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Wu S, Li L, Liang Q, Gao H, Tang T, Tang Y. A DFT study of sulforaphane adsorption on the group III nitrides (B12N12, Al12N12 and Ga12N12) nanocages. J Biomol Struct Dyn 2023:1-12. [PMID: 37882329 DOI: 10.1080/07391102.2023.2272755] [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: 06/23/2023] [Accepted: 09/04/2023] [Indexed: 10/27/2023]
Abstract
In this paper, the adsorption behavior of group III nitrides (B12N12, Al12N12, and Ga12N12) nanocages to sulforaphane (SF) anticancer medicine were studied by density functional theory (DFT). The adsorption energy, solvation energy, desorption time and related quantum molecular descriptors were calculated in neutral and acidic solutions. When the drugs were adsorbed to nanocages, the structure of nanocages and drugs changed after adsorption, indicating that the process was effective adsorption. The adsorption energy and solvation energy of the complexes created after adsorption were negative values, which indicated that the structure of complexes formed by adsorption were stable. According to charge decomposition analysis (CDA) and natural bonding orbitals (NBO), drugs act as charge donors and nanocages act as charge acceptors, so that the charge flows from drugs to nanocages. Thermodynamic calculations demonstrate that drugs adsorption on nanocages is a spontaneous exothermic process. The calculation of quantum molecular descriptors confirmed that drugs adsorption on nanocages increased the chemical reactivity and solubility of drugs, which facilitated its transfer in biological fluids. Both interaction region index (IRI) and topological analysis of atom in molecule (AIM) revealed Van Der Waals interaction between drugs and nanocages. Protonation studies demonstrated that acidic circumstances could improve the polarity of complexes, increase the solvation effect, and boost drugs release in target cancer cells. The results of this work indicate that X12N12(X = B, Al, Ga) nanocages can be used as the delivery vehicle of SF drug.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- ShiQuan Wu
- School of Physics, Guizhou University, Guiyang, China
| | - Li Li
- School of Physics, Guizhou University, Guiyang, China
| | - QiQi Liang
- School of Physics, Guizhou University, Guiyang, China
| | - HuaXu Gao
- School of Physics, Guizhou University, Guiyang, China
| | - TianYu Tang
- School of Physics, Guizhou University, Guiyang, China
| | - YanLin Tang
- School of Physics, Guizhou University, Guiyang, China
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Russo E, Grondona C, Brullo C, Spallarossa A, Villa C, Tasso B. Indole Antitumor Agents in Nanotechnology Formulations: An Overview. Pharmaceutics 2023; 15:1815. [PMID: 37514002 PMCID: PMC10385756 DOI: 10.3390/pharmaceutics15071815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/19/2023] [Accepted: 06/22/2023] [Indexed: 07/30/2023] Open
Abstract
The indole heterocycle represents one of the most important scaffolds in medicinal chemistry and is shared among a number of drugs clinically used in different therapeutic areas. Due to its varied biological activities, high unique chemical properties and significant pharmacological behaviors, indole derivatives have drawn considerable interest in the last decade as antitumor agents active against different types of cancers. The research of novel antiproliferative drugs endowed with enhanced efficacy and reduced toxicity led to the approval by U.S. Food and Drug Administration of the indole-based anticancer agents Sunitinib, Nintedanib, Osimertinib, Panobinostat, Alectinib and Anlotinib. Additionally, new drug delivery systems have been developed to protect the active principle from degradation and to direct the drug to the specific site for clinical use, thus reducing its toxicity. In the present work is an updated review of the recently approved indole-based anti-cancer agents and the nanotechnology systems developed for their delivery.
