6BNR

Carbonmonoxy hemoglobin in complex with the antisickling agent 5-methoxy-2-(pyridin-2-ylmethoxy)benzaldehyde (INN310)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Rational design of pyridyl derivatives of vanillin for the treatment of sickle cell disease.

Pagare, P.P.Ghatge, M.S.Musayev, F.N.Deshpande, T.M.Chen, Q.Braxton, C.Kim, S.Venitz, J.Zhang, Y.Abdulmalik, O.Safo, M.K.

(2018) Bioorg. Med. Chem. 26: 2530-2538

  • DOI: 10.1016/j.bmc.2018.04.015

  • PubMed Abstract: 
  • Hypoxia-induced polymerization of sickle hemoglobin (Hb S) is the principal phenomenon that underlays the pathophysiology and morbidity associated with sickle cell disease (SCD). Opportunely, as an allosteric protein, hemoglobin (Hb) serves as a conv ...

    Hypoxia-induced polymerization of sickle hemoglobin (Hb S) is the principal phenomenon that underlays the pathophysiology and morbidity associated with sickle cell disease (SCD). Opportunely, as an allosteric protein, hemoglobin (Hb) serves as a convenient and potentially critical druggable target. Consequently, molecules that prevent Hb S polymerization (Hb modifiers), and the associated erythrocyte sickling have been investigated-and retain significant interest-as a viable therapeutic strategy for SCD. This group of molecules, including aromatic aldehydes, form high oxygen affinity Schiff-base adducts with Hb S, which are resistant to polymerization. Here, we report the design and synthesis of novel potent antisickling agents (SAJ-009, SAJ-310 and SAJ-270) based on the pharmacophore of vanillin and INN-312, a previously reported pyridyl derivative of vanillin. These novel derivatives exhibited superior in vitro binding and pharmacokinetic properties compared to vanillin, which translated into significantly enhanced allosteric and antisickling properties. Crystal structure studies of liganded Hb in the R2 quaternary state in complex with SAJ-310 provided important insights into the allosteric and antisickling properties of this group of compounds. While these derivatives generally show similar in vitro biological potency, significant structure-dependent differences in their biochemical profiles would help predict the most promising candidates for successful in vivo pre-clinical translational studies and inform further structural modifications to improve on their pharmacologic properties.


    Organizational Affiliation

    Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, 800 East Leigh Street, Richmond, VA 23298, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin subunit alpha
A, C
141Homo sapiensMutation(s): 0 
Gene Names: HBA1, HBA2
Find proteins for P69905 (Homo sapiens)
Go to Gene View: HBA1 HBA2
Go to UniProtKB:  P69905
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin subunit beta
B, D
146Homo sapiensMutation(s): 0 
Gene Names: HBB
Find proteins for P68871 (Homo sapiens)
Go to Gene View: HBB
Go to UniProtKB:  P68871
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B, C, D
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
E0J
Query on E0J

Download SDF File 
Download CCD File 
A, C
2-[(4-methoxy-2-methylphenoxy)methyl]pyridine
C14 H15 N O2
IJQMLIQZWDSRCW-UHFFFAOYSA-N
 Ligand Interaction
CMO
Query on CMO

Download SDF File 
Download CCD File 
A, B, C, D
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 62.817α = 90.00
b = 83.550β = 90.00
c = 104.915γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CrystalCleardata reduction
CrystalCleardata collection
PHENIXphasing
d*TREKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Minority Health and Health DisparitiesUnited StatesRO1MD009124

Revision History 

  • Version 1.0: 2018-09-05
    Type: Initial release