a major concern in this case.
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Affiliation(s)
- Andrey A. Buglak
- A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia; (A.V.Z.); (B.B.D.)
- Physical Faculty, St. Petersburg State University, 7/9 Universitetskaya Naberezhnaya, 199034 St. Petersburg, Russia
- Correspondence: ; Tel.: +7-(495)-954-27-32
| | - Anatoly V. Zherdev
- A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia; (A.V.Z.); (B.B.D.)
- Institute of Physiologically Active Compounds, Russian Academy of Sciences, Severny Proezd 1, 142432 Chernogolovka, Moscow Region, Russia
| | - Boris B. Dzantiev
- A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia; (A.V.Z.); (B.B.D.)
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Al-Wahaibi LH, Sert Y, Ucun F, Al-Shaalan NH, Alsfouk A, El-Emam AA, Karakaya M. Theoretical and experimental spectroscopic studies, XPS analysis, dimer interaction energies and molecular docking study of 5-(adamantan-1-yl)-N-methyl-1,3,4-thiadiazol-2-amine. JOURNAL OF PHYSICS AND CHEMISTRY OF SOLIDS 2019. [DOI: 10.1016/j.jpcs.2019.109091] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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17
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Gao J, Guo C, Wang X, Zhang W, Wang Y, Vahabi V. Porphyrin-like porous nanomaterials as drug delivery systems for ibuprofen drug. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1678776] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jiali Gao
- Affiliated Hospital of Inner Mongolia Medical University Pharmacy Department, Hohhot, Inner Mongolia, China
| | - Chunyan Guo
- Affiliated Hospital of Inner Mongolia Medical University Pharmacy Department, Hohhot, Inner Mongolia, China
| | - Xin Wang
- Affiliated Hospital of Inner Mongolia Medical University Pharmacy Department, Hohhot, Inner Mongolia, China
| | - Wenxu Zhang
- Affiliated Hospital of Inner Mongolia Medical University Pharmacy Department, Hohhot, Inner Mongolia, China
| | - Yang Wang
- Affiliated Hospital of Inner Mongolia Medical University Pharmacy Department, Hohhot, Inner Mongolia, China
| | - Vahid Vahabi
- Young Researchers and Elite Club, Central Tehran Branch, Islamic Azad University, Tehran, Iran
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18
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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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19
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Kyzyma O, Bashmakova N, Gorshkova Y, Ivankov O, Mikheev I, Kuzmenko M, Kutovyy S, Nikolaienko T. Interaction between the plant alkaloid berberine and fullerene C70: Experimental and quantum-chemical study. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.01.062] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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20
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Farmanzadeh D, Keyhanian M. Computational assessment on the interaction of amantadine drug with B12N12 and Zn12O12 nanocages and improvement in adsorption behaviors by impurity Al doping. Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2400-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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21
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Chen M, Jabeen F, Rasulev B, Ossowski M, Boudjouk P. A computational structure–property relationship study of glass transition temperatures for a diverse set of polymers. ACTA ACUST UNITED AC 2018. [DOI: 10.1002/polb.24602] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Min Chen
- Center for Computationally Assisted Science and TechnologyNorth Dakota State UniversityFargo North Dakota58102
- Department of Computer ScienceNorth Dakota State UniversityFargo North Dakota58102
| | - Farukh Jabeen
- Center for Computationally Assisted Science and TechnologyNorth Dakota State UniversityFargo North Dakota58102
| | - Bakhtiyor Rasulev
- Center for Computationally Assisted Science and TechnologyNorth Dakota State UniversityFargo North Dakota58102
- Department of Coatings and Polymeric MaterialsNorth Dakota State UniversityFargo North Dakota58102
| | - Martin Ossowski
- Center for Computationally Assisted Science and TechnologyNorth Dakota State UniversityFargo North Dakota58102
| | - Philip Boudjouk
- Department of Chemistry and BiochemistryNorth Dakota State UniversityFargo North Dakota58102
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22
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Sizochenko N, Mikolajczyk A, Leszczynski J, Puzyn T. In Silico Methods for Nanotoxicity Evaluation: Opportunities and Challenges. Nanotoxicology 2018. [DOI: 10.1201/b21545-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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23
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Fullerene quinazolinone conjugates targeting Mycobacterium tuberculosis: a combined molecular docking, QSAR, and ONIOM approach. Struct Chem 2018. [DOI: 10.1007/s11224-018-1100-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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24
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Greber KE, Ciura K, Belka M, Kawczak P, Nowakowska J, Bączek T, Sawicki W. Characterization of antimicrobial and hemolytic properties of short synthetic cationic lipopeptides based on QSAR/QSTR approach. Amino Acids 2017; 50:479-485. [PMID: 29264738 PMCID: PMC5852172 DOI: 10.1007/s00726-017-2530-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 12/12/2017] [Indexed: 01/04/2023]
Abstract
In this study, we investigated the influence of molecular descriptors of cationic lipopeptides on their antimicrobial activity and hemolytic properties. The quantitative structure-activity relationship and quantitative structure-property relationship models were constructed. The antimicrobial, hemolytic and retention data were used as dependent variable and structural parameters as the independent ones. The obtained results suggest that the chromatographic indexes can be employed for prediction of antibacterial activity and that lipopeptides present nonspecific interaction between erythrocytes and bacterial membranes.
