Molecular Systems Design & Engineering最新文献_第2页

In silico investigation of the interaction between α-synuclein aggregates and organic supramolecular assemblies α-突触核蛋白聚集体与有机超分子组装体之间相互作用的硅学研究

IF 3.6 3区工程技术

Molecular Systems Design & Engineering Pub Date : 2024-08-19 DOI: 10.1039/d4me00071d

Laura Le Bras, Yves L. Dory, Benoît Champagne

{"title":"In silico investigation of the interaction between α-synuclein aggregates and organic supramolecular assemblies","authors":"Laura Le Bras, Yves L. Dory, Benoît Champagne","doi":"10.1039/d4me00071d","DOIUrl":"https://doi.org/10.1039/d4me00071d","url":null,"abstract":"α-Synuclein (αSYN), and its tendency to self-aggregate, plays an important role in the development of Parkinson's disease (PD). αSYN aggregates are characterized by a stacking of αSYN chains and an interaction between the stackings to form dimer-like structures. The stability of these supramolecular assemblies is ensured by the presence of numerous residues that adopt “β-strand” and then “β-sheet” conformations, implying multiple interactions within and between the chains of αSYN. Following our previous study on the ability of small organic molecules to form columnar supramolecular assemblies (organic nanotubes, ONs) [Le Bras, L.; Dory, Y. L.; Champagne, B. Computational prediction of the supramolecular self-assembling properties of organic molecules: the role of conformational flexibility of amide moieties. Phys. Chem. Chem. Phys., 2021, 23, 20453–20465], we propose here to unravel the ability of these ONs to interact with αSYN aggregates. More than an interaction, we expect the organic molecules to avoid the complete aggregation process and ideally to induce destabilization of the stacking. Both molecular dynamics simulation and quantum mechanical-based calculations are used to identify the key parameters of the interaction and the resulting (de)stabilization of the assembly.","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142209517","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Synthesis and theoretical studies of the conformational behaviour of N-vinylcaprolactam/N-vinylimidazole copolymers in selective solvent† 选择性溶剂中 N-乙烯基己内酰胺/N-乙烯基咪唑共聚物构象行为的合成与理论研究

IF 3.2 3区工程技术

Molecular Systems Design & Engineering Pub Date : 2024-08-12 DOI: 10.1039/D4ME00085D

A. I. Barabanova, A. V. Vorozheykina, M. K. Glagolev, P. V. Komarov and A. R. Khokhlov

引用次数: 0

Improving DNA aptamers against a heart failure protein biomarker using structure-guided random mutation approaches for colourimetric biosensor development† 利用结构引导的随机突变方法改进针对心力衰竭蛋白生物标记物的DNA适配体，以开发比色生物传感器

IF 3.2 3区工程技术

Molecular Systems Design & Engineering Pub Date : 2024-08-01 DOI: 10.1039/D4ME00073K

Donny Marcius, Bejo Ropii, Diah Ayu Safitri, Mokhamad Fakhrul Ulum, Husna Nugrahapraja and Isa Anshori

{"title":"Improving DNA aptamers against a heart failure protein biomarker using structure-guided random mutation approaches for colourimetric biosensor development†","authors":"Donny Marcius, Bejo Ropii, Diah Ayu Safitri, Mokhamad Fakhrul Ulum, Husna Nugrahapraja and Isa Anshori","doi":"10.1039/D4ME00073K","DOIUrl":"10.1039/D4ME00073K","url":null,"abstract":"Aptamers are short single-stranded oligonucleotides, which offer several advantages over antibodies as bioreceptors. The widely used method for generating aptamer sequences, SELEX, has some limitations such as a limited oligonucleotide library used and amplification bias of PCR. Bioinformatics approaches have been shown to optimise and increase aptamer affinity. This research aimed to enhance the affinity of the NT-proBNP (N-terminal pro-brain natriuretic peptide, a biomarker for heart failure)-targeting aptamer acquired from SELEX using computational strategies involving sequence truncation and secondary structure-guided random mutations. DNA aptamers and protein structures are predicted by MC-Fold + 3dDNA and Robetta, respectively, whereas the computational evaluations utilize molecular docking, interaction profiles, and molecular dynamics simulations. The structural and energetic analysis revealed that the in silico optimised aptamer had more stable and robust interactions in binding to the NT-proBNP protein than the SELEX-obtained aptamer. Furthermore, our approach was supported and confirmed by in vitro colourimetric assay based on gold nanoparticle aggregation, evidenced by a detection limit of 0.5 ng mL−1 which is lower than the SELEX-obtained aptamer (2.3 ng mL−1).","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142209413","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Synthesis and catalytic application of ZSM-48 zeolite ZSM-48 沸石的合成与催化应用

