The research team’s strategy rested on a deceptively simple premise: rather than studying the virus in isolation, they examined how human cells respond to infection. Viruses are obligate hijackers, and the genes a host cell switches on or off during infection often reveal the molecular levers the pathogen pulls. The investigators mined three independent transcriptomic profile datasets comparing gene expression in MPOX patients against healthy controls. By intersecting the results across datasets, they filtered out noise and arrived at 166 common host differentially expressed genes, or hDEGs, that consistently distinguish infected individuals from uninfected ones. Of these, 75 genes were upregulated, meaning their activity increased during infection, while 91 were downregulated, suggesting suppression of functions the virus may find inconvenient.

Identifying differentially expressed genes is only the first step in untangling a disease process. To separate genuine drivers from incidental bystanders, the team turned to protein-protein interaction network analysis, a technique that maps the web of physical and functional contacts among the proteins encoded by the altered genes. Genes sitting at highly connected nodes of such networks often exert outsized influence on cellular behavior. From this analysis, six top-ranked host key genes emerged as potential MPOX-causing genes: ALB, HSP90AA1, CDH1, PTPRC, IGF1, and ABL1. Each tells a plausible story. ALB encodes serum albumin, the body’s most abundant plasma protein and a marker of liver function and fluid balance. HSP90AA1 is a molecular chaperone that stabilizes many client proteins, including those involved in immune signaling. CDH1 produces E-cadherin, a cell adhesion molecule critical to maintaining epithelial barriers, the very front line that poxviruses breach. PTPRC, better known as CD45, is a tyrosine phosphatase essential for lymphocyte activation, pointing to immune cell involvement. IGF1 governs growth factor signaling, and ABL1 is a kinase with well-characterized roles in cell proliferation and DNA damage responses.

With these six hub genes in hand, the researchers performed functional enrichment analysis to determine which biological processes, molecular functions, cellular components, and signaling pathways the genes collectively implicate. Such enrichment analysis asks whether a set of genes is overrepresented in known functional categories compared with what chance would predict. The results painted a coherent picture of MPOX pathogenesis, highlighting processes tied to immune response regulation, epithelial integrity, and metabolic adaptation. The team also extended the analysis to KEGG pathways, a curated database of molecular interaction and reaction networks, which helped situate the hub genes within broader cellular circuits. Complementing this, a regulatory network analysis identified transcription factors and microRNAs that potentially control the expression of the key genes, adding another layer of mechanistic insight. Transcription factors are proteins that switch genes on or off, while microRNAs are small RNA molecules that fine-tune gene expression after transcription; mapping these regulators helps explain how the observed expression changes might arise during infection.

The second half of the study pivoted from understanding the disease to treating it. Rather than waiting years for a novel antiviral to be discovered and tested, the team pursued drug repurposing, the strategy of finding new uses for approved or well-characterized compounds. Repurposing offers a substantial speed advantage because existing drugs already have established safety profiles, manufacturing routes, and, in many cases, clinical experience in humans. The researchers screened candidate molecules against the proteins implicated in MPOX using molecular docking, a computational method that predicts how strongly and in what orientation a small molecule binds to a target protein’s binding site. From this screen, five top-ranked drug candidates emerged: Tecovirimat, Beclabuvir, Maraviroc, Raltegravir, and Brincidofovir.

Several of these nominations carry intriguing logic. Tecovirimat is an antiviral originally developed against smallpox that inhibits the VP37 envelope protein of orthopoxviruses, the viral family that includes monkeypox, and it has already seen emergency use during recent outbreaks. Brincidofovir is a lipid conjugate of cidofovir designed to accumulate in cells and disrupt viral DNA replication, and it too carries orthopoxvirus indications. Maraviroc, by contrast, is an HIV entry inhibitor that blocks the CCR5 receptor on immune cells, while Raltegravir is an HIV integrase strand transfer inhibitor, and Beclabuvir is an investigational hepatitis C NS5A inhibitor. That compounds developed for entirely different pathogens dock favorably onto host or viral proteins relevant to MPOX illustrates the core promise of repurposing: molecular interfaces evolved for one purpose can sometimes be exploited for another.

