Artificial intelligence for natural product drug discovery

被引:102
作者
Mullowney, Michael W. [1 ]
Duncan, Katherine R. [2 ]
Elsayed, Somayah S. [3 ]
Garg, Neha [4 ]
van der Hooft, Justin J. J. [5 ,6 ]
Martin, Nathaniel I. [7 ]
Meijer, David [5 ]
Terlouw, Barbara R. [5 ]
Biermann, Friederike [5 ,8 ,9 ]
Blin, Kai [10 ]
Durairaj, Janani [11 ]
Gonzalez, Marina Gorostiola
Helfrich, Eric J. N. [8 ,9 ]
Huber, Florian [13 ]
Leopold-Messer, Stefan [14 ]
Rajan, Kohulan [15 ]
de Rond, Tristan [16 ]
van Santen, Jeffrey A. [17 ]
Sorokina, Maria [18 ,19 ]
Balunas, Marcy J. [20 ,21 ]
Beniddir, Mehdi A. [22 ]
van Bergeijk, Doris A. [3 ]
Carroll, Laura M. [23 ]
Clark, Chase M. [24 ]
Clevert, Djork-Arne [25 ]
Dejong, Chris A. [26 ]
Du, Chao [3 ]
Ferrinho, Scarlet [27 ]
Grisoni, Francesca [28 ,29 ]
Hofstetter, Albert [30 ]
Jespers, Willem [12 ]
Kalinina, Olga V. [31 ,32 ,33 ]
Kautsar, Satria A. [34 ]
Kim, Hyunwoo [35 ,36 ]
Leao, Tiago F. [37 ]
Masschelein, Joleen [38 ,39 ]
Rees, Evan R. [24 ]
Reher, Raphael [40 ,41 ]
Reker, Daniel [42 ,43 ]
Schwaller, Philippe [44 ]
Segler, Marwin [45 ]
Skinnider, Michael A. [26 ,46 ]
Walker, Allison S. [47 ,48 ]
Willighagen, Egon L. [49 ]
Zdrazil, Barbara [50 ]
Ziemert, Nadine [51 ]
Goss, Rebecca J. M. [27 ]
Guyomard, Pierre [52 ]
Volkamer, Andrea [33 ,53 ]
Gerwick, William H. [54 ]
机构
[1] Univ Chicago, Duchossois Family Inst, Chicago, IL USA
[2] Univ Strathclyde, Strathclyde Inst Pharm & Biomed Sci, Glasgow, Scotland
[3] Leiden Univ, Inst Biol, Dept Mol Biotechnol, Leiden, Netherlands
[4] Georgia Inst Technol, Ctr Microbial Dynam & Infect, Sch Chem & Biochem, Atlanta, GA 30332 USA
[5] Wageningen Univ, Bioinformat Grp, Wageningen, Netherlands
[6] Univ Johannesburg, Dept Biochem, Johannesburg, South Africa
[7] Leiden Univ, Inst Biol, Biol Chem Grp, Leiden, Netherlands
[8] Goethe Univ Frankfurt, Inst Mol Bio Sci, Frankfurt, Germany
[9] LOEWE Ctr Translat Biodivers Genom TBG, Frankfurt, Germany
[10] Tech Univ Denmark, Novo Nord Fdn Ctr Biosustainabil, Lyngby, Denmark
[11] Univ Basel, Biozentrum, Basel, Switzerland
[12] Leiden Acad Ctr Drug Res, Drug Discovery & Safety, Leiden, Netherlands
[13] Hsch Dusseldorf, Ctr Digitalizat & Digital, Dusseldorf, Germany
[14] Eidgenoss TH ETH Zurich, Inst Mikrobiol, Zurich, Switzerland
[15] Friedrich Schiller Univ Jena, Inst Inorgan & Analyt Chem, Jena, Germany
[16] Univ Auckland, Sch Chem Sci, Auckland, New Zealand
[17] Simon Fraser Univ, Dept Chem, Burnaby, BC, Canada
[18] Friedrich Schiller Univ, Inst Inorgan & Analyt Chem, Jena, Germany
[19] Bayer AG, Pharmaceut R&D, Berlin, Germany
[20] Univ Michigan, Dept Microbiol & Immunol, Ann Arbor, MI USA
[21] Univ Michigan, Dept Med Chem, Ann Arbor, MI USA
[22] Univ Paris Saclay, Equipe Chim Subst Nat, CNRS, BioCIS, Orsay, France
[23] EMBL, Struct & Computat Biol Unit, Heidelberg, Germany
[24] Univ Wisconsin Madison, Sch Pharm, Div Pharmaceut Sci, Madison, WI USA
[25] Pfizer, WRDM Machine Learning Res, Berlin, Germany
[26] Adapsyn Biosci, Hamilton, ON, Canada
[27] Univ St Andrews, Chem Dept, St Andrews, Scotland
[28] Eindhoven Univ Technol, Inst Complex Mol Syst, Dept Biomed Engn, Eindhoven, Netherlands
