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Legru A, Batista FA, Puszko AK, Bouillon A, Maurel M, Martinez M, Ejjoummany A, Ortega Varga L, Adler P, Méchaly A, Hadjadj M, Sosnowski P, Hopfgartner G, Alzari PM, Blondel A, Haouz A, Barale JC, Hernandez JF. Insights from structure-activity relationships and the binding mode of peptidic α-ketoamide inhibitors of the malaria drug target subtilisin-like SUB1. Eur J Med Chem 2024; 269:116308. [PMID: 38503166 DOI: 10.1016/j.ejmech.2024.116308] [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: 12/11/2023] [Revised: 03/04/2024] [Accepted: 03/04/2024] [Indexed: 03/21/2024]
Abstract
Plasmodium multi-resistance, including against artemisinin, seriously threatens malaria treatment and control. Hence, new drugs are urgently needed, ideally targeting different parasitic stages, which are not yet targeted by current drugs. The SUB1 protease is involved in both hepatic and blood stages due to its essential role in the egress of parasites from host cells, and, as potential new target, it would meet the above criteria. We report here the synthesis as well as the biological and structural evaluation of substrate-based α-ketoamide SUB1 pseudopeptidic inhibitors encompassing positions P4-P2'. By individually substituting each position of the reference compound 1 (MAM-117, Ac-Ile-Thr-Ala-AlaCO-Asp-Glu (Oall)-NH2), we better characterized the structural determinants for SUB1 binding. We first identified compound 8 with IC50 values of 50 and 570 nM against Pv- and PfSUB1, respectively (about 3.5-fold higher potency compared to 1). Compound 8 inhibited P. falciparum merozoite egress in culture by 37% at 100 μM. By increasing the overall hydrophobicity of the compounds, we could improve the PfSUB1 inhibition level and antiparasitic activity, as shown with compound 40 (IC50 values of 12 and 10 nM against Pv- and PfSUB1, respectively, IC50 value of 23 μM on P. falciparum merozoite egress). We also found that 8 was highly selective towards SUB1 over three mammalian serine peptidases, supporting the promising value of this compound. Finally, several crystal 3D-structures of SUB1-inhibitor complexes, including with 8, were solved at high resolution to decipher the binding mode of these compounds.
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Affiliation(s)
- Alice Legru
- Institut des Biomolécules Max Mousseron (IBMM), CNRS, Univ Montpellier, ENSCM, Montpellier, France
| | - Fernando A Batista
- Structural Microbiology, UMR3528, Institut Pasteur, CNRS, Université de Paris, Paris, France
| | - Anna K Puszko
- Institut des Biomolécules Max Mousseron (IBMM), CNRS, Univ Montpellier, ENSCM, Montpellier, France
| | - Anthony Bouillon
- Structural Microbiology, UMR3528, Institut Pasteur, CNRS, Université de Paris, Paris, France
| | - Manon Maurel
- Institut des Biomolécules Max Mousseron (IBMM), CNRS, Univ Montpellier, ENSCM, Montpellier, France
| | - Mariano Martinez
- Structural Microbiology, UMR3528, Institut Pasteur, CNRS, Université de Paris, Paris, France
| | - Abdelaziz Ejjoummany
- Institut des Biomolécules Max Mousseron (IBMM), CNRS, Univ Montpellier, ENSCM, Montpellier, France
| | - Laura Ortega Varga
- Structural Bioinformatic, UMR3528, Institut Pasteur, CNRS, Université de Paris, Paris, France
| | - Pauline Adler
- Institut des Biomolécules Max Mousseron (IBMM), CNRS, Univ Montpellier, ENSCM, Montpellier, France
| | - Ariel Méchaly
- Cristallography Platform-C2RT, UMR3528, Institut Pasteur, CNRS, Université de Paris, Paris, France
| | - Margot Hadjadj
- Institut des Biomolécules Max Mousseron (IBMM), CNRS, Univ Montpellier, ENSCM, Montpellier, France
| | - Piotr Sosnowski
- Department of Inorganic and Analytical Chemistry, University of Geneva, CH-1211, Geneva, Switzerland
| | - Gérard Hopfgartner
- Department of Inorganic and Analytical Chemistry, University of Geneva, CH-1211, Geneva, Switzerland
| | - Pedro M Alzari
- Structural Microbiology, UMR3528, Institut Pasteur, CNRS, Université de Paris, Paris, France
| | - Arnaud Blondel
- Structural Bioinformatic, UMR3528, Institut Pasteur, CNRS, Université de Paris, Paris, France
| | - Ahmed Haouz
- Cristallography Platform-C2RT, UMR3528, Institut Pasteur, CNRS, Université de Paris, Paris, France
| | - Jean-Christophe Barale
- Structural Microbiology, UMR3528, Institut Pasteur, CNRS, Université de Paris, Paris, France.
