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Exploring The Interplay Between Scoring Functions and Physico-chemical Properties in Antibody-antigen Docking

IPSJ Transactions on bioinformatics 2024年 17卷 10-17页

作者： Ratnayake, Sangeetha Martinelli, Axel Endo, Toshinori Osada, Naoki Division of Bioinformatics and Bioengineering Graduate School of Information Science and Technology Hokkaido University Hokkaido Sapporo060–0814 Japan BigOmics Analytics Via Serafino Balestra 12 Lugano6900 Switzerland Faculty of Information Science and Technology Hokkaido University Hokkaido Sapporo060–0814 Japan

The advent of antibody therapy has brought about a change in the treatment of diseases. The efficacy of antibody modeling relies on the intricate atomic interactions between antibodies and antigens. Traditional methods for determining antibody structures, such as X-ray crystallography, are costly and time-consuming. Computational docking offers a faster and more cost-effective approach to obtaining complex antibody and antigen complexes even in challenging scenarios. Rosetta, a widely employed software for protein structure modeling, incorporates a scoring function specifically tailored for modeling antibody-antigen interactions. The unique characteristics of the antibody-antigen interface can result in inaccurate predictions. Therefore, it is essential to understand the existing scoring function and the behavior of the antibody-antigen interface. In this study, we evaluated specific parameters within Rosetta-derived scoring functions, with a particular focus on the energy landscape of the structures they generated. We found that performance in antibody-antigen docking simulations could be enhanced by omitting parameters related to solvation. Also, we delved into the physico-chemical properties of antibody-antigen interfaces, paying special attention to the complementarity-determining regions and epitopes. Our exploration helped identify certain parameters that significantly influence docking simulation performance. These insights pave the way for the creation of more accurate scoring functions tailored for specific antibody-antigen interactions. © 2024 Information Processing Society of Japan.

关键词： Antibodies

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Advancing Antibody-antigen Interface Analysis in Docking Scoring Functions for Precision Docking Analysis

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IPSJ Transactions on bioinformatics 2024年 17卷 40-47页

Molecular docking simulations utilizing scoring functions are pivotal for assessing the stability of complex formations. The unique biochemical characteristics of antibody-antigen interfaces, however, present challenges in applying general parameter sets of scoring functions to these molecules, necessitating the customization of the scoring function to enhance prediction accuracy for structural configurations and binding affinities. In response to this, we have developed models within the Rosetta software framework, widely recognized for its utility in predicting antigen-antibody docking, to optimize the parameters of its scoring function. Through a quantitative evaluation of the shape of decoy distribution generated by Rosetta, we have been able to refine the parameters for each antibody-antigen complex, yielding a notable improvement in the prediction accuracy of the software for a given dataset. Furthermore, we have identified a distinct parameter set that is effective for the majority of complexes in our dataset, though not universally applicable. This study introduces a novel approach to customizing scoring functions, potentially contributing to advancements in drug discovery and deepening our understanding of the complexities inherent in antibody-antigen interactions at a molecular level. © 2024 Information Processing Society of Japan.

关键词： Antibodies

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High-Speed Observations of Acoustic Droplet Ejection of a Shear-Thinning Polymer Solution in an External High-Voltage Electric Field

High-Speed Observations of Acoustic Droplet Ejection of a Sh...

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IEEE International Symposium on Applications of Ferroelectrics (ISAF)

作者： Joni Mäkinen Nobuki Kudo Jere Hyvönen Mamoru Hashimoto Edward Hæggström Ari Salmi Department of Physics Faculty of Science University of Helsinki Helsinki Finland Division of Bioengineering and Bioinformatics Faculty of Information Science and Technology Hokkaido University Sapporo Japan

