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Schade M, Merla B, Lesch B, Wagener M, Timmermanns S, Pletinckx K, Hertrampf T. Highly Selective Sub-Nanomolar Cathepsin S Inhibitors by Merging Fragment Binders with Nitrile Inhibitors. J Med Chem 2020; 63:11801-11808. [PMID: 32880457 DOI: 10.1021/acs.jmedchem.0c00949] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Pharmacological inhibition of cathepsin S (CatS) allows for a specific modulation of the adaptive immune system and many major diseases. Here, we used NMR fragment screening and crystal structure-aided merging to synthesize novel, highly selective CatS inhibitors with picomolar enzymatic Ki values and nanomolar functional activity in human Raji cells. Noncovalent fragment hits revealed binding hotspots, while the covalent inhibitor structure-activity relationship enabled efficient potency optimization.
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Affiliation(s)
- Markus Schade
- Grünenthal GmbH, Zieglerstr. 6, 52078 Aachen, Germany
| | - Beatrix Merla
- Grünenthal GmbH, Zieglerstr. 6, 52078 Aachen, Germany
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Zwicker JD, Smith D, Guerra AJ, Hitchens JR, Haug N, Vander Roest S, Lee P, Wen B, Sun D, Wang L, Keep RF, Xiang J, Carruthers VB, Larsen SD. Discovery and Optimization of Triazine Nitrile Inhibitors of Toxoplasma gondii Cathepsin L for the Potential Treatment of Chronic Toxoplasmosis in the CNS. ACS Chem Neurosci 2020; 11:2450-2463. [PMID: 32027110 DOI: 10.1021/acschemneuro.9b00674] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
With roughly 2 billion people infected, the neurotropic protozoan Toxoplasma gondii remains one of the most pervasive and infectious parasites. Toxoplasma infection is the second leading cause of death due to foodborne illness in the United States, causes severe disease in immunocompromised patients, and is correlated with several cognitive and neurological disorders. Currently, no therapies exist that are capable of eliminating the persistent infection in the central nervous system (CNS). In this study we report the identification of triazine nitrile inhibitors of Toxoplasma cathepsin L (TgCPL) from a high throughput screen and their subsequent optimization. Through rational design, we improved inhibitor potency to as low as 5 nM, identified pharmacophore features that can be exploited for isoform selectivity (up to 7-fold for TgCPL versus human isoform), and improved metabolic stability (t1/2 > 60 min in mouse liver microsomes) guided by a metabolite ID study. We demonstrated that this class of compounds is capable of crossing the blood-brain barrier in mice (1:1 brain/plasma at 2 h). Importantly, we also show for the first time that treatment of T. gondii bradyzoite cysts in vitro with triazine nitrile inhibitors reduces parasite viability with efficacy equivalent to a TgCPL genetic knockout.
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Affiliation(s)
- Jeffery D. Zwicker
- Vahlteich Medicinal Chemistry Core, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - David Smith
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Alfredo J. Guerra
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jacob R. Hitchens
- Vahlteich Medicinal Chemistry Core, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Nicole Haug
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Steve Vander Roest
- Center for Chemical Genomics, Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Pil Lee
- Vahlteich Medicinal Chemistry Core, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Bo Wen
- Pharmacokinetics Core, Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Duxin Sun
- Pharmacokinetics Core, Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Lu Wang
- Pharmacokinetics Core, Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Richard F. Keep
- Department of Neurosurgery, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jianming Xiang
- Department of Neurosurgery, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Vern B. Carruthers
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Scott D. Larsen
- Vahlteich Medicinal Chemistry Core, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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Cysteine proteases as therapeutic targets: does selectivity matter? A systematic review of calpain and cathepsin inhibitors. Acta Pharm Sin B 2015; 5:506-19. [PMID: 26713267 PMCID: PMC4675809 DOI: 10.1016/j.apsb.2015.08.001] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 07/09/2015] [Accepted: 07/14/2015] [Indexed: 01/17/2023] Open
Abstract
Cysteine proteases continue to provide validated targets for treatment of human diseases. In neurodegenerative disorders, multiple cysteine proteases provide targets for enzyme inhibitors, notably caspases, calpains, and cathepsins. The reactive, active-site cysteine provides specificity for many inhibitor designs over other families of proteases, such as aspartate and serine; however, a) inhibitor strategies often use covalent enzyme modification, and b) obtaining selectivity within families of cysteine proteases and their isozymes is problematic. This review provides a general update on strategies for cysteine protease inhibitor design and a focus on cathepsin B and calpain 1 as drug targets for neurodegenerative disorders; the latter focus providing an interesting query for the contemporary assumptions that irreversible, covalent protein modification and low selectivity are anathema to therapeutic safety and efficacy.
