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Naoto Hori

Assistant Professor, Faculty of Science

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Biography

Dr Naoto Hori is an Assistant Professor of Computational Biophysics in the School of Pharmacy at the 糖心原创. Born and raised in Osaka, Japan, Naoto received his BSc and MSc in Chemistry from Kobe University. After a year's experience working as a software engineer in a company, he worked at Kyoto University, where he obtained his PhD in Biophysics under the supervision of Prof. Shoji Takada. While a postdoctoral researcher with Prof. Dave Thirumalai at the University of Maryland and the University of Texas at Austin, Naoto investigated RNA folding and misfolding mechanisms using molecular simulations.

Since joining the 糖心原创 as an independent Nottingham Research Fellow in 2020, he has focused on computational modelling to investigate the complex, heterogeneous structures of long RNA molecules and their therapeutic potential. Passionate about the field, Naoto aims to contribute to a broader understanding of RNA biology and develop new approaches to RNA therapeutics using high-performance computing and unique molecular simulation models.

Academic & Professional Experience

  • 2023 - Present, Assistant Professor, 糖心原创
  • 2020 - 2023, Nottingham Research Fellow, 糖心原创
  • 2016 - 2019, Postdoctoral Fellow, University of Texas at Austin ()
  • 2014 - 2015, Research Associate, University of Maryland ()
  • 2010 - 2013, (Prof. Takada's lab.)
  • 2009 - 2010, Research Associate, Kyoto University ()
  • 2008 - 2009, Software Engineer,

Education

  • 2013, Ph.D. in Biophysics, Kyoto University ()
  • 2008, M.Sc. in Chemistry, Kobe University
  • 2006, B.Sc. in Chemistry, Kobe University

Research Summary

Overview

Our research focuses on the cutting-edge exploration of RNA structures, folding, interactions, and therapeutic applications using computational biophysics approaches. RNA plays a crucial role in numerous biological processes and has emerged as a promising target for therapeutic applications, particularly in RNA-based drugs and gene therapies. Through advanced molecular simulation techniques, we aim to uncover the fundamental mechanisms underlying RNA behavior and its interactions with various molecules.

1. RNA folding and dynamics

We investigate how RNA molecules fold into their functional structures and how their conformations evolve over time. Using molecular dynamics simulations, we explore the driving forces behind RNA folding and misfolding, which are key to understanding their biological functions and potential misfolding. We are now particularly interested in the relationship between biological function and structural ensemble of long RNA molecules such as mRNAs, lncRNAs and viral genomes.

2. RNA formulations for therapeutic delivery

One of our primary interests is the interactions between RNA and formulation agents such as cationic polymers and lipids designed for drug delivery. By modelling these complexes and simulating the assembly process, we aim to understand the molecular mechanisms that govern the formulation from a physicochemical point of view. By combining simulations and experiments, our ultimate goal is to design and optimise carriers to improve RNA stability, cellular uptake and therapeutic efficacy.

3. RNA-protein interactions and complex assembly

Another important aspect of RNA's biological role is to form various complexes with other proteins in order to function. These include large molecular machines involved in transcription, translation and many regulatory mechanisms in the cell, such as ribosomes and telomerase. RNA is also a key player in the formation of various types of condensates with intrinsically disordered proteins. We aim to address these problems using molecular simulation approaches.

