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Journal articles on the topic 'Scaffold hopping'

Author: Grafiati
Published: 4 June 2021
Last updated: 26 July 2025

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1

Böhm, Hans-Joachim, Alexander Flohr, and Martin Stahl. "Scaffold hopping." Drug Discovery Today: Technologies 1, no. 3 (2004): 217–24. http://dx.doi.org/10.1016/j.ddtec.2004.10.009.

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2

Lloyd, David G. "Approaches to Scaffold Hopping." Drug Discovery Today: Technologies 10, no. 4 (2013): e451-e452. http://dx.doi.org/10.1016/j.ddtec.2013.09.001.

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3

Kanakaveti, Vishnupriya, Sakthivel Rathinasamy, Suresh K. Rayala, and Michael Gromiha. "Forging New Scaffolds from Old: Combining Scaffold Hopping and Hierarchical Virtual Screening for Identifying Novel Bcl-2 Inhibitors." Current Topics in Medicinal Chemistry 19, no. 13 (2019): 1162–72. http://dx.doi.org/10.2174/1568026619666190618142432.

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Background: Though virtual screening methods have proven to be potent in various instances, the technique is practically incomplete to quench the need of drug discovery process. Thus, the quest for novel designing approaches and chemotypes for improved efficacy of lead compounds has been intensified and logistic approaches such as scaffold hopping and hierarchical virtual screening methods were evolved. Till now, in all the previous attempts these two approaches were applied separately. Objective: In the current work, we made a novel attempt in terms of blending scaffold hopping and hierarchic
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4

Grabowski, Kristina, Ewgenij Proschak, Karl-Heinz Baringhaus, Oliver Rau, Manfred Schubert-Zsilavecz, and Gisbert Schneider. "Bioisosteric Replacement of Molecular Scaffolds: From Natural Products to Synthetic Compounds." Natural Product Communications 3, no. 8 (2008): 1934578X0800300. http://dx.doi.org/10.1177/1934578x0800300821.

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Natural products often contain scaffolds or core structures that prevent immediate synthetic accessibility. It is, therefore, desirable to find isosteric chemotypes that allow for scaffold-hopping or re-scaffolding. The idea is to obtain simpler chemotypes that are synthetically feasible and exhibit either the same or similar bioactivity as the original natural product or reference compound. We developed and applied a virtual screening technique that represents a molecular scaffold by its side-chain attachment points (exit-vectors) and properties of the side-chain substituents. The technique w
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5

Hu, Ye, and Jürgen Bajorath. "Global assessment of scaffold hopping potential for current pharmaceutical targets." MedChemComm 1, no. 5 (2010): 339–44. http://dx.doi.org/10.1039/c0md00156b.

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6

Vainio, Mikko J., Thierry Kogej, Florian Raubacher, and Jens Sadowski. "Scaffold Hopping by Fragment Replacement." Journal of Chemical Information and Modeling 53, no. 7 (2013): 1825–35. http://dx.doi.org/10.1021/ci4001019.

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7

Hu, Ye, Dagmar Stumpfe, and Jürgen Bajorath. "Recent Advances in Scaffold Hopping." Journal of Medicinal Chemistry 60, no. 4 (2016): 1238–46. http://dx.doi.org/10.1021/acs.jmedchem.6b01437.

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8

Sun, Hongmao, Gregory Tawa, and Anders Wallqvist. "Classification of scaffold-hopping approaches." Drug Discovery Today 17, no. 7-8 (2012): 310–24. http://dx.doi.org/10.1016/j.drudis.2011.10.024.

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9

Schuffenhauer, Ansgar. "Computational methods for scaffold hopping." Wiley Interdisciplinary Reviews: Computational Molecular Science 2, no. 6 (2012): 842–67. http://dx.doi.org/10.1002/wcms.1106.

