1
|
Junior DBC, Lacerda PS, de Pilla Varotti F, Leite FHA. Towards development of new antimalarial compounds through in silico and in vitro assays. Comput Biol Chem 2024; 111:108093. [PMID: 38772047 DOI: 10.1016/j.compbiolchem.2024.108093] [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: 12/18/2023] [Revised: 02/17/2024] [Accepted: 05/01/2024] [Indexed: 05/23/2024]
Abstract
Malaria is one of most widespread infectious disease in world. The antimalarial therapy presents a series of limitations, such as toxicity and the emergence of resistance, which makes the search for new drugs urgent. Thus, it becomes necessary to explore essential and exclusive therapeutic targets of the parasite to achieve selective inhibition. Enoyl-ACP reductase is an enzyme of the type II fatty acid biosynthetic pathway and is responsible for the rate-limiting step in the fatty acid elongation cycle. In this work, we use hierarchical virtual screening and drug repositioning strategies to prioritize compounds for phenotypic assays and molecular dynamics studies. The molecules were tested against chloroquine-resistant W2 strain of Plasmodium falciparum (EC50 between 330.05 and 13.92 µM). Nitrofurantoin was the best antimalarial activity at low micromolar range (EC50 = 13.92 µM). However, a hit compound against malaria must have a biological activity value below 1 µM. A large number of molecules present problems with permeability in biological membranes and reaching an effective concentration in their target's microenvironment. Nitrofurantoin derivatives with inclusions of groups which confer increased lipid solubility (methyl groups, halogens and substituted and unsubstituted aromatic rings) have been proposed. These derivatives were pulled through the lipid bilayer in molecular dynamics simulations. Molecules 14, 18 and 21 presented lower free energy values than nitrofurantoin when crossing the lipid bilayer.
Collapse
Affiliation(s)
| | - Pedro Sousa Lacerda
- Laboratório de Bioinformática e Modelagem Molecular, Universidade Federal da Bahia, Brazil
| | | | - Franco Henrique Andrade Leite
- Programa de pós-graduação em Biotecnologia, Universidade Estadual de Feira de Santana, Brazil; Programa de pós-graduação em Ciências Farmacêuticas, Universidade Estadual de Feira de Santana, Brazil; Laboratório de Modelagem Molecular, Universidade Estadual de Feira de Santana, Brazil.
| |
Collapse
|
2
|
Costa Júnior DB, Araújo JSC, Oliveira LDM, Neri FSM, Moreira POL, Taranto AG, Fonseca AL, Varotti FDP, Leite FHA. A novel antiplasmodial compound: integration of in silico and in vitro assays. J Biomol Struct Dyn 2021; 40:6295-6307. [PMID: 33554762 DOI: 10.1080/07391102.2021.1882339] [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: 10/22/2022]
Abstract
Malaria is a disease caused by Plasmodium genus. which P. falciparum is responsible for the most severe form of the disease, cerebral malaria. In 2018, 405,000 people died of malaria. Antimalarial drugs have serious adverse effects and limited efficacy due to multidrug-resistant strains. One way to overcome these limitations is the use of computational approaches for prioritizing candidates to phenotypic assays and/or in vitro assays against validated targets. Plasmodium falciparum Enoyl-ACP reductase (PfENR) is noteworthy because it catalyzes the rate-limiting step of the biosynthetic pathway of fatty acid. Thus, the study aimed to identify potential PfENR inhibitors by ligand (2D molecular similarity and pharmacophore models) and structure-based virtual screening (molecular docking). 2D similarity-based virtual screening using Tanimoto Index (> 0.45) selected 29,236 molecules from natural products subset available in ZINC database (n = 181,603). Next, 10 pharmacophore models for PfENR inhibitors were generated and evaluated based on the internal statistical parameters from GALAHAD™ and ROC/AUC curve. These parameters selected a suitable pharmacophore model with one hydrophobic center and two hydrogen bond acceptors. The alignment of the filtered molecules on best pharmacophore model resulted in the selection of 10,977 molecules. These molecules were directed to the docking-based virtual screening by AutoDock Vina 1.1.2 program. These strategies selected one compound to phenotypic assays against parasite. ZINC630259 showed EC50 = 0.12 ± 0.018 µM in antiplasmodial assays and selective index similar to other antimalarial drugs. Finally, MM/PBSA method showed stability of molecule within PfENR binding site (ΔGbinding=-57.337 kJ/mol).Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- David Bacelar Costa Júnior
- Programa de pós-graduação em Biotecnologia, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | | | - Larissa de Mattos Oliveira
- Programa de pós-graduação em Biotecnologia, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | - Flávio Simas Moreira Neri
- Programa de pós-graduação em Ciências Farmacêuticas, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | | | - Alex Gutterres Taranto
