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Vivekanandhan P, Swathy K, Lucy A, Sarayut P, Patcharin K. Entomopathogenic fungi based microbial insecticides and their physiological and biochemical effects on Spodoptera frugiperda (J.E. Smith). Front Cell Infect Microbiol 2023; 13:1254475. [PMID: 38149005 PMCID: PMC10750404 DOI: 10.3389/fcimb.2023.1254475] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/20/2023] [Indexed: 12/28/2023] Open
Abstract
Background 'The fall armyworm, Spodoptera frugiperda', represents a significant threat to maize production, a major staple crop in Asian countries. Methods In pursuit of more effective control of this insect pest, our study assessed the physiological and biochemical effects of the entomopathogenic fungus Metarhizium anisopliae against the larvae of S. frugiperda. Results Results revealed that, following nine days of treatment, a high concentration of conidia (1.5x107 conidia/mL-1) was toxic to all stages of larvae (second to fifth instar), resulting in 97% mortality of the second instar, 89% mortality of the third instar, 77% mortality of the fourth instar, and 72% mortality of fifth instar. All larval instars were found to have dose-dependent mortality effects. Treated S. frugiperda larvae further displayed significant physiological, morphological, and behavioral changes. Here, treated larvae displayed significantly lower levels of acetylcholinesterase, α-carboxylesterase, and β-carboxylesterase enzyme activity when compared to control groups. Treated larvae underwent an outward morphological change as the result of a decrease in the exterior cuticle of the anal papillae and a demelanization of the interior cuticle. Treated larvae also exhibited abnormal feeding behaviors as a consequence of the negative impact of conidia treatment on the neuromuscular system. Investigation into the effect of M. anisopliae on the non-target organism, the earthworm Eudrilus eugeniae, revealed that M. anisopliae conidia did not produce significant pathogenicity following three days of treatment. Furthermore, histological analysis revealed no significant effect of the entomopathogenic fungi on the gut tissue of the non-target organism. Conclusion This study highlights the potential of M. anisopliae in the control of S. frugiperda.
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Affiliation(s)
- Perumal Vivekanandhan
- Office of Research Administration, Chiang Mai University, Chiang Mai, Thailand
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai, Thailand
| | - Kannan Swathy
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai, Thailand
| | - Alford Lucy
- School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol, United Kingdom
| | - Pittarate Sarayut
- Office of Research Administration, Chiang Mai University, Chiang Mai, Thailand
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai, Thailand
| | - Krutmuang Patcharin
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai, Thailand
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Szewczuk NA, Duchowicz PR, Pomilio AB, Lobayan RM. Resonance structure contributions, flexibility, and frontier molecular orbitals (HOMO-LUMO) of pelargonidin, cyanidin, and delphinidin throughout the conformational space: application to antioxidant and antimutagenic activities. J Mol Model 2022; 29:2. [PMID: 36480114 DOI: 10.1007/s00894-022-05392-5] [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: 07/29/2022] [Accepted: 11/15/2022] [Indexed: 12/13/2022]
Abstract
This research refers to the study and understanding of the conformational space of the positive-charged anthocyanidin structures in relation with the known chemical reactivities and bioactivities of these compounds. Therefore, the planar (P) and nonplanar (Z) conformers of the three hydroxylated anthocyanidins pelargonidin, cyanidin, and delphinidin were analyzed throughout the conformational space at the B3LYP/6-311 ++ G** level of theory. The outcome displayed eleven new conformers for pelargonidin, fifty-four for cyanidin, and thirty-one for delphinidin. Positive-charged quinoidal structures showed a significant statistical weight in the conformational space, thus coexisting simultaneously with other resonance structures, such that under certain reaction conditions, the anthocyanidins behave as positive-charged quinoidal structures instead of oxonium salts. The calculations of the permanent dipole moment and the polarizability showed relationships with the quantity and arrangement of hydroxyls in the structure. In addition, theoretical calculations were used to analyze the frontier molecular orbitals (HOMO-LUMO) of the three anthocyanidins. The novel conception of this work lies in the fact that dipole moment, polarizability, and HOMO-LUMO values were related to the reactivity/bioactivity of these three anthocyanidins. HOMO-LUMO energy gaps were useful to explain the antioxidant activity, while the percent atom contributions to HOMO were appropriate to demonstrate the antimutagenic activity as enzyme inhibitors, as well as the steric and electrostatic requirements to form the pharmacophore. Delphinidin was the strongest antioxidant anthocyanidin, and pelargonidin the best anthocyanidin with antimutagenic activity.
