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Plotnik JP, Richardson AE, Yang H, Rojas E, Bontcheva V, Dowell C, Parsons S, Wilson A, Ravanmehr V, Will C, Jung P, Zhu H, Partha SK, Panchal SC, Mali RS, Kohlhapp FJ, McClure RA, Ramathal CY, George MD, Jhala M, Elsen NL, Qiu W, Judge RA, Pan C, Mastracchio A, Henderson J, Meulbroek JA, Green MR, Pappano WN. Inhibition of MALT1 and BCL2 induces synergistic anti-tumor activity in models of B cell lymphoma. Mol Cancer Ther 2024:741916. [PMID: 38507740 DOI: 10.1158/1535-7163.mct-23-0518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/21/2023] [Accepted: 03/18/2024] [Indexed: 03/22/2024]
Abstract
The activated B cell (ABC) subset of diffuse large B cell lymphoma (DLBCL) is characterized by chronic B cell receptor signaling and associated with poor outcomes when treated with standard therapy. In ABC-DLBCL, MALT1 is a core enzyme that is constitutively activated by stimulation of the B cell receptor or gain-of-function mutations in upstream components of the signaling pathway, making it an attractive therapeutic target. We discovered a novel small molecule inhibitor, ABBV-MALT1, that potently shuts down B cell signaling selectively in ABC-DLBCL preclinical models leading to potent cell growth and xenograft inhibition. We also identified a rational combination partner for ABBV-MALT1 in the BCL2 inhibitor, venetoclax, which when combined significantly synergizes to elicit deep and durable responses in preclinical models. This work highlights the potential of ABBV-MALT1 monotherapy and combination with venetoclax as effective treatment options for patients with ABC-DLBCL.
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Affiliation(s)
| | | | - Haopeng Yang
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Estela Rojas
- MD Anderson Cancer Center, Houston, TX, United States
| | | | | | | | - Ashley Wilson
- MD Anderson Cancer Center, Houston, TX, United States
| | | | | | - Paul Jung
- AbbVie Inc., North Chicago, Il, United States
| | | | | | | | | | | | | | | | | | | | | | - Wei Qiu
- AbbVie Inc., North Chicago, Il, United States
| | | | - Chin Pan
- AbbVie Inc., South San Francisco, California, United States
| | | | - Jared Henderson
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | | | - Michael R Green
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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2
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Petros AM, Korepanova A, Jakob CG, Qiu W, Panchal SC, Wang J, Dietrich JD, Brewer JT, Pohlki F, Kling A, Wilcox K, Lakics V, Bahnassawy L, Reinhardt P, Partha SK, Bodelle PM, Lake M, Charych EI, Stoll VS, Sun C, Mohler EG. Fragment-Based Discovery of an Apolipoprotein E4 (apoE4) Stabilizer. J Med Chem 2019; 62:4120-4130. [PMID: 30933499 DOI: 10.1021/acs.jmedchem.9b00178] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Apolipoprotein E is a 299-residue lipid carrier protein produced in both the liver and the brain. The protein has three major isoforms denoted apoE2, apoE3, and apoE4 which differ at positions 112 and 158 and which occur at different frequencies in the human population. Genome-wide association studies indicate that the possession of two apoE4 alleles is a strong genetic risk factor for late-onset Alzheimer's disease (LOAD). In an attempt to identify a small molecule stabilizer of apoE4 function that may have utility as a therapy for Alzheimer's disease, we carried out an NMR-based fragment screen on the N-terminal domain of apoE4 and identified a benzyl amidine based fragment binder. In addition to NMR, binding was characterized using various other biophysical techniques, and a crystal structure of the bound core was obtained. Core elaboration ultimately yielded a compound that showed activity in an IL-6 and IL-8 cytokine release assay.
