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Mukhopadhyay T, Ghosh A, Datta A. Screening 2D Materials for Their Nanotoxicity toward Nucleic Acids and Proteins: An In Silico Outlook. ACS PHYSICAL CHEMISTRY AU 2024; 4:97-121. [PMID: 38560753 PMCID: PMC10979489 DOI: 10.1021/acsphyschemau.3c00053] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/04/2023] [Accepted: 11/06/2023] [Indexed: 04/04/2024]
Abstract
Since the discovery of graphene, two-dimensional (2D) materials have been anticipated to demonstrate enormous potential in bionanomedicine. Unfortunately, the majority of 2D materials induce nanotoxicity via disruption of the structure of biomolecules. Consequently, there has been an urge to synthesize and identify biocompatible 2D materials. Before the cytotoxicity of 2D nanomaterials is experimentally tested, computational studies can rapidly screen them. Additionally, computational analyses can provide invaluable insights into molecular-level interactions. Recently, various "in silico" techniques have identified these interactions and helped to develop a comprehensive understanding of nanotoxicity of 2D materials. In this article, we discuss the key recent advances in the application of computational methods for the screening of 2D materials for their nanotoxicity toward two important categories of abundant biomolecules, namely, nucleic acids and proteins. We believe the present article would help to develop newer computational protocols for the identification of novel biocompatible materials, thereby paving the way for next-generation biomedical and therapeutic applications based on 2D materials.
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Affiliation(s)
- Titas
Kumar Mukhopadhyay
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A and 2B Raja S.C. Mullick Road,
Jadavpur, Kolkata 700032, West Bengal, India
| | - Anupam Ghosh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A and 2B Raja S.C. Mullick Road,
Jadavpur, Kolkata 700032, West Bengal, India
| | - Ayan Datta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A and 2B Raja S.C. Mullick Road,
Jadavpur, Kolkata 700032, West Bengal, India
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Lan J, Peng Y, Liang L, Duan X, Kong Z, Zhang L, Shen JW. Theoretical study of protein adsorption on graphene/h-BN heterostructures. Phys Chem Chem Phys 2023; 25:31206-31221. [PMID: 37955184 DOI: 10.1039/d3cp03303a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
The biological characteristics of planar heterojunction nanomaterials and their interactions with biomolecules are crucial for the potential application of these materials in the biomedical field. This study employed molecular dynamics (MD) simulations to investigate the interactions between proteins with distinct secondary structures (a single α-helix representing the minimal oligomeric domain protein, a single β-sheet representing the WW structural domain of the Yap65 protein, and a mixed α/β structure representing the BBA protein) and a planar two-dimensional heterojunction (a GRA/h-BN heterojunction consisting of a graphene nanoplate (GRA) and a hexagonal boron nitride nanoplate (h-BN)). The results indicate that all three kinds of protein can be quickly and stably adsorbed on the GRA/h-BN heterojunction due to the strong van der Waals interaction, regardless of their respective types, structures and initial orientations. Moreover, the proteins exhibit a pronounced binding preference for the hBN region of the GRA/h-BN heterojunction. Upon adsorption, the α-helix structure of the minimal oligomeric domain protein experiences partial or complete denaturation. Conversely, while the secondary structure of the single β-sheet and mixed α/β structure (BBA protein) undergoes slight changes (focus on the coil and turn regions), the main α-helix and β-sheet structures remain intact. The initial orientation significantly impacts the degree of protein adsorption and its position on the GRA/h-BN heterojunction. However, regardless of the initial orientation, proteins can ultimately be adsorbed onto the GRA/h-BN heterojunction. Furthermore, the initial orientation has a minor influence on the structural changes of proteins. Significantly, the combination of different secondary structures helps mitigate the denaturation of a single α-helix structure to some extent. Overall, the adsorption of proteins on GRA/h-BN is primarily driven by van der Waals and hydrophobic interactions. Proteins with β-sheet or mixed structures exhibit stronger biocompatibility on the GRA/h-BN heterojunction. Our research elucidated the biological characteristics of GRA/h-BN heterojunction nanomaterials and their interactions with proteins possessing diverse secondary structures. It offers a theoretical foundation for considering heterojunction nanomaterials as promising candidates for biomedical applications.