| | - Jean-François Hernandez
- Institut des Biomolécules Max Mousseron (IBMM), CNRS, Univ Montpellier, ENSCM, Montpellier, France.
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Cui H, Zhou G, Ruan H, Zhao J, Hasi A, Zong N. Genome-Wide Identification and Analysis of the Maize Serine Peptidase S8 Family Genes in Response to Drought at Seedling Stage. PLANTS (BASEL, SWITZERLAND) 2023; 12:369. [PMID: 36679082 PMCID: PMC9865268 DOI: 10.3390/plants12020369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 06/17/2023]
Abstract
Subtilisin-like proteases (subtilases) are found in almost all plant species and are involved in regulating various biotic and abiotic stresses. Although the literature on subtilases in different plant species is vast, the gene function of the serine peptidase S8 family and its maize subfamily is still unknown. Here, a bioinformatics analysis of this gene family was conducted by describing gene structure, conserved motifs, phylogenetic relationships, chromosomal distributions, gene duplications, and promoter cis-elements. In total, we identified 18 ZmSPS8 genes in maize, distributed on 7 chromosomes, and half of them were hydrophilic. Most of these proteins were located at the cell wall and had similar secondary and tertiary structures. Prediction of cis-regulatory elements in promoters illustrated that they were mainly associated with hormones and abiotic stress. Maize inbred lines B73, Zheng58, and Qi319 were used to analyze the spatial-temporal expression patterns of ZmSPS8 genes under drought treatment. Seedling drought results showed that Qi319 had the highest percent survival after 14 d of withholding irrigation, while B73 was the lowest. Leaf relative water content (LRWC) declined more rapidly in B73 and to lower values, and the nitrotetrazolium blue chloride (NBT) contents of leaves were higher in Qi319 than in the other inbreds. The qPCR results indicated that 6 serine peptidase S8 family genes were positively or negatively correlated with plant tolerance to drought stress. Our study provides a detailed analysis of the ZmSPS8s in the maize genome and finds a link between drought tolerance and the family gene expression, which was established by using different maize inbred lines.
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Affiliation(s)
- Hongwei Cui
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010020, China
| | - Guyi Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hongqiang Ruan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jun Zhao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Agula Hasi
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010020, China
| | - Na Zong
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Brogi S, Giovani S, Brindisi M, Gemma S, Novellino E, Campiani G, Blackman MJ, Butini S. In silico study of subtilisin-like protease 1 (SUB1) from different Plasmodium species in complex with peptidyl-difluorostatones and characterization of potent pan-SUB1 inhibitors. J Mol Graph Model 2016; 64:121-130. [PMID: 26826801 PMCID: PMC5276822 DOI: 10.1016/j.jmgm.2016.01.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 12/04/2015] [Accepted: 01/16/2016] [Indexed: 11/23/2022]
Abstract
Homology models of four SUB1 orthologues from P. falciparum species were produced. We analyzed the binding mode of our previous difluorostatone inhibitors to six SUB1. In vitro activity of our difluorostatone-based inhibitors was correctly predicted. We derived a structure-based pan-SUB1 pharmacophore, and validated it in silico. We confirmed that development of pan-SUB1 inhibitors is a feasible task.
