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Barbaraci C, di Giacomo V, Maruca A, Patamia V, Rocca R, Dichiara M, Di Rienzo A, Cacciatore I, Cataldi A, Balaha M, Rapino M, Zagni C, Zampieri D, Pasquinucci L, Parenti C, Amata E, Rescifina A, Alcaro S, Marrazzo A. Discovery of first novel sigma/HDACi dual-ligands with a potent in vitro antiproliferative activity. Bioorg Chem 2023; 140:106794. [PMID: 37659146 DOI: 10.1016/j.bioorg.2023.106794] [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: 04/19/2023] [Revised: 08/09/2023] [Accepted: 08/15/2023] [Indexed: 09/04/2023]
Abstract
Designing and discovering compounds for dual-target inhibitors is challenging to synthesize new, safer, and more efficient drugs than single-target drugs, especially to treat multifactorial diseases such as cancer. The simultaneous regulation of multiple targets might represent an alternative synthetic approach to optimize patient compliance and tolerance, minimizing the risk of target-based drug resistance due to the modulation of a few targets. To this end, we conceived for the first time the design and synthesis of dual-ligands σR/HDACi to evaluate possible employment as innovative candidates to address this complex disease. Among all synthesized compounds screened for several tumoral cell lines, compound 6 (Kiσ1R = 38 ± 3.7; Kiσ2R = 2917 ± 769 and HDACs IC50 = 0.59 µM) is the most promising candidate as an antiproliferative agent with an IC50 of 0.9 µM on the HCT116 cell line and no significant toxicity to normal cells. Studies of molecular docking, which confirmed the affinity over σ1R and a pan-HDACs inhibitory behavior, support a possible balanced affinity and activity between both targets.
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Affiliation(s)
- Carla Barbaraci
- Department of Drug and Health Sciences, Medicinal Chemistry Section, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Viviana di Giacomo
- Department of Pharmacy, University "G. d'Annunzio", Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
| | - Annalisa Maruca
- Net4science academic spinoff srl, Università degli Studi "Magna Græcia" di Catanzaro, Campus "Salvatore Venuta", Viale Europa, 88100, Catanzaro, Italy
| | - Vincenzo Patamia
- Department of Drug and Health Sciences, Medicinal Chemistry Section, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Roberta Rocca
- Net4science academic spinoff srl, Università degli Studi "Magna Græcia" di Catanzaro, Campus "Salvatore Venuta", Viale Europa, 88100, Catanzaro, Italy
| | - Maria Dichiara
- Department of Drug and Health Sciences, Medicinal Chemistry Section, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Annalisa Di Rienzo
- Department of Pharmacy, University "G. d'Annunzio", Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
| | - Ivana Cacciatore
- Department of Pharmacy, University "G. d'Annunzio", Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
| | - Amelia Cataldi
- Department of Pharmacy, University "G. d'Annunzio", Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
| | - Marwa Balaha
- Department of Pharmacy, University "G. d'Annunzio", Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafr El Sheikh 33516, Egypt
| | - Monica Rapino
- Genetic Molecular Institute of CNR, Unit of Chieti, "G. d' Annunzio" University, Via dei Vestini 31, 66100 Chieti-Pescara, Italy
| | - Chiara Zagni
- Department of Drug and Health Sciences, Medicinal Chemistry Section, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Daniele Zampieri
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Lorella Pasquinucci
- Department of Drug and Health Sciences, Medicinal Chemistry Section, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Carmela Parenti
- Department of Drug and Health Sciences, Medicinal Chemistry Section, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Emanuele Amata
- Department of Drug and Health Sciences, Medicinal Chemistry Section, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Antonio Rescifina
- Department of Drug and Health Sciences, Medicinal Chemistry Section, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Stefano Alcaro
- Net4science academic spinoff srl, Università degli Studi "Magna Græcia" di Catanzaro, Campus "Salvatore Venuta", Viale Europa, 88100, Catanzaro, Italy; Dipartimento di Scienze della Salute, Università degli Studi "Magna Græcia" di Catanzaro, Campus "Salvatore Venuta", Viale Europa, 88100, Catanzaro, Italy.
| | - Agostino Marrazzo
- Department of Drug and Health Sciences, Medicinal Chemistry Section, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy.
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Abstract
Fatty acid–and retinol-binding proteins (FARs) belong to a unique family of excreted/secreted proteins (ESPs) found exclusively in nematodes. Much of our understanding of these proteins, however, is limited to their in vitro binding characteristics toward various fatty acids and retinol and has provided little insight into their in vivo functions or mechanisms. Recent research, however, has shown that FARs elicit an immunomodulatory role in plant and animal model systems, likely by sequestering lipids involved in immune signaling. This alludes to the intricate relationship between parasitic nematode effectors and their hosts.
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Szczepańska K, Podlewska S, Dichiara M, Gentile D, Patamia V, Rosier N, Mönnich D, Ruiz Cantero MC, Karcz T, Łażewska D, Siwek A, Pockes S, Cobos EJ, Marrazzo A, Stark H, Rescifina A, Bojarski AJ, Amata E, Kieć-Kononowicz K. Structural and Molecular Insight into Piperazine and Piperidine Derivatives as Histamine H 3 and Sigma-1 Receptor Antagonists with Promising Antinociceptive Properties. ACS Chem Neurosci 2022; 13:1-15. [PMID: 34908391 PMCID: PMC8739840 DOI: 10.1021/acschemneuro.1c00435] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 11/29/2021] [Indexed: 12/11/2022] Open
Abstract
In an attempt to extend recent studies showing that some clinically evaluated histamine H3 receptor (H3R) antagonists possess nanomolar affinity at sigma-1 receptors (σ1R), we selected 20 representative structures among our previously reported H3R ligands to investigate their affinity at σRs. Most of the tested compounds interact with both sigma receptors to different degrees. However, only six of them showed higher affinity toward σ1R than σ2R with the highest binding preference to σ1R for compounds 5, 11, and 12. Moreover, all these ligands share a common structural feature: the piperidine moiety as the fundamental part of the molecule. It is most likely a critical structural element for dual H3/σ1 receptor activity as can be seen by comparing the data for compounds 4 and 5 (hH3R Ki = 3.17 and 7.70 nM, σ1R Ki = 1531 and 3.64 nM, respectively), where piperidine is replaced by piperazine. We identified the putative protein-ligand interactions responsible for their high affinity using molecular modeling techniques and selected compounds 5 and 11 as lead structures for further evaluation. Interestingly, both ligands turned out to be high-affinity histamine H3 and σ1 receptor antagonists with negligible affinity at the other histamine receptor subtypes and promising antinociceptive activity in vivo. Considering that many literature data clearly indicate high preclinical efficacy of individual selective σ1 or H3R ligands in various pain models, our research might be a breakthrough in the search for novel, dual-acting compounds that can improve existing pain therapies. Determining whether such ligands are more effective than single-selective drugs will be the subject of our future studies.