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Affiliation(s)
- Katarzyna E Greber
- Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland.
| | - Krzesimir Ciura
- Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland
| | - Mariusz Belka
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland
| | - Piotr Kawczak
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland
| | - Joanna Nowakowska
- Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland
| | - Tomasz Bączek
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland
| | - Wiesław Sawicki
- Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Al. Gen. J. Hallera 107, 80-416, Gdańsk, Poland
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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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26
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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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Rasulev B, Jabeen F, Stafslien S, Chisholm BJ, Bahr J, Ossowski M, Boudjouk P. Polymer Coating Materials and Their Fouling Release Activity: A Cheminformatics Approach to Predict Properties. ACS APPLIED MATERIALS & INTERFACES 2017; 9:1781-1792. [PMID: 27982587 DOI: 10.1021/acsami.6b12766] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A novel cheminformatics-based approach has been employed to investigate a set of polymer coating materials designed to mitigate the accumulation of marine biofouling on surfaces immersed in the sea. Specifically, a set of 27 nontoxic, amphiphilic polysiloxane-based polymer coatings was synthesized using a combinatorial, high-throughput approach and characterized for fouling-release (FR) activity toward a number of relevant marine fouling organisms, including bacteria, microalgae, and adult barnacles. In order to model these complex systems adequately, a new computational technique was used in which all investigated polymer-based coating materials were considered as mixture systems comprising several compositional variables at a range of concentrations. By applying a combination of methodologies for mixture systems and a quantitative structure-activity relationship approach (QSAR), seven unique QSAR models were developed that were able to successfully predict the desired FR properties. Furthermore, the developed models identified several significant descriptors responsible for FR activity of investigated polymer-based coating materials, with correlation coefficients ranging from rtest2 = 0.63 to 0.94. The computational models derived from this study may serve as a powerful set of tools to predict optimal combinations of source components to produce amphiphilic polysiloxane-based coating systems with effective, broad-spectrum FR properties.
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Affiliation(s)
- Bakhtiyor Rasulev
- Center for Computationally Assisted Science and Technology, North Dakota State University , Fargo, North Dakota, United States
- Department of Coatings and Polymeric Materials, North Dakota State University , Fargo, North Dakota, United States
| | - Farukh Jabeen
- Center for Computationally Assisted Science and Technology, North Dakota State University , Fargo, North Dakota, United States
| | - Shane Stafslien
- Research and Creative Activities, North Dakota State University , Fargo, North Dakota, United States
| | - Bret J Chisholm
- Department of Coatings and Polymeric Materials, North Dakota State University , Fargo, North Dakota, United States
| | - James Bahr
- Research and Creative Activities, North Dakota State University , Fargo, North Dakota, United States
| | - Martin Ossowski
- Center for Computationally Assisted Science and Technology, North Dakota State University , Fargo, North Dakota, United States
| | - Philip Boudjouk
- Center for Computationally Assisted Science and Technology, North Dakota State University , Fargo, North Dakota, United States
