1
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Feral A, Martin AR, Desfoux A, Amblard M, Vezenkov LL. Covalent-reversible peptide-based protease inhibitors. Design, synthesis, and clinical success stories. Amino Acids 2023; 55:1775-1800. [PMID: 37330416 DOI: 10.1007/s00726-023-03286-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/22/2023] [Indexed: 06/19/2023]
Abstract
Dysregulated human peptidases are implicated in a large variety of diseases such as cancer, hypertension, and neurodegeneration. Viral proteases for their part are crucial for the pathogens' maturation and assembly. Several decades of research were devoted to exploring these precious therapeutic targets, often addressing them with synthetic substrate-based inhibitors to elucidate their biological roles and develop medications. The rational design of peptide-based inhibitors offered a rapid pathway to obtain a variety of research tools and drug candidates. Non-covalent modifiers were historically the first choice for protease inhibition due to their reversible enzyme binding mode and thus presumably safer profile. However, in recent years, covalent-irreversible inhibitors are having a resurgence with dramatic increase of their related publications, preclinical and clinical trials, and FDA-approved drugs. Depending on the context, covalent modifiers could provide more effective and selective drug candidates, hence requiring lower doses, thereby limiting off-target effects. Additionally, such molecules seem more suitable to tackle the crucial issue of cancer and viral drug resistances. At the frontier of reversible and irreversible based inhibitors, a new drug class, the covalent-reversible peptide-based inhibitors, has emerged with the FDA approval of Bortezomib in 2003, shortly followed by 4 other listings to date. The highlight in the field is the breathtakingly fast development of the first oral COVID-19 medication, Nirmatrelvir. Covalent-reversible inhibitors can hipothetically provide the safety of the reversible modifiers combined with the high potency and specificity of their irreversible counterparts. Herein, we will present the main groups of covalent-reversible peptide-based inhibitors, focusing on their design, synthesis, and successful drug development programs.
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Affiliation(s)
- Anthony Feral
- IBMM, University Montpellier, CNRS, ENSCM, Montpellier, France
| | | | | | - Muriel Amblard
- IBMM, University Montpellier, CNRS, ENSCM, Montpellier, France
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2
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Martins LC, de Oliveira RB, Lameira J, Ferreira RS. Experimental and Computational Study of Aryl-thiosemicarbazones Inhibiting Cruzain Reveals Reversible Inhibition and a Stepwise Mechanism. J Chem Inf Model 2023; 63:1506-1520. [PMID: 36802548 DOI: 10.1021/acs.jcim.2c01566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Trypanosoma cruzi is a parasite that infects about 6-7 million people worldwide, mostly in Latin America, causing Chagas disease. Cruzain, the main cysteine protease of T. cruzi, is a validated target for developing drug candidates for Chagas disease. Thiosemicarbazones are one of the most relevant warheads used in covalent inhibitors targeting cruzain. Despite its relevance, the mechanism of inhibition of cruzain by thiosemicarbazones is unknown. Here, we combined experiments and simulations to unveil the covalent inhibition mechanism of cruzain by a thiosemicarbazone-based inhibitor (compound 1). Additionally, we studied a semicarbazone (compound 2), which is structurally similar to compound 1 but does not inhibit cruzain. Assays confirmed the reversibility of inhibition by compound 1 and suggested a two-step mechanism of inhibition. The Ki was estimated to be 36.3 μM and Ki* to be 11.5 μM, suggesting the pre-covalent complex to be relevant for inhibition. Molecular dynamics simulations of compounds 1 and 2 with cruzain were used to propose putative binding modes for the ligands. One-dimensional (1D) quantum mechanics/molecular mechanics (QM/MM) potential of mean force (PMF) and gas-phase energies showed that the attack of Cys25-S- on the C═S or C═O bond yields a more stable intermediate than the attack on the C═N bond of the thiosemicarbazone/semicarbazone. Two-dimensional (2D) QM/MM PMF revealed a putative reaction mechanism for compound 1, involving the proton transfer to the ligand, followed by the Cys25-S- attack at C═S. The ΔG and energy barrier were estimated to be -1.4 and 11.7 kcal/mol, respectively. Overall, our results shed light on the inhibition mechanism of cruzain by thiosemicarbazones.
