Structure Report for: 6R8P

Atkinson, B.N., Steadman, D., Zhao, Y., Sipthorp, J., Vecchia, L., Ruza, R.R., Jegnathan, F., Lines, G., Frew, S., Monaghan, A., Kjaer, S., Bictash, M., Jones, Y., Fish, P.V.

Title: Structural Analysis and Development of Notum Fragment Screening Hits
Zhao Y, Mahy W, Willis NJ, Woodward HL, Steadman D, Bayle ED, Atkinson BN, Sipthorp J, Vecchia L and Jones EY <11 more author(s)> Zhao Y, Mahy W, Willis NJ, Woodward HL, Steadman D, Bayle ED, Atkinson BN, Sipthorp J, Vecchia L, Ruza RR, Harlos K, Jeganathan F, Constantinou S, Costa A, Kjaer S, Bictash M, Salinas PC, Whiting P, Vincent JP, Fish PV, Jones EY (- 11)
Ref: ACS Chem Neurosci, 13:2060, 2022 : PubMed
Abstract


ESTHER: Zhao_2022_ACS.Chem.Neurosci_13_2060
PubMedSearch: Zhao 2022 ACS.Chem.Neurosci 13 2060
PubMedID: 35731924
Gene_locus related to this paper: human-NOTUM
Inhibitor(s) related to this paper: CHEMBL57478, ARUK3001043, Fragment-823, Fragment-828, Fragment-810, Fragment-872, Fragment-863, Fragment-791, Fragment-772, Fragment-784, Fragment-792, Fragment-705, Fragment-722, Fragment-714, Fragment-658, Fragment-690, Fragment-923, Fragment-924, Fragment-900, Fragment-916, Fragment-934, Fragment-955, Fragment-927, ARUK3000223, Fragment-886, Fragment-067, Fragment-074, Fragment-077, Fragment-065, Fragment-154, Fragment-159, Felbinac, Fragment-174, Fragment-173, Fragment-110, Sulfapyridine, Fragment-147, Fragment-297, Fragment-290, Fragment-201, Fragment-210, Fragment-283, Fragment-282, Fragment-277, Fragment-276, Fragment-197, Fragment-193, Fragment-199, Fragment-588, Fragment-609, Fragment-634, Fragment-646, Fragment-830, 2-N-pyridin-2-ylbenzene-1,2-diamine, (4-fluoroanilino)thiourea, Fragment-063-notum-screen, Fragment-064-notum-screen, Fragment-049-notum-screen, SCHEMBL21776992, 4F-329S, N-[2-(5-fluoro-1H-indol-3-yl)ethyl]acetamide, JVB, CHEMBL4539054, ARUK3001185

Abstract

The Wnt signaling suppressor Notum is a promising target for osteoporosis, Alzheimer's disease, and colorectal cancers. To develop novel Notum inhibitors, we used an X-ray crystallographic fragment screen with the Diamond-SGC Poised Library (DSPL) and identified 59 fragment hits from the analysis of 768 data sets. Fifty-eight of the hits were found bound at the enzyme catalytic pocket with potencies ranging from 0.5 to >1000 microM. Analysis of the fragments' diverse binding modes, enzymatic inhibitory activities, and chemical properties led to the selection of six hits for optimization, and five of these resulted in improved Notum inhibitory potencies. One hit, 1-phenyl-1,2,3-triazole 7, and its related cluster members, have shown promising lead-like properties. These became the focus of our fragment development activities, resulting in compound 7d with IC(50) 0.0067 microM. The large number of Notum fragment structures and their initial optimization provided an important basis for further Notum inhibitor development.



        

Title: Discovery of 2-phenoxyacetamides as inhibitors of the Wnt-depalmitoleating enzyme NOTUM from an X-ray fragment screen
Atkinson BN, Steadman D, Zhao YG, Sipthorp J, Vecchia L, Ruza RR, Jeganathan F, Lines G, Frew S and Jones EY <6 more author(s)> Atkinson BN, Steadman D, Zhao YG, Sipthorp J, Vecchia L, Ruza RR, Jeganathan F, Lines G, Frew S, Monaghan A, Kjaer S, Bictash M, Jones Y, Fish PV, Zhao Y, Jones EY (- 6)
Ref: Medchemcomm, 10:1361, 2019 : PubMed
Abstract


ESTHER: Atkinson_2019_Medchemcomm_10_1361
PubMedSearch: Atkinson 2019 Medchemcomm 10 1361
PubMedID: 31534655
Gene_locus related to this paper: human-NOTUM
Inhibitor(s) related to this paper: Isoquinoline-45-JV8, Benzotriazole-39-JV5, JVB, CHEMBL4539054

Abstract

NOTUM is a carboxylesterase that has been shown to act by mediating the O-depalmitoleoylation of Wnt proteins resulting in suppression of Wnt signaling. Here, we describe the development of NOTUM inhibitors that restore Wnt signaling for use in in vitro disease models where NOTUM over activity is an underlying cause. A crystallographic fragment screen with NOTUM identified 2-phenoxyacetamide 3 as binding in the palmitoleate pocket with modest inhibition activity (IC50 33 muM). Optimization of hit 3 by SAR studies guided by SBDD identified indazole 38 (IC50 0.032 muM) and isoquinoline 45 (IC50 0.085 muM) as potent inhibitors of NOTUM. The binding of 45 to NOTUM was rationalized through an X-ray co-crystal structure determination which showed a flipped binding orientation compared to 3. However, it was not possible to combine NOTUM inhibition activity with metabolic stability as the majority of the compounds tested were rapidly metabolized in an NADPH-independent manner.