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Guerra Y, Valiente PA, Pons T, Berry C, Rudiño-Piñera E. Structures of a bi-functional Kunitz-type STI family inhibitor of serine and aspartic proteases: Could the aspartic protease inhibition have evolved from a canonical serine protease-binding loop? J Struct Biol 2016; 195:259-271. [PMID: 27329566 DOI: 10.1016/j.jsb.2016.06.014] [Citation(s) in RCA: 4] [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: 04/09/2016] [Revised: 06/14/2016] [Accepted: 06/18/2016] [Indexed: 01/06/2023]
Abstract
Bi-functional inhibitors from the Kunitz-type soybean trypsin inhibitor (STI) family are glycosylated proteins able to inhibit serine and aspartic proteases. Here we report six crystal structures of the wild-type and a non-glycosylated mutant of the bifunctional inhibitor E3Ad obtained at different pH values and space groups. The crystal structures show that E3Ad adopts the typical β-trefoil fold of the STI family exhibiting some conformational changes due to pH variations and crystal packing. Despite the high sequence identity with a recently reported potato cathepsin D inhibitor (PDI), three-dimensional structures obtained in this work show a significant conformational change in the protease-binding loop proposed for aspartic protease inhibition. The E3Ad binding loop for serine protease inhibition is also proposed, based on structural similarity with a novel non-canonical conformation described for the double-headed inhibitor API-A from the Kunitz-type STI family. In addition, structural and sequence analyses suggest that bifunctional inhibitors of serine and aspartic proteases from the Kunitz-type STI family are more similar to double-headed inhibitor API-A than other inhibitors with a canonical protease-binding loop.
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Affiliation(s)
- Yasel Guerra
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos CP 62210, Mexico.
| | - Pedro A Valiente
- Laboratorio de Biología Computacional y Diseño de Proteínas, Centro de Estudios de Proteínas (CEP), Facultad de Biología, Universidad de La Habana, Cuba
| | - Tirso Pons
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), C/Melchor Fernández Almagro 3, Madrid 28029, Spain
| | - Colin Berry
- Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AT, Wales, UK
| | - Enrique Rudiño-Piñera
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Avenida Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos CP 62210, Mexico.
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Meyers MJ, Anderson EJ, McNitt SA, Krenning TM, Singh M, Xu J, Zeng W, Qin L, Xu W, Zhao S, Qin L, Eickhoff CS, Oliva J, Campbell MA, Arnett SD, Prinsen MJ, Griggs DW, Ruminski PG, Goldberg DE, Ding K, Liu X, Tu Z, Tortorella MD, Sverdrup FM, Chen X. Evaluation of spiropiperidine hydantoins as a novel class of antimalarial agents. Bioorg Med Chem 2015; 23:5144-50. [PMID: 25797165 DOI: 10.1016/j.bmc.2015.02.050] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [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: 01/23/2015] [Revised: 02/23/2015] [Accepted: 02/25/2015] [Indexed: 02/07/2023]
Abstract
Given the rise of parasite resistance to all currently used antimalarial drugs, the identification of novel chemotypes with unique mechanisms of action is of paramount importance. Since Plasmodium expresses a number of aspartic proteases necessary for its survival, we have mined antimalarial datasets for drug-like aspartic protease inhibitors. This effort led to the identification of spiropiperidine hydantoins, bearing similarity to known inhibitors of the human aspartic protease β-secretase (BACE), as new leads for antimalarial drug discovery. Spiropiperidine hydantoins have a dynamic structure-activity relationship profile with positions identified as being tolerant of a variety of substitution patterns as well as a key piperidine N-benzyl phenol pharmacophore. Lead compounds 4e (CWHM-123) and 12k (CWHM-505) are potent antimalarials with IC50 values against Plasmodium falciparum 3D7 of 0.310 μM and 0.099 μM, respectively, and the former features equivalent potency on the chloroquine-resistant Dd2 strain. Remarkably, these compounds do not inhibit human aspartic proteases BACE, cathepsins D and E, or Plasmodium plasmepsins II and IV despite their similarity to known BACE inhibitors. Although the current leads suffer from poor metabolic stability, they do fit into a drug-like chemical property space and provide a new class of potent antimalarial agents for further study.
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Affiliation(s)
- Marvin J Meyers
- Center for World Health and Medicine, Saint Louis University School of Medicine, 1402 South Grand Blvd, M132 Schwitalla Hall, Saint Louis, MO 63104, USA.