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Affiliation(s)
- Eleonora Russo
- Section of Medicinal and Cosmetic Chemistry, Department of Pharmacy, University of Genova, Viale Benedetto XV, 3, 16132 Genova, Italy
| | - Carola Grondona
- Section of Medicinal and Cosmetic Chemistry, Department of Pharmacy, University of Genova, Viale Benedetto XV, 3, 16132 Genova, Italy
| | - Chiara Brullo
- Section of Medicinal and Cosmetic Chemistry, Department of Pharmacy, University of Genova, Viale Benedetto XV, 3, 16132 Genova, Italy
| | - Andrea Spallarossa
- Section of Medicinal and Cosmetic Chemistry, Department of Pharmacy, University of Genova, Viale Benedetto XV, 3, 16132 Genova, Italy
| | - Carla Villa
- Section of Medicinal and Cosmetic Chemistry, Department of Pharmacy, University of Genova, Viale Benedetto XV, 3, 16132 Genova, Italy
| | - Bruno Tasso
- Section of Medicinal and Cosmetic Chemistry, Department of Pharmacy, University of Genova, Viale Benedetto XV, 3, 16132 Genova, Italy
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Jiang Y, Wang C, Zhang M, Liu L, Gao X, Zhang S, Ye D. Study of folate-based carbon nanotube drug delivery systems targeted to folate receptor α by molecular dynamic simulations. Int J Biol Macromol 2023; 244:125386. [PMID: 37327924 DOI: 10.1016/j.ijbiomac.2023.125386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/03/2023] [Accepted: 06/12/2023] [Indexed: 06/18/2023]
Abstract
We designed targeted drug delivery systems containing folate (FOL), the functionalized carbon nanotube (f-CNT) and doxorubicin (DOX), and studied the targeting properties of folate, f-CNT-FOL and DOX/f-CNT-FOL to folate receptor α (FRα). Folate was actively targeted to FRα in molecular dynamics simulations, and the dynamic process, effect of folate receptor evolution, and characteristics were analyzed. On this basis, the f-CNT-FOL and DOX/f-CNT-FOL nano-drug-carrier systems were designed, and the drug delivery process targeted to FRα was studied by 4 times MD simulations. The system evolution and detailed interactions of f-CNT-FOL and DOX/f-CNT-FOL with FRα residues were examined. We found that though the connection of CNT with the FOL could decrease the insertion depth of the pterin of FOL into the pocket of FRα, the loading of drug molecules could reduce this effect. Representative snapshots from the MD simulations were analyzed, showing that the location of DOX on the surface of CNT was constantly changed during the MD simulation, but the surface of the four rings of DOX were almost always parallel to the surface of CNT. The RMSD and RMSF were used to further analyze. The results may provide new insights for the design of novel targeted nano-drug-delivery systems.
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Affiliation(s)
- Yue Jiang
- School of Science, Tianjin Chengjian University, Tianjin, China
| | - Cuihong Wang
- School of Science, Tianjin Chengjian University, Tianjin, China.
| | - Meiling Zhang
- School of Biomedical Engineering and Technology, Tianjin Medical University, Tianjin, China
| | - Lijuan Liu
- School of Science, Tianjin Chengjian University, Tianjin, China
| | - Xin Gao
- School of Science, Tianjin Chengjian University, Tianjin, China
| | - Shouchao Zhang
- School of Science, Tianjin Chengjian University, Tianjin, China
| | - Dan Ye
- School of Science, Tianjin Chengjian University, Tianjin, China
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4
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Hasan MM, Das AC, Hossain MR, Hossain MK, Hossain MA, Neher B, Ahmed F. The computational quantum mechanical investigation of the functionalized boron nitride nanocage as the smart carriers for favipiravir drug delivery: a DFT and QTAIM analysis. J Biomol Struct Dyn 2022; 40:13190-13206. [PMID: 34596003 DOI: 10.1080/07391102.2021.1982776] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Favipiravir (FPV) is an antiviral drug used for the cure of Influenza virus, Ebola virus, Lassa virus etc. because it has excellent preventing ability of entry/exit of the virus into/from the human cells. Boron nitride nanocages have already drawn enormous attention as the delivery vehicle of various drug molecules for their nontoxicity and other lucrative properties. In this research, we have scrutinized the adsorption mechanism of FPV molecule on the exterior surface of pristine, Zn functionalized, and Ni functionalized B12N12 (BN, Zn f-BN, and Ni f-BN) nanocages by applying the DFT/QTAIM method and B3LYP/6-31G(d,p) approach. The adsorption energy (EAd) data reveal that the functionalized BN adsorbents can adsorb FPV drug very efficiently compared with the pristine adsorbent (Highest EAd is -56.40 kcal/mol for FPV adsorbed Ni f-BN complex). The reduction of the HOMO-LUMO gap up to 67.79% indicates that this drug can be detected by the produced electrical signal very promisingly in the case of f-BN nanocages. The topological parameters also validate the ability of the f-BN nanocages to adsorb the FPV molecule. The effect of the biological environment of our investigated structures has been studied by using water as a solvent, and spontaneous adsorption with high solubility is observed in our calculations. This analysis also reveals that f-BN nanocages can be a potential nanocarrier for the delivery of FPV drug molecule.