{"title":"协助设计融合蛋白的开源硅学工作流程","authors":"","doi":"10.1016/j.compbiolchem.2024.108209","DOIUrl":null,"url":null,"abstract":"<div><p>Fusion proteins have the potential to become the new norm for targeted therapeutic treatments. Highly specific payload delivery can be achieved by combining custom targeting moieties, such as V<sub>HH</sub> domains, with active parts of proteins that have a particular activity not naturally targeted to the intended cells. Conversely, novel drug products may make use of the highly specific targeting properties of naturally occurring proteins and combine them with custom payloads. When designing such a product, there is rarely a known structure for the final construct which makes it difficult to assess molecular behaviour that may ultimately impact therapeutic outcome. Considering the time and cost of expressing a construct, optimising the purification procedure, obtaining sufficient quantities for biophysical characterisation, and performing structural studies <em>in vitro</em>, there is an enormous benefit to conduct <em>in silico</em> studies ahead of wet lab work.</p><p>By following a repeatable, streamlined, and fast workflow of molecular dynamics assessment, it is possible to eliminate low-performing candidates from costly experimental work. There are, however, many aspects to consider when designing a novel fusion protein and it is crucial not to overlook some elements. In this work, we suggest a set of user-friendly, open-source methods which can be used to screen fusion protein candidates from the sequence alone. We used the light chain and translocation domain of botulinum toxin A (BoNT/A) fused with a selected V<sub>HH</sub> domain, termed here LC-H<sub>N</sub>-V<sub>HH</sub>, as a case study for a general approach to designing, modelling, and simulating fusion proteins. Its behaviour <em>in silico</em> correlated well with initial <em>in vitro</em> work, with SEC HPLC showing multiple protein states in solution and a dynamic protein shifting between these states over time without loss of material.</p></div>","PeriodicalId":10616,"journal":{"name":"Computational Biology and Chemistry","volume":null,"pages":null},"PeriodicalIF":2.6000,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S147692712400197X/pdfft?md5=6a2955eabc805b598902561119497014&pid=1-s2.0-S147692712400197X-main.pdf","citationCount":"0","resultStr":"{\"title\":\"An open source in silico workflow to assist in the design of fusion proteins\",\"authors\":\"\",\"doi\":\"10.1016/j.compbiolchem.2024.108209\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>Fusion proteins have the potential to become the new norm for targeted therapeutic treatments. Highly specific payload delivery can be achieved by combining custom targeting moieties, such as V<sub>HH</sub> domains, with active parts of proteins that have a particular activity not naturally targeted to the intended cells. Conversely, novel drug products may make use of the highly specific targeting properties of naturally occurring proteins and combine them with custom payloads. When designing such a product, there is rarely a known structure for the final construct which makes it difficult to assess molecular behaviour that may ultimately impact therapeutic outcome. Considering the time and cost of expressing a construct, optimising the purification procedure, obtaining sufficient quantities for biophysical characterisation, and performing structural studies <em>in vitro</em>, there is an enormous benefit to conduct <em>in silico</em> studies ahead of wet lab work.</p><p>By following a repeatable, streamlined, and fast workflow of molecular dynamics assessment, it is possible to eliminate low-performing candidates from costly experimental work. There are, however, many aspects to consider when designing a novel fusion protein and it is crucial not to overlook some elements. In this work, we suggest a set of user-friendly, open-source methods which can be used to screen fusion protein candidates from the sequence alone. We used the light chain and translocation domain of botulinum toxin A (BoNT/A) fused with a selected V<sub>HH</sub> domain, termed here LC-H<sub>N</sub>-V<sub>HH</sub>, as a case study for a general approach to designing, modelling, and simulating fusion proteins. Its behaviour <em>in silico</em> correlated well with initial <em>in vitro</em> work, with SEC HPLC showing multiple protein states in solution and a dynamic protein shifting between these states over time without loss of material.</p></div>\",\"PeriodicalId\":10616,\"journal\":{\"name\":\"Computational Biology and Chemistry\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":2.6000,\"publicationDate\":\"2024-09-10\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.sciencedirect.com/science/article/pii/S147692712400197X/pdfft?md5=6a2955eabc805b598902561119497014&pid=1-s2.0-S147692712400197X-main.pdf\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Computational Biology and Chemistry\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S147692712400197X\",\"RegionNum\":4,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Computational Biology and Chemistry","FirstCategoryId":"99","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S147692712400197X","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOLOGY","Score":null,"Total":0}
An open source in silico workflow to assist in the design of fusion proteins
Fusion proteins have the potential to become the new norm for targeted therapeutic treatments. Highly specific payload delivery can be achieved by combining custom targeting moieties, such as VHH domains, with active parts of proteins that have a particular activity not naturally targeted to the intended cells. Conversely, novel drug products may make use of the highly specific targeting properties of naturally occurring proteins and combine them with custom payloads. When designing such a product, there is rarely a known structure for the final construct which makes it difficult to assess molecular behaviour that may ultimately impact therapeutic outcome. Considering the time and cost of expressing a construct, optimising the purification procedure, obtaining sufficient quantities for biophysical characterisation, and performing structural studies in vitro, there is an enormous benefit to conduct in silico studies ahead of wet lab work.
By following a repeatable, streamlined, and fast workflow of molecular dynamics assessment, it is possible to eliminate low-performing candidates from costly experimental work. There are, however, many aspects to consider when designing a novel fusion protein and it is crucial not to overlook some elements. In this work, we suggest a set of user-friendly, open-source methods which can be used to screen fusion protein candidates from the sequence alone. We used the light chain and translocation domain of botulinum toxin A (BoNT/A) fused with a selected VHH domain, termed here LC-HN-VHH, as a case study for a general approach to designing, modelling, and simulating fusion proteins. Its behaviour in silico correlated well with initial in vitro work, with SEC HPLC showing multiple protein states in solution and a dynamic protein shifting between these states over time without loss of material.
期刊介绍:
Computational Biology and Chemistry publishes original research papers and review articles in all areas of computational life sciences. High quality research contributions with a major computational component in the areas of nucleic acid and protein sequence research, molecular evolution, molecular genetics (functional genomics and proteomics), theory and practice of either biology-specific or chemical-biology-specific modeling, and structural biology of nucleic acids and proteins are particularly welcome. Exceptionally high quality research work in bioinformatics, systems biology, ecology, computational pharmacology, metabolism, biomedical engineering, epidemiology, and statistical genetics will also be considered.
Given their inherent uncertainty, protein modeling and molecular docking studies should be thoroughly validated. In the absence of experimental results for validation, the use of molecular dynamics simulations along with detailed free energy calculations, for example, should be used as complementary techniques to support the major conclusions. Submissions of premature modeling exercises without additional biological insights will not be considered.
Review articles will generally be commissioned by the editors and should not be submitted to the journal without explicit invitation. However prospective authors are welcome to send a brief (one to three pages) synopsis, which will be evaluated by the editors.