Improved RNA virus understanding is critical to studying animal and plant health, and environmental processes. However, the continuous and rapid RNA virus evolution makes their identification and char...

What a week we just had in Lisbon! After two years of communications we have organised the 2nd RdRP Summit: RdRp-based RNA virus discovery community (more rdrp.io )! This community.. absolutely fasci...

A community effort to create a shared resource for HMM-based RdRp discovery - dimitris-karapliafis/RdRpCATCH

Molecular simulations have been instrumental in elucidating the SARS-CoV-2 lifecycle, thereby supporting the design and development of antiviral therapies and diagnostic tools for COVID-19. Here, the molecular mechanism of the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp), a potential target for antiviral drugs to treat COVID-19, was explored based on QM/MM simulations with fixed-charge and polarizable force fields (cFF and pFF, respectively). The free energy perturbation (FEP) method allowed exploring the free energy landscape of the enzymatic reaction mechanism, addressing key questions about the initial deprotonation of the 3′-OH group of the terminal nucleotide before a nucleophilic attack on the incoming nucleotide takes place. Indeed, among the five mechanisms explored, the most favorable was identified as a three-step process. The first step consists of a proton transfer from the 3′-OH group of the terminal nucleotide to a hydroxide group coordinated with an Mg2+ ion. Subsequently, the O3′ atom nucleophilically attacks the Pα atom of the incoming ATP. Finally, a proton is transferred from the water molecule formed in the first step to the γ-phosphate group of the pyrophosphate leaving group, regenerating the Mg2+-coordinated hydroxide group. This mechanism was found to be exergonic, with the rate-determining step being the nucleophilic attack, having a free energy barrier of 15.2 kcal mol–1. Both cFF and pFF yield consistent energetic and geometrical descriptions of the full RdRp-catalyzed reaction. Noncovalent interaction (NCI) and electron localization function (ELF) analyses provide insights into the electronic evolution during the reaction, showing strong polarization on electronic basins associated with the reactive oxygens O3′ and O3α. Together, findings contribute to a deeper understanding of the RdRp mechanism, which could aid in the discovery of new antiviral inhibitors.

Molecular simulations have been instrumental in elucidating the SARS-CoV-2 lifecycle, thereby supporting the design and development of antiviral therapies and diagnostic tools for COVID-19. Here, the molecular mechanism of the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp), a potential target for antiviral drugs to treat COVID-19, was explored based on QM/MM simulations with fixed-charge and polarizable force fields (cFF and pFF, respectively). The free energy perturbation (FEP) method allowed exploring the free energy landscape of the enzymatic reaction mechanism, addressing key questions about the initial deprotonation of the 3′-OH group of the terminal nucleotide before a nucleophilic attack on the incoming nucleotide takes place. Indeed, among the five mechanisms explored, the most favorable was identified as a three-step process. The first step consists of a proton transfer from the 3′-OH group of the terminal nucleotide to a hydroxide group coordinated with an Mg2+ ion. Subsequently, the O3′ atom nucleophilically attacks the Pα atom of the incoming ATP. Finally, a proton is transferred from the water molecule formed in the first step to the γ-phosphate group of the pyrophosphate leaving group, regenerating the Mg2+-coordinated hydroxide group. This mechanism was found to be exergonic, with the rate-determining step being the nucleophilic attack, having a free energy barrier of 15.2 kcal mol–1. Both cFF and pFF yield consistent energetic and geometrical descriptions of the full RdRp-catalyzed reaction. Noncovalent interaction (NCI) and electron localization function (ELF) analyses provide insights into the electronic evolution during the reaction, showing strong polarization on electronic basins associated with the reactive oxygens O3′ and O3α. Together, findings contribute to a deeper understanding of the RdRp mechanism, which could aid in the discovery of new antiviral inhibitors.

AbstractRift Valley fever virus (Bunyavirales, Peribunyaviridae) or short RVFV is emerging arbovirus that can cause disease and death in humans and animals. There are no drugs to treat infection, and

Using population-based surveillance data, among adults hospitalized with influenza-associated pneumonia, delayed initiation of influenza antiviral treatmen

Within the hepatitis E virus (HEV) ORF1 polyprotein, the X domain interacts with viral RNA-dependent RNA polymerase (RdRp), forming a functional “pocket-like” cavity (PC) that is crucial for viral replication. Structure-based screening, surface plasmon resonance (SPR) assays, and HEV model validation collectively identify saikosaponin D and liriopesides B as PC-targeting compounds with potent anti-HEV activity, offering a novel therapeutic strategy. Abstract Hepatitis E virus (HEV) is the leading cause of acute viral hepatitis worldwide, yet no FDA-approved anti-HEV medication available. Elucidating HEV replication machinery is therefore crucial for identifying novel antiviral targets, and consequently developing potent antivirals. The nonstructural ORF1 polyprotein is pivotal for HEV replication. Herein, it is revealed that the ORF1 X domain is a critical component of HEV replication machinery. Interestingly, the ADP-ribose hydrolase activity of X domain per se is dispensable for HEV replication. Instead, the X domain supports HEV replication through its interdomain interaction with the RNA-dependent RNA polymerase (RdRp). Structure-based functional analysis reveals that X and RdRp jointly create a “pocket-like” cavity (PC) at their interaction interface. Site-directed mutagenesis disrupting the PC integrity completely abolishes HEV replication, demonstrating its crucial role in the viral life cycle. Through a PC-targeted high-throughput in silico screening pipeline, combined with molecular docking analysis, surface plasmon resonance assays, and advanced in vitro HEV models, saikosaponin D and liriopesides B are identified as potent HEV inhibitors targeting this critical interface. Collectively, this study identifies a novel structure within ORF1 polyprotein that is crucial for HEV replication, and demonstrates the feasibility of developing novel antivirals by targeting this PC structure.