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Acuña-Guzman V, Montoya-Alfaro ME, Negrón-Ballarte LP, Solis-Calero C. A Machine Learning Approach for Predicting Caco-2 Cell Permeability in Natural Products from the Biodiversity in Peru. Pharmaceuticals (Basel) 2024; 17:750. [PMID: 38931417 PMCID: PMC11206960 DOI: 10.3390/ph17060750] [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: 05/12/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND Peru is one of the most biodiverse countries in the world, which is reflected in its wealth of knowledge about medicinal plants. However, there is a lack of information regarding intestinal absorption and the permeability of natural products. The human colon adenocarcinoma cell line (Caco-2) is an in vitro assay used to measure apparent permeability. This study aims to develop a quantitative structure-property relationship (QSPR) model using machine learning algorithms to predict the apparent permeability of the Caco-2 cell in natural products from Peru. METHODS A dataset of 1817 compounds, including experimental log Papp values and molecular descriptors, was utilized. Six QSPR models were constructed: a multiple linear regression (MLR) model, a partial least squares regression (PLS) model, a support vector machine regression (SVM) model, a random forest (RF) model, a gradient boosting machine (GBM) model, and an SVM-RF-GBM model. RESULTS An evaluation of the testing set revealed that the MLR and PLS models exhibited an RMSE = 0.47 and R2 = 0.63. In contrast, the SVM, RF, and GBM models showcased an RMSE = 0.39-0.40 and R2 = 0.73-0.74. Notably, the SVM-RF-GBM model demonstrated superior performance, with an RMSE = 0.38 and R2 = 0.76. The model predicted log Papp values for 502 natural products falling within the applicability domain, with 68.9% (n = 346) showing high permeability, suggesting the potential for intestinal absorption. Additionally, we categorized the natural products into six metabolic pathways and assessed their drug-likeness. CONCLUSIONS Our results provide insights into the potential intestinal absorption of natural products in Peru, thus facilitating drug development and pharmaceutical discovery efforts.
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Affiliation(s)
| | | | | | - Christian Solis-Calero
- Faculty of Pharmacy and Biochemistry, Universidad Nacional Mayor de San Marcos, Lima 15001, Peru
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2
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Martínez-Urrutia F, Medina-Franco JL. BIOMX-DB: A web application for the BIOFACQUIM natural product database. Mol Inform 2024:e202400060. [PMID: 38837557 DOI: 10.1002/minf.202400060] [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: 02/16/2024] [Revised: 03/23/2024] [Accepted: 03/30/2024] [Indexed: 06/07/2024]
Abstract
Natural product databases are an integral part of chemoinformatics and computer-aided drug design. Despite their pivotal role, a distinct scarcity of projects in Latin America, particularly in Mexico, provides accessible tools of this nature. Herein, we introduce BIOMX-DB, an open and freely accessible web-based database designed to address this gap. BIOMX-DB enhances the features of the existing Mexican natural product database, BIOFACQUIM, by incorporating advanced search, filtering, and download capabilities. The user-friendly interface of BIOMX-DB aims to provide an intuitive experience for researchers. For seamless access, BIOMX-DB is freely available at www.biomx-db.com.
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Affiliation(s)
- Fernando Martínez-Urrutia
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - José L Medina-Franco
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Mexico City, Mexico
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3
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Zadra M, Menezes BBD, Frescura LM, Essi L, Amaro de Carvalho C, Barcellos da Rosa M. Ruellia angustiflora (Nees) Lindau ex Rambo: extraction and characterization of phenolic compounds and evaluation of antiradical, photoprotective and antimicrobial activities. Nat Prod Res 2024; 38:2082-2090. [PMID: 37548309 DOI: 10.1080/14786419.2023.2244124] [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: 02/16/2023] [Revised: 07/03/2023] [Accepted: 07/24/2023] [Indexed: 08/08/2023]
Abstract
Ruellia angustiflora is a shrub popularly known as flower of fire, used in traditional medicine as a healing agent. This study aims to verify the presence of characteristics of pharmaceutical interest in extracts from the root, stem and leaves of this species. The ideal time for ultrasound-assisted extraction is 60 min with a solid-liquid ratio of 1% (w/v). The kinetics of the reaction of the extracts with DPPH is biphasic, and IC50 values are related to the total phenolic compounds. Five phenolic compounds were identified in the extracts, where ferulic acid, rutin and quercetin showed to be the main responsible for the antiradical activity. The extracts displayed considerable photoprotective activity, mainly Ra-LE (SPF = 23). Ra-RE showed an inhibition halo similar to erythromycin against Streptococcus pyogenes. Taken together, these data reveal that Ruellia angustiflora is a source of phenolic compounds and has relevant antiradical, photoprotective and antibacterial activities.
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Affiliation(s)
- Marina Zadra
- Post-Graduate Program in Pharmaceutical Sciences, Federal University of Santa Maria, Santa Maria, Brazil
| | | | - Lucas Mironuk Frescura
- Post-Graduate Program in Chemistry, Federal University of Santa Maria, Santa Maria, Brazil
| | - Liliana Essi
- Department of Biology, Federal University of Santa Maria, Santa Maria, RS, Brazil
| | | | - Marcelo Barcellos da Rosa
- Post-Graduate Program in Pharmaceutical Sciences, Federal University of Santa Maria, Santa Maria, Brazil
- Post-Graduate Program in Chemistry, Federal University of Santa Maria, Santa Maria, Brazil
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4
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Goyzueta-Mamani LD, Barazorda-Ccahuana HL, Candia-Puma MA, Galdino AS, Machado-de-Avila RA, Giunchetti RC, Medina-Franco JL, Florin-Christensen M, Ferraz Coelho EA, Chávez-Fumagalli MA. Targeting Leishmania infantum Mannosyl-oligosaccharide glucosidase with natural products: potential pH-dependent inhibition explored through computer-aided drug design. Front Pharmacol 2024; 15:1403203. [PMID: 38873424 PMCID: PMC11169604 DOI: 10.3389/fphar.2024.1403203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 04/25/2024] [Indexed: 06/15/2024] Open
Abstract
Visceral Leishmaniasis (VL) is a serious public health issue, documented in more than ninety countries, where an estimated 500,000 new cases emerge each year. Regardless of novel methodologies, advancements, and experimental interventions, therapeutic limitations, and drug resistance are still challenging. For this reason, based on previous research, we screened natural products (NP) from Nuclei of Bioassays, Ecophysiology, and Biosynthesis of Natural Products Database (NuBBEDB), Mexican Compound Database of Natural Products (BIOFACQUIM), and Peruvian Natural Products Database (PeruNPDB) databases, in addition to structural analogs of Miglitol and Acarbose, which have been suggested as treatments for VL and have shown encouraging action against parasite's N-glycan biosynthesis. Using computer-aided drug design (CADD) approaches, the potential inhibitory effect of these NP candidates was evaluated by inhibiting the Mannosyl-oligosaccharide Glucosidase Protein (MOGS) from Leishmania infantum, an enzyme essential for the protein glycosylation process, at various pH to mimic the parasite's changing environment. Also, computational analysis was used to evaluate the Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) profile, while molecular dynamic simulations were used to gather information on the interactions between these ligands and the protein target. Our findings indicated that Ocotillone and Subsessiline have potential antileishmanial effects at pH 5 and 7, respectively, due to their high binding affinity to MOGS and interactions in the active center. Furthermore, these compounds were non-toxic and had the potential to be administered orally. This research indicates the promising anti-leishmanial activity of Ocotillone and Subsessiline, suggesting further validation through in vitro and in vivo experiments.
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Affiliation(s)
- Luis Daniel Goyzueta-Mamani
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, Arequipa, Peru
| | - Haruna Luz Barazorda-Ccahuana
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, Arequipa, Peru
| | - Mayron Antonio Candia-Puma
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, Arequipa, Peru
- Facultad de Ciencias Farmacéuticas, Bioquímicas y Biotecnológicas, Universidad Católica de Santa María, Arequipa, Peru
| | | | | | - Rodolfo Cordeiro Giunchetti
- Laboratório de Biologia das Interações Celulares, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Instituto Nacional de Ciência e Tecnologia de Doenças Tropicais (INCT-DT), Salvador, Brazil
| | - José L. Medina-Franco
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Mónica Florin-Christensen
- Instituto de Patobiología Veterinaria, CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Eduardo Antonio Ferraz Coelho
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Departamento de Patologia Clínica, Colégio Técnico da Universidade Federal de Minas Gerais (COLTEC), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Miguel Angel Chávez-Fumagalli
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, Arequipa, Peru
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5
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de Azevedo DQ, Campioni BM, Pedroz Lima FA, L Medina-Franco J, Castilho RO, Maltarollo VG. A critical assessment of bioactive compounds databases. Future Med Chem 2024; 16:1029-1051. [PMID: 38910575 DOI: 10.1080/17568919.2024.2342203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 04/03/2024] [Indexed: 06/25/2024] Open
Abstract
Compound databases (DBs) are essential tools for drug discovery. The number of DBs in public domain is increasing, so it is important to analyze these DBs. In this article, the main characteristics of 64 DBs will be presented. The methodological strategy used was a literature search. To analyze the characteristics obtained in the review, the DBs were categorized into two subsections: Open Access and Commercial DBs. Open access includes generalist DBs (containing compounds of diverse origins), DBs with specific applicability, DBs exclusive to natural products and those containing compounds with specific pharmacological action. The literature review showed that there are challenges to making these repositories available, such as standardizing information curation practices and funding to maintain and sustain them.
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Affiliation(s)
- Daniela Quadros de Azevedo
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Campus Pampulha, Belo Horizonte, Minas Gerais, 31270-900, Brazil
| | - Beatriz Mattos Campioni
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Campus Pampulha, Belo Horizonte, Minas Gerais, 31270-900, Brazil
| | - Felipe Augusto Pedroz Lima
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Campus Pampulha, Belo Horizonte, Minas Gerais, 31270-900, Brazil
| | - José L Medina-Franco
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, Mexico City, 04510, Mexico
| | - Rachel Oliveira Castilho
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Campus Pampulha, Belo Horizonte, Minas Gerais, 31270-900, Brazil
| | - Vinícius Gonçalves Maltarollo
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Campus Pampulha, Belo Horizonte, Minas Gerais, 31270-900, Brazil
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6
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Gomes PWP, Mannochio-Russo H, Schmid R, Zuffa S, Damiani T, Quiros-Guerrero LM, Caraballo-Rodríguez AM, Zhao HN, Yang H, Xing S, Charron-Lamoureux V, Chigumba DN, Sedio BE, Myers JA, Allard PM, Harwood TV, Tamayo-Castillo G, Kang KB, Defossez E, Koolen HHF, da Silva MN, E Silva CYY, Rasmann S, Walker TWN, Glauser G, Chaves-Fallas JM, David B, Kim H, Lee KH, Kim MJ, Choi WJ, Keum YS, de Lima EJSP, de Medeiros LS, Bataglion GA, Costa EV, da Silva FMA, Carvalho ARV, Reis JDE, Pamplona S, Jeong E, Lee K, Kim GJ, Kil YS, Nam JW, Choi H, Han YK, Park SY, Lee KY, Hu C, Dong Y, Sang S, Morrison CR, Borges RM, Teixeira AM, Lee SY, Lee BS, Jeong SY, Kim KH, Rutz A, Gaudry A, Bruelhart E, Kappers IF, Karlova R, Meisenburg M, Berdaguer R, Tello JS, Henderson D, Cayola L, Wright SJ, Allen DN, Anderson-Teixeira KJ, Baltzer JL, Lutz JA, McMahon SM, Parker GG, Parker JD, Northen TR, Bowen BP, Pluskal T, van der Hooft JJJ, Carver JJ, Bandeira N, Pullman BS, Wolfender JL, Kersten RD, Wang M, Dorrestein PC. plantMASST - Community-driven chemotaxonomic digitization of plants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.13.593988. [PMID: 38798440 PMCID: PMC11118438 DOI: 10.1101/2024.05.13.593988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Understanding the distribution of hundreds of thousands of plant metabolites across the plant kingdom presents a challenge. To address this, we curated publicly available LC-MS/MS data from 19,075 plant extracts and developed the plantMASST reference database encompassing 246 botanical families, 1,469 genera, and 2,793 species. This taxonomically focused database facilitates the exploration of plant-derived molecules using tandem mass spectrometry (MS/MS) spectra. This tool will aid in drug discovery, biosynthesis, (chemo)taxonomy, and the evolutionary ecology of herbivore interactions.
