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Llorach-Pares L, Nonell-Canals A, Avila C, Sanchez-Martinez M. Computer-Aided Drug Design (CADD) to De-Orphanize Marine Molecules: Finding Potential Therapeutic Agents for Neurodegenerative and Cardiovascular Diseases. Mar Drugs 2022; 20:53. [PMID: 35049908 PMCID: PMC8781171 DOI: 10.3390/md20010053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 12/24/2021] [Accepted: 12/27/2021] [Indexed: 11/30/2022] Open
Abstract
Computer-aided drug design (CADD) techniques allow the identification of compounds capable of modulating protein functions in pathogenesis-related pathways, which is a promising line on drug discovery. Marine natural products (MNPs) are considered a rich source of bioactive compounds, as the oceans are home to much of the planet's biodiversity. Biodiversity is directly related to chemodiversity, which can inspire new drug discoveries. Therefore, natural products (NPs) in general, and MNPs in particular, have been used for decades as a source of inspiration for the design of new drugs. However, NPs present both opportunities and challenges. These difficulties can be technical, such as the need to dive or trawl to collect the organisms possessing the compounds, or biological, due to their particular marine habitats and the fact that they can be uncultivable in the laboratory. For all these difficulties, the contributions of CADD can play a very relevant role in simplifying their study, since, for example, no biological sample is needed to carry out an in-silico analysis. Therefore, the amount of natural product that needs to be used in the entire preclinical and clinical study is significantly reduced. Here, we exemplify how this combination between CADD and MNPs can help unlock their therapeutic potential. In this study, using a set of marine invertebrate molecules, we elucidate their possible molecular targets and associated therapeutic potential, establishing a pipeline that can be replicated in future studies.
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Affiliation(s)
- Laura Llorach-Pares
- Mind the Byte S.L., 08028 Barcelona, Catalonia, Spain; (L.L.-P.); (A.N.-C.)
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology and Biodiversity Research Institute (IRBio), University of Barcelona, 08028 Barcelona, Catalonia, Spain;
| | | | - Conxita Avila
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology and Biodiversity Research Institute (IRBio), University of Barcelona, 08028 Barcelona, Catalonia, Spain;
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Cuyàs E, Verdura S, Lozano-Sánchez J, Viciano I, Llorach-Parés L, Nonell-Canals A, Bosch-Barrera J, Brunet J, Segura-Carretero A, Sanchez-Martinez M, Encinar JA, Menendez JA. The extra virgin olive oil phenolic oleacein is a dual substrate-inhibitor of catechol-O-methyltransferase. Food Chem Toxicol 2019; 128:35-45. [PMID: 30935952 DOI: 10.1016/j.fct.2019.03.049] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 03/25/2019] [Accepted: 03/26/2019] [Indexed: 12/13/2022]
Abstract
Catechol-containing polyphenols present in coffee and tea, while serving as excellent substrates for catechol-O-methyltransferase (COMT)-catalyzed O-methylation, can also operate as COMT inhibitors. However, little is known about the relationship between COMT and the characteristic phenolics present in extra virgin olive oil (EVOO). We here selected the EVOO dihydroxy-phenol oleacein for a computational study of COMT-driven methylation using classic molecular docking/molecular dynamics simulations and hybrid quantum mechanical/molecular mechanics, which were supported by in vitro activity studies using human COMT. Oleacein could be superimposed onto the catechol-binding site of COMT, maintaining the interactions with the atomic positions involved in methyl transfer from the S-adenosyl-L-methionine cofactor. The transition state structure for the meta-methylation in the O5 position of the oleacein benzenediol moiety was predicted to occur preferentially. Enzyme analysis of the conversion ratio of catechol to O-alkylated guaiacol confirmed the inhibitory effect of oleacein on human COMT, which remained unaltered when tested against the protein version encoded by the functional Val158Met polymorphism of the COMT gene. Our study provides a theoretical determination of how EVOO dihydroxy-phenols can be metabolized via COMT. The ability of oleacein to inhibit COMT adds a new dimension to the physiological and therapeutic utility of EVOO secoiridoids.
