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Muñoz-Vega MC, López-Hernández S, Sierra-Chavarro A, Scotti MT, Scotti L, Coy-Barrera E, Herrera-Acevedo C. Machine-Learning- and Structure-Based Virtual Screening for Selecting Cinnamic Acid Derivatives as Leishmania major DHFR-TS Inhibitors. Molecules 2023; 29:179. [PMID: 38202763 PMCID: PMC10779987 DOI: 10.3390/molecules29010179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 12/02/2023] [Accepted: 12/06/2023] [Indexed: 01/12/2024] Open
Abstract
The critical enzyme dihydrofolate reductase-thymidylate synthase in Leishmania major (LmDHFR-TS) serves a dual-purpose role and is essential for DNA synthesis, a cornerstone of the parasite's reproductive processes. Consequently, the development of inhibitors against LmDHFR-TS is crucial for the creation of novel anti-Leishmania chemotherapies. In this study, we employed an in-house database containing 314 secondary metabolites derived from cinnamic acid that occurred in the Asteraceae family. We conducted a combined ligand/structure-based virtual screening to identify potential inhibitors against LmDHFR-TS. Through consensus analysis of both approaches, we identified three compounds, i.e., lithospermic acid (237), diarctigenin (306), and isolappaol A (308), that exhibited a high probability of being inhibitors according to both approaches and were consequently classified as promising hits. Subsequently, we expanded the binding mode examination of these compounds within the active site of the test enzyme through molecular dynamics simulations, revealing a high degree of structural stability and minimal fluctuations in its tertiary structure. The in silico predictions were then validated through in vitro assays to examine the inhibitory capacity of the top-ranked naturally occurring compounds against LmDHFR-TS recombinant protein. The test compounds effectively inhibited the enzyme with IC50 values ranging from 6.1 to 10.1 μM. In contrast, other common cinnamic acid derivatives (i.e., flavonoid glycosides) from the Asteraceae family, such as hesperidin, isovitexin 4'-O-glucoside, and rutin, exhibited low activity against this target. The selective index (SI) for all tested compounds was determined using HsDHFR with moderate inhibitory effect. Among these hits, lignans 306 and 308 demonstrated the highest selectivity, displaying superior SI values compared to methotrexate, the reference inhibitor of DHFR-TS. Therefore, continued research into the anti-leishmanial potential of these C6C3-hybrid butyrolactone lignans may offer a brighter outlook for combating this neglected tropical disease.
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Affiliation(s)
- Maria Camila Muñoz-Vega
- Department of Chemical Engineering, Universidad ECCI, Bogotá, Distrito Capital 111311, Colombia; (M.C.M.-V.); (S.L.-H.); (A.S.-C.)
- Laboratorio de Investigación en Biocatálisis y Biotransformaciones (LIBB), Grupo de Investigación en Ingeniería de los Procesos Agroalimentarios y Biotecnológicos (GIPAB), Departamento de Química Universidad del Valle, Cali 760042, Colombia
| | - Sofía López-Hernández
- Department of Chemical Engineering, Universidad ECCI, Bogotá, Distrito Capital 111311, Colombia; (M.C.M.-V.); (S.L.-H.); (A.S.-C.)
| | - Adrián Sierra-Chavarro
- Department of Chemical Engineering, Universidad ECCI, Bogotá, Distrito Capital 111311, Colombia; (M.C.M.-V.); (S.L.-H.); (A.S.-C.)
| | - Marcus Tullius Scotti
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil; (M.T.S.); (L.S.)
| | - Luciana Scotti
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil; (M.T.S.); (L.S.)
| | - Ericsson Coy-Barrera
- Bioorganic Chemistry Laboratory, Facultad de Ciencias Básicas y Aplicadas, Universidad Militar Nueva Granada, Cajicá 250247, Colombia;
| | - Chonny Herrera-Acevedo
- Department of Chemical Engineering, Universidad ECCI, Bogotá, Distrito Capital 111311, Colombia; (M.C.M.-V.); (S.L.-H.); (A.S.-C.)
