Eduardo L. Tosado Rodriguez

The gut microbiome has emerged as an important determinant of the metabolism, efficacy, and safety of many therapeutic agents, expanding the traditional host-centered view of pharmacology. Direct microbial biotransformation is particularly relevant to orally administered compounds, whereas the gut microbiome can also influence systemically administered therapies indirectly through immune, inflammatory, barrier, and hepatic pathways. Beyond its established roles in nutrient metabolism, immune regulation, and maintenance of epithelial homeostasis, the microbiome functions as a metabolically active organ capable of transforming endogenous molecules, dietary compounds, xenobiotics, and therapeutic agents through an extensive repertoire of microbial enzymes and metabolites. These interactions influence virtually every stage of drug disposition by modifying pharmacokinetics, pharmacodynamics, bioavailability, therapeutic efficacy, and toxicity. This narrative review summarizes current knowledge of the composition and functional diversity of the gut microbiome and examines the molecular mechanisms underlying host–microbe–drug interactions, including direct microbial biotransformation, regulation of intestinal barrier integrity, immune modulation, bile acid metabolism, and microbial control of hepatic drug-metabolizing pathways. We further discuss the impact of these mechanisms across multiple therapeutic areas, including oncology, neurological and psychiatric disorders, cardiovascular medicine, diabetes, metabolic diseases, and microbiome-dependent activation of natural products. Emphasis is placed on recent advances in cancer therapy, where the microbiome has emerged as a key determinant of responses to chemotherapy, immune checkpoint inhibitors, oncolytic viruses, and other immunotherapies. The review also highlights the bidirectional relationship between drugs and microbial communities, illustrating how pharmaceuticals reshape the microbiome while microbial ecosystems simultaneously influence therapeutic outcomes. Finally, we discuss emerging technologies, including multi-omics approaches, artificial intelligence, organ-on-chip models, and microbiome-targeted interventions, that are accelerating the integration of pharmacomicrobiomics into drug discovery and precision medicine. Collectively, current evidence supports recognizing the microbiome as an integral component of human pharmacology and a promising source of predictive biomarkers and therapeutic targets for the development of safer, more effective, and personalized treatment strategies.

The human microbiome has emerged as a fundamental determinant of drug metabolism, efficacy, and safety, expanding the traditional host-centered view of pharmacology. Beyond its established roles in nutrient metabolism, immune regulation, and maintenance of epithelial homeostasis, the microbiome functions as a metabolically active organ capable of transforming endogenous molecules, dietary compounds, xenobiotics, and therapeutic agents through an extensive repertoire of microbial enzymes and metabolites. These interactions influence virtually every stage of drug disposition by modifying pharmacokinetics, pharmacodynamics, bioavailability, therapeutic efficacy, and toxicity. This narrative review summarizes current knowledge of the composition and functional diversity of the human microbiome and examines the molecular mechanisms underlying host–microbe–drug interactions, including direct microbial biotransformation, regulation of intestinal barrier integrity, immune modulation, bile acid metabolism, and microbial control of hepatic drug-metabolizing pathways. We further discuss the impact of these mechanisms across multiple therapeutic areas, including oncology, neurological and psychiatric disorders, cardiovascular medicine, diabetes, metabolic diseases, and microbiome-dependent activation of natural products. Emphasis is placed on recent advances in cancer therapy, where the microbiome has emerged as a key determinant of responses to chemotherapy, immune checkpoint inhibitors, oncolytic viruses, and other immunotherapies. The review also highlights the bidirectional relationship between drugs and microbial communities, illustrating how pharmaceuticals reshape the microbiome while microbial ecosystems simultaneously influence therapeutic outcomes. Finally, we discuss emerging technologies, including multi-omics approaches, artificial intelligence, organ-on-chip models, and microbiome-targeted interventions, that are accelerating the integration of pharmacomicrobiomics into drug discovery and precision medicine. Collectively, current evidence supports recognizing the microbiome as an integral component of human pharmacology and a promising source of predictive biomarkers and therapeutic targets for the development of safer, more effective, and personalized treatment strategies.

Anxiety disorders are the most prevalent mental health conditions worldwide, yet current treatments remain suboptimal, with benzodiazepines carrying risks of tolerance and dependence. These limitations motivate the search for novel anxiolytics. Tropical marine macroalgae represent a promising source of neuroactive metabolites. Here, we investigate the anxiolytic potential of Stypopodium zonale using a neuroproteomics-based approach in Drosophila melanogaster. Crude organic extracts were prepared via ultrasonic-assisted extraction and administered acutely to adult flies for six hours. Proteins from fly heads were quantified and analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS), revealing 66 significantly differentially abundant proteins (fold change ≥ |1.5|, p ≤ 0.05), 72.7% of which were less abundant in the extract-treated group. Principal component analysis demonstrated clear separation between control and experimental samples. Ingenuity Pathway Analysis (IPA) mapped 33 of the differentially abundant proteins to human orthologs and identified significant predicted inhibition of the Protein Kinase A (PKA) signaling pathway. An IPA Interaction Network enabled the construction of a preliminary working model, suggesting that the extract may antagonize Drosophila’s Dop1R2 (DAMB). Overall, this study integrates natural product drug discovery with neuroproteomics in an invertebrate model system, providing a foundation for future behavioral validation and isolation of bioactive compounds from S. zonale.