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Affiliation(s)
- Paulo Wender P Gomes
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Helena Mannochio-Russo
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Robin Schmid
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Simone Zuffa
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Tito Damiani
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Luis-Manuel Quiros-Guerrero
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU, 1211 Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, CMU, 1211 Geneva, Switzerland
| | - Andrés Mauricio Caraballo-Rodríguez
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Haoqi Nina Zhao
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Heejung Yang
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- College of Pharmacy, Kangwon National University, Chuncheon, Republic of Korea
| | - Shipei Xing
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Vincent Charron-Lamoureux
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Desnor N Chigumba
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA
| | - Brian E Sedio
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
- Smithsonian Tropical Research Institute, Republic of Panama
| | - Jonathan A Myers
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | | | - Thomas V Harwood
- The DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, 94720, United States
| | - Giselle Tamayo-Castillo
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José 11501-2060, Costa Rica
- Escuela de Química, Universidad de Costa Rica, 2061 San José, Costa Rica
| | - Kyo Bin Kang
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Sookmyung Women's University, Seoul, Republic of Korea
| | - Emmanuel Defossez
- Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
- Botanical garden of Neuchâtel
| | | | - Milton Nascimento da Silva
- Laboratory of Liquid Chromatography, Federal University of Pará, Belém 66075-110, Brazil
- Institute of Exact and Natural Sciences, Federal University of Pará, Belém 66075-110, Brazil
| | - Consuelo Yumiko Yoshioka E Silva
- Laboratory of Liquid Chromatography, Federal University of Pará, Belém 66075-110, Brazil
- Institute of Health Sciences, Faculty of Pharmacy, Federal University of Pará, Belém 66075-110, Brazil
| | - Sergio Rasmann
- Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - Tom W N Walker
- Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - Gaëtan Glauser
- Neuchâtel Platform of Analytical Chemistry, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - José Miguel Chaves-Fallas
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José 11501-2060, Costa Rica
- Department of Biology and Whitney R. Harris World Ecology Center, University of Missouri-St. Louis, St. Louis, MO 63121, USA
| | - Bruno David
- Green Mission Pierre Fabre, Institut de Recherche Pierre Fabre, 3 Avenue Hubert Curien, BP 13562, 31562 Toulouse, France
| | - Hyunwoo Kim
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University, 32, Dongguk-ro, Goyang, Gyeonggi-do 10326, Korea
| | - Kyu Hyeong Lee
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University, 32, Dongguk-ro, Goyang, Gyeonggi-do 10326, Korea
| | - Myeong Ji Kim
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University, 32, Dongguk-ro, Goyang, Gyeonggi-do 10326, Korea
| | - Won Jun Choi
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University, 32, Dongguk-ro, Goyang, Gyeonggi-do 10326, Korea
| | - Young-Sam Keum
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University, 32, Dongguk-ro, Goyang, Gyeonggi-do 10326, Korea
| | | | - Lívia Soman de Medeiros
- Federal University of São Paulo, Diadema, Brazil
- Department of Chemistry, Federal University of São Paulo, Diadema, SP, 09972-270, Brazil
| | | | | | | | - Alice Rhelly V Carvalho
- Laboratory of Liquid Chromatography, Federal University of Pará, Belém 66075-110, Brazil
- Institute of Health Sciences, Faculty of Pharmacy, Federal University of Pará, Belém 66075-110, Brazil
| | - José Diogo E Reis
- Laboratory of Liquid Chromatography, Federal University of Pará, Belém 66075-110, Brazil
- Institute of Exact and Natural Sciences, Federal University of Pará, Belém 66075-110, Brazil
| | - Sônia Pamplona
- Laboratory of Liquid Chromatography, Federal University of Pará, Belém 66075-110, Brazil
- Institute of Exact and Natural Sciences, Federal University of Pará, Belém 66075-110, Brazil
| | - Eunah Jeong
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Sookmyung Women's University, Seoul, Republic of Korea
| | - Kyungha Lee
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Sookmyung Women's University, Seoul, Republic of Korea
| | - Geum Jin Kim
- Department of Pharmacology, College of Medicine, Dongguk University, Gyeongju, Gyeongsangbuk-do, Republic of Korea
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan, Republic of Korea
| | - Yun-Seo Kil
- College of Pharmacy, Yeungnam University, Gyeongsan, Republic of Korea
- College of Pharmacy and Inje Institute of Pharmaceutical Sciences and Research, Inje University, Gimhae, Gyeongnam 50834, Republic of Korea
| | - Joo-Won Nam
- College of Pharmacy, Yeungnam University, Gyeongsan, Republic of Korea
- Core Research Support Center for Natural Products and Medical Materials, Yeungnam University, Gyeongsan, Republic of Korea
| | - Hyukjae Choi
- College of Pharmacy, Yeungnam University, Gyeongsan, Republic of Korea
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan, Republic of Korea
- Core Research Support Center for Natural Products and Medical Materials, Yeungnam University, Gyeongsan, Republic of Korea
| | - Yoo Kyong Han
- College of Pharmacy, Korea University, Sejong, Republic of Korea
| | - Si Young Park
- College of Pharmacy, Korea University, Sejong, Republic of Korea
| | - Ki Yong Lee
- College of Pharmacy, Korea University, Sejong, Republic of Korea
| | - Changling Hu
- Laboratory for Functional Foods and Human Health, Center for Excellence in Post-Harvest Technologies, North Carolina Agricultural and Technical State University, North Carolina Research Campus, Kannapolis, NC, USA
| | - Yilun Dong
- Laboratory for Functional Foods and Human Health, Center for Excellence in Post-Harvest Technologies, North Carolina Agricultural and Technical State University, North Carolina Research Campus, Kannapolis, NC, USA
| | - Shengmin Sang
- Laboratory for Functional Foods and Human Health, Center for Excellence in Post-Harvest Technologies, North Carolina Agricultural and Technical State University, North Carolina Research Campus, Kannapolis, NC, USA
| | - Colin R Morrison
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
- Brackenridge Field Laboratory, University of Texas at Austin, Austin, TX, USA
| | - Ricardo Moreira Borges
- Walter Mors Institute of Research on Natural Products, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Andrew Magno Teixeira
- Walter Mors Institute of Research on Natural Products, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Seo Yoon Lee
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Bum Soo Lee
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Se Yun Jeong
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Ki Hyun Kim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Adriano Rutz
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU, 1211 Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, CMU, 1211 Geneva, Switzerland
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Arnaud Gaudry
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU, 1211 Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, CMU, 1211 Geneva, Switzerland
| | - Edouard Bruelhart
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Iris F Kappers
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University, Wageningen, The Netherlands
| | - Rumyana Karlova
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University, Wageningen, The Netherlands
| | - Mara Meisenburg
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University, Wageningen, The Netherlands
| | - Roland Berdaguer
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University, Wageningen, The Netherlands
| | - J Sebastián Tello
- Latin America Department, Missouri Botanical Garden, St. Louis, MO, USA
| | - David Henderson
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
- Missouri Botanical Garden, St. Louis, MO, USA
| | - Leslie Cayola
- Herbario Nacional de Bolivia, Universidad Mayor de San Andrés, La Paz, Bolivia
| | - S Joseph Wright
- Smithsonian Tropical Research Institute, Balboa, Republic of Panama
| | - David N Allen
- Department of Biology, Middlebury College, Middlebury, VT, USA
| | | | | | - James A Lutz
- Department of Wildland Resources, Utah State University, Logan, UT, USA
| | - Sean M McMahon
- Smithsonian Environmental Research Center, Edgewater, MD, USA
- Forest Global Earth Observatory, Smithsonian Tropical Research Institute, Panama City, Panama
| | - Geoffrey G Parker
- Forest Ecology Group, Smithsonian Environmental Research Center, Edgewater, MD, USA
| | - John D Parker
- Forest Ecology Group, Smithsonian Environmental Research Center, Edgewater, MD, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology Division and the DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States
| | - Benjamin P Bowen
- Environmental Genomics and Systems Biology Division and the DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, United States
| | - Tomáš Pluskal
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Justin J J van der Hooft
- Bioinformatics Group, Wageningen University & Research, 6708 PB Wageningen, the Netherlands
- Department of Biochemistry, University of Johannesburg, Johannesburg 2006, South Africa
| | - Jeremy J Carver
- Center for Computational Mass Spectrometry, Department of Computer Science and Engineering, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego 92093-0404, United States
| | - Nuno Bandeira
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Benjamin S Pullman
- Center for Computational Mass Spectrometry, Department of Computer Science and Engineering, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego 92093-0404, United States
| | - Jean-Luc Wolfender
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU, 1211 Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, CMU, 1211 Geneva, Switzerland
| | - Roland D Kersten
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Mingxun Wang
- Department of Computer Science, University of California Riverside, Riverside, CA, 92521, United States
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
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7
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Das AP, Agarwal SM. Recent advances in the area of plant-based anti-cancer drug discovery using computational approaches. Mol Divers 2024; 28:901-925. [PMID: 36670282 PMCID: PMC9859751 DOI: 10.1007/s11030-022-10590-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 12/18/2022] [Indexed: 01/22/2023]
Abstract
Phytocompounds are a well-established source of drug discovery due to their unique chemical and functional diversities. In the area of cancer therapeutics, several phytocompounds have been used till date to design and develop new drugs. One of the desired interests of pharmaceutical companies and researchers globally is that new anti-cancer leads are discovered, for which phytocompounds can be considered a valuable source. Simultaneously, in recent years, the growth of computational approaches like virtual screening (VS), molecular dynamics (MD), pharmacophore modelling, Quantitative structure-activity relationship (QSAR), Absorption Distribution Metabolism Excretion and Toxicity (ADMET), network biology, and machine learning (ML) has gained importance due to their efficiency, reduced time-consuming nature, and cost-effectiveness. Therefore, the present review amalgamates the information on plant-based molecules identified for cancer lead discovery from in silico approaches. The mandate of this review is to discuss studies published in the last 5-6 years that aim to identify the phytomolecules as leads against cancer with the help of traditional computational approaches as well as newer techniques like network pharmacology and ML. This review also lists the databases and webservers available in the public domain for phytocompounds related information that can be harnessed for drug discovery. It is expected that the present review would be useful to pharmacologists, medicinal chemists, molecular biologists, and other researchers involved in the development of natural products (NPs) into clinically effective lead molecules.
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Affiliation(s)
- Agneesh Pratim Das
- Bioinformatics Division, ICMR-National Institute of Cancer Prevention and Research, I-7, Sector-39, Noida, Uttar Pradesh, 201301, India
| | - Subhash Mohan Agarwal
- Bioinformatics Division, ICMR-National Institute of Cancer Prevention and Research, I-7, Sector-39, Noida, Uttar Pradesh, 201301, India.
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8
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Alves MF, Katchborian-Neto A, Bueno PCP, Carnevale-Neto F, Casoti R, Ferreira MS, Murgu M, de Paula ACC, Dias DF, Soares MG, Chagas-Paula DA. LC-MS/DIA-based strategy for comprehensive flavonoid profiling: an Ocotea spp. applicability case. RSC Adv 2024; 14:10481-10498. [PMID: 38567345 PMCID: PMC10985591 DOI: 10.1039/d4ra01384k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 03/22/2024] [Indexed: 04/04/2024] Open
Abstract
We introduce a liquid chromatography - mass spectrometry with data-independent acquisition (LC-MS/DIA)-based strategy, specifically tailored to achieve comprehensive and reliable glycosylated flavonoid profiling. This approach facilitates in-depth and simultaneous exploration of all detected precursors and fragments during data processing, employing the widely-used open-source MZmine 3 software. It was applied to a dataset of six Ocotea plant species. This framework suggested 49 flavonoids potentially newly described for these plant species, alongside 45 known features within the genus. Flavonols kaempferol and quercetin, both exhibiting O-glycosylation patterns, were particularly prevalent. Gas-phase fragmentation reactions further supported these findings. For the first time, the apigenin flavone backbone was also annotated in most of the examined Ocotea species. Apigenin derivatives were found mainly in the C-glycoside form, with O. porosa displaying the highest flavone : flavonol ratio. The approach also allowed an unprecedented detection of kaempferol and quercetin in O. porosa species, and it has underscored the untapped potential of LC-MS/DIA data for broad and reliable flavonoid profiling. Our study annotated more than 50 flavonoid backbones in each species, surpassing the current literature.
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Affiliation(s)
- Matheus Fernandes Alves
- Institute of Chemistry, Federal University of Alfenas-MG 37130-001 Alfenas Minas Gerais Brazil
| | - Albert Katchborian-Neto
- Institute of Chemistry, Federal University of Alfenas-MG 37130-001 Alfenas Minas Gerais Brazil
| | - Paula Carolina Pires Bueno
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ) Theodor-Echtermeyer-Weg 1 14979 Großbeeren Germany
| | - Fausto Carnevale-Neto
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington 850 Republican Street Seattle Washington 98109 USA
| | - Rosana Casoti
- Antibiotics Department, Federal University of Pernambuco 50670-901 Recife Pernambuco Brazil
| | - Miller Santos Ferreira
- Institute of Chemistry, Federal University of Alfenas-MG 37130-001 Alfenas Minas Gerais Brazil
| | - Michael Murgu
- Waters Corporation Alameda Tocantins 125, Alphaville 06455-020 São Paulo Brazil
| | | | - Danielle Ferreira Dias
- Institute of Chemistry, Federal University of Alfenas-MG 37130-001 Alfenas Minas Gerais Brazil
| | - Marisi Gomes Soares
- Institute of Chemistry, Federal University of Alfenas-MG 37130-001 Alfenas Minas Gerais Brazil
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9
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Fernandes PO, Dias ALT, Dos Santos Júnior VS, Sá Magalhães Serafim M, Sousa YV, Monteiro GC, Coutinho ID, Valli M, Verzola MMSA, Ottoni FM, Pádua RMD, Oda FB, Dos Santos AG, Andricopulo AD, da Silva Bolzani V, Mota BEF, Alves RJ, de Oliveira RB, Kronenberger T, Maltarollo VG. Machine Learning-Based Virtual Screening of Antibacterial Agents against Methicillin-Susceptible and Resistant Staphylococcus aureus. J Chem Inf Model 2024; 64:1932-1944. [PMID: 38437501 DOI: 10.1021/acs.jcim.4c00087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
The application of computer-aided drug discovery (CADD) approaches has enabled the discovery of new antimicrobial therapeutic agents in the past. The high prevalence of methicillin-resistantStaphylococcus aureus(MRSA) strains promoted this pathogen to a high-priority pathogen for drug development. In this sense, modern CADD techniques can be valuable tools for the search for new antimicrobial agents. We employed a combination of a series of machine learning (ML) techniques to select and evaluate potential compounds with antibacterial activity against methicillin-susceptible S. aureus (MSSA) and MRSA strains. In the present study, we describe the antibacterial activity of six compounds against MSSA and MRSA reference (American Type Culture Collection (ATCC)) strains as well as two clinical strains of MRSA. These compounds showed minimal inhibitory concentrations (MIC) in the range from 12.5 to 200 μM against the different bacterial strains evaluated. Our results constitute relevant proven ML-workflow models to distinctively screen for novel MRSA antibiotics.
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Affiliation(s)
- Philipe Oliveira Fernandes
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Anna Letícia Teotonio Dias
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Valtair Severino Dos Santos Júnior
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Mateus Sá Magalhães Serafim
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Yamara Viana Sousa
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Gustavo Claro Monteiro
- Departamento de Química Orgânica, Instituto de Química, Universidade Estadual Paulista (UNESP), Araraquara, São Paulo 14.800-900, Brazil
| | - Isabel Duarte Coutinho
- Departamento de Química Orgânica, Instituto de Química, Universidade Estadual Paulista (UNESP), Araraquara, São Paulo 14.800-900, Brazil
| | - Marilia Valli
- Departamento de Física e Ciência Interdisciplinar, Instituto de Física, Universidade de São Paulo (USP), São Carlos, São Paulo 13.563-120, Brazil
| | - Marina Mol Sena Andrade Verzola
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Flaviano Melo Ottoni
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Rodrigo Maia de Pádua
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Fernando Bombarda Oda
- Departamento de Fármacos e Medicamentos, Faculdade de Ciências Farmacêuticas, Universidade Estadual Paulista (UNESP), Araraquara 14.800-903, Brazil
| | - André Gonzaga Dos Santos
- Departamento de Fármacos e Medicamentos, Faculdade de Ciências Farmacêuticas, Universidade Estadual Paulista (UNESP), Araraquara 14.800-903, Brazil
| | - Adriano Defini Andricopulo
- Departamento de Física e Ciência Interdisciplinar, Instituto de Física, Universidade de São Paulo (USP), São Carlos, São Paulo 13.563-120, Brazil
| | - Vanderlan da Silva Bolzani
- Departamento de Química Orgânica, Instituto de Química, Universidade Estadual Paulista (UNESP), Araraquara, São Paulo 14.800-900, Brazil
| | - Bruno Eduardo Fernandes Mota
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Ricardo José Alves
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Renata Barbosa de Oliveira
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
| | - Thales Kronenberger
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Vinícius Gonçalves Maltarollo
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais 31.270-901, Brazil
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10
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Mannochio-Russo H, Soleo de Funari C, Costa-Lotufo LV. Special Issue in Honor of Professor Vanderlan da Silva Bolzani. JOURNAL OF NATURAL PRODUCTS 2024; 87:453-455. [PMID: 38515368 DOI: 10.1021/acs.jnatprod.4c00195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
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11
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Dutra LL, Borges RJ, Maltarollo VG, Mendes TAO, Bressan GC, Leite JPV. In silico evaluation of pharmacokinetics properties of withanolides and simulation of their biological activities against Alzheimer's disease. J Biomol Struct Dyn 2024; 42:2616-2631. [PMID: 37166375 DOI: 10.1080/07391102.2023.2206909] [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: 08/26/2022] [Accepted: 04/19/2023] [Indexed: 05/12/2023]
Abstract
The withanolides are naturally occurring steroidal lactones found mainly in plants of the Solanaceae family. The subtribe Withaninae includes species like Withania sominifera, which are a source of many bioactive withanolides. In this work, we selected and evaluate the ADMET-related properties of 91 withanolides found in species of the subtribe Withaninae computationally, to predict the relationship between their structures and their pharmacokinetic profiles. We also evaluated the interaction of these withanolides with known targets of Alzheimer's disease (AD) through molecular docking and molecular dynamics. Withanolides presented favorable pharmacokinetic properties, like high gastrointestinal absorption, lipophilicity (logP ≤ 5), good distribution and excretion parameters, and a favorable toxicity profile. The specie Withania aristata stood out as an interesting source of the promising withanolides classified as 5-ene with 16-ene or 17-ene. These withanolides presented a favourable pharmacokinetic profile and were also highlighted as the best candidates for inhibition of AD-related targets. Our results also suggest that withanolides are likely to act as cholinesterase inhibitors by interacting with the catalytic pocket in an energy favorable and stable way.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Luana L Dutra
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Minas Gerais, Brazil
| | - Rafael J Borges
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Minas Gerais, Brazil
| | - Vinícius G Maltarollo
- Pharmaceutical Products Department- Faculty of Pharmacy, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
| | - Tiago A O Mendes
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Minas Gerais, Brazil
| | - Gustavo C Bressan
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Minas Gerais, Brazil
| | - João Paulo V Leite
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Minas Gerais, Brazil
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12
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da Rocha JAP, da Costa RA, da Costa ADSS, da Rocha ECM, Gomes AJB, Machado AK, Fagan SB, Brasil DDSB, Lima e Lima AH. Harnessing Brazilian biodiversity database: identification of flavonoids as potential inhibitors of SARS-CoV-2 main protease using computational approaches and all-atom molecular dynamics simulation. Front Chem 2024; 12:1336001. [PMID: 38456183 PMCID: PMC10917896 DOI: 10.3389/fchem.2024.1336001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/31/2024] [Indexed: 03/09/2024] Open
Abstract
SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) is the etiological agent responsible for the global outbreak of COVID-19 (Coronavirus Disease 2019). The main protease of SARS-CoV-2, Mpro, is a key enzyme that plays a vital role in mediating viral replication and transcription. In this study, a comprehensive computational approach was employed to investigate the binding affinity, selectivity, and stability of natural product candidates as potential new antivirals acting on the viral polyprotein processing mediated by SARS-CoV-2 Mpro. A library of 288 flavonoids extracted from Brazilian biodiversity was screened to select potential Mpro inhibitors. An initial filter based on Lipinski's rule of five was applied, and 204 compounds that did not violate any of the Lipinski rules were selected. The compounds were then docked into the active site of Mpro using the GOLD program, and the poses were subsequently re-scored using MM-GBSA (Molecular Mechanics Generalized Born Surface Area) binding free energy calculations performed by AmberTools23. The top five flavonoids with the best MM-GBSA binding free energy values were selected for analysis of their interactions with the active site residues of the protein. Next, we conducted a toxicity and drug-likeness analysis, and non-toxic compounds were subjected to molecular dynamics simulation and free energy calculation using the MM-PBSA (Molecular Mechanics Poisson-Boltzmann Surface Area) method. It was observed that the five selected flavonoids had lower MM-GBSA binding free energy with Mpro than the co-crystal ligand. Furthermore, these compounds also formed hydrogen bonds with two important residues, Cys145 and Glu166, in the active site of Mpro. Two compounds that passed the drug-likeness filter showed stable conformations during the molecular dynamics simulations. Among these, NuBBE_867 exhibited the best MM-PBSA binding free energy value compared to the crystallographic inhibitor. Therefore, this study suggests that NuBBE_867 could be a potential inhibitor against the main protease of SARS-CoV-2 and may be further examined to confirm our results.
