Post on 09-Aug-2020
Heat Shock Protein 90/70 (HSP90/70)
Targeted Library
June, 2012
YAI, ChemDiv, Inc.
The Core Strategy
Analyze the structures of reported HSP90/70 inhibitors (more than 1K
molecules);
► Analyze the structures of HSP90 and HSP70 proteins and conformational
shifts within the active binding site observed upon ligand binding;
► Binding modes and allosteric binding sites identification/analysis;
► Include selective HSP90 and HSP70 binders;
► 3D-model construction/validation;
► Select small-molecule compounds from ChemDiv store (more than 1.5 mil
molecules) with potential HSP90/70 activity following several structure
determinant, including similarity, privileged scaffolds and “med-chem” filters;
► Molecular Docking of selected compounds / “Pro-Drug” approach
Representative examples of reported HSP90 inhibitors
O
O
O O
N
OO
O
O
O
N
O
ONa
+
Novobiocin Hsp90 C-terminal inhibitor NB disrupts Bcr-Abl /Hsp90and Bcr-Abl /Hsp70 interactions Launched (anticancer) Pfizer
N
O
O
N
O
O
O O
O
N
O
Tanespimycin (17-AAG)ATP-site ligand, HSP90 Phase III (anticancer) Pfizer
N
NN
N
N
Cl
N
O
CNF-2024 Phase II (anticancer)ATP-site ligand, HSP90Conforma Therapeutics
N
N
OFF
F
O N
N
O
PF-04928473 Phase I (anticancer)ATP-site ligand, HSP90 Pfizer
N N
N O
O
O
N GanetespibPhase II/III (anticancer)ATP-site ligand, HSP90 Synta PharmaceuticalsN
N
N
S
N
N
N
O
O
I
PU-H71 Phase I (anticancer) ATP-site ligand, HSP90Memorial Sloan-Kettering Cancer Center Sloan-Kettering Institute
N
N
N
O
O O AT-13387AU Phase II (anticancer)ATP-site ligand, HSP90 Astex Pharmaceuticals
O
N
O
O
O
O
O
N
O
O
O KW-2478Phase I/II (anticancer) Kyowa Hakko Kirin
O
N
N
O
OO
O N
NVP-AUY922Phase II (anticancer) Novartis
NN
O
F
N O
N N
NVP-HSP990Phase I (anticancer) Novartis
N
O
N
O
N
N
N
O
XL-888 Phase I (anticancer)selective HSP90 inhibitor Exelixis
N
NN
N
N O
N
Biological Testingselective HSP90 inhibitor Sanofi
ClCl
ON
N
F
N
N
N
N
O
F F
N Biological Testingselective HSP90 inhibitor Pfizer
O
O
N
O O
KNK-437 PreclinicalInhibits the synthesis of HSP90 Kaneka
N
N
O
O
O
N
O
N O
O
O
O
O
N+
O
O
O
DMT series Biological TestingUniversity of Pittsburgh
NCl
Cl
NN
O
N
O
N
N
O
O
N
VER-155008 Preclinical VernalisIC50 = 0.5 mcM
NN
O
O
ON
N
O
O
O
N+O O
Mal-2-213 Biological Testing ATP-site ligandColumbia University IC50 ~30 nM
N
NN
N
O
S
N
N
O
N
N
O
YK-5 Biological Testing Allosteric site inhibitorMemorial Sloan-Kettering Cancer Center
S
N
N
S
N+
O
MKT-077 Phase II (anticancer) allosteric inhibitorDana-Farber Cancer Institute
O
OH
OH
OH
OH
OH
OH
O MyricetinAllosteric site inhibitor
Representative examples of reported HSP70 inhibitors
The final library content (more than 15K compounds)
compounds with „moderate-to-high‟ structural similarity (Tanimoto coeff. >0.5) to the
reported HSP90 and HSP70 inhibitors, isosteric modifications, topological analogues
compounds successfully passed through the developed 3D-models
O
OH
NH
O
OH
similarity = 0.52
O
NH
O
ID: K808-1985
Compound developed by Kyowa Hakko KirinHSP90 inhibitor under early biological evaluation Kitamura, Y. et al. US 7781485 Aug 24, 2010
N
N
N
OH
ID: G856-2554
N
N
O
O
similarity: 0.50
Compound developed by Emory UniversityHSP90 inhibitor under early biological evaluation Min, J. et al. US 022070, 2012
IC50=0.770 µM (Displacement of geldanamycin)
H417 human small-cell lung carcinoma cells
N NH
OOH
Me
MeO
HIGH SCRORE
O
NH
O
O
OH
OMe
K219_0094
MEDIUM SCRORE
G857_1210
EXAMPLES:
EXAMPLES:
non-trivial a-helix and b-sheet mimetics (HSP90/70-‟client protein‟ interaction mimetics)
compounds with a high diversity in structure (minor subset), including nature-like
compounds, e.g. spiro-compounds (Escape from flatland)
N
N
O
O
EtO
ID: K780-1065
N
N
OO Me
Me
Me
Me
ID: P681-0294
NS
NN
O
ClID: 5408-0495
N
NH
S
O
O Me
Me Me
ID: 3046-8072
N
O
O
NH
Me Me
Me
ID: C700-2278
NN
NN
O
O
O
O
F
ID: C796-0949
N
NN
NH
O
OO
Me
Cl
Me
MeMe
MeID: E223-2328
N
N
NH
O
O
ID: K788-9376
NO
O
OH
MeO
ID: K780-0501
EXAMPLES:
EXAMPLES:
Molecular weight H_acceptor
H_donor B_rotN
Key Properties
LogP logSw
PSA
Num. of unique heterocycles: 176;