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Affiliation(s)
- Elisabet Cuyàs
- ProCURE (Program Against Cancer Therapeutic Resistance), Metabolism & Cancer Group, Catalan Institute of Oncology, Girona, Spain; Girona Biomedical Research Institute (IDIBGI), Girona, Spain
| | - Sara Verdura
- ProCURE (Program Against Cancer Therapeutic Resistance), Metabolism & Cancer Group, Catalan Institute of Oncology, Girona, Spain; Girona Biomedical Research Institute (IDIBGI), Girona, Spain
| | - Jesús Lozano-Sánchez
- Department of Analytical Chemistry, Faculty of Sciences, University of Granada, Granada, Spain; Research and Development Functional Food Centre (CIDAF), PTS Granada, Granada, Spain
| | | | | | | | - Joaquim Bosch-Barrera
- Girona Biomedical Research Institute (IDIBGI), Girona, Spain; Medical Oncology, Catalan Institute of Oncology (ICO) Dr. Josep Trueta University Hospital, Girona, Spain; Department of Medical Sciences, Medical School University of Girona, Girona, Spain
| | - Joan Brunet
- Medical Oncology, Catalan Institute of Oncology (ICO) Dr. Josep Trueta University Hospital, Girona, Spain; Department of Medical Sciences, Medical School University of Girona, Girona, Spain; Hereditary Cancer Programme, Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL) L'Hospitalet del Llobregat, Barcelona, Spain; Hereditary Cancer Programme, Catalan Institute of Oncology (ICO) Girona Biomedical Research Institute (IDIBGI), Girona, Spain
| | - Antonio Segura-Carretero
- Department of Analytical Chemistry, Faculty of Sciences, University of Granada, Granada, Spain; Research and Development Functional Food Centre (CIDAF), PTS Granada, Granada, Spain
| | | | - José Antonio Encinar
- Institute of Research, Development and Innovation in Biotechnology of Elche (IDiBE) and Molecular and Cell Biology Institute (IBMC), Miguel Hernández University (UMH), Elche, Spain.
| | - Javier A Menendez
- ProCURE (Program Against Cancer Therapeutic Resistance), Metabolism & Cancer Group, Catalan Institute of Oncology, Girona, Spain; Girona Biomedical Research Institute (IDIBGI), Girona, Spain.
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Martí S, Bastida A, Świderek K. Theoretical Studies on Mechanism of Inactivation of Kanamycin A by 4'-O-Nucleotidyltransferase. Front Chem 2019; 6:660. [PMID: 30761287 PMCID: PMC6361787 DOI: 10.3389/fchem.2018.00660] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 12/18/2018] [Indexed: 01/31/2023] Open
Abstract
This work is focused on mechanistic studies of the transfer of an adenylyl group (Adenoside-5'-monophosfate) from adenosine 5'-triphosphate (ATP) to a OH-4' hydroxyl group of an antibiotic. Using hybrid quantum mechanics/molecular mechanics (QM/MM) techniques, we study the substrate and base-assisted mechanisms of the inactivation process of kanamycin A (KAN) catalyzed by 4'-O-Nucleotidyltransferase [ANT(4')], an active enzyme against almost all aminoglycoside antibiotics. Free energy surfaces, obtained with Free Energy Perturbation methods at the M06-2X/MM level of theory, show that the most favorable reaction path presents a barrier of 12.2 kcal·mol-1 that corresponds to the concerted activation of O4' from KAN by Glu145. In addition, the primary and secondary 18O kinetic isotope effects (KIEs) have been computed for bridge O3α, and non-bridge O1α, O2α, and O5' atoms of ATP. The observed normal 1°-KIE of 1.2% and 2°-KIE of 0.07% for the Glu145-assisted mechanism are in very good agreement with experimentally measured data. Additionally, based on the obtained results, the role of electrostatic and compression effects in enzymatic catalysis is discussed.