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil; (M.T.S.); (L.S.)
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Oliveira MCN, Cavalcante IL, de Araújo AN, Ferreira dos Santos AM, de Menezes RPB, Herrera-Acevedo C, Ferreira de Sousa N, de Souza Aquino J, Barbosa-Filho JM, de Castro RD, Almeida RN, Scotti L, Scotti MT, Da Silva Stiebbe Salvadori MG. Methyleugenol Has an Antidepressant Effect in a Neuroendocrine Model: In Silico and In Vivo Evidence. Pharmaceuticals (Basel) 2023; 16:1408. [PMID: 37895879 PMCID: PMC10610402 DOI: 10.3390/ph16101408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/18/2023] [Accepted: 08/21/2023] [Indexed: 10/29/2023] Open
Abstract
Major depressive disorder is a severe mood disorder characterized by different emotions and feelings. This study investigated the antidepressant activity of the phenylpropanoid methyleugenol (ME) in adult female mice exposed to a stress model induced by dexamethasone. The animals were randomly divided into groups containing eight animals and were pre-administered with dexamethasone (64 μg/kg subcutaneously). After 165 and 180 min, they were treated with ME (25, 50 and 100 mg/kg intraperitoneally) or imipramine (10 mg/kg intraperitoneally) after 45 min and 30 min, respectively; they were then submitted to tests which were filmed. The videos were analyzed blindly. In the tail suspension test, ME (50 mg/kg) increased latency and reduced immobility time. In the splash test, ME (50 mg/kg) decreased grooming latency and increased grooming time. In the open field, there was no statistical difference for the ME groups regarding the number of crosses, and ME (50 mg/kg) increased the number of rearing and time spent in the center. Regarding in silico studies, ME interacted with dopaminergic D1 and α1 adrenergic pathway receptors and with tryptophan hydroxylase inhibitor. In the in vivo evaluation of the pathways of action, the antidepressant potential of ME (50 mg/kg) was reversed by SCH23390 (4 mg/kg intraperitoneally) dopaminergic D1 receptor, Prazosin (1 mg/kg intraperitoneally) α1 adrenergic receptor, and PCPA (4 mg/kg intraperitoneally) tryptophan hydroxylase inhibitor. Our findings indicate that ME did not alter with the locomotor activity of the animals and shows antidepressant activity in female mice with the participation of the D1, α1 and serotonergic systems.
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Affiliation(s)
- Mayara Cecile Nascimento Oliveira
- Laboratory of Psychopharmacology, Institute for Research in Drugs and Medicines, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil (A.M.F.d.S.); (R.D.d.C.)
| | - Ikla Lima Cavalcante
- Laboratory of Psychopharmacology, Institute for Research in Drugs and Medicines, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil (A.M.F.d.S.); (R.D.d.C.)
| | - Alana Natalícia de Araújo
- Laboratory of Psychopharmacology, Institute for Research in Drugs and Medicines, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil (A.M.F.d.S.); (R.D.d.C.)
| | - Aline Matilde Ferreira dos Santos
- Laboratory of Psychopharmacology, Institute for Research in Drugs and Medicines, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil (A.M.F.d.S.); (R.D.d.C.)
| | - Renata Priscila Barros de Menezes
- Laboratory of Cheminformatics, Institute for Research in Drugs and Medicines, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil
| | - Chonny Herrera-Acevedo
- Laboratory of Cheminformatics, Institute for Research in Drugs and Medicines, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil
| | - Natália Ferreira de Sousa
- Laboratory of Cheminformatics, Institute for Research in Drugs and Medicines, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil
| | - Jailane de Souza Aquino
- Laboratory of Experimental Nutrition, Department of Nutrition, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil
| | - José Maria Barbosa-Filho
- Department of Pharmaceutical Sciences, Institute for Research in Drugs and Medicines, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil
| | - Ricardo Dias de Castro
- Laboratory of Psychopharmacology, Institute for Research in Drugs and Medicines, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil (A.M.F.d.S.); (R.D.d.C.)