Anxiety disorders are the most prevalent mental health conditions worldwide, yet current treatments remain suboptimal, with benzodiazepines carrying risks of tolerance and dependence. These limitations motivate the search for novel anxiolytics. Tropical marine macroalgae represents a promising source of neuroactive metabolites. Here, we investigate the anxiolytic potential of Stypopodium zonale using a neuroproteomics-based approach in Drosophila melanogaster. Crude organic extracts were prepared via ultrasonic-assisted extraction and administered acutely to adult flies for six hours. Proteins from fly heads were quantified and analyzed using LC-MS/MS, revealing 66 significantly differentially abundant proteins (fold change ≥ |1.5|, p ≤ 0.05), 72.7% of which were less abundant in the extract-treated group. Principal Component Analysis demonstrated clear separation between control and experimental samples. Ingenuity Pathway Analysis (IPA) mapped 33 of the differentially abundant proteins to human orthologs and identified significant predicted inhibition of the Protein Kinase A (PKA) signaling pathway. An IPA Interaction Network enabled the construction of a preliminary working model, suggesting that the extract may antagonize Drosophila’s Dop1R2 (DAMB). Overall, this study integrates natural product drug discovery with neuroproteomics in an invertebrate model system, providing a foundation for future behavioral validation and isolation of bioactive compounds from S. zonale.

Although antiviral therapy has improved quality of life, around 50% of people with HIV (PWH) experience neurodegeneration and cognitive decline. This is prompted in part by the migration of HIV-infected monocyte-derived macrophages (MDMs) to the brain, leading to neuronal death. Previous studies in our lab have shown that HIV-infected MDMs secrete cathepsin B (CATB), which is a pro-inflammatory neurotoxic enzyme that is reduced by the addition of cannabinoid receptor-2 (CB2R) agonist JWH-133 to cell cultures. In this study, we aimed to identify the proteins secreted (secretome) by HIV-infected macrophages exposed to JWH-133 and quantify them using tandem mass tag (TMT) mass spectrometry. Frozen 13-day MDM supernatants from (1) an MDM negative control; (2) HIV+MDM, and (3) HIV+MDM-JWH-133 were compared in triplicate by mass spectrometry (LC/MS/MS) and analyzed for protein identification. Subsequently, the same samples were labeled by TMT labeling and quantified by LC/MS/MS. After a database search, 528 proteins were identified from all groups. Thereafter, proteins with more than three unique peptides and more than 10% coverage were selected for protein identification. Venn diagrams revealed one unique protein secreted by MDM-HIV, 10 unique proteins in HIV+MDM-JWH-133, and 15 common proteins in the three groups. CATB was unique to HIV+MDM. HIV+MDM exposed to JWH-133 showed proteins related to metabolism, cell organization, antiviral activity, and stress response. TMT analysis revealed 1454 proteins with abundance for statistical analysis based on FC ≥ |1.5| and p-value ≤ 0.05, of which Ruvb-like 1 and Hornerin decreased significantly with JWH-133 treatment. Both proteins stimulate HIV replication. In addition, HIV infection upregulated proteins associated with pathways of viral latency that were inhibited by JWH-133. In conclusion, JWH-133 treatment in HIV-infected macrophages leads to the secretion of antiviral host factors and decreases the secretion of proviral, inflammatory, and neurotoxic host factors.

Extracellular signal-regulated kinase 1/2 (ERK1/2) inhibitors show therapeutic potential in triple-negative breast cancer (TNBC), but resistance through compensatory signaling limits their efficacy. We previously identified the secretory carrier membrane protein 3 (SCAMP3) as a regulator of TNBC progression and ERK1/2 activation. Here, we investigated the role of SCAMP3 in ERK1/2 signaling and therapeutic response using TMT-based LC-MS/MS phosphoproteomics of wild-type (WT) and SCAMP3 knockout (SC3KO) SUM-149 cells under basal conditions, after epidermal growth factor (EGF) stimulation, and during ERK1/2 inhibition with MK-8353. A total of 4408 phosphosites were quantified, with 1093 significantly changed. SC3KO abolished residual ERK activity under MK-8353 and affected the compensatory activation of oncogenic pathways observed in WT cells. SC3KO reduced the phosphorylation of ERK feedback regulators RAF proto-oncogene serine/threonine-protein kinase Raf-1 (S43) and the dual-specificity mitogen-activated protein kinase kinase 2 (MEK2) (T394), affected other ERK targets, including nucleoporins, transcription factors, and metabolic enzymes triosephosphate isomerase (TPI1) (S21) and ATP-citrate lyase (ACLY) (S455). SCAMP3 loss also impaired the mammalian target of rapamycin complex I (mTORC1) signaling and disrupted autophagic flux, evidenced by elevated sequestosome-1 (SQSTM1/p62) and microtubule-associated protein light chain 3 (LC3B-II) with reduced levels of the autophagosome lysosome maturation marker, Rab7A. Beyond ERK substrates, SC3KO affected phosphorylation events mediated by other kinases. These findings position SCAMP3 as a central coordinator of ERK signaling and autophagy. Our results support SCAMP3 as a potential therapeutic target to enhance ERK1/2 inhibitor clinical efficacy and overcome adaptive resistance mechanisms in TNBC.