- Department of Chemistry and Biochemistry, North Dakota State University , Fargo, North Dakota, United States
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28
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Samanta PN, Das KK. Noncovalent interaction assisted fullerene for the transportation of some brain anticancer drugs: A theoretical study. J Mol Graph Model 2017; 72:187-200. [PMID: 28110183 DOI: 10.1016/j.jmgm.2017.01.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Revised: 01/04/2017] [Accepted: 01/05/2017] [Indexed: 01/21/2023]
Abstract
The treatment of brain cancer like glioblastoma multiforme often uses chemotherapeutic drugs like temozolomide, procarbazine, carmustine, and lomustine. Fullerene loaded with these drugs help to cross the blood brain barriers. The adsorptions of the four drug molecules on the surface of the fullerene are studied mostly by using density functional theory (DFT) based method at the M06-2X/6-31G(d) level of calculations. In all four cases, the estimated interactions are noncovalent type and the average adsorption energy lies in between -5 and -11kcal/mol in the gas phase. In the aqueous and protein environment such interactions are weakened further. The binding affinity is further assessed by performing MP2 based calculations to provide interaction energies with a reasonable accuracy. Stabilities and reactivities of the drug adsorbed fullerene complexes are determined from chemical reactivity descriptors. The attached drug molecules increase the polarity of the pristine C60 thus facilitating the drug delivery within the biological systems. The semiconducting behavior of C60 is retained in the C60-drug composite systems. The computed DOS, IR, UV spectra, and molecular orbitals in the vicinity of Fermi level are analyzed to reveal the nature of the noncovalent interactions between C60 and drug molecules. The Wiberg bond order values are used to estimate the strength of the adsorption of the drug molecule on C60. In all four C60-drug interactions, the chemical characteristics of the drug molecule are least perturbed by the C60 moiety thereby suggesting it to be a good carrier for the delivery of these brain anticancer drug molecules to the target cells.
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Affiliation(s)
- Pabitra Narayan Samanta
- Department of Chemistry, Physical Chemistry Section, Jadavpur University, Kolkata 700 032, India
| | - Kalyan Kumar Das
- Department of Chemistry, Physical Chemistry Section, Jadavpur University, Kolkata 700 032, India.
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29
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Castro E, Martinez ZS, Seong CS, Cabrera-Espinoza A, Ruiz M, Hernandez Garcia A, Valdez F, Llano M, Echegoyen L. Characterization of New Cationic N,N-Dimethyl[70]fulleropyrrolidinium Iodide Derivatives as Potent HIV-1 Maturation Inhibitors. J Med Chem 2016; 59:10963-10973. [PMID: 28002960 DOI: 10.1021/acs.jmedchem.6b00994] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
HIV-1 maturation can be impaired by altering protease (PR) activity, the structure of the Gag-Pol substrate, or the molecular interactions of viral structural proteins. Here we report the synthesis and characterization of new cationic N,N-dimethyl[70]fulleropyrrolidinium iodide derivatives that inhibit more than 99% of HIV-1 infectivity at low micromolar concentrations. Analysis of the HIV-1 life cycle indicated that these compounds inhibit viral maturation by impairing Gag and Gag-Pol processing. Importantly, fullerene derivatives 2a-c did not inhibit in vitro PR activity and strongly interacted with HIV immature capsid protein in pull-down experiments. Furthermore, these compounds potently blocked infectivity of viruses harboring mutant PR that are resistant to multiple PR inhibitors or mutant Gag proteins that confer resistance to the maturation inhibitor Bevirimat. Collectively, our studies indicate fullerene derivatives 2a-c as potent and novel HIV-1 maturation inhibitors.
