Sahoo Sthitaprajna, Lee Hak-Kyo, Shin Donghyun
Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, Republic of Korea.
Department of Animal Biotechnology, Jeonbuk National University, Jeonju, Republic of Korea.
PLoS One. 2025 Apr 21;20(4):e0321079. doi: 10.1371/journal.pone.0321079. eCollection 2025.
The viral replication of foot-and-mouth disease virus (FMDV) and other picornaviruses primarily depends on the successful processing of a polyprotein precursor by the enzyme 3C protease (3Cpro) at specific sites. The crucial role of 3Cpro in viral replication and pathogenesis makes it a potential target for developing novel therapeutics against foot-and-mouth disease. The β-ribbon region (residues 138-150) containing the active site residues (C142) in 3Cpro is found to be conserved and contributes significantly to substrate specificity. Moreover, experimental reports suggest that mutations at position 142, particularly C142S and C142L, exhibit different functional activities. However, the intrinsic dynamics and conformational changes induced by active-site mutations of 3Cpro remain unclear, limiting the development of novel inhibitors of 3C protease. Accordingly, we carried out molecular dynamics (MD) simulations with multiple replicates for both the WT and mutants of 3Cpro. The observed results suggest that the C142S mutant induces substantial structural transitions compared to the WT and C142L. In contrast, the essential dynamics of the mutants significantly varied from those of the WT 3Cpro. Moreover, cross-correlation analysis revealed a similar pattern of anti-correlation between the amino acid residues of the WT and C142L mutant complexes. Analysis of the betweenness centrality of the WT and the mutants from the residue interaction networks revealed common residues for intra-residual signal propagation. The results from our study suggest that the active site mutant C142S may induce conformational changes, which can cause the β-ribbon region to bend towards the catalytic pocket and inhibit the enzymatic activity. C142L substitution may also alter the β-ribbon region conformation, which may impact the substrate binding process during proteolysis, as reported in previous studies. These results can provide a better understanding of the conformational dynamic behavior of 3Cpro active-site mutants and may assist in developing potential inhibitors against foot-and-mouth disease.
口蹄疫病毒（FMDV）和其他小RNA病毒的病毒复制主要取决于3C蛋白酶（3Cpro）在特定位点对多蛋白前体的成功加工。3Cpro在病毒复制和发病机制中的关键作用使其成为开发抗口蹄疫新型疗法的潜在靶点。发现3Cpro中包含活性位点残基（C142）的β-带状区域（残基138 - 150）是保守的，并且对底物特异性有显著贡献。此外，实验报告表明，142位的突变，特别是C142S和C142L，表现出不同的功能活性。然而，3Cpro活性位点突变诱导的内在动力学和构象变化仍不清楚，这限制了3C蛋白酶新型抑制剂的开发。因此，我们对3Cpro的野生型和突变体进行了多次重复的分子动力学（MD）模拟。观察结果表明，与野生型和C142L相比，C142S突变体诱导了大量的结构转变。相比之下，突变体的基本动力学与野生型3Cpro的基本动力学有显著差异。此外，交叉相关分析揭示了野生型和C142L突变体复合物氨基酸残基之间类似的反相关模式。从残基相互作用网络分析野生型和突变体之间的介数中心性，揭示了残基内信号传播的共同残基。我们的研究结果表明，活性位点突变体C142S可能诱导构象变化，这可能导致β-带状区域向催化口袋弯曲并抑制酶活性。如先前研究报道，C142L取代也可能改变β-带状区域构象，这可能影响蛋白水解过程中的底物结合过程。这些结果可以更好地理解3Cpro活性位点突变体的构象动态行为，并可能有助于开发抗口蹄疫的潜在抑制剂。