There is a present need to develop alternative biotherapeutic drugs to mitigate the exacerbated inflammatory immune responses characteristic of sepsis. The potent endotoxin lipopolysaccharide (LPS), a major component of Gram-negative bacterial outer membrane, activates the immune system via Toll-like receptor 4 (TLR4), triggering macrophages and a persistent cascade of inflammatory mediators. Our previous studies have demonstrated that Fh15, a recombinant member of the Fasciola hepatica fatty acid binding protein family, can significantly increase the survival rate by suppressing many inflammatory mediators induced by LPS in a septic shock mouse model. Although Fh15 has been proposed as a TLR4 antagonist, the specific mechanisms underlying its immunomodulatory effect remained unclear. In the present study, we employed a quantitative proteomics approach using tandem mass tag (TMT) followed by LC-MS/MS analysis to identify and quantify differentially expressed proteins that participate in signaling pathways downstream TLR4 of macrophages, which can be dysregulated by Fh15. Data are available via ProteomeXchange with identifier PXD065520. Based on significant fold change (FC) cut-off of 1.5 and p-value ≤ 0.05 criteria, we focused our attention to 114 proteins that were upregulated by LPS and downregulated by Fh15. From these proteins, TNFα, IL-1α, Lck, NOS2, SOD2 and CD36 were selected for validation by Western blot on murine bone marrow-derived macrophages due to their relevant roles in the NF-κB, iNOS, oxidative stress, and phagosome signaling pathways, which are closely associated with sepsis pathogenesis. These results suggest that Fh15 exerts a broad spectrum of action by simultaneously targeting multiple downstream pathways activated by TLR4, thereby modulating various aspects of the inflammatory responses during sepsis.

Introduction: Stressor-related disorders frequently co-occur with alcohol use disorder (AUD). This necessitates an understanding of the physiological and genetic factors contributing to this relationship. Binge drinking is the most common method of alcohol consumption among adolescent males and significantly increases the risk of developing comorbid stressor-related disorders and AUD. In experiments modeling the effects of a single binge-like alcohol exposure in male adolescent mice, we observed a clear deficit in context extinction learning. This exposure led to a significant initial increase in subsequent voluntary drinking on day one, as measured by the every-other-day (EOD) two-bottle choice drinking assay, which normalized thereafter. Methods: For this study we performed an mRNASeq analysis of mice nucleus accumbens (NAc), a region intricately involved in regulating both aversive contextual fear responses and reward, after EOD to profile the differential expression of mRNAs within this region. We also used immunohistochemistry of coronal brain slices to characterize expression of proteins associated with stress-related disorders and molecular alcohol tolerance, such as FKBP5, GSK3ß, and ß-catenin, within the striatum, nucleus accumbens (NAc), hippocampus, and basolateral amygdala (BLA). Results: Comparative mRNA profile analysis reveals significant long-term changes in gene expression induced by binge-like alcohol exposure, even 30 days after the initial exposure. Immunohistochemistry showed a full recovery of previously observed altered levels of target proteins prior to EOD. Conclusions: These findings suggest that the temporal activation of specific gene subsets plays a crucial role in the comorbidity of AUD and stressor-related diseases. Understanding these mechanisms can help develop more effective, integrated treatment approaches to improve outcomes for affected individuals.

Background: Understanding the dynamics of the gut microbiota in sea urchins is crucial for comprehending the ecological balance in marine ecosystems. The gut microbiota plays a vital role in nutrient metabolism, immune system modulation, and pathogen protection. The microbial composition and dynamics of naturally occurring sea urchin Tripneustes ventricosus have yet to be thoroughly investigated. We hypothesized the gut microbiota of T. ventricosus in the Caribbean, varies across life stages and seasons. Methods: Thirty-six naturally occurring large individuals and six small individuals (42 animals) were collected from shallow waters on the northeastern coast of Puerto Rico in February and August of 2019. The fecal pellet’s microbiota was characterized by sequencing V4 region of the 16S rRNA gene. Results: We found significant differences in the composition of fecal pellet microbiota between seasons and life stages. Phylum Bacteroidota had greater relative abundance in August, while Firmicutes was more dominant in February. Propionigenium and Roseimarinus had greater relative abundance in August, while Candidatus Hepatoplasma, and Kistimonas had greater relative abundance in February. Differences in the gut digest microbiota were not found between small and large urchins, but small urchins displayed a slightly higher diversity and dominance of Bacteroidota and Proteobacteria, while large urchins exhibited a greater relative abundance of Fusobacteria and Desulfobacterota. However, the genera Ferrominas and Propionigenium counts were significantly lower in small individuals. Discussion: This is the first report for this species in the Caribbean region and adds to our comprehension of the microbiota of the white sea urchin across collection periods and size classes, highlighting the dynamic nature of the gut microbiota.