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Affiliation(s)
- João Augusto Pereira da Rocha
- Laboratory of Modeling and Computational Chemistry, Federal Institute of Education, Science and Technology of Paraná (IFPA) Campus Bragança, Bragança, Brazil
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Brazil
- Laboratory of Biosolutions and Bioplastics of the Amazon, Graduate Program in Science and Environment, Institute of Exact and Natural Sciences, Federal University of Pará (UFPA), Belém, Brazil
- Graduate Program in Chemistry, Institute of Exact and Natural Sciences, Federal University of Pará, Belém, Brazil
| | - Renato Araújo da Costa
- Laboratory of Biosolutions and Bioplastics of the Amazon, Graduate Program in Science and Environment, Institute of Exact and Natural Sciences, Federal University of Pará (UFPA), Belém, Brazil
- Laboratory of Molecular Biology, Evolution and Microbiology, Federal Institute of Education Science and Technology of Paraná (IFPA) Campus Abaetetuba, Abaetetuba, Brazil
| | - Andreia do Socorro Silva da Costa
- Laboratory of Biosolutions and Bioplastics of the Amazon, Graduate Program in Science and Environment, Institute of Exact and Natural Sciences, Federal University of Pará (UFPA), Belém, Brazil
| | - Elaine Cristina Medeiros da Rocha
- Laboratory of Modeling and Computational Chemistry, Federal Institute of Education, Science and Technology of Paraná (IFPA) Campus Bragança, Bragança, Brazil
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Brazil
- Laboratory of Biosolutions and Bioplastics of the Amazon, Graduate Program in Science and Environment, Institute of Exact and Natural Sciences, Federal University of Pará (UFPA), Belém, Brazil
- Graduate Program in Chemistry, Institute of Exact and Natural Sciences, Federal University of Pará, Belém, Brazil
| | - Anderson José Bahia Gomes
- Laboratory of Molecular Biology, Evolution and Microbiology, Federal Institute of Education Science and Technology of Paraná (IFPA) Campus Abaetetuba, Abaetetuba, Brazil
| | | | | | - Davi do Socorro Barros Brasil
- Laboratory of Biosolutions and Bioplastics of the Amazon, Graduate Program in Science and Environment, Institute of Exact and Natural Sciences, Federal University of Pará (UFPA), Belém, Brazil
- Graduate Program in Chemistry, Institute of Exact and Natural Sciences, Federal University of Pará, Belém, Brazil
| | - Anderson Henrique Lima e Lima
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Brazil
- Graduate Program in Chemistry, Institute of Exact and Natural Sciences, Federal University of Pará, Belém, Brazil
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13
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Barazorda-Ccahuana HL, Cárcamo-Rodriguez EG, Centeno-Lopez AE, Galdino AS, Machado-de-Ávila RA, Giunchetti RC, Coelho EAF, Chávez-Fumagalli MA. Targeting with Structural Analogs of Natural Products the Purine Salvage Pathway in Leishmania (Leishmania) infantum by Computer-Aided Drug-Design Approaches. Trop Med Infect Dis 2024; 9:41. [PMID: 38393130 PMCID: PMC10891554 DOI: 10.3390/tropicalmed9020041] [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: 11/30/2023] [Revised: 01/27/2024] [Accepted: 01/29/2024] [Indexed: 02/25/2024] Open
Abstract
Visceral Leishmaniasis (VL) has a high death rate, with 500,000 new cases and 50,000 deaths occurring annually. Despite the development of novel strategies and technologies, there is no adequate treatment for the disease. Therefore, the purpose of this study is to find structural analogs of natural products as potential novel drugs to treat VL. We selected structural analogs from natural products that have shown antileishmanial activities, and that may impede the purine salvage pathway using computer-aided drug-design (CADD) approaches. For these, we started with the vastly studied target in the pathway, the adenine phosphoribosyl transferase (APRT) protein, which alone is non-essential for the survival of the parasite. Keeping this in mind, we search for a substance that can bind to multiple targets throughout the pathway. Computational techniques were used to study the purine salvage pathway from Leishmania infantum, and molecular dynamic simulations were used to gather information on the interactions between ligands and proteins. Because of its low homology to human proteins and its essential role in the purine salvage pathway proteins network interaction, the findings further highlight the significance of adenylosuccinate lyase protein (ADL) as a therapeutic target. An analog of the alkaloid Skimmianine, N,N-diethyl-4-methoxy-1-benzofuran-6-carboxamide, demonstrated a good binding affinity to APRT and ADL targets, no expected toxicity, and potential for oral route administration. This study indicates that the compound may have antileishmanial activity, which was granted in vitro and in vivo experiments to settle this finding in the future.
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Affiliation(s)
- Haruna Luz Barazorda-Ccahuana
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, Arequipa 04000, Peru
| | - Eymi Gladys Cárcamo-Rodriguez
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, Arequipa 04000, Peru
- Facultad de Ciencias Farmacéuticas, Bioquímicas y Biotecnológicas, Universidad Católica de Santa María, Arequipa 04000, Peru
| | - Angela Emperatriz Centeno-Lopez
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, Arequipa 04000, Peru
- Facultad de Ciencias Farmacéuticas, Bioquímicas y Biotecnológicas, Universidad Católica de Santa María, Arequipa 04000, Peru
| | - Alexsandro Sobreira Galdino
- Laboratório de Biotecnologia de Microrganismos, Universidade Federal São João Del-Rei, Divinópolis 35501-296, MG, Brazil
| | | | - Rodolfo Cordeiro Giunchetti
- Laboratório de Biologia das Interações Celulares, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
- Instituto Nacional de Ciência e Tecnologia em Doenças Tropicais, INCT-DT, Salvador 40015-970, BA, Brazil
| | - Eduardo Antonio Ferraz Coelho
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
- Departamento de Patologia Clínica, COLTEC, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
| | - Miguel Angel Chávez-Fumagalli
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, Arequipa 04000, Peru
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14
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Serafim MSM, Kronenberger T, Rocha REO, Rosa ADRA, Mello TLG, Poso A, Ferreira RS, Abrahão JS, Kroon EG, Mota BEF, Maltarollo VG. Aminopyrimidine Derivatives as Multiflavivirus Antiviral Compounds Identified from a Consensus Virtual Screening Approach. J Chem Inf Model 2024; 64:393-411. [PMID: 38194508 DOI: 10.1021/acs.jcim.3c01505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Around three billion people are at risk of infection by the dengue virus (DENV) and potentially other flaviviruses. Worldwide outbreaks of DENV, Zika virus (ZIKV), and yellow fever virus (YFV), the lack of antiviral drugs, and limitations on vaccine usage emphasize the need for novel antiviral research. Here, we propose a consensus virtual screening approach to discover potential protease inhibitors (NS3pro) against different flavivirus. We employed an in silico combination of a hologram quantitative structure-activity relationship (HQSAR) model and molecular docking on characterized binding sites followed by molecular dynamics (MD) simulations, which filtered a data set of 7.6 million compounds to 2,775 hits. Lastly, docking and MD simulations selected six final potential NS3pro inhibitors with stable interactions along the simulations. Five compounds had their antiviral activity confirmed against ZIKV, YFV, DENV-2, and DENV-3 (ranging from 4.21 ± 0.14 to 37.51 ± 0.8 μM), displaying aggregator characteristics for enzymatic inhibition against ZIKV NS3pro (ranging from 28 ± 7 to 70 ± 7 μM). Taken together, the compounds identified in this approach may contribute to the design of promising candidates to treat different flavivirus infections.
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Affiliation(s)
- Mateus Sá Magalhães Serafim
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Thales Kronenberger
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
- Excellence Cluster "Controlling Microbes to Fight Infections" (CMFI), Tübingen 72076, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio 70211, Finland
| | - Rafael Eduardo Oliveira Rocha
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Amanda Del Rio Abreu Rosa
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Thaysa Lara Gonçalves Mello
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Antti Poso
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio 70211, Finland
- Department of Medical Oncology and Pneumology, University Hospital of Tübingen, Tübingen 70211, Germany
| | - Rafaela Salgado Ferreira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Jonatas Santos Abrahão
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Erna Geessien Kroon
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Bruno Eduardo Fernandes Mota
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Vinícius Gonçalves Maltarollo
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
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Kamal M, Mukherjee S, Joshi B, Sindhu ZUD, Wangchuk P, Haider S, Ahmed N, Talukder MH, Geary TG, Yadav AK. Model nematodes as a practical innovation to promote high throughput screening of natural products for anthelmintics discovery in South Asia: Current challenges, proposed practical and conceptual solutions. Mol Biochem Parasitol 2023; 256:111594. [PMID: 37730126 DOI: 10.1016/j.molbiopara.2023.111594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/27/2023] [Accepted: 09/12/2023] [Indexed: 09/22/2023]
Abstract
With the increasing prevalence of anthelmintic resistance in animals recorded globally, and the threat of resistance in human helminths, the need for novel anthelmintic drugs is greater than ever. Most research aimed at discovering novel anthelmintic leads relies on high throughput screening (HTS) of large libraries of synthetic small molecules in industrial and academic settings in developed countries, even though it is the tropical countries that are most plagued by helminth infections. Tropical countries, however, have the advantage of possessing a rich flora that may yield natural products (NP) with promising anthelmintic activity. Focusing on South Asia, which produces one of the world's highest research outputs in NP and NP-based anthelmintic discovery, we find that limited basic research and funding, a lack of awareness of the utility of model organisms, poor industry-academia partnerships and lack of technological innovations greatly limit anthelmintics research in the region. Here we propose that utilizing model organisms including the free-living nematode Caenorhabditis elegans, that can potentially allow rapid target identification of novel anthelmintics, and Oscheius tipulae, a closely related, free-living nematode which is found abundantly in soil in hotter temperatures, could be a much-needed innovation that can enable cost-effective and efficient HTS of NPs for discovering compounds with anthelmintic/antiparasitic potential in South Asia and other tropical regions that historically have devoted limited funding for such research. Additionally, increased collaborations at the national, regional and international level between parasitologists and pharmacologists/ethnobotanists, setting up government-industry-academia partnerships to fund academic research, creating a centralized, regional collection of plant extracts or purified NPs as a dereplication strategy and HTS library, and holding regional C. elegans/O. tipulae-based anthelmintics workshops and conferences to share knowledge and resources regarding model organisms may collectively promote and foster a NP-based anthelmintics landscape in South Asia and beyond.
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Affiliation(s)
- Muntasir Kamal
- Department of Molecular Genetics, University of Toronto, Toronto, Canada.
| | - Suprabhat Mukherjee
- Department of Animal Science, Kazi Nazrul University, Asansol 713340, West Bengal, India
| | - Bishnu Joshi
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Zia-Ud-Din Sindhu
- Department of Parasitology, University of Agriculture Faisalabad, Pakistan
| | - Phurpa Wangchuk
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns Campus, QLD 4878, Australia
| | | | - Nurnabi Ahmed
- Department of Parasitology, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | | | - Timothy G Geary
- Institute of Parasitology, McGill University, Montreal, Canada; School of Biological Sciences, Queen's University-Belfast, Belfast, NI, UK
| | - Arun K Yadav
- Department of Zoology, North-Eastern Hill University, Shillong 793022, India
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16
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Lima RS, de Carvalho APA, Conte-Junior CA. Health from Brazilian Amazon food wastes: Bioactive compounds, antioxidants, antimicrobials, and potentials against cancer and oral diseases. Crit Rev Food Sci Nutr 2023; 63:12453-12475. [PMID: 35875893 DOI: 10.1080/10408398.2022.2101983] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Brazilian Amazon contains over 30,000 plant species and foods rich in bioactive compounds such as terpenes, phenolic acids, alkaloids, and flavonoids, of potential health benefits (antioxidant, antimicrobial, antiparasitic, anticancer, gastroprotection, prebiotic effects, among others). The existence of residues from non-edible parts of plants (leaves, roots, stems, branches, barks) or fruit wastes (peel, bagasse, seeds) in the agri-food industry and its supply chain is an important challenge in food loss and waste management. In this critical review several Amazon species, focusing on extracts/essential oils from nonedible parts or wastes, were analyzed in terms of phytochemicals, biological activity, and underlying mechanisms. We hope this review emphasizes the importance of Amazon's sustainability initiatives on population health due to the potential shown against cancer, infectious diseases, and prevention of oral diseases. It is urgent to think about the conversion of amazon food wastes and co-products into high-added-value raw materials to develop novel drugs, food packaging systems, or nutraceutical foods.
