Targeting the Main Protease (Mpro, nsp5) by Growth of Fragment Scaffolds Exploiting Structure-Based Methodologies

Nadide Altincekic, Nathalie Jores, Frank Löhr, Chrisitan Richter, Claus Ehrhardt, Marcel J.J. Blommers, Hannes Berg, Sare Öztürk, Santosh L. Gande, Verena Linhard, Julien Orts, Marie Jose Abdi Saad, Matthias Bütikofer, Janina Kaderli, B. Göran Karlsson, Ulrika Brath, Mattias Hedenström, Gerhard Gröbner, Uwe H. Sauer, Anastassis PerrakisJulian Langer, Lucia Banci, Francesca Cantini, Marco Fragai, Deborah Grifagni, Tatjana Barthel, Jan Wollenhaupt, Manfred S. Weiss, Angus Robertson, Adriaan Bax, Sridhar Sreeramulu, Harald Schwalbe

Research output: Contribution to journalArticlepeer-review


The main protease Mpro, nsp5, of SARS-CoV-2 (SCoV2) is one of its most attractive drug targets. Here, we report primary screening data using nuclear magnetic resonance spectroscopy (NMR) of four different libraries and detailed follow-up synthesis on the promising uracil-containing fragment Z604 derived from these libraries. Z604 shows time-dependent binding. Its inhibitory effect is sensitive to reducing conditions. Starting with Z604, we synthesized and characterized 13 compounds designed by fragment growth strategies. Each compound was characterized by NMR and/or activity assays to investigate their interaction with Mpro

These investigations resulted in the four-armed compound 35b that binds directly to Mpro. 35b could be cocrystallized with Mpro revealing its noncovalent binding mode, which fills all four active site subpockets. Herein, we describe the NMR-derived fragment-to-hit pipeline and its application for the development of promising starting points for inhibitors of the main protease of SCoV2.

Original languageEnglish
JournalACS Chemical Biology
Publication statusE-pub ahead of print - 2024
Externally publishedYes


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