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Affiliation(s)
- Luan Carvalho Martins
- Molecular Modeling and Drug Design Laboratory, Institute for Biological Sciences, Federal University of Minas Gerais, 6627, Antônio Carlos Avenue, 31270-901 Belo Horizonte, MG, Brazil
| | - Renata Barbosa de Oliveira
- Pharmaceutical Products Department, Faculty of Pharmacy, Federal University of Minas Gerais, 6627, Antônio Carlos Avenue, 31270-901 Belo Horizonte, MG, Brazil
| | - Jerônimo Lameira
- Institute of Biological Sciences, Federal University of Pará, 66075-110 Belém, Pará, Brazil
| | - Rafaela Salgado Ferreira
- Molecular Modeling and Drug Design Laboratory, Institute for Biological Sciences, Federal University of Minas Gerais, 6627, Antônio Carlos Avenue, 31270-901 Belo Horizonte, MG, Brazil
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3
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Differentiated Immunohistochemical Expression of Osteoclastogenic Markers in Radicular Cyst, Odontogenic Keratocyst, and Ameloblastoma. Appl Immunohistochem Mol Morphol 2021; 29:352-358. [PMID: 33944809 DOI: 10.1097/pai.0000000000000911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 12/29/2020] [Indexed: 11/25/2022]
Abstract
The aim of this study was to investigate the osteoclastogenesis process by means of immunohistochemical markers for receptor activator of nuclear factor κB ligand (RANKL), osteoprotegerin (OPG), interleukin-6 (IL-6), and cathepsin K (CTSK) antigens in osteolytic lesions of maxillary bones. The sample consisted of 23 radicular cysts (RC), 25 odontogenic keratocysts (OKC), and 25 ameloblastomas (AM). RANKL was statistically higher in RC (49.6±15.2/53.7±18) and OKC (48.6±15.1/51.4±16.8) when compared with AM (37.2±12.5/36.4±13) in the epithelium and connective tissue. OPG was lower in OKC (34.8±18.5) only in connective tissue when compared with RC (44.5±11.2). The expression of RANKL was statistically higher than OPG in RC (epithelium and connective tissue) and OKC (connective tissue). For IL-6, a statistical difference was observed only in the connective tissue between groups, with higher expression in RC (48.2±15) and lower in OKC (22±11.9). The expression of IL-6 was correlated with the intensity of the inflammatory infiltrate. CTSK was statistically higher in AM (34±19) and OKC (29±13.8) compared with RC (19±10.5). According to the results of the present research the bone resorption in cysts and odontogenic tumors occurs through different mechanisms. The ostoclastogenic process in lesions with aggressive clinical behavior, as AM and OKC, seems to be associated with the expression of CTSK. In contrast, lesions with inflammatory etiology, as RC, the expression of IL-6 seems to have an important role in the bone resorption process. The highest expression of RANKL under the expression of OPG also seems to contribute to the growth mechanism of RC and OKC.
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4
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Bogolubsky AV, Moroz YS, Mykhailiuk PK, Dmytriv YV, Pipko SE, Babichenko LN, Konovets AI, Tolmachev A. Facile one-pot synthesis of 4-substituted semicarbazides. RSC Adv 2015. [DOI: 10.1039/c4ra12425a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A simple one-pot approach to 4-substituted semicarbazides allowed us to synthesize a 25 member library.
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Affiliation(s)
| | - Yurii S. Moroz
- Enamine Ltd
- Kyiv
- Ukraine
- ChemBioCenter
- Kyiv National Taras Shevchenko University
| | - Pavel K. Mykhailiuk
- Enamine Ltd
- Kyiv
- Ukraine
- Department of Chemistry
- Kyiv National Taras Shevchenko University
| | | | - Sergey E. Pipko
- ChemBioCenter
- Kyiv National Taras Shevchenko University
- Kyiv
- Ukraine
| | | | - Anzhelika I. Konovets
- Enamine Ltd
- Kyiv
- Ukraine
- The Institute of High Technologies
- Kyiv National Taras Shevchenko University
| | - Andrey Tolmachev
- Enamine Ltd
- Kyiv
- Ukraine
- ChemBioCenter
- Kyiv National Taras Shevchenko University
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5
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Jung ME, Chamberlain BT, Ho CLC, Gillespie EJ, Bradley KA. Structure-Activity Relationship of Semicarbazone EGA Furnishes Photoaffinity Inhibitors of Anthrax Toxin Cellular Entry. ACS Med Chem Lett 2014; 5:363-7. [PMID: 24900841 DOI: 10.1021/ml400486k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 12/26/2013] [Indexed: 11/28/2022] Open
Abstract
EGA, 1, prevents the entry of multiple viruses and bacterial toxins into mammalian cells by inhibiting vesicular trafficking. The cellular target of 1 is unknown, and a structure-activity relationship study was conducted in order to develop a strategy for target identification. A compound with midnanomolar potency was identified (2), and three photoaffinity labels were synthesized (3-5). For this series, the expected photochemistry of the phenyl azide moiety is a more important factor than the IC50 of the photoprobe in obtaining a successful photolabeling event. While 3 was the most effective reversible inhibitor of the series, it provided no protection to cells against anthrax lethal toxin (LT) following UV irradiation. Conversely, 5, which possessed weak bioactivity in the standard assay, conferred robust irreversible protection vs LT to cells upon UV photolysis.
