在当前研究中，我们采用了结构信息学和分子模拟方法来改良OmoMyc，一种具有c-Myc负性优势的蛋白质，以设计能够中断肾癌中c-MYC-MAX复合物的新型突变体。在总共472个突变中，只有六个突变体A61Q、Q64E、Q64K、N77R、Q64E-N77R和Q64K-N77R被报道增加了结合亲和力，并被用于进一步的蛋白质-蛋白质对接分析。对接结果显示，预测的突变体不仅提高了OmoMyc的功能性，还增加了每个复合物中的vdW和静电能量，通过建立额外的氢键、盐桥和非键接触，进一步增强了工程化的OmoMyc的结合。分子模拟揭示了突变复合物与野生型OmoMyc相比具有更稳定的行为，但在结构上报告了DNA结合结构域（DBD）区域、环区域的扰动以及C末端结构域（CTD）的轻微偏差。此外，氢键和结合自由能结果进一步验证了我们预测的OmoMyc突变体的良好活性。结合自由能（TBE）的结果显示，每个复合物的TBE分别为-87.88±0.16kcal/mol（WT OmoMyc-MAX), -91.89±0.21kcal/mol（A61Q OmoMyc-MAX), -91.55±0.20kcal/mol（Q64E OmoMyc-MAX), -95.17±0.24kcal/mol（Q64K OmoMyc-MAX), -96.49±0.22kcal/mol（N77R OmoMyc-MAX), -97.76±0.22kcal/mol（Q64E-N77R OmoMyc-MAX), 和-95.31±0.20kcal/mol（Q64K-N77R OmoMyc-MAX)。结合自由能的结果表明，这些突变体可以更迅速地竞争性地抑制c-Myc-MAX复合物。此外，内部运动和能量景观也发生了改变。这些发现为OmoMyc突变体作为治疗癌症（尤其是肾癌）候选药物的潜力提供了重要的见解，并为开发更有效的临床版本的OmoMyc铺平了道路。版权所有© 2023 Elsevier Ltd. 保留所有权利。

In the current study, we employed, structural informatics, and molecular simulation-based methods to engineer OmoMyc, a c-Myc dominant negative protein, to design novel mutants that could abrogate the c-MYC-MAX complex in Renal Carcinoma (RC). Among the total 472 mutations, only six mutations A61Q, Q64E, Q64K, N77R, Q64E-N77R, and Q64K-N77R were reported to increase the binding affinity and subjected to subsequent analysis such as protein-protein docking. The docking results revealed that the predicted mutants improve the functionality of the OmoMyc by not only increasing the binding affinity but also vdW and electrostatic energy in each complex that consequently increase the binding of the engineered OmoMyc by establishing extra hydrogen bonds, salt-bridges, and non-bonded contacts. Molecular simulation revealed a more stable behavior by the mutant complexes in contrast to the native OmoMyc however structural perturbations were reported in the regions, DBD (DNA-binding domain), loop region, and minor deviations at CTD (C terminal domain). Moreover, the hydrogen bonding and binding free energy results further validated the promising activity of our predicted mutants of OmoMyc. The results for TBE (total binding energy) revealed that the for each complex the TBE was calculated to be -87.88 ± 0.16 kcal/mol (WT OmoMyc-MAX), -91.89 ± 0.21 kcal/mol (A61Q OmoMyc-MAX), -91.55 ± 0.20 kcal/mol (Q64E OmoMyc-MAX), -95.17 ± 0.24 kcal/mol (Q64K OmoMyc-MAX), -96.49 ± 0.22 kcal/mol (N77R OmoMyc-MAX), -97.76 ± 0.22 kcal/mol (Q64E-N77R OmoMyc-MAX), and -95.31 ± 0.20 kcal/mol (Q64K-N77R OmoMyc-MAX) respectively. The results for TBE revealed promising results that allow the mutants to competitively inhibit the c-Myc-MAX complex more swiftly. Additionally, the internal motion and energy landscape were altered. These findings provide important insights into the potential of the mutants of OmoMyc as a therapeutic candidate for cancer treatment, particularly renal carcinoma, and could pave the way for the development of more effective clinical versions of OmoMyc.Copyright © 2023 Elsevier Ltd. All rights reserved.