| | - Reinaldo Nóbrega Almeida
- Laboratory of Psychopharmacology, Institute for Research in Drugs and Medicines, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil (A.M.F.d.S.); (R.D.d.C.)
| | - Luciana Scotti
- Laboratory of Cheminformatics, Institute for Research in Drugs and Medicines, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil
| | - Marcus Tullius Scotti
- Laboratory of Cheminformatics, Institute for Research in Drugs and Medicines, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil
| | - Mirian Graciela Da Silva Stiebbe Salvadori
- Laboratory of Psychopharmacology, Institute for Research in Drugs and Medicines, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil (A.M.F.d.S.); (R.D.d.C.)
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Herrera-Acevedo C, de Menezes RPB, de Sousa NF, Scotti L, Scotti MT, Coy-Barrera E. Kaurane-Type Diterpenoids as Potential Inhibitors of Dihydrofolate Reductase-Thymidylate Synthase in New World Leishmania Species. Antibiotics (Basel) 2023; 12:antibiotics12040663. [PMID: 37107025 PMCID: PMC10135059 DOI: 10.3390/antibiotics12040663] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/14/2023] [Accepted: 03/26/2023] [Indexed: 03/30/2023] Open
Abstract
The bifunctional enzyme Dihydrofolate reductase-thymidylate synthase (DHFR-TS) plays a crucial role in the survival of the Leishmania parasite, as folates are essential cofactors for purine and pyrimidine nucleotide biosynthesis. However, DHFR inhibitors are largely ineffective in controlling trypanosomatid infections, largely due to the presence of Pteridine reductase 1 (PTR1). Therefore, the search for structures with dual inhibitory activity against PTR1/DHFR-TS is crucial in the development of new anti-Leishmania chemotherapies. In this research, using the Leishmania major DHFR-TS recombinant protein, enzymatic inhibitory assays were performed on four kauranes and two derivatives that had been previously tested against LmPTR1. The structure 302 (6.3 µM) and its derivative 302a (4.5 µM) showed the lowest IC50 values among the evaluated molecules. To evaluate the mechanism of action of these structures, molecular docking calculations and molecular dynamics simulations were performed using a DHFR-TS hybrid model. Results showed that hydrogen bond interactions are critical for the inhibitory activity against LmDHFR-TS, as well as the presence of the p-hydroxyl group of the phenylpropanoid moiety of 302a. Finally, additional computational studies were performed on DHFR-TS structures from Leishmania species that cause cutaneous and mucocutaneous leishmaniasis in the New World (L. braziliensis, L. panamensis, and L. amazonensis) to explore the targeting potential of these kauranes in these species. It was demonstrated that structures 302 and 302a are multi-Leishmania species compounds with dual DHFR-TS/PTR1 inhibitory activity.
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Affiliation(s)
- Chonny Herrera-Acevedo
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil (M.T.S.)
- Department of Chemical Engineering, Universidad ECCI, Bogotá, Distrito Capital 111311, Colombia
| | - Renata Priscila Barros de Menezes
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil (M.T.S.)
| | - Natália Ferreira de Sousa
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil (M.T.S.)
| | - Luciana Scotti
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil (M.T.S.)
| | - Marcus Tullius Scotti
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil (M.T.S.)
| | - Ericsson Coy-Barrera
- Bioorganic Chemistry Laboratory, Facultad de Ciencias Básicas y Aplicadas, Universidad Militar Nueva Granada, Cajicá 250247, Colombia
- Correspondence:
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Tullius Scotti M, Herrera-Acevedo C, Barros de Menezes RP, Martin HJ, Muratov EN, Ítalo de Souza Silva Á, Faustino Albuquerque E, Ferreira Calado L, Coy-Barrera E, Scotti L. MolPredictX: Online Biological Activity Predictions by Machine Learning Models. Mol Inform 2022; 41:e2200133. [PMID: 35961924 DOI: 10.1002/minf.202200133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/12/2022] [Indexed: 01/05/2023]
Abstract
Here we report the development of MolPredictX, an innovate and freely accessible web interface for biological activity predictions of query molecules. MolPredictX utilizes in-house QSAR models to provide 27 qualitative predictions (active or inactive), and quantitative probabilities for bioactivity against parasitic (Trypanosoma and Leishmania), viral (Dengue, Sars-CoV and Hepatitis C), pathogenic yeast (Candida albicans), bacterial (Salmonella enterica and Escherichia coli), and Alzheimer disease enzymes. In this article, we introduce the methodology and usability of this webtool, highlighting its potential role in the development of new drugs against a variety of diseases. MolPredictX is undergoing continuous development and is freely available at https://www.molpredictx.ufpb.br/.