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Affiliation(s)
- Michael E. Jung
- California
NanoSystems Institute, ‡Department of Chemistry and Biochemistry, §Department of Microbiology,
Immunology and Molecular Genetics, University of California, Los Angeles, Los
Angeles, California 90095, United States
| | - Brian T. Chamberlain
- California
NanoSystems Institute, ‡Department of Chemistry and Biochemistry, §Department of Microbiology,
Immunology and Molecular Genetics, University of California, Los Angeles, Los
Angeles, California 90095, United States
| | - Chi-Lee C. Ho
- California
NanoSystems Institute, ‡Department of Chemistry and Biochemistry, §Department of Microbiology,
Immunology and Molecular Genetics, University of California, Los Angeles, Los
Angeles, California 90095, United States
| | - Eugene J. Gillespie
- California
NanoSystems Institute, ‡Department of Chemistry and Biochemistry, §Department of Microbiology,
Immunology and Molecular Genetics, University of California, Los Angeles, Los
Angeles, California 90095, United States
| | - Kenneth A. Bradley
- California
NanoSystems Institute, ‡Department of Chemistry and Biochemistry, §Department of Microbiology,
Immunology and Molecular Genetics, University of California, Los Angeles, Los
Angeles, California 90095, United States
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6
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Álvarez R, Puebla P, Díaz JF, Bento AC, García-Navas R, de la Iglesia-Vicente J, Mollinedo F, Andreu JM, Medarde M, Peláez R. Endowing Indole-Based Tubulin Inhibitors with an Anchor for Derivatization: Highly Potent 3-Substituted Indolephenstatins and Indoleisocombretastatins. J Med Chem 2013; 56:2813-27. [DOI: 10.1021/jm3015603] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Raquel Álvarez
- Laboratorio de Química
Orgánica y Farmacéutica, CIETUS and IBSAL, Facultad
de Farmacia, Universidad de Salamanca,
Campus Miguel de Unamuno, E-37007 Salamanca, Spain
| | - Pilar Puebla
- Laboratorio de Química
Orgánica y Farmacéutica, CIETUS and IBSAL, Facultad
de Farmacia, Universidad de Salamanca,
Campus Miguel de Unamuno, E-37007 Salamanca, Spain
| | | | - Ana C. Bento
- Instituto de Biología Molecular
y Celular del Cáncer, Centro de Investigación del Cáncer, CSIC-Universidad de Salamanca, Campus Miguel de Unamuno,
E-37007 Salamanca, Spain
| | - Rósula García-Navas
- Instituto de Biología Molecular
y Celular del Cáncer, Centro de Investigación del Cáncer, CSIC-Universidad de Salamanca, Campus Miguel de Unamuno,
E-37007 Salamanca, Spain
| | - Janis de la Iglesia-Vicente
- Instituto de Biología Molecular
y Celular del Cáncer, Centro de Investigación del Cáncer, CSIC-Universidad de Salamanca, Campus Miguel de Unamuno,
E-37007 Salamanca, Spain
| | - Faustino Mollinedo
- Instituto de Biología Molecular
y Celular del Cáncer, Centro de Investigación del Cáncer, CSIC-Universidad de Salamanca, Campus Miguel de Unamuno,
E-37007 Salamanca, Spain
| | | | - Manuel Medarde
- Laboratorio de Química
Orgánica y Farmacéutica, CIETUS and IBSAL, Facultad
de Farmacia, Universidad de Salamanca,
Campus Miguel de Unamuno, E-37007 Salamanca, Spain
| | - Rafael Peláez
- Laboratorio de Química
Orgánica y Farmacéutica, CIETUS and IBSAL, Facultad
de Farmacia, Universidad de Salamanca,
Campus Miguel de Unamuno, E-37007 Salamanca, Spain
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7
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Yuan XY, Fu DY, Ren XF, Fang X, Wang L, Zou S, Wu Y. Highly selective aza-nitrile inhibitors for cathepsin K, structural optimization and molecular modeling. Org Biomol Chem 2013; 11:5847-52. [DOI: 10.1039/c3ob41165f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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8
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Allen JG, Fotsch C, Babij P. Emerging Targets in Osteoporosis Disease Modification. J Med Chem 2010; 53:4332-53. [PMID: 20218623 DOI: 10.1021/jm9018756] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- John G. Allen
- Chemistry Research and Discovery, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320
| | - Christopher Fotsch
- Chemistry Research and Discovery, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320
| | - Philip Babij
- Metabolic Disorders, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320
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9
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Bredihhin A, Mäeorg U. Effective strategy for the systematic synthesis of hydrazine derivatives. Tetrahedron 2008. [DOI: 10.1016/j.tet.2008.04.096] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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10
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Proteasome inhibition by peptide-semicarbazones. Bioorg Med Chem 2008; 16:4579-88. [PMID: 18313310 DOI: 10.1016/j.bmc.2008.02.042] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2007] [Revised: 02/07/2008] [Accepted: 02/12/2008] [Indexed: 11/23/2022]
Abstract
Peptide-semicarbazones derived from Z-Trp-Trp-Phe-aldehyde inhibit the chymotryptic activity of the human proteasome at nanomolar concentrations, but are less active in a NFkappaB reporter gene assay. Cyclic semicarbazones, in contrast, combine a strong inhibitory effect on the enzyme with an inhibition of NFkappaB signaling in the nanomolar range. In addition, a practical synthesis for scale-up of such compounds was developed.
