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Zheng JJ, Li QZ, Wang Z, Wang X, Zhao Y, Gao X. Computer-aided nanodrug discovery: recent progress and future prospects. Chem Soc Rev 2024; 53:9059-9132. [PMID: 39148378 DOI: 10.1039/d3cs00575e] [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: 08/17/2024]
Abstract
Nanodrugs, which utilise nanomaterials in disease prevention and therapy, have attracted considerable interest since their initial conceptualisation in the 1990s. Substantial efforts have been made to develop nanodrugs for overcoming the limitations of conventional drugs, such as low targeting efficacy, high dosage and toxicity, and potential drug resistance. Despite the significant progress that has been made in nanodrug discovery, the precise design or screening of nanomaterials with desired biomedical functions prior to experimentation remains a significant challenge. This is particularly the case with regard to personalised precision nanodrugs, which require the simultaneous optimisation of the structures, compositions, and surface functionalities of nanodrugs. The development of powerful computer clusters and algorithms has made it possible to overcome this challenge through in silico methods, which provide a comprehensive understanding of the medical functions of nanodrugs in relation to their physicochemical properties. In addition, machine learning techniques have been widely employed in nanodrug research, significantly accelerating the understanding of bio-nano interactions and the development of nanodrugs. This review will present a summary of the computational advances in nanodrug discovery, focusing on the understanding of how the key interfacial interactions, namely, surface adsorption, supramolecular recognition, surface catalysis, and chemical conversion, affect the therapeutic efficacy of nanodrugs. Furthermore, this review will discuss the challenges and opportunities in computer-aided nanodrug discovery, with particular emphasis on the integrated "computation + machine learning + experimentation" strategy that can potentially accelerate the discovery of precision nanodrugs.
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Affiliation(s)
- Jia-Jia Zheng
- Laboratory of Theoretical and Computational Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China.
| | - Qiao-Zhi Li
- Laboratory of Theoretical and Computational Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China.
| | - Zhenzhen Wang
- Laboratory of Theoretical and Computational Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China.
| | - Xiaoli Wang
- Laboratory of Theoretical and Computational Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China.
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Yuliang Zhao
- Laboratory of Theoretical and Computational Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China.
| | - Xingfa Gao
- Laboratory of Theoretical and Computational Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China.
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Akor FO, Edo GD, Nelson FA, Johnson AU, Iyam SO, Abubakar MN, Gulack AO, Ubah CB, Ekpong BO, Benjamin I. Surface modification of graphene and fullerene with Sulfur (S), Selenium (Se), and Oxygen (O): DFT Simulation for enhanced zidovudine delivery in HIV treatment. BMC Chem 2024; 18:156. [PMID: 39192298 PMCID: PMC11351320 DOI: 10.1186/s13065-024-01259-3] [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: 04/03/2024] [Accepted: 08/02/2024] [Indexed: 08/29/2024] Open
Abstract
HIV is one of the most threatening health conditions with a highly increasing rate, affecting millions of people globally, and from its time of discovery until now, its potential cure cannot be explicitly defined. This challenge of having no/low effective drugs for the subjected virus has called for serious attention in the scientific world of virus disease therapeutics. Most of these drugs yields low effectiveness due to poor delivery; hence, there is a need for novel engineering methods for efficient delivery. In this study, two nanomaterilas (graphene; GP, and fullerene; C60) were modelled and investigated with sulfur (S), selenium (Se), and oxygen (O) atoms, to facilitate the delivery of zidovudine (ZVD). This investigation was computationally investigated using the density functional theory (DFT), calculated at B3LYP functional and Gd3bj/Def2svp level of theory. Results from the frontier molecular orbital (FMO), revealed that the GP/C60_S_ZVD complex calculated the least energy gap of 0.668 eV, thus suggesting a favourable interactions. The study of adsorption energy revealed chemisorption among all the interacting complexes wherein GP/C60_S_ZVD complex (-1.59949 eV) was highlighted as the most interacting system, thereby proving its potential for the delivery of ZVD. The outcome of this research urges that a combination of GP and C60 modified with chalcogen particularly, O, S, and Se can aid in facilitating the delivery of zidovudine.
