Drug Discovery Today: Technologies最新文献

筛选
英文 中文
Efficient molecular encoders for virtual screening 用于虚拟筛选的高效分子编码器
Drug Discovery Today: Technologies Pub Date : 2019-12-01 DOI: 10.1016/j.ddtec.2020.08.004
Youjun Xu , Chenjing Cai , Shiwei Wang , Luhua Lai , Jianfeng Pei
{"title":"Efficient molecular encoders for virtual screening","authors":"Youjun Xu ,&nbsp;Chenjing Cai ,&nbsp;Shiwei Wang ,&nbsp;Luhua Lai ,&nbsp;Jianfeng Pei","doi":"10.1016/j.ddtec.2020.08.004","DOIUrl":"10.1016/j.ddtec.2020.08.004","url":null,"abstract":"<div><p>Molecular representations encoding molecular structure information play critical roles in molecular virtual screening (VS). In order to improve VS performance, an abundance of molecular encoders have been developed and tested by various VS challenges. Combinational strategies were also used to improve the performance. Deep learning (DL)-based molecular encoders have attracted much attention for their automatic information extraction ability. In this review, we present an overview of two-dimensional-, three-dimensional-, and DL-based molecular encoders, summarize recent progress of VS using DL technologies, and propose a general framework of DL molecular encoder-based VS. Perspectives on the future directions of molecular representations and applications in the prediction of active compounds are also provided.</p></div>","PeriodicalId":36012,"journal":{"name":"Drug Discovery Today: Technologies","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.ddtec.2020.08.004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39118926","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
The art of atom descriptor design 原子描述符设计的艺术
Drug Discovery Today: Technologies Pub Date : 2019-12-01 DOI: 10.1016/j.ddtec.2020.06.004
Andreas H. Göller
{"title":"The art of atom descriptor design","authors":"Andreas H. Göller","doi":"10.1016/j.ddtec.2020.06.004","DOIUrl":"10.1016/j.ddtec.2020.06.004","url":null,"abstract":"<div><p>This review provides an overview of descriptions of atoms applied to the understanding of phenomena like chemical reactivity and selectivity, pK<sub>a</sub> values, Site of Metabolism prediction, or hydrogen bond strengths, but also the substitution of quantum mechanical calculations by machine learning models for energies, forces or even spectrosocopic properties and finally the fast calculation of atomic charges for force field parametrization. The descriptor space ranges from derivatives of the wavefunctions or electron density via quantum mechanics derived descriptors to classical descriptions of atoms and their embedding in a molecule. The common denominator for all approaches is the thorough understanding of the physics of the chemical problem that guided the design of the atom descriptor. Quantum mechanics (QM) and machine learning (ML) finally are converging to a new discipline, namely QM/ML.</p></div>","PeriodicalId":36012,"journal":{"name":"Drug Discovery Today: Technologies","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.ddtec.2020.06.004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39118930","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 4
Graph-based generative models for de Novo drug design 基于图的新生药物设计生成模型
Drug Discovery Today: Technologies Pub Date : 2019-12-01 DOI: 10.1016/j.ddtec.2020.11.004
Xiaolin Xia, Jianxing Hu, Yanxing Wang, Liangren Zhang, Zhenming Liu
{"title":"Graph-based generative models for de Novo drug design","authors":"Xiaolin Xia,&nbsp;Jianxing Hu,&nbsp;Yanxing Wang,&nbsp;Liangren Zhang,&nbsp;Zhenming Liu","doi":"10.1016/j.ddtec.2020.11.004","DOIUrl":"10.1016/j.ddtec.2020.11.004","url":null,"abstract":"<div><p><span>The discovery of new chemical entities is a crucial part of drug discovery, which requires the lead compounds to have desired properties to be pharmaceutically active. </span><em>De novo</em><span> drug design aims to generate and optimize novel ligands for macromolecular targets from scratch. The development of graph-based deep generative neural networks has provided a new method. In this review, we gave a brief introduction to graph representation and graph-based generative models for </span><em>de novo</em> drug design, summarized them as four architectures, and concluded each’s characteristics. We also discussed generative models for scaffold- and fragment-based design and graph-based generative models’ future directions.</p></div>","PeriodicalId":36012,"journal":{"name":"Drug Discovery Today: Technologies","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.ddtec.2020.11.004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39118931","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 19
Recent advancements in DVD-Ig based therapeutic development 基于DVD-Ig的治疗发展的最新进展
Drug Discovery Today: Technologies Pub Date : 2019-12-01 DOI: 10.1016/j.ddtec.2020.10.002
Feng Dong, Tariq Ghayur