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Md Mehade Hasan
- Department of Physics, Jashore University of Science and Technology, Jashore, Bangladesh.,Department of Physics, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | | | - Md Rakib Hossain
- Department of Physics, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
| | - Md Kamal Hossain
- Department of Physics, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Md Abul Hossain
- Department of Physics, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Budrun Neher
- Department of Physics, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Farid Ahmed
- Department of Physics, Jahangirnagar University, Savar, Dhaka, Bangladesh
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5
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Khedri M, Afsharchi F, Souderjani AH, Rezvantalab S, Didandeh M, Maleki R, Musaie K, Santos HA, Shahbazi M. Molecular scale study on the interactions of biocompatible nanoparticles with macrophage membrane and blood proteins. NANO SELECT 2022. [DOI: 10.1002/nano.202200043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Mohammad Khedri
- Computational Biology and Chemistry Group (CBCG) Universal Scientific Education and Research Network (USERN) Tehran Iran
| | - Fatemeh Afsharchi
- Zanjan Pharmaceutical Nanotechnology Research Center (ZPNRC) Zanjan University of Medical Sciences Zanjan Iran
| | - Amirhosein Hasanpour Souderjani
- Department of Pharmaceutical Engineering, School of Chemical Engineering College of Engineering, University of Tehran Tehran Iran
| | - Sima Rezvantalab
- Renewable Energies Department Faculty of Chemical Engineering Urmia University of Technology Urmia Iran
| | - Mohsen Didandeh
- Department of Chemical Engineering Tarbiat Modares University Tehran Iran
| | - Reza Maleki
- Computational Biology and Chemistry Group (CBCG) Universal Scientific Education and Research Network (USERN) Tehran Iran
| | - Kiyan Musaie
- Zanjan Pharmaceutical Nanotechnology Research Center (ZPNRC) Zanjan University of Medical Sciences Zanjan Iran
| | - Hélder A. Santos
- Department of Biomedical Engineering University Medical Center Groningen University of Groningen Groningen The Netherlands
- W.J. Kolff Institute for Biomedical Engineering and Materials Science University of Groningen/University Medical Center Groningen Groningen The Netherlands
- Drug Research Program Division of Pharmaceutical Chemistry and Technology Faculty of Pharmacy University of Helsinki Helsinki Finland
| | - Mohammad‐Ali Shahbazi
- Department of Biomedical Engineering University Medical Center Groningen University of Groningen Groningen The Netherlands
- W.J. Kolff Institute for Biomedical Engineering and Materials Science University of Groningen/University Medical Center Groningen Groningen The Netherlands
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Zarghami Dehaghani M, Yousefi F, Seidi F, Sajadi SM, Rabiee N, Habibzadeh S, Esmaeili A, Hamed Mashhadzadeh A, Spitas C, Mostafavi E, Saeb MR. Dynamics of Antimicrobial Peptide Encapsulation in Carbon Nanotubes: The Role of Hydroxylation. Int J Nanomedicine 2022; 17:125-136. [PMID: 35058692 PMCID: PMC8765279 DOI: 10.2147/ijn.s335380] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 12/05/2021] [Indexed: 12/28/2022] Open
Affiliation(s)
- Maryam Zarghami Dehaghani
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources and Joint International Research Lab of Lignocellulosic Functional Materials, Nanjing Forestry University, Nanjing, 210037, People’s Republic of China
| | - Farrokh Yousefi
- Department of Physics, University of Zanjan, Zanjan, 45195-313, Iran
| | - Farzad Seidi
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources and Joint International Research Lab of Lignocellulosic Functional Materials, Nanjing Forestry University, Nanjing, 210037, People’s Republic of China
| | - S Mohammad Sajadi
- Department of Nutrition, Cihan University-Erbil, Erbil, Iraq