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Affiliation(s)
- Faith O Akor
- Department of Science Laboratory Technology, University of Calabar, Calabar, Nigeria
| | - Godwin D Edo
- Department of Science Laboratory Technology, University of Calabar, Calabar, Nigeria
| | - Favour A Nelson
- Department of Chemistry, University of Calabar, Calabar, Nigeria
| | | | - Solomon O Iyam
- Department of Microbiology, University of Calabar, Calabar, Nigeria
| | - Muhammad N Abubakar
- Department of Biotechnology, Moddibo Adama University of Yola, Yola, Nigeria
| | - Alpha O Gulack
- Department of Science Laboratory Technology, University of Calabar, Calabar, Nigeria
| | - Chioma B Ubah
- Department of Microbiology, University of Calabar, Calabar, Nigeria
| | - Bassey O Ekpong
- Department of Microbiology, University of Calabar, Calabar, Nigeria.
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Wu D, Ma A, Liu Z, Wang Z, Xu F, Fan G, Xu H. Adsorption of sulfur-containing contaminant gases by pristine, Cr and Mo doped NbS 2monolayers based on density functional theory. NANOTECHNOLOGY 2023; 34:505708. [PMID: 37725960 DOI: 10.1088/1361-6528/acfb13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/18/2023] [Indexed: 09/21/2023]
Abstract
The adsorption and sensor performance of hazardous gases containing sulfur (SO2, H2S and SO3) on pristine, Cr and Mo doped NbS2monolayers (Cr-NbS2and Mo-NbS2) were investigated in detail based on density functional theory. The comparative analysis of the parameters such as density of states, adsorption energy, charge transfer, recovery time and work function of the systems showed that the pristine NbS2monolayer have poor sensor performance for sulfur-containing hazardous gases due to weak adsorption capacity, insignificant charge transfer and insignificant changes in electronic properties after gas adsorption on the surface. After doping with Cr atoms, the adsorption performance of Cr-NbS2was significantly improved, and it can be used as a sensor for SO2and H2S gases and as an adsorbent for SO3gas. The adsorption performance of Mo-NbS2is also significantly improved by doping with Mo atoms, and it can be used as a sensor for H2S gas and as an adsorbent for SO2and SO3gas. Therefore, Cr-NbS2and Mo-NbS2are revealed to be sensing or elimination materials for the harmful gases containing sulfur (SO2, H2S and SO3) in the atmosphere.
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Affiliation(s)
- Dandan Wu
- School of Chemistry and Chemical Engineering, Anhui University of Technology, Maanshan, Anhui 243002, People's Republic of China
| | - Aling Ma
- School of Chemistry and Chemical Engineering, Anhui University of Technology, Maanshan, Anhui 243002, People's Republic of China
| | - Zhiyi Liu
- School of Chemistry and Chemical Engineering, Anhui University of Technology, Maanshan, Anhui 243002, People's Republic of China
| | - Zhenzhen Wang
- School of Chemistry and Chemical Engineering, Anhui University of Technology, Maanshan, Anhui 243002, People's Republic of China
| | - Fang Xu
- School of Chemistry and Chemical Engineering, Anhui University of Technology, Maanshan, Anhui 243002, People's Republic of China
| | - Guohong Fan
- School of Chemistry and Chemical Engineering, Anhui University of Technology, Maanshan, Anhui 243002, People's Republic of China
| | - Hong Xu
- School of Chemistry and Chemical Engineering, Anhui University of Technology, Maanshan, Anhui 243002, People's Republic of China
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Milon, Roy D, Ahmed F. A DFT study to investigate the physical, electrical, optical properties and thermodynamic functions of boron nanoclusters (M xB 2n0; x=1,2, n=3,4,5). Heliyon 2023; 9:e17886. [PMID: 37539100 PMCID: PMC10395302 DOI: 10.1016/j.heliyon.2023.e17886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/28/2023] [Accepted: 06/30/2023] [Indexed: 08/05/2023] Open