Recent Publications

  • LEWIS O'SHAUGHNESSY, AKOSUA ANANE-ADJEI, MARIAROSA MAZZA, NAOTO HORI, PRATIK GURNANI and CAMERON ALEXANDER, 2025. Polymer Chemistry.
  • ALFREDO D. SMART, MERRYN E. HUGHES, ANGELA DOWNIE RUIZ VELASCO, NAOTO HORI, SNOW STOLNIK and CATHERINE L. JOPLING, 2025. Molecular Therapy Nucleic Acids. 36(3), 102602
  • D. THIRUMALAI, NAOTO HORI and HUNG T. NGUYEN, 2025. Current Opinion in Structural Biology. 93, 103107
  • BALAKA MONDAL, DEBAYAN CHAKRABORTY, NAOTO HORI, HUNG T. NGUYEN and D. THIRUMALAI, 2024. Journal of Chemical Theory and Computation. 20(7), 2934-2946
  • LEWIS O'SHAUGHNESSY, AKOSUA ANANE-ADJEI, MARIAROSA MAZZA, NAOTO HORI, PRATIK GURNANI and CAMERON ALEXANDER, 2025. Polymer Chemistry.
  • ALFREDO D. SMART, MERRYN E. HUGHES, ANGELA DOWNIE RUIZ VELASCO, NAOTO HORI, SNOW STOLNIK and CATHERINE L. JOPLING, 2025. Molecular Therapy Nucleic Acids. 36(3), 102602
  • D. THIRUMALAI, NAOTO HORI and HUNG T. NGUYEN, 2025. Current Opinion in Structural Biology. 93, 103107
  • BALAKA MONDAL, DEBAYAN CHAKRABORTY, NAOTO HORI, HUNG T. NGUYEN and D. THIRUMALAI, 2024. Journal of Chemical Theory and Computation. 20(7), 2934-2946
  • HIRANMAY MAITY, HUNG T. NGUYEN, NAOTO HORI and D. THIRUMALAI, 2024. The Journal of Physical Chemistry Letters. 15(14), 3820-3827
  • HIRANMAY MAITY, HUNG T. NGUYEN, NAOTO HORI and D. THIRUMALAI, 2023. Proceedings of the National Academy of Sciences of the United States of America. 120(24), e2301409120
  • NAOTO HORI and D. THIRUMALAI, 2023. Nucleic Acids Research. 51(19), 10737鈥�10751
  • HUNG T. NGUYEN, NAOTO HORI and D. THIRUMALAI, 2022. Nature Chemistry. 14, 775-785
  • NAOTO HORI, NATALIA A. DENESYUK and D. THIRUMALAI, 2021. Proceedings of the National Academy of Sciences of the United States of America. 118(10), e2020837118
  • NAOTO HORI, NATALIA A. DENESYUK and D. THIRUMALAI, 2019. Biophysical Journal. 116(12), 2400-2410
  • HUNG T. NGUYEN, NAOTO HORI and D. THIRUMALAI, 2019. Proceedings of the National Academy of Sciences of the United States of America. 116(42), 21022-21030
  • JORJETHE ROCA, NAOTO HORI, SAROJ BARAL, YOGAMBIGAI VELMURUGU, RANJANI NARAYANAN, PRASANTH NARAYANAN, D. THIRUMALAI and ANJUM ANSARI, 2018. Proceedings of the National Academy of Sciences of the United States of America. 115(31), E7313-E7322
  • DEBAYAN CHAKRABORTY, NAOTO HORI and D. THIRUMALAI, 2018. Journal of Chemical Theory and Computation. 14(7), 3763-3779
  • NAOTO HORI, NATALIA A. DENESYUK and D. THIRUMALAI, 2018. Journal of Physical Chemistry B. 122(49), 11279-11288
  • NATALIA A. DENESYUK, NAOTO HORI and D. THIRUMALAI, 2018. Journal of Physical Chemistry B. 122(50), 11860-11867
  • HIMADRI S. SAMANTA, PAVEL I. ZHURAVLEV, MICHAEL HINCZEWSKI, NAOTO HORI, SHAON CHAKRABARTI and D. THIRUMALAI, 2017. Soft Matter. 13(19), 3622-3638
  • SHIBAPRASAD SEN, RAM SARKAR, KAUSHIK ROY and NAOTO HORI, 2017. In: Proceedings of the 5th International Conference on Frontiers in Intelligent Computing: Theory and Applications. 515. 541-549
  • NAOTO HORI, NATALIA A. DENESYUK and D. THIRUMALAI, 2016. Journal of Molecular Biology. 428(14), 2847-2859
  • TOMOHIRO TANAKA, NAOTO HORI and SHOJI TAKADA, 2015. PLOS Computational Biology. 11(7), e1004356
  • HIROO KENZAKI, NOBUYASU KOGA, NAOTO HORI, RYO KANADA, WENFEI LI, KEI-ICHI OKAZAKI, XIN-QIU YAO and SHOJI TAKADA, 2011. Journal of Chemical Theory and Computation. 7(6), 1979-1989
  • WENFEI LI, HIROAKI YOSHII, NAOTO HORI, TOMOSHI KAMEDA and SHOJI TAKADA, 2010. Methods. 52(1), 106-114
  • NAOTO HORI, GEORGE CHIKENJI, R. STEPHEN BERRY and SHOJI TAKADA, 2009. Proceedings of the National Academy of Sciences of the United States of America. 106(1), 73-78

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