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Saifi I, Bhat BA, Hamdani SS, Bhat UY, Lobato-Tapia CA, Mir MA, Dar TUH, Ganie SA. Artificial intelligence and cheminformatics tools: a contribution to the drug development and chemical science. J Biomol Struct Dyn 2024; 42:6523-6541. [PMID: 37434311 DOI: 10.1080/07391102.2023.2234039] [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: 02/12/2023] [Accepted: 07/03/2023] [Indexed: 07/13/2023]
Abstract
In the ever-evolving field of drug discovery, the integration of Artificial Intelligence (AI) and Machine Learning (ML) with cheminformatics has proven to be a powerful combination. Cheminformatics, which combines the principles of computer science and chemistry, is used to extract chemical information and search compound databases, while the application of AI and ML allows for the identification of potential hit compounds, optimization of synthesis routes, and prediction of drug efficacy and toxicity. This collaborative approach has led to the discovery, preclinical evaluations and approval of over 70 drugs in recent years. To aid researchers in the pursuit of new drugs, this article presents a comprehensive list of databases, datasets, predictive and generative models, scoring functions and web platforms that have been launched between 2021 and 2022. These resources provide a wealth of information and tools for computer-assisted drug development, and are a valuable asset for those working in the field of cheminformatics. Overall, the integration of AI, ML and cheminformatics has greatly advanced the drug discovery process and continues to hold great potential for the future. As new resources and technologies become available, we can expect to see even more groundbreaking discoveries and advancements in these fields.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ifra Saifi
- Chaudhary Charan Singh University, Meerut, Uttar Pradesh, India
| | - Basharat Ahmad Bhat
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, J&K, India
| | - Syed Suhail Hamdani
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, J&K, India
| | - Umar Yousuf Bhat
- Department of Zoology, School of Biological Sciences, University of Kashmir, Srinagar, J&K, India
| | | | - Mushtaq Ahmad Mir
- Department of Clinical Laboratory Sciences, College of Applied Medical Science, King Khalid University, KSA, Saudi Arabia
| | - Tanvir Ul Hasan Dar
- Department of Biotechnology, School of Biosciences and Biotechnology, BGSB University, Rajouri, India
| | - Showkat Ahmad Ganie
- Department of Clinical Biochemistry, School of Biological Sciences, University of Kashmir, Srinagar, J&K, India
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2
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Gómez-García A, Prinz AK, Jiménez DAA, Zamora WJ, Barazorda-Ccahuana HL, Chávez-Fumagalli MÁ, Valli M, Andricopulo AD, da S Bolzani V, Olmedo DA, Solís PN, Núñez MJ, Rodríguez Pérez JR, Sánchez HAV, Cortés Hernández HF, Mosquera Martinez OM, Koch O, Medina-Franco JL. Updating and profiling the natural product-likeness of Latin American compound libraries. Mol Inform 2024; 43:e202400052. [PMID: 38994633 DOI: 10.1002/minf.202400052] [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: 02/08/2024] [Revised: 04/03/2024] [Accepted: 04/13/2024] [Indexed: 07/13/2024]
Abstract
Compound databases of natural products play a crucial role in drug discovery and development projects and have implications in other areas, such as food chemical research, ecology and metabolomics. Recently, we put together the first version of the Latin American Natural Product database (LANaPDB) as a collective effort of researchers from six countries to ensemble a public and representative library of natural products in a geographical region with a large biodiversity. The present work aims to conduct a comparative and extensive profiling of the natural product-likeness of an updated version of LANaPDB and the individual ten compound databases that form part of LANaPDB. The natural product-likeness profile of the Latin American compound databases is contrasted with the profile of other major natural product databases in the public domain and a set of small-molecule drugs approved for clinical use. As part of the extensive characterization, we employed several chemoinformatics metrics of natural product likeness. The results of this study will capture the attention of the global community engaged in natural product databases, not only in Latin America but across the world.
