8PI3 | pdb_00008pi3

Cathepsin S Y132D mutant in complex with NNPI-C10 inhibitor

• PDB DOI: https://doi.org/10.2210/pdb8PI3/pdb

• Classification: ONCOPROTEIN
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Cricetulus griseus
• Mutation(s): Yes 


• Deposited: 2023-06-21 Released: 2024-06-05 
• Deposition Author(s): Petruzzella, A., Lau, K., Pojer, F., Oricchio, E.
• Funding Organization(s): Swiss Cancer League

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 
  0.206 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Antibody-peptide conjugates deliver covalent inhibitors blocking oncogenic cathepsins.

Petruzzella, A., Bruand, M., Santamaria-Martinez, A., Katanayeva, N., Reymond, L., Wehrle, S., Georgeon, S., Inel, D., van Dalen, F.J., Viertl, D., Lau, K., Pojer, F., Schottelius, M., Zoete, V., Verdoes, M., Arber, C., Correia, B.E., Oricchio, E.

(2024) Nat Chem Biol 20: 1188-1198

• PubMed: 38811854 
• DOI: https://doi.org/10.1038/s41589-024-01627-z
• Primary Citation Related Structures: 
  8PI3, 8RND


• PubMed Abstract: 
  

  Cysteine cathepsins are a family of proteases that are relevant therapeutic targets for the treatment of different cancers and other diseases. However, no clinically approved drugs for these proteins exist, as their systemic inhibition can induce deleterious side effects. To address this problem, we developed a modular antibody-based platform for targeted drug delivery by conjugating non-natural peptide inhibitors (NNPIs) to antibodies. NNPIs were functionalized with reactive warheads for covalent inhibition, optimized with deep saturation mutagenesis and conjugated to antibodies to enable cell-type-specific delivery. Our antibody-peptide inhibitor conjugates specifically blocked the activity of cathepsins in different cancer cells, as well as osteoclasts, and showed therapeutic efficacy in vitro and in vivo. Overall, our approach allows for the rapid design of selective cathepsin inhibitors and can be generalized to inhibit a broad class of proteases in cancer and other diseases.

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Organizational Affiliation: 
• Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland.
Institute of Chemical Sciences and Engineering (ISIC), Institute of Bioengineering, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
Laboratory of Protein Design and Immunoengineering, School of Engineering, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne, Switzerland.
Department of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland.
Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, The Netherlands.
Institute for Chemical Immunology, Nijmegen, The Netherlands.
Translational Radiopharmaceutical Sciences, Departments of Nuclear Medicine and Molecular Imaging and of Oncology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland.
In Vivo Imaging Facility, Department of Research and Training, University of Lausanne (UNIL), Lausanne, Switzerland.
Protein Production and Structure Core Facility, School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
AGORA Pôle de Recherche sur le Cancer, Lausanne, Switzerland.
Laboratory of Protein Design and Immunoengineering, School of Engineering, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland. [e-mail].
Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland. [e-mail].
Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 28.02 kDa 
• Atom Count: 1,928 
• Modeled Residue Count: 230 
• Deposited Residue Count: 239 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cathepsin S	A	228	Homo sapiens	Mutation(s): 1  Gene Names: CTSS EC: 3.4.22.27
UniProt & NIH Common Fund Data Resources
Find proteins for P25774 (Homo sapiens) Explore P25774  Go to UniProtKB:  P25774
PHAROS:  P25774 GTEx:  ENSG00000163131

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NNPI-C10 inhibitor	B	11	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	I [auth A], J [auth A], K [auth A], L [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
PEG	Q [auth A], T [auth A], U [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	G [auth A], H [auth A], O [auth A], R [auth A], S [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	N [auth A], P [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	C [auth A], D [auth A], E [auth A], M [auth A], V [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
A1H5W	B	L-PEPTIDE LINKING	C3 H7 N4 O2		ALA
YWF	B	PEPTIDE LINKING	C4 H7 N O2		ABU

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free:  0.206 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.706	α = 90
b = 87.706	β = 90
c = 69.436	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-06-05 
Deposition Author(s): Petruzzella, A., Lau, K., Pojer, F., Oricchio, E.

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Funding Organization	Location	Grant Number
Swiss Cancer League	Switzerland	KFS-5102-08-2020

Revision History  

• Version 1.0: 2024-06-05
  Type: Initial release
  
• Version 1.1: 2024-06-12
  Changes: Database references
• Version 1.2: 2024-09-11
  Changes: Database references