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Tahir A, Siddiqi AR, Maryam A, Chaitanya Vedithi S, Blundell TL. Structure-guided computational insecticide discovery targeting β-N-acetyl-D-hexosaminidase of Ostrinia furnacalis. J Biomol Struct Dyn 2023:1-14. [PMID: 37814544 DOI: 10.1080/07391102.2023.2264394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 09/20/2023] [Indexed: 10/11/2023]
Abstract
Ostrinia furnacalis is a species of moth in the Crambidae family that is harmful to maize and other corn crops in Southeast Asia and the Western Pacific regions. Ostrinia furnacalis causes devastating losses to economically important corn fields. The β-N-acetyl-D-hexosaminidase is an essential enzyme in O. furnacalis and its substrate binding +1 active site is different from that of the plants and humans β-N-acetyl-D-hexosaminidases. To develop environment-friendly insecticides against OfHex1, we conducted structure-guided computational insecticide discovery to identify potential inhibitors that can bind the active site and inhibit the substrate binding and activity of the enzyme. We adopted a three-pronged strategy to conduct virtual screening using Glide and virtual screening workflow (VSW) in Schrödinger Suite-2022-3, against crystal structures of OfHex1 (PDB Id:3NSN), its homologue in humans (PDB Id: 1NP0) and Alphafold model of β-N-acetyl-D-hexosaminidase from Trichogramma pretiosum, an egg parasitoid that protects the crops from O. furnacalis. A library of 20,313 commercially available and "insecticide-like" compounds was extracted from published literature. LigPrep enabled 44,943 ready-to-dock conformers generation. Glide docking revealed 18 OfHex1-specific hits that were absent in human and T. pretiosum screens. Reference docking was conducted using inhibitors/natural ligands in the crystal structures and hits with better docking scores than the reference were selected for MD simulations using Desmond to understand the stability of hit-target interactions. We noted five compounds that bound to OfHex1 TMX active-site based on their docking scores, consistent binding as noted by MD simulations and their insecticide/pesticide likeliness as noted by the Comprehensive Pesticide Likeness Analysis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Adeena Tahir
- Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad, Pakistan
| | - Abdul Rauf Siddiqi
- Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad, Pakistan
| | - Arooma Maryam
- Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad, Pakistan
| | - Sundeep Chaitanya Vedithi
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Heart and Lung Research Institute (HLRI), Cambridge, United Kingdom
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Heart and Lung Research Institute (HLRI), Cambridge, United Kingdom
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Xu Q, Zhao Z, Liang P, Wang S, Li F, Jin S, Zhang J. Identification of novel nematode succinate dehydrogenase inhibitors: Virtual screening based on ligand-pocket interactions. Chem Biol Drug Des 2023; 101:9-23. [PMID: 34981652 DOI: 10.1111/cbdd.14019] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/10/2021] [Accepted: 12/29/2021] [Indexed: 12/15/2022]
Abstract
To discover new nematicidal succinate dehydrogenase (SDH) inhibitors with novel structures, we conducted a virtual screening of the ChemBridge library with 1.7 million compounds based on ligand-pocket interactions. The homology model of Caenorhabditis elegans SDH was established, along with a pharmacophore model based on ligand-pocket interactions. After the pharmacophore-based and docking-based screening, 19 compounds were selected for the subsequent enzymatic assays. The results showed that compound 1 (ID: 7607321) exhibited inhibitory activity against SDH with a determined IC50 value of 19.6 μM. Structural modifications and nematicidal activity studies were then carried out, which provided further evidence that compound 1 exhibited excellent nematicidal activity. Molecular dynamics simulations were then conducted to investigate the underlying molecular basis for the potency of these inhibitors against SDH. This work provides a reliable strategy and useful information for the future design of nematode SDH inhibitors.