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Affiliation(s)
- Edison Castro
- Department of Chemistry, University of Texas at El Paso , 500 West University Avenue, CCSB #3.0302, El Paso, Texas 79968, United States
| | - Zachary S Martinez
- Department of Biological Sciences, University of Texas at El Paso , 500 West University Avenue, El Paso, Texas 79968, United States
| | - Chang-Soo Seong
- Department of Biological Sciences, University of Texas at El Paso , 500 West University Avenue, El Paso, Texas 79968, United States
| | - Andrea Cabrera-Espinoza
- Department of Chemistry, University of Texas at El Paso , 500 West University Avenue, CCSB #3.0302, El Paso, Texas 79968, United States
| | - Mauro Ruiz
- Department of Chemistry, University of Texas at El Paso , 500 West University Avenue, CCSB #3.0302, El Paso, Texas 79968, United States
| | - Andrea Hernandez Garcia
- Department of Chemistry, University of Texas at El Paso , 500 West University Avenue, CCSB #3.0302, El Paso, Texas 79968, United States
| | - Federico Valdez
- Department of Biological Sciences, University of Texas at El Paso , 500 West University Avenue, El Paso, Texas 79968, United States
| | - Manuel Llano
- Department of Biological Sciences, University of Texas at El Paso , 500 West University Avenue, El Paso, Texas 79968, United States
| | - Luis Echegoyen
- Department of Chemistry, University of Texas at El Paso , 500 West University Avenue, CCSB #3.0302, El Paso, Texas 79968, United States
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30
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Raies AB, Bajic VB. In silico toxicology: computational methods for the prediction of chemical toxicity. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2016; 6:147-172. [PMID: 27066112 PMCID: PMC4785608 DOI: 10.1002/wcms.1240] [Citation(s) in RCA: 315] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 10/27/2015] [Accepted: 11/10/2015] [Indexed: 01/08/2023]
Abstract
Determining the toxicity of chemicals is necessary to identify their harmful effects on humans, animals, plants, or the environment. It is also one of the main steps in drug design. Animal models have been used for a long time for toxicity testing. However, in vivo animal tests are constrained by time, ethical considerations, and financial burden. Therefore, computational methods for estimating the toxicity of chemicals are considered useful. In silico toxicology is one type of toxicity assessment that uses computational methods to analyze, simulate, visualize, or predict the toxicity of chemicals. In silico toxicology aims to complement existing toxicity tests to predict toxicity, prioritize chemicals, guide toxicity tests, and minimize late-stage failures in drugs design. There are various methods for generating models to predict toxicity endpoints. We provide a comprehensive overview, explain, and compare the strengths and weaknesses of the existing modeling methods and algorithms for toxicity prediction with a particular (but not exclusive) emphasis on computational tools that can implement these methods and refer to expert systems that deploy the prediction models. Finally, we briefly review a number of new research directions in in silico toxicology and provide recommendations for designing in silico models. WIREs Comput Mol Sci 2016, 6:147-172. doi: 10.1002/wcms.1240 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Arwa B Raies
- King Abdullah University of Science and Technology (KAUST) Computational Bioscience Research Centre (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE) Thuwal Saudi Arabia
| | - Vladimir B Bajic
- King Abdullah University of Science and Technology (KAUST) Computational Bioscience Research Centre (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE) Thuwal Saudi Arabia
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Abstract
The interest of scientists in nanostructures has been increased in the last years and proper methods for their assessment are needed.In silicomethods found their usefulness in the replacement of experimental evaluation and are successfully used as efficient alternatives for estimation and prediction of compound’s properties or activities. In this paper, it is shown that a Quantitative Structure-Property Relationship method is proper to be applied also on nanostructures. Based on computational experiment, several models to describe the total strain energy of C42fullerene isomers were obtained and their characteristics are presented. Furthermore, the best performing model obtained on C42fullerene isomers was validated on C40fullerene isomers.
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Jagiello K, Grzonkowska M, Swirog M, Ahmed L, Rasulev B, Avramopoulos A, Papadopoulos MG, Leszczynski J, Puzyn T. Advantages and limitations of classic and 3D QSAR approaches in nano-QSAR studies based on biological activity of fullerene derivatives. JOURNAL OF NANOPARTICLE RESEARCH : AN INTERDISCIPLINARY FORUM FOR NANOSCALE SCIENCE AND TECHNOLOGY 2016; 18:256. [PMID: 27642255 PMCID: PMC5003910 DOI: 10.1007/s11051-016-3564-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 08/18/2016] [Indexed: 05/19/2023]
Abstract
In this contribution, the advantages and limitations of two computational techniques that can be used for the investigation of nanoparticles activity and toxicity: classic nano-QSAR (Quantitative Structure-Activity Relationships employed for nanomaterials) and 3D nano-QSAR (three-dimensional Quantitative Structure-Activity Relationships, such us Comparative Molecular Field Analysis, CoMFA/Comparative Molecular Similarity Indices Analysis, CoMSIA analysis employed for nanomaterials) have been briefly summarized. Both approaches were compared according to the selected criteria, including: efficiency, type of experimental data, class of nanomaterials, time required for calculations and computational cost, difficulties in the interpretation. Taking into account the advantages and limitations of each method, we provide the recommendations for nano-QSAR modellers and QSAR model users to be able to determine a proper and efficient methodology to investigate biological activity of nanoparticles in order to describe the underlying interactions in the most reliable and useful manner.