Abstract
First Principle DFT calculations employing the B3LYP/LanL2DZ/SDD level of theory were used to analyze the various characteristics of boron nanoclusters (B6, B8, and B10). These pure structures were further doped with four transition metals (Ta, Ti, Tc, and V) to examine the enhancement of the pure structures' structural, electrical, and optical features. To study structural stability, we have estimated cohesion energy and imaginary frequencies. Cohesion energies were entirely negative, with a range of -3.37 eV to -8.07 eV, and most constructions had no imaginary frequencies, indicating their structural occurrences. The calculated adsorption energy suggests that the order of stability of the pristine boron nanoclusters is B10>B8>B6, and TcB10 and Tc2B10 are the more stable structures. Mulliken charge, DOS, HOMO-LUMO, and the HOMO-LUMO gap have all been examined in-depth to provide insight into electrical characteristics. UV-Vis and CD measurements show the doped boron nanoclusters have excellent optical properties. Aside from calculating thermodynamic functions, we have also calculated the global DFT parameters, which give us a deep quantum mechanical understanding of the optimized structure for further research and applications in the field of science and technology.
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Affiliation(s)
- Milon
- Department of Physics, Comilla University, Cumilla 3506, Bangladesh
| | - Debashis Roy
- Department of Physics, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Farid Ahmed
- Department of Physics, Jhangirnagar University, Savar, Dhaka 1342, Bangladesh
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Ogunwale G, Louis H, Unimuke TO, Mathias GE, Owen AE, Edet HO, Enudi OC, Oluwasanmi EO, Adeyinka AS, Doust Mohammadi M. Interaction of 5-Fluorouracil on the Surfaces of Pristine and Functionalized Ca 12O 12 Nanocages: An Intuition from DFT. ACS OMEGA 2023; 8:13551-13568. [PMID: 37091381 PMCID: PMC10116506 DOI: 10.1021/acsomega.2c03635] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 01/11/2023] [Indexed: 05/03/2023]
Abstract
The utilization of nanostructured materials for several biomedical applications has tremendously increased over the last few decades owing to their nanosizes, porosity, large surface area, sensitivity, and efficiency as drug delivery systems. Thus, the incorporation of functionalized and pristine nanostructures for cancer therapy offers substantial prospects to curb the persistent problems of ineffective drug administration and delivery to target sites. The potential of pristine (Ca12O12) and formyl (-CHO)- and amino (-NH2)-functionalized (Ca12O12-CHO and Ca12O12-NH2) derivatives as efficient nanocarriers for 5-fluorouracil (5FU) was studied at the B3LYP-GD3(BJ)/6-311++G(d,p) theoretical level in two electronic media (gas and solvent). To effectively account for all adsorption interactions of the drug on the investigated surfaces, electronic studies as well as topological analysis based on the quantum theory of atoms in molecules (QTAIM) and noncovalent interactions were exhaustively utilized. Interestingly, the obtained results divulged that the 5FU drug interacted favorably with both Ca12O12 and its functionalized derivatives. The adsorption energies of pristine and functionalized nanostructures were calculated to be -133.4, -96.9, and -175.6 kcal/mol, respectively, for Ca12O12, Ca12O12-CHO, and Ca12O12-NH2. Also, both topological analysis and NBO stabilization analysis revealed the presence of interactions among O3-H32, O27-C24, O10-C27, and N24-H32 atoms of the drug and the surface. However, 5FU@Ca12O12-CHO molecules portrayed the least adsorption energy due to considerable destabilization of the molecular complex as revealed by the computed deformation energy. Therefore, 5FU@Ca12O12 and 5FU@Ca12O12-NH2 acted as better nanovehicles for 5FU.