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Affiliation(s)
- Qingbo Xu
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Zhixiang Zhao
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Peibo Liang
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Simin Wang
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Fang Li
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Shuhui Jin
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Jianjun Zhang
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
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Shen S, Ding B, Jiang X, Yang M, Yang Q, Dong L. Discovery of novel inhibitors targeting nematode chitinase C eCht1: Virtual screening, biological evaluation, and molecular dynamics simulation. Front Chem 2022; 10:1021295. [PMID: 36405330 PMCID: PMC9669442 DOI: 10.3389/fchem.2022.1021295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 10/18/2022] [Indexed: 04/19/2024] Open
Abstract
Plant-parasitic nematodes are a main limiting factor for worldwide agriculture. To reduce the global burden of nematode infections, chemical nematicides are still the most effective methods to manage nematodes. With the increasing resistance of nematodes, the development of new anti-nematicides drug is urgent. Nematode chitinases are found to play important roles in various physiological functions, such as larva moulting, hatching from eggshell, and host infection. Inhibition of nematode chitinase is considered a promising strategy for the development of eco-friendly nematicides. In this study, to develop novel nematode chitinase CeCht1 inhibitors, virtual screening of the ZINC database was performed using the pesticide-likeness rules, pharmacophore-based and docking-based approach in turn. Compounds HAU-4 and HAU-7 were identified as potent CeCht1 inhibitors with the IC50 values of 4.2 μM and 10.0 μM, respectively. Moreover, molecular dynamics simulations combined with binding free energy and free energy decomposition calculations were conducted to investigate the basis for the potency of the two inhibitors toward CeCht1. This work gives an insight into the future rational development of novel and potent nematode chitinase inhibitors.
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Affiliation(s)
- Shengqiang Shen
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Baokang Ding
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Xi Jiang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Meiling Yang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Qing Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Lili Dong
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
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Fernandes MJG, Pereira RB, Rodrigues ARO, Vieira TF, Fortes AG, Pereira DM, Sousa SF, Gonçalves MST, Castanheira EMS. Liposomal Formulations Loaded with a Eugenol Derivative for Application as Insecticides: Encapsulation Studies and In Silico Identification of Protein Targets. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:3583. [PMID: 36296773 PMCID: PMC9611868 DOI: 10.3390/nano12203583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 10/08/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
A recently synthesized new eugenol derivative, ethyl 4-(2-methoxy-4-(oxiran-2-ylmethyl)phenoxy)butanoate, with a high insecticidal activity against Sf9 (Spodoptera frugiperda) insect cells, was encapsulated in the liposomal formulations of egg-phosphatidylcholine/cholesterol (Egg-PC:Ch) 70:30 and 100% dioleoylphosphatidylglycerol (DOPG), aiming at the future application as insecticides. Compound-loaded DOPG liposomes have sizes of 274 ± 12 nm, while Egg-PC:Ch liposomes exhibit smaller hydrodynamic diameters (69.5 ± 7 nm), high encapsulation efficiency (88.8 ± 2.7%), higher stability, and a more efficient compound release, thus, they were chosen for assays in Sf9 insect cells. The compound elicited a loss of cell viability up to 80% after 72 h of incubation. Relevantly, nanoencapsulation maintained the toxicity of the compound toward insect cells while lowering the toxicity toward human cells, thus showing the selectivity of the system. Structure-based inverted virtual screening was used to predict the most likely targets and molecular dynamics simulations and free energy calculations were used to demonstrate that this molecule can form a stable complex with insect odorant binding proteins and/or acetylcholinesterase. The results are promising for the future application of compound-loaded nanoliposome formulations as crop insecticides.