IF 3.2 3区工程技术

Molecular Systems Design & Engineering Pub Date : 2024-07-11 DOI: 10.1039/D4ME00076E

Wen Liu, Yanan Wang, Xinbao Zhang, Fucun Chen, Sujuan Xie, Longya Xu, Xiujie Li and Xiangxue Zhu

{"title":"Synthesis and catalytic application of ZSM-48 zeolite","authors":"Wen Liu, Yanan Wang, Xinbao Zhang, Fucun Chen, Sujuan Xie, Longya Xu, Xiujie Li and Xiangxue Zhu","doi":"10.1039/D4ME00076E","DOIUrl":"10.1039/D4ME00076E","url":null,"abstract":"ZSM-48 is a kind of high-silica zeolite with one dimensional (1D) 10-member ring (10-MR) channel structure. It is well known for its unique pore structure and acid properties, as well as exceptional catalytic performance in various reactions. However, the diffusion limitation and insufficient acid density pose significant challenges to its widespread application and promotion. This review aims to summarize the advancements in enhancing diffusivity and regulating acid properties of ZSM-48 zeolite, as well as its catalytic applications. To alleviate diffusion limitations, the construction of hierarchical ZSM-48 zeolites through post-treatment and in situ strategies is extensively summarized. Ongoing endeavors focus on determining the optimal balance between maintaining structural integrity and improving mass transfer capacity through post-treatment techniques. Concerning acid regulation, various strategies such as the use of a special organic structure directing agent (OSDA), seed-assisted synthesis, zeolite hybridization, and heteroatom doping strategies have been developed. The emphasis on acid regulation in ZSM-48 zeolite involves efforts to design or discover more cost-effective OSDAs. Additionally, researchers are exploring simpler and more economical seed-assisted synthesis routes to produce Al-rich candidates. In terms of catalytic application, extensive research has been conducted on various reactions including hydroisomerization of paraffin, isomerization of xylenes, cracking of hydrocarbons, and methanol conversion to hydrocarbons. Its distinctive catalytic performance is primarily related to the shape-selective advantage conferred by its 1D channel structure. In particular, ZSM-48 zeolite is widely regarded as the leading candidate in paraffin hydroisomerization reactions, attributed to its high proportion of multi-branched isomers in the catalytic products. The present review aims to provide a comprehensive reference for researchers dedicated to the synthesis, modification, and application of ZSM-48 zeolite.","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141586654","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Designing novel inhibitor derivatives targeting SARS-CoV-2 Mpro enzyme: a deep learning and structure biology approach† 设计针对 SARS-CoV-2 Mpro 酶的新型抑制剂衍生物：一种深度学习和结构生物学方法

IF 3.2 3区工程技术

Molecular Systems Design & Engineering Pub Date : 2024-07-10 DOI: 10.1039/D4ME00062E

Tushar Joshi, Shalini Mathpal, Priyanka Sharma, Akshay Abraham, Rajadurai Vijay Solomon and Subhash Chandra

