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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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2
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Li Y, Xu W, Wang X, Lai R, Qiu X, Zeng Z, Wang Z, Wang J. Molecular Dynamics and In Vitro Studies Elucidating the Tunable Features of Reconfigurable Nanodiscs for Guiding the Optimal Design of Curcumin Formulation. Bioengineering (Basel) 2024; 11:245. [PMID: 38534519 DOI: 10.3390/bioengineering11030245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/28/2024] Open
Abstract
In this study, we advance our exploration of Apolipoprotein A-I (apoA-I) peptide analogs (APAs) for their application in nanodisc (ND) assembly, focusing on the dynamic conformational characteristics and the potential for drug delivery. We explore APA-ND interactions with an emphasis on curcumin encapsulation, utilizing molecular dynamic simulations and in vitro assessments to evaluate the efficacy of various APA-ND formulations as drug carriers. The methodological approach involved the generation of three unique apoA-I α-11/3 helical mimics, resulting in fifteen distinct APAs. Their structural integrity was rigorously assessed using ColabFold-AF2, with particular attention to pLDDT and pTM scores. Extensive molecular dynamics simulations, covering 1.7 μs across 17 ND systems, were conducted to investigate the influence of APA sequence variations on ND stability and interactions. This study reveals that the composition of APAs, notably the presence of Proline, Serine, and Tryptophan, significantly impacts ND stability and morphology. Oligomeric APAs, in particular, demonstrated superior stability and distinct interaction patterns compared to their monomeric counterparts. Additionally, hydrodynamic diameter measurements over eight weeks indicated sequence-dependent stability, highlighting the potential of specific APA configurations for sustained colloidal stability. In vitro study successfully encapsulated curcumin in [AA]3/DMPC ND formulations, revealing concentration-dependent stability and interaction dynamics. The findings underscore the remarkable capability of APA-NDs to maintain structural integrity and efficient drug encapsulation, positioning them as a promising platform for drug delivery. The study concludes by emphasizing the tunability and versatility of APA-NDs in drug formulation, potentially revolutionizing nanomedicine by enabling customized APA sequences and ND properties for targeted drug delivery.
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Affiliation(s)
- Yongxiao Li
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Wanting Xu
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Xinpei Wang
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Ruizhi Lai
- Department of Pathology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China
| | - Xiaohui Qiu
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Zekai Zeng
- Department of Pathology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China
| | - Zhe Wang
- Department of Pathology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China
| | - Junqing Wang
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
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Wang Z, Wang X, Xu W, Li Y, Lai R, Qiu X, Chen X, Chen Z, Mi B, Wu M, Wang J. Translational Challenges and Prospective Solutions in the Implementation of Biomimetic Delivery Systems. Pharmaceutics 2023; 15:2623. [PMID: 38004601 PMCID: PMC10674763 DOI: 10.3390/pharmaceutics15112623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Biomimetic delivery systems (BDSs), inspired by the intricate designs of biological systems, have emerged as a groundbreaking paradigm in nanomedicine, offering unparalleled advantages in therapeutic delivery. These systems, encompassing platforms such as liposomes, protein-based nanoparticles, extracellular vesicles, and polysaccharides, are lauded for their targeted delivery, minimized side effects, and enhanced therapeutic outcomes. However, the translation of BDSs from research settings to clinical applications is fraught with challenges, including reproducibility concerns, physiological stability, and rigorous efficacy and safety evaluations. Furthermore, the innovative nature of BDSs demands the reevaluation and evolution of existing regulatory and ethical frameworks. This review provides an overview of BDSs and delves into the multifaceted translational challenges and present emerging solutions, underscored by real-world case studies. Emphasizing the potential of BDSs to redefine healthcare, we advocate for sustained interdisciplinary collaboration and research. As our understanding of biological systems deepens, the future of BDSs in clinical translation appears promising, with a focus on personalized medicine and refined patient-specific delivery systems.
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Affiliation(s)
- Zhe Wang
- Department of Pathology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China; (Z.W.); (R.L.)
| | - Xinpei Wang
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (X.W.); (W.X.); (Y.L.); (X.Q.); (X.C.); (Z.C.)
| | - Wanting Xu
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (X.W.); (W.X.); (Y.L.); (X.Q.); (X.C.); (Z.C.)
| | - Yongxiao Li
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (X.W.); (W.X.); (Y.L.); (X.Q.); (X.C.); (Z.C.)
| | - Ruizhi Lai
- Department of Pathology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China; (Z.W.); (R.L.)
| | - Xiaohui Qiu
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (X.W.); (W.X.); (Y.L.); (X.Q.); (X.C.); (Z.C.)
| | - Xu Chen
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (X.W.); (W.X.); (Y.L.); (X.Q.); (X.C.); (Z.C.)
| | - Zhidong Chen
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (X.W.); (W.X.); (Y.L.); (X.Q.); (X.C.); (Z.C.)
| | - Bobin Mi
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China;
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration, Wuhan 430022, China
| | - Meiying Wu
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (X.W.); (W.X.); (Y.L.); (X.Q.); (X.C.); (Z.C.)
| | - Junqing Wang
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (X.W.); (W.X.); (Y.L.); (X.Q.); (X.C.); (Z.C.)