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Affiliation(s)
- Sergio Martí
- Departament de Química Física i Analítica, Universitat Jaume I, Castelló de La Plana, Spain
| | - Agatha Bastida
- Departamento de Química Bio-orgánica, Instituto de Química Orgánica General (CSIC), Madrid, Spain
| | - Katarzyna Świderek
- Departament de Química Física i Analítica, Universitat Jaume I, Castelló de La Plana, Spain
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Wang X, Shi J, Liu Y. Oxidative Rearrangement Mechanism of Pentalenolactone F Catalyzed by Cytochrome P450 CYP161C2 (PntM). Inorg Chem 2018; 57:8933-8941. [PMID: 29999312 DOI: 10.1021/acs.inorgchem.8b00860] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The CYP161C2 (PntM) from Streptomyces arenae is a member of the cytochrome P450 enzymes, which catalyzes the unusual oxidative rearrangement of pentalenolactone F (1) to the sesquiterpenoid antibiotic pentalenolactone (3). On the basis of the crystal structure of PntM bound with substrate, quantum mechanical/molecular mechanics (QM/MM) calculations have been performed to explore the detailed mechanism of PntM-catalyzed oxidative rearrangement. The conversion from pentalenolactone F (1) to pentalenolactone (3) involves the stereospecific removal of the H-1 si from 1, the syn-1,2-migration of the 2 si methyl group, and the antarafacial loss of H-3 re. The abstraction of H-1 si by Cpd I is calculated to be rate limiting with an energy barrier of 20.3 kcal/mol, which basically agrees with the estimated free energy barrier from experiments (18.6 kcal/mol). It is the unfavorable geometry of Fe-OH-C1 that blocks the oxygen rebound reaction, and the subsequent intramolecular syn-1,2-methyl migration is accompanied by an electron transfer from the substrate to the porphyrin ring via an Fe-OH group, generating the carbocation intermediate. Owing to the positive charge, the intermediate can easily lose a proton to form the final products. Our calculation results indicate that both the carboxyl group of porphyrin and Fe-OH can act as bases to accept the proton of the substrate. The target product pentalenolactone and the three isomeric byproducts correspond to four different modes of deprotonation.
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Affiliation(s)
- Xiya Wang
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shandong University , Jinan , Shandong 250100 , People's Republic of China
| | - Junyou Shi
- College of Chemistry and Environmental Science , Qujing Normal University , Qujing , Yunnan 655011 , People's Republic of China
| | - Yongjun Liu
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shandong University , Jinan , Shandong 250100 , People's Republic of China
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Spinello A, Pavlin M, Casalino L, Magistrato A. A Dehydrogenase Dual Hydrogen Abstraction Mechanism Promotes Estrogen Biosynthesis: Can We Expand the Functional Annotation of the Aromatase Enzyme? Chemistry 2018; 24:10840-10849. [DOI: 10.1002/chem.201802025] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Indexed: 01/26/2023]
Affiliation(s)
- Angelo Spinello
- CNR-IOM-Democritos, c/o International School for Advanced Studies (SISSA); via Bonomea 265 34136 Trieste Italy
| | - Matic Pavlin
- CNR-IOM-Democritos, c/o International School for Advanced Studies (SISSA); via Bonomea 265 34136 Trieste Italy
| | - Lorenzo Casalino
- International School for Advanced Studies (SISSA); via Bonomea 265 34136 Trieste Italy
| | - Alessandra Magistrato
- CNR-IOM-Democritos, c/o International School for Advanced Studies (SISSA); via Bonomea 265 34136 Trieste Italy
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Alberro N, Torrent-Sucarrat M, Arrieta A, Rubiales G, Cossío FP. Density Functional Theory Study on the Demethylation Reaction between Methylamine, Dimethylamine, Trimethylamine, and Tamoxifen Catalyzed by a Fe(IV)-Oxo Porphyrin Complex. J Phys Chem A 2018; 122:1658-1671. [PMID: 29320849 DOI: 10.1021/acs.jpca.7b10654] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
In this work, we studied computationally the N-demethylation reaction of methylamine, dimethylamine, and trimethylamine as archetypal examples of primary, secondary, and tertiary amines catalyzed by high-field low-spin Fe-containing enzymes such as cytochromes P450. Using DFT calculations, we found that the expected C-H hydroxylation process was achieved for trimethylamine. When dimethylamine and methylamine were studied, two different reaction mechanisms (C-H hydroxylation and a double hydrogen atom transfer) were computed to be energetically accessible and both are equally preferred. Both processes led to the formation of formaldehyde and the N-demethylated substrate. Finally, as an illustrative example, the relative contribution of the three primary oxidation routes of tamoxifen was rationalized through energetic barriers obtained from density functional calculations and docking experiments involving CYP3A4 and CYP2D6 isoforms. We found that the N-demethylation process was the intrinsically favored one, whereas other oxidation reactions required most likely preorganization imposed by the residues close to the active sites.
