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Stankovic B, Marinkovic F. A novel procedure for selection of molecular descriptors: QSAR model for mutagenicity of nitroaromatic compounds. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:54603-54617. [PMID: 39207617 DOI: 10.1007/s11356-024-34800-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024]
Abstract
Nitroaromatic compounds (NACs) stand out as pervasive organic pollutants, prompting an imperative need to investigate their hazardous effects. Computational chemistry methods play a crucial role in this exploration, offering a safer and more time-efficient approach, mandated by various legislations. In this study, our focus lay on the development of transparent, interpretable, reproducible, and publicly available methodologies aimed at deriving quantitative structure-activity relationship models and testing them by modelling the mutagenicity of NACs against the Salmonella typhimurium TA100 strain. Descriptors were selected from Mordred and RDKit molecular descriptors, along with several quantum chemistry descriptors. For that purpose, the genetic algorithm (GA), as the most widely used method in the literature, and three alternative algorithms (Boruta, Featurewiz, and ForwardSelector) combined with the forward stepwise selection technique were used. The construction of models utilized the multiple linear regression method, with subsequent scrutiny of fitting and predictive performance, reliability, and robustness through various statistical validation criteria. The models were ranked by the Multi-Criteria Decision Making procedure. Findings have revealed that the proposed methodology for descriptor selection outperforms GA, with Featurewiz showing a slight advantage over Boruta and ForwardSelector. These constructed models can serve as valuable tools for the quick and reliable prediction of NACs mutagenicity.
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Affiliation(s)
- Branislav Stankovic
- Department for Nuclear and Plasma Physics, Vinča Institute of Nuclear Sciences -National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia.
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Araujo-Lima CF, de Cassia Castro Carvalho R, Rosario SL, Leite DI, Aguiar ACC, de Souza Santos LV, de Araujo JS, Salomão K, Kaiser CR, Krettli AU, Bastos MM, Aiub CAF, de Nazaré Correia Soeiro M, Boechat N, Felzenszwalb I. Antiplasmodial, Trypanocidal, and Genotoxicity In Vitro Assessment of New Hybrid α,α-Difluorophenylacetamide-statin Derivatives. Pharmaceuticals (Basel) 2023; 16:782. [PMID: 37375730 DOI: 10.3390/ph16060782] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 05/13/2023] [Accepted: 05/19/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Statins present a plethora of pleiotropic effects including anti-inflammatory and antimicrobial responses. A,α-difluorophenylacetamides, analogs of diclofenac, are potent pre-clinical anti-inflammatory non-steroidal drugs. Molecular hybridization based on the combination of pharmacophoric moieties has emerged as a strategy for the development of new candidates aiming to obtain multitarget ligands. METHODS Considering the anti-inflammatory activity of phenylacetamides and the potential microbicidal action of statins against obligate intracellular parasites, the objective of this work was to synthesize eight new hybrid compounds of α,α-difluorophenylacetamides with the moiety of statins and assess their phenotypic activity against in vitro models of Plasmodium falciparum and Trypanosoma cruzi infection besides exploring their genotoxicity safety profile. RESULTS None of the sodium salt compounds presented antiparasitic activity and two acetated compounds displayed mild anti-P. falciparum effect. Against T. cruzi, the acetate halogenated hybrids showed moderate effect against both parasite forms relevant for human infection. Despite the considerable trypanosomicidal activity, the brominated compound revealed a genotoxic profile impairing future in vivo testing. CONCLUSIONS However, the chlorinated derivative was the most promising compound with chemical and biological profitable characteristics, without presenting genotoxicity in vitro, being eligible for further in vivo experiments.