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11
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Ma S, Devi-Kesavan LS, Gao J. Molecular dynamics simulations of the catalytic pathway of a cysteine protease: a combined QM/MM study of human cathepsin K. J Am Chem Soc 2007; 129:13633-45. [PMID: 17935329 PMCID: PMC2556303 DOI: 10.1021/ja074222+] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Molecular dynamics simulations using a combined QM/MM potential have been performed to study the catalytic mechanism of human cathepsin K, a member of the papain family of cysteine proteases. We have determined the two-dimensional free energy surfaces of both acylation and deacylation steps to characterize the reaction mechanism. These free energy profiles show that the acylation step is rate limiting with a barrier height of 19.8 kcal/mol in human cathepsin K and of 29.3 kcal/mol in aqueous solution. The free energy of activation for the deacylation step is 16.7 kcal/mol in cathepsin K and 17.8 kcal/mol in aqueous solution. The reduction of free energy barrier is achieved by stabilization of the oxyanion in the transition state. Interestingly, although the "oxyanion hole" has been formed in the Michaelis complex, the amide units do not donate hydrogen bonds directly to the carbonyl oxygen of the substrate, but they stabilize the thiolate anion nucleophile. Hydrogen-bonding interactions are induced as the substrate amide group approaches the nucleophile, moving more than 2 A and placing the oxyanion in contact with Gln19 and the backbone amide of Cys25. The hydrolysis of peptide substrate shares a common mechanism both for the catalyzed reaction in human cathepsin K and for the uncatalyzed reaction in water. Overall, the nucleophilic attack by Cys25 thiolate and the proton-transfer reaction from His162 to the amide nitrogen are highly coupled, whereas a tetrahedral intermediate is formed along the nucleophilic reaction pathway.
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Affiliation(s)
- Shuhua Ma
- Department of Chemistry and Supercomputing Institute, Digital Technology Center, University of Minnesota, 207 Pleasant street SE, Minneapolis, MN 55455
| | - Lakshmi S. Devi-Kesavan
- Department of Chemistry and Supercomputing Institute, Digital Technology Center, University of Minnesota, 207 Pleasant street SE, Minneapolis, MN 55455
| | - Jiali Gao
- Department of Chemistry and Supercomputing Institute, Digital Technology Center, University of Minnesota, 207 Pleasant street SE, Minneapolis, MN 55455
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12
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Lecaille F, Brömme D, Lalmanach G. Biochemical properties and regulation of cathepsin K activity. Biochimie 2007; 90:208-26. [PMID: 17935853 DOI: 10.1016/j.biochi.2007.08.011] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2007] [Accepted: 08/24/2007] [Indexed: 02/02/2023]
Abstract
Cysteine cathepsins (11 in humans) are mostly located in the acidic compartments of cells. They have been known for decades to be involved in intracellular protein degradation as housekeeping proteases. However, the discovery of new cathepsins, including cathepsins K, V and F, has provided strong evidence that they also participate in specific biological events. This review focuses on the current knowledge of cathepsin K, the major bone cysteine protease, which is a drug target of clinical interest. Nevertheless, we will not discuss recent developments in cathepsin K inhibitor design since they have been extensively detailed elsewhere. We will cover features of cathepsin K structure, cellular and tissue distribution, substrate specificity, and regulation (pH, propeptide, glycosaminoglycans, oxidants), and its putative roles in physiological or pathophysiological processes. Finally, we will review the kinetic data of its inhibition by natural endogenous inhibitors (stefin B, cystatin C, H- and L-kininogens).
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Affiliation(s)
- Fabien Lecaille
- INSERM, U618, Protéases et Vectorisation Pulmonaires, Equipe Protéases et Pathologies Pulmonaires, Faculté de Médecine, Université François Rabelais, 10 Boulevard Tonnellé, F-37032 Tours Cedex, France.
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