Computational docking alone can be misleading, however, because a molecule that fits a binding site in a static snapshot may fail to maintain that interaction under the dynamic conditions of a living cell. To address this, the team evaluated the pharmacokinetic credentials of all five candidates using ADME/T analysis, which assesses absorption, distribution, metabolism, excretion, and toxicity, alongside drug-likeness filters that compare molecular properties against those of successful oral medicines. The candidates passed these evaluations with favorable profiles, suggesting that, in principle, they could reach their targets in the body at effective concentrations without unacceptable toxicity.

The strongest computational evidence came from molecular dynamics simulations, which model the physical motion of atoms over time to test whether a drug-protein complex remains stable in a realistic, fluctuating environment. The researchers ran 100-nanosecond simulations of the three most promising complexes: ALB bound to Tecovirimat, CDH1 bound to Maraviroc, and PPARG bound to Beclabuvir. PPARG, the nuclear receptor targeted by Beclabuvir in this analysis, adds an interesting metabolic dimension to the proposed mechanism. Throughout the simulations, the team tracked root-mean-square deviation, or RMSD, which measures how far the protein structure drifts from its starting conformation, and root-mean-square fluctuation, or RMSF, which quantifies how much individual residues wiggle locally. They also computed binding free energies using the MM-GBSA method, which estimates the thermodynamic favorability of the drug-protein interaction. All three complexes demonstrated strong binding stability across these metrics, indicating that the docked poses were not artifacts of a single frozen structure but held up under sustained atomic motion.

The convergence of transcriptomic evidence, network analysis, docking, pharmacokinetic screening, and dynamic simulation gives the study an unusually complete computational arc, moving from disease mechanism to therapeutic nomination within a single framework. The identification of host key genes such as ALB, CDH1, and PTPRC may also inform diagnostic development, since consistently dysregulated host transcripts can serve as biomarkers distinguishing MPOX from other febrile illnesses, a persistent challenge in regions where poxvirus, malaria, and other infections overlap clinically.

Yet the authors are careful to frame their findings as a starting point rather than a conclusion. Every result in the study, from the 166 differentially expressed genes to the stability of the simulated drug complexes, derives from computational inference and must be validated experimentally in the laboratory before it can inform clinical practice. Docking scores do not guarantee efficacy in infected cells, and transcriptomic correlations do not prove causation. Still, in a landscape where no approved MPOX drug exists and vaccine coverage remains sparse, computational pipelines like this one offer a rapid, systematic way to prioritize which existing molecules deserve the first laboratory look. As MPOX continues to circulate globally, such approaches may shorten the path from genomic data to actionable therapeutics, turning the growing archive of patient transcriptomes into a roadmap for fighting a disease the world can no longer afford to neglect.

Subject of Research: Host transcriptomic analysis of MPOX pathogenesis and computational drug repurposing

Article Title: Disclosing pathogenic processes of monkeypox (MPOX) and drug repurposing through host-transcriptomics analysis

Article References: Mahmud, S., Ajadee, A., Ali, M. A., Ahmed, M. F., Ahmmed, R., Rana, M. M., Noor, T., Faysal, M. F., Kabir, M. H., & Mollah, M. N. H. (2026). Disclosing pathogenic processes of monkeypox (MPOX) and drug repurposing through host-transcriptomics analysis. PLOS Neglected Tropical Diseases, 20(10), e0014797. https://doi.org/10.1371/journal.pntd.0014797

Image Credits: AI Generated

DOI: 10.1371/journal.pntd.0014797

Keywords: MPOX, monkeypox, host transcriptomics, drug repurposing, molecular docking, molecular dynamics, PLOS Neglected Tropical Diseases, Tecovirimat, Brincidofovir, differentially expressed genes, protein-protein interaction network, antiviral therapeutics