In Silico Investigation of BTK as a Potent Immunomodulatory Target: Exploring Novel Therapeutic Approaches for Multiple Sclerosis

Multiple sclerosis (MS) is a chronic autoimmune demyelinating disease characterized by progressive neurological impairment. Bruton’s tyrosine kinase (BTK) has emerged as a crucial therapeutic target due to its role in B-cell activation and innate immune signaling. While BTK inhibitors (BTKi) have shown promise for treating MS and inflammatory disorders, their high toxicity and off-target kinase inhibition pose challenges, particularly given that many patients experience mild symptoms. This study presents L2-a, a structurally optimized, highly selective BTKi designed to minimize drug-induced liver injury (DILI) and improve blood–brain barrier (BBB) permeability. Using scaffold hopping, the nitro-substituted aromatic scaffold was replaced with a trifluoromethyl-substituted heterocycle, significantly reducing hepatotoxicity while enhancing binding interactions with key BTK residues (CYS481, GLY480, and ASP539). L2-a also demonstrates lower CYP inhibition, reduced AMES toxicity, and improved membrane absorption, ensuring better druggability. Computational analyses, including site-directed mutation studies, molecular dynamics (MD) simulations, and quantum chemical analysis, confirmed L2-a’s high binding specificity, reduced off-target effects, and strong conformational stability across BTK variants. L2-a mitigates off-target effects through structural optimization of the BTK binding pocket, particularly at CYS481, enhancing binding specificity and reducing nonspecific interactions across BTK mutants. These findings establish L2-a as a next-generation BTKi with enhanced safety and therapeutic potential for autoimmune and inflammatory diseases, particularly MS.