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Affiliation(s)
- Carlos Fernando Araujo-Lima
- Laboratório de Biologia Celular, LBC Instituto Oswaldo Cruz-FIOCRUZ, Rio de Janeiro 21041-250, RJ, Brazil
- Laboratório de Mutagênese Ambiental, LabMut Instituto de Biologia Roberto Alcantara Gomes, IBRAG-UERJ, Rio de Janeiro 22050-020, RJ, Brazil
- Programa de Pós-Graduação em Biologia Molecular e Celular, Instituto Biomédico-UNIRIO, Rio de Janeiro 20211-030, RJ, Brazil
| | - Rita de Cassia Castro Carvalho
- Departamento de Síntese de Fármacos, Instituto de Tecnologia em Fármacos, Farmanguinhos-FIOCRUZ, Rua Sizenando Nabuco 100, Manguinhos, Rio de Janeiro 21041-250, RJ, Brazil
- Programa de Pós-Graduação em Química, PGQu, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-853, RJ, Brazil
| | - Sandra Loureiro Rosario
- Departamento de Síntese de Fármacos, Instituto de Tecnologia em Fármacos, Farmanguinhos-FIOCRUZ, Rua Sizenando Nabuco 100, Manguinhos, Rio de Janeiro 21041-250, RJ, Brazil
| | - Debora Inacio Leite
- Departamento de Síntese de Fármacos, Instituto de Tecnologia em Fármacos, Farmanguinhos-FIOCRUZ, Rua Sizenando Nabuco 100, Manguinhos, Rio de Janeiro 21041-250, RJ, Brazil
- Programa de Pós-Graduação em Farmacologia e Química Medicinal, ICB-UFRJ, Rio de Janeiro 21941-902, RJ, Brazil
| | - Anna Caroline Campos Aguiar
- Laboratório de Malária, Centro de Pesquisas René Rachou, CPqRR-FIOCRUZ, Belo Horizonte 30190-002, MG, Brazil
| | - Lizandra Vitoria de Souza Santos
- Laboratório de Mutagênese Ambiental, LabMut Instituto de Biologia Roberto Alcantara Gomes, IBRAG-UERJ, Rio de Janeiro 22050-020, RJ, Brazil
| | | | - Kelly Salomão
- Laboratório de Biologia Celular, LBC Instituto Oswaldo Cruz-FIOCRUZ, Rio de Janeiro 21041-250, RJ, Brazil
| | - Carlos Roland Kaiser
- Programa de Pós-Graduação em Química, PGQu, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-853, RJ, Brazil
| | - Antoniana Ursine Krettli
- Laboratório de Malária, Centro de Pesquisas René Rachou, CPqRR-FIOCRUZ, Belo Horizonte 30190-002, MG, Brazil
| | - Monica Macedo Bastos
- Departamento de Síntese de Fármacos, Instituto de Tecnologia em Fármacos, Farmanguinhos-FIOCRUZ, Rua Sizenando Nabuco 100, Manguinhos, Rio de Janeiro 21041-250, RJ, Brazil
| | - Claudia Alessandra Fortes Aiub
- Programa de Pós-Graduação em Biologia Molecular e Celular, Instituto Biomédico-UNIRIO, Rio de Janeiro 20211-030, RJ, Brazil
| | | | - Nubia Boechat
- Departamento de Síntese de Fármacos, Instituto de Tecnologia em Fármacos, Farmanguinhos-FIOCRUZ, Rua Sizenando Nabuco 100, Manguinhos, Rio de Janeiro 21041-250, RJ, Brazil
| | - Israel Felzenszwalb
- Laboratório de Mutagênese Ambiental, LabMut Instituto de Biologia Roberto Alcantara Gomes, IBRAG-UERJ, Rio de Janeiro 22050-020, RJ, Brazil
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Liggri PGV, Pérez-Garrido A, Tsitsanou KE, Dileep KV, Michaelakis A, Papachristos DP, Pérez-Sánchez H, Zographos SE. 2D finger-printing and molecular docking studies identified potent mosquito repellents targeting odorant binding protein 1. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2023:103961. [PMID: 37217081 DOI: 10.1016/j.ibmb.2023.103961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 04/27/2023] [Accepted: 05/10/2023] [Indexed: 05/24/2023]
Abstract
Personal protection measures against the mosquitoes like the use of repellents constitute valuable tools in the effort to prevent the transmission of vector-borne diseases. Therefore, the discovery of novel repellent molecules which will be effective at lower concentrations and provide a longer duration of protection remains an urgent need. Mosquito Odorant-Binding Proteins (OBPs) involved in the initial steps of the olfactory signal transduction cascade have been recognized not only as passive carriers of odors and pheromones but also as the first molecular filter to discriminate semiochemicals, hence serving as molecular targets for the design of novel pest control agents. Among the three-dimensional structures of mosquito OBPs solved in the last decades, the OBP1 complexes with known repellents have been widely used as reference structures in docking analysis and molecular dynamics simulation studies for the structure-based discovery of new molecules with repellent activity. Herein, ten compounds known to be active against mosquitoes and/or displaying a binding affinity for Anopheles gambiae AgamOBP1 were used as queries in an in silico screening of over 96 million chemical samples in order to detect molecules with structural similarity. Further filtering of the acquired hits on the basis of toxicity, vapor pressure, and commercial availability resulted in 120 unique molecules that were subjected to molecular docking studies against OBP1. For seventeen potential OBP1-binders, the free energy of binding (FEB) and mode of interaction with the protein were further estimated by molecular docking simulations leading to the selection of eight molecules exhibiting the highest similarity with their parental compounds and favorable energy values. The in vitro determination of their binding affinity to AgamOBP1 and the evaluation of their repellent activity against female Aedes albopictus mosquitoes revealed that our combined ligand similarity screening and OBP1 structure-based molecular docking successfully detected three molecules with enhanced repellent properties. A novel DEET-like repellent with lower volatility (8.55 × 10-4 mmHg) but a higher binding affinity for OBP1 than DEET (1.35 × 10-3 mmHg). A highly active repellent molecule that is predicted to bind to the secondary Icaridin (sIC)-binding site of OBP1 with higher affinity than to the DEET-site and, therefore, represents a new scaffold to be exploited for the discovery of binders targeting multiple OBP sites. Finally, a third potent repellent exhibiting a high degree of volatility was found to be a strong DEET-site binder of OBP1 that could be used in slow-release formulations.