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Affiliation(s)
- Rayssa S Lima
- Department of Biochemistry, Analytical and Molecular Laboratorial Center (CLAn), Institute of Chemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, Rio de Janeiro, Brazil
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
- Graduate Program in Sanitary Surveillance (PPGVS), National Institute of Health Quality Control, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Anna Paula Azevedo de Carvalho
- Department of Biochemistry, Analytical and Molecular Laboratorial Center (CLAn), Institute of Chemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, Rio de Janeiro, Brazil
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
- Graduate Program in Sanitary Surveillance (PPGVS), National Institute of Health Quality Control, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil
- Graduate Program in Chemistry (PGQu), Chemistry Institute, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Carlos A Conte-Junior
- Department of Biochemistry, Analytical and Molecular Laboratorial Center (CLAn), Institute of Chemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, Rio de Janeiro, Brazil
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
- Graduate Program in Sanitary Surveillance (PPGVS), National Institute of Health Quality Control, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil
- Graduate Program in Chemistry (PGQu), Chemistry Institute, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
- Graduate Program in Food Science (PPGCAL), Chemistry Institute, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
- Graduate Program in Veterinary Hygiene (PPGHV), Faculty of Veterinary Medicine, Fluminense Federal University (UFF), Niterói, Rio de Janeiro, Brazil
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17
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Simoben CV, Babiaka SB, Moumbock AFA, Namba-Nzanguim CT, Eni DB, Medina-Franco JL, Günther S, Ntie-Kang F, Sippl W. Challenges in natural product-based drug discovery assisted with in silico-based methods. RSC Adv 2023; 13:31578-31594. [PMID: 37908659 PMCID: PMC10613855 DOI: 10.1039/d3ra06831e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 10/19/2023] [Indexed: 11/02/2023] Open
Abstract
The application of traditional medicine by humans for the treatment of ailments as well as improving the quality of life far outdates recorded history. To date, a significant percentage of humans, especially those living in developing/underprivileged communities still rely on traditional medicine for primary healthcare needs. In silico-based methods have been shown to play a pivotal role in modern pharmaceutical drug discovery processes. The application of these methods in identifying natural product (NP)-based hits has been successful. This is very much observed in many research set-ups that use rationally in silico-based methods in combination with experimental validation techniques. The combination has rendered the use of in silico-based approaches even more popular and successful in the investigation of NPs. However, identifying and proposing novel NP-based hits for experimental validation comes with several challenges such as the availability of compounds by suppliers, the huge task of separating pure compounds from complex mixtures, the quantity of samples available from the natural source to be tested, not to mention the potential ecological impact if the natural source is exhausted. Because most peer-reviewed publications are biased towards "positive results", these challenges are generally not discussed in publications. In this review, we highlight and discuss these challenges. The idea is to give interested scientists in this field of research an idea of what they can come across or should be expecting as well as prompting them on how to avoid or fix these issues.
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Affiliation(s)
- Conrad V Simoben
- Center for Drug Discovery, Faculty of Science, University of Buea P.O. Box 63 Buea CM-00237 Cameroon
- Structural Genomics Consortium, University of Toronto Toronto Ontario M5G 1L7 Canada
- Department of Pharmacology & Toxicology, University of Toronto Toronto Ontario M5S 1A8 Canada
| | - Smith B Babiaka
- Center for Drug Discovery, Faculty of Science, University of Buea P.O. Box 63 Buea CM-00237 Cameroon
- Department of Chemistry, University of Buea Buea Cameroon
- Department of Microbial Bioactive Compounds, Interfaculty Institute for Microbiology and Infection Medicine, University of Tübingen 72076 Tübingen Germany
| | - Aurélien F A Moumbock
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg Freiburg Germany
| | - Cyril T Namba-Nzanguim
- Center for Drug Discovery, Faculty of Science, University of Buea P.O. Box 63 Buea CM-00237 Cameroon
- Department of Chemistry, University of Buea Buea Cameroon
| | - Donatus Bekindaka Eni
- Center for Drug Discovery, Faculty of Science, University of Buea P.O. Box 63 Buea CM-00237 Cameroon
- Department of Chemistry, University of Buea Buea Cameroon
| | - 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
| | - Stefan Günther
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg Freiburg Germany
| | - Fidele Ntie-Kang
- Center for Drug Discovery, Faculty of Science, University of Buea P.O. Box 63 Buea CM-00237 Cameroon
- Department of Chemistry, University of Buea Buea Cameroon
- Institute of Pharmacy, Martin-Luther University Halle-Wittenberg Halle (Saale) Germany
| | - Wolfgang Sippl
- Institute of Pharmacy, Martin-Luther University Halle-Wittenberg Halle (Saale) Germany
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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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19
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da Costa RA, da Costa ADSS, da Rocha JAP, Lima MRDC, da Rocha ECM, Nascimento FCDA, Gomes AJB, do Rego JDAR, Brasil DDSB. Exploring Natural Alkaloids from Brazilian Biodiversity as Potential Inhibitors of the Aedes aegypti Juvenile Hormone Enzyme: A Computational Approach for Vector Mosquito Control. Molecules 2023; 28:6871. [PMID: 37836714 PMCID: PMC10574778 DOI: 10.3390/molecules28196871] [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: 07/11/2023] [Revised: 08/26/2023] [Accepted: 09/02/2023] [Indexed: 10/15/2023] Open
Abstract
This study explores the potential inhibitory activity of alkaloids, a class of natural compounds isolated from Brazilian biodiversity, against the mJHBP enzyme of the Aedes aegypti mosquito. This mosquito is a significant vector of diseases such as dengue, zika, and chikungunya. The interactions between the ligands and the enzyme at the molecular level were evaluated using computational techniques such as molecular docking, molecular dynamics (MD), and molecular mechanics with generalized Born surface area (MMGBSA) free energy calculation. The findings suggest that these compounds exhibit a high binding affinity with the enzyme, as confirmed by the binding free energies obtained in the simulation. Furthermore, the specific enzyme residues that contribute the most to the stability of the complex with the compounds were identified: specifically, Tyr33, Trp53, Tyr64, and Tyr129. Notably, Tyr129 residues were previously identified as crucial in the enzyme inhibition process. This observation underscores the significance of the research findings and the potential of the evaluated compounds as natural insecticides against Aedes aegypti mosquitoes. These results could stimulate the development of new vector control agents that are more efficient and environmentally friendly.
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Affiliation(s)
- Renato Araújo da Costa
- Laboratory of Biosolutions and Bioplastics of the Amazon, Graduate Program in Science and Environment, Institute of Exact and Natural Sciences, Federal University of Pará (UFPA), Belém 66075-110, PA, Brazil; (A.d.S.S.d.C.); (F.C.d.A.N.); (J.d.A.R.d.R.); (D.d.S.B.B.)
- Laboratory of Molecular Biology, Evolution and Microbiology, Federal Institute of Education, Science and Technology of Pará (IFPA) Campus Abaetetuba, Abaetetuba 68440-000, PA, Brazil; (M.R.d.C.L.); (A.J.B.G.)
| | - Andréia do Socorro Silva da Costa
- Laboratory of Biosolutions and Bioplastics of the Amazon, Graduate Program in Science and Environment, Institute of Exact and Natural Sciences, Federal University of Pará (UFPA), Belém 66075-110, PA, Brazil; (A.d.S.S.d.C.); (F.C.d.A.N.); (J.d.A.R.d.R.); (D.d.S.B.B.)
| | - João Augusto Pereira da Rocha
- Graduate Program in Chemistry, Federal University of Pará (UFPA), Belém 66075-110, PA, Brazil; (J.A.P.d.R.); (E.C.M.d.R.)
| | - Marlon Ramires da Costa Lima
- Laboratory of Molecular Biology, Evolution and Microbiology, Federal Institute of Education, Science and Technology of Pará (IFPA) Campus Abaetetuba, Abaetetuba 68440-000, PA, Brazil; (M.R.d.C.L.); (A.J.B.G.)
| | | | - Fabiana Cristina de Araújo Nascimento
- Laboratory of Biosolutions and Bioplastics of the Amazon, Graduate Program in Science and Environment, Institute of Exact and Natural Sciences, Federal University of Pará (UFPA), Belém 66075-110, PA, Brazil; (A.d.S.S.d.C.); (F.C.d.A.N.); (J.d.A.R.d.R.); (D.d.S.B.B.)
| | - Anderson José Baia Gomes
- Laboratory of Molecular Biology, Evolution and Microbiology, Federal Institute of Education, Science and Technology of Pará (IFPA) Campus Abaetetuba, Abaetetuba 68440-000, PA, Brazil; (M.R.d.C.L.); (A.J.B.G.)
| | - José de Arimatéia Rodrigues do Rego
- Laboratory of Biosolutions and Bioplastics of the Amazon, Graduate Program in Science and Environment, Institute of Exact and Natural Sciences, Federal University of Pará (UFPA), Belém 66075-110, PA, Brazil; (A.d.S.S.d.C.); (F.C.d.A.N.); (J.d.A.R.d.R.); (D.d.S.B.B.)
| | - Davi do Socorro Barros Brasil
- Laboratory of Biosolutions and Bioplastics of the Amazon, Graduate Program in Science and Environment, Institute of Exact and Natural Sciences, Federal University of Pará (UFPA), Belém 66075-110, PA, Brazil; (A.d.S.S.d.C.); (F.C.d.A.N.); (J.d.A.R.d.R.); (D.d.S.B.B.)
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20
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López-Pérez K, López-López E, Medina-Franco JL, Miranda-Quintana RA. Sampling and Mapping Chemical Space with Extended Similarity Indices. Molecules 2023; 28:6333. [PMID: 37687162 PMCID: PMC10489020 DOI: 10.3390/molecules28176333] [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: 07/25/2023] [Revised: 08/24/2023] [Accepted: 08/26/2023] [Indexed: 09/10/2023] Open
Abstract
Visualization of the chemical space is useful in many aspects of chemistry, including compound library design, diversity analysis, and exploring structure-property relationships, to name a few. Examples of notable research areas where the visualization of chemical space has strong applications are drug discovery and natural product research. However, the sheer volume of even comparatively small sub-sections of chemical space implies that we need to use approximations at the time of navigating through chemical space. ChemMaps is a visualization methodology that approximates the distribution of compounds in large datasets based on the selection of satellite compounds that yield a similar mapping of the whole dataset when principal component analysis on a similarity matrix is performed. Here, we show how the recently proposed extended similarity indices can help find regions that are relevant to sample satellites and reduce the amount of high-dimensional data needed to describe a library's chemical space.
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Affiliation(s)
- Kenneth López-Pérez
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL 32611, USA;
| | - Edgar López-López
- DIFACQUIM Research Group, Department of Pharmacy, National Autonomous University of Mexico, Mexico City 04510, Mexico;
- Department of Chemistry and Graduate Program in Pharmacology, Center for Research and Advanced Studies of the National Polytechnic Institute, Mexico City 07000, Mexico
| | - José L. Medina-Franco
- DIFACQUIM Research Group, Department of Pharmacy, National Autonomous University of Mexico, Mexico City 04510, Mexico;
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21
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Barazorda-Ccahuana HL, Goyzueta-Mamani LD, Candia Puma MA, Simões de Freitas C, de Sousa Vieria Tavares G, Pagliara Lage D, Ferraz Coelho EA, Chávez-Fumagalli MA. Computer-aided drug design approaches applied to screen natural product's structural analogs targeting arginase in Leishmania spp. F1000Res 2023; 12:93. [PMID: 37424744 PMCID: PMC10323282 DOI: 10.12688/f1000research.129943.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/12/2023] [Indexed: 07/11/2023] Open
Abstract
Introduction: Leishmaniasis is a disease with high mortality rates and approximately 1.5 million new cases each year. Despite the new approaches and advances to fight the disease, there are no effective therapies. Methods: Hence, this study aims to screen for natural products' structural analogs as new drug candidates against leishmaniasis. We applied Computer-aided drug design (CADD) approaches, such as virtual screening, molecular docking, molecular dynamics simulation, molecular mechanics-generalized Born surface area (MM-GBSA) binding free estimation, and free energy perturbation (FEP) aiming to select structural analogs from natural products that have shown anti-leishmanial and anti-arginase activities and that could bind selectively against the Leishmania arginase enzyme. Results: The compounds 2H-1-benzopyran, 3,4-dihydro-2-(2-methylphenyl)-(9CI), echioidinin, and malvidin showed good results against arginase targets from three parasite species and negative results for potential toxicities. The echioidinin and malvidin ligands generated interactions in the active center at pH 2.0 conditions by MM-GBSA and FEP methods. Conclusions: This work suggests the potential anti-leishmanial activity of the compounds and thus can be further in vitro and in vivo experimentally validated.
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Affiliation(s)
- Haruna Luz Barazorda-Ccahuana
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Catolica de Santa Maria de Arequipa, Arequipa, Peru
| | - Luis Daniel Goyzueta-Mamani
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Catolica de Santa Maria de Arequipa, Arequipa, Peru
- Sustainable Innovative Biomaterials Department, Le Qara Research Center, Arequipa, Peru
| | - Mayron Antonio Candia Puma
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Catolica de Santa Maria de Arequipa, Arequipa, Peru
- Universidad Católica de Santa María, Facultad de Ciencias Farmacéuticas, Bioquímicas y Biotecnológicas, Arequipa, Peru
| | - Camila Simões de Freitas
- Universidade Federal de Minas Gerais, Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Belo Horizonte, Minas Gerais, Brazil
| | - Grasiele de Sousa Vieria Tavares
- Universidade Federal de Minas Gerais, Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Belo Horizonte, Minas Gerais, Brazil
| | - Daniela Pagliara Lage
- Universidade Federal de Minas Gerais, Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Belo Horizonte, Minas Gerais, Brazil
| | - Eduardo Antonio Ferraz Coelho
- Universidade Federal de Minas Gerais, Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Belo Horizonte, Minas Gerais, Brazil
- Universidade Federal de Minas Gerais, Departamento de Patologia Clínica, COLTEC, Belo Horizonte, Minas Gerais, Brazil
| | - Miguel Angel Chávez-Fumagalli
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Catolica de Santa Maria de Arequipa, Arequipa, Peru
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22
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Barazorda-Ccahuana HL, Ranilla LG, Candia-Puma MA, Cárcamo-Rodriguez EG, Centeno-Lopez AE, Davila-Del-Carpio G, Medina-Franco JL, Chávez-Fumagalli MA. PeruNPDB: the Peruvian Natural Products Database for in silico drug screening. Sci Rep 2023; 13:7577. [PMID: 37165197 PMCID: PMC10170056 DOI: 10.1038/s41598-023-34729-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/06/2023] [Indexed: 05/12/2023] Open
Abstract
Since the number of drugs based on natural products (NPs) represents a large source of novel pharmacological entities, NPs have acquired significance in drug discovery. Peru is considered a megadiverse country with many endemic species of plants, terrestrial, and marine animals, and microorganisms. NPs databases have a major impact on drug discovery development. For this reason, several countries such as Mexico, Brazil, India, and China have initiatives to assemble and maintain NPs databases that are representative of their diversity and ethnopharmacological usage. We describe the assembly, curation, and chemoinformatic evaluation of the content and coverage in chemical space, as well as the physicochemical attributes and chemical diversity of the initial version of the Peruvian Natural Products Database (PeruNPDB), which contains 280 natural products. Access to PeruNPDB is available for free ( https://perunpdb.com.pe/ ). The PeruNPDB's collection is intended to be used in a variety of tasks, such as virtual screening campaigns against various disease targets or biological endpoints. This emphasizes the significance of biodiversity protection both directly and indirectly on human health.
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Affiliation(s)
- Haruna L Barazorda-Ccahuana
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, 04000, Arequipa, Peru
| | - Lena Gálvez Ranilla
- Laboratory of Research in Food Science, Universidad Catolica de Santa Maria, 04000, Arequipa, Peru
- Escuela Profesional de Ingeniería de Industria Alimentaria, Facultad de Ciencias e Ingenierías Biológicas y Químicas, Universidad Catolica de Santa Maria, 04000, Arequipa, Peru
| | - Mayron Antonio Candia-Puma
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, 04000, Arequipa, Peru
- Facultad de Ciencias Farmacéuticas, Bioquímicas y Biotecnológicas, Universidad Católica de Santa María, 04000, Arequipa, Peru
| | - Eymi Gladys Cárcamo-Rodriguez
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, 04000, Arequipa, Peru
- Facultad de Ciencias Farmacéuticas, Bioquímicas y Biotecnológicas, Universidad Católica de Santa María, 04000, Arequipa, Peru
| | - Angela Emperatriz Centeno-Lopez
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, 04000, Arequipa, Peru
- Facultad de Ciencias Farmacéuticas, Bioquímicas y Biotecnológicas, Universidad Católica de Santa María, 04000, Arequipa, Peru
| | - Gonzalo Davila-Del-Carpio
- Facultad de Ciencias Farmacéuticas, Bioquímicas y Biotecnológicas, Universidad Católica de Santa María, 04000, Arequipa, Peru
| | - José L Medina-Franco
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Miguel Angel Chávez-Fumagalli
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, 04000, Arequipa, Peru.
