1
|
Yang HW, Ju SP, Hsieh YT, Yang YC. Design single-stranded DNA aptamer of cluster of differentiation 47 protein by stochastic tunnelling-basin hopping-discrete molecular dynamics method. J Biomol Struct Dyn 2024; 42:3969-3982. [PMID: 37261868 DOI: 10.1080/07391102.2023.2217511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 05/18/2023] [Indexed: 06/02/2023]
Abstract
The formation of the Cluster of Differentiation 47 (CD47, PDB code: 2JJT)/signal regulatory protein α (SIRPα) complex is very important as it protects healthy cells from immune clearance while promoting macrophage phagocytosis for tumour elimination. Although several antibodies have been developed for cancer therapy, new function-blocking aptamers are still under development. This study aims to design the aptamer AptCD47, which can block the formation of the CD47/SIRPα complex. This study employs the MARTINI coarse-grained (CG) force field and the stochastic tunnelling-basin hopping-discrete molecular dynamics (STUN-BH-DMD) method to identify the most stable AptCD47/CD47 complexes. Coarse-grained molecular dynamics (CGMD) simulations were used to obtain root-mean-square deviation (RMSD) and root-mean-square fluctuation (RMSF) analyses. The results demonstrate that the formation of AptCD47/CD47 complexes renders the CD47 structure more stable than the single CD47 molecule in a water environment. The minimum energy pathway (MEP) obtained by the nudged elastic band (NEB) method indicates that the binding processes of 5'-ATTCAATTCC-3' and 5'-AGTGCAATCT-3' to CD47 are barrierless, which is much lower than the binding barrier of SIRPα to CD47 of about 14.23 kcal/mol. Therefore, these two AptCD47/CD47 complexes can create a high spatial binding barrier for SIRPα, preventing the formation of a stable CD47/SIRPα complex. The proposed numerical process with the MARTINI CG force field can be used to design CD47 aptamers that efficiently block SIRPα from binding to CD47.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Hung-Wei Yang
- Department of Biomedical Engineering, National Cheng Kung University, Tainan City, Taiwan
- Medical Device Innovation Center, National Cheng Kung University, Tainan City, Taiwan
| | - Shin-Pon Ju
- Department of Mechanical and Electro-Mechanical Engineering, National Sun Yat-sen University, Kaohsiung, Taiwan
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yun-Te Hsieh
- Department of Mechanical and Electro-Mechanical Engineering, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Yung-Cheng Yang
- Department of Mechanical and Electro-Mechanical Engineering, National Sun Yat-sen University, Kaohsiung, Taiwan
| |
Collapse
|
2
|
Li S, Coffinier Y, Lagadec C, Cleri F, Nishiguchi K, Fujiwara A, Fujii T, Kim SH, Clément N. Redox-labelled electrochemical aptasensors with nanosupported cancer cells. Biosens Bioelectron 2022; 216:114643. [PMID: 36030742 DOI: 10.1016/j.bios.2022.114643] [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: 02/28/2022] [Revised: 07/31/2022] [Accepted: 08/16/2022] [Indexed: 11/30/2022]
Abstract
The transfer of redox-labelled bioelectrochemical sensors from proteins to cells is not straightforward because of the cell downward force issue on the surface of the sensors. In this paper, 20-nm-thick nanopillars are introduced to overcome this issue, in a well-controlled manner. We show on both molecular dynamics simulations and experiments that suspending cells a few nanometers above an electrode surface enables redox-labelled tethered DNA aptamer probes to move freely, while remaining at an interaction distance from a target membrane protein, i. e. epithelial cell adhesion molecule (EpCAM), which is typically overexpressed in cancer cells. By this nanopillar configuration, the interaction of aptamer with cancer cells is clearly observable, with 13 cells as the lower limit of detection. Nanoconfinement induced by the gap between the electrode surface and the cell membrane appears to improve the limit of detection and to lower the melting temperature of DNA aptamer hairpins, offering an additional degree of freedom to optimize molecular recognition mechanisms. This novel nanosupported electrochemical DNA cell sensor scheme including Brownian-fluctuating redox species opens new opportunities for the design of all-electrical sensors using redox-labelled probes.
