Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia.
International Laboratory for Supercomputer Atomistic Modelling and Multi-Scale Analysis, National Research University Higher School of Economics, 101000 Moscow, Russia.
Int J Mol Sci. 2022 May 3;23(9):5091. doi: 10.3390/ijms23095091.
Lipid modification of viral proteins with fatty acids of different lengths (S-acylation) is crucial for virus pathogenesis. The reaction is catalyzed by members of the DHHC family and proceeds in two steps: the autoacylation is followed by the acyl chain transfer onto protein substrates. The crystal structure of human DHHC20 (hDHHC20), an enzyme involved in the acylation of S-protein of SARS-CoV-2, revealed that the acyl chain may be inserted into a hydrophobic cavity formed by four transmembrane (TM) α-helices. To test this model, we used molecular dynamics of membrane-embedded hDHHC20 and its mutants either in the absence or presence of various acyl-CoAs. We found that among a range of acyl chain lengths probed only C16 adopts a conformation suitable for hDHHC20 autoacylation. This specificity is altered if the small or bulky residues at the cavity's ceiling are exchanged, e.g., the V185G mutant obtains strong preferences for binding C18. Surprisingly, an unusual hydrophilic ridge was found in TM helix 4 of hDHHC20, and the responsive hydrophilic patch supposedly involved in association was found in the 3D model of the S-protein TM-domain trimer. Finally, the exchange of critical Thr and Ser residues in the spike led to a significant decrease in its S-acylation. Our data allow further development of peptide/lipid-based inhibitors of hDHHC20 that might impede replication of Corona- and other enveloped viruses.
脂肪酸对病毒蛋白的脂质修饰（S-酰化）对于病毒发病机制至关重要。该反应由 DHHC 家族成员催化，并分两步进行：自动酰化后，酰基链转移到蛋白底物上。参与 SARS-CoV-2 S 蛋白酰化的人类 DHHC20（hDHHC20）酶的晶体结构表明，酰基链可能插入由四个跨膜（TM）α-螺旋形成的疏水性腔中。为了验证该模型，我们使用了膜嵌入 hDHHC20 及其突变体的分子动力学，无论是否存在各种酰基辅酶 A。我们发现，在所探测的一系列酰链长度中，只有 C16 采用适合 hDHHC20 自动酰化的构象。如果腔顶的小或大残基被交换，这种特异性会改变，例如，V185G 突变体对 C18 的结合具有强烈的偏好。令人惊讶的是，在 hDHHC20 的 TM 螺旋 4 中发现了一个不寻常的亲水脊，并且在 S 蛋白 TM 结构域三聚体的 3D 模型中发现了与该亲水脊响应的关联亲水斑。最后，在刺突中交换关键的 Thr 和 Ser 残基会导致 S-酰化显著减少。我们的数据允许进一步开发基于肽/脂质的 hDHHC20 抑制剂，这可能会阻碍 Corona 和其他包膜病毒的复制。
