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The efficiency of this process is unclear, at least partly because there is no random background for optimization against which to compare. Such a random background might emerge from synthetically accessible but otherwise systematic random small substitutions across starting ligands, measuring likelihood of achieving a substantial improvement in affinity\/potency or other property by any single perturbation. Recent literature and ligand-affinity\/potency databases suggest that perhaps 10% of analogs with minor modifications improve upon a parent\u2019s potency substantially (by \u226510-fold), but this number is clouded by reporting bias, intentional improvement, and inter-group reproducibility. To begin to establish a background expectation for ligand optimization, we comprehensively and systematically modified 18 lead molecules across six targets with single atom changes; 257 compounds were synthesized. Unexpectedly, 11.2% of these random small perturbation analogs improved potency by \u226510-fold over their parents. Conversely, these more potent analogs typically had worse\n                  <jats:italic>in vitro<\/jats:italic>\n                  pharmacokinetics (e.g. reduced metabolic stability, lower plasma free fraction). While it was possible to find analogs 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.\n                <\/jats:p>","DOI":"10.64898\/2026.05.10.724162","type":"posted-content","created":{"date-parts":[[2026,5,14]],"date-time":"2026-05-14T00:05:14Z","timestamp":1778717114000},"source":"Crossref","is-referenced-by-count":0,"title":["Toward a Random Background for Ligand Optimization"],"prefix":"10.64898","author":[{"given":"Xinyu","family":"Xu","sequence":"first","affiliation":[{"name":"Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Olivier","family":"Mailhot","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Galen J.","family":"Correy","sequence":"additional","affiliation":[{"name":"Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"XP","family":"Huang","sequence":"additional","affiliation":[{"name":"Department of Pharmacology, NIMH Psychoactive Drug Screening Program, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joao","family":"Braz","sequence":"additional","affiliation":[{"name":"Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Da","family":"Shi","sequence":"additional","affiliation":[{"name":"Schr\u00f6dinger Inc, San Diego, CA, USA; 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