Discovery of Non-Covalent Inhibitors for SARS-CoV-2 PLpro: Integrating Virtual Screening, Synthesis, and Experimental Validation

Bruna K P Sousa; Melina Mottin; Donald Seanego; Christopher D Jurisch; Beatriz S A Rodrigues; Verônica L S da Silva; Milene Aparecida Andrade; Gilberto S Morais; Diogo F Boerin; Thamires Q Froes; Flávia Nader Motta; M Cristina Nonato; Izabela D M Bastos; Kelly Chibale; Richard K Gessner; Carolina Horta Andrade

doi:10.1021/acsmedchemlett.4c00420

Discovery of Non-Covalent Inhibitors for SARS-CoV-2 PLpro: Integrating Virtual Screening, Synthesis, and Experimental Validation

ACS Med Chem Lett. 2024 Dec 2;15(12):2140-2149. doi: 10.1021/acsmedchemlett.4c00420. eCollection 2024 Dec 12.

Authors

Bruna K P Sousa^{1

2}, Melina Mottin^{1

2

3}, Donald Seanego⁴, Christopher D Jurisch⁴, Beatriz S A Rodrigues³, Verônica L S da Silva³, Milene Aparecida Andrade³, Gilberto S Morais³, Diogo F Boerin^{1

5}, Thamires Q Froes^{1

5}, Flávia Nader Motta^{3

6}, M Cristina Nonato^{1

5}, Izabela D M Bastos³, Kelly Chibale^{4

7

8}, Richard K Gessner⁴, Carolina Horta Andrade^{1

2

9}

Affiliations

¹ Center for the Research and Advancement in Fragments and Molecular Targets (CRAFT), Faculdade de Ciências Farmaceuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo 05508-070, Brazil.
² Laboratory for Molecular Modeling and Drug Design (LabMol), Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, Goiás 74690-900, Brazil.
³ Pathogen-Host Interface Laboratory, Department of Cell Biology, University of Brasilia, Brasilia 73345-010, Brazil.
⁴ Holistic Drug Discovery and Development Centre (H3D), University of Cape Town, Cape Town 7701, South Africa.
⁵ Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo 05508-070, Brazil.
⁶ Faculdade de Ceilândia, Universidade de Brasília, Brasília, Distrito Federal 73345-010, Brazil.
⁷ South African Medical Research Council Drug Discovery and Development Research Unit, University of Cape Town, Cape Town 7701, South Africa.
⁸ Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7701, South Africa.
⁹ Center for Excellence in Artificial Intelligence (CEIA), Instituto de Informática, Universidade Federal de Goiás, Goiânia, Goiás 74690-900, Brazil.

Abstract

The SARS-CoV-2 pandemic has significantly challenged global public health, highlighting the need for effective therapeutic options. This study focuses on the papain-like protease (PLpro) of SARS-CoV-2, which is a critical enzyme for viral polyprotein processing, maturation, and immune evasion. We employed a combined approach that began with computational models in a virtual screening campaign, prioritizing compounds from our in-house chemical library against PLpro. Out of 81 virtual hits evaluated through enzymatic and biophysical assays, we identified a modest inhibitor featuring a naphthyridine core with an IC₅₀ of 73.61 μM and a K _i of 22 μM. Expanding our exploration, we synthesized and assessed 30 naphthyridine analogues, three of which emerged as promising noncovalent, nonpeptidomimetic inhibitors with IC₅₀ values between 15.06 and 51.81 μM. Furthermore, in vitro ADMET assays revealed these compounds to possess moderate aqueous solubility, low cytotoxicity, and high microsomal stability, making them excellent candidates for further development targeting SARS-CoV-2 PLpro.