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Jiang T, Wang Z, Yu W, Wang J, Yu S, Bao X, Wei B, Xuan Q. Mix-Key: graph mixup with key structures for molecular property prediction. Brief Bioinform 2024; 25:bbae165. [PMID: 38706318 PMCID: PMC11070654 DOI: 10.1093/bib/bbae165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/21/2024] [Accepted: 04/04/2024] [Indexed: 05/07/2024] Open
Abstract
Molecular property prediction faces the challenge of limited labeled data as it necessitates a series of specialized experiments to annotate target molecules. Data augmentation techniques can effectively address the issue of data scarcity. In recent years, Mixup has achieved significant success in traditional domains such as image processing. However, its application in molecular property prediction is relatively limited due to the irregular, non-Euclidean nature of graphs and the fact that minor variations in molecular structures can lead to alterations in their properties. To address these challenges, we propose a novel data augmentation method called Mix-Key tailored for molecular property prediction. Mix-Key aims to capture crucial features of molecular graphs, focusing separately on the molecular scaffolds and functional groups. By generating isomers that are relatively invariant to the scaffolds or functional groups, we effectively preserve the core information of molecules. Additionally, to capture interactive information between the scaffolds and functional groups while ensuring correlation between the original and augmented graphs, we introduce molecular fingerprint similarity and node similarity. Through these steps, Mix-Key determines the mixup ratio between the original graph and two isomers, thus generating more informative augmented molecular graphs. We extensively validate our approach on molecular datasets of different scales with several Graph Neural Network architectures. The results demonstrate that Mix-Key consistently outperforms other data augmentation methods in enhancing molecular property prediction on several datasets.
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Affiliation(s)
- Tianyi Jiang
- Institute of Cyberspace Security, College of Information Engineering, Zhejiang University of Technology, 310023, Hangzhou, China
- Binjiang Institute of Artificial Intelligence, Zhejiang University of Technology, 310056, Hangzhou, China
| | - Zeyu Wang
- Institute of Cyberspace Security, College of Information Engineering, Zhejiang University of Technology, 310023, Hangzhou, China
- Binjiang Institute of Artificial Intelligence, Zhejiang University of Technology, 310056, Hangzhou, China
| | - Wenchao Yu
- the College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, 310014, Hangzhou, China
| | - Jinhuan Wang
- Institute of Cyberspace Security, College of Information Engineering, Zhejiang University of Technology, 310023, Hangzhou, China
- Binjiang Institute of Artificial Intelligence, Zhejiang University of Technology, 310056, Hangzhou, China
| | - Shanqing Yu
- Institute of Cyberspace Security, College of Information Engineering, Zhejiang University of Technology, 310023, Hangzhou, China
- Binjiang Institute of Artificial Intelligence, Zhejiang University of Technology, 310056, Hangzhou, China
| | - Xiaoze Bao
- the College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, 310014, Hangzhou, China
| | - Bin Wei
- the College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, 310014, Hangzhou, China
| | - Qi Xuan
- Institute of Cyberspace Security, College of Information Engineering, Zhejiang University of Technology, 310023, Hangzhou, China
- Binjiang Institute of Artificial Intelligence, Zhejiang University of Technology, 310056, Hangzhou, China
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2
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Wang X, Lu M, Su Q, Zhou M, Addepalli Y, Yao W, Wang Z, Lu Y. Phosphine‐Catalyzed [4+2] Cycloadditions of Allenic Ketones: Enantioselective Synthesis of Functionalized Tetrahydropyridines. Chem Asian J 2019; 14:3409-3413. [DOI: 10.1002/asia.201901104] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/09/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Xin Wang
- School of Pharmaceutical Sciences and Chongqing Key Laboratory of Natural Drug ResearchChongqing University Chongqing 401331 P.R. China
| | - Mengxue Lu
- School of Pharmaceutical Sciences and Chongqing Key Laboratory of Natural Drug ResearchChongqing University Chongqing 401331 P.R. China
| | - Qin Su
- School of Pharmaceutical Sciences and Chongqing Key Laboratory of Natural Drug ResearchChongqing University Chongqing 401331 P.R. China
| | - Minghui Zhou
- School of Pharmaceutical Sciences and Chongqing Key Laboratory of Natural Drug ResearchChongqing University Chongqing 401331 P.R. China
| | - Yesu Addepalli
- School of Pharmaceutical Sciences and Chongqing Key Laboratory of Natural Drug ResearchChongqing University Chongqing 401331 P.R. China