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Affiliation(s)
- Katarzyna Szczepańska
- Department
of Technology and Biotechnology of Drugs, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, Kraków 30-688, Poland
- Maj
Institute of Pharmacology, Polish Academy
of Sciences, Smętna 12, Kraków 31-343, Poland
| | - Sabina Podlewska
- Department
of Technology and Biotechnology of Drugs, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, Kraków 30-688, Poland
- Maj
Institute of Pharmacology, Polish Academy
of Sciences, Smętna 12, Kraków 31-343, Poland
| | - Maria Dichiara
- Department
of Drug and Health Sciences, University
of Catania, V.le A. Doria, 95125 Catania, Italy
| | - Davide Gentile
- Department
of Drug and Health Sciences, University
of Catania, V.le A. Doria, 95125 Catania, Italy
| | - Vincenzo Patamia
- Department
of Drug and Health Sciences, University
of Catania, V.le A. Doria, 95125 Catania, Italy
| | - Niklas Rosier
- Institute
of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Denise Mönnich
- Institute
of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Ma Carmen Ruiz Cantero
- Department
of Pharmacology and Neurosciences Institute (Biomedical Research Center)
and Biosanitary Research Institute ibs.GRANADA, University of Granada, Avenida de la Investigación 11, 18016 Granada, Spain
| | - Tadeusz Karcz
- Department
of Technology and Biotechnology of Drugs, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, Kraków 30-688, Poland
| | - Dorota Łażewska
- Department
of Technology and Biotechnology of Drugs, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, Kraków 30-688, Poland
| | - Agata Siwek
- Department
of Pharmacobiology, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, Kraków 30-688, Poland
| | - Steffen Pockes
- Institute
of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Enrique J. Cobos
- Department
of Pharmacology and Neurosciences Institute (Biomedical Research Center)
and Biosanitary Research Institute ibs.GRANADA, University of Granada, Avenida de la Investigación 11, 18016 Granada, Spain
| | - Agostino Marrazzo
- Department
of Drug and Health Sciences, University
of Catania, V.le A. Doria, 95125 Catania, Italy
| | - Holger Stark
- Institute
of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitaetsstr. 1, 40225 Duesseldorf, Germany
| | - Antonio Rescifina
- Department
of Drug and Health Sciences, University
of Catania, V.le A. Doria, 95125 Catania, Italy
| | - Andrzej J. Bojarski
- Maj
Institute of Pharmacology, Polish Academy
of Sciences, Smętna 12, Kraków 31-343, Poland
| | - Emanuele Amata
- Department
of Drug and Health Sciences, University
of Catania, V.le A. Doria, 95125 Catania, Italy
| | - Katarzyna Kieć-Kononowicz
- Department
of Technology and Biotechnology of Drugs, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, Kraków 30-688, Poland
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Floresta G, Fallica AN, Salerno L, Sorrenti V, Pittalà V, Rescifina A. Growing the molecular architecture of imidazole-like ligands in HO-1 complexes. Bioorg Chem 2021; 117:105428. [PMID: 34710668 DOI: 10.1016/j.bioorg.2021.105428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 08/27/2021] [Accepted: 10/11/2021] [Indexed: 12/11/2022]
Abstract
Up-regulation of HO-1 had been frequently reported in different cases and types of human malignancies. Since poor clinical outcomes are reported in these cases, this enzyme's inhibition is considered a valuable and proven anticancer approach. To identify novel HO-1 inhibitors suitable for drug development, we report a structure-guided fragment-based approach to identify new lead compounds. Different parts of the selected molecules were analyzed, and the different series of novel compounds were virtually evaluated. The growing experiments of the classical HO-1 inhibitors structure led us to different hit-compounds. A synthetic pathway for six selected molecules was designed, and the compounds were synthesized. The biological activity revealed that molecules 10 and 12 inhibit the HO-1 activity with an IC50 of 1.01 and 0.90 μM, respectively. This study suggested that our growing approach was successful, and these results are ongoing for further development.
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Affiliation(s)
- Giuseppe Floresta
- Department of Analytical, Environmental and Forensic Sciences, King's College London, London, UK.
| | - Antonino N Fallica
- Department of Drug and Health Sciences, University of Catania, Catania, Italy
| | - Loredana Salerno
- Department of Drug and Health Sciences, University of Catania, Catania, Italy
| | - Valeria Sorrenti
- Department of Drug and Health Sciences, University of Catania, Catania, Italy
| | - Valeria Pittalà
- Department of Drug and Health Sciences, University of Catania, Catania, Italy.
| | - Antonio Rescifina
- Department of Drug and Health Sciences, University of Catania, Catania, Italy
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Novel Functions of the Fatty Acid and Retinol Binding Protein (FAR) Gene Family Revealed by Fungus-Mediated RNAi in the Parasitic Nematode, Aphelenchoides besseyi. Int J Mol Sci 2021; 22:ijms221810057. [PMID: 34576221 PMCID: PMC8471444 DOI: 10.3390/ijms221810057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 11/17/2022] Open
Abstract
RNA interference (RNAi) is a powerful tool for the analysis of gene function in nematodes. Fatty acid and retinol binding protein (FAR) is a protein that only exists in nematodes and plays an important role in their life activities. The rice white-tip nematode (RWTN), Aphelenchoides besseyi, is a migratory endoparasitic plant nematode that causes serious damage in agricultural production. In this study, the expression levels of eight RWTN genes were effectively decreased when RWTN was fed Ab-far-n (n: 1–8) hairpin RNA transgenic Botrytis cinerea (ARTBn). These functions of the far gene family were identified to be consistent and diverse through phenotypic changes after any gene was silenced. Such consistency indicates that the body lengths of the females were significantly shortened after silencing any of the eight Ab-far genes. The diversities were mainly manifested as follows: (1) Reproduction of nematodes was clearly inhibited after Ab-far-1 to Ab-far-4 were silenced. In addition, silencing Ab-far-2 could inhibit the pathogenicity of nematodes to Arabidopsis; (2) gonad length of female nematodes was significantly shortened after Ab-far-2 and Ab-far-4 were silenced; (3) proportion of male nematodes significantly increased in the adult population after Ab-far-1, Ab-far-3, and Ab-far-5 were silenced, whereas the proportion of adult nematodes significantly decreased in the nematode population after Ab-far-4 were silenced. (4) Fat storage of nematodes significantly decreased after Ab-far-3, Ab-far-4, and Ab-far-7 were silenced. To our knowledge, this is the first study to demonstrate that Ab-far genes affect sex formation and lipid metabolism in nematodes, which provides valuable data for further study and control of RWTNs.