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10

Yamaguchi, Mayumi, Akira Matsuda, and Satoshi Ichikawa. "Synthesis of isoxazolidine-containing uridine derivatives as caprazamycin analogues." Organic & Biomolecular Chemistry 13, no. 4 (2015): 1187–97. http://dx.doi.org/10.1039/c4ob02142h.

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11

Hessler, Gerhard, and Karl-Heinz Baringhaus. "The scaffold hopping potential of pharmacophores." Drug Discovery Today: Technologies 7, no. 4 (2010): e263-e269. http://dx.doi.org/10.1016/j.ddtec.2010.09.001.

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12

Lamberth, Clemens. "Agrochemical lead optimization by scaffold hopping." Pest Management Science 74, no. 2 (2017): 282–92. http://dx.doi.org/10.1002/ps.4755.

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13

Mandal, Pubali, Jhimli Sarkar Manna, Debmallya Das, and Manoj Kumar Mitra. "Excitonic dynamics of Chlorophyll-a molecules in chitosan hydrogel scaffold." Photochemical & Photobiological Sciences 14, no. 4 (2015): 786–91. http://dx.doi.org/10.1039/c4pp00305e.

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14

Bathula, Chandramohan, Rajinikanth Mamidala, Chiranjeevi Thulluri та ін. "Substituted furopyridinediones as novel inhibitors of α-glucosidase". RSC Advances 5, № 110 (2015): 90374–85. http://dx.doi.org/10.1039/c5ra19255b.

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15

Kawamura, Shuhei, Yuka Unno, Takatsugu Hirokawa, Akira Asai, Mitsuhiro Arisawa, and Satoshi Shuto. "Rational hopping of a peptidic scaffold into non-peptidic scaffolds: structurally novel potent proteasome inhibitors derived from a natural product, belactosin A." Chem. Commun. 50, no. 19 (2014): 2445–47. http://dx.doi.org/10.1039/c3cc48818g.

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Rational scaffold hopping of a natural product belactosin A derivative based on the pharmacophore model constructed resulted in the identification of the significantly simplified highly potent non-peptide derivatives.
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16

Rodrigues, Tiago, Yen-Chu Lin, Markus Hartenfeller, Steffen Renner, Yi Fan Lim, and Gisbert Schneider. "Repurposing de novo designed entities reveals phosphodiesterase 3B and cathepsin L modulators." Chemical Communications 51, no. 35 (2015): 7478–81. http://dx.doi.org/10.1039/c5cc01376c.

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17

Wu, Deyan, Xuehua Zheng, Runduo Liu, et al. "Free energy perturbation (FEP)-guided scaffold hopping." Acta Pharmaceutica Sinica B 12, no. 3 (2022): 1351–62. http://dx.doi.org/10.1016/j.apsb.2021.09.027.

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18

Gardiner, Eleanor J., John D. Holliday, Caroline O’Dowd, and Peter Willett. "Effectiveness of 2D fingerprints for scaffold hopping." Future Medicinal Chemistry 3, no. 4 (2011): 405–14. http://dx.doi.org/10.4155/fmc.11.4.

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19

Nakano, Hiroshi, Tomoyuki Miyao, and Kimito Funatsu. "Exploring Topological Pharmacophore Graphs for Scaffold Hopping." Journal of Chemical Information and Modeling 60, no. 4 (2020): 2073–81. http://dx.doi.org/10.1021/acs.jcim.0c00098.

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20

Stiefl, Nikolaus, Ian A. Watson, Knut Baumann, and Andrea Zaliani. "ErG: 2D Pharmacophore Descriptions for Scaffold Hopping." Journal of Chemical Information and Modeling 46, no. 1 (2006): 208–20. http://dx.doi.org/10.1021/ci050457y.

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21

Gertsch, Jürg. "Scaffold and organism hopping with chemical probes." Nature Chemical Biology 15, no. 5 (2019): 428–29. http://dx.doi.org/10.1038/s41589-019-0275-9.