| | - Elizabeth J Anderson
- Center for World Health and Medicine, Saint Louis University School of Medicine, 1402 South Grand Blvd, M132 Schwitalla Hall, Saint Louis, MO 63104, USA
| | - Sarah A McNitt
- Center for World Health and Medicine, Saint Louis University School of Medicine, 1402 South Grand Blvd, M132 Schwitalla Hall, Saint Louis, MO 63104, USA
| | - Thomas M Krenning
- Center for World Health and Medicine, Saint Louis University School of Medicine, 1402 South Grand Blvd, M132 Schwitalla Hall, Saint Louis, MO 63104, USA
| | - Megh Singh
- Center for World Health and Medicine, Saint Louis University School of Medicine, 1402 South Grand Blvd, M132 Schwitalla Hall, Saint Louis, MO 63104, USA
| | - Jing Xu
- Drug Discovery Pipeline at the Guangzhou Institutes for Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Wentian Zeng
- Drug Discovery Pipeline at the Guangzhou Institutes for Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Limei Qin
- Laboratory of Pathogen Biology, State Key Laboratory of Respiratory Disease, Center for Infection and Immunity, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, #190, Kaiyuan Avenue, Guangzhou Science Park, Guangzhou 510530, China
| | - Wanwan Xu
- Laboratory of Pathogen Biology, State Key Laboratory of Respiratory Disease, Center for Infection and Immunity, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, #190, Kaiyuan Avenue, Guangzhou Science Park, Guangzhou 510530, China
| | - Siting Zhao
- Laboratory of Pathogen Biology, State Key Laboratory of Respiratory Disease, Center for Infection and Immunity, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, #190, Kaiyuan Avenue, Guangzhou Science Park, Guangzhou 510530, China
| | - Li Qin
- Laboratory of Pathogen Biology, State Key Laboratory of Respiratory Disease, Center for Infection and Immunity, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, #190, Kaiyuan Avenue, Guangzhou Science Park, Guangzhou 510530, China
| | - Christopher S Eickhoff
- Center for World Health and Medicine, Saint Louis University School of Medicine, 1402 South Grand Blvd, M132 Schwitalla Hall, Saint Louis, MO 63104, USA
| | - Jonathan Oliva
- Center for World Health and Medicine, Saint Louis University School of Medicine, 1402 South Grand Blvd, M132 Schwitalla Hall, Saint Louis, MO 63104, USA
| | - Mary A Campbell
- Center for World Health and Medicine, Saint Louis University School of Medicine, 1402 South Grand Blvd, M132 Schwitalla Hall, Saint Louis, MO 63104, USA
| | - Stacy D Arnett
- Center for World Health and Medicine, Saint Louis University School of Medicine, 1402 South Grand Blvd, M132 Schwitalla Hall, Saint Louis, MO 63104, USA
| | - Michael J Prinsen
- Center for World Health and Medicine, Saint Louis University School of Medicine, 1402 South Grand Blvd, M132 Schwitalla Hall, Saint Louis, MO 63104, USA
| | - David W Griggs
- Center for World Health and Medicine, Saint Louis University School of Medicine, 1402 South Grand Blvd, M132 Schwitalla Hall, Saint Louis, MO 63104, USA
| | - Peter G Ruminski
- Center for World Health and Medicine, Saint Louis University School of Medicine, 1402 South Grand Blvd, M132 Schwitalla Hall, Saint Louis, MO 63104, USA
| | - Daniel E Goldberg
- Departments of Medicine and Molecular Microbiology, Washington University in St. Louis, Saint Louis, MO, USA
| | - Ke Ding
- Key Laboratory of Regenerative Biology, Institute of Chemical Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xiaorong Liu
- Drug Discovery Pipeline at the Guangzhou Institutes for Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Zhengchao Tu
- Drug Discovery Pipeline at the Guangzhou Institutes for Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Micky D Tortorella
- Drug Discovery Pipeline at the Guangzhou Institutes for Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Francis M Sverdrup
- Center for World Health and Medicine, Saint Louis University School of Medicine, 1402 South Grand Blvd, M132 Schwitalla Hall, Saint Louis, MO 63104, USA
| | - Xiaoping Chen
- Laboratory of Pathogen Biology, State Key Laboratory of Respiratory Disease, Center for Infection and Immunity, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, #190, Kaiyuan Avenue, Guangzhou Science Park, Guangzhou 510530, China.
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Dos Santos ALS. Protease expression by microorganisms and its relevance to crucial physiological/pathological events. World J Biol Chem 2011; 2:48-58. [PMID: 21537490 PMCID: PMC3083995 DOI: 10.4331/wjbc.v2.i3.48] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2011] [Revised: 02/21/2011] [Accepted: 02/28/2011] [Indexed: 02/05/2023] Open
Abstract
The treatment of infections caused by fungi and trypanosomatids is difficult due to the eukaryotic nature of these microbial cells, which are similar in several biochemical and genetic aspects to host cells. Aggravating this scenario, very few antifungal and anti-trypanosomatidal agents are in clinical use and, therefore, therapy is limited by drug safety considerations and their narrow spectrum of activity, efficacy and resistance. The search for new bioactive agents against fungi and trypanosomatids has been expanded because progress in biochemistry and molecular biology has led to a better understanding of important and essential pathways in these microorganisms including nutrition, growth, proliferation, signaling, differentiation and death. In this context, proteolytic enzymes produced by these eukaryotic microorganisms are appointed and, in some cases, proven to be excellent targets for searching novel natural and/or synthetic pharmacological compounds, in order to cure or prevent invasive fungal/trypanosomatid diseases. With this task in mind, our research group and others have focused on aspartic-type proteases, since the activity of this class of hydrolytic enzymes is directly implicated in several facets of basic biological processes of both fungal and trypanosomatid cells as well as due to the participation in numerous events of interaction between these microorganisms and host structures. In the present paper, a concise revision of the beneficial effects of aspartic protease inhibitors, with emphasis on the aspartic protease inhibitors used in the anti-human immunodeficiency virus therapy, will be presented and discussed using our experience with the following microbial models: the yeast Candida albicans, the filamentous fungus Fonsecaea pedrosoi and the protozoan trypanosomatid Leishmania amazonensis.
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Affiliation(s)
- André Luis Souza Dos Santos
- André Luis Souza dos Santos, Laboratory of Multidisciplinary Studies on Microbial Biochemistry, Department of General Microbiology, Institute of Microbiology Prof. Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil
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