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Affiliation(s)
- Nicolas A Szewczuk
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), CONICET, Universidad Nacional de La Plata (UNLP), Diag. 113 Y 64, C.C. 16, Sucursal 4, B1900, La Plata, Argentina
| | - Pablo R Duchowicz
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), CONICET, Universidad Nacional de La Plata (UNLP), Diag. 113 Y 64, C.C. 16, Sucursal 4, B1900, La Plata, Argentina
| | - Alicia B Pomilio
- Laboratorio de Química y Bioquímica Estructural, Departamento de Bioquímica Clínica, Área Hematología, Hospital de Clínicas "José de San Martín", Universidad de Buenos Aires, Av. Córdoba 2351, C1120AAF, Buenos Aires, Argentina
| | - Rosana M Lobayan
- Departamento de Física, Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Avda. Libertad 5300, 3400, Corrientes, Argentina.
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Fermentation as an Alternative Process for the Development of Bioinsecticides. FERMENTATION 2020. [DOI: 10.3390/fermentation6040120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Currently, insect pest control is carried out through the application of synthetic insecticides which have been related to harmful effects on both human and environmental health, as well as to the development of resistant pest populations. In this context, the development of new and natural insecticides is necessary. Agricultural and forestry waste or by-products are very low-cost substrates that can be converted by microorganisms into useful value-added bioactive products through fermentation processes. In this review we discuss recent discoveries of compounds obtained from fermented substrates along with their insecticidal, antifeedant, and repellent activities. Fermentation products obtained from agricultural and forestry waste are described in detail. The fermentation of the pure secondary metabolite such as terpenes and phenols is also included.
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Muhire J, Li BQ, Zhai HL, Li SS, Mi JY. A Simple Approach to the Toxicity Prediction of Anilines and Phenols Towards Aquatic Organisms. ARCHIVES OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2020; 78:545-554. [PMID: 31915850 DOI: 10.1007/s00244-019-00703-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 12/27/2019] [Indexed: 06/10/2023]
Abstract
Chemicals pollution in the environment has attracted attention all over the world, and the toxicity prediction of chemical pollutants has become quite important. In this paper, we introduce a simple approach to predict the toxicity of some chemical components, in which the Tchebichef image moment (TM) method was employed to extract useful chemical information from the images of molecular structures to establish quantitative structure-activity relationship (QSAR) prediction models. The proposed approach was applied to predict the toxicity of anilines and phenols for the aquatic organisms of P. subcapitata and V. fischeri, in which the obtained TMs were defined as the independent variables, while the biological toxicity (pEC50) was regarded to be the dependent variable. Then, the predictive models were established by stepwise regression, respectively. The obtained squared correlation coefficients of leave-one-out cross-validation (Q2) for training sets and the predictive squared correlation coefficients (Rp2) for test sets of the two groups of data were higher than 0.79 and 0.75, respectively, which indicated that the obtained models possessed satisfactory accuracy and reliability. Compared with several reported methods, the proposed approach was more convenient and has a higher predictive capability. Our study provides another perspective in QSAR research.
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Affiliation(s)
- Jules Muhire
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Bao Qiong Li
- School of Biotechnology & Health Sciences, Wuyi University, Jiangmen, 529020, People's Republic of China
| | - Hong Lin Zhai
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou, 730000, People's Republic of China.
| | - Sha Sha Li
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Jia Ying Mi
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou, 730000, People's Republic of China
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Hassan B, Ahmed S, Kirker G, Mankowski ME, Misbah Ul Haq M. Synergistic effect of heartwood extracts in combination with linseed oil as wood preservatives against subterranean termite Heterotermes indicola (Blattodea: Rhinotermitidae). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:3076-3085. [PMID: 31838694 DOI: 10.1007/s11356-019-07202-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 11/28/2019] [Indexed: 06/10/2023]
Abstract
This study evaluated the effect of wood extracts from Tectona grandis, Dalbergia sissoo, Cedrus deodara, and Pinus roxburghii combined with linseed oil as protectants of two non-durable wood species against the termite, Heterotermes indicola. Heartwood blocks (19 × 19 × 19 mm) and wood shavings were extracted using an ethanol/toluene (2:1) solvent system. Results of choice and no-choice tests with solvent-extracted and non-extracted heartwood blocks showed greater wood mass loss from termite feeding on solvent-extracted blocks compared with non-extracted blocks for all wood species. Significantly higher termite mortality was observed after termite exposure to non-extracted blocks compared with extracted blocks for all durable species. Sapwood blocks of two non-durable wood species (southern pine and cottonwood) were vacuum/pressure impregnated separately with each of the four types of extract at a concentration of 7.5 mg ml-1, linseed oil (20%) and a mixture of oil (20%) and extracts (4.25 mg ml-1) for the laboratory and field tests. Results showed that extract-oil mixture imparted significantly higher termite resistance compared with linseed or extracts alone under laboratory conditions. This apparent synergistic effect was clearly noted when linseed oil was combined with extracts from T. grandis or D. sissoo followed by an extract-oil mixture using C. deodara. These extract oil mixtures showed significantly less weight loss for the treated non-durable wood species and higher termite mortality (83-100%) compared with the control treatments and other extract-linseed oil mixtures tested. Treatment of both non-durable wood species with T. grandis + oil and D. sissoo + oil prevented termite damage compared with other treatments when blocks and stakes were exposed in the field for a period of 2 years. Results of the current study indicated that a mixture of a particular heartwood extract with linseed oil has potential to be used as environmentally friendly wood protectants.