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Affiliation(s)
- Panagiota G V Liggri
- Institute of Chemical Biology, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635, Athens, Greece; Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500, Larissa, Greece.
| | - Alfonso Pérez-Garrido
- Structural Bioinformatics and High Performance Computing Research Group (BIO-HPC), Universidad Católica de Murcia (UCAM), 30107, Spain
| | - Katerina E Tsitsanou
- Institute of Chemical Biology, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635, Athens, Greece
| | - Kalarickal V Dileep
- Laboratory for Computational and Structural Biology, Jubilee Centre for Medical Research, Jubilee Mission Medical College and Research Institute, Thrissur, Kerala, 680005, India
| | - Antonios Michaelakis
- Benaki Phytopathological Institute, Department of Entomology and Agricultural Zoology, 8 S Delta Str. 14561, Kifissia, Athens, Greece
| | - Dimitrios P Papachristos
- Benaki Phytopathological Institute, Department of Entomology and Agricultural Zoology, 8 S Delta Str. 14561, Kifissia, Athens, Greece
| | - Horacio Pérez-Sánchez
- Structural Bioinformatics and High Performance Computing Research Group (BIO-HPC), Universidad Católica de Murcia (UCAM), 30107, Spain.
| | - Spyros E Zographos
- Institute of Chemical Biology, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635, Athens, Greece.
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Banegas-Luna AJ, Imbernón B, Llanes Castro A, Pérez-Garrido A, Cerón-Carrasco JP, Gesing S, Merelli I, D'Agostino D, Pérez-Sánchez H. Advances in distributed computing with modern drug discovery. Expert Opin Drug Discov 2018; 14:9-22. [PMID: 30484337 DOI: 10.1080/17460441.2019.1552936] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Computational chemistry dramatically accelerates the drug discovery process and high-performance computing (HPC) can be used to speed up the most expensive calculations. Supporting a local HPC infrastructure is both costly and time-consuming, and, therefore, many research groups are moving from in-house solutions to remote-distributed computing platforms. Areas covered: The authors focus on the use of distributed technologies, solutions, and infrastructures to gain access to HPC capabilities, software tools, and datasets to run the complex simulations required in computational drug discovery (CDD). Expert opinion: The use of computational tools can decrease the time to market of new drugs. HPC has a crucial role in handling the complex algorithms and large volumes of data required to achieve specificity and avoid undesirable side-effects. Distributed computing environments have clear advantages over in-house solutions in terms of cost and sustainability. The use of infrastructures relying on virtualization reduces set-up costs. Distributed computing resources can be difficult to access, although web-based solutions are becoming increasingly available. There is a trade-off between cost-effectiveness and accessibility in using on-demand computing resources rather than free/academic resources. Graphics processing unit computing, with its outstanding parallel computing power, is becoming increasingly important.
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Affiliation(s)
- Antonio Jesús Banegas-Luna
- a Bioinformatics and High Performance Computing Research Group (BIO-HPC) , Universidad Católica de Murcia (UCAM) , Murcia , Spain
| | - Baldomero Imbernón
- a Bioinformatics and High Performance Computing Research Group (BIO-HPC) , Universidad Católica de Murcia (UCAM) , Murcia , Spain
| | - Antonio Llanes Castro
- a Bioinformatics and High Performance Computing Research Group (BIO-HPC) , Universidad Católica de Murcia (UCAM) , Murcia , Spain
| | - Alfonso Pérez-Garrido
- a Bioinformatics and High Performance Computing Research Group (BIO-HPC) , Universidad Católica de Murcia (UCAM) , Murcia , Spain
| | - José Pedro Cerón-Carrasco
- a Bioinformatics and High Performance Computing Research Group (BIO-HPC) , Universidad Católica de Murcia (UCAM) , Murcia , Spain
| | - Sandra Gesing
- b Center for Research Computing , University of Notre Dame , Notre Dame , IN , USA
| | - Ivan Merelli
- c Institute for Biomedical Technologies , National Research Council of Italy , Segrate (Milan) , Italy
| | - Daniele D'Agostino
- d Institute for Applied Mathematics and Information Technologies "E. Magenes" , National Research Council of Italy , Genoa , Italy
| | - Horacio Pérez-Sánchez
- a Bioinformatics and High Performance Computing Research Group (BIO-HPC) , Universidad Católica de Murcia (UCAM) , Murcia , Spain
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Pérez-Garrido A, Rivero-Buceta V, Cano G, Kumar S, Pérez-Sánchez H, Bautista MT. Latest QSAR study of adenosine A $$_{\mathrm{2B}}$$ 2 B receptor affinity of xanthines and deazaxanthines. Mol Divers 2015; 19:975-89. [DOI: 10.1007/s11030-015-9608-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 06/24/2015] [Indexed: 12/24/2022]
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