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Affiliation(s)
- Marcus Tullius Scotti
- Programa de Pós-Graduação de Produtos Naturais e Sintéticos Bioativos, Universidade Federal da Paraíba, 58051-900, João Pessoa-PB, Brazil
| | - Chonny Herrera-Acevedo
- Programa de Pós-Graduação de Produtos Naturais e Sintéticos Bioativos, Universidade Federal da Paraíba, 58051-900, João Pessoa-PB, Brazil.,Department of Chemical Engineering, Universidad ECCI, Carrera 19 # 49-20, 111311, Bogotá D.C., Colombia
| | - Renata Priscila Barros de Menezes
- Programa de Pós-Graduação de Produtos Naturais e Sintéticos Bioativos, Universidade Federal da Paraíba, 58051-900, João Pessoa-PB, Brazil
| | - Holli-Joi Martin
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Eugene N Muratov
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Ávilla Ítalo de Souza Silva
- Programa de Pós-Graduação de Produtos Naturais e Sintéticos Bioativos, Universidade Federal da Paraíba, 58051-900, João Pessoa-PB, Brazil
| | - Emmanuella Faustino Albuquerque
- Programa de Pós-Graduação de Produtos Naturais e Sintéticos Bioativos, Universidade Federal da Paraíba, 58051-900, João Pessoa-PB, Brazil
| | - Lucas Ferreira Calado
- Programa de Pós-Graduação de Produtos Naturais e Sintéticos Bioativos, Universidade Federal da Paraíba, 58051-900, João Pessoa-PB, Brazil
| | - Ericsson Coy-Barrera
- Bioorganic Chemistry Laboratory, Facultad de Ciencias Básicas y Aplicadas, Universidad Militar Nueva Granada, Cajicá, 250247, Colombia
| | - Luciana Scotti
- Programa de Pós-Graduação de Produtos Naturais e Sintéticos Bioativos, Universidade Federal da Paraíba, 58051-900, João Pessoa-PB, Brazil
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Mathew B, Herrera-Acevedo C, Dev S, Rangarajan TM, Kuruniyan MS, Poonkuzhi NP, Scotti L, Scotti MT. Development of 2D, 3D-QSAR and Pharmacophore Modeling of Chalcones for the Inhibition of Monoamine Oxidase B. Comb Chem High Throughput Screen 2021; 25:1731-1744. [PMID: 34397324 DOI: 10.2174/1386207324666210816125738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 06/04/2021] [Accepted: 06/21/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Selective and reversible types of MAO-B inhibitors have emerged as promising candidates for the management of neurodegenerative diseases. Several functionalized chalcone derivatives were shown to have potential reversible MAO-B inhibitory activity, which have recently been reported from our laboratory. METHODS With the experimental results of about 70 chalcone derivatives, we further developed a pharmacophore modelling, and 2D and 3D- QSAR analyses of these reported chalcones for MAO-B inhibition. RESULTS The 2D-QSAR model presented four variables (MATS7v, GATS 1i and 3i, and C-006) from 143 Dragon 7 molecular descriptors, with a r2 value of 0.76 and a Q2cv for cross-validation equal to 0.72. An external validation also was performed using 11 chalcones, obtaining a Q2ext value of 0.74. The second 3D-QSAR model using MLR (multiple linear regression) was built starting from 128 Volsurf+ molecular descriptors, being identified as 4 variables (Molecular descriptors): D3, CW1 and LgS11, and L2LGS. Adetermination coefficient (r2) value of 0.76 and a Q2cv for cross-validation equal to 0.72 were obtained for this model. An external validation also was performed using 11 chalcones and a Q2ext value of 0.74 was found. CONCLUSION This report exhibited a good correlation and satisfactory agreement between experiment and theory.
