Major depressive disorder (MDD) represents a significant global health burden, affecting millions of individuals worldwide and leading to substantial disability [1,2]. While current pharmacological interventions, primarily monoamine antidepressants, form the cornerstone of treatment, their clinical utility is often constrained by notable limitations. These include delayed therapeutic onset, suboptimal response rates in a large subset of patients, high rates of relapse, and a spectrum of adverse effects that frequently compromise patient adherence and long-term outcomes [[3], [4], [5]]. This clinical landscape underscores an urgent need for a deeper understanding of antidepressant mechanisms to develop safer and more effective therapeutic strategies.

Flx, the prototypical selective serotonin reuptake inhibitor (SSRI), has been a cornerstone of MDD treatment for decades. Its primary therapeutic mechanism is well-established: the selective blockade of the serotonin transporter (SERT), which increases synaptic serotonin levels [6]. However, the clinical profile of Flx is not solely defined by its efficacy. It is also associated with a range of challenging adverse effects, including gastrointestinal disturbances, sexual dysfunction, and sleep disturbances [7,8]. The molecular pathways underlying these off-target effects remain incompletely understood, highlighting a critical gap in our knowledge of this classic antidepressant.

In parallel with synthetic drugs, phytomedicines have gained prominence, with SJW (Hypericum perforatum L.) being one of the most widely used herbal remedies for mild to moderate depression [9]. In stark contrast to the single-target action of Flx, SJW possesses a complex phytochemical profile, and its antidepressant effects are attributed to a pleiotropic mechanism. Key constituents, such as hyperforin, hypericin and flavonoids, are thought to modulate multiple neurotransmitter systems, including serotonin, norepinephrine, and dopamine, alongside potential monoamine oxidase (MAO) inhibition [[10], [11], [12]]. It has been extensively researched over the last two decades, however, there are still many open questions regarding the mechanism of action [13].

Despite the extensive clinical use of both Flx and SJW, a systematic, head-to-head comparison of their underlying molecular mechanisms at a systems level is conspicuously lacking. This knowledge gap presents a significant clinical challenge: without a clear understanding of their convergent and divergent pathways, it is difficult to rationalize their distinct adverse effect profiles, optimize treatment selection for individual patients, or provide evidence-based guidance on the safety and efficacy of their potential co-administration.

The combination of “omics” techniques has enhanced the comprehension of numerous particular biological systems and governing mechanisms [14]. Hundreds of potential molecular proteins and metabolites have been identified using omics techniques. The presence (or altered levels, i.e., up- or down-regulated) of these may be a predictor of depression [15]. Therefore, this study employs a comparative proteomics and metabolomics approach to systematically identify the molecular modulations underlying the effects of Flx and SJW. This head-to-head comparison aims to elucidate their shared and distinct molecular pathways. These findings are intended to provide a scientific basis for predicting adverse effects, optimizing their clinical use, evaluating the rationale for co-administration, and identifying novel targets for future antidepressant drug development.