Research

Functional genomics has transformed our understanding of gene regulation, disease mechanisms, and therapeutic potential. Despite advancements, precise manipulation of functional genomics using clinically accessible tools remains challenging. This research proposes to develop next-generation small molecules (SMs) as DNA and RNA modulators, innovating approaches for sequence-specific genome and transcriptome editing. By integrating advanced chemogenomic tools, our reserach aims to decode nucleic acid-drug interactions and design synthetic therapeutic strategies targeting various diseases such as cancer and neurodegenerative diseases.

All

2024

G-quadruplex DNA structure is a positive regulator of MYC transcription

Isabel Esain-Garcia, Angie Kirchner, Larry Melidis, Rafael de Cesaris Araujo Tavares, Somdutta Dhir, …, Zutao Yu, Sarah K. Madden, Regina Hermann, David Tannahill, Shankar Balasubramanian

Proceedings of the National Academy of Sciences  ·  05 Feb 2024  ·  doi:10.1073/pnas.2320240121

2023

Unveiling the role of G-quadruplex structure in promoter region: Regulation of ABCA1 expression in macrophages possibly via NONO protein recruitment

Chao-Da Xiao, Meng-Hao Jia, Ming-Qing Zhong, Yan Xu, Zu-Tao Yu, …, Xu Lu, Yan Zhang, Xue Zhou, Lin-Yun Fu, Xiang-Chun Shen

International Journal of Biological Macromolecules  ·  01 Aug 2023  ·  doi:10.1016/j.ijbiomac.2023.125443

Chem-map profiles drug binding to chromatin in cells

Zutao Yu, Jochen Spiegel, Larry Melidis, Winnie W. I. Hui, Xiaoyun Zhang, Antanas Radzevičius, Shankar Balasubramanian

Nature Biotechnology  ·  23 Jan 2023  ·  doi:10.1038/s41587-022-01636-0

Mitochondria and G-quadruplex evolution: an intertwined relationship

Vinodh J. Sahayasheela, Zutao Yu, Takuya Hidaka, Ganesh N. Pandian, Hiroshi Sugiyama

Trends in Genetics  ·  01 Jan 2023  ·  doi:10.1016/j.tig.2022.10.006

2022

Chemical Probe-Based Nanopore Sequencing to Selectively Assess the RNA Modifications

Soundhar Ramasamy, Vinodh J. Sahayasheela, Surbhi Sharma, Zutao Yu, Takuya Hidaka, Li Cai, Vaijayanthi Thangavel, Hiroshi Sugiyama, Ganesh N. Pandian

ACS Chemical Biology  ·  03 Oct 2022  ·  doi:10.1021/acschembio.2c00221

Inhibition of GLI-Mediated Transcription by Cyclic Pyrrole-Imidazole Polyamide in Cancer Stem Cells

Vinodh J Sahayasheela, Zutao Yu, Yuki Hirose, Ganesh N Pandian, Toshikazu Bando, Hiroshi Sugiyama

Bulletin of the Chemical Society of Japan  ·  08 Mar 2022  ·  doi:10.1246/bcsj.20210453

2020

A novel dual MEK/PDK1 inhibitor 9za retards the cell cycle at G₀/G₁ phase and induces mitochondrial apoptosis in non-small cell lung cancer cells

Rangru Liu, Zutao Yu, Zhuo Chen, Danqi Liu, Fengying Huang, …, Gaoyun Hu, Xinan Yi, Xi Li, Honghao Zhou, Zhaoqian Liu

PeerJ  ·  02 Oct 2020  ·  doi:10.7717/PEERJ.9981

Chemical probe-based Nanopore Sequencing to Selectively Assess the RNA modifications

Soundhar Ramasamy, Vinodh J Sahayasheela, Zutao Yu, Takuya Hidaka, Li Cai, Hiroshi Sugiyama, Ganesh N. Pandian

Cold Spring Harbor Laboratory  ·  20 May 2020  ·  doi:10.1101/2020.05.19.105338

Effective treatment of vancomycin nephrotoxicity with continuous venous‐venous haemodiafiltration (CVVHDF) in a paediatric patient

Meng Lv, Shuli Ma, Nan Chen, Yan Liu, Zutao Yu

Journal of Clinical Pharmacy and Therapeutics  ·  18 May 2020  ·  doi:10.1111/jcpt.13181

Artificial Assemblies with Cooperative DNA Recognition

Zutao YU

Springer Theses  ·  01 Jan 2020  ·  doi:10.1007/978-981-15-4423-1

A synthetic transcription factor pair mimic for precise recruitment of an epigenetic modifier to the targeted DNA locus

Zutao Yu, Mengting Ai, Soumen K. Samanta, Fumitaka Hashiya, Junichi Taniguchi, …, Kaori Hashiya, Toshikazu Bando, Ganesh N. Pandian, Lyle Isaacs, Hiroshi Sugiyama

Chemical Communications  ·  01 Jan 2020  ·  doi:10.1039/c9cc09608f

2019

Soluble Guanylate Cyclase Stimulators and Activators: Where are We and Where to Go?