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Affiliation(s)
- Alejandro Gómez-García
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Mexico City, 04510, Mexico
| | - Ann-Kathrin Prinz
- Institute of Pharmaceutical and Medicinal Chemistry, Westfälische Wilhelms-Universität Münster, 48149, Münster, Germany
| | - Daniel A Acuña Jiménez
- CBio3 Laboratory, School of Chemistry, University of Costa Rica, San Pedro, San José, 11501-2060, Costa Rica
| | - William J Zamora
- CBio3 Laboratory, School of Chemistry, University of Costa Rica, San Pedro, San José, 11501-2060, Costa Rica
- Laboratory of Computational Toxicology and Artificial Intelligence (LaToxCIA), Biological Testing Laboratory (LEBi), University of Costa Rica, San Pedro, San José, 11501-2060, Costa Rica
- Advanced Computing Lab (CNCA), National High Technology Center (CeNAT), Pavas, San José, 1174-1200, Costa Rica
| | - Haruna L Barazorda-Ccahuana
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa Maria, Arequipa, 04000, Peru
| | - Miguel Á Chávez-Fumagalli
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa Maria, Arequipa, 04000, Peru
| | - Marilia Valli
- Laboratory of Medicinal and Computational Chemistry (LQMC), Centre for Research and Innovation in Biodiversity and Drug Discovery (CIBFar), São Carlos Institute of Physics (IFSC), University of São Paulo (USP), Av. João Dagnone, 1100, São Carlos, SP, 13563-120, Brazil
| | - Adriano D Andricopulo
- Laboratory of Medicinal and Computational Chemistry (LQMC), Centre for Research and Innovation in Biodiversity and Drug Discovery (CIBFar), São Carlos Institute of Physics (IFSC), University of São Paulo (USP), Av. João Dagnone, 1100, São Carlos, SP, 13563-120, Brazil
| | - Vanderlan da S Bolzani
- Nuclei of Bioassays, Biosynthesis and Ecophysiology of Natural Products (NuBBE), Department of Organic Chemistry, Institute of Chemistry, São Paulo State University (UNESP), Av. Prof. Francisco Degni, 55, Araraquara, SP, 14800-900, Brazil
| | - Dionisio A Olmedo
- Center for Pharmacognostic Research on Panamanian Flora (CIFLORPAN), College of Pharmacy, University of Panama, Av. Manuel E. Batista and Jose De Fabrega, Panama City, 3366, Panama
| | - Pablo N Solís
- Center for Pharmacognostic Research on Panamanian Flora (CIFLORPAN), College of Pharmacy, University of Panama, Av. Manuel E. Batista and Jose De Fabrega, Panama City, 3366, Panama
| | - Marvin J Núñez
- Natural Product Research Laboratory, School of Chemistry and Pharmacy, University of El Salvador, Final Ave. Mártires Estudiantes del 30 de Julio, San Salvador, 01101, El Salvador
| | - Johny R Rodríguez Pérez
- GIFAMOL Research Group, School of Chemistry Technology, Universidad Tecnológica de Pereira, Pereira, 660003, Colombia
- GIEPRONAL Research Group, School of Basic Sciences, Technology and Engineering, Universidad Nacional Abierta y a Distancia, Dosquebradas, 661001, Colombia
| | - Hoover A Valencia Sánchez
- GIFAMOL Research Group, School of Chemistry Technology, Universidad Tecnológica de Pereira, Pereira, 660003, Colombia
| | - Héctor F Cortés Hernández
- GIFAMOL Research Group, School of Chemistry Technology, Universidad Tecnológica de Pereira, Pereira, 660003, Colombia
| | - Oscar M Mosquera Martinez
- GBPN Research Group, School of Chemistry Technology, Universidad Tecnológica de Pereira, Pereira, 660003, Colombia
| | - Oliver Koch
- Institute of Pharmaceutical and Medicinal Chemistry, Westfälische Wilhelms-Universität Münster, 48149, Münster, Germany
| | - José L Medina-Franco
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Mexico City, 04510, Mexico
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Gómez-García A, Jiménez DAA, Zamora WJ, Barazorda-Ccahuana HL, Chávez-Fumagalli MÁ, Valli M, Andricopulo AD, Bolzani VDS, Olmedo DA, Solís PN, Núñez MJ, Rodríguez Pérez JR, Valencia Sánchez HA, Cortés Hernández HF, Medina-Franco JL. Navigating the Chemical Space and Chemical Multiverse of a Unified Latin American Natural Product Database: LANaPDB. Pharmaceuticals (Basel) 2023; 16:1388. [PMID: 37895859 PMCID: PMC10609821 DOI: 10.3390/ph16101388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/22/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