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23
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Flores RMA, Pantaleão SQ, Araujo SC, Malpartida HMG, Honorio KM. Structural analysis of factors related to FAM3C/ILEI dimerization and identification of inhibitor candidates targeting cancer treatment. Comput Biol Chem 2023; 104:107869. [PMID: 37068312 DOI: 10.1016/j.compbiolchem.2023.107869] [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: 12/22/2022] [Revised: 04/05/2023] [Accepted: 04/09/2023] [Indexed: 04/19/2023]
Abstract
FAM3 is a superfamily of four cytokines that maintain a single globular structure β -β -α of three classes: FAM3A, B, C and D. FAM3C was the first member of this family related to cancer and is functionally characterized as an essential factor for the epithelial-mesenchymal transition (EMT), leading to late delays in tumor progression. Due to its crucial role in EMT and metastasis, FAM3C has been termed an interleukin-like EMT (ILEI) inducer. There are several studies on the part of FAM3C in the progression of cancer and other diseases. However, little is known about its cellular receptors and possible inhibitors. In this study, based on in silico approaches, we performed structural analyses of factors related to FAM3C/ILEI dimerization. We also identified four possible inhibitor candidates, expected to be exciting prototypes and could be submitted to future biological tests targeting cancer treatment.
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Affiliation(s)
| | - Simone Queiroz Pantaleão
- Center for Mathematics, Computing, and Cognition, Federal University of ABC, 09210-170 Santo André, SP, Brazil
| | - Sheila Cruz Araujo
- Center for Sciences Natural and Human, Federal University of ABC, 09210-170 Santo André, SP, Brazil
| | | | - Kathia Maria Honorio
- Center for Sciences Natural and Human, Federal University of ABC, 09210-170 Santo André, SP, Brazil; School of Arts, Sciences and Humanities, University of São Paulo, 03828-0000 São Paulo, SP, Brazil.
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24
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Faleschini T, Syafni N, Schulte HL, Garifulina A, Hering S, Espindola LS, Hamburger M. A neolignan from Connarus tuberosus as an allosteric GABA A receptor modulator at the neurosteroid binding site. Biomed Pharmacother 2023; 161:114498. [PMID: 36906973 DOI: 10.1016/j.biopha.2023.114498] [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: 01/25/2023] [Revised: 02/24/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
In a screening of a small library of extracts from plants of the Amazonian and Cerrado biomes, a hexane extract of Connarus tuberosus roots was found to significantly potentiate the GABA induced fluorescence in a fluorescence (FLIPR) assay in CHO cells stably expressing the α1β2γ2 subtype of human GABAA receptors. With the aid of HPLC-based activity profiling the activity was linked to the neolignan connarin. In CHO cells the activity of connarin was not abolished by increasing concentrations of flumazenil, while the effect of diazepam was increased by increasing concentrations of connarin. The effect of connarin was abolished by pregnenolone sulfate (PREGS) in a concentration-dependent manner, and the effect of allopregnanolone was further increased by increasing concentrations of connarin. In a two-microelectrode voltage clamp assay with Xenopus laevis oocytes transiently expressing GABAA receptors composed of human α1β2γ2S and α1β2 subunits connarin potentiated the GABA-induced currents, with EC50 values of 1.2 ± 0.3 μM (α1β2γ2S) and 1.3 ± 0.4 μM (α1β2), and with a maximum enhancement of currents Emax of 1959 ± 70% (α1β2γ2S) and 185 ± 48% (α1β2). The activation induced by connarin was abolished by increasing concentrations of PREGS.
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Affiliation(s)
- Teresa Faleschini
- Department of Pharmaceutical Sciences, University of Basel, 4056 Basel, Switzerland
| | - Nova Syafni
- Department of Pharmaceutical Sciences, University of Basel, 4056 Basel, Switzerland; Faculty of Pharmacy and Sumatran Biota Laboratory, Andalas University, 25163 Padang, West Sumatra, Indonesia
| | - Heidi Luise Schulte
- Department of Pharmaceutical Sciences, University of Basel, 4056 Basel, Switzerland; Universidade de Brasília, Laboratório de Farmacognosia, Campus Universitário Darcy Ribeiro, 70910-900 Brasília, DF, Brazil
| | - Aleksandra Garifulina
- Division of Pharmacology and Toxicology, Department of Pharmaceutical Sciences, University of Vienna, 1090 Vienna, Austria
| | - Steffen Hering
- Universidade de Brasília, Laboratório de Farmacognosia, Campus Universitário Darcy Ribeiro, 70910-900 Brasília, DF, Brazil
| | - Laila Salmen Espindola
- Universidade de Brasília, Laboratório de Farmacognosia, Campus Universitário Darcy Ribeiro, 70910-900 Brasília, DF, Brazil
| | - Matthias Hamburger
- Department of Pharmaceutical Sciences, University of Basel, 4056 Basel, Switzerland.
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25
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Zhang W, Zeng Y, Jiao M, Ye C, Li Y, Liu C, Wang J. Integration of high-throughput omics technologies in medicinal plant research: The new era of natural drug discovery. FRONTIERS IN PLANT SCIENCE 2023; 14:1073848. [PMID: 36743502 PMCID: PMC9891177 DOI: 10.3389/fpls.2023.1073848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 01/04/2023] [Indexed: 06/18/2023]
Abstract
Medicinal plants are natural sources to unravel novel bioactive compounds to satisfy human pharmacological potentials. The world's demand for herbal medicines is increasing year by year; however, large-scale production of medicinal plants and their derivatives is still limited. The rapid development of modern technology has stimulated multi-omics research in medicinal plants, leading to a series of breakthroughs on key genes, metabolites, enzymes involved in biosynthesis and regulation of active compounds. Here, we summarize the latest research progress on the molecular intricacy of medicinal plants, including the comparison of genomics to demonstrate variation and evolution among species, the application of transcriptomics, proteomics and metabolomics to explore dynamic changes of molecular compounds, and the utilization of potential resources for natural drug discovery. These multi-omics research provide the theoretical basis for environmental adaptation of medicinal plants and allow us to understand the chemical diversity and composition of bioactive compounds. Many medicinal herbs' phytochemical constituents and their potential health benefits are not fully explored. Given their large diversity and global distribution as well as the impacts of growth duration and environmental factors on bioactive phytochemicals in medicinal plants, it is crucial to emphasize the research needs of using multi-omics technologies to address basic and applied problems in medicinal plants to aid in developing new and improved medicinal plant resources and discovering novel medicinal ingredients.
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Affiliation(s)
- Wenting Zhang
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Engineering & Technology Research Center for Conservation and Utilization of the Genuine Southern Medicinal Resources, Guangzhou, China
| | - Yuan Zeng
- School of Plant and Environmental Sciences, Virginia Tech, VA, Blacksburg, United States
- Southern Piedmont Agricultural Research and Extension Center, Virginia Tech, VA, Blackstone, United States
| | - Meng Jiao
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Chanjuan Ye
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yanrong Li
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Chuanguang Liu
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Jihua Wang
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Engineering & Technology Research Center for Conservation and Utilization of the Genuine Southern Medicinal Resources, Guangzhou, China
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26
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Simões-Coelho M, Figueira AR, Russo E. Motivations for a sustainable ethos: evidence from the globally present Brazilian multinational Natura &Co. ENVIRONMENT SYSTEMS & DECISIONS 2023; 43:1-16. [PMID: 36628130 PMCID: PMC9815681 DOI: 10.1007/s10669-022-09890-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 12/16/2022] [Indexed: 01/07/2023]
Abstract
Driven by improvements in the understanding and the growing importance of sustainability engagement among individuals and companies, this study aims to analyze the sustainable development of a renowned Consumer Goods Company. Natura &Co is a Brazilian multinational that forms among the five largest global beauty corporations, owning four major brands-Avon, The Body Shop, Aesop, and Natura. This study used a case study methodology and had the objective of analyzing the strategies adopted by the company through time while engaging in the global sustainability agenda. It also covers a gap in the literature in analyzing Latin American multinationals. The company is assessed through a case summarized into a sustainability motivations framework of four quadrants, namely social insurance, market success, legitimacy, and process improvement. As one of the main findings, the case confirms literature indications of the evolution of sustainability motivations and strategies from simple compliance with the law and social rules into innovation and differentiation, which allowed the company to compete globally.
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Affiliation(s)
- Marco Simões-Coelho
- The COPPEAD Graduate School of Business, Federal University of Rio de Janeiro, Rua Pascoal Lemme, 355—Cidade Universitária, Rio de Janeiro, RJ 21941-918 Brazil
| | - Ariane Roder Figueira
- The COPPEAD Graduate School of Business, Federal University of Rio de Janeiro, Rua Pascoal Lemme, 355—Cidade Universitária, Rio de Janeiro, RJ 21941-918 Brazil
| | - Eduardo Russo
- The COPPEAD Graduate School of Business, Federal University of Rio de Janeiro, Rua Pascoal Lemme, 355—Cidade Universitária, Rio de Janeiro, RJ 21941-918 Brazil
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27
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Bajorath J, Chávez-Hernández AL, Duran-Frigola M, Fernández-de Gortari E, Gasteiger J, López-López E, Maggiora GM, Medina-Franco JL, Méndez-Lucio O, Mestres J, Miranda-Quintana RA, Oprea TI, Plisson F, Prieto-Martínez FD, Rodríguez-Pérez R, Rondón-Villarreal P, Saldívar-Gonzalez FI, Sánchez-Cruz N, Valli M. Chemoinformatics and artificial intelligence colloquium: progress and challenges in developing bioactive compounds. J Cheminform 2022; 14:82. [PMID: 36461094 PMCID: PMC9716667 DOI: 10.1186/s13321-022-00661-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022] Open
Abstract
We report the main conclusions of the first Chemoinformatics and Artificial Intelligence Colloquium, Mexico City, June 15-17, 2022. Fifteen lectures were presented during a virtual public event with speakers from industry, academia, and non-for-profit organizations. Twelve hundred and ninety students and academics from more than 60 countries. During the meeting, applications, challenges, and opportunities in drug discovery, de novo drug design, ADME-Tox (absorption, distribution, metabolism, excretion and toxicity) property predictions, organic chemistry, peptides, and antibiotic resistance were discussed. The program along with the recordings of all sessions are freely available at https://www.difacquim.com/english/events/2022-colloquium/ .
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Affiliation(s)
- Jürgen Bajorath
- grid.10388.320000 0001 2240 3300Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Friedrich-Hirzebruch-Allee 5/6, 53113 Bonn, Germany
| | - Ana L. Chávez-Hernández
- grid.9486.30000 0001 2159 0001DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, 04510 Mexico City, Mexico
| | - Miquel Duran-Frigola
- Ersilia Open Source Initiative, Cambridge, UK ,grid.7722.00000 0001 1811 6966Joint IRB-BSC-CRG Programme in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia Spain
| | - Eli Fernández-de Gortari
- grid.420330.60000 0004 0521 6935Nanosafety Laboratory, International Iberian Nanotechnology Laboratory, 4715-330 Braga, Portugal
| | - Johann Gasteiger
- grid.5330.50000 0001 2107 3311Computer-Chemie-Centrum, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Edgar López-López
- grid.9486.30000 0001 2159 0001DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, 04510 Mexico City, Mexico ,grid.512574.0Department of Pharmacology, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV), 07360 Mexico City, Mexico
| | - Gerald M. Maggiora
- grid.134563.60000 0001 2168 186XBIO5 Institute, University of Arizona, Tucson, AZ 85721 USA
| | - José L. Medina-Franco
- grid.9486.30000 0001 2159 0001DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, 04510 Mexico City, Mexico
| | | | - Jordi Mestres
- grid.5841.80000 0004 1937 0247Chemotargets SL, Baldiri Reixac 4, Parc Cientific de Barcelona (PCB), 08028 Barcelona, Catalonia Spain ,grid.20522.370000 0004 1767 9005Research Group on Systems Pharmacology, Research Program on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute and University Pompeu Fabra, Parc de Recerca Biomedica (PRBB), 08003 Barcelona, Catalonia Spain
| | | | - Tudor I. Oprea
- grid.266832.b0000 0001 2188 8502Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM 87131 USA ,grid.8761.80000 0000 9919 9582Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy at Gothenburg University, 40530 Gothenburg, Sweden ,grid.5254.60000 0001 0674 042XNovo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark ,Present Address: Roivant Discovery Sciences, Inc., 451 D Street, Boston, MA 02210 USA
| | - Fabien Plisson
- grid.512574.0Department of Biotechnology and Biochemistry, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV-IPN), Irapuato Unit, 36824 Irapuato, Gto Mexico
| | - Fernando D. Prieto-Martínez
- grid.9486.30000 0001 2159 0001Chemistry Institute, National Autonomous University of Mexico, 04510 Mexico City, Mexico
| | - Raquel Rodríguez-Pérez
- grid.419481.10000 0001 1515 9979Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Paola Rondón-Villarreal
- grid.442204.40000 0004 0486 1035Universidad de Santander, Facultad de Ciencias Médicas y de la Salud, Instituto de Investigación Masira, Calle 70 No. 55-210, 680003 Santander, Bucaramanga Colombia
| | - Fernanda I. Saldívar-Gonzalez
- grid.9486.30000 0001 2159 0001DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, 04510 Mexico City, Mexico
| | - Norberto Sánchez-Cruz
- grid.5841.80000 0004 1937 0247Chemotargets SL, Baldiri Reixac 4, Parc Cientific de Barcelona (PCB), 08028 Barcelona, Catalonia Spain ,grid.9486.30000 0001 2159 0001Instituto de Química, Unidad Mérida, Universidad Nacional Autónoma de México, Carretera Mérida-Tetiz Km. 4.5, Yucatán, 97357 Ucú, Mexico
| | - Marilia Valli
- grid.410543.70000 0001 2188 478XNuclei of Bioassays, Biosynthesis and Ecophysiology of Natural Products (NuBBE), Department of Organic Chemistry, Institute of Chemistry, São Paulo State University-UNESP, Araraquara, Brazil
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28
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Comparative analysis of an anthraquinone and chalcone derivatives-based virtual combinatorial library. A cheminformatics "proof-of-concept" study. J Mol Graph Model 2022; 117:108307. [PMID: 36096064 DOI: 10.1016/j.jmgm.2022.108307] [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: 06/15/2022] [Revised: 08/08/2022] [Accepted: 08/08/2022] [Indexed: 01/14/2023]
Abstract
A Laplacian scoring algorithm for gene selection and the Gini coefficient to identify the genes whose expression varied least across a large set of samples were the state-of-the-art methods used here. These methods have not been trialed for their feasibility in cheminformatics. This was a maiden attempt to investigate a complete comparative analysis of an anthraquinone and chalcone derivatives-based virtual combinatorial library. This computational "proof-of-concept" study illustrated the combinatorial approach used to explain how the structure of the selected natural products (NPs) undergoes molecular diversity analysis. A virtual combinatorial library (1.6 M) based on 20 anthraquinones and 24 chalcones was enumerated. The resulting compounds were optimized to the near drug-likeness properties, and the physicochemical descriptors were calculated for all datasets including FDA, Non-FDA, and NPs from ZINC 15. UMAP and PCA were applied to compare and represent the chemical space coverage of each dataset. Subsequently, the Laplacian score and Gini coefficient were applied to delineate feature selection and selectivity among properties, respectively. Finally, we demonstrated the diversity between the datasets by employing Murcko's and the central scaffolds systems, calculating three fingerprint descriptors and analyzing their diversity by PCA and SOM. The optimized enumeration resulted in 1,610,268 compounds with NP-Likeness, and synthetic feasibility mean scores close to FDA, Non-FDA, and NPs datasets. The overlap between the chemical space of the 1.6 M database was more prominent than with the NPs dataset. A Laplacian score prioritized NP-likeness and hydrogen bond acceptor properties (1.0 and 0.923), respectively, while the Gini coefficient showed that all properties have selective effects on datasets (0.81-0.93). Scaffold and fingerprint diversity indicated that the descending order for the tested datasets was FDA, Non-FDA, NPs and 1.6 M. Virtual combinatorial libraries based on NPs can be considered as a source of the combinatorial compound with NP-likeness properties. Furthermore, measuring molecular diversity is supposed to be performed by different methods to allow for comparison and better judgment.