Sijia Xiao, Qianbin Li, Liqing Hu, Zutao Yu, Jie Yang, Qi Chang, Zhuo Chen, Gaoyun Hu

Mini-Reviews in Medicinal Chemistry  ·  29 Nov 2019  ·  doi:10.2174/1389557519666190730110600

Current Advances in Idiopathic Pulmonary Fibrosis: The pathogenesis, Therapeutic Strategies and Candidate Molecules

Meng Lv, Yan Liu, Shuli Ma, Zutao Yu

Future Medicinal Chemistry  ·  01 Oct 2019  ·  doi:10.4155/FMC-2019-0111

Therapeutic gene regulation using pyrrole–imidazole polyamides

Zutao Yu, Ganesh N. Pandian, Takuya Hidaka, Hiroshi Sugiyama

Advanced Drug Delivery Reviews  ·  01 Jul 2019  ·  doi:10.1016/j.addr.2019.02.001

Binding pocket-based design, synthesis and biological evaluation of novel selective BRD4-BD1 inhibitors

Junlong Ma, Heng Chen, Jie Yang, Zutao Yu, Pan Huang, …, Bifeng Zheng, Rangru Liu, Qianbin Li, Gaoyun Hu, Zhuo Chen

Bioorganic & Medicinal Chemistry  ·  01 May 2019  ·  doi:10.1016/j.bmc.2019.03.037

Dual inhibitors of RAF-MEK-ERK and PI3K-PDK1-AKT pathways: Design, synthesis and preliminary anticancer activity studies of 3-substituted-5-(phenylamino) indolone derivatives

Zutao Yu, Zhuo Chen, Qiongli Su, Shiqi Ye, Hongbo Yuan, …, Zhijun Tu, Xiaoping Yang, RangRu Liu, Gaoyun Hu, Qianbin Li

Bioorganic & Medicinal Chemistry  ·  01 Mar 2019  ·  doi:10.1016/j.bmc.2019.01.028

Recent Progress of Targeted G-Quadruplex-Preferred Ligands Toward Cancer Therapy

Sefan Asamitsu, Shunsuke Obata, Zutao Yu, Toshikazu Bando, Hiroshi Sugiyama

Molecules  ·  24 Jan 2019  ·  doi:10.3390/molecules24030429

2018

Direct Observation of the Double‐Stranded DNA Formation through Metal Ion‐Mediated Base Pairing in the Nanoscale Structure

Xiwen Xing, Yihong Feng, Zutao Yu, Kumi Hidaka, Fenyong Liu, Akira Ono, Hiroshi Sugiyama, Masayuki Endo

Chemistry – A European Journal  ·  20 Dec 2018  ·  doi:10.1002/chem.201805394

Direct Observation of H3–H4 Octasome by High‐Speed AFM

Tingting Zou, Fumitaka Hashiya, Yulei Wei, Zutao Yu, Ganesh N. Pandian, Hiroshi Sugiyama

Chemistry – A European Journal  ·  04 Oct 2018  ·  doi:10.1002/chem.201804010

Orthogonal γPNA Dimerization Domains Empower DNA Binders with Cooperativity and Versatility Mimicking that of Transcription Factor Pairs

Zutao Yu, Wei‐Che Hsieh, Sefan Asamitsu, Kaori Hashiya, Toshikazu Bando, Danith H. Ly, Hiroshi Sugiyama

Chemistry – A European Journal  ·  27 Aug 2018  ·  doi:10.1002/chem.201801961

Synthetic DNA-Binding Inhibitor of HES1 Alters the Notch Signaling Pathway and Induces Neuronal Differentiation

Yulei Wei, Ganesh N. Pandian, Zutao Yu, Tingting Zou, Yue Li, Jayant Darokar, Kaori Hashiya, Toshikazu Bando, Hiroshi Sugiyama

ACS Omega  ·  30 Mar 2018  ·  doi:10.1021/acsomega.8b00220

Pip-HoGu: An Artificial Assembly with Cooperative DNA Recognition Capable of Mimicking Transcription Factor Pairs

Zutao Yu, Chuanxin Guo, Yulei Wei, Kaori Hashiya, Toshikazu Bando, Hiroshi Sugiyama

Journal of the American Chemical Society  ·  08 Feb 2018  ·  doi:10.1021/jacs.7b13275

UVA irradiation of BrU-substituted DNA in the presence of Hoechst 33258

Abhijit Saha, Seiichiro Kizaki, Ji Hoon Han, Zutao Yu, Hiroshi Sugiyama

Bioorganic & Medicinal Chemistry  ·  01 Jan 2018  ·  doi:10.1016/j.bmc.2017.11.011

2017

Antiproliferative and apoptotic activities of sequence-specific histone acetyltransferase inhibitors

Zutao Yu, Junichi Taniguchi, Yulei Wei, Ganesh N. Pandian, Kaori Hashiya, Toshikazu Bando, Hiroshi Sugiyama

European Journal of Medicinal Chemistry  ·  01 Sep 2017  ·  doi:10.1016/j.ejmech.2017.06.037

2016

“One-Pot” Synthesis of 1-Phenyl-1H-benzimidazole Derivatives Facilitated by Fe

Zutao Yu, Zeyu Wang, Xiao Wu, Gaoyun Hu, Qianbin Li

Chinese Journal of Organic Chemistry  ·  01 Jan 2016  ·  doi:10.6023/cjoc201512007

2015

The RAF-MEK-ERK Pathway: Targeting ERK to Overcome Obstacles of Effective Cancer Therapy

Zutao Yu, Shiqi Ye, Gaoyun Hu, Meng Lv, Zhijun Tu, Kun Zhou, Qianbin Li

Future Medicinal Chemistry  ·  01 Mar 2015  ·  doi:10.4155/fmc.14.143