Collapse
Affiliation(s)
- S Li
- IIS, LIMMS/CNRS-IIS IRL2820, The Univ. of Tokyo, 4-6-1 Komaba, Meguro-ku Tokyo, 153-8505, Japan.
| | - Y Coffinier
- IEMN, CNRS UMR8520, Univ. Lille Avenue Poincaré, BP 60069, Villeneuve D'Ascq Cedex, 59652, France
| | - C Lagadec
- Univ. Lille, CNRS, Inserm, CHU Lille, Centre Oscar Lambret, UMR9020 - UMR-S 1277 - Canther - Cancer Heterogeneity, Plasticity and Resistance to Therapies, F-59000, Lille, France
| | - F Cleri
- IEMN, CNRS UMR8520, Univ. Lille Avenue Poincaré, BP 60069, Villeneuve D'Ascq Cedex, 59652, France
| | - K Nishiguchi
- NTT Basic Research Laboratories, NTT Corporation, 3-1, Morinosato-Wakamiya, Atsugi-shi, 243-0198, Japan
| | - A Fujiwara
- NTT Basic Research Laboratories, NTT Corporation, 3-1, Morinosato-Wakamiya, Atsugi-shi, 243-0198, Japan
| | - T Fujii
- IIS, LIMMS/CNRS-IIS IRL2820, The Univ. of Tokyo, 4-6-1 Komaba, Meguro-ku Tokyo, 153-8505, Japan
| | - S-H Kim
- IIS, LIMMS/CNRS-IIS IRL2820, The Univ. of Tokyo, 4-6-1 Komaba, Meguro-ku Tokyo, 153-8505, Japan
| | - N Clément
- IIS, LIMMS/CNRS-IIS IRL2820, The Univ. of Tokyo, 4-6-1 Komaba, Meguro-ku Tokyo, 153-8505, Japan.
| |
Collapse
|
3
|
Exploring the most stable aptamer/target molecule complex by the stochastic tunnelling-basin hopping-discrete molecular dynamics method. Sci Rep 2021; 11:11406. [PMID: 34075115 PMCID: PMC8169667 DOI: 10.1038/s41598-021-90907-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 05/07/2021] [Indexed: 11/29/2022] Open
Abstract
The stochastic tunnelling-basin hopping-discrete molecular dynamics (STUN-BH-DMD) method was applied to the search for the most stable biomolecular complexes in water by using the MARTINI coarse-grained (CG) model. The epithelial cell adhesion molecule (EpCAM, PDB code: 4MZV) was used as an EpCAM adaptor for an EpA (AptEpA) benchmark target molecule. The effects of two adsorption positions on the EpCAM were analysed, and it is found that the AptEpA adsorption configuration located within the EpCAM pocket-like structure is more stable and the energy barrier is lower due to the interaction with water. By the root mean square deviation (RMSD), the configuration of EpCAM in water is more conservative when the AptEpA binds to EpCAM by attaching to the pocket space of the EpCAM dimer. For AptEpA, the root mean square fluctuation (RMSF) analysis result indicates Nucleobase 1 and Nucleobase 2 display higher flexibility during the CGMD simulation. Finally, from the binding energy contour maps and histogram plots of EpCAM and each AptEpA nucleobase, it is clear that the binding energy adsorbed to the pocket-like structure is more continuous than that energy not adsorbed to the pocket-like structure. This study has proposed a new numerical process for applying the STUN-BH-DMD with the CG model, which can reduce computational details and directly find a more stable AptEpA/EpCAM complex in water.