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Affiliation(s)
- Bijo Mathew
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi-682 041, India
| | - Chonny Herrera-Acevedo
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, 58051-900, João Pessoa, Brazil
| | - Sanal Dev
- Department of Pharmaceutical Chemistry, Al-Shifa College of Pharmacy, Perinthalmanna - 679322, Kerala, India
| | - T M Rangarajan
- Department of Chemistry, Sri Venketeswara College, University of Delhi, New Delhi-110021, India
| | | | | | - Luciana Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, 58051-900, João Pessoa, Brazil
| | - Marcus Tullius Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, 58051-900, João Pessoa, Brazil
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Herrera-Acevedo C, Perdomo-Madrigal C, Herrera-Acevedo K, Coy-Barrera E, Scotti L, Scotti MT. Machine learning models to select potential inhibitors of acetylcholinesterase activity from SistematX: a natural products database. Mol Divers 2021; 25:1553-1568. [PMID: 34132933 DOI: 10.1007/s11030-021-10245-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/03/2021] [Indexed: 11/29/2022]
Abstract
Alzheimer's disease is the most common form of dementia, representing 60-70% of dementia cases. The enzyme acetylcholinesterase (AChE) cleaves the ester bonds in acetylcholine and plays an important role in the termination of acetylcholine activity at cholinergic synapses in various regions of the nervous system. The inhibition of acetylcholinesterase is frequently used to treat Alzheimer's disease. In this study, a merged BindingDB and ChEMBL dataset containing molecules with reported half-maximal inhibitory concentration (IC50) values for AChE (7032 molecules) was used to build machine learning classification models for selecting potential AChE inhibitors from the SistematX dataset (8593 secondary metabolites). A total of seven fivefold models with accuracy above 80% after cross-validation were obtained using three types of molecular descriptors (VolSurf, DRAGON 5.0, and bit-based fingerprints). A total of 521 secondary metabolites (6.1%) were classified as active in this stage. Subsequently, virtual screening was performed, and 25 secondary metabolites were identified as potential inhibitors of AChE. Separately, the crystal structure of AChE in complex with (-)-galantamine was used to perform molecular docking calculations with the entire SistematX dataset. Consensus analysis of both methodologies was performed. Only eight structures achieved combined probability values above 0.5. Finally, two sesquiterpene lactones, structures 15 and 24, were predicted to be able to cross the blood-brain barrier, which was confirmed in the VolSurf+ quantitative model, revealing these two structures as the most promising secondary metabolites for AChE inhibition among the 8593 molecules tested. A consensus analysis of classification models and molecular docking calculations identified four potential inhibitors of acetylcholinesterase from the SistematX dataset (8593 structures).
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Affiliation(s)
- Chonny Herrera-Acevedo
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa, PB, 58051-900, Brazil.,Bioorganic Chemistry Laboratory, Facultad de Ciencias Básicas y Aplicadas, Universidad Militar Nueva Granada, 250247, Cajicá, Colombia
| | - Camilo Perdomo-Madrigal
- School of Science, Universidad de Ciencias Aplicadas y Ambientales, Calle 222 # 55-37, Bogotá D.C., Colombia
| | - Kenyi Herrera-Acevedo
- Departamento de Química, Facultad de Ciencias, Universidad Nacional de Colombia, Carrera 45 # 26- 85, Bogotá D.C., Colombia
| | - Ericsson Coy-Barrera
- Bioorganic Chemistry Laboratory, Facultad de Ciencias Básicas y Aplicadas, Universidad Militar Nueva Granada, 250247, Cajicá, Colombia
| | - Luciana Scotti
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa, PB, 58051-900, Brazil
| | - Marcus Tullius Scotti
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa, PB, 58051-900, Brazil.