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Affiliation(s)
- Maria José G. Fernandes
- Centre of Chemistry (CQUM), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Renato B. Pereira
- REQUIMTE/LAQV, Laboratory of Pharmacognosy, Department of Chemistry, Faculty of Pharmacy, University of Porto, R. Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Ana Rita O. Rodrigues
- Physics Centre of Minho and Porto Universities (CF-UM-UP), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- Associate Laboratory LaPMET, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Tatiana F. Vieira
- UCIBIO/REQUIMTE, BioSIM—Department of Medicine, Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
| | - A. Gil Fortes
- Centre of Chemistry (CQUM), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - David M. Pereira
- REQUIMTE/LAQV, Laboratory of Pharmacognosy, Department of Chemistry, Faculty of Pharmacy, University of Porto, R. Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Sérgio F. Sousa
- UCIBIO/REQUIMTE, BioSIM—Department of Medicine, Faculty of Medicine, University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
| | - M. Sameiro T. Gonçalves
- Centre of Chemistry (CQUM), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Elisabete M. S. Castanheira
- Physics Centre of Minho and Porto Universities (CF-UM-UP), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- Associate Laboratory LaPMET, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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The Role of Chitooligosaccharidolytic β- N-Acetylglucosamindase in the Molting and Wing Development of the Silkworm Bombyx mori. Int J Mol Sci 2022; 23:ijms23073850. [PMID: 35409210 PMCID: PMC8998872 DOI: 10.3390/ijms23073850] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/21/2022] [Accepted: 03/27/2022] [Indexed: 02/01/2023] Open
Abstract
The insect glycoside hydrolase family 20 β-N-acetylhexosaminidases (HEXs) are key enzymes involved in chitin degradation. In this study, nine HEX genes in Bombyx mori were identified by genome-wide analysis. Bioinformatic analysis based on the transcriptome database indicated that each gene had a distinct expression pattern. qRT-PCR was performed to detect the expression pattern of the chitooligosaccharidolytic β-N-acetylglucosaminidase (BmChiNAG). BmChiNAG was highly expressed in chitin-rich tissues, such as the epidermis. In the wing disc and epidermis, BmChiNAG has the highest expression level during the wandering stage. CRISPR/Cas9-mediated BmChiNAG deletion was used to study the function. In the BmChiNAG-knockout line, 39.2% of female heterozygotes had small and curly wings. The ultrastructure of a cross-section showed that the lack of BmChiNAG affected the stratification of the wing membrane and the formation of the correct wing vein structure. The molting process of the homozygotes was severely hindered during the larva to pupa transition. Epidermal sections showed that the endocuticle of the pupa was not degraded in the mutant. These results indicate that BmChiNAG is involved in chitin catabolism and plays an important role in the molting and wing development of the silkworm, which highlights the potential of BmChiNAG as a pest control target.
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Chen T, Li WQ, Liu Z, Jiang W, Liu T, Yang Q, Zhu XL, Yang GF. Discovery of Biphenyl-Sulfonamides as Novel β- N-Acetyl-d-Hexosaminidase Inhibitors via Structure-Based Virtual Screening. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:12039-12047. [PMID: 34587743 DOI: 10.1021/acs.jafc.1c01642] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Novel insecticidal targets are always in demand due to the development of resistance. OfHex1, a β-N-acetyl-d-hexosaminidase identified in Ostrinia furnacalis (Asian corn borer), is involved in insect chitin catabolism and has proven an ideal target for insecticide development. In this study, structure-based virtual screening, structure simplification, and biological evaluation are used to show that compounds with a biphenyl-sulfonamide skeleton have great potential as OfHex1 inhibitors. Specifically, compounds 10k, 10u, and 10v have Ki values of 4.30, 3.72, and 4.56 μM, respectively, and thus, they are more potent than some reported nonglycosyl-based inhibitors such as phlegmacin B1 (Ki = 26 μM), berberine (Ki = 12 μM), 2 (Ki = 11.2 μM), and 3 (Ki = 28.9 μM). Furthermore, inhibitory kinetic assessments reveal that the target compounds are competitive inhibitors with respect substrate, and based on toxicity predictions, most of them have potent drug properties. The obtained results indicate that the biphenyl-sulfonamide skeleton characterized by simple chemical structure, synthetic tractability, potent activity, and low toxicity has potential for further development in pest management targeting OfHex1.
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Affiliation(s)
- Tao Chen
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Chemical Biology Center, Central China Normal University, Wuhan 430079, P.R. China
| | - Wen-Qin Li
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, P.R. China
| | - Zheng Liu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Chemical Biology Center, Central China Normal University, Wuhan 430079, P.R. China
| | - Wen Jiang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Chemical Biology Center, Central China Normal University, Wuhan 430079, P.R. China
| | - Tian Liu
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, P.R. China
| | - Qing Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection and Shenzhen Agricultural Genome Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R. China
| | - Xiao-Lei Zhu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Chemical Biology Center, Central China Normal University, Wuhan 430079, P.R. China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Chemical Biology Center, Central China Normal University, Wuhan 430079, P.R. China
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