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Affiliation(s)
- Andrew M Petros
- Research & Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
| | - Alla Korepanova
- Research & Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
| | - Clarissa G Jakob
- Research & Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
| | - Wei Qiu
- Research & Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
| | - Sanjay C Panchal
- Research & Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
| | - Jie Wang
- Research & Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
| | - Justin D Dietrich
- Research & Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
| | - Jason T Brewer
- Research & Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
| | - Frauke Pohlki
- Neuroscience Research , AbbVie Deutschland GmbH & Co. KG , Knollstrasse , 67061 Ludwigshafen , Germany
| | - Andreas Kling
- Neuroscience Research , AbbVie Deutschland GmbH & Co. KG , Knollstrasse , 67061 Ludwigshafen , Germany
| | - Kyle Wilcox
- Research & Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
| | - Viktor Lakics
- Neuroscience Research , AbbVie Deutschland GmbH & Co. KG , Knollstrasse , 67061 Ludwigshafen , Germany
| | - Lamiaa Bahnassawy
- Neuroscience Research , AbbVie Deutschland GmbH & Co. KG , Knollstrasse , 67061 Ludwigshafen , Germany
| | - Peter Reinhardt
- Neuroscience Research , AbbVie Deutschland GmbH & Co. KG , Knollstrasse , 67061 Ludwigshafen , Germany
| | - Sarathy Karunan Partha
- Research & Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
| | - Pierre M Bodelle
- Research & Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
| | - Marc Lake
- Research & Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
| | - Erik I Charych
- AbbVie Neuroscience Research , 200 Sydney Street , Cambridge , Massachusetts 02139 , United States
| | - Vincent S Stoll
- Research & Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
| | - Chaohong Sun
- Research & Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
| | - Eric G Mohler
- Research & Development , AbbVie , 1 North Waukegan Road , North Chicago , Illinois 60064 , United States
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Low KE, Karunan Partha S, Davies PL, Campbell RL. Allosteric inhibitors of calpains: Reevaluating inhibition by PD150606 and LSEAL. Biochim Biophys Acta Gen Subj 2014; 1840:3367-73. [PMID: 25196359 DOI: 10.1016/j.bbagen.2014.08.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 08/26/2014] [Accepted: 08/28/2014] [Indexed: 10/24/2022]
Abstract
BACKGROUND The mercaptoacrylate calpain inhibitor, PD150606, has been shown by X-ray crystallography to bind to a hydrophobic groove in the enzyme's penta-EF-hand domains far away from the catalytic cleft and has been previously described as an uncompetitive inhibitor of calpains. The penta-peptide LSEAL has been reported to be an inhibitor of calpain and was predicted to bind in the same hydrophobic groove. The X-ray crystal structure of calpain-2 bound to its endogenous calpain inhibitor, calpastatin, shows that calpastatin also binds to the hydrophobic grooves in the two penta-EF-hand domains, but its inhibitory domain binds to the protease core domains and blocks the active site cleft directly. METHODS The mechanisms of inhibition by PD150606 and LSEAL were investigated using steady-state kinetics of cleavage of a fluorogenic substrate by calpain-2 and the protease core of calpain1, as well as by examining the inhibition of casein hydrolysis by calpain and the autoproteolysis of calpain. RESULTS PD150606 inhibits both full-length calpain-2 and the protease core of calpain-1 with an apparent noncompetitive kinetic model. The penta-peptide LSEAL failed to inhibit either whole calpain or its protease core in vitro. CONCLUSIONS PD150606 cannot inhibit cleavage by calpain-2 of small substrates via binding to the penta-EF-hand domain. GENERAL SIGNIFICANCE PD150606 is often described as a calpain-specific inhibitor due to its ability to target the penta-EF-hand domains of calpain, but we show that it must be acting at a site on the protease core domain instead.
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Affiliation(s)
- Kristin E Low
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada.
| | - Sarathy Karunan Partha
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada.
| | - Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada.
| | - Robert L Campbell
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada.