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Affiliation(s)
- Babar Hassan
- South China Agricultural University, Guangzhou, 510642, People's Republic of China.
| | - Sohail Ahmed
- University of Agriculture Faisalabad, University Main Rd., Faisalabad, Punjab, 38000, Pakistan
| | - Grant Kirker
- USDA-FS, Forest Products Laboratory, 1 Gifford Pinchot Dr, Madison, WI, 53726, USA
| | - Mark E Mankowski
- USDA-FS, Forest Products Laboratory, 1 Gifford Pinchot Dr, Madison, WI, 53726, USA
- USDA-FS, Forest Products Laboratory, 201 Lincoln Green, Starkville, MS, 39759, USA
| | - Muhammad Misbah Ul Haq
- Nuclear Institute for Food and Agriculture (NIFA) Peshawar, Peshawar, Khyber-Pakhtunkhwa Province, Pakistan
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Boucherle B, Peuchmaur M, Boumendjel A, Haudecoeur R. Occurrences, biosynthesis and properties of aurones as high-end evolutionary products. PHYTOCHEMISTRY 2017; 142:92-111. [PMID: 28704688 DOI: 10.1016/j.phytochem.2017.06.017] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 05/22/2017] [Accepted: 06/30/2017] [Indexed: 05/06/2023]
Abstract
Recent years have witnessed a considerable renewed interest for the uncommon flavonoid class of aurones. The characterization of two major biosynthetic machineries involved in their biosynthesis in flowers has encouraged the revival of phytochemical studies and identification of original structures, a process started almost seventy-five years ago. This review draws up an exhaustive map of natural occurrences of aurones their biosynthetic pathways and roles, with the aim to link their original structural properties among flavonoids to their place in evolution and the selective advantages they bring to some of the most advanced taxa in the plant kingdom.
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Affiliation(s)
- Benjamin Boucherle
- Univ. Grenoble-Alpes, CNRS, DPM UMR 5063, CS 40700, 38058, Grenoble, France
| | - Marine Peuchmaur
- Univ. Grenoble-Alpes, CNRS, DPM UMR 5063, CS 40700, 38058, Grenoble, France
| | - Ahcène Boumendjel
- Univ. Grenoble-Alpes, CNRS, DPM UMR 5063, CS 40700, 38058, Grenoble, France
| | - Romain Haudecoeur
- Univ. Grenoble-Alpes, CNRS, DPM UMR 5063, CS 40700, 38058, Grenoble, France.
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7
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Duchowicz PR, Bacelo DE, Fioressi SE, Palermo V, Ibezim NE, Romanelli GP. QSAR studies of indoyl aryl sulfides and sulfones as reverse transcriptase inhibitors. Med Chem Res 2017. [DOI: 10.1007/s00044-017-2069-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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8
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Saavedra LM, Ruiz D, Romanelli GP, Duchowicz PR. Quantitative Structure-Antifungal Activity Relationships for cinnamate derivatives. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2015; 122:521-527. [PMID: 26410195 DOI: 10.1016/j.ecoenv.2015.09.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 09/09/2015] [Accepted: 09/14/2015] [Indexed: 06/05/2023]
Abstract
Quantitative Structure-Activity Relationships (QSAR) are established with the aim of analyzing the fungicidal activities of a set of 27 active cinnamate derivatives. The exploration of more than a thousand of constitutional, topological, geometrical and electronic molecular descriptors, which are calculated with Dragon software, leads to predictions of the growth inhibition on Pythium sp and Corticium rolfsii fungi species, in close agreement to the experimental values extracted from the literature. A set containing 21 new structurally related cinnamate compounds is prepared. The developed QSAR models are applied to predict the unknown fungicidal activity of this set, showing that cinnamates like 38, 28 and 42 are expected to be highly active for Pythium sp, while this is also predicted for 28 and 34 in C. rolfsii.