| | - Weijun Yao
- Department of ChemistryZhejiang Sci-Tech University Hangzhou 310018 P.R. China
| | - Zhen Wang
- School of Pharmaceutical Sciences and Chongqing Key Laboratory of Natural Drug ResearchChongqing University Chongqing 401331 P.R. China
| | - Yixin Lu
- Department of ChemistryNational University of Singapore Singapore 117543 Singapore
- National University of Singapore (Suzhou) Research Institute Suzhou 215123 P.R. China
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3
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Xing JJ, Gao YN, Shi M. Phosphine-Initiated Cascade Annulation of β′-Acetoxy Allenoate and p
-Quinols: Access to Ring Fused Hexahydroindeno Furan Derivatives. Adv Synth Catal 2018. [DOI: 10.1002/adsc.201800319] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Jiao-Jiao Xing
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals, School of Chemistry & Molecular Engineering; East China University of Science and Technology; 130 Mei Long Road Shanghai 200237 People's Republic of China
| | - Yu-Ning Gao
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals, School of Chemistry & Molecular Engineering; East China University of Science and Technology; 130 Mei Long Road Shanghai 200237 People's Republic of China
| | - Min Shi
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals, School of Chemistry & Molecular Engineering; East China University of Science and Technology; 130 Mei Long Road Shanghai 200237 People's Republic of China
- State Key Laboratory and Institute of Elemento-organic Chemistry; Nankai University; Tianjin 300071 People's Republic of China
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 354 Fenglin Lu Shanghai 200032 People's Republic of China
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4
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Ni H, Tang X, Zheng W, Yao W, Ullah N, Lu Y. Enantioselective Phosphine-Catalyzed Formal [4+4] Annulation of α,β-Unsaturated Imines and Allene Ketones: Construction of Eight-Membered Rings. Angew Chem Int Ed Engl 2017; 56:14222-14226. [DOI: 10.1002/anie.201707183] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 08/12/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Huanzhen Ni
- Graduate School for Integrative Sciences & Engineering (NGS); National University of Singapore; 28 Medical Drive 117456 Singapore Singapore
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 117543 Singapore Singapore
| | - Xiaodong Tang
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 117543 Singapore Singapore
- National University of Singapore (Suzhou) Research Institute; 377 Lin Quan Street, Suzhou Industrial Park Suzhou Jiangsu 215123 P. R. China
| | - Wenrui Zheng
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 117543 Singapore Singapore
- National University of Singapore (Suzhou) Research Institute; 377 Lin Quan Street, Suzhou Industrial Park Suzhou Jiangsu 215123 P. R. China
| | - Weijun Yao
- Department of chemistry; Zhejiang Sci-Tech University; Hangzhou Zhejiang 310018 P. R. China
| | - Nisar Ullah
- Chemistry Department; King Fahd University of Petroleum and Materials; Dhahran 31261 Saudi Arabia
| | - Yixin Lu
- Graduate School for Integrative Sciences & Engineering (NGS); National University of Singapore; 28 Medical Drive 117456 Singapore Singapore
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 117543 Singapore Singapore
- National University of Singapore (Suzhou) Research Institute; 377 Lin Quan Street, Suzhou Industrial Park Suzhou Jiangsu 215123 P. R. China
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5
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Ni H, Tang X, Zheng W, Yao W, Ullah N, Lu Y. Enantioselective Phosphine-Catalyzed Formal [4+4] Annulation of α,β-Unsaturated Imines and Allene Ketones: Construction of Eight-Membered Rings. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707183] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Huanzhen Ni
- Graduate School for Integrative Sciences & Engineering (NGS); National University of Singapore; 28 Medical Drive 117456 Singapore Singapore
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 117543 Singapore Singapore
| | - Xiaodong Tang
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 117543 Singapore Singapore
- National University of Singapore (Suzhou) Research Institute; 377 Lin Quan Street, Suzhou Industrial Park Suzhou Jiangsu 215123 P. R. China
| | - Wenrui Zheng
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 117543 Singapore Singapore
- National University of Singapore (Suzhou) Research Institute; 377 Lin Quan Street, Suzhou Industrial Park Suzhou Jiangsu 215123 P. R. China
| | - Weijun Yao
- Department of chemistry; Zhejiang Sci-Tech University; Hangzhou Zhejiang 310018 P. R. China
| | - Nisar Ullah