- Laboratório de Bioinformática e Desenho de Fármacos, Universidade Federal de São João Del-Rei, Feira de Santana, Brazil
| | - Amanda Luisa Fonseca
- Laboratório de Bioquímica Medicinal, Universidade Federal de São João Del-Rei, Feira de Santana, Brazil
| | - Fernando de Pilla Varotti
- Laboratório de Bioquímica Medicinal, Universidade Federal de São João Del-Rei, Feira de Santana, Brazil
| | - Franco Henrique Andrade Leite
- Programa de pós-graduação em Biotecnologia, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil.,Programa de pós-graduação em Ciências Farmacêuticas, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil.,Laboratório de Qumioinformática e Avaliação Biológica, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| |
Collapse
|
3
|
Costa Júnior DB, Araújo JSC, de Mattos Oliveira L, Neri FSM, Moreira POL, Taranto AG, Fonseca AL, de Pilla Varotti F, Leite FHA. Identification of novel antiplasmodial compound by hierarquical virtual screening and in vitro assays. J Biomol Struct Dyn 2020; 39:3378-3386. [PMID: 32364060 DOI: 10.1080/07391102.2020.1763837] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Malaria is an infectious disease caused by protozoa of the genus Plasmodium spp. with approximately 219 million cases in 2017. P. falciparum is main responsible for the most severe form of the disease, cerebral malaria. Despite of public health impacts, chemotherapy against malaria is still limited due to the emergence of drug resistance cases used in monotherapy and combination therapies. Thus, the development of new antimalarial drugs becomes emergency. One way of achieve this goal is to explore essential and/or unique therapeutic targets of the parasite, or at least sufficiently different to ensure selective inhibition. Enoil-ACP reductase (ENR) is a NADH-dependent enzyme responsible for the limiting step of the type II fatty acid biosynthetic pathway (FAS II). Thus, pharmacophore and docking based virtual screening were applied to prioritize molecules for in vitro assays against P. falciparum W2 strain. The application of successive filters at OOCC database (n = 618) resulted in the identification of one molecule (13) (EC50 = 0.098 ± 0.021 μM) with similar biological activity to artemether. The molecule 13 is a typical drug repurposing case due to previous other approved therapeutic uses on Chinese medicine as a non-specific cholinergic antagonist, thus it could be accelerated the drug development process. Additionally, molecular dynamics studies were used to confirm stability of the molecular interactions identified by molecular docking. Thus, representative structures of P. falciparum ENR can be used in a study to propose new derivatives for evaluation of biological activity in vitro and in vivo. Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- David Bacelar Costa Júnior
- Programa de pós-graduação em Ciências Farmacêuticas, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | | | - Larissa de Mattos Oliveira
- Programa de pós-graduação em Biotecnologia, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | - Flávio Simas Moreira Neri
- Programa de pós-graduação em Ciências Farmacêuticas, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | | | - Alex Gutterres Taranto
- Laboratório de Química Farmacêutica Medicinal, Universidade Federal de São João Del-Rei, Sao Joao del-Rei, Brazil
| | - Amanda Luisa Fonseca
- Laboratório de Bioquímica Medicinal, Universidade Federal de São João Del-Rei, Sao Joao del-Rei, Brazil
| | - Fernando de Pilla Varotti
- Laboratório de Bioquímica Medicinal, Universidade Federal de São João Del-Rei, Sao Joao del-Rei, Brazil
| | - Franco Henrique Andrade Leite
- Programa de pós-graduação em Ciências Farmacêuticas, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil.,Programa de pós-graduação em Biotecnologia, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil.,Laboratório de Modelagem Molecular, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| |
Collapse
|
4
|
Kamata K, Birrer RB, Tokuda Y. Travel medicine: Part 1-The basics. J Gen Fam Med 2017; 18:52-55. [PMID: 29263991 PMCID: PMC5689387 DOI: 10.1002/jgf2.39] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 09/07/2016] [Indexed: 12/30/2022] Open
Abstract
International travels for tourism and business purposes continue to increase annually, while the global terrorism and the risk of lethal viral infections are currently real concerns. It is important that primary care physicians assess travel risk and adequately prepare the prospective traveler for trips. Appropriate vaccines should be administered and an emergency self‐kit recommended. Patient should be educated about safe travel habits and a posttravel follow‐up process established. Further, traveling healthcare professionals may be called upon to assist an ill patient at any time during their journey. In these 2‐part special articles, we provide a practical brief summary of up‐to‐date travel medicine basics for primary care physicians.