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Herrera-Acevedo C, Flores-Gaspar A, Scotti L, Mendonça-Junior FJB, Scotti MT, Coy-Barrera E. Identification of Kaurane-Type Diterpenes as Inhibitors of Leishmania Pteridine Reductase I. Molecules 2021; 26:molecules26113076. [PMID: 34063939 PMCID: PMC8196580 DOI: 10.3390/molecules26113076] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/18/2021] [Accepted: 05/18/2021] [Indexed: 12/16/2022] Open
Abstract
The current treatments against Leishmania parasites present high toxicity and multiple side effects, which makes the control and elimination of leishmaniasis challenging. Natural products constitute an interesting and diverse chemical space for the identification of new antileishmanial drugs. To identify new drug options, an in-house database of 360 kauranes (tetracyclic diterpenes) was generated, and a combined ligand- and structure-based virtual screening (VS) approach was performed to select potential inhibitors of Leishmania major (Lm) pteridine reductase I (PTR1). The best-ranked kauranes were employed to verify the validity of the VS approach through LmPTR1 enzyme inhibition assay. The half-maximal inhibitory concentration (IC50) values of selected bioactive compounds were examined using the random forest (RF) model (i.e., 2β-hydroxy-menth-6-en-5β-yl ent-kaurenoate (135) and 3α-cinnamoyloxy-ent-kaur-16-en-19-oic acid (302)) were below 10 μM. A compound similar to 302, 3α-p-coumaroyloxy-ent-kaur-16-en-19-oic acid (302a), was also synthesized and showed the highest activity against LmPTR1. Finally, molecular docking calculations and molecular dynamics simulations were performed for the VS-selected, most-active kauranes within the active sites of PTR1 hybrid models, generated from three Leishmania species that are known to cause cutaneous leishmaniasis in the new world (i.e., L. braziliensis, L. panamensis, and L. amazonensis) to explore the targeting potential of these kauranes to other species-dependent variants of this enzyme.
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Affiliation(s)
- Chonny Herrera-Acevedo
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil; (C.H.-A.); (L.S.)
- Bioorganic Chemistry Laboratory, Facultad de Ciencias Básicas y Aplicadas, Universidad Militar Nueva Granada, Cajicá 250247, Colombia;
| | - Areli Flores-Gaspar
- Departamento de Química, Facultad de Ciencias Básicas y Aplicadas, Universidad Militar Nueva Granada, Cajicá 250247, Colombia
- Correspondence: (A.F.-G.); (M.T.S.); Tel.: +57-1-650-00-00 (ext. 1526) (A.F.-G.); +55-83-99869-0415 (M.T.S.)
| | - Luciana Scotti
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil; (C.H.-A.); (L.S.)
| | | | - Marcus Tullius Scotti
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil; (C.H.-A.); (L.S.)
- Correspondence: (A.F.-G.); (M.T.S.); Tel.: +57-1-650-00-00 (ext. 1526) (A.F.-G.); +55-83-99869-0415 (M.T.S.)
| | - Ericsson Coy-Barrera
- Bioorganic Chemistry Laboratory, Facultad de Ciencias Básicas y Aplicadas, Universidad Militar Nueva Granada, Cajicá 250247, Colombia;
- Departamento de Química, Facultad de Ciencias Básicas y Aplicadas, Universidad Militar Nueva Granada, Cajicá 250247, Colombia
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Costa RPO, Lucena LF, Silva LMA, Zocolo GJ, Herrera-Acevedo C, Scotti L, Da-Costa FB, Ionov N, Poroikov V, Muratov EN, Scotti MT. The SistematX Web Portal of Natural Products: An Update. J Chem Inf Model 2021; 61:2516-2522. [PMID: 34014674 DOI: 10.1021/acs.jcim.1c00083] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Natural products and their secondary metabolites are promising starting points for the development of drug prototypes and new drugs, as many current treatments for numerous diseases are directly or indirectly related to such compounds. State-of-the-art, curated, integrated, and frequently updated databases of secondary metabolites are thus highly relevant to drug discovery. The SistematX Web Portal, introduced in 2018, is undergoing development to address this need and documents crucial information about plant secondary metabolites, including the exact location of the species from which the compounds were isolated. SistematX also allows registered users to log in to the data management area and gain access to administrative pages. This study reports recent updates and modifications to the SistematX Web Portal, including a batch download option, the generation and visualization of 1H and 13C nuclear magnetic resonance spectra, and the calculation of physicochemical (drug-like and lead-like) properties and biological activity profiles. The SistematX Web Portal is freely available at http://sistematx.ufpb.br.