The number of databases of natural products (NPs) has increased substantially. Latin America is extraordinarily rich in biodiversity, enabling the identification of novel NPs, which has encouraged both the development of databases and the implementation of those that are being created or are under development. In a collective effort from several Latin American countries, herein we introduce the first version of the Latin American Natural Products Database (LANaPDB), a public compound collection that gathers the chemical information of NPs contained in diverse databases from this geographical region. The current version of LANaPDB unifies the information from six countries and contains 12,959 chemical structures. The structural classification showed that the most abundant compounds are the terpenoids (63.2%), phenylpropanoids (18%) and alkaloids (11.8%). From the analysis of the distribution of properties of pharmaceutical interest, it was observed that many LANaPDB compounds satisfy some drug-like rules of thumb for physicochemical properties. The concept of the chemical multiverse was employed to generate multiple chemical spaces from two different fingerprints and two dimensionality reduction techniques. Comparing LANaPDB with FDA-approved drugs and the major open-access repository of NPs, COCONUT, it was concluded that the chemical space covered by LANaPDB completely overlaps with COCONUT and, in some regions, with FDA-approved drugs. LANaPDB will be updated, adding more compounds from each database, plus the addition of databases from other Latin American countries.
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Affiliation(s)
- Alejandro Gómez-García
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México Avenida Universidad 3000, Mexico City 04510, Mexico;
| | - Daniel A. Acuña Jiménez
- CBio3 Laboratory, School of Chemistry, University of Costa Rica, San Pedro, San José 11501-2060, Costa Rica; (D.A.A.J.); (W.J.Z.)
| | - William J. Zamora
- CBio3 Laboratory, School of Chemistry, University of Costa Rica, San Pedro, San José 11501-2060, Costa Rica; (D.A.A.J.); (W.J.Z.)
- Laboratory of Computational Toxicology and Artificial Intelligence (LaToxCIA), Biological Testing Laboratory (LEBi), University of Costa Rica, San Pedro, San José 11501-2060, Costa Rica
- Advanced Computing Lab (CNCA), National High Technology Center (CeNAT), Pavas, San José 1174-1200, Costa Rica
| | - Haruna L. Barazorda-Ccahuana
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa Maria, Arequipa 04000, Peru; (H.L.B.-C.); (M.Á.C.-F.)
| | - Miguel Á. Chávez-Fumagalli
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa Maria, Arequipa 04000, Peru; (H.L.B.-C.); (M.Á.C.-F.)
| | - Marilia Valli
- Laboratory of Medicinal and Computational Chemistry (LQMC), Centre for Research and Innovation in Biodiversity and Drug Discovery (CIBFar), São Carlos Institute of Physics (IFSC), University of São Paulo (USP), Av. João Dagnone, 1100, São Carlos 13563-120, SP, Brazil; (M.V.); (A.D.A.)
| | - Adriano D. Andricopulo
- Laboratory of Medicinal and Computational Chemistry (LQMC), Centre for Research and Innovation in Biodiversity and Drug Discovery (CIBFar), São Carlos Institute of Physics (IFSC), University of São Paulo (USP), Av. João Dagnone, 1100, São Carlos 13563-120, SP, Brazil; (M.V.); (A.D.A.)
| | - Vanderlan da S. Bolzani
- Nuclei of Bioassays, Biosynthesis and Ecophysiology of Natural Products (NuBBE), Department of Organic Chemistry, Institute of Chemistry, São Paulo State University (UNESP), Av. Prof. Francisco Degni, 55, Araraquara 14800-900, SP, Brazil;
| | - Dionisio A. Olmedo
- Center for Pharmacognostic Research on Panamanian Flora (CIFLORPAN), College of Pharmacy, University of Panama, Av. Manuel E. Batista and Jose De Fabrega, Panama City 3366, Panama; (D.A.O.); (P.N.S.)
