6UCG

Retinoic acid receptor-related orphan receptor (ROR) gamma in complex with allosteric compound 28

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.87 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 

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Literature

Discovery ofN-(Indazol-3-yl)piperidine-4-carboxylic Acids as ROR gamma t Allosteric Inhibitors for Autoimmune Diseases.

Zhang, H., Lapointe, B.T., Anthony, N., Azevedo, R., Cals, J., Correll, C.C., Daniels, M., Deshmukh, S., van Eenenaam, H., Ferguson, H., Hegde, L.G., Karstens, W.J., Maclean, J., Miller, J.R., Moy, L.Y., Simov, V., Nagpal, S., Oubrie, A., Palte, R.L., Parthasarathy, G., Sciammetta, N., van der Stelt, M., Woodhouse, J.D., Trotter, B.W., Barr, K.

(2020) ACS Med Chem Lett 11: 114-119

  • DOI: https://doi.org/10.1021/acsmedchemlett.9b00431
  • Primary Citation of Related Structures:  
    6UCG

  • PubMed Abstract: 

    • The clinical success of anti-IL-17 monoclonal antibodies (i.e., Cosentyx and Taltz) has validated Th17 pathway modulation for the treatment of autoimmune diseases. The nuclear hormone receptor RORγt is a master regulator of Th17 cells and affects the production of a host of cytokines, including IL-17A, IL-17F, IL-22, IL-26, and GM-CSF ...

    The clinical success of anti-IL-17 monoclonal antibodies (i.e., Cosentyx and Taltz) has validated Th17 pathway modulation for the treatment of autoimmune diseases. The nuclear hormone receptor RORγt is a master regulator of Th17 cells and affects the production of a host of cytokines, including IL-17A, IL-17F, IL-22, IL-26, and GM-CSF. Substantial interest has been spurred across both academia and industry to seek small molecules suitable for RORγt inhibition. A variety of RORγt inhibitors have been reported in the past few years, the majority of which are orthosteric binders. Here we disclose the discovery and optimization of a class of inhibitors, which bind differently to an allosteric binding pocket. Starting from a weakly active hit 1 , a tool compound 14 was quickly identified that demonstrated superior potency, selectivity, and off-target profile. Further optimization focused on improving metabolic stability. Replacing the benzoic acid moiety with piperidinyl carboxylate, modifying the 4-aza-indazole core in 14 to 4-F-indazole, and incorporating a key hydroxyl group led to the discovery of 25 , which possesses exquisite potency and selectivity, as well as an improved pharmacokinetic profile suitable for oral dosing.

    Organizational Affiliation: 

    Medicinal Chemistry, Discovery Biology, Discovery Process Chemistry, Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Discovery Pharmaceutical Sciences, Modeling & Informatics, In Vitro and In Vivo Pharmacology, and Computational and Structural Chemistry, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear receptor ROR-gamma241Homo sapiensMutation(s): 0 
Gene Names: RORC, NR1F3, RORG, RZRG
UniProt & NIH Common Fund Data Resources
Find proteins for P51449 (Homo sapiens)
Explore P51449 
Go to UniProtKB:  P51449
PHAROS:  P51449
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51449
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Q3Y (Subject of Investigation/LOI)
Query on Q3Y
Download Ideal Coordinates CCD File 
B [auth A](3S,4R)-1-[1-(2-chloro-6-cyclopropylbenzene-1-carbonyl)-4-fluoro-1H-indazol-3-yl]-3-hydroxypiperidine-4-carboxylic acid
C23 H21 Cl F N3 O4
IBIKHMZPHNKTHM-RDTXWAMCSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
Q3Y BindingDB:  6UCG IC50: min: 1, max: 49 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.87 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.44α = 90
b = 108.44β = 90
c = 104.32γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-04
    Type: Initial release