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22

Brown, Nathan. "Bioisosteres and Scaffold Hopping in Medicinal Chemistry." Molecular Informatics 33, no. 6-7 (2014): 458–62. http://dx.doi.org/10.1002/minf.201400037.

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23

Schneider, Gisbert, Petra Schneider, and Steffen Renner. "Scaffold-Hopping: How Far Can You Jump?" QSAR & Combinatorial Science 25, no. 12 (2006): 1162–71. http://dx.doi.org/10.1002/qsar.200610091.

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24

Burslem, George M., Daniel P. Bondeson, and Craig M. Crews. "Scaffold hopping enables direct access to more potent PROTACs with in vivo activity." Chemical Communications 56, no. 50 (2020): 6890–92. http://dx.doi.org/10.1039/d0cc02201b.

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25

Yue, Liyan, Juanjuan Du, Fei Ye, et al. "Identification of novel small-molecule inhibitors targeting menin–MLL interaction, repurposing the antidiarrheal loperamide." Organic & Biomolecular Chemistry 14, no. 36 (2016): 8503–19. http://dx.doi.org/10.1039/c6ob01248e.

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26

Yu, Zhiyong, James A. Brannigan, Kaveri Rangachari, et al. "Discovery of pyridyl-based inhibitors of Plasmodium falciparum N-myristoyltransferase." MedChemComm 6, no. 10 (2015): 1767–72. http://dx.doi.org/10.1039/c5md00242g.

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27

Nepali, Kunal, Sunil Kumar, Hsiang-Ling Huang, et al. "2-Aroylquinoline-5,8-diones as potent anticancer agents displaying tubulin and heat shock protein 90 (HSP90) inhibition." Organic & Biomolecular Chemistry 14, no. 2 (2016): 716–23. http://dx.doi.org/10.1039/c5ob02100f.

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28

Rabal, Obdulia, Fares Ibrahim Amr, and Julen Oyarzabal. "Novel Scaffold Fingerprint (SFP): Applications in Scaffold Hopping and Scaffold-Based Selection of Diverse Compounds." Journal of Chemical Information and Modeling 55, no. 1 (2015): 1–18. http://dx.doi.org/10.1021/ci500542e.

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29

Zhao, Hongyu. "Scaffold selection and scaffold hopping in lead generation: a medicinal chemistry perspective." Drug Discovery Today 12, no. 3-4 (2007): 149–55. http://dx.doi.org/10.1016/j.drudis.2006.12.003.

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30

Chaudhary, Vikas, Sarita Das, Anmada Nayak, Sankar K. Guchhait, and Chanakya N. Kundu. "Scaffold-hopping and hybridization based design and building block strategic synthesis of pyridine-annulated purines: discovery of novel apoptotic anticancer agents." RSC Advances 5, no. 33 (2015): 26051–60. http://dx.doi.org/10.1039/c5ra00052a.

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31

Cesarini, Silvia, Ilaria Vicenti, Federica Poggialini, et al. "Serendipitous Identification of Azine Anticancer Agents Using a Privileged Scaffold Morphing Strategy." Molecules 29, no. 7 (2024): 1452. http://dx.doi.org/10.3390/molecules29071452.

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The use of privileged scaffolds as a starting point for the construction of libraries of bioactive compounds is a widely used strategy in drug discovery and development. Scaffold decoration, morphing and hopping are additional techniques that enable the modification of the chosen privileged framework and better explore the chemical space around it. In this study, two series of highly functionalized pyrimidine and pyridine derivatives were synthesized using a scaffold morphing approach consisting of triazine compounds obtained previously as antiviral agents. Newly synthesized azines were evalua
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32

Castagna, Diana, Emma L. Duffy, Dima Semaan, et al. "Identification of a novel class of autotaxin inhibitors through cross-screening." MedChemComm 6, no. 6 (2015): 1149–55. http://dx.doi.org/10.1039/c5md00081e.

