RNAi-based therapeutics targeting the F gene in human metapneumovirus: An in-silico approach

Abstract

Background: Human metapneumovirus (HMPV) is a major cause of acute respiratory tract infections, particularly in young children, older adults, and immunocompromised individuals. Despite its significant clinical burden, no approved antiviral therapies or vaccines are currently available. This study aimed to identify potential RNA interference (RNAi)-based therapeutic candidates targeting the highly conserved fusion (F) gene of HMPV. Methods: An in silico pipeline was employed to design and evaluate small interfering RNA (siRNA) candidates targeting the HMPV F gene. A total of 869 siRNA sequences were initially generated using siDirect 2.1 software, which were sequentially filtered to 34 and then to 10 candidates based on sequence characteristics and predicted silencing efficiency. Molecular docking was performed to assess interactions between selected siRNAs and the human Argonaute-2 (AGO2) protein, followed by 100-ns molecular dynamics simulations to evaluate structural stability. Principal component analysis and free-energy landscape analyses were also performed. Results: Three siRNA candidates (F11, F19, and F26) demonstrated favorable RNAi characteristics, including high predicted silencing efficiency and strong target binding. Among them, F11 exhibited the highest sequence conservation across global HMPV strains, the highest melting temperature, favorable AGO2 interaction, and stable dynamic behavior. Principal component analysis indicated that F11 sampled the most constrained conformational subspace, which had a well-defined low-energy basin, thereby identifying it as the most promising candidate. Conclusions: This study identified F11 as the most promising siRNA candidate targeting the highly conserved HMPV fusion (F) gene, demonstrating strong potential as an RNAi-based therapeutic agent according to computational analyses. However, further in vitro and in vivo validation is required to confirm its efficacy and safety.