- Chemistry Department; King Fahd University of Petroleum and Materials; Dhahran 31261 Saudi Arabia
| | - Yixin Lu
- Graduate School for Integrative Sciences & Engineering (NGS); National University of Singapore; 28 Medical Drive 117456 Singapore Singapore
- Department of Chemistry; National University of Singapore; 3 Science Drive 3 117543 Singapore Singapore
- National University of Singapore (Suzhou) Research Institute; 377 Lin Quan Street, Suzhou Industrial Park Suzhou Jiangsu 215123 P. R. China
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6
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Xu H, Laraia L, Schneider L, Louven K, Strohmann C, Antonchick AP, Waldmann H. Highly Enantioselective Catalytic Vinylogous Propargylation of Coumarins Yields a Class of Autophagy Inhibitors. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Hao Xu
- Max-Planck-Institut für Molekulare Physiologie; Abteilung Chemische Biologie; Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Luca Laraia
- Max-Planck-Institut für Molekulare Physiologie; Abteilung Chemische Biologie; Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Laura Schneider
- Max-Planck-Institut für Molekulare Physiologie; Abteilung Chemische Biologie; Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Kathrin Louven
- Technische Universität Dortmund; Fakultät Chemie und Chemische Biologie; Anorganische Chemie; Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Carsten Strohmann
- Technische Universität Dortmund; Fakultät Chemie und Chemische Biologie; Anorganische Chemie; Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Andrey P. Antonchick
- Max-Planck-Institut für Molekulare Physiologie; Abteilung Chemische Biologie; Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Technische Universität Dortmund; Fakultät Chemie and Chemische Biologie; Chemische Biologie; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
- Faculty of Science; Peoples' Friendship University of Russia; 6 Miklukho-Maklaya Street 117198 Moscow Russia
| | - Herbert Waldmann
- Max-Planck-Institut für Molekulare Physiologie; Abteilung Chemische Biologie; Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Technische Universität Dortmund; Fakultät Chemie and Chemische Biologie; Chemische Biologie; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
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7
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Xu H, Laraia L, Schneider L, Louven K, Strohmann C, Antonchick AP, Waldmann H. Highly Enantioselective Catalytic Vinylogous Propargylation of Coumarins Yields a Class of Autophagy Inhibitors. Angew Chem Int Ed Engl 2017; 56:11232-11236. [DOI: 10.1002/anie.201706005] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Indexed: 12/28/2022]
Affiliation(s)
- Hao Xu
- Max-Planck-Institut für Molekulare Physiologie; Abteilung Chemische Biologie; Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Luca Laraia
- Max-Planck-Institut für Molekulare Physiologie; Abteilung Chemische Biologie; Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Laura Schneider
- Max-Planck-Institut für Molekulare Physiologie; Abteilung Chemische Biologie; Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Kathrin Louven
- Technische Universität Dortmund; Fakultät Chemie und Chemische Biologie; Anorganische Chemie; Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Carsten Strohmann
- Technische Universität Dortmund; Fakultät Chemie und Chemische Biologie; Anorganische Chemie; Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Andrey P. Antonchick
- Max-Planck-Institut für Molekulare Physiologie; Abteilung Chemische Biologie; Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Technische Universität Dortmund; Fakultät Chemie and Chemische Biologie; Chemische Biologie; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
- Faculty of Science; Peoples' Friendship University of Russia; 6 Miklukho-Maklaya Street 117198 Moscow Russia
| | - Herbert Waldmann
- Max-Planck-Institut für Molekulare Physiologie; Abteilung Chemische Biologie; Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Technische Universität Dortmund; Fakultät Chemie and Chemische Biologie; Chemische Biologie; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
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8
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Kesava-Reddy N, Golz C, Strohmann C, Kumar K. Silver(I)-Catalyzed Enantioselective [3+2]-Cycloaddition Reaction of α-Silylimines: A Facile Route to Quaternary-Carbon-Rich Scaffolds. Chemistry 2016; 22:18373-18377. [DOI: 10.1002/chem.201604793] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Naredla Kesava-Reddy
- Abteilung Chemische Biologie; Max-Planck-Institut für Molekulare Physiologie; Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Christopher Golz
- Fakultät Chemie und Chemische Biologie; Technische Universität Dortmund; Otto-Hahn-Straße 6 44221 Dortmund Germany
