7IJC

PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z8929428675

This is a non-PDB format compatible entry.

Summary for 7IJC

• Entry DOI: 10.2210/pdb7ijc/pdb
• Group deposition: PanDDA analysis group deposition of SARS-CoV-2 NSP3 macrodomain ligand screen - ligands from Z5398393122 small moves analogues (G_1002350)
• Descriptor: Non-structural protein 3, DIMETHYL SULFOXIDE, (3S)-3-(pyridin-3-yl)-3-[(7H-pyrrolo[2,3-d]pyrimidine-4-carbonyl)amino]propanoic acid, ... (4 entities in total)
• Functional Keywords: macrodomain, adp-ribose, sars-cov-2, fragment-based drug discovery, viral protein
• Biological source: Severe acute respiratory syndrome coronavirus 2
• Total number of polymer chains: 2
• Total formula weight: 37058.25

Authors

Correy, G.J.,Fraser, J.S. (deposition date: 2025-07-22, release date: 2025-09-17, Last modification date: 2026-09-30)

Primary citation

Xu, X.,Mailhot, O.,Correy, G.J.,Huang, X.P.,Braz, J.M.,Shi, D.,Srinivasan, K.,Zielinski, K.,Holota, Y.,Kuziv, Y.,Iliopoulos-Tsoutsouvas, C.,Levinzon, N.D.,Doruk, Y.U.,Rachman, M.M.,Diolaiti, M.E.,Stevens, M.G.V.,Liu, F.,Holland, K.L.,Hubner, H.,Wang, J.,Wu, Y.,Ashworth, A.,Makriyannis, A.,Zhang, Y.,Moroz, Y.S.,Gmeiner, P.,Abel, R.,Manglik, A.,Basbaum, A.I.,Roth, B.L.,Fraser, J.S.,Shoichet, B.K.
Development of a random background to understand ligand optimization.
Nature, 2026

PubMed Abstract: Ligand optimization is central to drug discovery, with hundreds of analogues often designed and synthesized between an initial hit and a therapeutic candidate. The efficiency of this process is unclear, partly because there is no random background for optimization to compare against. Such a random background might emerge from systematic random small substitutions across starting ligands, measuring the likelihood of achieving a substantial improvement in affinity or potency, or other property by any single perturbation. Recent literature has suggested that perhaps 10% of analogues with minor modifications improve upon the potency of a parent by tenfold or more, but this number is clouded by reporting bias, intentional improvement and inter-group variability. To begin to establish a background expectation for ligand optimization, here we systematically modified 18 lead molecules across six targets with single-atom changes; 257 compounds were synthesized. Unexpectedly, 11.3% of these random small perturbation analogues improved potency by tenfold or more. Conversely, they typically had worse in vitro pharmacokinetics. Although it was possible to find analogues where the potency increase compensated for inferior exposure and half-life, resulting in more potent compounds in vivo, overall, a frustrated landscape for ligand optimization is revealed. This study begins to establish a background expectation for ligand potency optimization and offers a simple strategy to do so. It also begins to quantify the challenges confronting the field in moving beyond in vitro potency.

PubMed: 42749805
DOI: 10.1038/s41586-026-11013-5

Experimental method

X-RAY DIFFRACTION (1 Å)