ISBN: (数字)9798350371901

ISBN: (纸本)9798350371918

High-speed observations of ultrasonic ejection of a viscoelastic, shear-thinning, polymer solution, 1 wt% PEO dissolved in water, for the purpose of electrospinning initiation are presented. A focused ultrasound source at 2.68 MHz is used for the ejection. A high-voltage electric field is applied between the solution and a conducting plate above. With a suitable ultrasonic ejection of the solution, electrospinning is initiatied as the electric field pulls a thinning jet from the solution, eventually producing a *** ultrasonic pulse regimes are investigated for the ejection: short (≤ 100 cycles) but high-amplitude (≈ 4.4 MPa), and long (≥ 5000 cycles) but low-amplitude (≈ 0.8 MPa) pulsing. Three different types of ejections leading to the electric field being able to pull a jet from the solution are observed. Most notably, we observed an unstable drop-chain formation which lead to the jetting of liquid from the drop-chain, which was further pulled by the electric field into a thinning jet.

关键词： Ultrasonic imaging Liquids High-voltage techniques Acoustics Polymers Electric fields Frequency control

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Single-cell RNA-sequencing and subcellular spatial transcriptomics facilitate the translation of liver microphysiological systems for regulatory application

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Journal of Pharmaceutical Analysis 2023年第7期13卷 691-693页

作者： Dan Li Zhou Fang Qiang Shi Nicholas Zhang Binsheng Gong Weida Tong Ahmet F.Coskun Joshua Xu Division of Bioinformatics and Biostatistics National Center for Toxicological ResearchU.S.Food and Drug AdministrationJeffersonAR72079USA Wallace H.Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory UniversityAtlantaGA30332USA Machine Learning Graduate Program Georgia Institute of TechnologyAtlantaGA30332USA Division of Systems Biology National Center for Toxicological ResearchU.S.Food and Drug AdministrationJeffersonAR72079USA Interdisciplinary Bioengineering Graduate Program Georgia Institute of TechnologyAtlantaGA30332USA Parker H.Petit Institute for Bioengineering and Bioscience Georgia Institute of TechnologyAtlantaGA30332USA

Reducing the use of animal models in drug development and safety assessment has long been supported by the *** and Drug Administration(FDA).The report by Royal Society for the Prevention of Cruelty to Animals indicates that in 2020,experiments involved the use of over 100 million animals,with the United States leading the list by utilizing 20 million *** ethical considerations associated with animal testing and the costs in terms of time and money,animal models are not always effective in predicting human reactions to drug *** animal testing has been the traditional method for assessing the safety and efficacy of drugs.

关键词： money utilizing testing

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Biosynthesis, therapeutic characteristics, origin and strategies to improve the yield of vasicine in plants

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Vegetos 2025年 1-15页

作者： Padmanabhan, Deepthi Manimekalai, Ramaswamy Senthil-Nathan, Sengottayan Suganthi, Muthusamy Palanisamy, Senthilkumar Department of Genetic Engineering School of Bioengineering SRM Institute of Science and Technology Kattankulathur 603203 India Molecular Biology and Bioinformatics Sugarcane Breeding Institute Tamil Nadu Coimbatore 641 007 India Division of Biopesticides and Environmental Toxicology Sri Paramakalyani Centre for Excellence in Environmental Sciences Manonmaniam Sundaranar University Tamil Nadu Alwarkurichi India Department of Biotechnology Vels Institute of Science Technology and Advanced Studies (VISTAS) Pallavaram Chennai 600 117 India

From the year 2016 to 2019, a total of 196 botanical drugs were registered for clinical trials, out of which 81 drugs were in phase II or III laid an environment for further trials and marketing of the drugs. Vasicine, a pyrroquinazoline alkaloidal compound found in some medicinal plants such as Justicia adhatoda and Sida cordifolia to name a few. Due to its broad range of health-promoting properties, the compound has piqued the attention of nutritionists and medicinal chemists. The compound’s recent pharmacological applications include antiviral activity against SARS-Co-V2, antimicrobial activity against E. aerogenes, S. epidermidis and P. aeruginosa, cytotoxic effect against lung adenocarcinoma and free radical scavenging activity, implying a potential role as an antioxidant. Vasicine was also discovered to have a possible anti-inflammatory property in carrageenan-induced inflammation, as well as neuroprotective efficacy in in vitro experiments on neuroblastoma cells by blocking cholinesterases in Alzheimer’s disease and improving memory and cognition. The integration of a multi-omics approach to elucidate the biosynthetic pathway and key regulatory enzymes laid the basis for metabolically engineering the entire pathway in microbial systems, as well as polyculture of microbes for robust biosynthesis strategies to overcome the limitations of traditional monoculture techniques for bioactive production. Genome editing with CRISPR Cas technologies plays a major role in the transformation of vasicine metabolite engineering to alter the process of biosynthesis and increase large-scale production in plants. © The Author(s) under exclusive licence to Society for Plant Research 2025.