| | - Carsten Strohmann
- Fakultät Chemie und Chemische Biologie; Technische Universität Dortmund; Otto-Hahn-Straße 6 44221 Dortmund Germany
| | - Kamal Kumar
- Abteilung Chemische Biologie; Max-Planck-Institut für Molekulare Physiologie; Otto-Hahn-Straße 11 44227 Dortmund Germany
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9
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Sankar MG, Garcia-Castro M, Golz C, Strohmann C, Kumar K. Engaging Allene-Derived Zwitterions in an Unprecedented Mode of Asymmetric [3+2]-Annulation Reaction. Angew Chem Int Ed Engl 2016; 55:9709-13. [DOI: 10.1002/anie.201603936] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Indexed: 01/09/2023]
Affiliation(s)
- Muthukumar G. Sankar
- Max-Planck-Institut für Molekulare Physiologie, Abteilung Chemische Biologie; Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Miguel Garcia-Castro
- Max-Planck-Institut für Molekulare Physiologie, Abteilung Chemische Biologie; Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Christopher Golz
- Fakultät Chemie und Chemische Biologie, Technische Universität Dortmund; Otto-Hahn-Strasse 6 44221 Dortmund Germany
| | - Carsten Strohmann
- Fakultät Chemie und Chemische Biologie, Technische Universität Dortmund; Otto-Hahn-Strasse 6 44221 Dortmund Germany
| | - Kamal Kumar
- Max-Planck-Institut für Molekulare Physiologie, Abteilung Chemische Biologie; Otto-Hahn-Strasse 11 44227 Dortmund Germany
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10
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Sankar MG, Garcia-Castro M, Golz C, Strohmann C, Kumar K. Engaging Allene-Derived Zwitterions in an Unprecedented Mode of Asymmetric [3+2]-Annulation Reaction. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201603936] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Muthukumar G. Sankar
- Max-Planck-Institut für Molekulare Physiologie, Abteilung Chemische Biologie; Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Miguel Garcia-Castro
- Max-Planck-Institut für Molekulare Physiologie, Abteilung Chemische Biologie; Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Christopher Golz
- Fakultät Chemie und Chemische Biologie, Technische Universität Dortmund; Otto-Hahn-Strasse 6 44221 Dortmund Germany
| | - Carsten Strohmann
- Fakultät Chemie und Chemische Biologie, Technische Universität Dortmund; Otto-Hahn-Strasse 6 44221 Dortmund Germany
| | - Kamal Kumar
- Max-Planck-Institut für Molekulare Physiologie, Abteilung Chemische Biologie; Otto-Hahn-Strasse 11 44227 Dortmund Germany
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11
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Xu H, Golz C, Strohmann C, Antonchick AP, Waldmann H. Enantiodivergent Combination of Natural Product Scaffolds Enabled by Catalytic Enantioselective Cycloaddition. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602084] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Hao Xu
- Max-Planck-Institut für Molekulare Physiologie; Abteilung Chemische Biologie; Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Christopher Golz
- Technische Universität Dortmund; Fakultät Chemie und Chemische Biologie, Anorganische Chemie; Otto-Hahn-Strasse 6 44221 Dortmund Germany
| | - Carsten Strohmann
- Technische Universität Dortmund; Fakultät Chemie und Chemische Biologie, Anorganische Chemie; Otto-Hahn-Strasse 6 44221 Dortmund Germany
| | - Andrey P. Antonchick
- Max-Planck-Institut für Molekulare Physiologie; Abteilung Chemische Biologie; Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Technische Universität Dortmund; Fakultät Chemie and Chemische Biologie, Chemische Biologie; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Herbert Waldmann
- Max-Planck-Institut für Molekulare Physiologie; Abteilung Chemische Biologie; Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Technische Universität Dortmund; Fakultät Chemie and Chemische Biologie, Chemische Biologie; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
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12
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Xu H, Golz C, Strohmann C, Antonchick AP, Waldmann H. Enantiodivergent Combination of Natural Product Scaffolds Enabled by Catalytic Enantioselective Cycloaddition. Angew Chem Int Ed Engl 2016; 55:7761-5. [PMID: 27193834 DOI: 10.1002/anie.201602084] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Indexed: 11/06/2022]
Abstract
An efficient strategy has been established for the enantiodivergent synthesis of natural product inspired compounds embodying both tropane and pyrrolidine natural product fragments. This strategy includes the enantioselective kinetic resolution of racemic tropanes by means of a copper(I)-catalyzed [3+2] cycloaddition and allows the preparation of two enantiopure products in a one-pot reaction in high yield and with high diastereo- and enantioselectivity by using one chiral catalyst.