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Affiliation(s)
- Renan P O Costa
- Laboratory of Cheminformatics, Instituto de Pesquisa em Fármacos e Medicamentos (IPeFarM), Universidade Federal da Paraíba, Campus I, Cidade Universitária, João Pessoa 58051-900, PB, Brazil
| | - Lucas F Lucena
- Laboratory of Cheminformatics, Instituto de Pesquisa em Fármacos e Medicamentos (IPeFarM), Universidade Federal da Paraíba, Campus I, Cidade Universitária, João Pessoa 58051-900, PB, Brazil
| | - Lorena Mara A Silva
- Laboratório Multiusuário de Química de Produtos Naturais, Embrapa Agroindústria Tropical, Rua Doutora Sara Mesquita 2270, Planalto do Pici, Fortaleza 60511110, CE, Brazil
| | - Guilherme Julião Zocolo
- Laboratório Multiusuário de Química de Produtos Naturais, Embrapa Agroindústria Tropical, Rua Doutora Sara Mesquita 2270, Planalto do Pici, Fortaleza 60511110, CE, Brazil
| | - Chonny Herrera-Acevedo
- Laboratory of Cheminformatics, Instituto de Pesquisa em Fármacos e Medicamentos (IPeFarM), Universidade Federal da Paraíba, Campus I, Cidade Universitária, João Pessoa 58051-900, PB, Brazil
| | - Luciana Scotti
- Laboratory of Cheminformatics, Instituto de Pesquisa em Fármacos e Medicamentos (IPeFarM), Universidade Federal da Paraíba, Campus I, Cidade Universitária, João Pessoa 58051-900, PB, Brazil
| | - Fernando Batista Da-Costa
- AsterBioChem Research Team, Laboratory of Pharmacognosy, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av do café s/n, Ribeirão Preto 14040-903, SP, Brazil
| | - Nikita Ionov
- Laboratory of Structure-Function Based Drug Design, Department of Bioinformatics, Institute of Biomedical Chemistry, Pogodinskaya Str. 10, bldg. 8, Moscow 119121, Russia
| | - Vladimir Poroikov
- Laboratory of Structure-Function Based Drug Design, Department of Bioinformatics, Institute of Biomedical Chemistry, Pogodinskaya Str. 10, bldg. 8, Moscow 119121, Russia
| | - Eugene N Muratov
- Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Marcus T Scotti
- Laboratory of Cheminformatics, Instituto de Pesquisa em Fármacos e Medicamentos (IPeFarM), Universidade Federal da Paraíba, Campus I, Cidade Universitária, João Pessoa 58051-900, PB, Brazil
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Herrera-Acevedo C, Perdomo-Madrigal C, Muratov EN, Scotti L, Scotti MT. Discovery of Alternative Chemotherapy Options for Leishmaniasis through Computational Studies of Asteraceae. ChemMedChem 2021; 16:1234-1245. [PMID: 33336460 DOI: 10.1002/cmdc.202000862] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/15/2020] [Indexed: 12/12/2022]
Abstract
Leishmaniasis is a complex disease caused by over 20 Leishmania species that primarily affects populations with poor socioeconomic conditions. Currently available drugs for treating leishmaniasis include amphotericin B, paromomycin, and pentavalent antimonials, which have been associated with several limitations, such as low efficacy, the development of drug resistance, and high toxicity. Natural products are an interesting source of new drug candidates. The Asteraceae family includes more than 23 000 species worldwide. Secondary metabolites that can be found in species from this family have been widely explored as potential new treatments for leishmaniasis. Recently, computational tools have become more popular in medicinal chemistry to establish experimental designs, identify new drugs, and compare the molecular structures and activities of novel compounds. Herein, we review various studies that have used computational tools to examine various compounds identified in the Asteraceae family in the search for potential drug candidates against Leishmania.