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de Mattos Pereira L, de Jezuz MPG, Rangel AR, Baldasso BD, Zaluski AB, Graeff-Teixeira C, Morassutti AL. De novo transcriptome reveals blood coagulation/antithrombin factors and infection mechanisms in Angiostrongylus cantonensis adult worms. Parasitology 2021; 148:857-870. [PMID: 33729108 PMCID: PMC11010222 DOI: 10.1017/s0031182021000469] [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: 12/12/2020] [Revised: 02/17/2021] [Accepted: 03/05/2021] [Indexed: 11/06/2022]
Abstract
Angiostrongylus cantonensis is the main aetiological agent of eosinophilic meningoencephalitis in humans. Several outbreaks have been documented around the world, cementing its status as an emerging global public health concern. As a result, new strategies for the diagnosis, prophylaxis and treatment of cerebral angiostrongyliasis are urgently needed. In this study, we report on the de novo assembly of the A. cantonensis transcriptome, its full functional annotation and a reconstruction of complete metabolic pathways. All results are available at AngiostrongylusDB (http://angiostrongylus.lad.pucrs.br/admin/welcome). The aim of this study was to identify the active genes and metabolic pathways involved in the mechanisms of infection and survival inside Rattus norvegicus. Among 389 metabolic mapped pathways, the blood coagulation/antithrombin pathways of heparan sulphate/heparin are highlighted. Moreover, we identified genes codified to GP63 (leishmanolysin), CALR (calreticulin), ACE (peptidyl-dipeptidase A), myoglobin and vWD (von Willebrand factor type D domain protein) involved in the infection invasion and survival of the parasite. The large dataset of functional annotations provided and the full-length transcripts identified in this research may facilitate future functional genomics studies and provides a basis for the development of new techniques for the diagnosis, prevention and treatment of cerebral angiostrongyliasis.
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Affiliation(s)
- Leandro de Mattos Pereira
- Laboratório de Biologia Parasitária, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Escola de Ciências, Porto Alegre, RS, Brazil
- Databiomics, Parque Tecnológico Tecnovates, Lajeado, RS95914-014, Brazil
| | - Milene Pereira Guimarães de Jezuz
- Laboratório de Biologia Parasitária, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Escola de Ciências, Porto Alegre, RS, Brazil
| | - Amaranta Ramos Rangel
- Laboratório de Biologia Parasitária, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Escola de Ciências, Porto Alegre, RS, Brazil
| | - Bruna Dalcin Baldasso
- Laboratório de Biologia Parasitária, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Escola de Ciências, Porto Alegre, RS, Brazil
| | - Amanda Bungi Zaluski
- Laboratório de Biologia e Desenvolvimento do Sistema Nervoso, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Escola de Ciências, Porto Alegre, RS, Brazil
| | - Carlos Graeff-Teixeira
- Laboratório de Biologia Parasitária, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Escola de Ciências, Porto Alegre, RS, Brazil
- Núcleo de Doenças Infecciosas, Centro de Ciências da Saúde, Universidade Federal do Espírito Santo, Vitoria, ES, Brazil
| | - Alessandra Loureiro Morassutti
- Escola de Medicina IMED, Passo Fundo, RS99070-220, Brazil
- Instituto de Patologia de Passo Fundo, Passo Fundo, RS99010-081, Brazil
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Floresta G, Abbate V. Machine learning vs. field 3D-QSAR models for serotonin 2A receptor psychoactive substances identification. RSC Adv 2021; 11:14587-14595. [PMID: 35424006 PMCID: PMC8697832 DOI: 10.1039/d1ra01335a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/13/2021] [Indexed: 02/06/2023] Open
Abstract
Serotonergic psychedelics, substances exerting their effects primarily through the serotonin 2A receptor (5HT2AR), continue to comprise a substantial portion of reported new psychoactive substances (NPS). In this paper five quantitative structure-activity relationship (QSAR) models for predicting the affinity of 5-HT2AR ligands have been developed. The resulting models, exploiting the accessibility of the QSAR equations, generate a useful tool for the investigation and identification of unclassified molecules. The models have been built using a set of 375 molecules using Forge software, and the quality was confirmed by statistical analysis, resulting in effective tools with respect to their predictive and descriptive capabilities. The best performing algorithm among the machine learning approaches and the classical field 3D-QSAR model were then combined to produce a consensus model and were exploited, together with a pharmacophorefilter, to explore the 5-HT2AR activity of 523 105 natural products, to classify a set of recently reported 5-HT2AR NPS and to design new potential active molecules. The findings of this study should facilitate the identification and classification of emerging 5-HT2AR ligands including NPS.