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Affiliation(s)
- Nerea Alberro
- Department of Organic Chemistry I, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Centro de Innovación en Química Avanzada (ORFEO-CINQA) , Manuel Lardizabal Ibilbidea 3, 20018 San Sebastián/Donostia, Spain
| | - Miquel Torrent-Sucarrat
- Department of Organic Chemistry I, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Centro de Innovación en Química Avanzada (ORFEO-CINQA) , Manuel Lardizabal Ibilbidea 3, 20018 San Sebastián/Donostia, Spain.,Donostia International Physics Center (DIPC) , Manuel Lardizabal Ibilbidea 4, 20018 San Sebastián/Donostia, Spain.,Ikerbasque, Basque Foundation for Science , María Díaz de Haro 3, 6°, 48013 Bilbao, Spain
| | - Ana Arrieta
- Department of Organic Chemistry I, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Centro de Innovación en Química Avanzada (ORFEO-CINQA) , Manuel Lardizabal Ibilbidea 3, 20018 San Sebastián/Donostia, Spain
| | - Gloria Rubiales
- Department of Organic Chemistry I, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Centro de Innovación en Química Avanzada (ORFEO-CINQA) , Manuel Lardizabal Ibilbidea 3, 20018 San Sebastián/Donostia, Spain
| | - Fernando P Cossío
- Department of Organic Chemistry I, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Centro de Innovación en Química Avanzada (ORFEO-CINQA) , Manuel Lardizabal Ibilbidea 3, 20018 San Sebastián/Donostia, Spain.,Donostia International Physics Center (DIPC) , Manuel Lardizabal Ibilbidea 4, 20018 San Sebastián/Donostia, Spain
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Viciano I, Martí S. Theoretical Study of the Mechanism of Exemestane Hydroxylation Catalyzed by Human Aromatase Enzyme. J Phys Chem B 2016; 120:3331-43. [PMID: 26972150 DOI: 10.1021/acs.jpcb.6b01014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human aromatase (CYP19A1) aromatizes the androgens to form estrogens via a three-step oxidative process. The estrogens are necessary in humans, mainly in women, because of the role they play in sexual and reproductive development. However, these also are involved in the development and growth of hormone-dependent breast cancer. Therefore, inhibition of the enzyme aromatase, by means of drugs known as aromatase inhibitors, is the frontline therapy for these types of cancers. Exemestane is a suicidal third-generation inhibitor of aromatase, currently used in breast cancer treatment. In this study, the hydroxylation of exemestane catalyzed by aromatase has been studied by means of hybrid QM/MM methods. The Free Energy Perturbation calculations provided a free energy of activation for the hydrogen abstraction step (rate-limiting step) of 17 kcal/mol. The results reveal that the hydroxylation of exemestane is not the inhibition stage, suggesting a possible competitive mechanism between the inhibitor and the natural substrate androstenedione in the first catalytic subcycle of the enzyme. Furthermore, the analysis of the interaction energy for the substrate and the cofactor in the active site shows that the role of the enzymatic environment during this reaction consists of a transition state stabilization by means of electrostatic effects.
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Affiliation(s)
- Ignacio Viciano
- Departament de Química Física i Analítica, Universitat Jaume I , 12071 Castelló, Spain
| | - Sergio Martí
- Departament de Química Física i Analítica, Universitat Jaume I , 12071 Castelló, Spain
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