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Yu J, Wang J, Zhao H, Gao J, Kang Y, Cao D, Wang Z, Hou T. Organic Compound Synthetic Accessibility Prediction Based on the Graph Attention Mechanism. J Chem Inf Model 2022; 62:2973-2986. [PMID: 35675668 DOI: 10.1021/acs.jcim.2c00038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Accurate estimation of the synthetic accessibility of small molecules is needed in many phases of drug discovery. Several expert-crafted scoring methods and descriptor-based quantitative structure-activity relationship (QSAR) models have been developed for synthetic accessibility assessment, but their practical applications in drug discovery are still quite limited because of relatively low prediction accuracy and poor model interpretability. In this study, we proposed a data-driven interpretable prediction framework called GASA (Graph Attention-based assessment of Synthetic Accessibility) to evaluate the synthetic accessibility of small molecules by distinguishing compounds to be easy- (ES) or hard-to-synthesize (HS). GASA is a graph neural network (GNN) architecture that makes self-feature deduction by applying an attention mechanism to automatically capture the most important structural features related to synthetic accessibility. The sampling around the hypothetical classification boundary was used to improve the ability of GASA to distinguish structurally similar molecules. GASA was extensively evaluated and compared with two descriptor-based machine learning methods (random forest, RF; eXtreme gradient boosting, XGBoost) and four existing scores (SYBA: SYnthetic Bayesian Accessibility; SCScore: Synthetic Complexity score; RAscore: Retrosynthetic Accessibility score; SAscore: Synthetic Accessibility score). Our analysis demonstrates that GASA achieved remarkable performance in distinguishing similar molecules compared with other methods and had a broader applicability domain. In addition, we show how GASA learns the important features that affect molecular synthetic accessibility by assigning attention weights to different atoms. An online prediction service for GASA was offered at http://cadd.zju.edu.cn/gasa/.
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Affiliation(s)
- Jiahui Yu
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Jike Wang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China.,School of Computer Science, Wuhan University, Wuhan 430072, Hubei, P. R. China
| | - Hong Zhao
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Junbo Gao
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Yu Kang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Dongsheng Cao
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410004, Hunan, P. R. China
| | - Zhe Wang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China.,State Key Lab of CAD&CG, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Tingjun Hou
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China.,State Key Lab of CAD&CG, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
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Agonigi G, Ciancaleoni G, Funaioli T, Zacchini S, Pineider F, Pinzino C, Pampaloni G, Zanotti V, Marchetti F. Controlled Dissociation of Iron and Cyclopentadienyl from a Diiron Complex with a Bridging C3 Ligand Triggered by One-Electron Reduction. Inorg Chem 2018; 57:15172-15186. [DOI: 10.1021/acs.inorgchem.8b02445] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Gabriele Agonigi
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Gianluca Ciancaleoni
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Tiziana Funaioli
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Stefano Zacchini
- Dipartimento di Chimica Industriale “Toso Montanari”, University of Bologna, Viale Risorgimento 4, I-40136 Bologna, Italy
| | - Francesco Pineider
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Calogero Pinzino
- Area della Ricerca, ICCOM-CNR, Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Guido Pampaloni
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Valerio Zanotti
- Dipartimento di Chimica Industriale “Toso Montanari”, University of Bologna, Viale Risorgimento 4, I-40136 Bologna, Italy
| | - Fabio Marchetti
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
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Li X, Liu Y, Zhang YK, Plattner JJ, Baker SJ, Bu W, Liu L, Zhou Y, Ding CZ, Zhang S, Kazmierski WM, Hamatake R, Duan M, Wright LL, Smith GK, Jarvest RL, Ji JJ, Cooper JP, Tallant MD, Crosby RM, Creech K, Wang A. Synthesis and antiviral activity of novel HCV NS3 protease inhibitors with P4 capping groups. Bioorg Med Chem Lett 2012; 22:7351-6. [DOI: 10.1016/j.bmcl.2012.10.075] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 10/08/2012] [Accepted: 10/15/2012] [Indexed: 12/29/2022]
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Franssen NMG, Walters AJC, Reek JNH, de Bruin B. Carbene insertion into transition metal–carbon bonds: a new tool for catalytic C–C bond formation. Catal Sci Technol 2011. [DOI: 10.1039/c0cy00065e] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Busetto L, Marchetti F, Zacchini S, Zanotti V. Synthesis and reactivity with amines of new diiron alkynyl methoxy carbene complexes. Inorganica Chim Acta 2005. [DOI: 10.1016/j.ica.2004.08.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Zhen H, Wang C, Hu Y, Flood TC. Reactions of (Trimethyltriazacyclononane)Rh(vinyl)3, −Rh(Z-propenyl)3, and −Rh(vinyl)2Me with Protic Acids. The Relative Migratory Aptitude of Methyl and Vinyl Groups to an (Ethylidene)Rh Alkylidene Carbon. Organometallics 1998. [DOI: 10.1021/om980423y] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hongshi Zhen
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0744
| | - Chunming Wang
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0744
| | - Yonghan Hu
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0744
| | - Thomas C. Flood
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0744
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Alías FM, Poveda ML, Sellin M, Carmona E, Gutiérrez-Puebla E, Monge A. Synthesis and Structural Characterization of Stable Hydride−Alkylidene Complexes of Iridium(III). Organometallics 1998. [DOI: 10.1021/om980313r] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Estieu K, Ollivier J, Salaün J. Regioselective synthesis of α,α-dialkylcyclopentanones from 1-hydroxycyclobutanecarboxylic acid or from O-protected cyclobutanone cyanohydrin. Tetrahedron 1998. [DOI: 10.1016/s0040-4020(98)00448-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Lee L, Chen DJ, Lin YC, Lo YH, Lin CH, Lee GH, Wang Y. Acid-Catalyzed Carbonylation of Lactone to Cyclic Anhydride on Tungsten Metal. Organometallics 1997. [DOI: 10.1021/om970431z] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lien Lee
- Department of Chemistry, National Taiwan University, Taipei, Taiwan 10764, Republic of China
| | - Ding-Jen Chen
- Department of Chemistry, National Taiwan University, Taipei, Taiwan 10764, Republic of China
| | - Ying-Chih Lin
- Department of Chemistry, National Taiwan University, Taipei, Taiwan 10764, Republic of China
| | - Yih-Hsing Lo
- Department of Chemistry, National Taiwan University, Taipei, Taiwan 10764, Republic of China
| | - Chien Hsing Lin
- Department of Chemistry, National Taiwan University, Taipei, Taiwan 10764, Republic of China
| | - Gene-Hsiang Lee
- Department of Chemistry, National Taiwan University, Taipei, Taiwan 10764, Republic of China
| | - Yu Wang
- Department of Chemistry, National Taiwan University, Taipei, Taiwan 10764, Republic of China
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Hui-Jean C, Chao-Shiuan L. Activation of carbon-carbon bond in the Mn-mediated cycloaddition reaction between disilacyclobutene and cyclohepta-1,3-diene. J Organomet Chem 1992. [DOI: 10.1016/0022-328x(92)88026-f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Trace RL, Jones W. In search of α-eliminations of carbon induced by sixteen electron iron: photolysis and thermolysis of derivatives of phenyl substituted cyclobutanes and cyclopropanes. J Organomet Chem 1989. [DOI: 10.1016/0022-328x(89)88078-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Winter MJ, Woodward S. Synthesis and reactions of the tungsten nonheteroatom-stabilised carbene anion [CpW(CO)2(CHPh)]−. J Organomet Chem 1989; 361:C18-20. [DOI: 10.1016/0022-328x(89)87365-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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