- Department of Phytochemistry, SRC, Soran University, Soran, Iraq
| | - Navid Rabiee
- Department of Physics, Sharif University of Technology, Tehran, Iran
| | - Sajjad Habibzadeh
- Department of Chemical Engineering, Amirkabir University of Technology (Tehran Polytechnic), Tehran, 1591639675, Iran
| | - Amin Esmaeili
- Department of Chemical Engineering, School of Engineering Technology and Industrial Trades, College of the North Atlantic — Qatar, Doha, Qatar
| | - Amin Hamed Mashhadzadeh
- Mechanical and Aerospace Engineering, School of Engineering and Digital Sciences, Nazarbayev University, Nur-Sultan, 010000, Kazakhstan
- Correspondence: Amin Hamed Mashhadzadeh Mechanical and Aerospace Engineering, School of Engineering and Digital Sciences, Nazarbayev University, Nur-Sultan, 010000, Kazakhstan Email ;
| | - Christos Spitas
- Mechanical and Aerospace Engineering, School of Engineering and Digital Sciences, Nazarbayev University, Nur-Sultan, 010000, Kazakhstan
| | - Ebrahim Mostafavi
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Ebrahim Mostafavi Stanford Cardiovascular Institute, Stanford University School of Medicine, Biomedical Innovation Building, 240 Pasteur Drive, Palo Alto, Stanford, CA94304, USA Email ;
| | - Mohammad Reza Saeb
- Department of Polymer Technology, Faculty of Chemistry, Gdańsk University of Technology, Gdańsk, 80-233, Poland
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Molecular dynamics simulation study of doxorubicin adsorption on functionalized carbon nanotubes with folic acid and tryptophan. Sci Rep 2021; 11:24210. [PMID: 34930942 PMCID: PMC8688492 DOI: 10.1038/s41598-021-03619-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 11/30/2021] [Indexed: 12/05/2022] Open
Abstract
In this work, molecular dynamics (MD) simulation is used to study the adsorption of the anticancer drug, doxorubicin (DOX), on the wall or surface of pristine and functionalized carbon nanotubes (FCNTs) in an aqueous solution. Initially, the CNTs were functionalized by tryptophan (Trp) and folic acid (FA), and then the DOX molecules were added to the system. The simulation results showed that the drug molecules can intensely interact with the FCNTs at physiological pH. Furthermore, it was found that as a result of functionalization, the solubility of FCNTs in an aqueous solution increases significantly. The effect of pH variation on drug release from both pristine and FCNTs was also investigated. The obtained results indicated that in acidic environments due to protonation of functional groups (Trp) and as a result of repulsive interaction between the DOX molecule and functional groups, the release of DOX molecules from FCNT’s surface is facilitated. The drug release is also strongly dependent on the pH and protonated state of DOX and FCNT.
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Encapsulation of an anticancer drug Isatin inside a host nano-vehicle SWCNT: a molecular dynamics simulation. Sci Rep 2021; 11:18753. [PMID: 34548596 PMCID: PMC8455564 DOI: 10.1038/s41598-021-98222-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 08/06/2021] [Indexed: 11/09/2022] Open
Abstract
The use of carbon nanotubes as anticancer drug delivery cargo systems is a promising modality as they are able to perforate cellular membranes and transport the carried therapeutic molecules into the cellular components. Our work describes the encapsulation process of a common anticancer drug, Isatin (1H-indole-2,3-dione) as a guest molecule, in a capped single-walled carbon nanotube (SWCNT) host with chirality of (10,10). The encapsulation process was modelled, considering an aqueous solution, by a molecular dynamics (MD) simulation under a canonical NVT ensemble. The interactions between the atoms of Isatin were obtained from the DREIDING force filed. The storage capacity of the capped SWCNT host was evaluated to quantify its capacity to host multiple Isatin molecules. Our results show that the Isatin can be readily trapped inside the volume cavity of the capped SWCNT and it remained stable, as featured by a reduction in the van der Waals forces between Isatin guest and the SWCNT host (at approximately - 30 kcal mol-1) at the end of the MD simulation (15 ns). Moreover, the free energy of encapsulation was found to be - 34 kcal mol-1 suggesting that the Isatin insertion procedure into the SWCNT occurred spontaneously. As calculated, a capped SWCNT (10,10) with a length of 30 Å, was able to host eleven (11) molecules of Isatin, that all remained steadily encapsulated inside the SWCNT volume cavity, showing a potential for the use of carbon nanotubes as drug delivery cargo systems.