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Affiliation(s)
- Karolina Jagiello
- Laboratory of Environmental Chemometrics, Faculty of Chemistry, Institute for Environmental and Human Health Protection, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Monika Grzonkowska
- Laboratory of Environmental Chemometrics, Faculty of Chemistry, Institute for Environmental and Human Health Protection, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Marta Swirog
- Laboratory of Environmental Chemometrics, Faculty of Chemistry, Institute for Environmental and Human Health Protection, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Lucky Ahmed
- Interdisciplinary Nanotoxicity Center, Department of Chemistry and Biochemistry, Jackson State University, 1400 JR Lynch Street, Jackson, MS 39217-0510 USA
| | - Bakhtiyor Rasulev
- Interdisciplinary Nanotoxicity Center, Department of Chemistry and Biochemistry, Jackson State University, 1400 JR Lynch Street, Jackson, MS 39217-0510 USA
- Center for Computationally Assisted Science and Technology, North Dakota State University, 1805 NDSU Research Park Drive, Post Office Box 6050, Fargo, ND 58108 USA
| | - Aggelos Avramopoulos
- Institute of Biology, Pharmaceutical Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Ave., 11635 Athens, Greece
| | - Manthos G. Papadopoulos
- Institute of Biology, Pharmaceutical Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Ave., 11635 Athens, Greece
| | - Jerzy Leszczynski
- Interdisciplinary Nanotoxicity Center, Department of Chemistry and Biochemistry, Jackson State University, 1400 JR Lynch Street, Jackson, MS 39217-0510 USA
| | - Tomasz Puzyn
- Laboratory of Environmental Chemometrics, Faculty of Chemistry, Institute for Environmental and Human Health Protection, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
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33
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Erzincan P, Saçan MT, Yüce-Dursun B, Danış Ö, Demir S, Erdem SS, Ogan A. QSAR models for antioxidant activity of new coumarin derivatives. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2015; 26:721-737. [PMID: 26470736 DOI: 10.1080/1062936x.2015.1088571] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 08/26/2015] [Indexed: 06/05/2023]
Abstract
This study presents 37 new antioxidant coumarin derivatives and strategies for structural modification to improve their antioxidant activities, the main ferric-reducing antioxidant power (FRAP) assay used to evaluate their antioxidant properties and the generation of validated quantitative structure-activity (antioxidant activity) relationship (QSAR) models. In an attempt to generate QSAR models, structures of all coumarin derivatives in the data set were fully optimized by semi-empirical PM6 method using SPARTAN 10 software. Descriptors were calculated by DRAGON 6.0 software. Multiple linear regression (MLR) models were developed with different training/test set combinations using QSARINS 2.2.1 software. Robustness, reliability and predictive power of the models were tested by internal and external validations. Applicability domain of the best two-descriptor model (nTR = 30; r(2) = 0.924; RMSETR = 0.213; nTEST = 7; r(2)ext = 0.887; RMSEext = 0.255; CCCext = 0.939) was determined. Descriptors appeared in the model revealed that complexity, H-bond donor and lipophilic character are important parameters in describing the antioxidant activity. Apart from the compounds in the data set, we also designed 31 new antioxidant coumarin derivatives and predicted their antioxidant activity using the best two-descriptor model. Most of these compounds are promising antioxidants.
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Affiliation(s)
- P Erzincan
- a Marmara University , Chemistry Department, Faculty of Arts and Sciences , Istanbul , Turkey
| | - M T Saçan
- b Boğaziçi University, Institute of Environmental Sciences , Istanbul , Turkey
| | - B Yüce-Dursun
- a Marmara University , Chemistry Department, Faculty of Arts and Sciences , Istanbul , Turkey
| | - Ö Danış
- a Marmara University , Chemistry Department, Faculty of Arts and Sciences , Istanbul , Turkey
| | - S Demir
- a Marmara University , Chemistry Department, Faculty of Arts and Sciences , Istanbul , Turkey
| | - S S Erdem
- a Marmara University , Chemistry Department, Faculty of Arts and Sciences , Istanbul , Turkey
| | - A Ogan
- a Marmara University , Chemistry Department, Faculty of Arts and Sciences , Istanbul , Turkey
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34
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Warr WA. Many InChIs and quite some feat. J Comput Aided Mol Des 2015; 29:681-94. [PMID: 26081259 DOI: 10.1007/s10822-015-9854-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 06/10/2015] [Indexed: 12/14/2022]
Affiliation(s)
- Wendy A Warr
- Wendy Warr & Associates, Holmes Chapel, Crewe, Cheshire, CW4 7HZ, UK,
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Yilmaz H, Sizochenko N, Rasulev B, Toropov A, Guzel Y, Kuz'min V, Leszczynska D, Leszczynski J. Amino substituted nitrogen heterocycle ureas as kinase insert domain containing receptor (KDR) inhibitors: Performance of structure–activity relationship approaches. J Food Drug Anal 2015; 23:168-175. [PMID: 28911371 PMCID: PMC9351780 DOI: 10.1016/j.jfda.2015.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
A quantitative structure–activity relationship (QSAR) study was performed on a set of amino-substituted nitrogen heterocyclic urea derivatives. Two novel approaches were applied: (1) the simplified molecular input-line entry systems (SMILES) based optimal descriptors approach; and (2) the fragment-based simplex representation of molecular structure (SiRMS) approach. Comparison with the classic scheme of building up the model and balance of correlation (BC) for optimal descriptors approach shows that the BC scheme provides more robust predictions than the classic scheme for the considered pIC50 of the heterocyclic urea derivatives. Comparison of the SMILES-based optimal descriptors and SiRMS approaches has confirmed good performance of both techniques in prediction of kinase insert domain containing receptor (KDR) inhibitory activity, expressed as a logarithm of inhibitory concentration (pIC50) of studied compounds.
