Cancer development and progression are based on the dysregulated function of the kinases namely tyrosine and serine/threonine [1,2]. PIM kinases (pro viral insertion site for Moloney Murine leukemia virus) are the members of serine/threonine kinases in the CAMK (calmodulin dependent protein kinases) family with three isoforms, namely PIM-1, PIM-2 and PIM-3 [3]. These isoforms are distinctly homologous to each other, PIM-2 showed 53% sequence similarity with PIM-1 [4]. PIM kinases were predominantly incriminated in the development of human prostate carcinoma evidenced by the DNA microarray analysis which divulged the overexertion in human prostate tumor and its articulation harmonized with the clinical denouement [5]. PIM kinases demonstrate numerous roles in cancer namely metabolism, survival, metastasis and therapeutic resistance to the available therapy [6,7]. Signaling of PIM kinase is fundamentally regulated on the basis of protein stabilization and gene transcription that is primarily based on JAK/STAT signaling. The signaling is initiated by the binding of growth factors to the receptors that activates JAK which generates the site for binding of STAT. STAT binds to the ISFR/GAS sequence located on the PIM-1 gene that synthesizes PIM protein. Further, PIM phosphorylates numerous cellular proteins namely CDC25A/C, MYC, CXCR4 authorized for cell survival, cell growth and progression. The dysregulation in the kinase function i.e., hyper phosphorylation leads to cancer [8,9].

The crystal structure of PIM kinases is peculiar from other kinases that are defined by the presence of additional Pro123 in the hinge region that is inadequate in developing hydrogen bond with ATP due to absence of the carbonyl functionality. This feature of PIM is essential for its exploration to design novel molecules. Based on the fact that till date there is no drug in the market targeting PIM kinase and due to this fact, PIM kinases are in limelight for the discovery and development of novel antitumor agents as inhibitors of PIM kinases [10]. Numerous PIM kinase inhibitors have been documented since decades from which none of them have cleared the clinical trials pipeline due to the toxicities [11,12].

A scaffold-hopping strategy was employed to design and develop novel analogs based on the previously documented tetrahydrobenzothieno-4-pyrimidinone scaffold, which demonstrated promising PIM kinase inhibitory activity but did not advance to clinical trials. This study focuses on the systematic design of tetrahydrobenzothieno-4-pyrimidine amides, leveraging pharmacophore modelling, python/RdKit enumerator tool, machine learning modelling, molecular docking and molecular dynamics simulations. The target compound was identified and its analogs were designed and docked with PIM-1 kinase to evaluate their binding interactions. Furthermore, molecular dynamics simulations were conducted to assess the stability of ligand binding within the active site. The synthesized compounds will be tested for their anti-proliferative effects on PC3, A549 and HT29 cancer cell lines and subsequently analyzed in a PIM kinase enzyme inhibition assay to identify promising lead candidates.