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Guo S, Garnham CP, Karunan Partha S, Campbell RL, Allingham JS, Davies PL. Role of Ca2+in folding the tandem β-sandwich extender domains of a bacterial ice-binding adhesin. FEBS J 2013; 280:5919-32. [DOI: 10.1111/febs.12518] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 08/24/2013] [Accepted: 09/02/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Shuaiqi Guo
- The Protein Function Discovery Group; Department of Biomedical and Molecular Sciences; Queen's University; Kingston Ontario Canada
| | - Christopher P. Garnham
- The Protein Function Discovery Group; Department of Biomedical and Molecular Sciences; Queen's University; Kingston Ontario Canada
| | - Sarathy Karunan Partha
- The Protein Function Discovery Group; Department of Biomedical and Molecular Sciences; Queen's University; Kingston Ontario Canada
| | - Robert L. Campbell
- The Protein Function Discovery Group; Department of Biomedical and Molecular Sciences; Queen's University; Kingston Ontario Canada
| | - John S. Allingham
- The Protein Function Discovery Group; Department of Biomedical and Molecular Sciences; Queen's University; Kingston Ontario Canada
| | - Peter L. Davies
- The Protein Function Discovery Group; Department of Biomedical and Molecular Sciences; Queen's University; Kingston Ontario Canada
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Karunan Partha S, Sadeghi-Khomami A, Cren S, Robinson RI, Woodward S, Slowski K, Berast L, Zheng B, Thomas NR, Sanders DAR. Identification of Novel Inhibitors of UDP-Galactopyranose Mutase by Structure-Based Virtual Screening. Mol Inform 2011; 30:873-83. [PMID: 27468107 DOI: 10.1002/minf.201100085] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Accepted: 07/25/2010] [Indexed: 11/08/2022]
Abstract
UDP-galactopyranose mutase (UGM) is a flavo-enzyme involved in the bacterial cell wall biosynthesis. UGM catalyzes the reversible isomerization of UDP-galactopyranose (UDP-Galp) to UDP-galactofuranose (UDP-Galf). UDP-Galf is the activated precursor of galactofuranose (Galf) residues that are essential components of the cell wall of certain pathogenic bacteria such as Klebsiella pneumoniae and Mycobacterium tuberculosis. Neither UGM nor Galf residues are found in humans, making Galf biosynthesis a potential drug target for developing antibacterial agents. We report the identification of novel inhibitors of UGM by in silico docking of the LeadQuest compound database against UGM from Escherichia coli. The 13 most promising inhibitors were then evaluated against K. pneumonia and M. tuberculosis UGMs by enzyme inhibition studies. Two inhibitors were identified with IC50 values of ∼1 µM and subsequently these compounds were docked into the recently solved X-ray structure of Deinococcus radiodurans UGM. The structure-activity relationships of the initial 13 compounds evaluated as inhibitors are discussed.
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Affiliation(s)
- Sarathy Karunan Partha
- Department of Chemistry, University of Saskatchewa, 110 Science Place, Saskatoon, SK, Canada S7N 5C9
| | - Ali Sadeghi-Khomami
- Centre for Biomolecular Sciences, School of Chemistry, The University of Nottingham, University Park, Nottingham, UK
| | - Sylvaine Cren
- Centre for Biomolecular Sciences, School of Chemistry, The University of Nottingham, University Park, Nottingham, UK
| | - Richard I Robinson
- Centre for Biomolecular Sciences, School of Chemistry, The University of Nottingham, University Park, Nottingham, UK
| | - Simon Woodward
- Centre for Biomolecular Sciences, School of Chemistry, The University of Nottingham, University Park, Nottingham, UK
| | - Kate Slowski
- Department of Chemistry, University of Saskatchewa, 110 Science Place, Saskatoon, SK, Canada S7N 5C9
| | - Lindsey Berast
- Department of Chemistry, University of Saskatchewa, 110 Science Place, Saskatoon, SK, Canada S7N 5C9
| | - Blake Zheng
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Neil R Thomas
- Centre for Biomolecular Sciences, School of Chemistry, The University of Nottingham, University Park, Nottingham, UK.
| | - David A R Sanders
- Department of Chemistry, University of Saskatchewa, 110 Science Place, Saskatoon, SK, Canada S7N 5C9.
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Partha SK, Sadeghi-Khomami A, Slowski K, Kotake T, Thomas NR, Jakeman DL, Sanders DAR. Chemoenzymatic synthesis, inhibition studies, and X-ray crystallographic analysis of the phosphono analog of UDP-Galp as an inhibitor and mechanistic probe for UDP-galactopyranose mutase. J Mol Biol 2010; 403:578-90. [PMID: 20850454 DOI: 10.1016/j.jmb.2010.08.053] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 08/27/2010] [Accepted: 08/30/2010] [Indexed: 12/01/2022]
Abstract
UDP (uridine diphosphate) galactopyranose mutase (UGM) is involved in the cell wall biosynthesis of many pathogenic microorganisms. UGM catalyzes the reversible conversion of UDP-α-D-galactopyranose into UDP-α-D-galactofuranose, with the latter being the precursor of galactofuranose (Galf) residues in cell walls. Glycoconjugates of Galf are essential components in the cell wall of various pathogenic bacteria, including Mycobacterium tuberculosis, the causative agent of tuberculosis. The absence of Galf in humans and its bacterial requirement make UGM a potential target for developing novel antibacterial agents. In this article, we report the synthesis, inhibitory activity, and X-ray crystallographic studies of UDP-phosphono-galactopyranose, a nonhydrolyzable C-glycosidic phosphonate. This is the first report on the synthesis of a phosphonate analog of UDP-α-D-galactopyranose by a chemoenzymatic phosphoryl coupling method. The phosphonate was evaluated against three bacterial UGMs and showed only moderate inhibition. We determined the crystal structure of the phosphonate analog bound to Deinococcus radiodurans UGM at 2.6 Å resolution. The phosphonate analog is bound in a novel conformation not observed in UGM-substrate complex structures or in other enzyme-sugar nucleotide phosphonate complexes. This complex structure provides a structural basis for the observed micromolar inhibition towards UGM. Steric clashes, loss of electrostatic stabilization between an active-site arginine (Arg305) and the phosphonate analog, and a 180° flip of the hexose moiety account for the differences in the binding orientations of the isosteric phosphonate analog and the physiological substrate. This provides new insight into the ability of a sugar-nucleotide-binding enzyme to orient a substrate analog in an unexpected geometry and should be taken into consideration in designing such enzyme inhibitors.