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Zarghami Dehaghani M, Yousefi F, Sajadi SM, Tajammal Munir M, Abida O, Habibzadeh S, Mashhadzadeh AH, Rabiee N, Mostafavi E, Saeb MR. Theoretical Encapsulation of Fluorouracil (5-FU) Anti-Cancer Chemotherapy Drug into Carbon Nanotubes (CNT) and Boron Nitride Nanotubes (BNNT). Molecules 2021; 26:4920. [PMID: 34443508 PMCID: PMC8398462 DOI: 10.3390/molecules26164920] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/03/2021] [Accepted: 08/05/2021] [Indexed: 12/24/2022] Open
Abstract
INTRODUCTION Chemotherapy with anti-cancer drugs is considered the most common approach for killing cancer cells in the human body. However, some barriers such as toxicity and side effects would limit its usage. In this regard, nano-based drug delivery systems have emerged as cost-effective and efficient for sustained and targeted drug delivery. Nanotubes such as carbon nanotubes (CNT) and boron nitride nanotubes (BNNT) are promising nanocarriers that provide the cargo with a large inner volume for encapsulation. However, understanding the insertion process of the anti-cancer drugs into the nanotubes and demonstrating drug-nanotube interactions starts with theoretical analysis. METHODS First, interactions parameters of the atoms of 5-FU were quantified from the DREIDING force field. Second, the storage capacity of BNNT (8,8) was simulated to count the number of drugs 5-FU encapsulated inside the cavity of the nanotubes. In terms of the encapsulation process of the one drug 5-FU into nanotubes, it was clarified that the drug 5-FU was more rapidly adsorbed into the cavity of the BNNT compared with the CNT due to the higher van der Waals (vdW) interaction energy between the drug and the BNNT. RESULTS The obtained values of free energy confirmed that the encapsulation process of the drug inside the CNT and BNNT occurred spontaneously with the free energies of -14 and -25 kcal·mol-1, respectively. DISCUSSION However, the lower value of the free energy in the system containing the BNNT unraveled more stability of the encapsulated drug inside the cavity of the BNNT comparing the system having CNT. The encapsulation of Fluorouracil (5-FU) anti-cancer chemotherapy drug (commercial name: Adrucil®) into CNT (8,8) and BNNT (8,8) with the length of 20 Å in an aqueous solution was discussed herein applying molecular dynamics (MD) simulation.
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Affiliation(s)
- Maryam Zarghami Dehaghani
- Center of Excellence in Electrochemistry, School of Chemistry, College of Science, University of Tehran, Tehran 11155-4563, Iran;
| | - Farrokh Yousefi
- Department of Physics, University of Zanjan, Zanjan 45195-313, Iran;
| | - S. Mohammad Sajadi
- Department of Nutrition, Cihan University-Erbil, Kurdistan Region, Erbil P.O. Box 625, Iraq;
- Department of Phytochemistry, SRC, Soran University, Soran P.O. Box 624, Iraq
| | - Muhammad Tajammal Munir
- College of Engineering and Technology, American University of the Middle East, Egaila 54200, Kuwait; (M.T.M.); (O.A.)
| | - Otman Abida
- College of Engineering and Technology, American University of the Middle East, Egaila 54200, Kuwait; (M.T.M.); (O.A.)
| | - Sajjad Habibzadeh
- Department of Chemical Engineering, Amirkabir University of Technology (Tehran Polytechnic), Tehran 1591639675, Iran
| | - Amin Hamed Mashhadzadeh
- Mechanical and Aerospace Engineering, School of Engineering and Digital Sciences, Nazarbayev University, Nur-Sultan 010000, Kazakhstan
| | - Navid Rabiee
- Department of Physics, Sharif University of Technology, Tehran P.O. Box 11155-9161, Iran;
| | - Ebrahim Mostafavi
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mohammad Reza Saeb
- Department of Polymer Technology, Faculty of Chemistry, Gdańsk University of Technology, G. Narutowicza 11/12, 80-233 Gdańsk, Poland;
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Tracking the interaction between single-wall carbon nanotube and SARS-Cov-2 spike glycoprotein: A molecular dynamics simulations study. Comput Biol Med 2021; 136:104692. [PMID: 34333227 PMCID: PMC8314789 DOI: 10.1016/j.compbiomed.2021.104692] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 12/26/2022]
Abstract
COVID-19, a newly discovered type of coronavirus, is the cause of the pandemic infection that was first reported in Wuhan, China, in December 2019. One of the most critical problems in this regard is to identify innovative drugs that may reduce or manage this global health concern. Nanoparticles have shown a pivotal role in drug delivery systems in recent decades. The surface of nanoparticles could be covered by a layer composed of different biomolecules (e.g., proteins and macromolecules) following the incubation with a biological fluid. This protein-rich layer is called “Protein Corona.” In this study, an all-atom molecular dynamics simulation was used for investigating the monomeric B domain of the spike glycoprotein due to its role in the accessibility of the spike glycoprotein to single-wall carbon nanotubes (SWCNTs). The interaction energy values between the carbon nanotube and B domain of the viral spike glycoprotein were evaluated. The obtained results, based on Lennard-Jones potentials, demonstrated that SWCNTs had an affinity to the B domain of the S1 subunit in the spike glycoprotein. The adsorption of SWCNTs on the B domain surface led to a significant change in solvent-accessible surface, internal hydrogen bonds, and finally in the tertiary structure, which could provide a reasonable method to impede the interaction between the angiotensin-converting enzyme II and SARS-CoV-2 spike glycoprotein. A decrease in the mean square displacement of the B domain was shown after the adsorption of SWCNTs as a result of increasing the hydrophobic-hydrophilic properties of the B domain. The arrangement of SWCNTs on the B domain surface and their interaction using the 2-acetamido-2-deoxy-β-d-glucopyranose group (988, 991, and 992) demonstrated that a change in the affinity of the S1 subunit could be used as a barrier to viral replication. The analysis of the SWCNT-B domain complex indicated that the presence of SWCNTs is able to cause alterations in the S1 subunit of the spike protein, and these nanotubes could be employed for further in-vitro and in-vivo antiviral studies. Also, SWCNTs are able to be utilized in drug delivery systems.