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Affiliation(s)
- Giuseppe Floresta
- Department of Analytical, Environmental and Forensic Sciences, King's College London London UK
| | - Vincenzo Abbate
- Department of Analytical, Environmental and Forensic Sciences, King's College London London UK
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Ding S, Wang D, Xu C, Yang S, Cheng X, Peng X, Chen C, Xie H. A new fungus-mediated RNAi method established and used to study the fatty acid and retinol binding protein function of the plant-parasitic nematode Aphelenchoides besseyi. RNA Biol 2020; 18:1424-1433. [PMID: 33218290 DOI: 10.1080/15476286.2020.1852779] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
RNA interference (RNAi) is a powerful tool for gene functional analysis of plant-parasitic nematodes (PPNs). RNAi involving soaking in a dsRNA solution and in planta methods is commonly applied in the study of gene function in PPNs. However, certain problems restrict the application of these methods. Therefore, more convenient and effective RNAi methods need to be established for different PPNs according to their biological characteristics. In this study, the fatty acid and retinoid binding protein genes (Ab-far-1, Ab-far-4, and combinatorial Ab-far-1 and Ab-far-4) of the rice white tip nematode (RWTN), Aphelenchoides besseyi, were used as target genes to construct a fungal RNAi vector, and the Ab-far-n dsRNA transgenic Botrytis cinerea (ARTBn) were generated using Agrobacterium-mediated transformation technology. After RWTN feeding on ARTBn, the expression of Ab-far-1 and Ab-far-4 in the nematodes was efficiently silenced, and the reproduction and pathogenicity of the nematodes were clearly inhibited. The Ab-far-1 and Ab-far-4 co-RNAi effects were better than the effects when each gene was individually targeted with RNAi. Additionally, the RNAi induced when RWTNs fed on ARTB1 were persistent and heritable. Thus, a new method of fungus-mediated RNAi was established for fungivorous PPNs and was verified as effective and applicable to the study of nematode gene function. This technique will remove the technological bottlenecks and provide a new method to studying the multiple genes with polygene co-RNAi in fungivorous PPNs. This study also provides a theoretical basis and new thought for further study of the gene function in PPNs.Abbreviations: FAR(Fatty acid and retinol-binding proteins); RWTN (The rice white tip nematode, Aphelenchoides besseyi); Ab-far-n (Fatty acid and retinol binding protein gene of A. besseyi); ARTB1 (Ab-far-1 hpRNA transgenic Botrytis cinerea); ARTB4 (Ab-far-4 hpRNA transgenic Botrytis cinerea); ARTB1/4 (combinatorial Ab-far-1 and Ab-far-4 hpRNA transgenic B. cinerea); EVTB (Empty vector transgenic B. cinerea); GRTB (eGFP hpRNA transgenic B. cinerea); WTB (Wild-type B. cinerea).
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Affiliation(s)
- Shanwen Ding
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, People's Republic of China
| | - Dongwei Wang
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, People's Republic of China.,Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, People's Republic of China
| | - Chunling Xu
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, People's Republic of China
| | - Sihua Yang
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, People's Republic of China
| | - Xi Cheng
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, People's Republic of China
| | - Xiaofang Peng
- Center for Disease Control and Prevention of Guangdong Province, Guangzhou, People's Republic of China
| | - Chun Chen
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, People's Republic of China
| | - Hui Xie
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, People's Republic of China
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9
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Gentile D, Patamia V, Scala A, Sciortino MT, Piperno A, Rescifina A. Putative Inhibitors of SARS-CoV-2 Main Protease from A Library of Marine Natural Products: A Virtual Screening and Molecular Modeling Study. Mar Drugs 2020; 18:E225. [PMID: 32340389 PMCID: PMC7231030 DOI: 10.3390/md18040225] [Citation(s) in RCA: 204] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/10/2020] [Accepted: 04/20/2020] [Indexed: 12/14/2022] Open
Abstract
The current emergency due to the worldwide spread of the COVID-19 caused by the new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a great concern for global public health. Already in the past, the outbreak of severe acute respiratory syndrome (SARS) in 2003 and Middle Eastern respiratory syndrome (MERS) in 2012 demonstrates the potential of coronaviruses to cross-species borders and further underlines the importance of identifying new-targeted drugs. An ideal antiviral agent should target essential proteins involved in the lifecycle of SARS-CoV. Currently, some HIV protease inhibitors (i.e., Lopinavir) are proposed for the treatment of COVID-19, although their effectiveness has not yet been assessed. The main protease (Mpr) provides a highly validated pharmacological target for the discovery and design of inhibitors. We identified potent Mpr inhibitors employing computational techniques that entail the screening of a Marine Natural Product (MNP) library. MNP library was screened by a hyphenated pharmacophore model, and molecular docking approaches. Molecular dynamics and re-docking further confirmed the results obtained by structure-based techniques and allowed this study to highlight some crucial aspects. Seventeen potential SARS-CoV-2 Mpr inhibitors have been identified among the natural substances of marine origin. As these compounds were extensively validated by a consensus approach and by molecular dynamics, the likelihood that at least one of these compounds could be bioactive is excellent.
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Affiliation(s)
- Davide Gentile
- Department of Drug Sciences, University of Catania, V.le A. Doria, 95125 Catania, Italy;
| | - Vincenzo Patamia
- Department of Drug Sciences, University of Catania, V.le A. Doria, 95125 Catania, Italy;
| | - Angela Scala
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, V.le F. Stagno d’Alcontres 31, 98166 Messina, Italy; (A.S.); (M.T.S.); (A.P.)
| | - Maria Teresa Sciortino
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, V.le F. Stagno d’Alcontres 31, 98166 Messina, Italy; (A.S.); (M.T.S.); (A.P.)
| | - Anna Piperno
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, V.le F. Stagno d’Alcontres 31, 98166 Messina, Italy; (A.S.); (M.T.S.); (A.P.)
| | - Antonio Rescifina
- Department of Drug Sciences, University of Catania, V.le A. Doria, 95125 Catania, Italy;
- Consorzio Interuniversitario Nazionale di ricerca in Metodologie e Processi Innovativi di Sintesi (CINMPS), Via E. Orabona, 4, 70125 Bari, Italy
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10
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Identification and Characterization of a Fatty Acid- and Retinoid-Binding Protein Gene ( Ar-far-1) from the Chrysanthemum Foliar Nematode, Aphelenchoides ritzemabosi. Int J Mol Sci 2019; 20:ijms20225566. [PMID: 31703422 PMCID: PMC6888133 DOI: 10.3390/ijms20225566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 10/28/2019] [Accepted: 11/04/2019] [Indexed: 12/04/2022] Open
Abstract
The chrysanthemum foliar nematode (CFN), Aphelenchoides ritzemabosi, is a migratory, plant-parasitic nematode that is widely distributed and infects the aboveground parts of many plants. The fatty acid- and retinoid-binding proteins (FAR) are nematode-specific proteins that are involved in the development, reproduction, and infection of nematodes and are secreted into the tissues to disrupt the plant defense reaction. In this study, we obtained the full-length sequence of the FAR gene (Ar-far-1) from CFN, which is 727 bp and includes a 546 bp ORF that encodes 181 amino acids. Ar-FAR-1 from CFN has the highest sequence similarity to Ab-FAR-1 from A. besseyi, and they are located within the same branch of the phylogenetic tree. Fluorescence-based ligand-binding analysis confirmed that recombinant Ar-FAR-1 was bound to fatty acids and retinol. Ar-far-1 mRNA was expressed in the muscle layer, intestine, female genital system, and egg of CFN, and more highly expressed in females than in males among the four developmental stages of CFN. We demonstrated that the reproduction number and infection capacity of CFN decreased significantly when Ar-far-1 was effectively silenced by in vitro RNAi. Ar-far-1 plays an important role in the development, reproduction, infectivity, and pathogenesis of CFN and may be used as an effective target gene for the control of CFN. The results provide meaningful data about the parasitic and pathogenic genes of CFN to study the interaction mechanism between plant-parasitic nematodes and hosts.