Collapse
|
4
|
Shang X, Guan Z, Zhang S, Shi L, You H. Predicting the aptamer SYL3C-EpCAM complex's structure with the Martini-based simulation protocol. Phys Chem Chem Phys 2021; 23:7066-7079. [PMID: 33496283 DOI: 10.1039/d0cp05003b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Aptamers (small single strand DNA/RNAs) such as SYL3C are considered as ideal alternatives to antibodies in cancer related research studies. However, 3D structure predictions for aptamers and aptamer-protein complexes are scarce due to the high cost of experimental measurements and unreliable computer-based methods. Thus aptamers' diagnostic and therapeutic applications are severely restricted. To meet the challenge, we proposed a Martini-based aptamer-protein complex prediction protocol. By combining the base-base contact map from simulation and secondary structure prediction from various tools, improved secondary structure predictions can be obtained. This method reduced the risk of providing incorrect or incomplete base pairs in secondary structure prediction. Thus 3D structure modeling based on the secondary structure can be more reliable. We introduced the soft elastic network to the hairpin folded regions of the Martini ssDNAs to preserve their canonical structure. Using our protocol, we predicted the first 3D structure of the aptamer SYL3C and the SYL3C-EpCAM complex. We believe that our work could contribute to the future aptamer-related research studies and medical implications.
Collapse
Affiliation(s)
- Xu Shang
- State Key Laboratory of Computer Architecture, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China.
| | | | | | | | | |
Collapse
|
5
|
Santini BL, Zúñiga-Bustos M, Vidal-Limon A, Alderete JB, Águila SA, Jiménez VA. In Silico Design of Novel Mutant Anti-MUC1 Aptamers for Targeted Cancer Therapy. J Chem Inf Model 2019; 60:786-793. [PMID: 31657548 DOI: 10.1021/acs.jcim.9b00756] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The transmembrane glycoprotein mucin 1 (MUC1) is an attractive tumor marker for cancer therapy and diagnosis. The nine amino acid extracellular epitope APDTRPAPG of this protein is selectively recognized by the S2.2 single-stranded DNA anti-MUC1 aptamer, which has emerged as a promising template for designing novel targeting agents for MUC1-directed therapy. In this work, 100 ns molecular dynamics (MD) simulations, MM/GBSA binding free energy calculations, and conformational analysis were employed to propose a novel prospective anti-MUC1 aptamer with increased affinity toward the MUC1 epitope resulting from the double mutation of the T11 and T12 residues with PSU and U nucleosides, respectively. The double mutant aptamer exhibits a tight interaction with the MUC1 epitope and adopts a groove conformation that structurally favors the intermolecular contact with the epitope through the intermediate T11-A18 region leaving the 3' and 5' ends free for further chemical conjugation with a nanocarrier or pharmaceutical. These results are valuable to gain understanding about the molecular features governing aptamer-epitope interactions and constitute a first key step for the design of novel aptamer-based nanocarriers for MUC1-targeted cancer therapy.
Collapse
Affiliation(s)
- Brianda L Santini
- Centro de Nanociencias y Nanotecnología , Universidad Nacional Autónoma de México , Km. 107 Carretera Tijuana-Ensenada , Ensenada , Baja California , Mexico , C.P. 22860
| | - Matías Zúñiga-Bustos
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas , Universidad Andres Bello , Sede Concepción, Autopista Concepción-Talcahuano 7100 , Talcahuano 4260000 , Chile
| | - Abraham Vidal-Limon
- Centro de Nanociencias y Nanotecnología , Universidad Nacional Autónoma de México , Km. 107 Carretera Tijuana-Ensenada , Ensenada , Baja California , Mexico , C.P. 22860
| | - Joel B Alderete
- Instituto de Química de Recursos Naturales , Universidad de Talca , Casilla 747 , Talca 3460000 , Chile
| | - Sergio A Águila
- Centro de Nanociencias y Nanotecnología , Universidad Nacional Autónoma de México , Km. 107 Carretera Tijuana-Ensenada , Ensenada , Baja California , Mexico , C.P. 22860
| | - Verónica A Jiménez
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas , Universidad Andres Bello , Sede Concepción, Autopista Concepción-Talcahuano 7100 , Talcahuano 4260000 , Chile
| |
Collapse
|