6W50

FACTOR XIA IN COMPLEX WITH THE INHIBITOR METHYL ((10R,14S)- 14-(4-(3-CHLORO-2,6-DIFLUOROPHENYL)-6-OXO-3,6-DIHYDRO- 1(2H)-PYRIDINYL)-10-METHYL-9-OXO-8,16- DIAZATRICYCLO[13.3.1.0~2,7~]NONADECA-1(19),2,4,6,15,17- HEXAEN-5-YL)CARBAMATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of a High Affinity, Orally Bioavailable Macrocyclic FXIa Inhibitor with Antithrombotic Activity in Preclinical Species.

Yang, W.Wang, Y.Lai, A.Clark, C.G.Corte, J.R.Fang, T.Gilligan, P.J.Jeon, Y.Pabbisetty, K.B.Rampulla, R.A.Mathur, A.Kaspady, M.Neithnadka, P.R.Arumugam, A.Raju, S.Rossi, K.A.Myers Jr., J.E.Sheriff, S.Lou, Z.Zheng, J.J.Chacko, S.A.Bozarth, J.M.Wu, Y.Crain, E.J.Wong, P.C.Seiffert, D.A.Luettgen, J.M.Lam, P.Y.S.Wexler, R.R.Ewing, W.R.

(2020) J Med Chem 63: 7226-7242

  • DOI: 10.1021/acs.jmedchem.0c00464
  • Primary Citation of Related Structures:  
    6W50

  • PubMed Abstract: 
  • Oral factor XIa (FXIa) inhibitors may provide a promising new antithrombotic therapy with an improved benefit to bleeding risk profile over existing antithrombotic agents. Herein, we report application of a previously disclosed cyclic carbamate P1 linker which provided improved oral bioavailability in the imidazole-based 13-membered macrocycle to the 12-membered macrocycle ...

    Oral factor XIa (FXIa) inhibitors may provide a promising new antithrombotic therapy with an improved benefit to bleeding risk profile over existing antithrombotic agents. Herein, we report application of a previously disclosed cyclic carbamate P1 linker which provided improved oral bioavailability in the imidazole-based 13-membered macrocycle to the 12-membered macrocycle. This resulted in identification of compound 4 with desired FXIa inhibitory potency and good oral bioavailability but high in vivo clearance. Further structure-activity relationship (SAR) studies of heterocyclic core modifications to replace the imidazole core as well as various linkers to the P1 group led to the discovery of compound 6f , a potent FXIa inhibitor with selectivity against most of the relevant serine proteases. Compound 6f also demonstrated excellent pharmacokinetics (PK) profile (high oral bioavailability and low clearance) in multiple preclinical species. Compound 6f achieved robust antithrombotic efficacy in a rabbit efficacy model at doses which preserved hemostasis.