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Bunker A, Róg T. Mechanistic Understanding From Molecular Dynamics Simulation in Pharmaceutical Research 1: Drug Delivery. Front Mol Biosci 2020; 7:604770. [PMID: 33330633 PMCID: PMC7732618 DOI: 10.3389/fmolb.2020.604770] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/02/2020] [Indexed: 12/12/2022] Open
Abstract
In this review, we outline the growing role that molecular dynamics simulation is able to play as a design tool in drug delivery. We cover both the pharmaceutical and computational backgrounds, in a pedagogical fashion, as this review is designed to be equally accessible to pharmaceutical researchers interested in what this new computational tool is capable of and experts in molecular modeling who wish to pursue pharmaceutical applications as a context for their research. The field has become too broad for us to concisely describe all work that has been carried out; many comprehensive reviews on subtopics of this area are cited. We discuss the insight molecular dynamics modeling has provided in dissolution and solubility, however, the majority of the discussion is focused on nanomedicine: the development of nanoscale drug delivery vehicles. Here we focus on three areas where molecular dynamics modeling has had a particularly strong impact: (1) behavior in the bloodstream and protective polymer corona, (2) Drug loading and controlled release, and (3) Nanoparticle interaction with both model and biological membranes. We conclude with some thoughts on the role that molecular dynamics simulation can grow to play in the development of new drug delivery systems.
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Affiliation(s)
- Alex Bunker
- Division of Pharmaceutical Biosciences, Drug Research Program, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Tomasz Róg
- Department of Physics, University of Helsinki, Helsinki, Finland
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12
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Mirsalari H, Maleki A, Raissi H, Soltanabadi A. Investigation of the Pristine and Functionalized Carbon Nanotubes as a Delivery System for the Anticancer Drug Dacarbazine: Drug Encapsulation. J Pharm Sci 2020; 110:2005-2016. [PMID: 33186581 DOI: 10.1016/j.xphs.2020.10.062] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 12/17/2022]
Abstract
Carbon Nanotubes (CNTs) have been used as the systems in drug delivery due to their exceptional physical and chemical properties. In this study, the adsorption of an anticancer drug Dacarbazine (DAC) into the inner and outer surface of pristine and Functionalized Carbon Nanotubes (FCNTs) with four carboxylic acid groups was investigated in aqueous solution using the Molecular Dynamics (MD) simulations. Our simulation results showed that in spite of the adsorption of drug molecules on the outer sidewall of pristine and functionalized nanotubes, the spontaneous encapsulation of DAC molecule into the cavity of CNTs and FCNTs is observed. The simulations show that the arrangement of the DAC molecule into the CNTs and FCNTs is controlled by π-π interactions.
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Affiliation(s)
- Halimeh Mirsalari
- Department of Chemistry, Omidiyeh Branch, Islamic Azad University, Omidiyeh, Iran
| | - Afsaneh Maleki
- Department of Chemistry, Omidiyeh Branch, Islamic Azad University, Omidiyeh, Iran.