{"title":"Designing novel inhibitor derivatives targeting SARS-CoV-2 Mpro enzyme: a deep learning and structure biology approach†","authors":"Tushar Joshi, Shalini Mathpal, Priyanka Sharma, Akshay Abraham, Rajadurai Vijay Solomon and Subhash Chandra","doi":"10.1039/D4ME00062E","DOIUrl":"10.1039/D4ME00062E","url":null,"abstract":"The emerging variants of SARS-CoV-2 have raised serious concerns worldwide due to their infectivity, lethality, and unpredictability. Moreover, the ability of these variants to bypass vaccine protection and immunity has compelled the research community to design novel compounds against SARS-CoV-2. This study focuses on designing novel molecules using artificial intelligence methods for the development of new therapeutics against SARS-CoV-2. Furthermore, these molecules were validated against main protease (Mpro) using in-silico methods. In this study, we used the DeepScreening RNN-based web server to design novel molecules using potential inhibitors of Mpro from CHEMBL4495582. Screened compounds were further validated by molecular docking and molecular dynamics (MD) simulation studies. One hundred molecules were obtained and studied through molecular docking and MD simulations. Additionally, eight molecules, based on their docking scores, were also evaluated for electronic structure properties by conducting Density Functional Theory (DFT) calculations using the B3LYP method and a 6-31G basis set. A total of three compounds, namely L18, L36, and L26, showed very good binding and stability with the active site of the Mpro protein. The results of this study demonstrate that potential molecules can be designed using artificial intelligence methods for the rapid development of drug candidates against SARS-CoV-2, addressing the alarming worldwide situation of emerging deadly SARS-CoV-2 variants. We hope that our study will attract the attention of the scientific community to increase the application of artificial intelligence techniques in the drug discovery process.","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141571627","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Unravelling the impact of sulfur atom oxidation and donor–acceptor effects on the performance of blue TADF emitters: a detailed computational study† 揭示硫原子氧化和供体-受体效应对蓝色 TADF 发射器性能的影响：一项详细的计算研究

IF 3.2 3区工程技术

Molecular Systems Design & Engineering Pub Date : 2024-07-04 DOI: 10.1039/D4ME00035H

Singaravel Nathiya

{"title":"Unravelling the impact of sulfur atom oxidation and donor–acceptor effects on the performance of blue TADF emitters: a detailed computational study†","authors":"Singaravel Nathiya","doi":"10.1039/D4ME00035H","DOIUrl":"10.1039/D4ME00035H","url":null,"abstract":"Blue TADF materials demonstrate significant potential for OLED and photovoltaic applications. Nevertheless, systematic studies are essential to explore the relationship between molecular structures and luminescence properties to develop blue-TADF emitters. In this study, a series of new 24 donor–acceptor–donor (D–A–D) type molecules with different electron donors and acceptors are designed theoretically, and their photophysical properties are analyzed by using DFT and TD-DFT methods. We examined the combined impact of sulfur oxidation and the symmetric incorporation of a nitrogen heteroatom, with positional modifications (2-dipyridyl and 3-dipyridyl), within the phenyl ring of the acceptor group. The findings suggest that enhancing both the donating and accepting strength of the molecules results in an orthogonal geometry and a small ΔEST, accompanied by an enhanced charge-transfer (CT) character. Upon sulfur oxidation, the magnitude of SOC decreases, resulting in a reduction of ΔEST attributed to screening and lone pair effects. Through quantum chemical calculations, we have theoretically identified 12 promising blue TADF molecules, featuring small ΔEST, increased SOC magnitude, and higher RISC (∼10+07 s−1) rates. Overall, our current study provides a robust molecular design approach and reliable computational method for designing a blue TADF emitter.","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141548321","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Empowering tomorrow's medicine: energy-driven micro/nano-robots redefining biomedical applications 赋能未来医学：能源驱动的微型/纳米机器人重新定义生物医学应用

IF 3.2 3区工程技术

Molecular Systems Design & Engineering Pub Date : 2024-07-02 DOI: 10.1039/D4ME00090K

Subham Preetam, Pingal Pritam, Richa Mishra, Sarvesh Rustagi, Smita Lata and Sumira Malik