Num. of unique screens: 3,663;
Diversity: 0,801 (cosine coefficient);
Num. of comb.templates: 340
Statistic
Hsp90 exists as two isoforms: Hsp90α and Hsp90β
► Hsp90 consists of a highly conserved N-terminal domain, a charged linker, and a highly
conserved C-terminal region, in general, the charged linker is not important for Hsp90 function,
and the inhibitors of Hsp90 mainly bind to the N-and C-terminal regions. The N-terminal
domain binds the natural products geldanamycin (GDA), radicicol and their derivatives, which
modulate at least two different conformational states. Novobiocin binds to the C-terminal
nucleotide binding site and inhibits Hsp90 function
► The first Hsp90 inhibitor drug is geldanamycin, a natural product isolated from
Streptomyces hygroscopicus. The geldanamycin analogue 17AAG (17-allylamino-17-
demethoxy-geldanamycin) possesses all the Hsp90-related characteristics of geldanamycin
but with lower toxicity. Another natural Hsp90 inhibitor is radicicol.
Geldanamycin 17AAG Radicicol
3D-molecular Docking
Besides the natural compounds, some synthesized inhibitors have also shown promising
effects on Hsp90, for example, purine-based inhibitors the Pyrazole-isoxazole analogues,
Novobiocin and coumarin scaffold analogues, such as 4TCNA
► Benzamide tetrahydro-4H-carbazol-4-one analogs (BT), AT13387 derivatives (AT) and
Dihydroxylphenyl amides (DA) have been developed as further potent Hsp90 inhibitors
3D-QSAR, CoMFA, CoMSIA, ANN and 3D-pharmacophore as well as 3D-docking methods
were employed to investigate several HSP90 purine-based inhibitors, which provided useful
models for designing the Hsp90 targeted compounds
► the common pharmacophoric features, i.e., one H-bond donor, one H-bond acceptor, one
hydrophobic (aromatic), and two hydrophobic (aliphatic) features, which might be of import
to develop inhibitors as anti-cancer agents
Novobiocin
BT AT
DA
to date, there are no 3D-QSAR studies of many ligands reported except very few classes.
Moreover, no comprehensive feature for the ligand-receptor interactions, such as the
hydrophobic contact between the key amino acid residues has been demonstrated
Purine-based HSP90 pharmacophore
developed by Chen includes
hydrophobic (blue), hydrogen bond
acceptor (green) and hydrogen bond
donor (purple). The distances of
features were labeled by blue lines
Chen CY. Insights into designing the dual-targeted HER2/HSP90 inhibitors. J. Mol. Graph. Model. 2010, 29(1), 21-31
► More than 50 crystallographic complexes of small-molecule compounds including several
BBs with HSP90 have been described to date. A majority of these complexes were
investigated during the study
► MolSoft SoftwareTM was used to analyzed these complexes with regard to their structural
homology and the ligand binding modes
► the ATP-binding site was thoroughly reconstructed based on the 3D-alignment of many
protein-ligand complexes
reported HSP90 ligands were flexibly redocked to the binding site of Hsp90 protein to
internaly evaluate the model. The optimum docking conformations as the most probable
binding conformation corresponding with a low energy score were analyzed
Hsp90a N-terminal domain bound to ATP (3T0Z)
Homo sapiens
The 3D-alignment of two crystallographic
data obtained for ATP and geldanamycin
D93, T184 and G97 are the most crucial conservative (rigid) points in the first
common binding mode
► AAs which coordinate the cofactor (Mg2+) are the second target
► there are several other AAs which can also provide significant contacts with
ligands within the ATP-binding site, including N106 (adjusted), K112, K58 (adjusted),
F138 and G137, N106 (adjusted), L107 (adjusted), N51, G97
Radicicol analogue bound to the ATP-
binding site of HSP90 (orange), VHD in the
site (yellow). Crystallographic data,
superposition
VHD
Woodhead AJ, et al. Discovery of (2,4-dihydroxy-5-isopropylphenyl)-[5-(4-methylpiperazin-1-ylmethyl)-1,3-dihydroisoindol-2-
yl]methanone (AT13387), a novel inhibitor of the molecular chaperone Hsp90 by fragment based drug design. J Med Chem. 2010
Aug 26;53(16):5956-69.