[29] UMC Utrecht, Alliance TU E, WUR, UU,Ctr Living Technol, Utrecht, Netherlands
[30] Swiss Fed Inst Technol, Lab Phys Chem, Zurich, Switzerland
[31] Helmholtz Ctr Infect Res HZI, Helmholtz Inst Pharmaceut Res Saarland HIPS, Saarbrucken, Germany
[32] Saarland Univ, Med Fac, Drug Bioinformat, Homburg, Germany
[33] Saarland Univ, Ctr Bioinformat, Saarbrucken, Germany
[34] Scripps Res, Dept Chem, Jupiter, FL USA
[35] Dongguk Univ Seoul, Coll Pharm, Goyang Si, South Korea
[36] Dongguk Univ Seoul, Integrated Res Inst Drug Dev, Goyang Si, South Korea
[37] Univ Sao Paulo, Ctr Nucl Energy Agr, Piracicaba, Brazil
[38] VIB KU Leuven, Ctr Microbiol, Heverlee, Belgium
[39] Katholieke Univ Leuven, Dept Biol, Heverlee, Belgium
[40] Univ Marburg, Inst Pharmaceut Biol & Biotechnol, Fachbereich Pharm, Marburg, Germany
[41] Martin Luther Univ Halle Wittenberg, Inst Pharm, Halle, Saale, Germany
[42] Duke Univ, Dept Biomed Engn, Durham, NC USA
[43] Duke Univ, Duke Microbiome Ctr, Durham, NC USA
[44] Ecole Polytech Fed Lausanne EPFL, Inst Sci & Ingn Chim, Lab Artificial Chem Intelligence, Lausanne, Switzerland
[45] Microsoft Res, Cambridge, England
[46] Univ British Columbia, Michael Smith Labs, Vancouver, BC, Canada
[47] Vanderbilt Univ, Dept Chem, Nashville, TN USA
[48] Vanderbilt Univ, Dept Biol Sci, Nashville, TN USA
[49] Maastricht Univ, Dept Bioinformat BiGCaT, NUTRIM, Maastricht, Netherlands
[50] European Bioinformat Inst EMBL EBI, Wellcome Genome Campus, Hinxton, Cambs, England
基金
美国国家科学基金会; 英国科研创新办公室; 比利时弗兰德研究基金会; 欧洲研究理事会; 英国生物技术与生命科学研究理事会; 瑞士国家科学基金会; 新加坡国家研究基金会;
关键词
MASS-SPECTROMETRY DATA; MACROMOLECULAR TARGETS; STRUCTURE ELUCIDATION; NONRIBOSOMAL PEPTIDE; LIGAND-BINDING; PREDICTION; DATABASE; SPECTRA; DESIGN; MODELS;
D O I
10.1038/s41573-023-00774-7
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
Developments in computational omics technologies have provided new means to access the hidden diversity of natural products, unearthing new potential for drug discovery. In parallel, artificial intelligence approaches such as machine learning have led to exciting developments in the computational drug design field, facilitating biological activity prediction and de novo drug design for molecular targets of interest. Here, we describe current and future synergies between these developments to effectively identify drug candidates from the plethora of molecules produced by nature. We also discuss how to address key challenges in realizing the potential of these synergies, such as the need for high-quality datasets to train deep learning algorithms and appropriate strategies for algorithm validation. Advances in computational omics technologies are enabling access to the hidden diversity of natural products, and artificial intelligence approaches are facilitating key steps in harnessing the therapeutic potential of such compounds, including biological activity prediction. This article discusses synergies between these fields to effectively identify drug candidates from the plethora of molecules produced by nature, and how to address the challenges in realizing the potential of these synergies.
引用
收藏
页码:895 / 916
页数:22
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