| | - Pablo N. Solís
- Center for Pharmacognostic Research on Panamanian Flora (CIFLORPAN), College of Pharmacy, University of Panama, Av. Manuel E. Batista and Jose De Fabrega, Panama City 3366, Panama; (D.A.O.); (P.N.S.)
| | - Marvin J. Núñez
- Natural Product Research Laboratory, School of Chemistry and Pharmacy, University of El Salvador, Final Ave. Mártires Estudiantes del 30 de Julio, San Salvador 01101, El Salvador;
| | - Johny R. Rodríguez Pérez
- GIFES Research Group, School of Chemistry Technology, Universidad Tecnológica de Pereira, Pereira 660003, Colombia; (J.R.R.P.); (H.A.V.S.); (H.F.C.H.)
- GIEPRONAL Research Group, School of Basic Sciences, Technology and Engineering, Universidad Nacional Abierta y a Distancia, Dosquebradas 661001, Colombia
| | - Hoover A. Valencia Sánchez
- GIFES Research Group, School of Chemistry Technology, Universidad Tecnológica de Pereira, Pereira 660003, Colombia; (J.R.R.P.); (H.A.V.S.); (H.F.C.H.)
| | - Héctor F. Cortés Hernández
- GIFES Research Group, School of Chemistry Technology, Universidad Tecnológica de Pereira, Pereira 660003, Colombia; (J.R.R.P.); (H.A.V.S.); (H.F.C.H.)
| | - José L. Medina-Franco
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México Avenida Universidad 3000, Mexico City 04510, Mexico;
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Corrêa EJA, Carvalho FC, de Castro Oliveira JA, Bertolucci SKV, Scotti MT, Silveira CH, Guedes FC, Melo JOF, de Melo-Minardi RC, de Lima LHF. Elucidating the molecular mechanisms of essential oils' insecticidal action using a novel cheminformatics protocol. Sci Rep 2023; 13:4598. [PMID: 36944648 PMCID: PMC10028760 DOI: 10.1038/s41598-023-29981-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 02/14/2023] [Indexed: 03/23/2023] Open
Abstract
Essential oils (EOs) are a promising source for novel environmentally safe insecticides. However, the structural diversity of their compounds poses challenges to accurately elucidate their biological mechanisms of action. We present a new chemoinformatics methodology aimed at predicting the impact of essential oil (EO) compounds on the molecular targets of commercial insecticides. Our approach merges virtual screening, chemoinformatics, and machine learning to identify custom signatures and reference molecule clusters. By assigning a molecule to a cluster, we can determine its most likely interaction targets. Our findings reveal that the main targets of EOs are juvenile hormone-specific proteins (JHBP and MET) and octopamine receptor agonists (OctpRago). Three of the twenty clusters show strong similarities to the juvenile hormone, steroids, and biogenic amines. For instance, the methodology successfully identified E-Nerolidol, for which literature points indications of disrupting insect metamorphosis and neurochemistry, as a potential insecticide in these pathways. We validated the predictions through experimental bioassays, observing symptoms in blowflies that were consistent with the computational results. This new approach sheds a higher light on the ways of action of EO compounds in nature and biotechnology. It also opens new possibilities for understanding how molecules can interfere with biological systems and has broad implications for areas such as drug design.
