6HX8

Tubulin-STX3451 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.402 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Tetrahydroisoquinoline Sulfamates as Potent Microtubule Disruptors: Synthesis, Antiproliferative and Antitubulin Activity of Dichlorobenzyl-Based Derivatives, and a Tubulin Cocrystal Structure.

Dohle, W.Prota, A.E.Menchon, G.Hamel, E.Steinmetz, M.O.Potter, B.V.L.

(2019) ACS Omega 4: 755-764

  • DOI: 10.1021/acsomega.8b02879

  • PubMed Abstract: 
  • Tetrahydroisoquinoline (THIQ) 6- <i>O </i>-sulfamate-based anticancer agents, inspired by the endogenous steroid 2-methoxyestradiol and its sulfamate derivatives, are further explored for antiproliferative and microtubule disruptor activity. Based on ...

    Tetrahydroisoquinoline (THIQ) 6- O -sulfamate-based anticancer agents, inspired by the endogenous steroid 2-methoxyestradiol and its sulfamate derivatives, are further explored for antiproliferative and microtubule disruptor activity. Based on recently designed C3-methyl C7-methoxy-substituted THIQ derivatives, compounds with mono- and dichloro-substitutions on the pendant N -benzyl ring were synthesized and evaluated. Although improved antiproliferative activity was observed, for example, 4a versus 4b and 4b versus 8c , it was relatively modest. Compound 8c , a 2',5'-dichlorobenzyl derivative was, however, identified as a promising antiproliferative agent with in vitro activities exceeding that of the parent steroid (e.g., GI 50 90 nM in DU-145 cells) and was highly potent against a range of tumor cell lines (e.g., GI 50 26 nM for OVCAR-3). 8c inhibited the polymerization of tubulin in vitro with an IC 50 only twofold less potent than combretastatin A-4 and inhibited colchicine binding to tubulin. Tubulin polymerization assays showed the parent THIQ 4a to be only a very weak inhibitor, but a striking potency difference was seen between compounds with C2' methoxy and chloro substituents, whereas this was much smaller when these substituents were positioned at C5'. To confirm the target in atomic detail and because 8c is a racemic mixture, an achiral parent THIQ 6- O -sulfamate derivative 10 was successfully cocrystallized with the αβ-tubulin heterodimer. The derivative 10 binds at the colchicine site on tubulin, the first example of this compound class investigated in such detail, with its sulfamate group interacting with residues beyond the reach of colchicine itself, similar to a recently reported quinazolinone sulfamate derivative, 6a . The structure also suggests that for racemic C3-methyl-substituted THIQ derivatives, such as 8c , the (S)-enantiomer is likely to be preferentially accommodated within the colchicine site for steric reasons. The results further confirm the potential of nonsteroidal THIQ sulfamate derivatives for oncology and suggest that the mechanism of microtubule destabilization for the THIQ compound class is to prevent the curved-to-straight conformational transition of tubulin required for polymerization.


    Organizational Affiliation

    University of Basel, Biozentrum, Basel CH-4056, Switzerland.,Medicinal Chemistry & Drug Discovery, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, U.K.,Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, Villigen PSI CH-5232, Switzerland.,Screening Technologies Branch, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Frederick National Laboratory for Cancer Research, Frederick 21702, Maryland, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tubulin alpha-1B chain
A, C
451Bos taurusMutation(s): 0 
Find proteins for P81947 (Bos taurus)
Go to UniProtKB:  P81947
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tubulin beta-2B chain
B, D
445Bos taurusMutation(s): 0 
Gene Names: TUBB2B
Find proteins for Q6B856 (Bos taurus)
Go to Gene View: TUBB2B
Go to UniProtKB:  Q6B856
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Stathmin-4
E
143Rattus norvegicusMutation(s): 0 
Gene Names: Stmn4
Find proteins for P63043 (Rattus norvegicus)
Go to UniProtKB:  P63043
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Tubulin-Tyrosine Ligase
F
384Gallus gallusMutation(s): 0 
Gene Names: TTL
Find proteins for E1BQ43 (Gallus gallus)
Go to Gene View: TTL
Go to UniProtKB:  E1BQ43
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

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B, D
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
GXN
Query on GXN

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B, D
[2-[(3-bromanyl-4,5-dimethoxy-phenyl)methyl]-7-methoxy-3,4-dihydro-1~{H}-isoquinolin-6-yl] sulfamate
C19 H23 Br N2 O6 S
AAQOREQGNICBFR-UHFFFAOYSA-N
 Ligand Interaction
GTP
Query on GTP

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Download CCD File 
A, C
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
CA
Query on CA

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A, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A, B, C, D, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES

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B
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
ACP
Query on ACP

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F
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.402 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 105.670α = 90.00
b = 159.920β = 90.00
c = 181.010γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
PHENIXrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland31003A_166608

Revision History 

  • Version 1.0: 2019-02-27
    Type: Initial release