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Affiliation(s)
- Hayriye Yilmaz
- Kayseri Vocational School, Biomedical Devices and Technologies, Erciyes University, 38039, Kayseri, Turkey; Interdisciplinary Center for Nanotoxicity, Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS, 39217, USA
| | - Natalia Sizochenko
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS, 39217, USA; Odessa I.I. Mechnikov National University, Department of Chemistry, Dvoryanskaya Street, 2, 65082, Odessa, Ukraine
| | - Bakhtiyor Rasulev
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS, 39217, USA
| | - Andrey Toropov
- Laboratory of Environmental Chemistry and Toxicology, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, 20156, Via La Masa 19, Milano, Italy
| | - Yahya Guzel
- Department of Chemistry, Faculty of Science, Erciyes University, 38039, Kayseri, Turkey
| | - Viktor Kuz'min
- Odessa I.I. Mechnikov National University, Department of Chemistry, Dvoryanskaya Street, 2, 65082, Odessa, Ukraine
| | - Danuta Leszczynska
- Department of Civil and Environmental Engineering, Jackson State University, Jackson, MS, 39217, USA
| | - Jerzy Leszczynski
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS, 39217, USA.
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36
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Yilmaz H, Rasulev B, Leszczynski J. Modeling the Dispersibility of Single Walled Carbon Nanotubes in Organic Solvents by Quantitative Structure-Activity Relationship Approach. NANOMATERIALS 2015; 5:778-791. [PMID: 28347035 PMCID: PMC5312907 DOI: 10.3390/nano5020778] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 04/29/2015] [Accepted: 05/04/2015] [Indexed: 01/28/2023]
Abstract
The knowledge of physico-chemical properties of carbon nanotubes, including behavior in organic solvents is very important for design, manufacturing and utilizing of their counterparts with improved properties. In the present study a quantitative structure-activity/property relationship (QSAR/QSPR) approach was applied to predict the dispersibility of single walled carbon nanotubes (SWNTs) in various organic solvents. A number of additive descriptors and quantum-chemical descriptors were calculated and utilized to build QSAR models. The best predictability is shown by a 4-variable model. The model showed statistically good results (R2training = 0.797, Q2 = 0.665, R2test = 0.807), with high internal and external correlation coefficients. Presence of the X0Av descriptor and its negative term suggest that small size solvents have better SWCNTs solubility. Mass weighted descriptor ATS6m also indicates that heavier solvents (and small in size) most probably are better solvents for SWCNTs. The presence of the Dipole Z descriptor indicates that higher polarizability of the solvent molecule increases the solubility. The developed model and contributed descriptors can help to understand the mechanism of the dispersion process and predictorganic solvents that improve the dispersibility of SWNTs.
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Affiliation(s)
- Hayriye Yilmaz
- Department of Biomedical Devices and Technology, Kayseri Vocational School, Erciyes University, Kayseri 38039, Turkey.
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS 39217, USA.
| | - Bakhtiyor Rasulev
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS 39217, USA.
- Center for Computationally Assisted Science and Technology (CCAST), North Dakota State University, Fargo, ND 58108, USA.
| | - Jerzy Leszczynski
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS 39217, USA.
