Repurposing a Library of Human Cathepsin L Ligands: Identification of Macrocyclic Lactams as Potent Rhodesain and<i>Trypanosoma brucei</i>Inhibitors

Giroud, Maude; Dietzel, Uwe; Anselm, Lilli; Banner, David W.; Kuglstatter, A.; Benz, Jörg; Blanc, Jean-Baptiste; Gaufreteau, Delphine; Liu, Haixia; Lin, Xianfeng; Stich, August; Kuhn, Bernd; Schuler, Franz; Kaiser, Marcel; Brun, Reto; Schirmeister, Tanja; Kisker, Caroline; Diederich, François; Haap, Wolfgang

doi:10.1021/acs.jmedchem.7b01869

Cited by 37 publications

(44 citation statements)

References 79 publications

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“…For example, Shenoy et al showed that although Z-Phe-Tyr (O-tert-Butyl)-DMK binds to the same subsites of cathepsin L as observed for the Z-Phe-Tyr (O-tert-Butyl)-C(O)C(H)O ligand and finds some alternative interactions with residues from the active site pocket. This finding has been corroborated by other studies as well that suggest that structural features of ligands can influence the subsite composition of the cathepsin L enzyme [94,95,97,98]. Such information has been duly capitalized to develop different classes of inhibitors that are discussed next.…”

Section: Inhibitory Ligand Inhibition Constant (K I )supporting

confidence: 56%

“…Much excitement remains as new cathepsin L functions continue to emerge from specific cell types in the coming years. 4AXL X-ray 1.92 [190] 4AXM X-ray 2.80 [190] 5F02 X-ray 1.43 [191] 5I4H X-ray 1.42 [192] 5MAE X-ray 1.00 [145] 5MAJ X-ray 1.00 [145] 5MQY X-ray 1.13 [123] 6EZP X-ray 1.37 [98] 6EZX X-ray 2.34 [98] 6F06 X-ray 2.02 [98] Funding: S.K.P. gratefully acknowledges the financial support from the National Science Foundation (NSF); Grant no.…”

Section: Final Perspectivesmentioning

confidence: 99%

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A Review of Small Molecule Inhibitors and Functional Probes of Human Cathepsin L

Dana

Pathak

2020

Molecules

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Human cathepsin L belongs to the cathepsin family of proteolytic enzymes with primarily an endopeptidase activity. Although its primary functions were originally thought to be only of a housekeeping enzyme that degraded intracellular and endocytosed proteins in lysosome, numerous recent studies suggest that it plays many critical and specific roles in diverse cellular settings. Not surprisingly, the dysregulated function of cathepsin L has manifested itself in several human diseases, making it an attractive target for drug development. Unfortunately, several redundant and isoform-specific functions have recently emerged, adding complexities to the drug discovery process. To address this, a series of chemical biology tools have been developed that helped define cathepsin L biology with exquisite precision in specific cellular contexts. This review elaborates on the recently developed small molecule inhibitors and probes of human cathepsin L, outlining their mechanisms of action, and describing their potential utilities in dissecting unknown function.Molecules 2020, 25, 698 2 of 41 also now well established and has been a subject of elegant reviews elsewhere [25][26][27]. Unfortunately, several overlapping and redundant functions of cathepsin L have also emerged [5,[28][29][30]. It is therefore critically important that its functional biology in both normal and disease-specific cell types be clearly annotated before significant resources are directed in drug discovery endeavors. In this review, we will briefly outline the biogenesis of cathepsin L, describe its post-translational processing and trafficking, and highlight key structural features required for formation of an active and mature cathepsin L. A brief summary of cathepsin L biology and its role in human diseases is provided next. Finally, a detailed and up-to-date report on existing cathepsin L-targeting small molecule inhibitors and functional probes with their mechanistic details is described.Human cathepsin L gene, CTHL (Uniprot primary accession number: P07711), located at the 9q21-q22 position of chromosome 9, encodes for a total of 333 amino acid peptide sequence (M.W. = 37,564 kDa) [31]. The coding space includes the regions of a N-terminal signal peptide, two pro-peptides, and two mature peptides comprising of a heavy (H) chain and a light (L) chain ( Figure 1). After transcription, the signal peptide is co-translationally removed in polysome and the resulting 41 kDa pro-cathepsin L is translocated to endoplasmic reticulum where it undergoes N-linked glycosylation with mannose rich sugars. The mannose sugars on the pro-cathepsin L are then phosphorylated in cis Golgi by UDP-N-acetylglucosamine:N-acetylglucosaminephosphotransferase enzyme [32]. The mannose-6-phosphate (M6P) receptors located on the surface of the trans Golgi network recognize the M6P-pro-cathepsin peptide and deliver the pro-cathepsin L peptide to the lysosome via the endolysosomal pathway. The weakly acidic environment of endosome/lysosome releases M6P receptors and the phosphate ...