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29
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Valli M, Souza JM, Chelucci RC, Biasetto CR, Araujo AR, Bolzani VDS, Andricopulo AD. Identification of natural cytochalasins as leads for neglected tropical diseases drug discovery. PLoS One 2022; 17:e0275002. [PMID: 36190979 PMCID: PMC9529094 DOI: 10.1371/journal.pone.0275002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/15/2022] [Indexed: 11/19/2022] Open
Abstract
Investigating the chemical diversity of natural products from tropical environments is an inspiring approach to developing new drug candidates for neglected tropical diseases (NTDs). In the present study, phenotypic screenings for antiprotozoal activity and a combination of computational and biological approaches enabled the identification and characterization of four cytochalasins, which are fungal metabolites from Brazilian biodiversity sources. Cytochalasins A-D exhibited IC50 values ranging from 2 to 20 μM against intracellular Trypanosoma cruzi and Leishmania infantum amastigotes, values comparable to those of the standard drugs benznidazole and miltefosine for Chagas disease and leishmaniasis, respectively. Furthermore, cytochalasins A-D reduced L. infantum infections by more than 80% in THP-1 cells, most likely due to the inhibition of phagocytosis by interactions with actin. Molecular modelling studies have provided useful insights into the mechanism of action of this class of compounds. Furthermore, cytochalasins A-D showed moderate cytotoxicity against normal cell lines (HFF-1, THP-1, and HepG2) and a good overall profile for oral bioavailability assessed in vitro. The results of this study support the use of natural products from Brazilian biodiversity sources to find potential drug candidates for two of the most important NTDs.
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Affiliation(s)
- 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), São Carlos, SP, Brazil
- * E-mail: (ADA); (MV)
| | - Julia Medeiros Souza
- 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), São Carlos, SP, Brazil
| | - Rafael Consolin Chelucci
- 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), São Carlos, SP, Brazil
| | - Carolina Rabal Biasetto
- Nuclei of Bioassays, Biosynthesis and Ecophysiology of Natural Products (NuBBE), Department of Organic Chemistry, Institute of Chemistry, São Paulo State University (UNESP), Araraquara, SP, Brazil
| | - Angela Regina Araujo
- Nuclei of Bioassays, Biosynthesis and Ecophysiology of Natural Products (NuBBE), Department of Organic Chemistry, Institute of Chemistry, São Paulo State University (UNESP), Araraquara, SP, Brazil
| | - Vanderlan da Silva Bolzani
- Nuclei of Bioassays, Biosynthesis and Ecophysiology of Natural Products (NuBBE), Department of Organic Chemistry, Institute of Chemistry, São Paulo State University (UNESP), Araraquara, SP, Brazil
| | - Adriano Defini 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), São Carlos, SP, Brazil
- * E-mail: (ADA); (MV)
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30
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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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31
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Veríssimo GC, Serafim MSM, Kronenberger T, Ferreira RS, Honorio KM, Maltarollo VG. Designing drugs when there is low data availability: one-shot learning and other approaches to face the issues of a long-term concern. Expert Opin Drug Discov 2022; 17:929-947. [PMID: 35983695 DOI: 10.1080/17460441.2022.2114451] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Modern drug discovery generally is accessed by useful information from previous large databases or uncovering novel data. The lack of biological and/or chemical data tends to slow the development of scientific research and innovation. Here, approaches that may help provide solutions to generate or obtain enough relevant data or improve/accelerate existing methods within the last five years were reviewed. AREAS COVERED One-shot learning (OSL) approaches, structural modeling, molecular docking, scoring function space (SFS), molecular dynamics (MD), and quantum mechanics (QM) may be used to amplify the amount of available data to drug design and discovery campaigns, presenting methods, their perspectives, and discussions to be employed in the near future. EXPERT OPINION Recent works have successfully used these techniques to solve a range of issues in the face of data scarcity, including complex problems such as the challenging scenario of drug design aimed at intrinsically disordered proteins and the evaluation of potential adverse effects in a clinical scenario. These examples show that it is possible to improve and kickstart research from scarce available data to design and discover new potential drugs.
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Affiliation(s)
- Gabriel C Veríssimo
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Mateus Sá M Serafim
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Thales Kronenberger
- Department of Medical Oncology and Pneumology, Internal Medicine VIII, University Hospital of Tübingen, Tübingen, Germany.,School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
| | - Rafaela S Ferreira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Kathia M Honorio
- Escola de Artes, Ciências e Humanidades, Universidade de São Paulo (USP), São Paulo, Brazil.,Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, Brazil
| | - Vinícius G Maltarollo
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
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Identification of Putative Plant-Based ALR-2 Inhibitors to Treat Diabetic Peripheral Neuropathy. Curr Issues Mol Biol 2022; 44:2825-2841. [PMID: 35877418 PMCID: PMC9319673 DOI: 10.3390/cimb44070194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/15/2022] [Accepted: 06/19/2022] [Indexed: 11/17/2022] Open
Abstract
Diabetic peripheral neuropathy (DPN) is a common diabetes complication (DM). Aldose reductase -2 (ALR-2) is an oxidoreductase enzyme that is most extensively studied therapeutic target for diabetes-related complications that can be inhibited by epalrestat, which has severe adverse effects; hence the discovery of potent natural inhibitors is desired. In response, a pharmacophore model based on the properties of eplarestat was generated. The specified pharmacophore model searched the NuBBEDB database of natural compounds for prospective lead candidates. To assess the drug-likeness and ADMET profile of the compounds, a series of in silico filtering procedures were applied. The compounds were then put through molecular docking and interaction analysis. In comparison to the reference drug, four compounds showed increased binding affinity and demonstrated critical residue interactions with greater stability and specificity. As a result, we have identified four potent inhibitors: ZINC000002895847, ZINC000002566593, ZINC000012447255, and ZINC000065074786, that could be used as pharmacological niches to develop novel ALR-2 inhibitors.
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de Oliveira MVD, Bittencourt Fernandes GM, da Costa KS, Vakal S, Lima AH. Virtual screening of natural products against 5-enolpyruvylshikimate-3-phosphate synthase using the Anagreen herbicide-like natural compound library. RSC Adv 2022; 12:18834-18847. [PMID: 35873314 PMCID: PMC9240924 DOI: 10.1039/d2ra02645g] [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: 04/26/2022] [Accepted: 06/14/2022] [Indexed: 11/21/2022] Open
Abstract
The shikimate pathway enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) catalyzes a reaction involved in the production of amino acids essential for plant growth and survival. EPSPS is the main target of glyphosate, a broad-spectrum herbicide that acts as a competitive inhibitor concerning phosphoenolpyruvate (PEP), which is the natural substrate of EPSPS. In the present study, we introduce a natural compound library, named Anagreen, which is a compendium of herbicide-like compounds obtained from different natural product databases. Herein, we combined the structure- and ligand-based virtual screening strategies to explore Anagreen against EPSPS using the structure of glyphosate complexed with a T102I/P106S mutant of EPSPS from Eleusine indica (EiEPSPS) as a starting point. First, ligand-based pharmacophore screening was performed to select compounds with a similar pharmacophore to glyphosate. Then, structure-based pharmacophore modeling was applied to build a model which represents the molecular features of glyphosate. Then, consensus docking was performed to rank the best poses of the natural compounds against the PEP binding site, and then molecular dynamics simulations were performed to analyze the stability of EPSPS complexed with the selected ligands. Finally, we have investigated the binding affinity of the complexes using free energy calculations. The selected hit compound, namely AG332841, showed a stable conformation and binding affinity to the EPSPS structure and showed no structural similarity to the already known weed EPSPS inhibitors. Our computational study aims to clarify the inhibition of the mutant EiEPSPS, which is resistant to glyphosate, and identify new potential herbicides from natural products.
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Affiliation(s)
- Maycon Vinicius Damasceno de Oliveira
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará 66075-110 Belém Pará Brazil
| | - Gilson Mateus Bittencourt Fernandes
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará 66075-110 Belém Pará Brazil
| | - Kauê S da Costa
- Institute of Biodiversity, Federal University of Western Pará Santarém Pará Brazil
| | - Serhii Vakal
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University Turku Finland
| | - Anderson H Lima
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará 66075-110 Belém Pará Brazil
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34
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Rutz A, Sorokina M, Galgonek J, Mietchen D, Willighagen E, Gaudry A, Graham JG, Stephan R, Page R, Vondrášek J, Steinbeck C, Pauli GF, Wolfender JL, Bisson J, Allard PM. The LOTUS initiative for open knowledge management in natural products research. eLife 2022; 11:e70780. [PMID: 35616633 PMCID: PMC9135406 DOI: 10.7554/elife.70780] [Citation(s) in RCA: 74] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 03/22/2022] [Indexed: 12/17/2022] Open
Abstract
Contemporary bioinformatic and chemoinformatic capabilities hold promise to reshape knowledge management, analysis and interpretation of data in natural products research. Currently, reliance on a disparate set of non-standardized, insular, and specialized databases presents a series of challenges for data access, both within the discipline and for integration and interoperability between related fields. The fundamental elements of exchange are referenced structure-organism pairs that establish relationships between distinct molecular structures and the living organisms from which they were identified. Consolidating and sharing such information via an open platform has strong transformative potential for natural products research and beyond. This is the ultimate goal of the newly established LOTUS initiative, which has now completed the first steps toward the harmonization, curation, validation and open dissemination of 750,000+ referenced structure-organism pairs. LOTUS data is hosted on Wikidata and regularly mirrored on https://lotus.naturalproducts.net. Data sharing within the Wikidata framework broadens data access and interoperability, opening new possibilities for community curation and evolving publication models. Furthermore, embedding LOTUS data into the vast Wikidata knowledge graph will facilitate new biological and chemical insights. The LOTUS initiative represents an important advancement in the design and deployment of a comprehensive and collaborative natural products knowledge base.
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Affiliation(s)
- Adriano Rutz
- School of Pharmaceutical Sciences, University of GenevaGenevaSwitzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of GenevaGenevaSwitzerland
| | - Maria Sorokina
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University JenaJenaGermany
| | - Jakub Galgonek
- Institute of Organic Chemistry and Biochemistry of the CASPragueCzech Republic
| | - Daniel Mietchen
- Ronin InstituteMontclairUnited States
- Leibniz Institute of Freshwater Ecology and Inland FisheriesBerlinGermany
- School of Data Science, University of VirginiaCharlottesvilleUnited States
| | - Egon Willighagen
- Department of Bioinformatics-BiGCaT, Maastricht UniversityMaastrichtNetherlands
| | - Arnaud Gaudry
- School of Pharmaceutical Sciences, University of GenevaGenevaSwitzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of GenevaGenevaSwitzerland
| | - James G Graham
- Center for Natural Product Technologies and WHO Collaborating Centre for Traditional Medicine (WHO CC/TRM), Pharmacognosy Institute; College of Pharmacy, University of Illinois at ChicagoChicagoUnited States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at ChicagoChicagoUnited States
| | - Ralf Stephan
- Ontario Institute for Cancer Research (OICR), University Ave SuiteTorontoCanada
| | | | - Jiří Vondrášek
- Institute of Organic Chemistry and Biochemistry of the CASPragueCzech Republic
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University JenaJenaGermany
| | - Guido F Pauli
- Center for Natural Product Technologies and WHO Collaborating Centre for Traditional Medicine (WHO CC/TRM), Pharmacognosy Institute; College of Pharmacy, University of Illinois at ChicagoChicagoUnited States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at ChicagoChicagoUnited States
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, University of GenevaGenevaSwitzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of GenevaGenevaSwitzerland
| | - Jonathan Bisson
- Center for Natural Product Technologies and WHO Collaborating Centre for Traditional Medicine (WHO CC/TRM), Pharmacognosy Institute; College of Pharmacy, University of Illinois at ChicagoChicagoUnited States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at ChicagoChicagoUnited States
| | - Pierre-Marie Allard
- School of Pharmaceutical Sciences, University of GenevaGenevaSwitzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of GenevaGenevaSwitzerland
- Department of Biology, University of FribourgFribourgSwitzerland
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35
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Combination of GC-MS Molecular Networking and Larvicidal Effect against Aedes aegypti for the Discovery of Bioactive Substances in Commercial Essential Oils. Molecules 2022; 27:molecules27051588. [PMID: 35268689 PMCID: PMC8912102 DOI: 10.3390/molecules27051588] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/20/2022] [Accepted: 02/24/2022] [Indexed: 01/11/2023] Open
Abstract
Dengue is a neglected disease, present mainly in tropical countries, with more than 5.2 million cases reported in 2019. Vector control remains the most effective protective measure against dengue and other arboviruses. Synthetic insecticides based on organophosphates, pyrethroids, carbamates, neonicotinoids and oxadiazines are unattractive due to their high degree of toxicity to humans, animals and the environment. Conversely, natural-product-based larvicides/insecticides, such as essential oils, present high efficiency, low environmental toxicity and can be easily scaled up for industrial processes. However, essential oils are highly complex and require modern analytical and computational approaches to streamline the identification of bioactive substances. This study combined the GC-MS spectral similarity network approach with larvicidal assays as a new strategy for the discovery of potential bioactive substances in complex biological samples, enabling the systematic and simultaneous annotation of substances in 20 essential oils through LC50 larvicidal assays. This strategy allowed rapid intuitive discovery of distribution patterns between families and metabolic classes in clusters, and the prediction of larvicidal properties of acyclic monoterpene derivatives, including citral, neral, citronellal and citronellol, and their acetate forms (LC50 < 50 µg/mL).
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36
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Medina-Franco JL, López-López E, Andrade E, Ruiz-Azuara L, Frei A, Guan D, Zuegg J, Blaskovich MA. Bridging informatics and medicinal inorganic chemistry: toward a database of metallodrugs and metallodrug candidates. Drug Discov Today 2022; 27:1420-1430. [DOI: 10.1016/j.drudis.2022.02.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/04/2021] [Accepted: 02/22/2022] [Indexed: 12/11/2022]
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37
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The Brazilian compound library (BraCoLi) database: a repository of chemical and biological information for drug design. Mol Divers 2022; 26:3387-3397. [PMID: 35089481 DOI: 10.1007/s11030-022-10386-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/13/2022] [Indexed: 10/19/2022]
Abstract
The Brazilian Compound Library (BraCoLi) is a novel open access and manually curated electronic library of compounds developed by Brazilian research groups to support further computer-aided drug design works, available on https://www.farmacia.ufmg.br/qf/downloads/ . Herein, the first version of the database is described comprising 1176 compounds. Also, the chemical diversity and drug-like profiles of BraCoLi were defined to analyze its chemical space. A significant amount of the compounds fitted Lipinski and Veber's rules, alongside other drug-likeness properties. A comparison using principal component analysis showed that BraCoLi is similar to other databases (FDA-approved drugs and NuBBEDB) regarding structural and physicochemical patterns. Furthermore, a scaffold analysis showed that BraCoLi presents several privileged chemical skeletons with great diversity. Despite the similar distribution in the structural and physicochemical spaces, Tanimoto coefficient values indicated that compounds present in the BraCoLi are generally different from the two other databases, where they showed different kernel distributions and low similarity. These facts show an interesting innovative aspect, which is a desirable feature for novel drug design purposes.