{"title":"Empowering tomorrow's medicine: energy-driven micro/nano-robots redefining biomedical applications","authors":"Subham Preetam, Pingal Pritam, Richa Mishra, Sarvesh Rustagi, Smita Lata and Sumira Malik","doi":"10.1039/D4ME00090K","DOIUrl":"10.1039/D4ME00090K","url":null,"abstract":"Micro/nano-robots (MNRs) have gained attention as a rapidly developing field with significant potential in advanced therapies and futuristic solutions. These self-propelled robots offer a promising strategy to enhance monitoring, overcome diffusion limitations, and interact effectively with target factors. Research in MNRs has become highly influential, especially in addressing critical issues like cancer. The progression from passive micro- and nanomaterials to active MNRs and ultimately to intelligent MNRs has led to advancements in motion abilities, multifunctionality, adaptive responses, swarming behaviour, and communication among robots. Nanorobotics, featuring sophisticated submicron devices made from nanocomponents, holds great promise for revolutionizing the healthcare industry. This review aims to highlight recent progress in propulsion mechanisms, including chemically controlled micromotors, field control, and biohybrid approaches, which serve as power sources for various biomedical and environmental applications. These applications utilize different energy sources such as magnetic, light, auditory, electric, and chemical reactions, particularly in drug delivery systems for cancer treatment. This review also discusses the challenges and future directions in the practical implementation of smart MNRs, paving the way for their real-world applications.","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141548322","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Outstanding Reviewers for Molecular Systems Design & Engineering in 2023 2023 年《分子系统设计与工程》杰出审稿人

IF 3.2 3区工程技术

Molecular Systems Design & Engineering Pub Date : 2024-06-28 DOI: 10.1039/D4ME90024C

引用次数: 0

Machine learning-based epoxy resin property prediction† 基于机器学习的环氧树脂性能预测

IF 3.2 3区工程技术

Molecular Systems Design & Engineering Pub Date : 2024-06-25 DOI: 10.1039/D4ME00060A

Huiwon Jang, Dayoung Ryu, Wonseok Lee, Geunyeong Park and Jihan Kim

{"title":"Machine learning-based epoxy resin property prediction†","authors":"Huiwon Jang, Dayoung Ryu, Wonseok Lee, Geunyeong Park and Jihan Kim","doi":"10.1039/D4ME00060A","DOIUrl":"10.1039/D4ME00060A","url":null,"abstract":"Epoxy resins have been utilized across various industries due to their superior mechanical and chemical properties. However, discovering the optimal design of epoxy resins is challenging because of the large chemical space of polymer systems. In this study, we adopted a data-driven approach to develop an effective prediction system for epoxy resin. In particular, we constructed a database of 789 epoxy resins, encompassing four key properties: density, coefficient of thermal expansion, glass transition temperature, and Young's modulus, obtained through molecular dynamics simulations. We devised descriptors that effectively represent epoxy resins. Ultimately, a machine learning model was trained, successfully predicting properties with reasonable accuracy. Our predictive model is a generalized model that was verified across various types of epoxy resins, making it applicable to all kinds of epoxy and hardener combinations. This achievement enables large-scale screening over numerous polymers, accelerating the discovery process. Further, we conducted an in-depth analysis of the important features that have a high impact on the epoxy resin. This provides valuable insights into the structure–property relationship which can guide researchers in designing new epoxy resins.","PeriodicalId":91,"journal":{"name":"Molecular Systems Design & Engineering","volume":null,"pages":null},"PeriodicalIF":3.2,"publicationDate":"2024-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141548324","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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Design of ionic liquid crystals enabled by [2]rotaxane structure formation† 通过形成 [2]rotaxane 结构设计离子液晶

IF 3.2 3区工程技术

Molecular Systems Design & Engineering Pub Date : 2024-06-20 DOI: 10.1039/D4ME00034J

Gosuke Washino, Takashi Kajitani, Suzushi Nishimura and Atsushi Shishido

引用次数: 0