VHD is one compound among a wide
fragment-based library screened recently
against HSP90. For many fragments the
related crystallographic data was
obtained. We also used these data to
develop our 3D-docking model
ATP bound to the binding site of HSP90
(orange), direct ATP analogues in the site
(yellow). Crystallographic data, superposition
From the
fragment-based
library
Crystal Structure of HSP90
with N-Aryl-benzimidazolone
Key contacts: G97, T184, D93
K58-sylfonyl oxygen (weak)
Another binding mode was
revealed for several tricyclic HSP90
inhibitors
H-bonding: Y139, L103
Hydrophobic and stacking contacts:
Phe138, Y139, Leu103, Ala111, Leu107,
Phe170, Gly106, Phe22, W162
Combined features form the third
binding mode for HSP90 ligands
Vallée F. et al. J Med Chem. Tricyclic series of heat shock protein 90 (Hsp90) inhibitors part I: discovery of tricyclic imidazo[4,5-
c]pyridines as potent inhibitors of the Hsp90 molecular chaperone. 2011; 54(20): 7206-19
N
N
NN N
NO
N(conf):24
minE:-99.97
maxE:-71.49
Energy (calc):-82.78
RMSD: 6.401e-007
H
N
N
N
N
O
N(conf):15
minE:-85.68
maxE:-54.12
Energy (calc):-85.68
RMSD: 6.915e-007
N
NN
O
N(conf):17
minE:-77.63
maxE:-41.11
Energy (calc):-77.63
RMSD: 6.718e-007
N
N N
N
O
O
N
N(conf):21
minE:-111.7
maxE:-67.89
Energy (calc):-111.7
RMSD:6.193e-007
S
O
ON
N
ON
O
O
Cl
N(conf):11
minE:-86.47
maxE:-32.4
Energy (calc):-69.8
RMSD: 6.119e-007
0.1 sens
N
N N
N
O
N
N(conf):11
minE:-100.1
maxE:-22.38
Energy (calc):-100.1
RMSD: 6.924e-007
0.1 sens
H
N
N N
H N
O
N
N(conf):24
minE:-77.57
maxE:-58.96
Energy (calc):-77.57
RMSD:6.581e-007
N(conf):24
minE:-108.2
maxE:-70.52
Energy (calc):-108.2
RMSD:6.589e-007
N
N
N
NO
N N
3D-Molecular Docking Hsp70► Hsp70 chaperones are key to cellular protein homeostasis
► Hsp70 proteins are allosteric machines and offer, besides classical active-site targets,
also opportunities to target the mechanism of allostery
► Potent anticancer compound MKT-077 has recently been described as an "allosteric
drug“
► Using NMR spectroscopy the compound's binding site on human Hsc70 (hHsc70 has
85% identity with human Hsp70) was identified. Fractional shifts upon addition of MKT-
077 in the 15N,2H-labeled hHsc70 include T222, A223, D225, H227, L228. For each
resonance, the shift at a molar ratio of 0.5 was defined as 50% completed
► We have reconstructed the allosteric binding site using this data and docked MKT-
077
Rousaki A elt al. Allosteric drugs: the interaction of antitumor compound MKT-077 with human Hsp70 chaperones. J Mol Biol. 2011, 411(3):614-32
MKT-077
N(conf):23
minE:-58.95
maxE:-46.94
Energy (calc):-58.27
RMSD:5.131e-007
S
N
N
S
N+
O E231
R261
V59
P91
K257
P63
Y41
2.43.2
2.8
ATP-binding site for
competitive inhibitors
Selective Binding to HSP90
► XL888 is a potent and selective ATP-competitive inhibitor of HSP90 developed by Exelixis
► XL888 binds to the target in a manner that is structurally distinct from other HSP90
inhibitors currently in the clinic
► XL888 selectively inhibits members of the HSP90 family and it is inactive against HSP70,
the structurally related Bergerat-fold ATPase Topoisomerase II, and a diverse panel of
serine/threonine and tyrosine kinases
► Crystallographic analysis of XL888 bound to HSP90 has showed that XL888 extends
across the width of the ATP-binding domain. A flexible region of ~30 amino acids referred to
as the “lid” (magenta ribbon) adopts a different conformation when bound to XL888 compared
with ADP or Geldanamycin
N
O
N
O
N
N
N
O
XL888A co-crystal structure of XL888 bound to the N-terminal
domain of HSP90a: comparison to ADP and Geldanamycin.