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37
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Sizochenko N, Rasulev B, Gajewicz A, Mokshyna E, Kuz'min VE, Leszczynski J, Puzyn T. Causal inference methods to assist in mechanistic interpretation of classification nano-SAR models. RSC Adv 2015. [DOI: 10.1039/c5ra11399g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Causal inference methods are helpful with finding possible biological mechanisms of nanoparticles' toxicity.
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Affiliation(s)
- Natalia Sizochenko
- Laboratory of Environmental Chemometrics
- Faculty of Chemistry
- University of Gdansk
- Gdansk
- Poland
| | - Bakhtiyor Rasulev
- Interdisciplinary Center for Nanotoxicity
- Department of Chemistry
- Jackson State University
- Jackson
- USA
| | - Agnieszka Gajewicz
- Laboratory of Environmental Chemometrics
- Faculty of Chemistry
- University of Gdansk
- Gdansk
- Poland
| | - Elena Mokshyna
- A.V. Bogatsky Physical–Chemical Institute National Academy of Sciences of Ukraine
- Odessa
- Ukraine
| | - Victor E. Kuz'min
- A.V. Bogatsky Physical–Chemical Institute National Academy of Sciences of Ukraine
- Odessa
- Ukraine
| | - Jerzy Leszczynski
- Interdisciplinary Center for Nanotoxicity
- Department of Chemistry
- Jackson State University
- Jackson
- USA
| | - Tomasz Puzyn
- Laboratory of Environmental Chemometrics
- Faculty of Chemistry
- University of Gdansk
- Gdansk
- Poland
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38
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Sizochenko N, Rasulev B, Gajewicz A, Kuz'min V, Puzyn T, Leszczynski J. From basic physics to mechanisms of toxicity: the "liquid drop" approach applied to develop predictive classification models for toxicity of metal oxide nanoparticles. NANOSCALE 2014; 6:13986-13993. [PMID: 25317542 DOI: 10.1039/c4nr03487b] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Many metal oxide nanoparticles are able to cause persistent stress to live organisms, including humans, when discharged to the environment. To understand the mechanism of metal oxide nanoparticles' toxicity and reduce the number of experiments, the development of predictive toxicity models is important. In this study, performed on a series of nanoparticles, the comparative quantitative-structure activity relationship (nano-QSAR) analyses of their toxicity towards E. coli and HaCaT cells were established. A new approach for representation of nanoparticles' structure is presented. For description of the supramolecular structure of nanoparticles the "liquid drop" model was applied. It is expected that a novel, proposed approach could be of general use for predictions related to nanomaterials. In addition, in our study fragmental simplex descriptors and several ligand-metal binding characteristics were calculated. The developed nano-QSAR models were validated and reliably predict the toxicity of all studied metal oxide nanoparticles. Based on the comparative analysis of contributed properties in both models the LDM-based descriptors were revealed to have an almost similar level of contribution to toxicity in both cases, while other parameters (van der Waals interactions, electronegativity and metal-ligand binding characteristics) have unequal contribution levels. In addition, the models developed here suggest different mechanisms of nanotoxicity for these two types of cells.
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Affiliation(s)
- Natalia Sizochenko
- I. I. Mechnikov Odessa National University, Department of Chemistry, Dvoryanskaya str., 2, 65082, Odessa, Ukraine
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Grinter SZ, Zou X. Challenges, applications, and recent advances of protein-ligand docking in structure-based drug design. Molecules 2014; 19:10150-76. [PMID: 25019558 PMCID: PMC6270832 DOI: 10.3390/molecules190710150] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 06/13/2014] [Accepted: 07/02/2014] [Indexed: 11/16/2022] Open
Abstract
The docking methods used in structure-based virtual database screening offer the ability to quickly and cheaply estimate the affinity and binding mode of a ligand for the protein receptor of interest, such as a drug target. These methods can be used to enrich a database of compounds, so that more compounds that are subsequently experimentally tested are found to be pharmaceutically interesting. In addition, like all virtual screening methods used for drug design, structure-based virtual screening can focus on curated libraries of synthesizable compounds, helping to reduce the expense of subsequent experimental verification. In this review, we introduce the protein-ligand docking methods used for structure-based drug design and other biological applications. We discuss the fundamental challenges facing these methods and some of the current methodological topics of interest. We also discuss the main approaches for applying protein-ligand docking methods. We end with a discussion of the challenging aspects of evaluating or benchmarking the accuracy of docking methods for their improvement, and discuss future directions.
