8PTR | pdb_00008ptr

COMPLEX CRYSTAL STRUCTURE OF MUTANT HUMAN MONOGLYCERIDE LIPASE WITH COMPOUND 5r

• PDB DOI: https://doi.org/10.2210/pdb8PTR/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-07-14 Released: 2024-01-31 
• Deposition Author(s): Butini, S., Benz, J., Grether, U., Leibrock, L., Papa, A., Maramai, S., Carullo, G., Federico, S., Grillo, A., Di Guglielmo, B., Lamponi, S., Gemma, S., Campiani, G.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 
  0.210 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Development of Potent and Selective Monoacylglycerol Lipase Inhibitors. SARs, Structural Analysis, and Biological Characterization.

Butini, S., Grether, U., Jung, K.M., Ligresti, A., Allara, M., Postmus, A.G.J., Maramai, S., Brogi, S., Papa, A., Carullo, G., Sykes, D., Veprintsev, D., Federico, S., Grillo, A., Di Guglielmo, B., Ramunno, A., Stevens, A.F., Heer, D., Lamponi, S., Gemma, S., Benz, J., Di Marzo, V., van der Stelt, M., Piomelli, D., Campiani, G.

(2024) J Med Chem 67: 1758-1782

• PubMed: 38241614 
• DOI: https://doi.org/10.1021/acs.jmedchem.3c01278
• Primary Citation Related Structures: 
  8PTC, 8PTQ, 8PTR


• PubMed Abstract: 
  

  New potent, selective monoacylglycerol lipase (MAGL) inhibitors based on the azetidin-2-one scaffold ((±)- 5a - v , (±)- 6a - j , and (±)- 7a - d ) were developed as irreversible ligands, as demonstrated by enzymatic and crystallographic studies for (±)- 5d , (±)- 5l , and (±)- 5r . X-ray analyses combined with extensive computational studies allowed us to clarify the binding mode of the compounds. 5v was identified as selective for MAGL when compared with other serine hydrolases. Solubility, in vitro metabolic stability, cytotoxicity, and absence of mutagenicity were determined for selected analogues. The most promising compounds ((±)- 5c , (±)- 5d , and (±)- 5v ) were used for in vivo studies in mice, showing a decrease in MAGL activity and increased 2-arachidonoyl- sn -glycerol levels in forebrain tissue. In particular, 5v is characterized by a high eudysmic ratio and (3 R ,4 S )- 5v is one of the most potent irreversible inhibitors of h / m MAGL identified thus far. These results suggest that the new MAGL inhibitors have therapeutic potential for different central and peripheral pathologies.

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Organizational Affiliation: 
• Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy.
Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, CH-4070 Basel, Switzerland.
Department of Anatomy and Neurobiology, University of California Irvine, Irvine, California 92697, United States.
Institute of Biomolecular Chemistry, National Research Council of Italy, Via Campi Flegrei 34, 80078 Pozzuoli, Italy.
Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University and Oncode Institute, 2300 CC, Leiden, Netherlands.
Department of Pharmacy, University of Pisa, via Bonanno, 56126 Pisa, Italy.
Faculty of Medicine & Health Sciences, University of Nottingham, Nottingham NG7 2UH, United Kingdom.
Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Edgbaston, B15 2TT Birmingham, Midlands, United Kingdom.
Department of Pharmacy/DIFARMA, University of Salerno, via Giovanni Paolo II 132, Salerno 84084, Fisciano, Italy.
Centre Nutrition, Santé et Société (NUTRISS), Institut sur La Nutrition Et Les Aliments Fonctionnels (INAF), École de Nutrition, Université Laval, 2440 Boulevard Hochelaga, Québec G1V 0A6, Canada.
Canada Excellence Research Chair in the Microbiome-Endocannabinoidome Axis in Metabolic Health, PO Box 2325, Quebec G1V 0A6, Canada.
Centre de Recherche de l'Institut de Cardiologie et de Pneumologie de Québec, Faculté de Médecine, Département de Médecine, Université Laval, PO Box 2725, Québec G1V 4G5, Canada.
Unité Mixte Internationale en Recherche Chimique et Biomoléculaire sur le Microbiome et Son Impact Sur la Santé Métabolique et la Nutrition (UMI-MicroMeNu), Université Laval, PO Box 2325, Quebec G1V 0A6, Canada.
Bioinformatics Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan 81746-7346, Iran.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 36.23 kDa 
• Atom Count: 2,495 
• Modeled Residue Count: 280 
• Deposited Residue Count: 323 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Monoglyceride lipase	A	323	Homo sapiens	Mutation(s): 3  Gene Names: MGLL EC: 3.1.1.23
UniProt & NIH Common Fund Data Resources
Find proteins for Q99685 (Homo sapiens) Explore Q99685  Go to UniProtKB:  Q99685
PHAROS:  Q99685 GTEx:  ENSG00000074416

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EFH (Subject of Investigation/LOI)	B [auth A]	(3~{R},4~{S})-4-(1,3-benzodioxol-5-yl)-1-[1-(benzotriazol-1-ylcarbonyl)piperidin-4-yl]-3-(3-fluorophenyl)azetidin-2-one C28 H24 F N5 O4 ZYBYLXKHKPMAIL-CLJLJLNGSA-N
EDO	C [auth A], D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
EFH	BindingDB:  8PTR	IC50: min: 0.05, max: 8.4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free:  0.210 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.883	α = 90
b = 126.5	β = 90
c = 60.177	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SADABS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-01-31 
Deposition Author(s): Butini, S., Benz, J., Grether, U., Leibrock, L., Papa, A., Maramai, S., Carullo, G., Federico, S., Grillo, A., Di Guglielmo, B., Lamponi, S., Gemma, S., Campiani, G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-01-31
  Type: Initial release
  
• Version 1.1: 2024-02-21
  Changes: Database references
• Version 1.2: 2024-10-16
  Changes: Structure summary