Journal Article

Exploring the impact of deleterious missense nonsynonymous single nucleotide polymorphisms in the DRD4 gene using computational approaches

Sarker, Dipto Kumer, Ray, Pallobi, Uddin, Shaikh Jamal, Salam, Fayad Bin Abdus

2025

Overview

Dopamine receptor D4 (DRD4) plays a vital role in regulating various physiological functions, including attention, impulse control, and sleep, as well as being associated with various neurological diseases, including attention deficit hyperactivity disorder, novelty seeking, and so on. However, a comprehensive analysis of harmful nonsynonymous single nucleotide polymorphisms (nsSNPs) of the DRD4 gene and their effects remains unexplored. The aim of this study is to uncover novel damaging missense nsSNPs and their structural and functional effects on the DRD4 receptor. From the dbSNP database, we found 677 nsSNPs, and then we analyzed their functional consequences, disease associations, and effects on protein stability with fifteen in silico tools. Five variants, including L65 ICL1 P (rs1459150721), V116 3.33 D (rs761875546), I129 3.46 S (rs751467198), I156 4.46 T (rs757732258), and F201 5.47 S (rs199609858), were identified as the most deleterious mutations that were also present in the conserved region and showed lower interactions with neighboring residues. To comprehensively understand their impact, we docked agonist dopamine and antagonist nemonapride at the binding site of the receptor, followed by 200 ns molecular dynamics simulations. We identified the V116D and I129S mutations as the most damaging, followed by F201S in the dopamine-bound states. Both the V116D and I129S variants demonstrated significantly high RMSD, Rg, and SASA, and low thermodynamic stability. The F201S-dopamine complex exhibited lower compactness and higher motions, along with a significant loss of hydrogen bonds and active site interactions. By contrast, while interacting with nemonapride, the impact of the I156T and L65P mutations was highly deleterious; both showed lower stability, higher flexibility, and higher motions. Additionally, nemonapride significantly lost interactions with the active site, notably in the I156T variant. We also found the V116D-nemonapride complex as structurally damaging; however, the interaction patterns of nemonapride were less altered in the MMPBSA analysis. Overall, this study revealed five novel deleterious variants along with a comprehensive understanding of their effect in the presence of an agonist and antagonist, which could be helpful for understanding disease susceptibility, precision medicine, and developing potential drugs.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 631/114 / 631/208 / 631/45 / 631/535/1267 / Agonists / Attention deficit hyperactivity disorder / Computational Biology - methods / Dopamine / Dopamine D4 receptors / Dopamine receptor D4 / Humanities and Social Sciences / Humans / Hydrogen bonding / Impulsive behavior / Molecular Dynamics Simulation / multidisciplinary / Mutation / Mutation, Missense / Neurological diseases / NsSNPs / Polymorphism / Polymorphism, Single Nucleotide / Precision medicine / Protein Stability / Receptors, Dopamine D4 - chemistry / Receptors, Dopamine D4 - genetics / Receptors, Dopamine D4 - metabolism / Science / Science (multidisciplinary) / Single-nucleotide polymorphism / Structure-function relationships