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Partha SK, van Straaten KE, Sanders DAR. Structural basis of substrate binding to UDP-galactopyranose mutase: crystal structures in the reduced and oxidized state complexed with UDP-galactopyranose and UDP. J Mol Biol 2009; 394:864-77. [PMID: 19836401 DOI: 10.1016/j.jmb.2009.10.013] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Revised: 10/07/2009] [Accepted: 10/08/2009] [Indexed: 11/25/2022]
Abstract
D-Galactofuranose (Galf) residues are found in the cell walls of pathogenic microbes such as Mycobacterium tuberculosis, and are essential for viability. UDP-galactopyranose mutase (UGM) is a unique flavo-enzyme that catalyzes the reversible conversion of UDP-galactopyranose (UDP-Galp) and UDP-galactofuranose (UDP-Galf). UDP-Galf is the active precursor of Galf residues found in cell walls. Despite the wealth of biochemical/mechanistic data generated for UGM, the structural basis of substrate binding is still lacking. Here, we report the crystal structures of UGM from Deinococcus radiodurans (drUGM) in complex with its natural substrate (UDP-Galp) and UDP. Crystal structures of drUGM:UDP-Galp complexes with oxidized and reduced FAD were determined at 2.36 A and 2.50 A resolution, respectively. The substrate is buried in the active site in an unusual folded conformation and the anomeric carbon of the galactose is at a favorable distance (2.8 A) from N5 of FAD to form an FAD-galactose adduct. The mobile loops in the substrate complex structure exist in a closed conformation. The drUGM-UDP complex structure was determined at 2.55 A resolution and its overall structure is identical with that of the oxidized and reduced complexes, including the conformation of the mobile loops. Comparison with the recently reported UGM:UDP-glucose complex structure reveals key differences and the structures reported here are likely to represent the productive/active conformation of UGM. These structures provide valuable insights into substrate recognition and a basis for understanding the mechanism. These complex structures may serve as a platform for structure-guided design of inhibitors of UGM.
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Affiliation(s)
- Sarathy Karunan Partha
- Department of Chemistry, 110 Science Place, University of Saskatchewan, Saskatoon, Canada S7N 5C9
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Karunan Partha S, Bonderoff SA, van Straaten KE, Sanders DAR. Expression, purification and preliminary X-ray crystallographic analysis of UDP-galactopyranose mutase from Deinococcus radiodurans. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:843-5. [PMID: 19652355 PMCID: PMC2720349 DOI: 10.1107/s1744309109027754] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2009] [Accepted: 07/14/2009] [Indexed: 11/10/2022]
Abstract
UDP-galactopyranose mutase (UGM) catalyzes the interconversion of UDP-galactopyranose and UDP-galactofuranose. A UGM-substrate complex from Deinococccus radiodurans has been expressed, purified and crystallized. Crystals were obtained by the microbatch-under-oil method at room temperature. The crystals diffracted to 2.36 A resolution at the Canadian Light Source. The space group was found to be P2(1)2(1)2(1), with unit-cell parameters a = 134.0, b = 176.6, c = 221.6 A. The initial structure solution was determined by molecular replacement using UGM from Mycobacterium tuberculosis (PDB code 1v0j) as a template model.
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Affiliation(s)
- Sarathy Karunan Partha
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, Saskatchewan S7N 5C9, Canada
| | - Sara A. Bonderoff
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, Saskatchewan S7N 5C9, Canada
| | - Karin E. van Straaten
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, Saskatchewan S7N 5C9, Canada
| | - David A. R. Sanders
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, Saskatchewan S7N 5C9, Canada
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