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Affiliation(s)
- Hao Xu
- Max-Planck-Institut für Molekulare Physiologie, Abteilung Chemische Biologie, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
| | - Christopher Golz
- Technische Universität Dortmund, Fakultät Chemie und Chemische Biologie, Anorganische Chemie, Otto-Hahn-Strasse 6, 44221, Dortmund, Germany
| | - Carsten Strohmann
- Technische Universität Dortmund, Fakultät Chemie und Chemische Biologie, Anorganische Chemie, Otto-Hahn-Strasse 6, 44221, Dortmund, Germany
| | - Andrey P Antonchick
- Max-Planck-Institut für Molekulare Physiologie, Abteilung Chemische Biologie, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany. .,Technische Universität Dortmund, Fakultät Chemie and Chemische Biologie, Chemische Biologie, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany.
| | - Herbert Waldmann
- Max-Planck-Institut für Molekulare Physiologie, Abteilung Chemische Biologie, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany. .,Technische Universität Dortmund, Fakultät Chemie and Chemische Biologie, Chemische Biologie, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany.
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13
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Garcia-Castro M, Zimmermann S, Sankar MG, Kumar K. Gerüstdiversitätsbasierte Synthese und ihre Anwendung bei der Sonden- und Wirkstoffsuche. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201508818] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Miguel Garcia-Castro
- Abteilung Chemische Biologie; Max-Planck-Institut für molekulare Physiologie; Otto-Hahn-Straße 11 44227 Dortmund Deutschland
| | - Stefan Zimmermann
- Abteilung Chemische Biologie; Max-Planck-Institut für molekulare Physiologie; Otto-Hahn-Straße 11 44227 Dortmund Deutschland
| | - Muthukumar G. Sankar
- Abteilung Chemische Biologie; Max-Planck-Institut für molekulare Physiologie; Otto-Hahn-Straße 11 44227 Dortmund Deutschland
| | - Kamal Kumar
- Abteilung Chemische Biologie; Max-Planck-Institut für molekulare Physiologie; Otto-Hahn-Straße 11 44227 Dortmund Deutschland
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14
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Garcia-Castro M, Zimmermann S, Sankar MG, Kumar K. Scaffold Diversity Synthesis and Its Application in Probe and Drug Discovery. Angew Chem Int Ed Engl 2016; 55:7586-605. [DOI: 10.1002/anie.201508818] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Revised: 01/19/2016] [Indexed: 01/19/2023]
Affiliation(s)
- Miguel Garcia-Castro
- Department of Chemical Biology; Max Planck Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Stefan Zimmermann
- Department of Chemical Biology; Max Planck Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Muthukumar G. Sankar
- Department of Chemical Biology; Max Planck Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Kamal Kumar
- Department of Chemical Biology; Max Planck Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
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15
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Schröder P, Förster T, Kleine S, Becker C, Richters A, Ziegler S, Rauh D, Kumar K, Waldmann H. Neuritogenic militarinone-inspired 4-hydroxypyridones target the stress pathway kinase MAP4K4. Angew Chem Int Ed Engl 2015; 54:12398-403. [PMID: 25908259 DOI: 10.1002/anie.201501515] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Indexed: 11/09/2022]
Abstract
Progressive loss and impaired restoration of neuronal activity are hallmarks of neurological diseases, and new small molecules with neurotrophic activity are in high demand. The militarinone alkaloids and structurally simplified analogues with 4-hydroxy-2-pyridone core structure induce pronounced neurite outgrowth, but their protein target has not been identified. Reported herein is the synthesis of a militarinone-inspired 4-hydroxy-2-pyridone collection, its investigation for enhancement of neurite outgrowth, and the discovery of the stress pathway kinase MAP4K4 as a target of the discovered neuritogenic pyridones. The most potent 4-hydroxy-2-pyridone is a selective ATP-competitive inhibitor of MAP4K4 but not of the other stress pathway related kinases, as proven by biochemical analysis and by a crystal structure of the inhibitor in complex with MAP4K4. The findings support the notion that MAP4K4 may be a new target for the treatment of neurodegenerative diseases.