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Affiliation(s)
- Laura M Saavedra
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas INIFTA (UNLP, CCT La Plata-CONICET), Diagonal 113 y 64, Sucursal 4, C.C. 16, 1900 La Plata, Argentina
| | - Diego Ruiz
- Curso de Química Orgánica, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata (UNLP), 60 y 119, B1904AAN La Plata, Buenos Aires, Argentina
| | - Gustavo P Romanelli
- Curso de Química Orgánica, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata (UNLP), 60 y 119, B1904AAN La Plata, Buenos Aires, Argentina; Centro de Investigación y Desarrollo en Ciencias Aplicadas "Dr. J.J. Ronco" (CINDECA), Departamento de Química, Facultad de Ciencias Exactas, UNLP-CCT-CONICET, Calle 47 No. 257, B1900AJK La Plata, Argentina
| | - Pablo R Duchowicz
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas INIFTA (UNLP, CCT La Plata-CONICET), Diagonal 113 y 64, Sucursal 4, C.C. 16, 1900 La Plata, Argentina.
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9
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Chen JF, Liu ZQ. Ferrocenyl-Appended Aurone and Flavone: Which Possesses Higher Inhibitory Effects on DNA Oxidation and Radicals? Chem Res Toxicol 2014; 28:451-9. [DOI: 10.1021/tx500405b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jia-Feng Chen
- Department of Organic Chemistry,
College of Chemistry, Jilin University, No. 2519 Jiefang Road, Changchun 130021, China
| | - Zai-Qun Liu
- Department of Organic Chemistry,
College of Chemistry, Jilin University, No. 2519 Jiefang Road, Changchun 130021, China
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10
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Łozowicka B, Kaczyński P, Magdziarz T, Dubis AT. Synthesis, antifeedant activity against Coleoptera and 3D QSAR study of alpha-asarone derivatives. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2014; 25:173-188. [PMID: 24601760 DOI: 10.1080/1062936x.2013.875061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
For the first time, a set of 56 compounds representing structural derivatives of naturally occurring alpha-asarone as an antifeedants against stored product pests Sitophilus granarius L., Trogoderma granarium Ev., and Tribolium confusum Duv., were subjected to the 3D QSAR studies. Three-dimensional quantitative structure-activity relationships (3D-QSAR) for 56 compounds, including 15 newly synthesized, were performed using comparative molecular field analysis s-CoMFA and SOM-CoMSA techniques. QSAR was conducted based on a combination of biological activity (against Coleoptera larvae and beetles) and various geometrical, topological, quantum-mechanical, electronic, and chromatographic descriptors. The CoMSA formalism coupled with IVE (CoMSA-IVE) allowed us to obtain highly predictive models for Trogoderma granarium Ev. larvae. We have found that this novel method indicates a clear molecular basis for activity and lipophilicity. This investigation will facilitate optimization of the design of new potential antifeedants.
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Affiliation(s)
- B Łozowicka
- a Institute of Plant Protection - National Research Institute , Bialystok , Poland
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11
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Shahlaei M. Descriptor selection methods in quantitative structure-activity relationship studies: a review study. Chem Rev 2013; 113:8093-103. [PMID: 23822589 DOI: 10.1021/cr3004339] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mohsen Shahlaei
- Department of Medicinal Chemistry and Novel Drug Delivery Research Center, School of Pharmacy, Kermanshah University of Medical Sciences , Kermanshah 81746-73461, Iran
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Pasquale G, Romanelli GP, Autino JC, García J, Ortiz EV, Duchowicz PR. Quantitative structure-activity relationships of mosquito larvicidal chalcone derivatives. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2012; 60:692-697. [PMID: 22217234 DOI: 10.1021/jf203374r] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The mosquito larvicidal activities of a series of chalcones and some derivatives were subjected to a quantitative structure-activity relationship (QSAR) study, using more than a thousand constitutional, topological, geometrical, and electronic molecular descriptors calculated with Dragon software. The larvicidal activity values for 28 active compounds of the series were predicted, showing in general a good approximation to the experimental values found in the literature. Chalcones having one or both electron-rich rings showed high toxicity. However, the activity of chalcones was reduced by electron-withdrawing groups, and this was roughly diminished by derivatization of the carbonyl group. A set of six chalcones being structurally similar to some of the active ones, with a still unknown larvicidal activity, were prepared. Their activity values were predicted by applying the developed QSAR models, showing that two chalcones of such set, both 32 and 34, were expected to be highly active.