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Key Words
- AD, Alzheimer׳s disease
- ALS, amyotrophic lateral sclerosis
- APP, amyloid precursor protein
- APP/PS1, Aβ overexpressing mice APP (K670N/M671L) and PS1 (M146L) mutants
- Ala, alanine
- Alzheimer׳s disease
- AppLon, London familial amyloid precursor protein mutation, APP (V717I)
- AppSwe, Swedish amyloid precursor protein mutation, APP (K670N/M671L)
- Arg, arginine
- Aβ, amyloid β
- Aβ1-42, amyloid β, 42 amino acid protein
- BACE-1, β-amyloid cleaving enzyme
- BBB, blood–brain barrier
- CANP, calcium-activated neutral protease
- CNS, central nervous system
- CREB, cyclic adenosine monophosphate response element binding protein
- CaMKII, Ca2+/calmodulin-dependent protein kinases II
- Calpain
- Cathepsin
- Cdk5/p35, activator of cyclin-dependent kinase 5
- Cysteine protease
- DTT, dithioerythritol
- EGFR, epidermal growth factor receptor
- ERK1/2, extracellular signal-regulated kinase 1/2
- Enzyme inhibitors
- GSH, glutathione
- Gln, glutamine
- Glu, glutamic acid
- Gly, glutamine
- Hsp70.1, heat shock protein 70.1
- Ile, isoleucine
- KO, knockout
- Leu, leucine
- Lys, lysine
- MAP-2, microtubule-associated protein 2
- MMP-9, matrix metalloproteinase 9
- Met, methionine
- NFT, neurofibrilliary tangles
- Neurodegeneration
- Nle, norleucine
- PD, Parkinson׳s disease
- PK, pharmacokinetic
- PKC, protein kinase C
- PTP1B, protein-tyrosine phosphatase 1B
- Phe, phenylalanine
- Pro, proline
- SP, senile plaques
- TBI, traumatic brain injury
- TNF, tumor necrosis factor
- Thr, threonine
- Tyr, tyrosine
- Val, valine
- WRX, Trp-Arg containing epoxysuccinate cysteine protease inhibitor
- WT, wildtype
- isoAsp, isoaspartate
- pGlu, pyroglutamate
- pyroGluAβ, pyroglutamate-amyloid β
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Ehmke V, Winkler E, Banner DW, Haap W, Schweizer WB, Rottmann M, Kaiser M, Freymond C, Schirmeister T, Diederich F. Optimization of triazine nitriles as rhodesain inhibitors: structure-activity relationships, bioisosteric imidazopyridine nitriles, and X-ray crystal structure analysis with human cathepsin L. ChemMedChem 2013; 8:967-75. [PMID: 23658062 DOI: 10.1002/cmdc.201300112] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Indexed: 11/10/2022]
Abstract
The cysteine protease rhodesain of Trypanosoma brucei parasites causing African sleeping sickness has emerged as a target for the development of new drug candidates. Based on a triazine nitrile moiety as electrophilic headgroup, optimization studies on the substituents for the S1, S2, and S3 pockets of the enzyme were performed using structure-based design and resulted in inhibitors with inhibition constants in the single-digit nanomolar range. Comprehensive structure-activity relationships clarified the binding preferences of the individual pockets of the active site. The S1 pocket tolerates various substituents with a preference for flexible and basic side chains. Variation of the S2 substituent led to high-affinity ligands with inhibition constants down to 2 nM for compounds bearing cyclohexyl substituents. Systematic investigations on the S3 pocket revealed its potential to achieve high activities with aromatic vectors that undergo stacking interactions with the planar peptide backbone forming part of the pocket. X-ray crystal structure analysis with the structurally related enzyme human cathepsin L confirmed the binding mode of the triazine ligand series as proposed by molecular modeling. Sub-micromolar inhibition of the proliferation of cultured parasites was achieved for ligands decorated with the best substituents identified through the optimization cycles. In cell-based assays, the introduction of a basic side chain on the inhibitors resulted in a 35-fold increase in antitrypanosomal activity. Finally, bioisosteric imidazopyridine nitriles were studied in order to prevent off-target effects with unselective nucleophiles by decreasing the inherent electrophilicity of the triazine nitrile headgroup. Using this ligand, the stabilization by intramolecular hydrogen bonding of the thioimidate intermediate, formed upon attack of the catalytic cysteine residue, compensates for the lower reactivity of the headgroup. The imidazopyridine nitrile ligand showed excellent stability toward the thiol nucleophile glutathione in a quantitative in vitro assay and fourfold lower cytotoxicity than the parent triazine nitrile.