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Affiliation(s)
- Peter Schröder
- Max-Planck-Institut für Molekulare Physiologie, Abteilung Chemische Biologie, Otto-Hahn-Straße 11, 44227 Dortmund (Germany).,Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Straße 6, 44221 Dortmund (Germany)
| | - Tim Förster
- Max-Planck-Institut für Molekulare Physiologie, Abteilung Chemische Biologie, Otto-Hahn-Straße 11, 44227 Dortmund (Germany).,Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Straße 6, 44221 Dortmund (Germany)
| | - Stefan Kleine
- Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Straße 6, 44221 Dortmund (Germany)
| | - Christian Becker
- Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Straße 6, 44221 Dortmund (Germany)
| | - André Richters
- Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Straße 6, 44221 Dortmund (Germany)
| | - Slava Ziegler
- Max-Planck-Institut für Molekulare Physiologie, Abteilung Chemische Biologie, Otto-Hahn-Straße 11, 44227 Dortmund (Germany)
| | - Daniel Rauh
- Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Straße 6, 44221 Dortmund (Germany)
| | - Kamal Kumar
- Max-Planck-Institut für Molekulare Physiologie, Abteilung Chemische Biologie, Otto-Hahn-Straße 11, 44227 Dortmund (Germany).,Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Straße 6, 44221 Dortmund (Germany)
| | - Herbert Waldmann
- Max-Planck-Institut für Molekulare Physiologie, Abteilung Chemische Biologie, Otto-Hahn-Straße 11, 44227 Dortmund (Germany). .,Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Straße 6, 44221 Dortmund (Germany).
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16
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Schröder P, Förster T, Kleine S, Becker C, Richters A, Ziegler S, Rauh D, Kumar K, Waldmann H. Neuritogenic Militarinone-Inspired 4-Hydroxypyridones Target the Stress Pathway Kinase MAP4K4. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201501515] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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17
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Potowski M, Golz C, Strohmann C, Antonchick AP, Waldmann H. Biology-oriented synthesis of benzopyrano[3,4-c]pyrrolidines. Bioorg Med Chem 2015; 23:2895-903. [PMID: 25792140 DOI: 10.1016/j.bmc.2015.02.044] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 02/20/2015] [Accepted: 02/24/2015] [Indexed: 12/20/2022]
Abstract
A natural product inspired synthesis of 6,6,5-tricyclic compounds via a silver(I)-catalyzed formal 1,3-dipolar cycloaddition of coumarins with α-iminoesters was developed. The reaction proceeds in a stepwise reaction course under formation of the trans-substituted diastereomer with respect to the 1,3-dipole and shows a broad substrate scope.
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Affiliation(s)
- Marco Potowski
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany; Chemical Biology, Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 6, 44221 Dortmund, Germany
| | - Christopher Golz
- Inorganic Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 6, 44221 Dortmund, Germany
| | - Carsten Strohmann
- Inorganic Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 6, 44221 Dortmund, Germany
| | - Andrey P Antonchick
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany; Chemical Biology, Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 6, 44221 Dortmund, Germany.
| | - Herbert Waldmann
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany; Chemical Biology, Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 6, 44221 Dortmund, Germany.
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18
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Potowski M, Merten C, Antonchick AP, Waldmann H. Catalytic Aerobic Oxidation and Tandem Enantioselective Cycloaddition in Cascade Multicomponent Synthesis. Chemistry 2015; 21:4913-7. [PMID: 25676025 DOI: 10.1002/chem.201500125] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Marco Potowski
- Max-Planck-Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, 44227 Dortmund (Germany), Fax: (+49) 231-133-2499; Fakultät Chemie und Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund (Germany)
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19
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Vidadala SR, Golz C, Strohmann C, Daniliuc CG, Waldmann H. Highly Enantioselective Intramolecular 1,3-Dipolar Cycloaddition: A Route to Piperidino-Pyrrolizidines. Angew Chem Int Ed Engl 2014; 54:651-5. [DOI: 10.1002/anie.201409942] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Indexed: 12/21/2022]
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20
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Vidadala SR, Golz C, Strohmann C, Daniliuc CG, Waldmann H. Highly Enantioselective Intramolecular 1,3-Dipolar Cycloaddition: A Route to Piperidino-Pyrrolizidines. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201409942] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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21
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Ziegler DT, Riesgo L, Ikeda T, Fujiwara Y, Fu GC. Biphenyl-derived phosphepines as chiral nucleophilic catalysts: enantioselective [4+1] annulations to form functionalized cyclopentenes. Angew Chem Int Ed Engl 2014; 53:13183-7. [PMID: 25287684 DOI: 10.1002/anie.201405854] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 07/15/2014] [Indexed: 11/10/2022]
Abstract
Because of the frequent occurrence of cyclopentane subunits in bioactive compounds, the development of efficient catalytic asymmetric methods for their synthesis is an important objective. Introduced herein is a new family of chiral nucleophilic catalysts, biphenyl-derived phosphepines, and we apply them to an enantioselective variant of a useful [4+1] annulation. A range of one-carbon coupling partners can be employed, thereby generating cyclopentenes which bear a fully substituted stereocenter [either all-carbon or heteroatom-substituted (sulfur and phosphorus)]. Stereocenters at the other four positions of the cyclopentane ring can also be introduced with good stereoselectivity. An initial mechanistic study indicates that phosphine addition to the electrophilic four-carbon coupling partner is not the turnover-limiting step of the catalytic cycle.