关键词： Medicinal plants Natural products Novel drugs Secondary metabolites

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End-to-end computational approach to the design of RNA biosensors for detecting miRNA biomarkers of cervical cancer

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Synthetic and Systems Biotechnology 2022年第2期7卷 802-814页

作者： Priyannth Ramasami S.Baabu Shivaramakrishna Srinivasan Swetha Nagarajan Sangeetha Muthamilselvan Thamarai Selvi Raghavv R.Suresh Ashok Palaniappan Department of Bioinformatics School of Chemical and BiotechnologySASTRA Deemed UniversityThanjavurTamil Nadu 613401India Department of Bioengineering School of Chemical and BiotechnologySASTRA Deemed UniversityThanjavurTamil Nadu613401India School of Advanced Materials Science and Engineering Sungkyunkwan University(SKKU)Suwon16419Republic of Korea Life Sciences Division TCS ResearchTata Consultancy ServicesChennaiTamil Nadu600042India

Cervical cancer is a global public health subject as it affects women in the reproductive ages,and accounts for the second largest burden among cancer patients worldwide with an unforgiving 50%mortality *** scant awareness and limited access to effective diagnosis have led to this enormous disease burden,calling for point-of-care,minimally invasive diagnosis ***,an end-to-end quantitative unified pipeline for diagnosis has been developed,beginning with identification of optimal biomarkers,concurrent design of toehold switch sensors,and finally simulation of the designed diagnostic circuits to assess *** miRNA expression data in the public domain,we identified miR-21-5p and miR-20a-5p as blood-based miRNA biomarkers specific to early-stage cervical cancer employing a multi-tier algorithmic *** riboregulators called toehold switches specific to the biomarker panel were then *** predict the dynamic range of toehold switches for use in genetic circuits as biosensors,we used a generic grammar of these switches,and built a neural network model of dynamic range using thermodynamic features derived from mRNA secondary structure and ***-generation toehold switches were used to overcome the design challenges associated with miRNA *** resultant model yielded an adj.R^(2)~0.71,outperforming earlier models of toehold-switch dynamic *** kinetics modelling was performed to predict the sensitivity of the second-generation toehold switches to the miRNA *** showed a linear response between 10 nM and 100 nM before *** study demonstrates an end-to-end computational workflow for the efficient design of genetic circuits geared towards the effective detection of unique genomic/nucleic-acid *** approach has the potential to replace iterative experimental trial and error,and focus time,money,and *** software including the toehold grammar parser,neu

关键词： Cervical cancer biosensor miRNA biomarker Synthetic toehold switches Genetic circuit design Reaction network modelling Toehold efficacy modelling Toehold switch grammar Machine learning

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Mitigating antibiotic pollution in wastewater by harnessing the potential of microalgae-based bioremediation technologies

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Vegetos 2024年 1-20页

作者： Singh, Amantika Singh, Pooja Kashyap, Jayant Tripathi, Pooja Choudhary, Krishna Kumar Sharma, Pradeep Kumar Karmakar, Rachan Shah, Maulin P. Tripathi, Vijay Department of Botany Mahila Mahavidyalaya Banaras Hindu University U.P. Varanasi 221005 India Department of Biosciences and Biomedical Engineering Indian Institute of Technology-Indore M.P. Indore 453552 India Department of Bioinformatics and Computational Biology Jacob Institute of Biotechnology and Bioengineering Sam Higginbottom University of Agriculture Technology and Sciences U.P. Prayagraj 211007 India Department of Environmental Science Graphic Era Deemed to Be University Clement Town U.K. Dehradun 248002 India Industrial Wastewater Research Lab Division of Applied and Environmental Microbiology Enviro Technology Limited Alankeshwar India Department of Microbiology Graphic Era Deemed to Be University Clement Town U.K Dehradun 248002 India Department of Molecular and Cellular Engineering Jacob Institute of Biotechnology and Bioengineering Sam Higginbottom University of Agriculture Technology and Sciences U.P. Prayagraj 211007 India

