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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. [PMID: 39148378 DOI: 10.1039/d3cs00575e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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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Wu C, Deng C, Zhang JX, Pan W, Yang L, Pan K, Tan QG, Yue T, Miao AJ. Silica nanoparticles inhibit cadmium uptake by the protozoan Tetrahymena thermophila without the need for adsorption. JOURNAL OF HAZARDOUS MATERIALS 2024; 466:133569. [PMID: 38266583 DOI: 10.1016/j.jhazmat.2024.133569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/06/2024] [Accepted: 01/17/2024] [Indexed: 01/26/2024]
Abstract
The simultaneous presence of nanoparticles (NPs) and heavy metals in the environment may affect their mutual biological uptake. Although previous studies showed that NPs could alter the cellular uptake of heavy metals by their adsorption of heavy metals, whether they could affect metal uptake without the need for adsorption is unknown. This study examined the effects of silica (SiO2) NPs on the uptake of Cd ion by the protozoan Tetrahymena thermophila. We found that, even with negligible levels of adsorption, SiO2 NPs at concentrations of 3 to 100 mg/L inhibited Cd uptake. This inhibitory effect decreased as the ambient Cd concentration increased from 1 to 100 μg/L, suggesting the involvement of at least two transporters with different affinities for Cd. The transporters were subsequently identified by the specific protein inhibitors amiloride and tariquidar as NCX and ABCB1, which are responsible for the uptake of Cd at low and high Cd levels, respectively. RT-qPCR and molecular dynamics simulation further showed that the inhibitory effects of SiO2 NPs were attributable to the down-regulated expression of the genes Ncx and Abcb1, steric hindrance of Cd uptake by NCX and ABCB1, and the shrinkage of the central channel pore of the transporters in the presence of SiO2 NPs. SiO2 NPs more strongly inhibited Cd transport by NCX than by ABCB1, due to the higher binding affinity of SiO2 NPs with NCX. Overall, our study sheds new light on a previously overlooked influence of NPs on metal uptake and the responsible mechanism.
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Affiliation(s)
- Chao Wu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu Province 210023, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong Province 518060, China
| | - Chaofan Deng
- Institute of Coastal Environmental Pollution Control, Key Laboratory of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, Shandong Province 266100, China
| | - Jia-Xin Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu Province 210023, China
| | - Wei Pan
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu Province 210023, China
| | - Liuyan Yang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu Province 210023, China
| | - Ke Pan
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong Province 518060, China
| | - Qiao-Guo Tan
- Key Laboratory of the Coastal and Wetland Ecosystems of Ministry of Education, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Tongtao Yue
- Institute of Coastal Environmental Pollution Control, Key Laboratory of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao, Shandong Province 266100, China.
| | - Ai-Jun Miao
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu Province 210023, China.
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Cheng S, Zhou K, Wang F, Ye Z, Ye C, Lian C, Shang Y, Liu H. Unraveling the Molecular Mechanisms of Alcohol-Mediated Skin Permeation Enhancement: Insights from Molecular Dynamics Simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:594-603. [PMID: 38115608 DOI: 10.1021/acs.langmuir.3c02809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
The application of alcohols as permeation enhancers in pharmaceutical and cosmetic formulations has attracted considerable attention, owing to their skin permeation-enhancing effect. Nonetheless, the elucidation of the fundamental mechanisms underlying the skin permeation-enhancing effect remains elusive. In this study, molecular dynamics (MD) simulations were employed to investigate the effect of 1,2-propanediol (1,2-PDO), 1,2-butanediol (1,2-BDO), and ethanol (EtOH) on the stratum corneum (SC) model membrane. The results showed that the effect of alcohols on the SC model membrane displayed a concentration-dependent nature. The alcohols can interact with SC lipids and exhibit a remarkable ability to selectively extract free fatty acid (FFA) molecules from the SC model membrane and make the SC looser. Meanwhile, 1,2-BDO and EtOH can penetrate into SC lipid bilayers at higher concentrations, leading to the formation of continuous hydrophilic defects in SC. The FFA extraction and the formation of continuous hydrophilic defects induced ceramide (CER) tail chains to become more disordered and fluid and also weakened the hydrogen bonding (H-bonding) network among SC lipids. Both the FFA extraction and the continuous hydrophilic defect formation endowed alcohols with the permeation-enhancing effect. The constrained simulations revealed that the free energy barriers decreased for the permeation of the hydrophilic model molecule (COL) across the SC model membranes containing alcohols, particularly for 1,2-BDO and EtOH. The possible permeation-enhancing mechanisms of alcohols were proposed correspondingly. This work not only provided a deep understanding of the transdermal permeation-enhancing behavior of alcohols at the molecular level but also provided necessary reference information for designing effective transdermal drug delivery systems in applications.