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11
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Computational Tools in the Discovery of FABP4 Ligands: A Statistical and Molecular Modeling Approach. Mar Drugs 2019; 17:md17110624. [PMID: 31683588 PMCID: PMC6891735 DOI: 10.3390/md17110624] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 10/17/2019] [Accepted: 10/29/2019] [Indexed: 12/12/2022] Open
Abstract
Small molecule inhibitors of adipocyte fatty-acid binding protein 4 (FABP4) have received interest following the recent publication of their pharmacologically beneficial effects. Recently, it was revealed that FABP4 is an attractive molecular target for the treatment of type 2 diabetes, other metabolic diseases, and some type of cancers. In past years, hundreds of effective FABP4 inhibitors have been synthesized and discovered, but, unfortunately, none have reached the clinical research phase. The field of computer-aided drug design seems to be promising and useful for the identification of FABP4 inhibitors; hence, different structure- and ligand-based computational approaches have been used for their identification. In this paper, we searched for new potentially active FABP4 ligands in the Marine Natural Products (MNP) database. We retrieved 14,492 compounds from this database and filtered through them with a statistical and computational filter. Seven compounds were suggested by our methodology to possess a potential inhibitory activity upon FABP4 in the range of 97–331 nM. ADMET property prediction was performed to validate the hypothesis of the interaction with the intended target and to assess the drug-likeness of these derivatives. From these analyses, three molecules that are excellent candidates for becoming new drugs were found.
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12
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Transcriptional profiling of wheat (Triticum aestivum L.) during a compatible interaction with the cereal cyst nematode Heterodera avenae. Sci Rep 2019; 9:2184. [PMID: 30778126 PMCID: PMC6379437 DOI: 10.1038/s41598-018-37824-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 10/26/2018] [Indexed: 12/27/2022] Open
Abstract
Cereal cyst nematode (CCN, Heterodera avenae) presents severe challenges to wheat (Triticum aestivum L.) production worldwide. An investigation of the interaction between wheat and CCN can greatly improve our understanding of how nematodes alter wheat root metabolic pathways for their development and could contribute to new control strategies against CCN. In this study, we conducted transcriptome analyses of wheat cv. Wen 19 (Wen19) by using RNA-Seq during the compatible interaction with CCN at 1, 3 and 8 days past inoculation (dpi). In total, 71,569 transcripts were identified, and 10,929 of them were examined as differentially expressed genes (DEGs) in response to CCN infection. Based on the functional annotation and orthologous findings, the protein phosphorylation, oxidation-reduction process, regulation of transcription, metabolic process, transport, and response process as well as many other pathways previously reported were enriched at the transcriptional level. Plant cell wall hydrolysis and modifying proteins, auxin biosynthesis, signalling and transporter genes were up-regulated by CCN infection to facilitate penetration, migration and syncytium establishment. Genes responding to wounding and jasmonic acid stimuli were enriched at 1 dpi. We found 16 NBS-LRR genes, 12 of which were down-regulated, indicating the repression of resistance. The expression of genes encoding antioxidant enzymes, glutathione S-transferases and UDP-glucosyltransferase was significantly up-regulated during CCN infection, indicating that they may play key roles in the compatible interaction of wheat with CCN. Taken together, the results obtained from the transcriptome analyses indicate that the genes involved in oxidation-reduction processes, induction and suppression of resistance, metabolism, transport and syncytium establishment may be involved in the compatible interaction of Wen 19 with CCN. This study provides new insights into the responses of wheat to CCN infection. These insights could facilitate the elucidation of the potential mechanisms of wheat responses to CCN.
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13
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Floresta G, Amata E, Gentile D, Romeo G, Marrazzo A, Pittalà V, Salerno L, Rescifina A. Fourfold Filtered Statistical/Computational Approach for the Identification of Imidazole Compounds as HO-1 Inhibitors from Natural Products. Mar Drugs 2019; 17:md17020113. [PMID: 30759842 PMCID: PMC6409521 DOI: 10.3390/md17020113] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 02/08/2019] [Accepted: 02/09/2019] [Indexed: 12/16/2022] Open
Abstract
Over-regulation of Heme oxygenase 1 (HO-1) has been recently identified in many types of human cancer, and in these cases, poor clinical outcomes are normally reported. Indeed, the inhibition of HO-1 is being considered as an anticancer approach. Imidazole scaffold is normally present in most of the classical HO-1 inhibitors and seems indispensable to the inhibitory activity due to its strong interaction with the Fe(II) of the heme group. In this paper, we searched for new potentially HO-1 inhibitors among three different databases: Marine Natural Products (MNP), ZINC Natural Products (ZNP) and Super Natural II (SN2). 484,527 compounds were retrieved from the databases and filtered through four statistical/computational filters (2D descriptors, 2D-QSAR pharmacophoric model, 3D-QSAR pharmacophoric model, and docking). Different imidazole-based compounds were suggested by our methodology to be potentially active in inhibiting the HO-1, and the results have been rationalized by the bioactivity of the filtered molecules reported in the literature.