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33

Hu, Lizhao, Yuyao Yang, Shuangjia Zheng, Jun Xu, Ting Ran, and Hongming Chen. "Kinase Inhibitor Scaffold Hopping with Deep Learning Approaches." Journal of Chemical Information and Modeling 61, no. 10 (2021): 4900–4912. http://dx.doi.org/10.1021/acs.jcim.1c00608.

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34

Nakano, Hiroshi, Tomoyuki Miyao, Jasial Swarit, and Kimito Funatsu. "Sparse Topological Pharmacophore Graphs for Interpretable Scaffold Hopping." Journal of Chemical Information and Modeling 61, no. 7 (2021): 3348–60. http://dx.doi.org/10.1021/acs.jcim.1c00409.

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35

Gooyit, Major, Tyler L. Harris, Nancy Tricoche, Sacha Javor, Sara Lustigman, and Kim D. Janda. "Onchocerca volvulus Molting Inhibitors Identified through Scaffold Hopping." ACS Infectious Diseases 1, no. 5 (2015): 198–202. http://dx.doi.org/10.1021/acsinfecdis.5b00017.

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36

Bergmann, Rikke, Anna Linusson, and Ismael Zamora. "SHOP: Scaffold HOPping by GRID-Based Similarity Searches." Journal of Medicinal Chemistry 50, no. 11 (2007): 2708–17. http://dx.doi.org/10.1021/jm061259g.

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37

Vrijdag, Johannes L., An M. Van den Bogaert, and Wim M. De Borggraeve. "Scaffold Hopping via a Transannular Rearrangement–Encompassing Cascade." Organic Letters 15, no. 5 (2013): 1052–55. http://dx.doi.org/10.1021/ol4000444.

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38

Renner, Steffen, and Gisbert Schneider. "Scaffold-Hopping Potential of Ligand-Based Similarity Concepts." ChemMedChem 1, no. 2 (2006): 181–85. http://dx.doi.org/10.1002/cmdc.200500005.

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39

Merk, Daniel, Francesca Grisoni, Lukas Friedrich, Elena Gelzinyte, and Gisbert Schneider. "Scaffold hopping from synthetic RXR modulators by virtual screening and de novo design." MedChemComm 9, no. 8 (2018): 1289–92. http://dx.doi.org/10.1039/c8md00134k.

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The concept of virtual screening and automated de novo design has been corroborated as a viable strategy for scaffold hopping from bioactive natural products to isofunctional, synthetically accessible mimetics.
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40

Wang, Li-Jiao, Zhi-Xing Cao, and Li Guo. "Design, Synthesis, and Preliminary Antitumor Activity Evaluation of Novel Alkaloid Derivatives." Natural Product Communications 15, no. 2 (2020): 1934578X2090353. http://dx.doi.org/10.1177/1934578x20903534.

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A novel alkaloid scaffold was designed through scaffold-hopping strategy based on the active pyrazines alkaloid isolated previously. A total of 25 derivatives were synthesized based on this scaffold and evaluated for their antitumor activities. Among all these tested compounds, 9f exhibited most excellent antitumor activities toward H460 cells, TMD-8 cells, and MV4-11 cells in vitro by 3-(4, 5-dimethyl-2-thiazolyl)-2,5-diphenyl-2 H-tetrazolium bromide assay with IC50 values of 29.8, 14.9, and 18.8 μM, respectively.
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41

Lazzara, Phillip R., and Terry W. Moore. "Scaffold-hopping as a strategy to address metabolic liabilities of aromatic compounds." RSC Medicinal Chemistry 11, no. 1 (2020): 18–29. http://dx.doi.org/10.1039/c9md00396g.