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Affiliation(s)
- Shiqiang Cheng
- Key Laboratory for Advanced Materials, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Kangfu Zhou
- Yunnan Botanee Bio-technology Group Co., Ltd., Yunnan 650106, China
| | - Feifei Wang
- Yunnan Botanee Bio-technology Group Co., Ltd., Yunnan 650106, China
- Yunnan Yunke Characteristic Plant Extraction Laboratory Co., Ltd., Yunnan 650106, China
| | - Zhicheng Ye
- Key Laboratory for Advanced Materials, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Chuanjun Ye
- Yunnan Botanee Bio-technology Group Co., Ltd., Yunnan 650106, China
| | - Cheng Lian
- Key Laboratory for Advanced Materials, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yazhuo Shang
- Key Laboratory for Advanced Materials, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Honglai Liu
- Key Laboratory for Advanced Materials, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
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Leibe R, Fritsch-Decker S, Gussmann F, Wagbo AM, Wadhwani P, Diabaté S, Wenzel W, Ulrich AS, Weiss C. Key Role of Choline Head Groups in Large Unilamellar Phospholipid Vesicles for the Interaction with and Rupture by Silica Nanoparticles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2207593. [PMID: 37098631 DOI: 10.1002/smll.202207593] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 03/22/2023] [Indexed: 06/19/2023]
Abstract
For highly abundant silica nanomaterials, detrimental effects on proteins and phospholipids are postulated as critical molecular initiating events that involve hydrogen-bonding, hydrophobic, and/or hydrophilic interactions. Here, large unilamellar vesicles with various well-defined phospholipid compositions are used as biomimetic models to recapitulate membranolysis, a process known to be induced by silica nanoparticles in human cells. Differential analysis of the dominant phospholipids determined in membranes of alveolar lung epithelial cells demonstrates that the quaternary ammonium head groups of phosphatidylcholine and sphingomyelin play a critical and dose-dependent role in vesicle binding and rupture by amorphous colloidal silica nanoparticles. Surface modification by either protein adsorption or by covalent coupling of carboxyl groups suppresses the disintegration of these lipid vesicles, as well as membranolysis in human A549 lung epithelial cells by the silica nanoparticles. Furthermore, molecular modeling suggests a preferential affinity of silanol groups for choline head groups, which is also modulated by the pH value. Biomimetic lipid vesicles can thus be used to better understand specific phospholipid-nanoparticle interactions at the molecular level to support the rational design of safe advanced materials.
