Computer-Assisted Systematic Chemical-Space Mapping of a First-in-Class Peripherally Restricted α2AAR Agonist through Scaffold-Seeded Enumeration
- 1Alpherabio LLC
Abstract
CC10137 is a first-in-class peripherally restricted 2A-adrenergic receptor (2AAR) agonist with broad-spectrum analgesic efficacy and a favorable safety profile. Systematic exploration of the chemical space surrounding first-in-class leads is important for defining series boundaries and guiding continued optimization, but conventional analogue-by-analogue medicinal chemistry samples only a small fraction of the accessible structural space. Here, we used a scaffold-seeded enumeration strategy to expand the chemical space surrounding CC10137 from four SAR-informed seed compounds comprising CC10137 and three closely related structural variants. Application of predefined medicinal chemistry transformation rules in StarDrop generated a virtual library of 16,601,163 unique structures. Morgan fingerprint-based principal component analysis indicated that the library occupied a highly multidimensional structural space involving variation in scaffold substitution, peripheral functional groups, and side-chain composition. A retrospective comparison set of 43 compounds independently designed and experimentally characterized in the earlier CC10137 program represented only approximately 0.00026% of the 16.6-million-member library, yet all 43 were recovered as exact structural matches. Three compounds selected directly from the virtual library retained 2AAR binding affinity and agonist potency below 25 nM. Five representative compounds further showed significant anti-allodynic effects in the in vivo spared nerve injury model, with inhibition rates ranging from 39.3% to 55.7%. These findings support scaffold-seeded computational enumeration as a practical strategy for systematic chemical-space mapping around a first-in-class lead and for identifying additional pharmacologically active structural regions for further optimization.
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BibTeX
@misc{moore2026computerassisted,
title = {{Computer-Assisted Systematic Chemical-Space Mapping of a First-in-Class Peripherally Restricted α2AAR Agonist through Scaffold-Seeded Enumeration}},
author = {C. Moore and L. Zhu and Z. Cheng},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.16.751790},
url = {https://www.biorxiv.org/content/10.64898/2026.09.16.751790v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Computer-Assisted Systematic Chemical-Space Mapping of a First-in-Class Peripherally Restricted α2AAR Agonist through Scaffold-Seeded Enumeration
AU - C. Moore
AU - L. Zhu
AU - Z. Cheng
PY - 2026
DA - 2026/09/16
PB - bioRxiv
DO - 10.64898/2026.09.16.751790
UR - https://www.biorxiv.org/content/10.64898/2026.09.16.751790v1
AB - CC10137 is a first-in-class peripherally restricted 2A-adrenergic receptor (2AAR) agonist with broad-spectrum analgesic efficacy and a favorable safety profile. Systematic exploration of the chemical space surrounding first-in-class leads is important for defining series boundaries and guiding continued optimization, but conventional analogue-by-analogue medicinal chemistry samples only a small fraction of the accessible structural space. Here, we used a scaffold-seeded enumeration strategy to expand the chemical space surrounding CC10137 from four SAR-informed seed compounds comprising CC10137 and three closely related structural variants. Application of predefined medicinal chemistry transformation rules in StarDrop generated a virtual library of 16,601,163 unique structures. Morgan fingerprint-based principal component analysis indicated that the library occupied a highly multidimensional structural space involving variation in scaffold substitution, peripheral functional groups, and side-chain composition. A retrospective comparison set of 43 compounds independently designed and experimentally characterized in the earlier CC10137 program represented only approximately 0.00026% of the 16.6-million-member library, yet all 43 were recovered as exact structural matches. Three compounds selected directly from the virtual library retained 2AAR binding affinity and agonist potency below 25 nM. Five representative compounds further showed significant anti-allodynic effects in the in vivo spared nerve injury model, with inhibition rates ranging from 39.3% to 55.7%. These findings support scaffold-seeded computational enumeration as a practical strategy for systematic chemical-space mapping around a first-in-class lead and for identifying additional pharmacologically active structural regions for further optimization.
ER -