Contact
Biography
Dr Naoto Hori is an Assistant Professor of Computational Biophysics in the School of Pharmacy at the University of Nottingham. 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 University of Nottingham 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, University of Nottingham
- 2020 - 2023, Nottingham Research Fellow, University of Nottingham
- 2016 - 2019, Postdoctoral Fellow, University of Texas at Austin (Prof. Thirumalai's lab)
- 2014 - 2015, Research Associate, University of Maryland (Prof. Thirumalai's lab)
- 2010 - 2013, JSPS Research Fellow (DC1) (Prof. Takada's lab.)
- 2009 - 2010, Research Associate, Kyoto University (Prof. Takada's lab.)
- 2008 - 2009, Software Engineer, Kozo Keikaku Engineering Inc.
Education
- 2013, Ph.D. in Biophysics, Kyoto University (Prof. Takada's lab.)
- 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. Synthesis and cell-induced luminescence of post-functionalisable ionisable polyesters from the Passerini 3-component polymerisation Polymer Chemistry. BALAKA MONDAL, DEBAYAN CHAKRABORTY, NAOTO HORI, HUNG T. NGUYEN and D. THIRUMALAI, 2024. Competition between stacking and divalent cation-mediated electrostatic interactions determines the conformations of short DNA sequences Journal of Chemical Theory and Computation. 20(7), 2934-2946 HIRANMAY MAITY, HUNG T. NGUYEN, NAOTO HORI and D. THIRUMALAI, 2024. Salt-dependent self-association of trinucleotide repeat RNA sequences The Journal of Physical Chemistry Letters. 15(14), 3820-3827 HIRANMAY MAITY, HUNG T. NGUYEN, NAOTO HORI and D. THIRUMALAI, 2023. Odd-even disparity in the population of slipped hairpins in RNA repeat sequences with implications for phase separation Proceedings of the National Academy of Sciences of the United States of America. 120(24), e2301409120