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Affiliation(s)
- Veronika Ehmke
- Laboratorium für Organische Chemie, ETH Zürich, Zürich, Switzerland
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Wiener JJ, Wickboldt AT, Nguyen S, Sun S, Rynberg R, Rizzolio M, Karlsson L, Edwards JP, Grice CA. Pyrazole-based arylalkyne Cathepsin S inhibitors. Part III: Modification of P4 region. Bioorg Med Chem Lett 2013; 23:1070-4. [DOI: 10.1016/j.bmcl.2012.12.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 11/28/2012] [Accepted: 12/10/2012] [Indexed: 11/25/2022]
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1H-Imidazo[4,5-c]pyridine-4-carbonitrile as cathepsin S inhibitors: Separation of desired cellular activity from undesired tissue accumulation through optimization of basic nitrogen pka. Bioorg Med Chem Lett 2011; 21:932-5. [DOI: 10.1016/j.bmcl.2010.12.065] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Revised: 12/14/2010] [Accepted: 12/15/2010] [Indexed: 11/18/2022]
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Standara S, Bouzková K, Straka M, Zacharová Z, Hocek M, Marek J, Marek R. Interpretation of substituent effects on 13C and 15N NMR chemical shifts in 6-substituted purines. Phys Chem Chem Phys 2011; 13:15854-64. [DOI: 10.1039/c1cp20680j] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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van den Hoorn T, Paul P, Jongsma MLM, Neefjes J. Routes to manipulate MHC class II antigen presentation. Curr Opin Immunol 2010; 23:88-95. [PMID: 21112200 DOI: 10.1016/j.coi.2010.11.002] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Accepted: 11/02/2010] [Indexed: 11/28/2022]
Abstract
MHC class II molecules (MHC-II) present antigenic fragments acquired in the endocytic route to the immune system for recognition and activation of CD4+ T cells. This ignites a series of immune responses. MHC-II strongly correlates to most autoimmune diseases. Understanding the biology of MHC-II is therefore expected to translate into novel means of autoimmunity control or immune response improvement. Although the basic cell biology of MHC-II antigen presentation is well understood, many novel aspects have been uncovered in recent years including means of antigen delivery, preparation for MHC-II loading, transport processes and vaccination strategies. We will discuss past, present and future of these insights into the biology of MHC-II.
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Affiliation(s)
- Tineke van den Hoorn
- Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, Netherlands
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Cai J, Robinson J, Belshaw S, Everett K, Fradera X, van Zeeland M, van Berkom L, van Rijnsbergen P, Popplestone L, Baugh M, Dempster M, Bruin J, Hamilton W, Kinghorn E, Westwood P, Kerr J, Rankovic Z, Arbuckle W, Bennett DJ, Jones PS, Long C, Martin I, Uitdehaag JCM, Meulemans T. Trifluoromethylphenyl as P2 for ketoamide-based cathepsin S inhibitors. Bioorg Med Chem Lett 2010; 20:6890-4. [PMID: 21030256 DOI: 10.1016/j.bmcl.2010.10.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Revised: 10/04/2010] [Accepted: 10/05/2010] [Indexed: 10/19/2022]
Abstract
The trifluoromethylphenyl P2 motif from previously reported heteroarylnitrile series has been successfully applied for the design and synthesis of highly potent novel ketoamide-based cathepsin S inhibitors. The key in this process is the change of the torsion angle between the P2 phenyl ring and the attached secondary amide by adding a small Cl, F, or Me group at the 2-position.
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Affiliation(s)
- Jiaqiang Cai
- Merck Research Laboratories, MSD, Newhouse, Lanarkshire, United Kingdom.
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