The papain-like protease (PL^pro) is vital for the replication of coronaviruses (CoVs), as well as for escaping innate-immune responses of the host. Hence, it has emerged as an attractive antiviral drug-target. In this study, computational approaches were employed, mainly the structure-based virtual screening coupled with all-atom molecular dynamics (MD) simulations to computationally identify specific inhibitors of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) PL^pro, which can be further developed as potential pan-PL^pro based broad-spectrum antiviral drugs. The sequence, structure, and functional conserveness of most deadly human CoVs PL^pro were explored, and it was revealed that functionally important catalytic triad residues are well conserved among SARS-CoV, SARS-CoV-2, and middle east respiratory syndrome coronavirus (MERS-CoV). The subsequent screening of a focused protease inhibitors database composed of ∼7,000 compounds resulted in the identification of three candidate compounds, ADM_13083841, LMG_15521745, and SYN_15517940. These three compounds established conserved interactions which were further explored through MD simulations, free energy calculations, and residual energy contribution estimated by MM-PB(GB)SA method. All these compounds showed stable conformation and interacted well with the active residues of SARS-CoV-2 PL^pro, and showed consistent interaction profile with SARS-CoV PL^pro and MERS-CoV PL^pro as well. Conclusively, the reported SARS-CoV-2 PL^pro specific compounds could serve as seeds for developing potent pan-PL^pro based broad-spectrum antiviral drugs against deadly human coronaviruses. Moreover, the presented information related to binding site residual energy contribution could lead to further optimization of these compounds.

类木瓜蛋白酶 (PL ^pro ) 对于冠状病毒 (CoV) 的复制以及逃避宿主的先天免疫反应至关重要。因此，它已成为一个有吸引力的抗病毒药物靶点。在这项研究中，采用了计算方法，主要是基于结构的虚拟筛选与全原子分子动力学（MD）模拟相结合，以计算方式识别严重急性呼吸综合征冠状病毒2（SARS-CoV-2）PL pro的特异性抑制剂^，其中可以进一步开发为潜在的基于泛PL ^pro的广谱抗病毒药物。^{对最致命的人类冠状病毒 PL pro}的序列、结构和功能保守性进行了探索，结果表明，功能重要的催化三联体残基在 SARS-CoV、SARS-CoV-2 和中东呼吸综合征冠状病毒 (MERS) 中高度保守。 -冠状病毒）。随后对由约 7,000 种化合物组成的重点蛋白酶抑制剂数据库进行筛选，鉴定出三种候选化合物：ADM_13083841、LMG_15521745 和 SYN_15517940。这三种化合物建立了保守的相互作用，并通过 MD 模拟、自由能计算和 MM-PB(GB)SA 方法估计的残余能量贡献进一步探讨了这些相互作用。^{所有这些化合物均表现出稳定的构象，并与 SARS-CoV-2 PL pro}的活性残基具有良好的相互作用，并且与 SARS-CoV PL ^pro和 MERS-CoV PL ^pro也表现出一致的相互作用特征。总之，所报告的 SARS-CoV-2 PL ^pro特异性化合物可以作为开发基于泛 PL ^{pro 的}有效广谱抗病毒药物的种子，以对抗致命的人类冠状病毒。此外，所提供的与结合位点残余能量贡献相关的信息可能导致这些化合物的进一步优化。