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Affiliation(s)
- Eduardo José Azevedo Corrêa
- Multicenter Program in Postgraduate in Biochemistry and Molecular Biology, Federal University of São João del-Rei, Campus Divinópolis, Divinópolis, MG, Brazil
- Minas Gerais Agricultural Research Company (EPAMIG), Pitangui, MG, Brazil
| | - Frederico Chaves Carvalho
- Department of Computer Science, Institute of Exact Sciences-ICEx, Federal University of Minas Gerais, Campus Belo Horizonte, Belo Horizonte, MG, Brazil
| | | | - Suzan Kelly Vilela Bertolucci
- Laboratory of Phytochemistry and Medicinal Plants, Department of Agriculture, Federal University of Lavras, Lavras, MG, Brazil
| | - Marcus Tullius Scotti
- Chemistry Department, Exact and Nature Sciences Center, Federal University of Paraiba, Campus I, João Pessoa, PB, Brazil
| | | | - Fabiana Costa Guedes
- Technological Sciences Institute, Federal University of Itajubá, Itabira, MG, Brazil
| | - Júlio Onésio Ferreira Melo
- Department of Exact and Biological Sciences, Federal University of São João Del-Rei, Sete Lagoas Campus, Sete Lagoas, MG, Brazil
| | - Raquel Cardoso de Melo-Minardi
- Department of Computer Science, Institute of Exact Sciences-ICEx, Federal University of Minas Gerais, Campus Belo Horizonte, Belo Horizonte, MG, Brazil
| | - Leonardo Henrique França de Lima
- Multicenter Program in Postgraduate in Biochemistry and Molecular Biology, Federal University of São João del-Rei, Campus Divinópolis, Divinópolis, MG, Brazil.
- Department of Exact and Biological Sciences, Federal University of São João Del-Rei, Sete Lagoas Campus, Sete Lagoas, MG, Brazil.
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5
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Progress and Impact of Latin American Natural Product Databases. Biomolecules 2022; 12:biom12091202. [PMID: 36139041 PMCID: PMC9496143 DOI: 10.3390/biom12091202] [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] [Received: 08/11/2022] [Revised: 08/27/2022] [Accepted: 08/29/2022] [Indexed: 11/17/2022] Open
Abstract
Natural products (NPs) are a rich source of structurally novel molecules, and the chemical space they encompass is far from being fully explored. Over history, NPs have represented a significant source of bioactive molecules and have served as a source of inspiration for developing many drugs on the market. On the other hand, computer-aided drug design (CADD) has contributed to drug discovery research, mitigating costs and time. In this sense, compound databases represent a fundamental element of CADD. This work reviews the progress toward developing compound databases of natural origin, and it surveys computational methods, emphasizing chemoinformatic approaches to profile natural product databases. Furthermore, it reviews the present state of the art in developing Latin American NP databases and their practical applications to the drug discovery area.
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Barros de Menezes RP, Fechine Tavares J, Kato MJ, da Rocha Coelho FA, Sousa Dos Santos AL, da Franca Rodrigues KA, Sessions ZL, Muratov EN, Scotti L, Tullius Scotti M. Natural Products from Annonaceae as Potential Antichagasic Agents. ChemMedChem 2022; 17:e202200196. [PMID: 35678042 DOI: 10.1002/cmdc.202200196] [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: 04/06/2022] [Revised: 06/06/2022] [Indexed: 11/12/2022]
Abstract
Chagas disease, a neglected tropical disease, is endemic in 21 Latin American countries and particularly prevalent in Brazil. Chagas disease has drawn more attention in recent years due to its expansion into non-endemic areas. The aim of this work was to computationally identify and experimentally validate the natural products from an Annonaceae family as antichagasic agents. Through the ligand-based virtual screening, we identified 57 molecules with potential activity against the epimastigote form of T. cruzi. Then, 16 molecules were analyzed in the in vitro study, of which, six molecules displayed previously unknown antiepimastigote activity. We also evaluated these six molecules for trypanocidal activity. We observed that all six molecules have potential activity against the amastigote form, but no molecules were active against the trypomastigote form. 13-Epicupressic acid seems to be the most promising, as it was predicted as an active compound in the in silico study against the amastigote form of T. cruzi, in addition to having in vitro activity against the epimastigote form.