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Affiliation(s)
- Giuseppe Floresta
- Department of Drug Sciences, University of Catania, V.le A. Doria, 95125 Catania, Italy.
| | - Emanuele Amata
- Department of Drug Sciences, University of Catania, V.le A. Doria, 95125 Catania, Italy.
| | - Davide Gentile
- Department of Drug Sciences, University of Catania, V.le A. Doria, 95125 Catania, Italy.
| | - Giuseppe Romeo
- Department of Drug Sciences, University of Catania, V.le A. Doria, 95125 Catania, Italy.
| | - Agostino Marrazzo
- Department of Drug Sciences, University of Catania, V.le A. Doria, 95125 Catania, Italy.
| | - Valeria Pittalà
- Department of Drug Sciences, University of Catania, V.le A. Doria, 95125 Catania, Italy.
| | - Loredana Salerno
- Department of Drug Sciences, University of Catania, V.le A. Doria, 95125 Catania, Italy.
| | - Antonio Rescifina
- Department of Drug Sciences, University of Catania, V.le A. Doria, 95125 Catania, Italy.
- Consorzio Interuniversitario Nazionale di ricerca in Metodologie e Processi Innovativi di Sintesi (C.I.N.M.P.S.), Via E. Orabona, 4, 70125 Bari, Italy.
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14
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Floresta G, Rescifina A. Metyrapone-β-cyclodextrin supramolecular interactions inferred by complementary spectroscopic/spectrometric and computational studies. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.09.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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15
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Sousa DM, Cunha NMFD, Silva DRD, Aragão PDTTDD, Aguiar MVDA, Lobo MDP, Moreira ACDOM, Cunha RMSD, Miranda RRCD, Bevilaqua CML. Differences in protein expression associated with ivermectin resistance in Caenorhabditis elegans. REVISTA BRASILEIRA DE PARASITOLOGIA VETERINARIA = BRAZILIAN JOURNAL OF VETERINARY PARASITOLOGY : ORGAO OFICIAL DO COLEGIO BRASILEIRO DE PARASITOLOGIA VETERINARIA 2019; 28:105-112. [PMID: 30916256 DOI: 10.1590/s1984-29612019013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 02/06/2019] [Indexed: 06/09/2023]
Abstract
The indiscriminate administration of synthetic anthelmintics such as ivermectin contributes to the selection of subpopulations capable of resisting the drugs' effects. To understand the mechanisms of ivermectin resistance in Caenorhabditis elegans, this study attempted to identify molecular targets. C. elegans lineages that were sensitive and resistant to ivermectin were used. Collected nematodes were added to an extraction buffer and macerated in liquid nitrogen for protein extraction. The extracted proteins were separated according to molecular weight by SDS-PAGE to verify their integrity. Subsequently, proteins from both lineages were separated using two-dimensional electrophoresis. The gels were analyzed and the relevant spots were excised and identified by mass spectrometry (NanoESI-Q-TOF and MASCOT®) and subsequently assessed by GO enrichment and STRING® analyses. The increased expression of proteins associated with high metabolic activity, such as ATP-2 and ENOL-1, which are responsible for ATP synthesis, was observed. Furthermore, proteins with involvement in mediating muscular function (MLC-1, ACT-1, and PDI-2), signaling (FAR-1 and FAR-2), and embryo development (VHA-2) were identified. Protein interaction analysis indicated that the majority of the identified proteins in the resistant lineages participated in the same reaction triggered by ivermectin.
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Affiliation(s)
- Dauana Mesquita Sousa
- Laboratório de Doenças Parasitárias, Programa de Pós-graduação em Ciências Veterinárias, Faculdade de Veterinária, Universidade Estadual do Ceará - UECE, Fortaleza, CE, Brasil
| | - Nivea Maria Ferreira da Cunha
- Laboratório de Biologia Molecular, Núcleo de Biotecnologia de Sobral, Universidade Estadual Vale do Acaraú - UVA, Sobral, CE, Brasil
| | - Deisianne Rodrigues da Silva
- Laboratório de Biologia Molecular, Núcleo de Biotecnologia de Sobral, Universidade Estadual Vale do Acaraú - UVA, Sobral, CE, Brasil
| | - Paulo de Tarso Teles Dourado de Aragão
- Laboratório de Biologia Molecular, Núcleo de Biotecnologia de Sobral, Programa de Pós-graduação em Biotecnologia, Universidade Federal do Ceará - UFC, Sobral, CE, Brasil
| | - Mônica Valéria de Almeida Aguiar
- Laboratório de Biologia Molecular, Núcleo de Biotecnologia de Sobral, Universidade Estadual Vale do Acaraú - UVA, Sobral, CE, Brasil
| | | | | | - Rodrigo Maranguape Silva da Cunha
- Laboratório de Biologia Molecular, Núcleo de Biotecnologia de Sobral, Universidade Estadual Vale do Acaraú - UVA, Sobral, CE, Brasil
| | | | - Claudia Maria Leal Bevilaqua
- Laboratório de Doenças Parasitárias, Programa de Pós-graduação em Ciências Veterinárias, Faculdade de Veterinária, Universidade Estadual do Ceará - UECE, Fortaleza, CE, Brasil
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16
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Floresta G, Amata E, Barbaraci C, Gentile D, Turnaturi R, Marrazzo A, Rescifina A. A Structure- and Ligand-Based Virtual Screening of a Database of "Small" Marine Natural Products for the Identification of "Blue" Sigma-2 Receptor Ligands. Mar Drugs 2018; 16:md16100384. [PMID: 30322188 PMCID: PMC6212963 DOI: 10.3390/md16100384] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 10/10/2018] [Accepted: 10/11/2018] [Indexed: 12/17/2022] Open
Abstract
Sigma receptors are a fascinating receptor protein class whose ligands are actually under clinical evaluation for the modulation of opioid analgesia and their use as positron emission tomography radiotracers. In particular, peculiar biological and therapeutic functions are associated with the sigma-2 (σ2) receptor. The σ2 receptor ligands determine tumor cell death through apoptotic and non-apoptotic pathways, and the overexpression of σ2 receptors in several tumor cell lines has been well documented, with significantly higher levels in proliferating tumor cells compared to quiescent ones. This acknowledged feature has found practical application in the development of cancer cell tracers and for ligand-targeting therapy. In this context, the development of new ligands that target the σ2 receptors is beneficial for those diseases in which this protein is involved. In this paper, we conducted a search of new potential σ2 receptor ligands among a database of 1517 “small” marine natural products constructed by the union of the Seaweed Metabolite and the Chemical Entities of Biological Interest (ChEBI) Databases. The structures were passed through two filters that were constituted by our developed two-dimensional (2D) and three-dimensional Quantitative Structure-Activity Relationship (3D-QSAR) statistical models, and successively docked upon a σ2 receptor homology model that we built according to the FASTA sequence of the σ2/TMEM97 (SGMR2_HUMAN) receptor.