The excessive use of antibiotics and their increasing environmental concentrations is a severe threat and potential hazard to public health. Unfortunately, traditional wastewater treatment technologies aren’t efficient against antibiotic- and other emerging contaminant-rich wastewater. Recently, nature-based methods for wastewater treatment, such as algal-based technologies, have been observed to be viable and capable of the significant bioremediation of antibiotics in wastewater environments. Microalgae, including Scenedesmus quadricauda and Chlorella psychrophile, have already been reported as capable of absorbing and removing tetracycline and azithromycin antibiotics, respectively. Numerous algal species can also remove a significant proportion of different numbers of antibiotics through biodegradation when global wastewater pollution is at a record high. Microalgae may even affect the solubility of antibiotics through hydrolysis, leading to a breakdown of the β-lactam ring structure where present or through the resulting changes in pH, etc. This review provides critical insight into the important factors in removing antibiotic pollution from wastewater and enhancing the removal efficiency. © The Author(s) under exclusive licence to Society for Plant Research 2024.

关键词： Antibiotics Bioremediation Microalgae Wastewater Wastewater treatment

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From bulk, single-cell to spatial RNA sequencing

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International Journal of Oral Science 2021年第4期13卷 339-344页

作者： Xinmin Li Cun-Yu Wang UCLA Technology Center for Genomics&Bioinformatics Department of Pathology and Laboratory MedicineDavid Geffen School of MedicineUCLALos AngelesCAUSA Laboratory of Molecular Signaling Division of Oral Biology and MedicineSchool of Dentistry and Jonsson Comprehensive Cancer CenterUCLALos AngelesCAUSA Department of Bioengineering Henry Samueli School of Engineering and Applied ScienceUCLALos AngelesCAUSA

RNA sequencing(RNAseq)can reveal gene fusions,splicing variants,mutations/indels in addition to differential gene expression,thus providing a more complete genetic picture than DNA *** most widely used technology in genomics tool box has evolved from classic bulk RNA sequencing(RNAseq),popular single cell RNA sequencing(scRNAseq)to newly emerged spatial RNA sequencing(spRNAseq).Bulk RNAseq studies average global gene expression,scRNAseq investigates single cell RNA biology up to 20,000 individual cells simultaneously,while spRNAseq has ability to dissect RNA activities spatially,representing next generation of RNA *** article highlights these technologies,characteristic features and suitable applications in precision oncology.

关键词： representing RNAseq spatially

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Enabling technology and core theory of synthetic biology

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Science China(Life Sciences) 2023年第8期66卷 1742-1785页

作者： Xian-En Zhang Chenli Liu Junbiao Dai Yingjin Yuan Caixia Gao Yan Feng Bian Wu Ping Wei Chun You Xiaowo Wang Tong Si Faculty of Synthetic Biology Shenzhen Institute of Advanced TechnologyShenzhen 518055China Institute of Synthetic Biology Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen 518055China National Laboratory of Biomacromolecules Institute of BiophysicsChinese Academy of SciencesBeijing 100101China Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering(Ministry of Education) School of Chemical Engineering and TechnologyTianjin UniversityTianjin 300072China State Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China State Key Laboratory of Microbial Metabolism Shanghai Jiao Tong UniversityShanghai 200240China State Key Laboratory of Microbial Resources Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China Tianjin Institute of Industrial Biotechnology Chinese Academy of SciencesTianjin 300308China Ministry of Education Key Laboratory of Bioinformatics Center for Synthetic and Systems BiologyBioinformatics DivisionBeijing National Research Center for Information Science and TechnologyDepartment of AutomationTsinghua UniversityBeijing 100084China