Collapse
Affiliation(s)
- Kazuhiro Kamata
- Department of Medicine JCHO Tokyo Joto Hospital Kotoku Tokyo Japan
| | - Richard B Birrer
- Department of Emergency Medicine Cornell University School of Medicine New York NY USA
| | | |
Collapse
|
5
|
Ma DM, Wang Z, Wang L, Alejos-Gonzales F, Sun MA, Xie DY. A Genome-Wide Scenario of Terpene Pathways in Self-pollinated Artemisia annua. MOLECULAR PLANT 2015; 8:1580-98. [PMID: 26192869 DOI: 10.1016/j.molp.2015.07.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 06/07/2015] [Accepted: 07/08/2015] [Indexed: 05/18/2023]
Abstract
Scenarios of genes to metabolites in Artemisia annua remain uninvestigated. Here, we report the use of an integrated approach combining metabolomics, transcriptomics, and gene function analyses to characterize gene-to-terpene and terpene pathway scenarios in a self-pollinating variety of this species. Eighty-eight metabolites including 22 sesquiterpenes (e.g., artemisinin), 26 monoterpenes, two triterpenes, one diterpene and 38 other non-polar metabolites were identified from 14 tissues. These metabolites were differentially produced by leaves and flowers at lower to higher positions. Sequences from cDNA libraries of six tissues were assembled into 18 871 contigs and genome-wide gene expression profiles in tissues were strongly associated with developmental stages and spatial specificities. Sequence mining identified 47 genes that mapped to the artemisinin, non-amorphadiene sesquiterpene, monoterpene, triterpene, 2-C-methyl-D-erythritol 4-phosphate and mevalonate pathways. Pearson correlation analysis resulted in network integration that characterized significant correlations of gene-to-gene expression patterns and gene expression-to-metabolite levels in six tissues simultaneously. More importantly, manipulations of amorpha-4,11-diene synthase gene expression not only affected the activity of this pathway toward artemisinin, artemisinic acid, and arteannuin b but also altered non-amorphadiene sesquiterpene and genome-wide volatile profiles. Such gene-to-terpene landscapes associated with different tissues are fundamental to the metabolic engineering of artemisinin.
Collapse
Affiliation(s)
- Dong-Ming Ma
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Zhilong Wang
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Liangjiang Wang
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - Fatima Alejos-Gonzales
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Ming-An Sun
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - De-Yu Xie
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA.
| |
Collapse
|
6
|
Hunt S, Yoshida M, Davis CE, Greenhill NS, Davis PF. An extract of the medicinal plant Artemisia annua modulates production of inflammatory markers in activated neutrophils. J Inflamm Res 2015; 8:9-14. [PMID: 25609991 PMCID: PMC4298291 DOI: 10.2147/jir.s75484] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
PURPOSE To investigate the ability of a commercial extract from the medicinal plant Artemisia annua to modulate production of the cytokine, tumor necrosis factor-alpha (TNF-α), and the cyclooxygenase (COX) inflammatory marker, prostaglandin E2 (PGE2) in activated neutrophils. METHODS Neutrophils were harvested from rat whole blood and cultured in the presence of plant extract or control samples. Neutrophils, except unactivated control cells, were activated with 10 μg/mL lipopolysaccharide (LPS). The cells were cultured with a range of different concentrations of the A. annua extracts (400-1 μg/mL) and artemisinin (200 and 100 μg/mL) and the supernatants were then tested by enzyme-linked immunosorbent assay (ELISA) for the concentrations of TNF-α and PGE2. Each sample was assayed in triplicate. Positive controls with an inhibitor were assayed in triplicate: chloroquine 2.58 and 5.16 μg/mL for TNF-α, and ibuprofen 400 μg/mL for PGE2. An unsupplemented group was also assessed in triplicate as a baseline control. RESULTS Neutrophils were stimulated to an inflammatory state by the addition of LPS. A. annua extract significantly inhibited TNF-α production by activated neutrophils in a dose-dependent manner. There was complete inhibition by the A. annua extract at 200, 100, and 50 μg/mL (all P≤0.0003). At A. annua extract concentrations of 25, 10, and 5 μg/mL, TNF-α production was inhibited by 89% (P<0.0001), 54% (P=0.0002), and 38% (P=0.0014), respectively. A. annua 1 μg/mL did not significantly inhibit TNF-α production (8.8%; P>0.05). Concentrations of 400, 200, and 100 μg/mL A. annua extract significantly inhibited PGE2 production by 87% (P=0.0128), 91% (P=0.0017), and 93% (P=0.0114), respectively. CONCLUSION An extract of A. annua was shown to be a potent inhibitor of TNF-α and a strong inhibitor of PGE2 production in activated neutrophils at the concentrations tested. Further studies are warranted with this promising plant extract.