{"title":"Recent advancements in DVD-Ig based therapeutic development","authors":"Feng Dong,&nbsp;Tariq Ghayur","doi":"10.1016/j.ddtec.2020.10.002","DOIUrl":"10.1016/j.ddtec.2020.10.002","url":null,"abstract":"","PeriodicalId":36012,"journal":{"name":"Drug Discovery Today: Technologies","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.ddtec.2020.10.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38747319","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Editorial for the Special Section "Artificial Intelligence in Drug Discovery" “药物发现中的人工智能”专区社论
Drug Discovery Today: Technologies Pub Date : 2019-12-01 DOI: 10.1016/j.ddtec.2020.12.001
Johannes Kirchmair
{"title":"Editorial for the Special Section \"Artificial Intelligence in Drug Discovery\"","authors":"Johannes Kirchmair","doi":"10.1016/j.ddtec.2020.12.001","DOIUrl":"10.1016/j.ddtec.2020.12.001","url":null,"abstract":"","PeriodicalId":36012,"journal":{"name":"Drug Discovery Today: Technologies","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.ddtec.2020.12.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39118928","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The good, the bad, and the ugly in chemical and biological data for machine learning 机器学习中化学和生物数据的优点、缺点和缺点。
Drug Discovery Today: Technologies Pub Date : 2019-12-01 DOI: 10.1016/j.ddtec.2020.07.001
Tiago Rodrigues
{"title":"The good, the bad, and the ugly in chemical and biological data for machine learning","authors":"Tiago Rodrigues","doi":"10.1016/j.ddtec.2020.07.001","DOIUrl":"10.1016/j.ddtec.2020.07.001","url":null,"abstract":"<div><p>Machine learning and artificial intelligence (ML/AI) have become important research tools in molecular medicine and chemistry. Their rise and recent success in drug discovery promises a rapid progression of development pipelines while reshaping how fundamental and clinical research is conducted. By taking advantage of the ever-growing wealth of publicly available and proprietary data, learning algorithms now provide an attractive means to generate statistically motivated research hypotheses. Hitherto unknown data patterns may guide and prioritize experiments, and augment expert intuition. Therefore, data is a key component in the model building workflow. Herein, I aim to discuss types of chemical and biological data according to their quality and reemphasize general recommendations for their use in ML/AI.</p></div>","PeriodicalId":36012,"journal":{"name":"Drug Discovery Today: Technologies","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.ddtec.2020.07.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39118929","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 19
Liver targeted gene therapy: Insights into emerging therapies 肝脏靶向基因治疗:对新兴疗法的见解
Drug Discovery Today: Technologies Pub Date : 2019-12-01 DOI: 10.1016/j.ddtec.2020.11.001
Carlos G. Moscoso , Clifford J. Steer
{"title":"Liver targeted gene therapy: Insights into emerging therapies","authors":"Carlos G. Moscoso ,&nbsp;Clifford J. Steer","doi":"10.1016/j.ddtec.2020.11.001","DOIUrl":"10.1016/j.ddtec.2020.11.001","url":null,"abstract":"<div><p><span>The large number of monogenic metabolic disorders originating in the liver poses a unique opportunity for development of gene therapy modalities to pursue curative approaches. Various disorders have been successfully treated </span><em>via</em><span> liver-directed gene therapy, though most of the advances have been in animal models<span>, with only limited success in clinical trials. Pre-clinical data in animals using non-viral approaches, including the </span></span><em>Sleeping Beauty</em><span> transposon<span><span> system, are discussed. The various advances with viral vectors for liver-directed gene therapy are also a focus of this review, including retroviral, adenoviral, recombinant adeno-associated viral, and SV40 vectors. Genome editing techniques, including zinc finger nucleases<span>, transcription activator-like effector nucleases and clustered regularly interspaced short palindromic repeats (CRISPR), are also described. Further, the various controversies in the field with regards to somatic vs. </span></span>germline editing using CRISPR in humans are explored, while also highlighting the myriad of preclinical advances. Lastly, newer technologies are reviewed, including base editing and prime editing, which use CRISPR with exciting adjunctive properties to avoid double-stranded breaks and thus the recruitment of endogenous repair mechanisms. While encouraging results have been achieved recently, there are still significant challenges to overcome prior to the broad use of vector-based and genome editing techniques in the clinical arena. As these technologies mature, the promise of a cure for many disabling inherited metabolic disorders is within reach, and urgently needed.</span></span></p></div>","PeriodicalId":36012,"journal":{"name":"Drug Discovery Today: Technologies","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.ddtec.2020.11.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38747316","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Current methods and challenges for deep learning in drug discovery 药物发现中深度学习的当前方法和挑战