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Affiliation(s)
- Renata Priscila Barros de Menezes
- Programa de Pós-Graduação de Produtos Naturais e Sintéticos Bioativos, Universidade federal da Paraíba, 58051-900, João Pessoa, PB, Brazil
| | - Josean Fechine Tavares
- Programa de Pós-Graduação de Produtos Naturais e Sintéticos Bioativos, Universidade federal da Paraíba, 58051-900, João Pessoa, PB, Brazil
| | - Massuo Jorge Kato
- Instituto de Química, Universidade de São Paulo, 05508-000, São Paulo, SP, Brazil
| | | | | | | | - Zoe L Sessions
- Molecular Modeling Lab, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, 27599, NC, USA
| | - Eugene N Muratov
- Molecular Modeling Lab, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, 27599, NC, USA
| | - Luciana Scotti
- Programa de Pós-Graduação de Produtos Naturais e Sintéticos Bioativos, Universidade federal da Paraíba, 58051-900, João Pessoa, PB, Brazil
| | - Marcus Tullius Scotti
- Programa de Pós-Graduação de Produtos Naturais e Sintéticos Bioativos, Universidade federal da Paraíba, 58051-900, João Pessoa, PB, Brazil
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7
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Fakhri S, Piri S, Moradi SZ, Khan H. Phytochemicals Targeting Oxidative Stress, Interconnected Neuroinflammatory, and Neuroapoptotic Pathways Following Radiation. Curr Neuropharmacol 2022; 20:836-856. [PMID: 34370636 PMCID: PMC9881105 DOI: 10.2174/1570159x19666210809103346] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/19/2021] [Accepted: 06/28/2021] [Indexed: 11/22/2022] Open
Abstract
The radiation for therapeutic purposes has shown positive effects in different contexts; however, it can increase the risk of many age-related and neurodegenerative diseases such as Alzheimer's disease (AD), amyotrophic lateral sclerosis (ALS), Huntington's disease (HD), and Parkinson's disease (PD). These different outcomes highlight a dose-response phenomenon called hormesis. Prevailing studies indicate that high doses of radiation could play several destructive roles in triggering oxidative stress, neuroapoptosis, and neuroinflammation in neurodegeneration. However, there is a lack of effective treatments in combating radiation-induced neurodegeneration, and the present drugs suffer from some drawbacks, including side effects and drug resistance. Among natural entities, polyphenols are suggested as multi-target agents affecting the dysregulated pathogenic mechanisms in neurodegenerative disease. This review discusses the destructive effects of radiation on the induction of neurodegenerative diseases by dysregulating oxidative stress, apoptosis, and inflammation. We also describe the promising effects of polyphenols and other candidate phytochemicals in preventing and treating radiation-induced neurodegenerative disorders, aiming to find novel/potential therapeutic compounds against such disorders.
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Affiliation(s)
- Sajad Fakhri
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah 6734667149, Iran;,Address correspondence to these author at the Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah 6734667149, Iran; E-mail: Department of Pharmacy, Abdul Wali Khan University Mardan, 23200, Pakistan; E-mail:
| | - Sana Piri
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah 6734667149, Iran;,These authors have contributed equally to this work.
| | - Seyed Zachariah Moradi
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah 6734667149, Iran;,Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah 6734667149, Iran;,These authors have contributed equally to this work.
| | - Haroon Khan
- Department of Pharmacy, Abdul Wali Khan University Mardan, 23200, Pakistan,Address correspondence to these author at the Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah 6734667149, Iran; E-mail: Department of Pharmacy, Abdul Wali Khan University Mardan, 23200, Pakistan; E-mail:
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8
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Saldívar-González FI, Aldas-Bulos VD, Medina-Franco JL, Plisson F. Natural product drug discovery in the artificial intelligence era. Chem Sci 2022; 13:1526-1546. [PMID: 35282622 PMCID: PMC8827052 DOI: 10.1039/d1sc04471k] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/10/2021] [Indexed: 12/19/2022] Open
Abstract
Natural products (NPs) are primarily recognized as privileged structures to interact with protein drug targets. Their unique characteristics and structural diversity continue to marvel scientists for developing NP-inspired medicines, even though the pharmaceutical industry has largely given up. High-performance computer hardware, extensive storage, accessible software and affordable online education have democratized the use of artificial intelligence (AI) in many sectors and research areas. The last decades have introduced natural language processing and machine learning algorithms, two subfields of AI, to tackle NP drug discovery challenges and open up opportunities. In this article, we review and discuss the rational applications of AI approaches developed to assist in discovering bioactive NPs and capturing the molecular "patterns" of these privileged structures for combinatorial design or target selectivity.