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Affiliation(s)
- Goodness
J. Ogunwale
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar540221, Nigeria
- Department
of Chemistry, Faculty of Science, University
of Ibadan, Ibadan200005, Nigeria
| | - Hitler Louis
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar540221, Nigeria
- Department
of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar540221, Nigeria
| | - Tomsmith O. Unimuke
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar540221, Nigeria
- Department
of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar540221, Nigeria
| | - Gideon E. Mathias
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar540221, Nigeria
- Department
of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar540221, Nigeria
| | - Aniekan E. Owen
- School
of Chemistry, University of St Andrews, St AndrewsKY16 9ST, Scotland
| | - Henry O. Edet
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar540221, Nigeria
- Department
of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar540221, Nigeria
| | - Obieze C. Enudi
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar540221, Nigeria
- Department
of Chemistry, Faculty of Science, University
of Ibadan, Ibadan200005, Nigeria
| | - Esther O. Oluwasanmi
- Computational
and Bio-Simulation Research Group, University
of Calabar, Calabar540221, Nigeria
- Department
of Chemistry, Faculty of Science, University
of Ibadan, Ibadan200005, Nigeria
| | - Adedapo S. Adeyinka
- Department
of Chemical Sciences, University of Johannesburg, Johannesburg2006, South-Africa
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Wu D, Xu F, Liu X, Li C, Chu X, Fan G, Xu H. Adsorption of CO, NO, and SO2 gases on pristine and single Ni3 cluster doped arsenene monolayer for its potential application as sensor or adsorbent by density functional theory study. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Theoretical study of transition metal doped α-borophene nanosheet as promising electrocatalyst for electrochemical reduction of N2. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113732] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Andrade-Zavaleta K, Chacon-Laiza Y, Asmat-Campos D, Raquel-Checca N. Green Synthesis of Superparamagnetic Iron Oxide Nanoparticles with Eucalyptus globulus Extract and Their Application in the Removal of Heavy Metals from Agricultural Soil. Molecules 2022; 27:1367. [PMID: 35209154 PMCID: PMC8880537 DOI: 10.3390/molecules27041367] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/03/2022] [Accepted: 02/13/2022] [Indexed: 11/16/2022] Open
Abstract
The green synthesis of metal oxide nanoparticles is presented as an excellent sustainable alternative for achieving nanostructures, with potential applications. This research provides important information regarding the influence of the type of solvent used in extracting organic reducing agents from E. globulus on the FeO NPs green synthesis protocol. A broad approach to characterization is presented, where UV-vis spectrophotometry suggests the presence of this type of nanoparticulate material. Likewise, the reduction mechanism was evaluated by FT-IR and the magnetic properties were evaluated by PPSM. In addition, characterizations were linked via elemental analysis (EDX), crystallographic characterization (XRD), electron microscopy (SEM/STEM), and Z potential to evaluate colloidal stability. The results show the influence of the type of solvent used for the extraction of organic reducing agents from E. globulus, and the effect on the synthesis of FeO NPs. In addition, the nanostructure material obtained showed excellent efficiency in the remediation of agricultural soil, eliminating metals such as Cr-VI, Cd, and, to a lesser extent, Pb.
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Affiliation(s)
- Karin Andrade-Zavaleta
- Facultad de Ingeniería, Ingeniería Ambiental, Universidad Privada del Norte, Trujillo 13011, Peru; (K.A.-Z.); (Y.C.-L.)
| | - Yessica Chacon-Laiza
- Facultad de Ingeniería, Ingeniería Ambiental, Universidad Privada del Norte, Trujillo 13011, Peru; (K.A.-Z.); (Y.C.-L.)
| | - David Asmat-Campos
- Dirección de Investigación, Innovación & Responsabilidad Social, Universidad Privada del Norte, Trujillo 13011, Peru
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