    Related Citations: 
    • Tetrahydroquinoline derivatives as potent and selective factor XIa inhibitors
      Quan, M.L., Wong, P.C., Wang, C., Woerner, F., Smallheer, J.M., Barbera, F.A., Bozarth, J.M., Brown, R.L., Harpel, M.R., Luettgen, J.M., Morin, P.E., Peterson, T., Ramamurthy, V., Rendina, A.R., Rossi, K.A., Watson, C.A., Wei, A., Zhang, G., Seiffert, D., Wexler, R.R.
      (2014) J Med Chem 57: 955
    • Phenylimidazoles as potent and selective inhibitors of coagulation factor XIa with in vivo antithrombotic activity.
      Quan, M.L., Wong, P.C., Wang, C., Woerner, F., Smallheer, J.M., Barbera, F.A., Bozarth, J.M., Brown, R.L., Harpel, M.R., Luettgen, J.M., Morin, P.E., Peterson, T., Ramamurthy, V., Rendina, A.R., Rossi, K.A., Watson, C.A., Wei, A., Zhang, G., Seiffert, D., Wexler, R.R.
      (2014) J Med Chem 57: 955
    • Phenylimidazoles as potent and selective inhibitors of coagulation factor XIa with in vivo antithrombotic activity
      Hangeland, J.J., Friends, T.J., Rossi, K.A., Smallheer, J.M., Wang, C., Sun, Z., Corte, J.R., Fang, T., Wong, P.C., Rendina, A.R., Barbera, F.A., Bozarth, J.M., Luettgen, J.M., Watson, C.A., Zhang, G., Wei, A., Ramamurthy, V., Morin, P.E., Bisacchi, G.S., Subramaniam, S., Arunachalam, P., Mathur, A., Seiffert, D.A., Wexler, R.R., Quan, M.L.
      (2014) J Med Chem 57: 9915
    • Pyridine and pyridinone-based factor XIa inhibitors.
      Corte, J.R., Fang, T., Hangeland, J.J., Friends, T.J., Rendina, A.R., Luettgen, J.M., Bozarth, J.M., Barbera, F.A., Rossi, K.A., Wei, A., Ramamurthy, V., Morin, P.E., Seiffert, D.A., Wexler, R.R., Quan, M.L.
      (2015) Bioorg Med Chem Lett 25: 925
    • Structure-based design of inhibitors of coagulation factor XIa with novel P1 moieties.
      Pinto, D.J., Smallheer, J.M., Corte, J.R., Austin, E.J., Wang, C., Fang, T., Smith II, L.M., Rossi, K.A., Rendina, A.R., Bozarth, J.M., Zhang, G., Wei, A., Ramamurthy, V., Sheriff, S., Myers Jr., J.E., Morin, P.E., Luettgen, J.M., Seiffert, D.A., Quan, M.L., Wexler, R.R.
      (2015) Bioorg Med Chem Lett 25: 1635
    • Discovery of a Potent Parenterally Administered Factor XIa Inhibitor with Hydroxyquinolin-2(1H)-one as the P2' Moiety.
      Hu, Z., Wong, P.C., Gilligan, P.J., Han, W., Pabbisetty, K.B., Bozarth, J.M., Crain, E.J., Harper, T., Luettgen, J.M., Myers Jr., J.E., Ramamurthy, V., Rossi, K.A., Sheriff, S., Watson, C.A., Wei, A., Zheng, J.J., Seiffert, D.A., Wexler, R.R., Quan, M.L.
      (2015) ACS Med Chem Lett 6: 590
    • Novel phenylalanine derived diamides as Factor XIa inhibitors.
      Smith II, L.M., Orwat, M.J., Hu, Z., Han, W., Wang, C., Rossi, K.A., Gilligan, P.J., Pabbisetty, K.B., Osuna, H., Corte, J.R., Rendina, A.R., Luettgen, J.M., Wong, P.C., Narayanan, R., Harper, T.W., Bozarth, J.M., Crain, E.J., Wei, A., Ramamurthy, V., Morin, P.E., Xin, B., Zheng, J., Seiffert, D.A., Quan, M.L., Lam, P.Y.S., Wexler, R.R., Pinto, D.J.P.
      (2016) Bioorg Med Chem Lett 26: 472
    • Orally bioavailable pyridine and pyrimidine-based Factor XIa inhibitors: Discovery of the methyl N-phenyl carbamate P2 prime group.
      Corte, J.R., Fang, T., Pinto, D.J., Orwat, M.J., Rendina, A.R., Luettgen, J.M., Rossi, K.A., Wei, A., Ramamurthy, V., Myers Jr., J.E., Sheriff, S., Narayanan, R., Harper, T.W., Zheng, J.J., Li, Y.X., Seiffert, D.A., Wexler, R.R., Quan, M.L.
      (2016) Bioorg Med Chem 24: 2257
    • Structure-Based Design of Macrocyclic Factor XIa Inhibitors: Discovery of the Macrocyclic Amide Linker.
      Corte, J.R., Fang, T., Osuna, H., Pinto, D.J., Rossi, K.A., Myers Jr., J.E., Sheriff, S., Lou, Z., Zheng, J.J., Harper, T.W., Bozarth, J.M., Wu, Y., Luettgen, J.M., Seiffert, D.A., Decicco, C.P., Wexler, R.R., Quan, M.L.
      (2017) J Med Chem 60: 1060
    • Macrocyclic inhibitors of Factor XIa: Discovery of alkyl-substituted macrocyclic amide linkers with improved potency.
      Corte, J.R., Yang, W., Fang, T., Wang, Y., Osuna, H., Lai, A., Ewing, W.R., Rossi, K.A., Myers Jr., J.E., Sheriff, S., Lou, Z., Zheng, J.J., Harper, T.W., Bozarth, J.M., Wu, Y., Luettgen, J.M., Seiffert, D.A., Quan, M.L., Wexler, R.R., Lam, P.Y.S.
      (2017) Bioorg Med Chem Lett 27: 3833
    • Macrocyclic factor XIa inhibitors.
      Wang, C., Corte, J.R., Rossi, K.A., Bozarth, J.M., Wu, Y., Sheriff, S., Myers Jr., J.E., Luettgen, J.M., Seiffert, D.A., Wexler, R.R., Quan, M.L.
      (2017) Bioorg Med Chem Lett 27: 4056
    • Discovery of a Parenteral Small Molecule Coagulation Factor XIa Inhibitor Clinical Candidate (BMS-962212).
      Pinto, D.J.P., Orwat, M.J., Smith II, L.M., Quan, M.L., Lam, P.Y.S., Rossi, K.A., Apedo, A., Bozarth, J.M., Wu, Y., Zheng, J.J., Xin, B., Toussaint, N., Stetsko, P., Gudmundsson, O., Maxwell, B., Crain, E.J., Wong, P.C., Lou, Z., Harper, T.W., Chacko, S.A., Myers Jr., J.E., Sheriff, S., Zhang, H., Hou, X., Mathur, A., Seiffert, D.A., Wexler, R.R., Luettgen, J.M., Ewing, W.R.
      (2017) J Med Chem 60: 9703
    • Structure based design of macrocyclic factor XIa inhibitors: Discovery of cyclic P1 linker moieties with improved oral bioavailability.
      Clark, C.G., Rossi, K.A., Corte, J.R., Fang, T., Smallheer, J.M., De Lucca, I., Nirschl, D.S., Orwat, M.J., Pinto, D.J.P., Hu, Z., Wang, Y., Yang, W., Jeon, Y., Ewing, W.R., Myers Jr., J.E., Sheriff, S., Lou, Z., Bozarth, J.M., Wu, Y., Rendina, A., Harper, T., Zheng, J., Xin, B., Xiang, Q., Leuttgen, J.M., Seiffert, D.A., Wexler, R.R., Lam, P.Y.S.
      (2019) Bioorg Med Chem Lett 29: 126604
    • Potent, Orally Bioavailable and Efficacious Macrocyclic Inhibitors of Factor XIa. Discovery of Pyridine-Based Macrocycles Possessing Phenylazole Carboxamide P1 Groups.
      Corte, J.R., Pinto, D.J.P., Fang, T., Osuna, H., Yang, W., Wang, Y., Lai, A., Clark, C.G., Sun, J.-H., Rampulla, R., Mathur, A., Kaspady, M., Neithnadka, P.R., Li, Y.-X.C., Rossi, K.A., Myers Jr., J.E., Sheriff, S., Lou, Z., Harper, T.W., Huang, C., Zheng, J.J., Bozarth, J.M., Wu, Y., Wong, P.C., Crain, E.J., Seiffert, D.A., Luettgen, J.M., Lam, P.Y.S., Wexler, R.R., Ewing, W.R.
      (2019) J Med Chem 63: 784
    • Orally bioavailable amine-linked macrocyclic inhibitors of factor XIa.
      Fang, T., Corte, J.R., Gilligan, P.J., Jeon, Y., Osuna, H., Rossi, K.A., Myers Jr., J.E., Sheriff, S., Lou, Z., Zheng, J.J., Harper, T.W., Bozarth, J.M., Wu, Y., Luettgen, J.M., Seiffert, D.A., Wexler, R.R., Lam, P.Y.S.
      (2020) Bioorg Med Chem Lett 30: 126949