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Affiliation(s)
- Giuseppe Floresta
- Department of Drug Sciences, University of Catania, V.le A. Doria, 95125 Catania, Italy.
- Department of Chemical Sciences, University of Catania, V.le A. Doria, 95125 Catania, Italy.
| | - Emanuele Amata
- Department of Chemical Sciences, University of Catania, V.le A. Doria, 95125 Catania, Italy.
| | - Carla Barbaraci
- Department of Drug Sciences, University of Catania, V.le A. Doria, 95125 Catania, Italy.
| | - Davide Gentile
- Department of Drug Sciences, University of Catania, V.le A. Doria, 95125 Catania, Italy.
| | - Rita Turnaturi
- Department of Drug Sciences, University of Catania, V.le A. Doria, 95125 Catania, Italy.
| | - Agostino Marrazzo
- Department of Drug Sciences, University of Catania, V.le A. Doria, 95125 Catania, Italy.
| | - Antonio Rescifina
- Department of Drug Sciences, University of Catania, V.le A. Doria, 95125 Catania, Italy.
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17
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Floresta G, Apirakkan O, Rescifina A, Abbate V. Discovery of High-Affinity Cannabinoid Receptors Ligands through a 3D-QSAR Ushered by Scaffold-Hopping Analysis. Molecules 2018; 23:molecules23092183. [PMID: 30200181 PMCID: PMC6225167 DOI: 10.3390/molecules23092183] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 08/26/2018] [Accepted: 08/28/2018] [Indexed: 01/08/2023] Open
Abstract
Two 3D quantitative structure–activity relationships (3D-QSAR) models for predicting Cannabinoid receptor 1 and 2 (CB1 and CB2) ligands have been produced by way of creating a practical tool for the drug-design and optimization of CB1 and CB2 ligands. A set of 312 molecules have been used to build the model for the CB1 receptor, and a set of 187 molecules for the CB2 receptor. All of the molecules were recovered from the literature among those possessing measured Ki values, and Forge was used as software. The present model shows high and robust predictive potential, confirmed by the quality of the statistical analysis, and an adequate descriptive capability. A visual understanding of the hydrophobic, electrostatic, and shaping features highlighting the principal interactions for the CB1 and CB2 ligands was achieved with the construction of 3D maps. The predictive capabilities of the model were then used for a scaffold-hopping study of two selected compounds, with the generation of a library of new compounds with high affinity for the two receptors. Herein, we report two new 3D-QSAR models that comprehend a large number of chemically different CB1 and CB2 ligands and well account for the individual ligand affinities. These features will facilitate the recognition of new potent and selective molecules for CB1 and CB2 receptors.
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MESH Headings
- Cannabinoid Receptor Agonists/chemistry
- Cannabinoid Receptor Agonists/metabolism
- Cannabinoid Receptor Antagonists/chemistry
- Cannabinoid Receptor Antagonists/metabolism
- Drug Design
- Hydrophobic and Hydrophilic Interactions
- Ligands
- Models, Molecular
- Molecular Conformation
- Molecular Docking Simulation
- Molecular Dynamics Simulation
- Molecular Structure
- Protein Binding
- Quantitative Structure-Activity Relationship
- Receptor, Cannabinoid, CB1/chemistry
- Receptor, Cannabinoid, CB1/metabolism
- Receptor, Cannabinoid, CB2/chemistry
- Receptor, Cannabinoid, CB2/metabolism
- Receptors, Cannabinoid/chemistry
- Receptors, Cannabinoid/metabolism
- Software
- Static Electricity
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Affiliation(s)
- Giuseppe Floresta
- Department of Drug Sciences, University of Catania, V.le A. Doria, 95125 Catania, Italy.
- Department of Chemical Sciences, University of Catania, V.le A. Doria, 95125 Catania, Italy.
- Institute of Pharmaceutical Science, King's College London, Stamford Street, London SE1 9NH, UK.
| | - Orapan Apirakkan
- King's Forensics, School of Population Health & Environmental Sciences, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, UK.
| | - Antonio Rescifina
- Department of Drug Sciences, University of Catania, V.le A. Doria, 95125 Catania, Italy.
| | - Vincenzo Abbate
- King's Forensics, School of Population Health & Environmental Sciences, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, UK.
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18
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Wang DW, Xu CL, Ding SW, Huang X, Cheng X, Zhang C, Chen C, Xie H. Identification and function of FAR protein family genes from a transcriptome analysis of Aphelenchoides besseyi. Bioinformatics 2018; 34:2936-2943. [DOI: 10.1093/bioinformatics/bty209] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 03/29/2018] [Indexed: 11/14/2022] Open
Affiliation(s)
- Dong-Wei Wang
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Chun-Ling Xu
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Shan-Wen Ding
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Xin Huang
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Xi Cheng
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, College of plant Protection, Fujian Agriculture and Forestry University, Fuzhou, People’s Republic of China
| | - Chao Zhang
- Institute of Genetic Engineering, Department of biochemistry, College of Basic Medicine, Southern Medical University, Guangzhou, People’s Republic of China
| | - Chun Chen
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Hui Xie
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology/Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, People’s Republic of China
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19
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Cui JK, Peng H, Qiao F, Wang GF, Huang WK, Wu DQ, Peng D. Characterization of Putative Effectors from the Cereal Cyst Nematode Heterodera avenae. PHYTOPATHOLOGY 2018; 108:264-274. [PMID: 28945520 DOI: 10.1094/phyto-07-17-0226-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Few molecular details of effectors of Heterodera avenae parasitism are known. We performed a high-throughput sequencing analysis of the H. avenae transcriptome at five developmental stages. A total of 82,549 unigenes were ultimately obtained, and 747 transcripts showed best hits to genes putatively encoding carbohydrate-active enzymes in plant-parasitic nematodes that play an important role in the invasion process. A total of 1,480 unigenes were homologous to known phytonematode effectors, and 63 putative novel effectors were identified in the H. avenae transcriptomes. Twenty-three unigenes were analyzed by qRT-PCR and confirmed to be highly expressed during at least one developmental stage. For in situ hybridization, 17 of the 22 tested putative effectors were specifically expressed and located in the subventral gland cells, and five putative novel effectors were specifically expressed in the dorsal gland. Furthermore, 115 transcripts were found to have putative lethal RNA interference (RNAi) phenotypes. Three target genes with lethal RNAi phenotypes and two of the four tested putative effectors were associated with a decrease in the number of cysts through in vitro RNAi technology. These transcriptomic data lay a foundation for further studies of interactions of H. avenae with cereal and H. avenae parasitic control.