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Affiliation(s)
- Jun Lan
- College of Automation, Hangzhou Dianzi University, Hangzhou, 310018, China.
| | - Yiran Peng
- College of Automation, Hangzhou Dianzi University, Hangzhou, 310018, China.
| | - Lijun Liang
- College of Automation, Hangzhou Dianzi University, Hangzhou, 310018, China.
| | - Xing Duan
- Center of Advanced Optoelectronic Materials and Devices, Key Laboratory of Novel Materials for Sensor of Zhejiang Province, College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Zhe Kong
- Center of Advanced Optoelectronic Materials and Devices, Key Laboratory of Novel Materials for Sensor of Zhejiang Province, College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Li Zhang
- Department of Chemistry, Key Laboratory of Surface & Interface Science of Polymer Materials of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Jia-Wei Shen
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang 311121, China.
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Adalikwu SA, Louis H, Iloanya AC, Edet HO, Akem MU, Eno EA, Manicum ALE. B- and Al-Doped Porous 2D Covalent Organic Frameworks as Nanocarriers for Biguanides and Metformin Drugs. ACS APPLIED BIO MATERIALS 2022; 5:5887-5900. [PMID: 36413624 DOI: 10.1021/acsabm.2c00855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Nanostructures such as nanosheets, nanotubes, nanocages, and fullerenes have been extensively studied as potential candidates in various fields since the advancement of nanoscience. Herein, the interaction between biguanides (BGN) and metformin (MET) on the modified covalent organic framework (COF), COF-B, and COF-Al was investigated using density functional theory at the ωB97XD/6-311+G (d, p) level of computation to explore a new drug delivery system. The electronic properties evaluation reveals that the studied surfaces are suited for the delivery of both drug molecules. The calculated adsorption energies and basis set superposition errors (BSSE) ranged between -21.20 and -65.86 kJ/mol. The negative values obtained are an indication of excellent interaction between the drug molecules and the COF surfaces. Moreover, BGN is better adsorbed on COF-B with Eads of -65.86 kJ/mol, while MET is better adsorbed on COF-Al with Eads = -47.30 kJ/mol. The analysis of the quantum theory of atom in molecules (QTAIM) explained the nature and strength of intermolecular interaction existing between the drug molecules BGN and MET with the adsorbing surfaces. The analysis of noncovalent interaction (NCI) shows a weak hydrogen-bond interaction. Other properties such as quantum chemical descriptors and natural bond orbital (NBO) analysis also agree with the potential of COF surfaces as drug delivery systems. The electron localization function (ELF) is discussed, and it confirms the transitions occurring in the NBO analysis of the complexes. In conclusion, COF-B and COF-Al are suitable candidates for the effective delivery of BGN and MET.
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Affiliation(s)
- Stephen A Adalikwu
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, P.M.B1115, Nigeria
| | - Hitler Louis
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, P.M.B1115, Nigeria.,Department of Pure and Applied Chemistry, University of Calabar, Calabar, P.M.B1115, Nigeria
| | - Anthony C Iloanya
- Department of Physics, Lehigh University, Bethlehem, Pennsylvania18015, United States
| | - Henry O Edet
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, P.M.B1115, Nigeria
| | - Martilda U Akem
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, P.M.B1115, Nigeria.,Department of Pure and Applied Chemistry, University of Calabar, Calabar, P.M.B1115, Nigeria
| | - Ededet A Eno
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, P.M.B1115, Nigeria.,Department of Pure and Applied Chemistry, University of Calabar, Calabar, P.M.B1115, Nigeria
| | - Amanda-Lee E Manicum
- Department of Chemistry, Tshwane University of Technology, Pretoria0183, South Africa
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