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Affiliation(s)
- Daniel T Ziegler
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125 (USA)
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22
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Ziegler DT, Riesgo L, Ikeda T, Fujiwara Y, Fu GC. Biphenyl-Derived Phosphepines as Chiral Nucleophilic Catalysts: Enantioselective [4+1] Annulations To Form Functionalized Cyclopentenes. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405854] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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23
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Wang Y, Bauer JO, Strohmann C, Kumar K. A Bioinspired Catalytic Oxygenase Cascade to Generate Complex Oxindoles. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403415] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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24
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Wang Y, Bauer JO, Strohmann C, Kumar K. A Bioinspired Catalytic Oxygenase Cascade to Generate Complex Oxindoles. Angew Chem Int Ed Engl 2014; 53:7514-8. [DOI: 10.1002/anie.201403415] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 04/08/2014] [Indexed: 12/26/2022]
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25
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Narayan R, Bauer JO, Strohmann C, Antonchick AP, Waldmann H. Catalytic Enantioselective Synthesis of Functionalized Tropanes Reveals Novel Inhibitors of Hedgehog Signaling. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201307392] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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26
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Narayan R, Bauer JO, Strohmann C, Antonchick AP, Waldmann H. Catalytic enantioselective synthesis of functionalized tropanes reveals novel inhibitors of hedgehog signaling. Angew Chem Int Ed Engl 2013; 52:12892-6. [PMID: 24151037 DOI: 10.1002/anie.201307392] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Indexed: 01/06/2023]
Abstract
Dipolar cycloaddition: A highly efficient copper(I)-catalyzed enantioselective [3+2] cycloaddition reaction of 1,3-fused cyclic azomethine ylides and nitroalkenes has been developed. This method provides access to functionalized tropane scaffolds with several quaternary and tertiary stereocenters in a single step under mild reaction conditions.
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Affiliation(s)
- Rishikesh Narayan
- Max-Planck-Institut für Molekulare Physiologie, Abteilung Chemische Biologie, Otto-Hahn-Strasse 11, 44227 Dortmund (Germany)
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27
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Takayama H, Jia ZJ, Kremer L, Bauer JO, Strohmann C, Ziegler S, Antonchick AP, Waldmann H. Discovery of inhibitors of the Wnt and Hedgehog signaling pathways through the catalytic enantioselective synthesis of an iridoid-inspired compound collection. Angew Chem Int Ed Engl 2013; 52:12404-8. [PMID: 24115579 DOI: 10.1002/anie.201306948] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Indexed: 01/12/2023]
Abstract
Cousins you can count on: An iridoid-inspired compound collection was synthesized efficiently by the resolution of cyclic enones in an asymmetric cycloaddition with azomethine ylides. The collection contained novel potent inhibitors of the Wnt and Hedgehog signaling pathways.
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Affiliation(s)
- Hiroshi Takayama
- Max-Planck-Institut für Molekulare Physiologie, Abteilung Chemische Biologie, Otto-Hahn-Strasse 11, 44227 Dortmund (Germany)
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28
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Takayama H, Jia ZJ, Kremer L, Bauer JO, Strohmann C, Ziegler S, Antonchick AP, Waldmann H. Discovery of Inhibitors of the Wnt and Hedgehog Signaling Pathways through the Catalytic Enantioselective Synthesis of an Iridoid-Inspired Compound Collection. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201306948] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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