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38
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Singla RK, Joon S, Shen L, Shen B. Translational Informatics for Natural Products as Antidepressant Agents. Front Cell Dev Biol 2022; 9:738838. [PMID: 35127696 PMCID: PMC8811306 DOI: 10.3389/fcell.2021.738838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 12/13/2021] [Indexed: 12/18/2022] Open
Abstract
Depression, a neurological disorder, is a universally common and debilitating illness where social and economic issues could also become one of its etiologic factors. From a global perspective, it is the fourth leading cause of long-term disability in human beings. For centuries, natural products have proven their true potential to combat various diseases and disorders, including depression and its associated ailments. Translational informatics applies informatics models at molecular, imaging, individual, and population levels to promote the translation of basic research to clinical applications. The present review summarizes natural-antidepressant-based translational informatics studies and addresses challenges and opportunities for future research in the field.
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Affiliation(s)
- Rajeev K. Singla
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- iGlobal Research and Publishing Foundation, New Delhi, India
| | - Shikha Joon
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- iGlobal Research and Publishing Foundation, New Delhi, India
| | - Li Shen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Bairong Shen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Bairong Shen,
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39
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Alves LA, Ferreira NCDS, Maricato V, Alberto AVP, Dias EA, Jose Aguiar Coelho N. Graph Neural Networks as a Potential Tool in Improving Virtual Screening Programs. Front Chem 2022; 9:787194. [PMID: 35127645 PMCID: PMC8811035 DOI: 10.3389/fchem.2021.787194] [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: 10/18/2021] [Accepted: 12/10/2021] [Indexed: 11/23/2022] Open
Abstract
Despite the increasing number of pharmaceutical companies, university laboratories and funding, less than one percent of initially researched drugs enter the commercial market. In this context, virtual screening (VS) has gained much attention due to several advantages, including timesaving, reduced reagent and consumable costs and the performance of selective analyses regarding the affinity between test molecules and pharmacological targets. Currently, VS is based mainly on algorithms that apply physical and chemistry principles and quantum mechanics to estimate molecule affinities and conformations, among others. Nevertheless, VS has not reached the expected results concerning the improvement of market-approved drugs, comprising less than twenty drugs that have reached this goal to date. In this context, graph neural networks (GNN), a recent deep-learning subtype, may comprise a powerful tool to improve VS results concerning natural products that may be used both simultaneously with standard algorithms or isolated. This review discusses the pros and cons of GNN applied to VS and the future perspectives of this learnable algorithm, which may revolutionize drug discovery if certain obstacles concerning spatial coordinates and adequate datasets, among others, can be overcome.
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Affiliation(s)
- Luiz Anastacio Alves
- Laboratory of Cellular Communication, Oswaldo Cruz Institute – Fiocruz, Rio de Janeiro, Brazil
- *Correspondence: Luiz Anastacio Alves,
| | | | - Victor Maricato
- Laboratory of Cellular Communication, Oswaldo Cruz Institute – Fiocruz, Rio de Janeiro, Brazil
| | | | - Evellyn Araujo Dias
- Laboratory of Cellular Communication, Oswaldo Cruz Institute – Fiocruz, Rio de Janeiro, Brazil
| | - Nt Jose Aguiar Coelho
- National Institute of Industrial Property - INPI and Veiga de Almeida University - UVA, Rio de Janeiro, Brazil
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40
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Oliveira VM, Andreote FD, Cortelo PC, Castro-Gamboa I, Costa-Lotufo LV, Polizeli MDLTM, Thiemann OH, Setubal JC. Microorganisms: the secret agents of the biosphere, and their key roles in biotechnology. BIOTA NEOTROPICA 2022. [DOI: 10.1590/1676-0611-bn-2022-1343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Abstract
Abstract We present a survey of projects that have been funded by FAPESP under the BIOTA-Microorganisms program. These projects generated a wide variety of results, including the identification of novel antibacterial-producing microorganisms, the characterization of novel microbial enzymes for industrial applications, taxonomic classification of novel microorganisms in several environments, investigation of the soil and mangrove microbial ecosystems and its influence on endangered plant species, and the sequencing of novel metagenome-assembled genomes. The results surveyed demonstrate the importance of microorganisms in environments that play important roles in human activities as well as the potential that many of these microorganisms have in contributing to biotechnological applications crucial for human survival in the 21st century.
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41
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Dunn TB, Seabra GM, Kim TD, Juárez-Mercado KE, Li C, Medina-Franco JL, Miranda-Quintana RA. Diversity and Chemical Library Networks of Large Data Sets. J Chem Inf Model 2021; 62:2186-2201. [PMID: 34723537 DOI: 10.1021/acs.jcim.1c01013] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The quantification of chemical diversity has many applications in drug discovery, organic chemistry, food, and natural product chemistry, to name a few. As the size of the chemical space is expanding rapidly, it is imperative to develop efficient methods to quantify the diversity of large and ultralarge chemical libraries and visualize their mutual relationships in chemical space. Herein, we show an application of our recently introduced extended similarity indices to measure the fingerprint-based diversity of 19 chemical libraries typically used in drug discovery and natural products research with over 18 million compounds. Based on this concept, we introduce the Chemical Library Networks (CLNs) as a general and efficient framework to represent visually the chemical space of large chemical libraries providing a global perspective of the relation between the libraries. For the 19 compound libraries explored in this work, it was found that the (extended) Tanimoto index offers the best description of extended similarity in combination with RDKit fingerprints. CLNs are general and can be explored with any structure representation and similarity coefficient for large chemical libraries.
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Affiliation(s)
- Timothy B Dunn
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Gustavo M Seabra
- Department of Medicinal Chemistry, University of Florida, Gainesville, Florida 32610, United States.,Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, Florida 32610, United States
| | - Taewon David Kim
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - K Eurídice Juárez-Mercado
- DIFACQUIM Research Group, Department of Pharmacy, National Autonomous University of Mexico, Mexico City 04510, Mexico
| | - Chenglong Li
- Department of Medicinal Chemistry, University of Florida, Gainesville, Florida 32610, United States.,Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, Florida 32610, United States
| | - José L Medina-Franco
- DIFACQUIM Research Group, Department of Pharmacy, National Autonomous University of Mexico, Mexico City 04510, Mexico
| | - Ramón Alain Miranda-Quintana
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States.,Quantum Theory Project, University of Florida, Gainesville, Florida 32611, United States
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42
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Sun X, Zhang Y, Zhou Y, Lian X, Yan L, Pan T, Jin T, Xie H, Liang Z, Qiu W, Wang J, Li Z, Zhu F, Sui X. NPCDR: natural product-based drug combination and its disease-specific molecular regulation. Nucleic Acids Res 2021; 50:D1324-D1333. [PMID: 34664659 PMCID: PMC8728151 DOI: 10.1093/nar/gkab913] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/16/2021] [Accepted: 09/25/2021] [Indexed: 01/15/2023] Open
Abstract
Natural product (NP) has a long history in promoting modern drug discovery, which has derived or inspired a large number of currently prescribed drugs. Recently, the NPs have emerged as the ideal candidates to combine with other therapeutic strategies to deal with the persistent challenge of conventional therapy, and the molecular regulation mechanism underlying these combinations is crucial for the related communities. Thus, it is urgently demanded to comprehensively provide the disease-specific molecular regulation data for various NP-based drug combinations. However, no database has been developed yet to describe such valuable information. In this study, a newly developed database entitled ‘Natural Product-based Drug Combination and Its Disease-specific Molecular Regulation (NPCDR)’ was thus introduced. This database was unique in (a) providing the comprehensive information of NP-based drug combinations & describing their clinically or experimentally validated therapeutic effect, (b) giving the disease-specific molecular regulation data for a number of NP-based drug combinations, (c) fully referencing all NPs, drugs, regulated molecules/pathways by cross-linking them to the available databases describing their biological or pharmaceutical characteristics. Therefore, NPCDR is expected to have great implications for the future practice of network pharmacology, medical biochemistry, drug design, and medicinal chemistry. This database is now freely accessible without any login requirement at both official (https://idrblab.org/npcdr/) and mirror (http://npcdr.idrblab.net/) sites.
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Affiliation(s)
- Xueni Sun
- School of Pharmacy and Department of Medical Oncology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Yintao Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ying Zhou
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, Zhejiang University, 79 QingChun Road, Hangzhou, Zhejiang 310000, China
| | - Xichen Lian
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lili Yan
- School of Pharmacy and Department of Medical Oncology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Ting Pan
- School of Pharmacy and Department of Medical Oncology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Ting Jin
- School of Pharmacy and Department of Medical Oncology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Han Xie
- School of Pharmacy and Department of Medical Oncology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Zimao Liang
- School of Pharmacy and Department of Medical Oncology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Wenqi Qiu
- Department of Surgery, HKU-SZH & Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Jianxin Wang
- School of Computer Science and Engineering, Central South University, Changsha 410083, China
| | - Zhaorong Li
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Xinbing Sui
- School of Pharmacy and Department of Medical Oncology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
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43
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Ntie-Kang F, Telukunta KK, Fobofou SAT, Chukwudi Osamor V, Egieyeh SA, Valli M, Djoumbou-Feunang Y, Sorokina M, Stork C, Mathai N, Zierep P, Chávez-Hernández AL, Duran-Frigola M, Babiaka SB, Tematio Fouedjou R, Eni DB, Akame S, Arreyetta-Bawak AB, Ebob OT, Metuge JA, Bekono BD, Isa MA, Onuku R, Shadrack DM, Musyoka TM, Patil VM, van der Hooft JJJ, da Silva Bolzani V, Medina-Franco JL, Kirchmair J, Weber T, Tastan Bishop Ö, Medema MH, Wessjohann LA, Ludwig-Müller J. Computational Applications in Secondary Metabolite Discovery (CAiSMD): an online workshop. J Cheminform 2021; 13:64. [PMID: 34488889 PMCID: PMC8419829 DOI: 10.1186/s13321-021-00546-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 08/23/2021] [Indexed: 11/12/2022] Open
Abstract
We report the major conclusions of the online open-access workshop "Computational Applications in Secondary Metabolite Discovery (CAiSMD)" that took place from 08 to 10 March 2021. Invited speakers from academia and industry and about 200 registered participants from five continents (Africa, Asia, Europe, South America, and North America) took part in the workshop. The workshop highlighted the potential applications of computational methodologies in the search for secondary metabolites (SMs) or natural products (NPs) as potential drugs and drug leads. During 3 days, the participants of this online workshop received an overview of modern computer-based approaches for exploring NP discovery in the "omics" age. The invited experts gave keynote lectures, trained participants in hands-on sessions, and held round table discussions. This was followed by oral presentations with much interaction between the speakers and the audience. Selected applicants (early-career scientists) were offered the opportunity to give oral presentations (15 min) and present posters in the form of flash presentations (5 min) upon submission of an abstract. The final program available on the workshop website ( https://caismd.indiayouth.info/ ) comprised of 4 keynote lectures (KLs), 12 oral presentations (OPs), 2 round table discussions (RTDs), and 5 hands-on sessions (HSs). This meeting report also references internet resources for computational biology in the area of secondary metabolites that are of use outside of the workshop areas and will constitute a long-term valuable source for the community. The workshop concluded with an online survey form to be completed by speakers and participants for the goal of improving any subsequent editions.
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Affiliation(s)
- Fidele Ntie-Kang
- Department of Chemistry, University of Buea, P. O. Box 63, Buea, Cameroon
- Institute of Pharmacy, Martin-Luther University of Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle, Germany
- Institute of Botany, Technische Universität Dresden, Zellescher Weg 20b, 01062 Dresden, Germany
| | - Kiran K. Telukunta
- Tarunavadaanenasaha Muktbharatonnayana Samstha Foundation, Hyderabad, India
| | - Serge A. T. Fobofou
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Mendelssohnstrasse 1, 38106 Braunschweig, Germany
| | - Victor Chukwudi Osamor
- Department of Computer and Information Sciences, Colege of Science and Technology, Covenant University, Km. 10 Idiroko Rd, Ogun Ota, Nigeria
| | - Samuel A. Egieyeh
- School of Pharmacy, University of the Western Cape, Cape Town, 7535 South Africa
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Cape Town, 7535 South Africa
| | - Marilia Valli
- Nuclei of Bioassays, Biosynthesis and Ecophysiology of Natural Products (NuBBE), Department of Organic Chemistry, Institute of Chemistry, Sao Paulo State University–UNESP, Araraquara, Brazil
| | | | - Maria Sorokina
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
| | - Conrad Stork
- Center for Bioinformatics, Universität Hamburg, 20146 Hamburg, Germany
| | - Neann Mathai
- Department of Chemistry and Computational Biology Unit (CBU), University of Bergen, 5020 Bergen, Norway
| | - Paul Zierep
- Pharmaceutical Bioinformatics, Albert-Ludwigs-University, Freiburg, Germany
| | - Ana L. Chávez-Hernández
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Miquel Duran-Frigola
- Ersilia Open Source Initiative, Cambridge, UK
- Joint IRB-BSC-CRG Programme in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia Spain
| | - Smith B. Babiaka
- Department of Chemistry, University of Buea, P. O. Box 63, Buea, Cameroon
| | | | - Donatus B. Eni
- Department of Chemistry, University of Buea, P. O. Box 63, Buea, Cameroon
| | - Simeon Akame
- Department of Immunology, School of Health Sciences, Catholic University of Central Africa, BP 7871, Yaoundé, Cameroon
| | | | - Oyere T. Ebob
- Department of Chemistry, University of Buea, P. O. Box 63, Buea, Cameroon
| | - Jonathan A. Metuge
- Department of Biochemistry and Molecular Biology, University of Buea, P. O. Box 63, Buea, Cameroon
| | - Boris D. Bekono
- Department of Physics, Ecole Normale Supérieure, University of Yaoundé I, BP. 47, Yaoundé, Cameroon
| | - Mustafa A. Isa
- Bioinformatics and Computational Biology Lab, Department of Microbiology, Faculty of Sciences, University of Maiduguri, P.M.B. 1069, Maiduguri, Borno State Nigeria
| | - Raphael Onuku
- Department of Pharmaceutical and Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Nigeria Nsukka, Nsukka, Nigeria
| | - Daniel M. Shadrack
- Department of Chemistry, St. John’s University of Tanzania, P. O. Box 47, Dodoma, Tanzania
| | - Thommas M. Musyoka
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, 6140 South Africa
| | - Vaishali M. Patil
- Computer Aided Drug Design Lab, KIET Group of Institutions, Delhi-NCR, Ghaziabad, 201206 India
| | | | - Vanderlan da Silva Bolzani
- Nuclei of Bioassays, Biosynthesis and Ecophysiology of Natural Products (NuBBE), Department of Organic Chemistry, Institute of Chemistry, Sao Paulo State University–UNESP, Araraquara, Brazil
| | - José L. Medina-Franco
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Johannes Kirchmair
- Department of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, 6140 South Africa
| | - Marnix H. Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Ludger A. Wessjohann
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, 06120 Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv), Puschstraße 4, 04103 Leipzig, Germany
| | - Jutta Ludwig-Müller
- Institute of Botany, Technische Universität Dresden, Zellescher Weg 20b, 01062 Dresden, Germany
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da Costa KS, Galúcio JM, de Jesus DA, Gomes GC, Lima E Lima AH, Taube PS, Dos Santos AM, Lameira J. Targeting Peptidyl-prolyl Cis-trans Isomerase NIMA-interacting 1: A Structure-based Virtual Screening Approach to Find Novel Inhibitors. Curr Comput Aided Drug Des 2021; 16:605-617. [PMID: 31654518 DOI: 10.2174/1573409915666191025114009] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 09/11/2019] [Accepted: 10/10/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (Pin1) is an enzyme that isomerizes phosphorylated serine or threonine motifs adjacent to proline residues. Pin1 has important roles in several cellular signaling pathways, consequently impacting the development of multiple types of cancers. METHODS Based on the previously reported inhibitory activity of pentacyclic triterpenoids isolated from the gum resin of Boswellia genus against Pin1, we designed a computational experiment using molecular docking, pharmacophore filtering, and structural clustering allied to molecular dynamics (MD) simulations and binding free energy calculations to explore the inhibitory activity of new triterpenoids against Pin1 structure. RESULTS Here, we report different computational evidence that triterpenoids from neem (Azadirachta indica A. Juss), such as 6-deacetylnimbinene, 6-Oacetylnimbandiol, and nimbolide, replicate the binding mode of the Pin1 substrate peptide, interacting with high affinity with the binding site and thus destabilizing the Pin1 structure. CONCLUSIONS Our results are supported by experimental data, and provide interesting structural insights into their molecular mechanism of action, indicating that their structural scaffolds could be used as a start point to develop new inhibitors against Pin1.
