6DI4

Rational Modification of Vanillin Derivatives to Stereospecifically Destabilize Sickle Hemoglobin Polymer Formation

  • Classification: OXYGEN TRANSPORT
  • Organism(s): Homo sapiens

  • Deposited: 2018-05-22 Released: 2018-09-05 
  • Deposition Author(s): Pagare, P.P., Musayev, F.N.
  • Funding Organization(s): National Institutes of Health/National Institute on Minority Health and Health Disparities; National Institutes of Health/National Center for Research Resources 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Rational modification of vanillin derivatives to stereospecifically destabilize sickle hemoglobin polymer formation.

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

(2018) Acta Crystallogr D Struct Biol 74: 956-964

  • DOI: 10.1107/S2059798318009919

  • PubMed Abstract: 
  • Increasing the affinity of hemoglobin for oxygen represents a feasible and promising therapeutic approach for sickle cell disease by mitigating the primary pathophysiological event, i.e. the hypoxia-induced polymerization of sickle hemoglobin (Hb S) ...

    Increasing the affinity of hemoglobin for oxygen represents a feasible and promising therapeutic approach for sickle cell disease by mitigating the primary pathophysiological event, i.e. the hypoxia-induced polymerization of sickle hemoglobin (Hb S) and the concomitant erythrocyte sickling. Investigations on a novel synthetic antisickling agent, SAJ-310, with improved and sustained antisickling activity have previously been reported. To further enhance the biological effects of SAJ-310, a structure-based approach was employed to modify this compound to specifically inhibit Hb S polymer formation through interactions which perturb the Hb S polymer-stabilizing αF-helix, in addition to primarily increasing the oxygen affinity of hemoglobin. Three compounds, TD-7, TD-8 and TD-9, were synthesized and studied for their interactions with hemoglobin at the atomic level, as well as their functional and antisickling activities in vitro. X-ray crystallographic studies with liganded hemoglobin in complex with TD-7 showed the predicted mode of binding, although the interaction with the αF-helix was not as strong as expected. These findings provide important insights and guidance towards the development of molecules that would be expected to bind and make stronger interactions with the αF-helix, resulting in more efficacious novel therapeutics for sickle cell disease.


    Organizational Affiliation

    Department of Pharmaceutics, School of Pharmacy, Virginia Commonwealth University, 800 East Leigh Street, Richmond, VA 23219, USA.,Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, 800 East Leigh Street, Richmond, VA 23219, USA.,Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, 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
GJ1
Query on GJ1

Download SDF File 
Download CCD File 
A, C
{6-[(4-methoxy-2-methylphenoxy)methyl]pyridin-2-yl}methanol
C15 H17 N O3
GBTFLQPUSKDFPL-UHFFFAOYSA-N
 Ligand Interaction
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
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: 1.9 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 62.696α = 90.00
b = 83.404β = 90.00
c = 104.934γ = 90.00
Software Package:
Software NamePurpose
PHENIXmodel building
CrysalisProdata reduction
CNSrefinement
CrystalCleardata scaling
CrystalCleardata collection

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 StatesMD009124
National Institutes of Health/National Center for Research ResourcesUnited StatesS10-OD021756

Revision History 

  • Version 1.0: 2018-09-05
    Type: Initial release
  • Version 1.1: 2018-10-17
    Type: Data collection, Database references