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Affiliation(s)
- Gustavo Pasquale
- Cátedra de Química Orgánica, Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata (UNLP), La Plata, Buenos Aires, Argentina
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13
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Quantitative structure–activity relationship and design of polysubstituted quinoline derivatives as inhibitors of phosphodiesterase 4. Med Chem Res 2011. [DOI: 10.1007/s00044-011-9831-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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García J, Duchowicz PR, Rozas MF, Caram JA, Mirífico MV, Fernández FM, Castro EA. A comparative QSAR on 1,2,5-thiadiazolidin-3-one 1,1-dioxide compounds as selective inhibitors of human serine proteinases. J Mol Graph Model 2011; 31:10-9. [PMID: 21908217 DOI: 10.1016/j.jmgm.2011.07.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Revised: 07/28/2011] [Accepted: 07/31/2011] [Indexed: 11/30/2022]
Abstract
Selective inhibitors of target serine proteinases have a potential therapeutic role for the treatment of various inflammatory and related diseases. We develop a comparative quantitative structure-activity relationships based analysis on compounds embodying the 1,2,5-thiadiazolidin-3-one 1,1-dioxide scaffold. By means of classical Molecular Dynamics we obtain the conformation of each lowest-energy molecular structure from which we derive more than a thousand of structural descriptors necessary for building predictive QSAR models. We resort to two different modeling approaches with the purpose of testing the consistency of our results: (a) multivariable linear regressions based on the replacement method and forward stepwise regression, and (b) the calculation of flexible descriptors with the CORAL program. All the models are properly validated by means of standard procedures. The resulting QSAR models are supposed to be of great utility for the rational search and design (including synthesis and/or in vitro biochemical studies) of new effective non-peptidyl inhibitors of serine proteinases.
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Affiliation(s)
- Javier García
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA, CCT La Plata-CONICET), Casilla de Correo 16, La Plata, Argentina
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15
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Carbó-Dorca R, Besalú E, Mercado LD. Communications on quantum similarity, part 3: a geometric-quantum similarity molecular superposition algorithm. J Comput Chem 2010; 32:582-99. [PMID: 20812322 DOI: 10.1002/jcc.21644] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Revised: 07/02/2010] [Accepted: 07/03/2010] [Indexed: 12/26/2022]
Abstract
This work describes a new procedure to obtain optimal molecular superposition based on quantum similarity (QS): the geometric-quantum similarity molecular superposition (GQSMS) algorithm. It has been inspired by the QS Aufbau principle, already described in a previous work, to build up coherently quantum similarity matrices (QSMs). The cornerstone of the present superposition technique relies upon the fact that quantum similarity integrals (QSIs), defined using a GTO basis set, depend on the squared intermolecular atomic distances. The resulting QSM structure, constructed under the GQSMS algorithm, becomes not only optimal in terms of its QSI elements but can also be arranged to produce a positive definite matrix global structure. Kruskal minimum spanning trees are also discussed as a device to order molecular sets described in turn by means of QSM. Besides the main subject of this work, focused on MS and QS, other practical considerations are also included in this study: essentially the use of elementary Jacobi rotations as QSM refinement tools and inward functions as QSM scaling methods.
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Affiliation(s)
- Ramon Carbó-Dorca
- Institut de Química Computacional, Universitat de Girona, Girona 17071, Catalonia, Spain.
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Mercader AG, Duchowicz PR, Fernández FM, Castro EA. Replacement Method and Enhanced Replacement Method Versus the Genetic Algorithm Approach for the Selection of Molecular Descriptors in QSPR/QSAR Theories. J Chem Inf Model 2010; 50:1542-8. [DOI: 10.1021/ci100103r] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Andrew G. Mercader
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA, UNLP, CCT La Plata-CONICET), Diag. 113 y 64, Sucursal 4, C.C. 16, 1900 La Plata, Argentina, and PRALIB (UBA-CONICET), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, C1113AAD Buenos Aires, Argentina
| | - Pablo R. Duchowicz
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA, UNLP, CCT La Plata-CONICET), Diag. 113 y 64, Sucursal 4, C.C. 16, 1900 La Plata, Argentina, and PRALIB (UBA-CONICET), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, C1113AAD Buenos Aires, Argentina
| | - Francisco M. Fernández
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA, UNLP, CCT La Plata-CONICET), Diag. 113 y 64, Sucursal 4, C.C. 16, 1900 La Plata, Argentina, and PRALIB (UBA-CONICET), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, C1113AAD Buenos Aires, Argentina
| | - Eduardo A. Castro
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA, UNLP, CCT La Plata-CONICET), Diag. 113 y 64, Sucursal 4, C.C. 16, 1900 La Plata, Argentina, and PRALIB (UBA-CONICET), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, C1113AAD Buenos Aires, Argentina
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