Collapse
Affiliation(s)
- Sheena Hunt
- Promisia Integrative Ltd, Wellington, New Zealand
| | | | | | | | | |
Collapse
|
7
|
Na YJ, Chai JY, Jung BK, Lee HJ, Song JY, Je JH, Seo JH, Park SH, Choi JS, Kim MJ. An imported case of severe falciparum malaria with prolonged hemolytic anemia clinically mimicking a coinfection with babesiosis. THE KOREAN JOURNAL OF PARASITOLOGY 2014; 52:667-72. [PMID: 25548419 PMCID: PMC4277030 DOI: 10.3347/kjp.2014.52.6.667] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 10/01/2014] [Accepted: 10/01/2014] [Indexed: 01/12/2023]
Abstract
While imported falciparum malaria has been increasingly reported in recent years in Korea, clinicians have difficulties in making a clinical diagnosis as well as in having accessibility to effective anti-malarial agents. Here we describe an unusual case of imported falciparum malaria with severe hemolytic anemia lasting over 2 weeks, clinically mimicking a coinfection with babesiosis. A 48-year old Korean man was diagnosed with severe falciparum malaria in France after traveling to the Republic of Benin, West Africa. He received a 1-day course of intravenous artesunate and a 7-day course of Malarone (atovaquone/proguanil) with supportive hemodialysis. Coming back to Korea 5 days after discharge, he was readmitted due to recurrent fever, and further treated with Malarone for 3 days. Both the peripheral blood smears and PCR test were positive for Plasmodium falciparum. However, he had prolonged severe hemolytic anemia (Hb 5.6 g/dl). Therefore, 10 days after the hospitalization, Babesia was considered to be potentially coinfected. A 7-day course of Malarone and azithromycin was empirically started. He became afebrile within 3 days of this babesiosis treatment, and hemolytic anemia profiles began to improve at the completion of the treatment. He has remained stable since his discharge. Unexpectedly, the PCR assays failed to detect DNA of Babesia spp. from blood. In addition, during the retrospective review of the case, the artesunate-induced delayed hemolytic anemia was considered as an alternative cause of the unexplained hemolytic anemia.
Collapse
Affiliation(s)
- Young Ju Na
- Department of Internal Medicine, Korea University Anam Hospital, Seoul 136-705, Korea
| | - Jong-Yil Chai
- Department of Parasitology and Tropical Medicine, Seoul National University College of Medicine, Seoul 110-799, Korea
| | - Bong-Kwang Jung
- Department of Parasitology and Tropical Medicine, Seoul National University College of Medicine, Seoul 110-799, Korea
| | - Hyun Jung Lee
- Department of Internal Medicine, Korea University Anam Hospital, Seoul 136-705, Korea
| | - Ji Young Song
- Department of Internal Medicine, Korea University Anam Hospital, Seoul 136-705, Korea
| | - Ji Hye Je
- Department of Internal Medicine, Korea University Anam Hospital, Seoul 136-705, Korea
| | - Ji Hye Seo
- Department of Internal Medicine, Korea University Anam Hospital, Seoul 136-705, Korea
| | - Sung Hun Park
- Department of Internal Medicine, Korea University Anam Hospital, Seoul 136-705, Korea
| | - Ji Seon Choi
- Department of Laboratory Medicine, Korea University Anam Hospital, Seoul 136-705, Korea
| | - Min Ja Kim
- Department of Internal Medicine, Korea University Anam Hospital, Seoul 136-705, Korea
| |
Collapse
|
8
|
Artemisinins: Pharmacological actions beyond anti-malarial. Pharmacol Ther 2014; 142:126-39. [DOI: 10.1016/j.pharmthera.2013.12.001] [Citation(s) in RCA: 309] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 11/26/2013] [Indexed: 12/23/2022]
|