    Organizational Affiliation

    Research and Development, Bristol Myers Squibb Company, P.O. Box 5400, Princeton, New Jersey 08540, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor XIA244Homo sapiensMutation(s): 2 
Gene Names: F11
EC: 3.4.21.27
UniProt & NIH Common Fund Data Resources
Find proteins for P03951 (Homo sapiens)
Explore P03951 
Go to UniProtKB:  P03951
PHAROS:  P03951
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SWP (Subject of Investigation/LOI)
Query on SWP

Download Ideal Coordinates CCD File 
B [auth A]methyl ((10R,14S)-14-(4-(3-chloro-2,6-difluorophenyl)-6-oxo-3,6-dihydro- 1(2h)-pyridinyl)-10-methyl-9-oxo-8,16-diazatricyclo[13.3.1.0~2,7~]nonadeca- 1(19),2,4,6,15,17-hexaen-5-yl)carbamate
C31 H29 Cl F2 N4 O4
AXXYATYQRMPQSN-QUGAMOGWSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A] , F [auth A] , G [auth A] , H [auth A] , I [auth A] , J [auth A] , K [auth A] , L [auth A] , 
E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.86α = 90
b = 78.86β = 90
c = 106.62γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
SCALAdata scaling
AMoREphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2020-03-12 
  • Released Date: 2020-06-10 
  • Deposition Author(s): Sheriff, S.

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-10
    Type: Initial release
  • Version 1.1: 2020-07-22
    Changes: Database references