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Affiliation(s)
- Sam Z Grinter
- Informatics Institute, University of Missouri, Columbia, MO 65211, USA.
| | - Xiaoqin Zou
- Informatics Institute, University of Missouri, Columbia, MO 65211, USA.
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Turabekova M, Rasulev B, Theodore M, Jackman J, Leszczynska D, Leszczynski J. Immunotoxicity of nanoparticles: a computational study suggests that CNTs and C60 fullerenes might be recognized as pathogens by Toll-like receptors. NANOSCALE 2014; 6:3488-95. [PMID: 24548972 DOI: 10.1039/c3nr05772k] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Over the last decade, a great deal of attention has been devoted to study the inflammatory response upon exposure to multi/single-walled carbon nanotubes (CNTs) and different fullerene derivatives. In particular, carbon nanoparticles are reported to provoke substantial inflammation in alveolar and bronchial epithelial cells, epidermal keratinocytes, cultured monocyte-macrophage cells, etc. We suggest a hypothetical model providing the potential mechanistic explanation for immune and inflammatory responses observed upon exposure to carbon nanoparticles. Specifically, we performed a theoretical study to analyze CNT and C60 fullerene interactions with the available X-ray structures of Toll-like receptors (TLRs) homo- and hetero-dimer extracellular domains. This assumption was based on the fact that similar to the known TLR ligands both CNTs and fullerenes induce, in cells, the secretion of certain inflammatory protein mediators, such as interleukins and chemokines. These proteins are observed within inflammation downstream processes resulted from the ligand molecule dependent inhibition or activation of TLR-induced signal transduction. Our computational studies have shown that the internal hydrophobic pockets of some TLRs might be capable of binding small-sized carbon nanostructures (5,5 armchair SWCNTs containing 11 carbon atom layers and C60 fullerene). High binding scores and minor structural alterations induced in TLR ectodomains upon binding C60 and CNTs further supported our hypothesis. Additionally, the proposed hypothesis is strengthened by the indirect experimental findings indicating that CNTs and fullerenes induce an excessive expression of specific cytokines and chemokines (i.e. IL-8 and MCP1).
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Affiliation(s)
- M Turabekova
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Jackson State University, 1400 J. R. Lynch Street, P. O. Box 17910, Jackson, MS 39217, USA.
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Turabekova MA, Rasulev BF, Dzhakhangirov FN, Toropov AA, Leszczynska D, Leszczynski J. Aconitum and delphinium diterpenoid alkaloids of local anesthetic activity: comparative QSAR analysis based on GA-MLRA/PLS and optimal descriptors approach. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART C, ENVIRONMENTAL CARCINOGENESIS & ECOTOXICOLOGY REVIEWS 2014; 32:213-238. [PMID: 25226219 DOI: 10.1080/10590501.2014.938886] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The duration of anesthesia (related to protein binding of a drug) and the onset time (determined by the pKa) are important characteristics in assessment of local anesthetic agents. They are known to be affected by a number of factors. Early studies of antiarrhythmic diterpenoid alkaloids from plants Aconitum and Delphinium suggested that they possess local anesthetic activity due to their ability to suppress sodium currents of excited membranes. In this study we utilized toxicity, duration, and onset of action as endpoints to construct Quantitative Structure-Activity Relationship (QSAR) models for the series of 34 diterpenoid alkaloids characterized by local anesthetic activity using genetic algorithm-based multiple linear regression analysis/partial least squares and simplified molecular input line entry system (SMILES)-based optimal descriptors approach. The developed QSAR models correctly reflected factors that determine three endpoints of interest. Toxicity correlates with descriptors describing partition and reactivity of compounds. The duration of anesthesia was encoded by the parameters defining the ability of a compound to bind at the receptor site. The size and number of H-bond acceptor atoms were found not to favor the speed of onset, while topographic electronic descriptor demonstrated strong positive effect on it. SMILES-based optimal descriptors approach resulted in overall improvement of models. This approach was shown to be more sensitive to structural peculiarities of molecules than regression methods. The results clearly indicate that obtained QSARs are able to provide distinct rationales for compounds optimization with respect to particular endpoint.
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Affiliation(s)
- M A Turabekova
- a Interdisciplinary Center for Nanotoxicity , Jackson State University , Jackson , Mississippi , USA
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