Synthetic biology provides a new paradigm for life science research(“build to learn”)and opens the future journey of biotechnology(“build to use”).Here,we discuss advances of various principles and technologies in the mainstream of the enabling technology of synthetic biology,including synthesis and assembly of a genome,DNA storage,gene editing,molecular evolution and de novo design of function proteins,cell and gene circuit engineering,cell-free synthetic biology,artificial intelligence(AI)-aided synthetic biology,as well as *** also introduce the concept of quantitative synthetic biology,which is guiding synthetic biology towards increased accuracy and predictability or the real rational *** conclude that synthetic biology will establish its disciplinary system with the iterative development of enabling technologies and the maturity of the core theory.

关键词： synthetic biology quantitative synthetic biology genome synthesis and assembly DNA storage molecular evolution de novo design computer-aided design cell engineering gene circuit chassis cell artificial intelligent(AI) biofoundry

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Impact of phytoconstituents on oral health practices:a post COVID-19 observation

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Food Science and Human Wellness 2024年第5期13卷 2386-2400页

作者： Harsh Kumar Reena Singh Daljeet Singh Dhanjal Chirag Chopra Natália Cruz-Martins Gheyath K.Nasrallah Amin F.Majdalawieh Sivakumar Manickam Shahida Anusha Siddiqui Dinesh Kumar Indu Sharma Varun Sharma School of Bioengineering&Food Technology Shoolini University of Biotechnology and Management SciencesSolan 173229India School of Bioengineering and Biosciences Lovely Professional UniversityPunjab 144402India Faculty of Medicine University of PortoPorto 4200-319Portugal Institute for Research and Innovation in Health(i3S) University of PortoPorto 4200-135Portugal Institute of Research and Advanced Training in Health Sciences and Technologies(CESPU) RuaCentral de GandraGandra 4585-116Portugal TOXRUN-Toxicology Research Unit University Institute of Health SciencesCESPUCRLGandra 4585-116Portugal Biomedical Research Center Qatar UniversityDoha 2713Qatar Department of Biomedical Science College of Health SciencesQatar UniversityDoha 2713Qatar Department of Biology Chemistryand Environmental SciencesCollege of Arts and SciencesAmerican University of SharjahSharjah 26666United Arab Emirates Petroleum and Chemical Engineering Faculty of EngineeringUniversiti Teknologi BruneiBandar Seri Begawan BE1410Brunei Campus Straubing for Biotechnology and Sustainability Technical University of MunichStraubing 94315Germany Genetic Heritage Group New York UniversityAbu Dhabi 129188United Arab Emirates Bioinformatics Division NMC Genetics India Pvt.Ltd.Gurugram 122001India

Appropriate oral hygiene significantly reduces the possibility of oral ***,dental caries and periodontal diseases are major oral health issues causing chronic diseases due to poor oral ***,herbal compounds have gained interest in maintaining oral *** of burdock root(Arctium),noni fruit(Morinda citrifolia),and neem leaf(Azadirachta indica)are now used as intracanal medicaments in endodontics and *** amboinicus species and other plants produces essential oil likeβ-caryophyllene,p-cymene,andγ-terpinene can exhibit antibacterial activity;highlighting phytoconstituents plays a vital role in oral *** COVID-19 pandemic highlighted the importance of hygiene and sanitization,to curb *** cavity is among the gateways for virus entry into *** is a potential reservoir of SARS-CoV-2,and there is an increased risk of infection if there is any fissure in the *** enables entry of virus into the vascular system through gingival or periodontal pocket,possibly reaching lung periphery then to lung vessels by interacting with endothelial surface receptors triggering pulmonary vasoconstriction and lung damage due to endothelial *** review aims to draw attention to the possible route of SARS-CoV-2 infection via the oral cavity and the importance of oral hygiene against COVID-19.

关键词： COVID-19 SARS-CoV-2 Oral Hygiene Microbiota Phytochemicals

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