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Affiliation(s)
- Chonny Herrera-Acevedo
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Cidade Universitária-Castelo Branco III, Joao Pessoa, PB, Brazil
| | - Camilo Perdomo-Madrigal
- School of Science, Universidad de Ciencias Aplicadas y Ambientales, Calle 222 n° 55-37, Bogotá D.C., Colombia
| | - Eugene N Muratov
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Cidade Universitária-Castelo Branco III, Joao Pessoa, PB, Brazil
| | - Luciana Scotti
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Cidade Universitária-Castelo Branco III, Joao Pessoa, PB, Brazil
| | - Marcus Tullius Scotti
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Cidade Universitária-Castelo Branco III, Joao Pessoa, PB, Brazil
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Herrera-Acevedo C, Dos Santos Maia M, Cavalcanti ÉBVS, Coy-Barrera E, Scotti L, Scotti MT. Selection of antileishmanial sesquiterpene lactones from SistematX database using a combined ligand-/structure-based virtual screening approach. Mol Divers 2020; 25:2411-2427. [PMID: 32909084 DOI: 10.1007/s11030-020-10139-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 08/30/2020] [Indexed: 12/20/2022]
Abstract
Leishmaniasis refers to a complex of diseases, caused by the intracellular parasitic protozoans belonging to the genus Leishmania. Among the three types of disease manifestations, the most severe type is visceral leishmaniasis, which is caused by Leishmania donovani, and is diagnosed in more than 20,000 cases annually, worldwide. Because the current therapeutic options for disease treatment are associated with several limitations, the identification of new potential leads/drugs remains necessary. In this study, a combined approach was used, based on two different virtual screening (VS) methods, which were designed to select promising antileishmanial agents from among the entire sesquiterpene lactone (SL) dataset registered in SistematX, a web interface for managing a secondary metabolite database that is accessible by multiple platforms on the Internet. Thus, a ChEMBL dataset, including 3159 and 1569 structures that were previously tested against L. donovani amastigotes and promastigotes in vitro, respectively, was used to develop two random forest models, which performed with greater than 74% accuracy in both the cross-validation and test sets. Subsequently, a ligand-based VS assay was performed against the 1306 SistematX-registered SLs. In parallel, the crystal structures of three L. donovani target proteins, N-myristoyltransferase, ornithine decarboxylase, and mitogen-activated protein kinase 3, and a homology model of pteridine reductase 1 were used to perform a structure-based VS, using molecular docking, of the entire SistematX SL dataset. The consensus analysis of these two VS approaches resulted in the normalization of probability scores and identified 13 promising, enzyme-targeting, antileishmanial SLs from SistematX that may act against L. donovani. A combined approach based on two different virtual screening methods (structure-based and ligand-based) was performed using an in-house dataset composed of 1306 sesquiterpene lactones to identify potential antileishmanial (Leishmania donovani) structures.
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Affiliation(s)
- Chonny Herrera-Acevedo
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa, PB, 58051-900, Brazil.,Bioorganic Chemistry Laboratory, Facultad de Ciencias Básicas y Aplicadas, Universidad Militar Nueva Granada, Cajicá, 250247, Colombia
| | - Mayara Dos Santos Maia
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa, PB, 58051-900, Brazil
| | | | - Ericsson Coy-Barrera
- Bioorganic Chemistry Laboratory, Facultad de Ciencias Básicas y Aplicadas, Universidad Militar Nueva Granada, Cajicá, 250247, Colombia
| | - Luciana Scotti
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa, PB, 58051-900, Brazil
| | - Marcus Tullius Scotti
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa, PB, 58051-900, Brazil.
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