Drug Discovery Today: Technologies Pub Date : 2019-12-01 DOI: 10.1016/j.ddtec.2020.07.003
Stefan Schroedl
{"title":"Current methods and challenges for deep learning in drug discovery","authors":"Stefan Schroedl","doi":"10.1016/j.ddtec.2020.07.003","DOIUrl":"10.1016/j.ddtec.2020.07.003","url":null,"abstract":"<div><p>Driven by rapid advances in computer hardware and publicly available datasets over the past decade, deep learning has achieved tremendous success in the transformation of many computational disciplines. These novel technologies have had considerable impact on computer-aided drug design as well, throughout all stages of the development pipeline. A flexible toolbox of neural architectures has been developed that are well-suited to represent the sequential, topological, or geometrical concepts of chemistry and biology; and that are able to either discriminate existing molecules or to generate new ones from scratch. For some biochemical prediction tasks, the state of the art has been advanced; however, for complex and practically relevant projects, the outcomes are less clear-cut. Current deep learning methods rely on massive amounts of labeled examples, but drug discovery data is comparatively limited in quantity and quality. These problems need to be resolved and existing sources used more effectively to demonstrate that deep learning can revolutionize the field in general.</p></div>","PeriodicalId":36012,"journal":{"name":"Drug Discovery Today: Technologies","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.ddtec.2020.07.003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38770812","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 9
Structurally-defined deubiquitinase inhibitors provide opportunities to investigate disease mechanisms 结构明确的去泛素酶抑制剂为研究疾病机制提供了机会
Drug Discovery Today: Technologies Pub Date : 2019-04-01 DOI: 10.1016/j.ddtec.2019.02.003
Ingrid E. Wertz , Jeremy M. Murray
{"title":"Structurally-defined deubiquitinase inhibitors provide opportunities to investigate disease mechanisms","authors":"Ingrid E. Wertz ,&nbsp;Jeremy M. Murray","doi":"10.1016/j.ddtec.2019.02.003","DOIUrl":"10.1016/j.ddtec.2019.02.003","url":null,"abstract":"<div><p>The Ubiquitin/Proteasome System comprises an essential cellular mechanism for regulated protein degradation. Ubiquitination may also promote the assembly of protein complexes that initiate intracellular signaling cascades. Thus, proper regulation of substrate protein ubiquitination is essential for maintaining normal cellular physiology. Deubiquitinases are the class of enzymes responsible for removing ubiquitin modifications from target proteins and have been implicated in regulating human disease. As such, deubiquitinases are now recognized as emerging drug targets. Small molecule deubiquitinase inhibitors have been developed; among those, inhibitors for the deubiquitinases USP7 and USP14 are the best-characterized given that they are structurally validated. In this review we discuss the normal physiological roles of the USP7 and USP14 deubiquitinases as well as the pathological conditions associated with their dysfunction, with a focus on oncology and neurodegenerative diseases. We also review structural biology of USP7 and USP14 enzymes and the characterization of their respective inhibitors, highlighting the various molecular mechanisms by which these deubiquitinases may be functionally inhibited. Finally, we summarize the cellular and <em>in vivo</em> studies performed using the structurally-validated USP7 and USP14 inhibitors.</p></div>","PeriodicalId":36012,"journal":{"name":"Drug Discovery Today: Technologies","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.ddtec.2019.02.003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37330623","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 35
Protein degradation for drug discovery 蛋白质降解用于药物发现
Drug Discovery Today: Technologies Pub Date : 2019-04-01 DOI: 10.1016/j.ddtec.2019.04.002
Alessio Ciulli, William Farnaby
{"title":"Protein degradation for drug discovery","authors":"Alessio Ciulli,&nbsp;William Farnaby","doi":"10.1016/j.ddtec.2019.04.002","DOIUrl":"10.1016/j.ddtec.2019.04.002","url":null,"abstract":"","PeriodicalId":36012,"journal":{"name":"Drug Discovery Today: Technologies","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.ddtec.2019.04.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37330622","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 10
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信