Plasmodium falciparum subtilisin-like protease 1 (SUB1) is a novel target for the development of innovative antimalarials. We recently described the first potent difluorostatone-based inhibitors of the enzyme ((4S)-(N-((N-acetyl-l-lysyl)-l-isoleucyl-l-threonyl-l-alanyl)-2,2-difluoro-3-oxo-4-aminopentanoyl)glycine (1) and (4S)-(N-((N-acetyl-l-isoleucyl)-l-threonyl-l-alanylamino)-2,2-difluoro-3-oxo-4-aminopentanoyl)glycine (2)). As a continuation of our efforts towards the definition of the molecular determinants of enzyme-inhibitor interaction, we herein propose the first comprehensive computational investigation of the SUB1 catalytic core from six different Plasmodium species, using homology modeling and molecular docking approaches. Investigation of the differences in the binding sites as well as the interactions of our inhibitors 1,2 with all SUB1 orthologues, allowed us to highlight the structurally relevant regions of the enzyme that could be targeted for developing pan-SUB1 inhibitors. According to our in silico predictions, compounds 1,2 have been demonstrated to be potent inhibitors of SUB1 from all three major clinically relevant Plasmodium species (P. falciparum, P. vivax, and P. knowlesi). We next derived multiple structure-based pharmacophore models that were combined in an inclusive pan-SUB1 pharmacophore (SUB1-PHA). This latter was validated by applying in silico methods, showing that it may be useful for the future development of potent antimalarial agents.
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Affiliation(s)
- Simone Brogi
- European Research Centre for Drug Discovery and Development (NatSynDrugs), University of Siena, via Aldo Moro 2, 53100, Siena, Italy; Dipartimento di Biotecnologie, Chimica e Farmacia, University of Siena, via Aldo Moro 2, 53100, Siena, Italy; Centro Interuniversitario di Ricerche sulla Malaria (CIRM), University of Perugia, Perugia, Italy
| | - Simone Giovani
- European Research Centre for Drug Discovery and Development (NatSynDrugs), University of Siena, via Aldo Moro 2, 53100, Siena, Italy; Dipartimento di Biotecnologie, Chimica e Farmacia, University of Siena, via Aldo Moro 2, 53100, Siena, Italy; Centro Interuniversitario di Ricerche sulla Malaria (CIRM), University of Perugia, Perugia, Italy
| | - Margherita Brindisi
- European Research Centre for Drug Discovery and Development (NatSynDrugs), University of Siena, via Aldo Moro 2, 53100, Siena, Italy; Dipartimento di Biotecnologie, Chimica e Farmacia, University of Siena, via Aldo Moro 2, 53100, Siena, Italy; Centro Interuniversitario di Ricerche sulla Malaria (CIRM), University of Perugia, Perugia, Italy
| | - Sandra Gemma
- European Research Centre for Drug Discovery and Development (NatSynDrugs), University of Siena, via Aldo Moro 2, 53100, Siena, Italy; Dipartimento di Biotecnologie, Chimica e Farmacia, University of Siena, via Aldo Moro 2, 53100, Siena, Italy; Centro Interuniversitario di Ricerche sulla Malaria (CIRM), University of Perugia, Perugia, Italy.
| | - Ettore Novellino
- European Research Centre for Drug Discovery and Development (NatSynDrugs), University of Siena, via Aldo Moro 2, 53100, Siena, Italy; Dipartimento di Farmacia, University of Naples Federico II, Via D. Montesano 49, 80131, Naples, Italy
| | - Giuseppe Campiani
- European Research Centre for Drug Discovery and Development (NatSynDrugs), University of Siena, via Aldo Moro 2, 53100, Siena, Italy; Dipartimento di Biotecnologie, Chimica e Farmacia, University of Siena, via Aldo Moro 2, 53100, Siena, Italy; Centro Interuniversitario di Ricerche sulla Malaria (CIRM), University of Perugia, Perugia, Italy.
| | - Michael J Blackman
- Division of Parasitology, MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK
| | - Stefania Butini
- European Research Centre for Drug Discovery and Development (NatSynDrugs), University of Siena, via Aldo Moro 2, 53100, Siena, Italy; Dipartimento di Biotecnologie, Chimica e Farmacia, University of Siena, via Aldo Moro 2, 53100, Siena, Italy; Centro Interuniversitario di Ricerche sulla Malaria (CIRM), University of Perugia, Perugia, Italy
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