7ZYJ

Leishmania tarentolae proteasome 20S subunit in complex with compound 2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Discovery of Novel Quinoline-Based Proteasome Inhibitors for Human African Trypanosomiasis (HAT).

Koester, D.C.Marx, V.M.Williams, S.Jiricek, J.Dauphinais, M.Rene, O.Miller, S.L.Zhang, L.Patra, D.Chen, Y.L.Cheung, H.Gable, J.Lakshminarayana, S.B.Osborne, C.Galarneau, J.R.Kulkarni, U.Richmond, W.Bretz, A.Xiao, L.Supek, F.Wiesmann, C.Honnappa, S.Be, C.Maser, P.Kaiser, M.Ritchie, R.Barrett, M.P.Diagana, T.T.Sarko, C.Rao, S.P.S.

(2022) J Med Chem 65: 11776-11787

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c00791
  • Primary Citation of Related Structures:  
    7ZYJ

  • PubMed Abstract: 

    Human African Trypanosomiasis (HAT) is a vector-borne disease caused by kinetoplastid parasites of the Trypanosoma genus. The disease proceeds in two stages, with a hemolymphatic blood stage and a meningo-encephalic brain stage. In the latter stage, the parasite causes irreversible damage to the brain leading to sleep cycle disruption and is fatal if untreated. An orally bioavailable treatment is highly desirable. In this study, we present a brain-penetrant, parasite-selective 20S proteasome inhibitor that was rapidly optimized from an HTS singleton hit to drug candidate compound 7 that showed cure in a stage II mouse efficacy model. Here, we describe hit expansion and lead optimization campaign guided by cryo-electron microscopy and an in silico model to predict the brain-to-plasma partition coefficient K p as an important parameter to prioritize compounds for synthesis. The model combined with in vitro and in vivo experiments allowed us to advance compounds with favorable unbound brain-to-plasma ratios ( K p,uu ) to cure a CNS disease such as HAT.


  • Organizational Affiliation

    Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Emeryville, California 94608, United States.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha typeA,
O [auth a]
250Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KZP5 (Leishmania tarentolae)
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UniProt GroupA0A640KZP5
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha typeB,
P [auth b]
231Leishmania tarentolaeMutation(s): 0 
UniProt
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UniProt GroupA0A640KGL4
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha typeC,
Q [auth c]
285Leishmania tarentolaeMutation(s): 0 
UniProt
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UniProt GroupA0A640KBV2
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha typeD,
R [auth d]
248Leishmania tarentolaeMutation(s): 0 
UniProt
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UniProt GroupA0A640KXA2
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome alpha 5 subunit, putativeE,
S [auth e]
344Leishmania tarentolaeMutation(s): 0 
UniProt
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UniProt GroupA0A640KG82
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome alpha 1 subunit, putativeF,
T [auth f]
428Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome alpha 7 subunit, putativeG,
U [auth g]
238Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit betaH,
V [auth h]
229Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit betaI,
W [auth i]
225Leishmania tarentolaeMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit betaJ,
X [auth j]
205Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KQX8 (Leishmania tarentolae)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit betaK,
Y [auth k]
206Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KTY7 (Leishmania tarentolae)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit betaL,
Z [auth l]
203Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome beta 6 subunit, putativeAA [auth m],
M
339Leishmania tarentolaeMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit betaBA [auth n],
N
219Leishmania tarentolaeMutation(s): 0 
UniProt
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KFC (Subject of Investigation/LOI)
Query on KFC

Download Ideal Coordinates CCD File 
CA [auth L],
DA [auth l]
~{N}-cyclopentyl-6-methyl-4-phenylazanyl-quinoline-2-carboxamide
C22 H23 N3 O
YSFGQDYFFHGWOC-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2022-09-28 
  • Deposition Author(s): Srinivas, H.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-28
    Type: Initial release