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Mitigating oxidative drug metabolism is an important component of lead optimization. This review focuses on scaffold-hopping strategies used in the recent medicinal chemistry literature to address metabolic liabilities of aromatic compounds.
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42

La Monica, Gabriele, Federica Alamia, Alessia Bono, Antonino Lauria, and Annamaria Martorana. "Scaffold-Hopping Strategies in Aurone Optimization: A Comprehensive Review of Synthetic Procedures and Biological Activities of Nitrogen and Sulfur Analogues." Molecules 29, no. 12 (2024): 2813. http://dx.doi.org/10.3390/molecules29122813.

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Aurones, particular polyphenolic compounds belonging to the class of minor flavonoids and overlooked for a long time, have gained significative attention in medicinal chemistry in recent years. Indeed, considering their unique and outstanding biological properties, they stand out as an intriguing reservoir of new potential lead compounds in the drug discovery context. Nevertheless, several physicochemical, pharmacokinetic, and pharmacodynamic (P3) issues hinder their progression in more advanced phases of the drug discovery pipeline, making lead optimization campaigns necessary. In this contex
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43

Woo, Jisoo, Alec H. Christian, Samantha A. Burgess, Yuan Jiang, Umar Faruk Mansoor, and Mark D. Levin. "Scaffold hopping by net photochemical carbon deletion of azaarenes." Science 376, no. 6592 (2022): 527–32. http://dx.doi.org/10.1126/science.abo4282.

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Discovery chemists routinely identify purpose-tailored molecules through an iterative structural optimization approach, but the preparation of each successive candidate in a compound series can rarely be conducted in a manner matching their thought process. This is because many of the necessary chemical transformations required to modify compound cores in a straightforward fashion are not applicable in complex contexts. We report a method that addresses one facet of this problem by allowing chemists to hop directly between chemically distinct heteroaromatic scaffolds. Specifically, we show tha
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44

Waugh, Barnali, Ambarnil Ghosh, Dhananjay Bhattacharyya, Nanda Ghoshal, and Rahul Banerjee. "In silico work flow for scaffold hopping in Leishmania." BMC Research Notes 7, no. 1 (2014): 802. http://dx.doi.org/10.1186/1756-0500-7-802.

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45

Ho, Soo Yei, Jenefer Alam, Duraiswamy Athisayamani Jeyaraj, et al. "Scaffold Hopping and Optimization of Maleimide Based Porcupine Inhibitors." Journal of Medicinal Chemistry 60, no. 15 (2017): 6678–92. http://dx.doi.org/10.1021/acs.jmedchem.7b00662.

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46

Tsunoyama, Kazuhisa, Ata Amini, Michael J. E. Sternberg, and Stephen H. Muggleton. "Scaffold Hopping in Drug Discovery Using Inductive Logic Programming." Journal of Chemical Information and Modeling 48, no. 5 (2008): 949–57. http://dx.doi.org/10.1021/ci700418f.

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47

Nair, Pramod C., and M. Elizabeth Sobhia. "Fingerprint Directed Scaffold Hopping for Identification of CCR2 Antagonists." Journal of Chemical Information and Modeling 48, no. 9 (2008): 1891–902. http://dx.doi.org/10.1021/ci800157j.

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48

Wang, Lingle, Yuqing Deng, Yujie Wu, et al. "Accurate Modeling of Scaffold Hopping Transformations in Drug Discovery." Journal of Chemical Theory and Computation 13, no. 1 (2016): 42–54. http://dx.doi.org/10.1021/acs.jctc.6b00991.

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49

Gopalsamy, Ariamala, Mengxiao Shi, Yongbo Hu, et al. "B-Raf kinase inhibitors: Hit enrichment through scaffold hopping." Bioorganic & Medicinal Chemistry Letters 20, no. 8 (2010): 2431–34. http://dx.doi.org/10.1016/j.bmcl.2010.03.030.

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50

Barker, Edward J., David Buttar, David A. Cosgrove, et al. "Scaffold Hopping Using Clique Detection Applied to Reduced Graphs." Journal of Chemical Information and Modeling 46, no. 2 (2006): 503–11. http://dx.doi.org/10.1021/ci050347r.

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