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Chen L, Yu C, Xu W, Xiong Y, Cheng P, Lin Z, Zhang Z, Knoedler L, Panayi AC, Knoedler S, Wang J, Mi B, Liu G. Dual-Targeted Nanodiscs Revealing the Cross-Talk between Osteogenic Differentiation of Mesenchymal Stem Cells and Macrophages. ACS NANO 2023; 17:3153-3167. [PMID: 36715347 PMCID: PMC9933878 DOI: 10.1021/acsnano.2c12440] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
Ongoing research has highlighted the significance of the cross-play of macrophages and mesenchymal stem cells (MSCs). Lysine-specific demethylase 6B (KDM6B) has been shown to control osteogenic differentiation of MSCs by depleting trimethylated histone 3 lysine 27 (H3K27me3). However, to date, the role of KDM6B in bone marrow-derived macrophages (BMDMs) remains controversial. Here, a chromatin immunoprecipitation assay (ChIP) proved that KDM6B derived from osteogenic-induced BMSCs could bind to the promoter region of BMDMs' brain and muscle aryl hydrocarbon receptor nuclear translocator-like protein-1 (BMAL1) gene in a coculture system and activate BMAL1. Transcriptome sequencing and experiments in vitro showed that the overexpression of BMAL1 in BMDM could inhibit the TLR2/NF-κB signaling pathway, reduce pyroptosis, and decrease the M1/M2 ratio, thereby promoting osteogenic differentiation of BMSCs. Furthermore, bone and macrophage dual-targeted GSK-J4 (KDM6B inhibitor)-loaded nanodiscs were synthesized via binding SDSSD-apoA-1 peptide analogs (APA) peptide, which indirectly proved the critical role of KDM6B in osteogenesis in vivo. Overall, we demonstrated that KDM6B serves as a positive circulation trigger during osteogenic differentiation by decreasing the ratio of M1/M2 both in vitro and in vivo. Collectively, these results provide insight into basic research in the field of osteoporosis and bone repair.
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Affiliation(s)
- Lang Chen
- Department
of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Hubei
Province Key Laboratory of Oral and Maxillofacial Development and
Regeneration, Wuhan 430022, China
| | - Chenyan Yu
- Department
of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Hubei
Province Key Laboratory of Oral and Maxillofacial Development and
Regeneration, Wuhan 430022, China
| | - Wanting Xu
- Department
of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- School
of Pharmaceutical Sciences, Shenzhen Campus
of Sun Yat-sen University, Shenzhen 518100, China
| | - Yuan Xiong
- Department
of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Hubei
Province Key Laboratory of Oral and Maxillofacial Development and
Regeneration, Wuhan 430022, China
| | - Peng Cheng
- Department
of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Hubei
Province Key Laboratory of Oral and Maxillofacial Development and
Regeneration, Wuhan 430022, China
| | - Ze Lin
- Department
of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Hubei
Province Key Laboratory of Oral and Maxillofacial Development and
Regeneration, Wuhan 430022, China
| | - Zhenhe Zhang
- Department
of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Hubei
Province Key Laboratory of Oral and Maxillofacial Development and
Regeneration, Wuhan 430022, China
| | - Leonard Knoedler
- Department
of Plastic, Hand and Reconstructive Surgery, University Hospital Regensburg, Regensburg 93053, Germany
- Leibniz
Institute of Immunotherapy, University of
Regensburg, Regensburg 93053, Germany
| | - Adriana C. Panayi
- Department
of Plastic Surgery, Brigham and Women’s
Hospital, Harvard Medical School, Boston, Massachusetts 02152, United States
- Department
of Hand, Plastic and Reconstructive Surgery, Microsurgery, Burn Center,
BG Trauma Center Ludwigshafen, University
of Heidelberg, Ludwig-Guttmann-Strasse
13, Ludwigshafen/Rhine 67071, Germany
| | - Samuel Knoedler
- Department
of Plastic Surgery, Brigham and Women’s
Hospital, Harvard Medical School, Boston, Massachusetts 02152, United States
- Institute
of Regenerative Biology and Medicine, Helmholtz
Zentrum München, Max-Lebsche-Platz 31, Munich 81377, Germany
| | - Junqing Wang
- Department
of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- School
of Pharmaceutical Sciences, Shenzhen Campus
of Sun Yat-sen University, Shenzhen 518100, China
| | - Bobin Mi
- Department
of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Hubei
Province Key Laboratory of Oral and Maxillofacial Development and
Regeneration, Wuhan 430022, China
| | - Guohui Liu
- Department
of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Hubei
Province Key Laboratory of Oral and Maxillofacial Development and
Regeneration, Wuhan 430022, China
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Chen Z, Chen X, Liu G, Han K, Chen J, Wang J. Editorial: The Application of Nanoengineering in Advanced Drug Delivery and Translational Research. Front Bioeng Biotechnol 2022; 10:886109. [PMID: 35402399 PMCID: PMC8988031 DOI: 10.3389/fbioe.2022.886109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 03/07/2022] [Indexed: 12/05/2022] Open
Affiliation(s)
- Zhidong Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Xu Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Gan Liu
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
- *Correspondence: Gan Liu, ; Kai Han, ; Jingxiao Chen, ; Junqing Wang,
| | - Kai Han
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, United States
- *Correspondence: Gan Liu, ; Kai Han, ; Jingxiao Chen, ; Junqing Wang,
| | - Jingxiao Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China
- *Correspondence: Gan Liu, ; Kai Han, ; Jingxiao Chen, ; Junqing Wang,
| | - Junqing Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
- *Correspondence: Gan Liu, ; Kai Han, ; Jingxiao Chen, ; Junqing Wang,
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