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Affiliation(s)
- Regina Leibe
- Institute of Biological and Chemical Systems - Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Susanne Fritsch-Decker
- Institute of Biological and Chemical Systems - Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Florian Gussmann
- Institute of Nanotechnology (INT), KIT, Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Ane Marit Wagbo
- Institute of Biological and Chemical Systems - Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Parvesh Wadhwani
- Institute of Biological Interfaces (IBG-2), KIT, Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Silvia Diabaté
- Institute of Biological and Chemical Systems - Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Wolfgang Wenzel
- Institute of Nanotechnology (INT), KIT, Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Anne S Ulrich
- Institute of Biological Interfaces (IBG-2), KIT, Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Carsten Weiss
- Institute of Biological and Chemical Systems - Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
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Cheng S, Ye Z, Wang X, Lian C, Shang Y, Liu H. The effects of adsorbed benzo(a)pyrene on dynamic behavior of polystyrene nanoplastics through phospholipid membrane: A molecular simulation study. Colloids Surf B Biointerfaces 2023; 224:113211. [PMID: 36863250 DOI: 10.1016/j.colsurfb.2023.113211] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/20/2023] [Accepted: 02/18/2023] [Indexed: 02/22/2023]
Abstract
Nanoplastics (NPs) are mainly generated from the decomposition of plastic waste and industrial production, which have attracted much attention due to the potential risk for humans. The ability of NPs to penetrate different biological barriers has been proved, but the understanding of molecular details is very limited, especially for organic pollutant-NP combinations. Here, we investigated the uptake process of polystyrene NPs (PSNPs) combined with benzo(a)pyrene (BAP) molecules by dipalmitoylphosphatidylcholine (DPPC) bilayers by molecular dynamics (MD) simulations. The results showed that the PSNPs can adsorb and accumulate BAP molecules in water phase and then carried BAP molecules to enter DPPC bilayers. At the same time, the adsorbed BAP promoted the penetration of PSNPs into DPPC bilayers effectively by hydrophobic effect. The process of BAP-PSNP combinations penetrating into DPPC bilayers can be summarized into four steps including adhesion on the DPPC bilayer surface, uptake by the DPPC bilayer, BAP molecules detached from the PSNPs, and the PSNPs depolymerized in the bilayer interior. Furthermore, the amount of adsorbed BAP on PSNPs affected the properties of DPPC bilayers directly, especially the fluidity of DPPC bilayers that determine the physiologic function. Obviously, the combined effect of PSNPs and BAP enhanced the cytotoxicity. This work not only presented a vivid transmembrane process of BAP-PSNP combinations and revealed the nature of the effects of adsorbed benzo(a)pyrene on the dynamic behavior of polystyrene nanoplastics through phospholipid membrane, but also provide some necessary information of the potential damage for organic pollutant-nanoplastic combinations on human health at a molecular level.
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Affiliation(s)
- Shiqiang Cheng
- Key Laboratory for Advanced Materials, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Zhicheng Ye
- Key Laboratory for Advanced Materials, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Xiong Wang
- Department of Dermatology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Cheng Lian
- Key Laboratory for Advanced Materials, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yazhuo Shang
- Key Laboratory for Advanced Materials, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Honglai Liu
- Key Laboratory for Advanced Materials, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
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Zhang Z, Qiao M, Zhao H, Ran Q, Yuan S. Effect of sodium alkyl sulfate chain length on foam stability: A molecular dynamics study. Colloids Surf A Physicochem Eng Asp 2023. [DOI: 10.1016/j.colsurfa.2022.130394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Cui X, Wang W, Du M, Ma D, Zhang X. Molecular Simulation to Explore the Dissolution Behavior of Sulfur in Carbon Disulfide. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27144402. [PMID: 35889275 PMCID: PMC9322742 DOI: 10.3390/molecules27144402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/04/2022] [Accepted: 07/06/2022] [Indexed: 11/16/2022]
Abstract
Soluble sulfur (S8) and insoluble sulfur (IS) have different application fields, and molecular dynamics simulation can reveal their differences in solubility in solvents. It is found that in the simulated carbon disulfide (CS2) solvent, soluble sulfur in the form of clusters mainly promotes the dissolution of clusters through van der Waals interaction between solvent molecules (CS2) and S8, and the solubility gradually increases with the increase in temperature. However, the strong interaction between polymer chains of insoluble sulfur in the form of polymer hinders the diffusion of IS into CS2 solvent, which is not conducive to high-temperature dissolution. The simulated solubility parameter shows that the solubility parameter of soluble sulfur is closer to that of the solvent, which is consistent with the above explanation that soluble sulfur is easy to dissolve.
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Affiliation(s)
- Xiangyu Cui
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250014, China
| | - Wenbo Wang
- Shandong Yanggu Huatai Chemical Co., Ltd., Yanggu, Liaocheng 252300, China
| | - Mengcheng Du
- Shandong Yanggu Huatai Chemical Co., Ltd., Yanggu, Liaocheng 252300, China
| | - Delong Ma
- Shandong Yanggu Huatai Chemical Co., Ltd., Yanggu, Liaocheng 252300, China
| | - Xiaolai Zhang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250014, China
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