Viral proteases are central targets in antiviral drug discovery and development because they play essential roles in viral replication and maturation. Although protease inhibitors have achieved major clinical success, traditional design strategies face challenges, including resistance development, poor oral exposure of early peptidomimetics, and off-target toxicity of highly reactive covalent warheads. Classical approaches, such as peptidomimetics, macrocyclization, and covalent warhead engineering, are discussed alongside contemporary strategies, including allosteric modulation and targeted protease degradation via proteolysis-targeting chimeras (PROTAC) technology. Particular emphasis is placed on how these strategies address key obstacles, such as resistance evolution, selectivity, metabolic stability, and oral bioavailability. Several quantitative case studies have also demonstrated the growing significance of computational tools in contemporary antiviral discovery. For SARS-CoV-2 main protease (Mpro), these workflows were enabled by the rapid availability of high-resolution experimental crystal structures of the target protein. The evolution of a weak fragment (Kd ≈ 1.7 mM; ΔG ≈ -3.6 kcal/mol) into a covalent inhibitor (QUB-00006-Int-07) with enzymatic inhibition (IC50 ≈ 830 nM) was successfully guided by molecular dynamics (MD) simulations and absolute binding free energy calculations. This was subsequently confirmed experimentally using NMR, ESI-MS, and FRET assays. Furthermore, out of 25 computationally prioritized candidates with Ki values less than 4 μM, 15 active Mpro inhibitors were identified using accelerated free-energy perturbation-based repurposing campaigns. Long-range allosteric pathways connecting the catalytic site to resistance-associated regions and experimentally verified allosteric pockets have also been discovered using dynamic nonequilibrium MD. Together, these integrated in silico approaches enable the early prioritization of high-affinity ligands, mechanistic understanding of resistance, and significant reduction of late-stage attrition in antiviral drug discovery. Through detailed case studies on SARS-CoV-2 main protease (Mpro), Zika virus NS2B-NS3 protease, and Dengue virus NS2B-NS3 protease, the review illustrates how medicinal chemistry principles translate molecular insights into clinically relevant antivirals. Finally, a forward-looking development roadmap is proposed that integrates potency, selectivity, pharmacokinetics, manufacturability, and resistance management toward the goal of broad-spectrum, durable, and adaptable protease-targeted therapeutics development.

BVDV NS5A promotes mitochondria-associated endoplasmic reticulum membrane (MAM) formation to enhance viral replication.

Narciclasine restricts pseudorabies virus replication in vitro and in vivo and has potential broad-spectrum antiviral activity.

Research advances in chikungunya virus: Epidemiology, pathogenesis, and control.

Characterization of bacteriophage Henu4_2 lytic for Escherichia coli and its therapeutic efficacy in infection models.

Ornithodoros lahorensis as a biological vector of African swine fever virus.

Identification of MA-104 cells as a novel continuous cell line for the direct primary isolation of lumpy skin disease virus.

Plant-positive single-stranded RNA viruses induce vesicles that are crucial for viral infection, replication and spread. However, the mechanisms underlying the vesicle biogenesis induced by negative single-stranded RNA viruses remain largely unknown. Here, a negative single-stranded RNA virus, tomato spotted wilt orthotospovirus (TSWV) which is a representative member of genus Orthotospovirus in the Tospoviridae family, was used as a model to investigate the mechanisms involving the interaction between the viral and the host plant proteins in vesicle formation and function. We found that the nonstructural protein (NSm) of TSWV, could induce endoplasmic reticulum (ER)-derived pathological vesicle biogenesis. In addition, NSm might hijack the host immunity proteins, NtPOX1 (a peroxidase) and pathogenesis-related protein NtPR-4A, to form a potential tetrameric protein complex with Sar1 (a small GTPase), which was crucial for NSm-induced vesicle biogenesis. The results also showed that these ER-derived pathological vesicles provided sites for TSWV replication. These findings provide novel and robust insights for understanding the infection processes and mechanisms of plant-negative single-stranded RNA viruses.

The evolution of in vitro culture systems for the study of hepatitis E virus infection.

Oncolytic virus hijacks GOT1 and pyrimidinosomes to fuel pyrimidine synthesis for replication in tumor cells.

Atg5-mediated autophagy modulation shapes the outcome of Bombyx mori Nucleopolyhedrovirus infection in silkworms.

Exploring the potential therapeutic effects of ultradiluted Crotalus horridus on antibody-dependent enhancement in dengue virus pathogenesis.

Caffeic acid inhibits replication of an Asian lineage Zika virus and attenuates virus-induced inflammatory responses.

Longitudinal multi-omics reveal phase-dependent viral adaptive strategies and functional potential during formation of algal-bacterial granular sludge.

Novel antiviral compounds: Synthesis, biological studies on SARS-CoV-2, and structure-activity relationship analysis.

Oxysterols in the defense against viral infections in humans.

From 2020 to 2025: Comprehensive review Decoding novel structural inhibitors for Mpro of SARS-CoV-2.

Animal coronaviruses (CoVs) have emerged as significant pathogens with considerable implications for both animal and human health. This review provides an in-depth analysis of the origins, transmission dynamics, and pathogenic mechanisms of animal CoVs. We examine the viral entry, replication processes, and immune evasion strategies that enable CoVs to infect a variety of host species. Additionally, the review highlights recent advancements in prevention and therapeutic strategies, including the development of species-specific vaccines, enhanced biosecurity measures, and surveillance systems aimed at controlling zoonotic spillover. Furthermore, we discuss the latest antiviral strategies, including repurposed drugs, targeted molecular therapies, and the development of novel antiviral agents. This review emphasizes the importance of interdisciplinary research in advancing our understanding of animal CoVs and in developing effective interventions to mitigate their impact on global health.

Fluorescence polarization-based high-throughput screening identifies SAM-competitive inhibitors of monkeypox virus N7-methyltransferase.

ERAD inhibitor Eeyarestatin I (EerI) suppresses duck plague virus by restoring STING-mediated antiviral immunity.