Cancer is a complex disease associated with various hallmarks. One such hallmark is altered glucose metabolism in aerobic conditions, termed ‘aerobic glycolysis’ [1], and the whole phenomenon is termed the Warburg effect [2]. Aerobic glycolysis acts as a metabolic switch in cancer, shifting the energy production to glycolysis and aiding cancer survival in various ways. However, the primary energy source in normal cells is oxidative phosphorylation (OXPHOS). The inactivated pyruvate dehydrogenase complex (PDHC) and glycolysis as a primary energy source further leads to lactate accumulation in the cytoplasm, termed as cell acidosis. The acidic environment of the cell also confers survival benefits to cancer cells [3,4]. Cancer is the second‑leading cause of mortality despite significant advancements in cancer therapeutics. Various factors are responsible for the failure of the existing therapeutic approaches, including multi-drug resistance [5].

The enzyme protein kinases (PKs) are a subset of many proteins, altogether working on phosphorylating other target proteins. Kinases use high-energy ATP as a phosphate source by dissociating ATP into ADP and utilizing the released γ-phosphate [6]. The function of phosphorylation performed by PKs is a critical mechanism to regulate various cellular functions, including cell cycle regulation, growth, signaling, apoptosis, etc. Modulations in kinase activity can alter standard cellular machinery in many forms. Moreover, dysregulated protein kinases are a hallmark associated with cancer onset, development and metastasis [7]. PKs, a significant part of various signaling pathways, show overexpression and contribute to the up-regulation of several oncogenic pathways. Design and development of potent inhibitors against kinases has emerged as an exciting domain in cancer therapeutics [8,9]. In the past few decades, PKs have gained attention as a potential target in cancer therapeutics, metabolic syndromes, neurodegeneration and many other diseases [[10], [11], [12]]. Various PKs such as MAP, tyrosine, and cell-cycle kinases have been studied extensively for their role in various disorders and have FDA-approved inhibitors against them. Various other small molecule inhibitors against PKs are in different phases of clinical trials [[13], [14], [15]].

Energy metabolism is an essential cellular process for efficient energy generation for the proper functioning of human machinery. Various proteins form a complex to govern these critical processes. PDHC is one such complex associated with glucose homeostasis and mammalian energy production. The complex connects cytosolic glycolysis with the citric acid cycle. The multi-subunit protein complex PDHC is regulated through a schematic series of phosphorylation and de-phosphorylation reactions by pyruvate dehydrogenase complex [16]. The coordination between the pyruvate dehydrogenase kinases (PDKs) and the phosphatases ensures efficient functioning of the complex. PDKs reversibly phosphorylate PDHC at specific serine residues of the E1α subunit, inhibiting the complex [17]. Pyruvate dehydrogenase kinases (PDK3) binds most efficiently to the PDHC, majorly at the L2-domain among all the isoforms of the kinase [18]. The association of PDK3 with the complex inactivates the complex and is associated with various cancers [19]. PDK3 is an important enzyme, primarily involved in the metabolic reprogramming of cancer cells. Its central role in orchestrating the cancer metabolic switch involves the inhibition of pyruvate catabolism within the tricarboxylic acid (TCA) cycle. This regulatory function is particularly significant in the context of cancer cell progression, making PDK3 as a promising drug target for the development of effective therapeutic interventions against diverse cancer types [20].

PDK3 is overexpressed in the presence of various factors, including hypoxia-induced factor-1α (HIF-1α) which is responsible for uncontrolled transcription [21]. The overexpression of the PDKs results in blockage of the mitochondrial respiration machinery and is accounted for by the changes in energy production roles [22]. PDK3 emerges as a key player in this metabolic reprogramming, as its activity contributes to the preferential utilization of glycolytic intermediates and suppression of oxidative phosphorylation [23,24]. By inhibiting pyruvate entry into the TCA cycle, PDK3 supports the Warburg effect and contributes to maintaining an environment conducive to cancer cell survival and proliferation. This metabolic adaptation is a hallmark of many cancer types and is associated with increased aggressiveness and resistance to conventional therapies. Therefore, targeting PDK3 holds immense therapeutic potential. Inhibiting PDK3 activity opens up new avenues for developing innovative therapeutics tailored to combat the diverse landscape of cancer biology.

In the last few years, an increased interest has shifted towards nature as a reservoir of medical treatments. Plant-derived chemical entities have shown their effect as a potent anti-cancer agent with minimal side and therapeutic effects [[25], [26], [27], [28], [29]]. Phytochemicals have considerable variations in structural and chemical entities and have been used for ages for various ailments [30]. Phytochemicals include polyphenols, alkaloids, volatile oils and many other chemical entities with potent anti-cancer properties [31,32]. Many have been approved as an anti-cancer agent [33,34]. The consumption of plant-based products is recommended not only for their numerous health benefits and nutritional value but also for their medicinal properties. Many plant-derived compounds have established roles as potent anti-cancer agents, with over 60 % of known plants being utilized in pharmaceutical research without causing significant side effects. Thymol, a colourless monoterpene phenol, is chemically classified as 2-isopropyl-5-methylphenol and is an essential dietary constituent of thyme. Traditionally, the plant has shown various bioactive properties, including anti-tumor activities [35].

In the current report, the role of thymol as an anti-cancer agent has been established by showing its inhibitory effect against PDK3. PDK3 has been studied previously for its anticancer targeting by various natural compounds [20,36]. Initially, molecular docking studies were carried out to evaluate the interactions between thymol and PDK3. Further, a detailed molecular dynamics (MD) simulation study was conducted for 100 ns, computing all the significant parameters for protein-ligand interactions [36,37]. Changes in secondary structure after ligand binding over time were also analyzed, followed by free binding energy analysis to estimate various components of energies involved in the binding. Following in silico experiments, the ligand's effect on the protein's structure and function was analyzed by kinase inhibition and fluorescence quenching assays. Our findings confirm that thymol interacts with PDK3 with distinct binding efficiencies. Thus, it could be further assessed for potential therapeutic applications after clinical validation processes.