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Section: Inhibitory Ligand Inhibition Constant (K I )supporting

confidence: 56%

Section: Final Perspectivesmentioning

confidence: 99%

A Review of Small Molecule Inhibitors and Functional Probes of Human Cathepsin L

Dana

Pathak

2020

Molecules

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“…Insilico testing offers immediate insight into pathways and drugs that interact with these pathways to promote or inhibit their activity. Eleven studies have been published about previous drugrepositioning efforts for SARS-FCoVs [9][10][11][12][13][14][15][16][17][18][19]. These studies were identified using the keywords ("Drug Repurposing" OR "Drug Repositioning") AND (SARS OR MERS OR coronavirus OR COVID-19 OR SARS-CoV-2).…”

Section: Introductionmentioning

confidence: 99%

Drug Repositioning Suggests a Role for the Heat Shock Protein 90 Inhibitor Geldanamycin in Treating COVID-19 Infection

Sultan¹,

Howard²,

Tbakhi³

2020

Preprint

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Drug repositioning offers an unmatched opportunity to offer novel therapeutics to treat SARS family of coronaviruses (SARS-FCoVs); an issue that became extremely urgent with the spreading of a novel virus with potential to threaten the lives of millions of people. Hereby, we analyzed a dataset of patients who presented with SARS during the 2003 outbreak. We established a gene signature that defines differential gene expression in patients who were sick with SARS vs. healthy controls and convalescent patients. We used a robust platform to conduct drug repositioning based on clustered gene expression and pathway enrichment to identify best matching drugs. We identified 55 agents of potential benefit. In most of these drugs we were able to establish a link to previous related research, use as antiviral, or at least a hypothetical role in treating SARS-FCoVs. Most notably, the heat shock protein 90 (hsp90) emerged as a major component that enables viruses to hijack infected cells through the process of autophagy. Almost half of the drugs identified could be linked to hsp90. As such, we propose using hsp90 inhibitors, mainly geldanamycin and its derivatives, to treat COVID-19.

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“…[54] For structure determination, the previously determined structure of mature rhodesain in complex with a macrolactam inhibitor (PDB: 6EX8) was used as a model for molecular replacement with PhaserMR of the phenix work suites after removal of the ligand and all water molecules. [24,[54][55][56] The prodomain was then built into the remaining electron density and final refinement was done with WinCoot. [57] MD simulations MD simulations were performed with the crystal structure of pro-rhodesain described in this manuscript but containing an active site cysteine residue instead of alanine.…”

Section: X-ray Crystallographymentioning

confidence: 99%

“…[18][19][20][21] The cleavage site is located in the linker between the pro-domain and the core protease domain. [22,23] While the rhodesain core protease domain has been crystallized in complex with different inhibitors including K11777 (PDB: 2P7U) [23][24][25][26] , a structure of the zymogen as an important intermediate of the parasitic protease maturation process is currently not available. In addition, the molecular details of the pH-dependent cleavage process remain unclear.…”

Section: Introductionmentioning

confidence: 99%

Structure, interdomain dynamics and pH-dependent autoactivation of pro-rhodesain, the main lysosomal cysteine protease from African trypanosomes

Johé¹,

Jaenicke²,

Neuweiler³

et al. 2020

Preprint

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Rhodesain is the lysosomal cathepsin L-like cysteine protease of T. brucei rhodesiense, the causative agent of Human African Trypanosomiasis. The enzyme is essential for the proliferation and pathogenicity of the parasite as well as its ability to overcome the blood-brain barrier of the host. Lysosomal cathepsins are expressed as zymogens with an inactivating pro-domain that is cleaved under acidic conditions. A structure of the uncleaved maturation intermediate from a trypanosomal cathepsin L-like protease is currently not available. We thus established the heterologous expression of T. brucei rhodesiense pro-rhodesain in E. coli and determined its crystal structure. The trypanosomal pro-domain differs from non-parasitic pro-cathepsins by a unique, extended α-helix that blocks the active site and whose interactions resemble that of the antiprotozoal inhibitor K11777. Interdomain dynamics between pro- and core protease domain as observed by photoinduced electron transfer fluorescence correlation spectroscopy increase at low pH, where pro-rhodesain also undergoes autocleavage. Using the crystal structure, molecular dynamics simulations and mutagenesis, we identify a conserved interdomain salt bridge that prevents premature intramolecular cleavage at higher pH values and may thus present a control switch for the observed pH-sensitivity of pro-enzyme cleavage in (trypanosomal) CathL-like proteases.

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Repurposing a Library of Human Cathepsin L Ligands: Identification of Macrocyclic Lactams as Potent Rhodesain andTrypanosoma bruceiInhibitors

Cited by 37 publications

References 79 publications

A Review of Small Molecule Inhibitors and Functional Probes of Human Cathepsin L

A Review of Small Molecule Inhibitors and Functional Probes of Human Cathepsin L

Drug Repositioning Suggests a Role for the Heat Shock Protein 90 Inhibitor Geldanamycin in Treating COVID-19 Infection

Structure, interdomain dynamics and pH-dependent autoactivation of pro-rhodesain, the main lysosomal cysteine protease from African trypanosomes

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