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Affiliation(s)
- Kauê Santana da Costa
- Institute of Biodiversity, Federal University of Western Para, Santarem, Para, Brazil
| | - João M Galúcio
- Institute of Biodiversity, Federal University of Western Para, Santarem, Para, Brazil
| | | | - Guelber Cardoso Gomes
- Institute of Pharmaceutical Sciences, Federal University of Para, 66075-110, Belem, Para, Brazil
| | | | - Paulo S Taube
- Institute of Biodiversity, Federal University of Western Para, Santarem, Para, Brazil
| | - Alberto M Dos Santos
- Institute of Biodiversity, Federal University of Western Para, Santarem, Para, Brazil
| | - Jerônimo Lameira
- Institute of Biological Sciences. Federal University of Para, 66075-110, Belem, Para, Brazil
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45
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Silva-Júnior NR, Cabrera YM, Barbosa SL, Barros RDA, Barros E, Vital CE, Ramos HJO, Oliveira MGA. Intestinal proteases profiling from Anticarsia gemmatalis and their binding to inhibitors. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2021; 107:e21792. [PMID: 33948994 DOI: 10.1002/arch.21792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/25/2021] [Accepted: 03/14/2021] [Indexed: 06/12/2023]
Abstract
Although the importance of intestinal hydrolases is recognized, there is little information on the intestinal proteome of lepidopterans such as Anticarsia gemmatalis. Thus, we carried out the proteomic analysis of the A. gemmatalis intestine to characterize the proteases by LC/MS. We examined the interactions of proteins identified with protease inhibitors (PI) using molecular docking. We found 54 expressed antigens for intestinal protease, suggesting multiple important isoforms. The hydrolytic arsenal featured allows for a more comprehensive understanding of insect feeding. The docking analysis showed that the soybean PI (SKTI) could bind efficiently with the trypsin sequences and, therefore, insect resistance does not seem to involve changing the sequences of the PI binding site. In addition, a SERPIN was identified and the interaction analysis showed the inhibitor binding site is in contact with the catalytic site of trypsin, possibly acting as a regulator. In addition, this SERPIN and the identified PI sequences can be targets for the control of proteolytic activity in the caterpillar intestine and serve as a support for the rational design of a molecule with greater stability, less prone to cleavage by proteases and viable for the control of insect pests such as A. gemmatalis.
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Affiliation(s)
- Neilier R Silva-Júnior
- Department of Biochemistry and Molecular Biology, Laboratory of Enzymology and Biochemistry of Proteins and Peptides, Universidade Federal de Viçosa, UFV, BIOAGRO/INCT-IPP, Viçosa, Minas Gerais, Brazil
| | - Yaremis M Cabrera
- Department of Biochemistry and Molecular Biology, Laboratory of Enzymology and Biochemistry of Proteins and Peptides, Universidade Federal de Viçosa, UFV, BIOAGRO/INCT-IPP, Viçosa, Minas Gerais, Brazil
| | - Samuel L Barbosa
- Department of Biochemistry and Molecular Biology, Laboratory of Enzymology and Biochemistry of Proteins and Peptides, Universidade Federal de Viçosa, UFV, BIOAGRO/INCT-IPP, Viçosa, Minas Gerais, Brazil
| | - Rafael de A Barros
- Department of Biochemistry and Molecular Biology, Laboratory of Enzymology and Biochemistry of Proteins and Peptides, Universidade Federal de Viçosa, UFV, BIOAGRO/INCT-IPP, Viçosa, Minas Gerais, Brazil
| | - Edvaldo Barros
- Núcleo de Análise de Biomoléculas, NuBioMol, Centro de Ciências Biológicas e da Saúde - CCB, Universidade Federal de Viçosa - UFV, Viçosa, Minas Gerais, Brazil
| | - Camilo E Vital
- Department of Biochemistry and Molecular Biology, Laboratory of Enzymology and Biochemistry of Proteins and Peptides, Universidade Federal de Viçosa, UFV, BIOAGRO/INCT-IPP, Viçosa, Minas Gerais, Brazil
| | - Humberto J O Ramos
- Department of Biochemistry and Molecular Biology, Laboratory of Enzymology and Biochemistry of Proteins and Peptides, Universidade Federal de Viçosa, UFV, BIOAGRO/INCT-IPP, Viçosa, Minas Gerais, Brazil
- Núcleo de Análise de Biomoléculas, NuBioMol, Centro de Ciências Biológicas e da Saúde - CCB, Universidade Federal de Viçosa - UFV, Viçosa, Minas Gerais, Brazil
| | - Maria Goreti A Oliveira
- Department of Biochemistry and Molecular Biology, Laboratory of Enzymology and Biochemistry of Proteins and Peptides, Universidade Federal de Viçosa, UFV, BIOAGRO/INCT-IPP, Viçosa, Minas Gerais, Brazil
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46
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Liu N, Lai J, Lyu C, Qiang B, Wang H, Jin H, Zhang L, Liu Z. Chemical Space, Scaffolds, and Halogenated Compounds of CMNPD: A Comprehensive Chemoinformatic Analysis. J Chem Inf Model 2021; 61:3323-3336. [PMID: 34156848 DOI: 10.1021/acs.jcim.1c00162] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The comprehensive marine natural products database (CMNPD) is a new free access and comprehensive database developed originally by Lyu's team of our research group, including more than 30 000 marine natural products (MNPs) reported from the 1960s. In this article, we aimed to present CMNPD's value in drug discovery and to present several characteristics of MNPs based on our new comprehensive data. We used chemoinformatic analysis methods to report the molecular properties, chemical space, and several scaffold assessments of CMNPD compared with several databases. Then, we reported the characteristics of MNPs from the aspect of halogens, comparing MNPs with terrestrial natural products (TNPs) and drugs. We found that CMNPD had a low proportion (2.91%) of scaffolds utilized by drugs, and high similarities between CMNPD and NPAtlas (a microbial natural products database), which are worth further investigation. The proportion of bromides in MNPs is outstandingly higher (11.0%) in contrast to other halogens. Furthermore, the results showed great differences in halogenated structures between MNPs and drugs, especially brominated substructures. Finally, we found that many marine species (2.52%) reported only halogenated compounds. It can be concluded from these results that CMNPD is a promising source for drug discovery and has many scientific issues relative to MNPs that need to be further investigated.
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Affiliation(s)
- Ningfeng Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 100191 Beijing, P. R. China
| | - Junyong Lai
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 100191 Beijing, P. R. China
| | - Chuanyu Lyu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 100191 Beijing, P. R. China
| | - Bo Qiang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 100191 Beijing, P. R. China
| | - Heyu Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 100191 Beijing, P. R. China
| | - Hongwei Jin
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 100191 Beijing, P. R. China
| | - Liangren Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 100191 Beijing, P. R. China
| | - Zhenming Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 100191 Beijing, P. R. China
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47
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Jin Y, Wang Z, Dong AY, Huang YQ, Hao GF, Song BA. Web repositories of natural agents promote pests and pathogenic microbes management. Brief Bioinform 2021; 22:6294160. [PMID: 34098581 DOI: 10.1093/bib/bbab205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 05/10/2021] [Accepted: 05/10/2021] [Indexed: 12/30/2022] Open
Abstract
The grand challenge to meet the increasing demands for food by a rapidly growing global population requires protecting crops from pests. Natural active substances play a significant role in the sustainable pests and pathogenic microbes management. In recent years, natural products- (NPs), antimicrobial peptides- (AMPs), medicinal plant- and plant essential oils (EOs)-related online resources have greatly facilitated the development of pests and pathogenic microbes control agents in an efficient and economical manner. However, a comprehensive comparison, analysis and summary of these existing web resources are still lacking. Here, we surveyed these databases of NPs, AMPs, medicinal plants and plant EOs with insecticidal, antibacterial, antiviral and antifungal activity, and we compared their functionality, data volume, data sources and applicability. We comprehensively discussed the limitation of these web resources. This study provides a toolbox for bench scientists working in the pesticide, botany, biomedical and pharmaceutical engineering fields. The aim of the review is to hope that these web resources will facilitate the discovery and development of potential active ingredients of pests and pathogenic microbes control agents.
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Affiliation(s)
- Yin Jin
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, P. R. China
| | - Zheng Wang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, P. R. China
| | - An-Yu Dong
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, P. R. China
| | - Yuan-Qin Huang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, P. R. China
| | - Ge-Fei Hao
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, P. R. China
| | - Bao-An Song
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, P. R. China
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Jeon J, Kang S, Kim HU. Predicting biochemical and physiological effects of natural products from molecular structures using machine learning. Nat Prod Rep 2021; 38:1954-1966. [PMID: 34047331 DOI: 10.1039/d1np00016k] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Covering: 2016 to 2021Discovery of novel natural products has been greatly facilitated by advances in genome sequencing, genome mining and analytical techniques. As a result, the volume of data for natural products has increased over the years, which started to serve as ingredients for developing machine learning models. In the past few years, a number of machine learning models have been developed to examine various aspects of a molecule by effectively processing its molecular structure. Understanding of the biological effects of natural products can benefit from such machine learning approaches. In this context, this Highlight reviews recent studies on machine learning models developed to infer various biological effects of molecules. A particular attention is paid to molecular featurization, or computational representation of a molecular structure, which is an essential process during the development of a machine learning model. Technical challenges associated with the use of machine learning for natural products are further discussed.
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Affiliation(s)
- Junhyeok Jeon
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.
| | - Seongmo Kang
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.
| | - Hyun Uk Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea. and KAIST Institute for Artificial Intelligence, KAIST, Daejeon 34141, Republic of Korea and BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, Daejeon 34141, Republic of Korea
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de Carvalho Martins V, França LP, da Silva Ferreira Y, Pires DC, de Souza Cardoso B, Pessanha de Araújo Santiago MC, Pacheco S, da Costa Souza M, Riger CJ, de Oliveira Godoy RL, Geraldo de Carvalho M. Determination of the Phytochemical Composition and Antioxidant Potential of Eugenia copacabanensis and Myrciaria tenella Leaves (Myrtaceae) Using a Saccharomyces cerevisiae Model. Chem Biodivers 2021; 18:e2100054. [PMID: 33915032 DOI: 10.1002/cbdv.202100054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 04/29/2021] [Indexed: 11/08/2022]
Abstract
Eugenia copacabanensis and Myrciaria tenella are present in restingas of the Atlantic Forest, but little information is available about their chemical and biological potential. In this context, the hexane, dichloromethane, ethyl acetate and butanol fractions from the leaves of methanolic extract were analyzed by GC/MS and HPLC-DAD and the antioxidant potential was determined by DPPH and ABTS assays and using a Saccharomyces cerevisiae model. Dereplication allowed the identification of 68 compounds, 42 and 41 of which, respectively, are first reported here for E. copacabanensis and M. tenella. In vivo results revealed that the ethyl acetate and butanol fractions showed expressive antioxidant protection in the BY4741 and Δgsh1 strains, with greater impact on glutathione-deficient cells. With a high diversity of phenolic compounds, these polar fractions of E. copacabanensis and M. tenella leaves are potential protectors against intracellular oxidative stress.
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Affiliation(s)
- Víctor de Carvalho Martins
- Laboratório de Química de Produtos Naturais, Instituto de Química, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, 23897-000, Brasil.,Laboratório de Cromatografia Líquida, Embrapa Agroindústria de Alimentos, Rio de Janeiro, RJ, 23020-470, Brasil
| | - Liliana Princisval França
- Laboratório de Química de Produtos Naturais, Instituto de Química, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, 23897-000, Brasil
| | - Yasmim da Silva Ferreira
- Laboratório de Química de Produtos Naturais, Instituto de Química, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, 23897-000, Brasil
| | - Daniele Cabral Pires
- Laboratório de Estresse Oxidativo em Microrganismos, Instituto de Química, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, 23897-000, Brasil
| | - Bárbara de Souza Cardoso
- Laboratório de Estresse Oxidativo em Microrganismos, Instituto de Química, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, 23897-000, Brasil
| | | | - Sidney Pacheco
- Laboratório de Cromatografia Líquida, Embrapa Agroindústria de Alimentos, Rio de Janeiro, RJ, 23020-470, Brasil
| | - Marcelo da Costa Souza
- Herbário RBR, Instituto de Ciências Biológicas e da Saúde, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, 23897-000, Brasil
| | - Cristiano Jorge Riger
- Laboratório de Estresse Oxidativo em Microrganismos, Instituto de Química, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, 23897-000, Brasil
| | | | - Mario Geraldo de Carvalho
- Laboratório de Química de Produtos Naturais, Instituto de Química, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, 23897-000, Brasil
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50
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Martins VDC, Santiago MCPDA, Pacheco S, Borguini RG, Souza MDC, de Carvalho MG, Godoy RLDO. Myrcia eriopus DC. (Myrtaceae) fruits, a new endemic Brazilian source of bioactive anthocyanins. Nat Prod Res 2021; 36:2853-2858. [PMID: 33949267 DOI: 10.1080/14786419.2021.1919106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Myrcia eriopus DC. (Myrtaceae) is a native and endemic Brazilian species, and there is no information about its chemical composition. In our study, five different anthocyanins and two other phenolic compounds were described for the first time in M. eriopus fruits. Delphinidin 3-O-glucoside (1), cyanidin 3-O-glucoside (2), petunidin 3-O-glucoside (3), peonidin 3-O-glucoside (4), malvidin 3-O-glucoside (5), gallic acid (6) and myricetin (7) were identified by offline system RP-HPLC-DAD/ESI-QTOF-MS and compared to the scientific literature. Furthermore, the lyophilized powder of M. eriopus fruits showed a high anthocyanin content (1878.14 mg cy-3-glu eqv/100 g f.w.), with greater levels of compounds 1 and 3, and an antioxidant potential in DPPH and ABTS assays (EC50 2419 μg/mL and 339 μmol Trolox/g f.w.), results superior to other non-conventional Brazilian fruits. This first report about the chemical composition of M. eriopus fruit reveals the potential of this fruit as a new source of bioactive anthocyanins.
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Affiliation(s)
- Víctor de Carvalho Martins
- Laboratório de Cromatografia Líquida, Embrapa Agroindústria de Alimentos, Rio de Janeiro, RJ, Brazil.,Laboratório de Química de Produtos Naturais, Instituto de Química, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, Brazil
| | | | - Sidney Pacheco
- Laboratório de Cromatografia Líquida, Embrapa Agroindústria de Alimentos, Rio de Janeiro, RJ, Brazil
| | - Renata Galhardo Borguini
- Laboratório de Cromatografia Líquida, Embrapa Agroindústria de Alimentos, Rio de Janeiro, RJ, Brazil
| | - Marcelo da Costa Souza
- Herbário RBR, Instituto de Ciências Biológicas e da Saúde, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, Brazil
| | - Mario Geraldo de Carvalho
- Laboratório de Química de Produtos Naturais, Instituto de Química, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, Brazil
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