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Affiliation(s)
- Jiang-Kuan Cui
- First, second, third, fourth, fifth, sixth, and seventh authors: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; first author: College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China; fourth author: College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; and sixth author: Center for Plant Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Huan Peng
- First, second, third, fourth, fifth, sixth, and seventh authors: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; first author: College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China; fourth author: College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; and sixth author: Center for Plant Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Fen Qiao
- First, second, third, fourth, fifth, sixth, and seventh authors: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; first author: College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China; fourth author: College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; and sixth author: Center for Plant Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Gao-Feng Wang
- First, second, third, fourth, fifth, sixth, and seventh authors: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; first author: College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China; fourth author: College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; and sixth author: Center for Plant Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Wen-Kun Huang
- First, second, third, fourth, fifth, sixth, and seventh authors: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; first author: College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China; fourth author: College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; and sixth author: Center for Plant Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Du-Qing Wu
- First, second, third, fourth, fifth, sixth, and seventh authors: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; first author: College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China; fourth author: College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; and sixth author: Center for Plant Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Deliang Peng
- First, second, third, fourth, fifth, sixth, and seventh authors: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; first author: College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China; fourth author: College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; and sixth author: Center for Plant Sciences, University of Leeds, Leeds, LS2 9JT, UK
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20
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Phani V, Shivakumara TN, Davies KG, Rao U. Meloidogyne incognita Fatty Acid- and Retinol- Binding Protein (Mi-FAR-1) Affects Nematode Infection of Plant Roots and the Attachment of Pasteuria penetrans Endospores. Front Microbiol 2017; 8:2122. [PMID: 29209280 PMCID: PMC5701614 DOI: 10.3389/fmicb.2017.02122] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 10/18/2017] [Indexed: 11/13/2022] Open
Abstract
Root-knot nematode (RKN) Meloidogyne incognita is an economically important pest of crops. Pasteuria penetrans, is a nematode hyperparasitic bacterium capable of suppressing the reproduction of RKN and thereby useful for its management. Secreted fatty acid and retinol-binding proteins are unique in nematodes and are engaged in nutrient acquisition, development and reproduction; they are also a component of the nematode cuticle and thought to be involved in the interface between hosts and parasites. Attachment of endospores to the cuticle of second stage juveniles of RKN is the primary step of infection and several factors have been identified to facilitate attachment. In this study, the full length of Mi-far-1 (573 bp) was cloned from M. incognita and characterized. Analysis revealed that the Mi-far-1 was rich in α-helix structure, contained a predicted consensus casein kinase II phosphorylation site and a glycosylation site. Quantitative PCR showed the highest expression in the fourth stage juveniles and in situ hybridization revealed the presence of Mi-far-1 mRNA in the hypodermis below the cuticle. Single copy insertion pattern of Mi-far-1 in M. incognita genome was detected by Southern blotting. Knockdown of Mi-far-1 showed significantly increased attachment of P. penetrans’ endospores on juvenile cuticle surface and also affected host finding, root infection and nematode fecundity.
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Affiliation(s)
- Victor Phani
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Keith G Davies
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, United Kingdom.,Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Uma Rao
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, India
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Yang D, Chen C, Liu Q, Jian H. Comparative analysis of pre- and post-parasitic transcriptomes and mining pioneer effectors of Heterodera avenae. Cell Biosci 2017; 7:11. [PMID: 28289537 PMCID: PMC5309974 DOI: 10.1186/s13578-017-0138-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 02/06/2017] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The cereal cyst nematode (CCN, Heterodera avenae) is a devastating pathogen of wheat and barley crops in many countries. We aimed to prioritize genetic and molecular targets for H. avenae control via the powerful and integrative bioinformatics platform. RESULTS Here, we sequenced mRNA isolated from Chinese H. avenae at pre-parasitic (consisting of egg, J1 and hatched-J2) stages and post-parasitic (consisting of parasitic-J2, J3, J4 and adults) stages. Total 1,066,719 reads of whole life cycle transcriptomes were assembled into 10,811 contigs with N50 length of 1754 bp and 71,401 singletons. Comparative analyses of orthologous among H. avenae and 7 other nematodes with various life-styles revealed the significance and peculiarity of neurological system for sedentary phytonematode. KEGG pathway enrichment demonstrated active crosstalk events of nervous system at pre-parasitic stages, and 6 FMRFamide-like neuropeptides were verified to display an expression peak at the hatched-J2 stage in H. avenae. Furthermore, multiple approaches were undertaken to mine putative effectors and parasitism-specific genes. Notably, H. avenae might represent the first phytonematode reported to possess the pioneer effectors with RxLR motif and potential effectors with homologies to Ant-5/Ant-34. CONCLUSION Our work provides valuable resources for in-depth understanding the parasitism and pathogenicity of H. avenae, as well as developing new targets-oriented strategies on effective managements.
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Affiliation(s)
- Dan Yang
- Department of Plant Pathology, China Agricultural University, Beijing, 100193 China
| | - Changlong Chen
- Department of Plant Pathology, China Agricultural University, Beijing, 100193 China
- Institute of Crop Research, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Qian Liu
- Department of Plant Pathology, China Agricultural University, Beijing, 100193 China
| | - Heng Jian
- Department of Plant Pathology, China Agricultural University, Beijing, 100193 China
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Correction: Characterization of Three Novel Fatty Acid- and Retinoid-Binding Protein Genes (Ha-far-1, Ha-far-2 and Hf-far-1) from the Cereal Cyst Nematodes Heterodera avenae and H. filipjevi. PLoS One 2016; 11:e0165356. [PMID: 27764248 PMCID: PMC5072580 DOI: 10.1371/journal.pone.0165356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pone.0160003.].
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