| | - Heidar Raissi
- Chemistry Department, University of Birjand, Birjand, Iran
| | - Azim Soltanabadi
- Department of Physical Chemistry, Faculty of Chemistry, Razi University, Kermanshah. Iran
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13
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Hasanzade Z, Raissi H. Molecular mechanism for the encapsulation of the doxorubicin in the cucurbit[n]urils cavity and the effects of diameter, protonation on loading and releasing of the anticancer drug:Mixed quantum mechanical/ molecular dynamics simulations. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2020; 196:105563. [PMID: 32531653 DOI: 10.1016/j.cmpb.2020.105563] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/06/2020] [Accepted: 05/20/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND AND OBJECTIVES Doxorubicin is a common apoptotic chemotherapeutic which has shown an obvious inhibitory effect in cancer chemotherapy. Here, cucurbit[n]urils (n = 7,10) have been proposed as a doxorubicin carrier, and the effects of diameter, protonation on loading and releasing of the anticancer drug doxorubicin has been studied. METHODS The Density Functional Theory (DFT) calculation and Molecular Dynamics (MD) simulation are performed to study the adsorption process of the (guest) Doxorubicin molecule in the neutral and protonated states within the (host) cucurbit[n]urils (n = 7,10). RESULTS DFT results show that the adsorption process in water is thermodynamically favorable. It is found that the binding energies for protonated drug encapsulation in cucurbit[n]urils are weaker than those of the neutral drug, implying the protonation of doxorubicin can promote the drug release from the adsorption situation. The electron density values and their Laplacian are evaluated to identify the nature of the intermolecular interactions through the topological parameters using the Bader's theory of atoms in molecules. Furthermore, the natural bond orbital analysis shows that the electrons aretransferred from cucurbit[n]urils to drug in all complexes. MD simulation results indicate that value of drug diffusion coefficient is small, therefore, we expect DOX to be slowly released from the CB cavity. CONCLUSIONS Based on obtained results, cucurbit[n]urils may be a prominent nano-carrier to loading and release drug on to target cells.
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Affiliation(s)
| | - Heidar Raissi
- Chemistry Department, University of Birjand, Birjand, Iran.
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El-Mageed HRA, Mustafa FM, Abdel-Latif MK. Boron nitride nanoclusters, nanoparticles and nanotubes as a drug carrier for isoniazid anti-tuberculosis drug, computational chemistry approaches. J Biomol Struct Dyn 2020; 40:226-235. [DOI: 10.1080/07391102.2020.1814871] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- H. R. Abd El-Mageed
- Micro-analysis and environmental research and community services center, Faculty of Science, Beni-Suef university, Beni-Suef City, Egypt
| | - F. M. Mustafa
- Chemistry Department, Faculty of Science, Beni-Suef University, Egypt
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15
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Farzad F, Hashemzadeh H. Probing the effect of polyethene glycol on the adsorption mechanisms of Gem on the hexagonal boron nitride as a highly efficient polymer-based drug delivery system: DFT, classical MD and Well-tempered Metadynamics simulations. J Mol Graph Model 2020; 98:107613. [DOI: 10.1016/j.jmgm.2020.107613] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 03/27/2020] [Accepted: 03/28/2020] [Indexed: 10/24/2022]
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16
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Molecular Interpretation of Pharmaceuticals’ Adsorption on Carbon Nanomaterials: Theory Meets Experiments. Processes (Basel) 2020. [DOI: 10.3390/pr8060642] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The ability of carbon-based nanomaterials (CNM) to interact with a variety of pharmaceutical drugs can be exploited in many applications. In particular, they have been studied both as carriers for in vivo drug delivery and as sorbents for the treatment of water polluted by pharmaceuticals. In recent years, the large number of experimental studies was also assisted by computational work as a tool to provide understanding at molecular level of structural and thermodynamic aspects of adsorption processes. Quantum mechanical methods, especially based on density functional theory (DFT) and classical molecular dynamics (MD) simulations were mainly applied to study adsorption/release of various drugs. This review aims to compare results obtained by theory and experiments, focusing on the adsorption of three classes of compounds: (i) simple organic model molecules; (ii) antimicrobials; (iii) cytostatics. Generally, a good agreement between experimental data (e.g. energies of adsorption, spectroscopic properties, adsorption isotherms, type of interactions, emerged from this review) and theoretical results can be reached, provided that a selection of the correct level of theory is performed. Computational studies are shown to be a valuable tool for investigating such systems and ultimately provide useful insights to guide CNMs materials development and design.
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17
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Pulling Simulations and Hydrogen Sorption Modelling on Carbon Nanotube Bundles. C — JOURNAL OF CARBON RESEARCH 2020. [DOI: 10.3390/c6010011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Recent progress in molecular simulation technology has developed an interest in modernizing the usual computational methods and approaches. For instance, most of the theoretical work on hydrogen adsorption on carbon nanotubes was conducted a decade ago. It should be insightful to reinvestigate the field and take advantage of code improvements and features implemented in contemporary software. One example of such features is the pulling simulation modules now available in many molecular dynamics programs. We conduct pulling simulations on pairs of carbon nanotubes and measure the inter-tube distance before they dissociate in water. We use this distance to set the interval size between adjacent nanotubes as we arrange them in bundle configurations. We consider bundles with triangular, intermediate and honeycomb patterns, and armchair nanotubes with a chiral index from n = 5 to n = 10. Then, we simulate low pressure hydrogen adsorption isotherms at 77 K, using the grand canonical Monte Carlo method. The different bundle configurations adsorb great hydrogen amounts that may exceed 2% wt at ambient pressures. The computed hydrogen capacities are considered large for physisorption on carbon nanostructures and attributed to the ultra-microporous network and extraordinary high surface area of the configured models.
