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Khalymbadzha IA, Fatykhov RF, Butorin II, Sharapov AD, Potapova AP, Muthipeedika NJ, Zyryanov GV, Melekhin VV, Tokhtueva MD, Deev SL, Kukhanova MK, Mochulskaya NN, Tsurkan MV. Bioinspired Pyrano[2,3- f]chromen-8-ones: Ring C-Opened Analogues of Calanolide A: Synthesis and Anti-HIV-1 Evaluation. Biomimetics (Basel) 2024; 9:44. [PMID: 38248618 PMCID: PMC10813249 DOI: 10.3390/biomimetics9010044] [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: 12/08/2023] [Revised: 12/23/2023] [Accepted: 01/09/2024] [Indexed: 01/23/2024] Open
Abstract
We have designed and synthesized a series of bioinspired pyrano[2,3-f]coumarin-based Calanolide A analogs with anti-HIV activity. The design of these new calanolide analogs involved incorporating nitrogen heterocycles or aromatic groups in lieu of ring C, effectively mimicking and preserving their bioactive properties. Three directions for the synthesis were explored: reaction of 5-hydroxy-2,2-dimethyl-10-propyl-2H,8H-pyrano[2,3-f]chromen-8-one with (i) 1,2,4-triazines, (ii) sulfonylation followed by Suzuki cross-coupling with (het)aryl boronic acids, and (iii) aminomethylation by Mannich reaction. Antiviral assay of the synthesized compounds showed that compound 4 has moderate activity against HIV-1 on enzymes and poor activity on the cell model. A molecular docking study demonstrates a good correlation between in silico and in vitro HIV-1 reverse transcriptase (RT) activity of the compounds when docked to the nonnucleoside RT inhibitor binding site, and alternative binding modes of the considered analogs of Calanolide A were established.
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Affiliation(s)
- Igor A. Khalymbadzha
- Department of Organic and Biomolecular Chemistry, Ural Federal University, 620002 Yekaterinburg, Russia; (R.F.F.); (I.I.B.); (A.D.S.); (A.P.P.); (N.J.M.); (G.V.Z.); (V.V.M.); (M.D.T.); (S.L.D.); (N.N.M.)
| | - Ramil F. Fatykhov
- Department of Organic and Biomolecular Chemistry, Ural Federal University, 620002 Yekaterinburg, Russia; (R.F.F.); (I.I.B.); (A.D.S.); (A.P.P.); (N.J.M.); (G.V.Z.); (V.V.M.); (M.D.T.); (S.L.D.); (N.N.M.)
| | - Ilya I. Butorin
- Department of Organic and Biomolecular Chemistry, Ural Federal University, 620002 Yekaterinburg, Russia; (R.F.F.); (I.I.B.); (A.D.S.); (A.P.P.); (N.J.M.); (G.V.Z.); (V.V.M.); (M.D.T.); (S.L.D.); (N.N.M.)
| | - Ainur D. Sharapov
- Department of Organic and Biomolecular Chemistry, Ural Federal University, 620002 Yekaterinburg, Russia; (R.F.F.); (I.I.B.); (A.D.S.); (A.P.P.); (N.J.M.); (G.V.Z.); (V.V.M.); (M.D.T.); (S.L.D.); (N.N.M.)
| | - Anastasia P. Potapova
- Department of Organic and Biomolecular Chemistry, Ural Federal University, 620002 Yekaterinburg, Russia; (R.F.F.); (I.I.B.); (A.D.S.); (A.P.P.); (N.J.M.); (G.V.Z.); (V.V.M.); (M.D.T.); (S.L.D.); (N.N.M.)
| | - Nibin Joy Muthipeedika
- Department of Organic and Biomolecular Chemistry, Ural Federal University, 620002 Yekaterinburg, Russia; (R.F.F.); (I.I.B.); (A.D.S.); (A.P.P.); (N.J.M.); (G.V.Z.); (V.V.M.); (M.D.T.); (S.L.D.); (N.N.M.)
| | - Grigory V. Zyryanov
- Department of Organic and Biomolecular Chemistry, Ural Federal University, 620002 Yekaterinburg, Russia; (R.F.F.); (I.I.B.); (A.D.S.); (A.P.P.); (N.J.M.); (G.V.Z.); (V.V.M.); (M.D.T.); (S.L.D.); (N.N.M.)
| | - Vsevolod V. Melekhin
- Department of Organic and Biomolecular Chemistry, Ural Federal University, 620002 Yekaterinburg, Russia; (R.F.F.); (I.I.B.); (A.D.S.); (A.P.P.); (N.J.M.); (G.V.Z.); (V.V.M.); (M.D.T.); (S.L.D.); (N.N.M.)
- Department of Medical Biology and Genetics, Ural State Medical University, 620028 Yekaterinburg, Russia
| | - Maria D. Tokhtueva
- Department of Organic and Biomolecular Chemistry, Ural Federal University, 620002 Yekaterinburg, Russia; (R.F.F.); (I.I.B.); (A.D.S.); (A.P.P.); (N.J.M.); (G.V.Z.); (V.V.M.); (M.D.T.); (S.L.D.); (N.N.M.)
| | - Sergey L. Deev
- Department of Organic and Biomolecular Chemistry, Ural Federal University, 620002 Yekaterinburg, Russia; (R.F.F.); (I.I.B.); (A.D.S.); (A.P.P.); (N.J.M.); (G.V.Z.); (V.V.M.); (M.D.T.); (S.L.D.); (N.N.M.)
| | | | - Nataliya N. Mochulskaya
- Department of Organic and Biomolecular Chemistry, Ural Federal University, 620002 Yekaterinburg, Russia; (R.F.F.); (I.I.B.); (A.D.S.); (A.P.P.); (N.J.M.); (G.V.Z.); (V.V.M.); (M.D.T.); (S.L.D.); (N.N.M.)