Lyman SK, et al. High-content, high-throughput analysis of cell cycle perturbations induced by the HSP90 inhibitor XL888. PLoS One. 2011;6(3):e17692;
Paraiso KH, et al. The HSP90 Inhibitor XL888 Overcomes BRAF Inhibitor Resistance Mediated through Diverse Mechanisms. Clin Cancer Res. 2012
;18(9):2502-14.
NH
N
N
NH
O
O
NH2
Compound 1
Vallée F, et al. Tricyclic series of heat shock protein 90 (Hsp90) inhibitors part I: discovery of tricyclic
imidazo[4,5-c]pyridines as potent inhibitors of the Hsp90 molecular chaperone. J Med Chem.
2011;54(20):7206-19.
yellow – ATP; orange – compound 1 Terminal region adjustment and alternative
binding cavity formation for penetration
Insight into the selectivity, XL888 binding mode
yellow – docking results
orange – crystallographic data
Selective HSP90 inhibitors docked into the reconstructed binding site
XL888
N
N
OF F
F
N
O
ON
SNX-2112
Huang KH, et al. Discovery of
novel aminoquinazolin-7-yl 6,7-
dihydro-indol-4-ones as potent,
selective inhibitors of heat shock
protein 90. Bioorg Med Chem
Lett. 2012;22(7):2550-4
NVP-AUY922 O
N
O
O
NO
N
O
(Novartis)
Eccles SA, et al. NVP-AUY922: a novel
heat shock protein 90 inhibitor active
against xenograft tumor growth,
angiogenesis, and metastasis. Cancer
Res. 2008 ;68(8):2850-60
(Pfizer)
ClCl
ON
N
F
N
N
N
N
O
F F
N
(Pfizer)
Zehnder L, et al. Optimization of potent, selective,
and orally bioavailable pyrrolodinopyrimidine-
containing inhibitors of heat shock protein 90.
Identification of development candidate 2-amino-4-
{4-chloro-2-[2-(4-fluoro-1H-pyrazol-1-yl)ethoxy]-6-
methylphenyl}-N-(2,2-difluoropropyl)-5,7-dihydro-
6H-pyrrolo[3,4-d]pyrimidine-6-carboxamide. J Med
Chem. 2011,12;54(9):3368-85
Overlapping of several inhibitors
Yellow - XL888
Orange – compound 1
Green - SNX_2112
Blue - NVP_AUY922
Core residues (H-bonding): T184,
D93, S52, K58;
Planar Stacking: F138
Additional H-bonding: Y139, W162,
F22, Q23, L103
Representative examples of compounds from HSP90/70 library
N NH
OOH
Me
OMe
G857_1210
Possible O-dealkylation by CYP3A4
G97
T184
D93N51
H2O
HIGH SCRORE
Ep = -60 kcal/mol
O
NH
O
O
OH
OCH
3
K219_0094
presumably> Pgp-target> poor BBB permeability
T184
K58 H20H20
MEDIUM SCRORE
Ep = -64 kcal/mol
N
O
O
O
Me
Me
Me
N
O
OH
OH
Me
D398_0454 D398_0454_1
D93
S52
H2O
N52O-dealkylatyon
CYP3A4
Pro-Drug Strategy
MEDIUM SCRORE
Ep = -47 kcal/mol
N
N
SNH
OO
O Me
Me
Cl
NH
NH
SNH
OO
O
Cl
N-dealkylation
CYP3A4
D93
S52
N51/S52
H2O
G801_0201 G801_0201_1
Pro-Drug Strategy
MEDIUM SCRORE
Ep = -74 kcal/mol
N
N
NH
N
OO
CH3
OH
OH
N
N
NH
N
OO
CH3
metabolic sites
hydroxylation
CYP3A4
possibledeacetylasesite S062-1044 S062-1044-1
D93
N51
T184
G97
K58
H2O
Pro-Drug Strategy
HIGH SCRORE
Ep = -74 kcal/mol