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Affiliation(s)
- F I Saldívar-González
- DIFACQUIM Research Group, School of Chemistry, Department of Pharmacy, Universidad Nacional Autónoma de México Avenida Universidad 3000 04510 Mexico Mexico
| | - V D Aldas-Bulos
- Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Centro de Investigación y de Estudios Avanzados del IPN Irapuato Guanajuato Mexico
| | - J L Medina-Franco
- DIFACQUIM Research Group, School of Chemistry, Department of Pharmacy, Universidad Nacional Autónoma de México Avenida Universidad 3000 04510 Mexico Mexico
| | - F Plisson
- CONACYT - Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Centro de Investigación y de Estudios Avanzados del IPN Irapuato Guanajuato Mexico
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9
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de Menezes RPB, Viana JDO, Muratov E, Scotti L, Scotti MT. Computer-Assisted Discovery of Alkaloids with Schistosomicidal Activity. Curr Issues Mol Biol 2022; 44:383-408. [PMID: 35723407 PMCID: PMC8929062 DOI: 10.3390/cimb44010028] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/08/2022] [Accepted: 01/09/2022] [Indexed: 11/28/2022] Open
Abstract
Schistosomiasis is a chronic parasitic disease caused by trematodes of the genus Schistosoma; it is commonly caused by Schistosoma mansoni, which is transmitted by Bioamphalaria snails. Studies show that more than 200 million people are infected and that more than 90% of them live in Africa. Treatment with praziquantel has the best cost–benefit result on the market. However, hypersensitivity, allergy, and drug resistance are frequently presented after administration. From this perspective, ligand-based and structure-based virtual screening (VS) techniques were combined to select potentially active alkaloids against S. mansoni from an internal dataset (SistematX). A set of molecules with known activity against S. mansoni was selected from the ChEMBL database to create two different models with accuracy greater than 84%, enabling ligand-based VS of the alkaloid bank. Subsequently, structure-based VS was performed through molecular docking using four targets of the parasite. Finally, five consensus hits (i.e., five alkaloids with schistosomicidal potential), were selected. In addition, in silico evaluations of the metabolism, toxicity, and drug-like profile of these five selected alkaloids were carried out. Two of them, namely, 11,12-methylethylenedioxypropoxy and methyl-3-oxo-12-methoxy-n(1)-decarbomethoxy-14,15-didehydrochanofruticosinate, had plausible toxicity, metabolomics, and toxicity profiles. These two alkaloids could serve as starting points for the development of new schistosomicidal compounds based on natural products.
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Affiliation(s)
- Renata Priscila Barros de Menezes
- Post-Graduate Program in Natural Synthetic Bioactive Products, Federal University of Paraiba, João Pessoa 58051-900, PB, Brazil; (R.P.B.d.M.); (J.d.O.V.); (L.S.)
| | - Jéssika de Oliveira Viana
- Post-Graduate Program in Natural Synthetic Bioactive Products, Federal University of Paraiba, João Pessoa 58051-900, PB, Brazil; (R.P.B.d.M.); (J.d.O.V.); (L.S.)
| | - Eugene Muratov
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA;
| | - Luciana Scotti
- Post-Graduate Program in Natural Synthetic Bioactive Products, Federal University of Paraiba, João Pessoa 58051-900, PB, Brazil; (R.P.B.d.M.); (J.d.O.V.); (L.S.)
| | - Marcus Tullius Scotti
- Post-Graduate Program in Natural Synthetic Bioactive Products, Federal University of Paraiba, João Pessoa 58051-900, PB, Brazil; (R.P.B.d.M.); (J.d.O.V.); (L.S.)
- Correspondence: ; Tel.: +55-83-998690415
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