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Flachsenberg F, Ehrt C, Gutermuth T, Rarey M. Redocking the PDB. J Chem Inf Model 2024; 64:219-237. [PMID: 38108627 DOI: 10.1021/acs.jcim.3c01573] [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: 12/19/2023]
Abstract
Molecular docking is a standard technique in structure-based drug design (SBDD). It aims to predict the 3D structure of a small molecule in the binding site of a receptor (often a protein). Despite being a common technique, it often necessitates multiple tools and involves manual steps. Here, we present the JAMDA preprocessing and docking workflow that is easy to use and allows fully automated docking. We evaluate the JAMDA docking workflow on binding sites extracted from the complete PDB and derive key factors determining JAMDA's docking performance. With that, we try to remove most of the bias due to manual intervention and provide a realistic estimate of the redocking performance of our JAMDA preprocessing and docking workflow for any PDB structure. On this large PDBScan22 data set, our JAMDA workflow finds a pose with an RMSD of at most 2 Å to the crystal ligand on the top rank for 30.1% of the structures. When applying objective structure quality filters to the PDBScan22 data set, the success rate increases to 61.8%. Given the prepared structures from the JAMDA preprocessing pipeline, both JAMDA and the widely used AutoDock Vina perform comparably on this filtered data set (the PDBScan22-HQ data set).
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Affiliation(s)
- Florian Flachsenberg
- Universität Hamburg, ZBH - Center for Bioinformatics, Bundesstraße 43, 20146 Hamburg, Germany
| | - Christiane Ehrt
- Universität Hamburg, ZBH - Center for Bioinformatics, Bundesstraße 43, 20146 Hamburg, Germany
| | - Torben Gutermuth
- Universität Hamburg, ZBH - Center for Bioinformatics, Bundesstraße 43, 20146 Hamburg, Germany
| | - Matthias Rarey
- Universität Hamburg, ZBH - Center for Bioinformatics, Bundesstraße 43, 20146 Hamburg, Germany
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Şen A, Özbeyli D, Teralı K, Göger F, Yıldırım A, Ertaş B, Doğan A, Bitiş L, Şener G. Protective effects of Rubus tereticaulis leaves ethanol extract on rats with ulcerative colitis and bio-guided isolation of its active compounds: A combined in silico, in vitro and in vivo study. Chem Biol Interact 2023; 369:110263. [PMID: 36375516 DOI: 10.1016/j.cbi.2022.110263] [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: 09/11/2022] [Revised: 11/01/2022] [Accepted: 11/11/2022] [Indexed: 11/13/2022]
Abstract
The aim of this study was to evaluate the therapeutic effect of active ethanol extract obtained from the leaves of Rubus tereticaulis (RTME) against colitis, and to purify major compounds from this extract by bioassay-directed isolation. Rats with colitis induced via intra-rectal acetic acid administration (5%, v/v) received RTME or sulfasalazine for three consecutive days. On day four, all rats were decapitated, and the colonic tissue samples were collected for macroscopic score, colon weight, reduced glutathione (GSH), myeloperoxidase (MPO), and malondialdehyde (MDA) analyses. The active compounds and chemical composition of RTME were determined by bio-guided isolation and LC-MS/MS, respectively. Compared to the colitis group, the rats treated with RTME displayed significantly lowered macroscopic scores and colon wet weights (p < 0.001). These effects were confirmed biochemically by a decrease in colonic MPO activity (p < 0.001), MDA levels (p < 0.001), and an increase in GSH levels (p < 0.001). Kaempferol-3-O-β-d-glucuronide (RT1) and quercetin-3-O-β-d-glucuronide (RT2) were found to be the major compounds of RTME, as evidenced by in vitro anti-inflammatory and antioxidant activity-guided isolation. Their anti-inflammatory/antioxidant activities were also predicted by docking simulations. Additionally, quinic acid, 5-caffeoylquinic acid, quercetin pentoside, quercetin glucoside, quercetin-3-O-β-d-glucuronide, kaempferol-3-O-β-d-glucuronide, and kaempferol rutinoside were identified in RTME via using LC-MS/MS. RT2, along with other compounds, may be responsible for the observed protective action of RTME against colitis. This study represents the first report on the beneficial effects of RTME in an experimental model of colitis and highlights the potential future use of RTME as a natural alternative to alleviate colitis.
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Affiliation(s)
- Ali Şen
- Department of Pharmacognosy, Faculty of Pharmacy, Marmara University, Istanbul, Turkey.
| | - Dilek Özbeyli
- Department of Medical Services and Techniques, Vocational School of Health Services, Marmara University, Istanbul, Turkey.
| | - Kerem Teralı
- Department of Medical Biochemistry, Faculty of Medicine, Cyprus International University, 99258, Nicosia, Cyprus.
| | - Fatih Göger
- Department of Pharmaceutical Botany, Faculty of Pharmacy, Afyonkarahisar Health Sciences University, Afyonkarahisar, Turkey.
| | - Aybeniz Yıldırım
- Department of Pharmacognosy, Faculty of Pharmacy, Marmara University, Istanbul, Turkey.
| | - