1.Xiaoran Wang＃, Yahong Tan＃, Yawen Yang＃, Haipeng Yu, Jie Cheng, Zhengan Zhang, Chun Song, Youming Zhang,Yizhen Yin*. A Multi-Channel Machine Learning Model for Predicting the Bioactivity Potential of Macrocyclic Peptides.J. Med. Chem.2026, 69, 1628–1640.
2. Min Wang＃, Jinyue Yang＃, Yahong Tan＃, Shuofeng Yuan＃, Guoli Shi＃, Qi Peng, Yongqi Li, Vincent Kwok-Man Poon, Chris Chung-Sing Chan, Na Xiao, Anna Jinxia Zhang, Yubin Xie, Junhua Li, Hao Luo, Yaning Fu, Yong Chen, Alex A. Compton, Youming Zhang, Yang Yang, George Fu Gao, Hongwei Hou*, Jasper Fuk-Woo Chan*,Yizhen Yin*, Yi Shi*. Intranasal administration of broad-spectrum macrocyclic peptide inhibitor protects against SARS-CoV-2 Omicron variants.Nat.Commun.2026,in press;https://www.nature.com/articles/s41467-026-68462-9.
3. Jian Zheng＃, Junjie Wu＃, Hang Yin＃, Zhiyue Zhang＃, Qifeng Zhao, Xiaoshen Wang, Xuzichao Li, Yang Liu, Youming Zhang, Zhi Yao, Heng Zhang*,Yizhen Yin*, Long Li*. A human-STING specific macrocyclic peptide suppresses cGAS-STING-induced inflammation.Ann. Rheum. Dis.2026, in press;https://doi.org/10.1016/j.ard.2025.10.023.
4. Athanasios Chatzopoulos＃, Constantinos Kolliopoulos＃,Yizhen Yin＃, Theodoros Karalis, Aya Komine, Sophie T. PhuongDung Tran, Jongchan Hwang, Nohara Goto, Hiroaki Suga, Peter ten Dijke, Christopher John Hipolito*, Spyridon S. Skandalis*, Paraskevi Heldin*. Macrocyclic peptides targeting human CD44 inhibit cell adhesion.Cell. Signal.2025, 136, 112178.
5. ChunMei An＃, Wenfeng Cai＃, Peiying Li＃, Jian Li, Na Zhao, Xu Yang, Keqiang Li, Ningning Pang, Xing Cheng, Naiyuan Wang, Dong Guo*,Yizhen Yin*, Xiaochun Xiong*. De Novo Discovery of a Macrocyclic Peptide Antagonist of Interleukin-11 with Antirenal Fibrotic Efficacy.J. Med. Chem.2025, 68, 20377–20388.
6.Yawen Yang＃,Pei Liu＃,Xi-Yang Cui＃,Junjie Wu,Wenfeng Cai,Jie Cheng,Chuanjie Lu,Xiaowei Fan,Youming Zhang,Zhibo Liu*,Yizhen Yin*.Ribosomal Incorporation of Fluorosulfonyloxy-L-Phenylalanine into Macrocyclic Peptides for De Novo Target-Specific Covalent Binders.J. Am. Chem. Soc.2025,147, 27095–27104.
7. Hongtan Liu＃,Lulu Song＃,Xiaoting Meng＃,Jinjing Li,Shihui Fan,Huilei Dong,Xiaoran Wang,Maolin Li,Haipeng Yu,Yu-Hsuan Tsai*,Yizhen Yin*,Chuanliu Wu*.Proline-Mediated Enhancement in Evolvability of Disulfide-Rich Peptides for Discovering Protein Binders.J. Am. Chem. Soc.2025, 147, 24870–24883.
8. Maolin Li, Haipeng Yu, Jie Cheng, Wenfeng Cai, Youming Zhang, Yizhen Yin*.Ribosomal incorporation of N-acetyl-3,5-bis(chloromethyl)benzylthio-l-alanine for developing an mRNA-displayed bicyclic peptide library cyclized via 1,3,5-tris(methyl)benzene.Org. Biomol. Chem., 2025,https://doi.org/10.1039/D5OB00693G. (Invited manuscript for New Talent Themed issue)
9. Fengwei Li#*, Mengmeng Zhang#, Chao Liu#, Jie Cheng, Yawen Yang, Xiangda Peng, Zhifeng Li, Wenfeng Cai, Haipeng Yu, Junjie Wu, Yuyu Guo, Hongkun Geng, Yun Fa, Youming Zhang, Dalei Wu*,Yizhen Yin*.De novo discovery of a molecular glue-like macrocyclic peptide that induces MCL1 homodimerization.Proc. Natl. Acad Sci U S A.2025, 122(13): e2426006122.
10. Yahong Tan＃, Jinyue Yang＃, Min Wang＃, Qi Peng, Yongqi Li, Lifeng Fu, Mengmeng Zhang, Jiang Wu, Guanya Yang, Christopher John Hipolito, Youming Zhang, Jianxun Qi, Yi Shi*,Yizhen Yin*.De NovoDiscovery of a Noncovalent Cell-Penetrating BicyclicPeptide Inhibitor Targeting SARS-CoV‑2 Main Protease.J. Med. Chem.2024, 67, 20258–20274.
11. Junjie Wu, Yuchan Wang, Wenfeng Cai, Danyan Chen, Xiangda Peng, Huilei Dong, Jinjing Li, Hongtan Liu, Shuting Shi, Sen Tang, Zhifeng Li, Haiyan Sui, Yan Wang, Chuanliu Wu, Youming Zhang,* Xinmiao Fu,*Yizhen Yin*.Ribosomal Translation of Fluorinated Non-Canonical Amino Acids for De Novo Biologically Active Fluorinated Macrocyclic Peptides.Chem. Sci.2024, 15, 13889–13898.
12. Lulu Song＃, Hongtan Liu＃, Maolin Li, Yawen Yang, Huilei Dong, Jinjing Li, Jiaqi Shao, Lixu Zhi, Hao Sun, Zhifeng Li, Haiyan Sui, Youming Zhang, Chuanliu Wu*,Yizhen Yin*. Ribosomal incorporation of lithocholic acid into peptides for the de novo discovery of peptide-lithocholic acid hybrid macrocyclic peptides.ACS Chem. Biol.2024, 19, 1440–1446.
13. Silong Zhai＃, Yahong Tan＃, Cheng Zhu, Chengyun Zhang, Yan Gao, Qingyi Mao, Youming Zhang, Hongliang Duan*, Yizhen Yin*. PepExplainer: an explainable deep learning model for selection-based macrocyclic peptide bioactivity prediction and optimization.Eur. J. Med. Chem.2024, 275, 116628.
14.Yizhen Yin*, Christopher John Hipolito*. Recent advances in non-standard macrocyclic peptide ligand discovery using mRNA display.Isr. J. Chem.2024, e202300167.
15. Silong Zhai＃, Yahong Tan＃, Chengyun Zhang, Christopher John Hipolito, Lulu Song, Cheng Zhu, Youming Zhang, Hongliang Duan*,Yizhen Yin*. PepScaf: Harnessing Machine Learning with In Vitro Selection toward De Novo Macrocyclic Peptides against IL-17C/IL-17RE Interaction.J.Med. Chem.2023, 66, 11187–11200.
16. Huilei Dong＃, Jinjing Li＃, Hongtan Liu, Shuaimin Lu, Junjie Wu, Youming Zhang,Yizhen Yin*, Yibing Zhao, Chuanliu Wu*. Design and Ribosomal Incorporationof Noncanonical Disulfide-Directing Motifs for the Development of MulticyclicPeptide Libraries.J. Am. Chem. Soc.2022, 144, 5116–5125.
17. Daisuke Hazama＃,Yizhen Yin＃, Yoji Murata*, Makoto Matsuda, TakeshiOkamoto, Daisuke Tanaka, Naohiro Terasaka, Jinxuan Zhao, Mariko Sakamoto,Yuka Kakuchi, Yasuyuki Saito, Takenori Kotani, Yoshihiro Nishimura, AtsushiNakagawa, Hiroaki Suga*, Takashi Matozaki*. Macrocyclic Peptide-MediatedBlockade of the CD47-SIRPα Interaction as a Potential Cancer Immunotherapy.Cell Chem. Biol.2020, 27, 1181-1191. (Co-first author)
18.Yizhen Yin, Nobuaki Ochi, Timothy W. Craven, David Baker, Nagio Takigawa,Hiroaki Suga*. De novo carborane-containing macrocyclic peptides targetinghuman EGFR.J. Am. Chem. Soc.2019, 141, 19193–19197.
19.Yizhen Yin＃, Qianran Fei＃, Weidong Liu, Zhuoru Li, Hiroaki Suga*, Chuanliu Wu*.Chemical and Ribosomal Synthesis of Topologically Controlled Bicyclic andTricyclic Peptide Scaffolds Primed by Selenoether Formation.Angew. Chem. Int.Edit.2019, 58, 4880-4885.
20. Alex Vinogradov,Yizhen Yin, Hiroaki Suga*. Macrocyclic peptides as drugcandidates: recent progress and remaining challenges.J. Am. Chem. Soc.2019,141, 4167-4181.
