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Abstract The Papain-like protease (PLpro) is a domain of a multi-functional, non-structural protein 3 of coronaviruses. PLpro cleaves viral polyproteins and posttranslational conjugates with poly-ubiquitin and protective ISG15, composed of two ubiquitin-like (UBL) domains. Across coronaviruses, PLpro showed divergent selectivity for recognition and cleavage of posttranslational conjugates despite sequence conservation. We show that SARS-CoV-2 PLpro binds human ISG15 and K48-linked di-ubiquitin (K48-Ub₂) with nanomolar affinity and detect alternate weaker-binding modes. Crystal structures of untethered PLpro complexes with ISG15 and K48-Ub₂combined with solution NMR and cross-linking mass spectrometry revealed how the two domains of ISG15 or K48-Ub₂are differently utilized in interactions with PLpro. Analysis of protein interface energetics predicted differential binding stabilities of the two UBL/Ub domains that were validated experimentally. We emphasize how substrate recognition can be tuned to cleave specifically ISG15 or K48-Ub₂modifications while retaining capacity to cleave mono-Ub conjugates. These results highlight alternative druggable surfaces that would inhibit PLpro function. 

Abstract We report that the direct macrocyclization of naphthalene monomers bearing ethyl ester functional groups delivers prism[5]arene derivatives, which can be deprotected to yield water‐soluble prism[5]arenes (H1andH3).¹H NMR spectroscopy showed that dicationic guests bind with the hydrophobic cores buried inside the anisotropic magnetically shielding cavity. Isothermal titration calorimetry measurements showed thatH1andH3are high‐affinity hosts in PBS‐buffered water with K_avalues exceeding 10⁹ M⁻¹for a select guest. The complexation events are driven by the non‐classical hydrophobic effect, CH⋅⋅⋅π interactions, and electrostatic interactions. HostH1displays somewhat higher affinity toward a common guest than pillar[6]arene bearing carboxylic acid functional groups but is significantly less potent than pillar[6]arene bearing sulfate groups.H1andH3should be considered alongside other high affinity hosts for a variety of chemical and biological applications.