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Gao Z, Hu B, Wang H, Wang J, Cheng M. Computational insights into the sorption mechanism of environmental contaminants by carbon nanoparticles through molecular dynamics simulation and density functional theory. Phys Chem Chem Phys 2020; 22:27308-27319. [DOI: 10.1039/d0cp03459b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Carbon nanomaterials like carbon nanotube, graphene or graphene oxide could significantly enhance contaminant sorption in aqueous solutions, offering a promising opportunity in water and air purification for removal of environmental contaminants.
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Affiliation(s)
- Zisen Gao
- Key Laboratory of Structure-Based Drug Design & Discovery
- Ministry of Education
- Shenyang Pharmaceutical University
- Shenyang 110016
- P. R. China
| | - Baichun Hu
- Key Laboratory of Structure-Based Drug Design & Discovery
- Ministry of Education
- Shenyang Pharmaceutical University
- Shenyang 110016
- P. R. China
| | - Hanxun Wang
- Key Laboratory of Structure-Based Drug Design & Discovery
- Ministry of Education
- Shenyang Pharmaceutical University
- Shenyang 110016
- P. R. China
| | - Jian Wang
- Key Laboratory of Structure-Based Drug Design & Discovery
- Ministry of Education
- Shenyang Pharmaceutical University
- Shenyang 110016
- P. R. China
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design & Discovery
- Ministry of Education
- Shenyang Pharmaceutical University
- Shenyang 110016
- P. R. China
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19
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Rahmani Z, Edjlali L, Vessally E, Hosseinian A, Nezhad PDK. A density functional theory outlook on the possible sensing ability of boron nitride nanotubes and their Al- and Si-doped derivatives for sulfonamide drugs. J Sulphur Chem 2019. [DOI: 10.1080/17415993.2019.1687702] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Zahra Rahmani
- Department of Chemistry, Tabriz Branch, Islamic Azad University, Tabriz, Iran
| | - Ladan Edjlali
- Department of Chemistry, Tabriz Branch, Islamic Azad University, Tabriz, Iran
| | - Esmail Vessally
- Department of Chemistry, Payame Noor University, Tehran, Iran
| | - Akram Hosseinian
- School of Engineering Science, College of Engineering, University of Tehran, Tehran, Iran
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Ai L, Xu Z, Yang B, He Q, Luo P. Sorafenib-associated hand-foot skin reaction: practical advice on diagnosis, mechanism, prevention, and management. Expert Rev Clin Pharmacol 2019; 12:1121-1127. [PMID: 31679411 DOI: 10.1080/17512433.2019.1689122] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: Sorafenib is a multitargeted tyrosine kinase inhibitor, which has been mainly used in the treatment of advanced hepatocellular carcinoma and renal cancer. However, hand-foot skin reaction (HFSR), as one of the most common adverse reactions, have hindered its long-term clinical application. At present, the mechanism of its occurrence has not been clearly studied and it leads to the lack of effective means of intervention. This article reviews known mechanism and management methods of HFSR caused by sorafenib.Areas covered: The author reviews HFSR caused by the treatment of sorafenib including the mechanism and management. English language reports located through PubMed are reviewed.Expert opinion: There are some conjectures about the mechanism of HFSR. However, the mechanism of HFSR induced by sorafenib is still unclear at present. In the absence of understanding the mechanism of HFSR, the most common method for clinical treatment of sorafenib-induced HFSR is dose down-regulation or discontinuation of treatment, which affects efficacy and even survival. Future research should focus on the mechanism of HFSR to find out new ways for prevention. Precautionary measures before the occurrence of HFSR can also be studied in the future.
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Affiliation(s)
- Leilei Ai
- Institute of Pharmacology & Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Ziheng Xu
- Institute of Pharmacology & Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Bo Yang
- Institute of Pharmacology & Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Qiaojun He
- Institute of Pharmacology & Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Peihua Luo
- Institute of Pharmacology & Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
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21
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Alinejad A, Raissi H, Hashemzadeh H. Understanding co-loading of doxorubicin and camptothecin on graphene and folic acid-conjugated graphene for targeting drug delivery: classical MD simulation and DFT calculation. J Biomol Struct Dyn 2019; 38:2737-2745. [DOI: 10.1080/07391102.2019.1645044] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
| | - Heidar Raissi
- Department of Chemistry, University of Birjand, Birjand, Iran
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