21.Sayaka Imanishi, Takayuki Katoh,Yizhen Yin, Mituhiro Yamada, Marina Kawai,Hiroaki Suga*. In Vitro Selection of Macrocyclic D/L-Hybrid Peptides against Human EGFR.J. Am. Chem. Soc.2021, 143, 5680–5684.
22. Emiko Mihara, Satoshi Watanabe, Nasir K. Bashiruddin, Nozomi Nakamura,Kyoko Matoba, Yumi Sano, Rumit Maini,Yizhen Yin, Katsuya Sakai, TakaoArimori, Kunio Matsumoto, Hiroaki Suga*, Junichi Takagi*. Lasso-grafting ofmacrocyclic peptide pharmacophores yields multi-functional proteins.Nat.Commun.2021, 12, 1543.
23. Junjie Wu, Mengmeng Zhang, Lulu Song, Yahong Tan, Yosuke Taniguchi, Christopher John Hipolito, Youming Zhang*,Yizhen Yin*.Implications of N7-hydrogen and C8-keto on the base pairing, mutagenic potential and repair of 8-oxo-2′-deoxy-adenosine: Investigation by nucleotide analogues.Bioorg. Chem.2022, 127, 106029.
24. Changsheng Wu＃*,Yizhen Yin＃, Lele Zhu, Youming Zhang, Yue-Zhong Li*.Metagenomic sequencing-driven multidisciplinary approaches to shed light on theuntapped microbial natural products.Drug Discov. Today2022, 27, 730–742.
25. Yahong Tan＃, Junjie Wu＃, Lulu Song, Mengmeng Zhang, Christopher JohnHipolito, Changsheng Wu, Siyuan Wang*, Youming Zhang,Yizhen Yin*.Merging the Versatile Functionalities of Boronic Acid with Peptides.Int. J. Mol.Sci.2021, 22, 12958.
26. Jia-Qi Hu, Jing-Jing Wang, Yue-Lan Li, Li Zhuo, Ai Zhang, Hai-Yan Sui, Xiao-JuLi, Tao Shen,Yizhen Yin, Zhi-Hong Wu, Wei Hu, Yue-Zhong Li*, ChangshengWu*. Combining NMR-Based Metabolic Profiling and Genome Mining for theAccelerated Discovery of Archangiumide, an Allenic Macrolide from theMyxobacterium Archangium violaceum SDU8.Org. Lett.2021, 23,2114–2119.
27.Yizhen Yin, Fener Chen*. Targeting human MutT homolog 1 (MTH1) for cancer eradication: current progress and perspectives.Acta Pharm. Sin. B, 2020, 10,2259–2271.
28.Yizhen Yin, Shigeki Sasaki, Yosuke Taniguchi*. Effects of8-halo-7-deaza-2'-deoxyguanosine triphosphate on DNA synthesis by DNApolymerases and cell proliferation.Bioorg. Med. Chem.2016, 24,3856-3861.
29.Yizhen Yin, Shigeki Sasaki, Yosuke Taniguchi*. Inhibitory Effect of8-Halogenated-7-deaza-2'-deoxyguanosine Triphosphates on Human8-Oxo-2'-deoxyguanosine Triphosphatase, hMTH1, Activities.ChemBioChem2016, 17, 566-569.
30.Yizhen Yin, Shigeki Sasaki, Yosuke Taniguchi*. Recognition and excisionproperties of 8-halogenated-7-deaza-2'-deoxyguanosine as8-oxo-2'-deoxyguanosine analogues and Fpg and hOGG1 inhibitors.ChemBioChem2015, 16, 1190-1198.
31.Yizhen Yin, Yosuke Taniguchi*, Shigeki Sasaki*. Synthesis of 8-Halogenated-7-deaza-2'-deoxyguanosine as an 8-Oxo-2'-deoxyguanosine Analogue andEvaluation of its Base Pairing Properties.Tetrahedron2014, 70, 2040-2047.
32.Yizhen Yin, Chao Liu, Long-Qian Tang and Zhao-Peng Liu*. Recoverable Pd/C catalyst mediated dehydrogenation of sterols and an improved synthesis of1α-hydroxydehydroepiandrosterone.Steroids2012, 77, 1419–1422.
33.Yizhen Yin, Jian-Ping Li, Chao Liu, Long-Qian Tang and Zhao-Peng Liu*.Advances in the Synthesis of A-Ring 1,7-Enyne Synthons for Active Vitamin D3Analogues.Curr. Org. Synth.2011, 8, 374-392.
34. Bing-Lei Gao, Cheng-Mei Zhang,Yi-Zhen Yin, Long-Qian Tang, Zhao-Peng Liu*.Design and synthesis of potent HIV-1 protease inhibitors incorporatinghydroxyprolinamides as novel P2 ligands.Bioorg. Med. Chem.Lett.2011, 21, 3730-3733.
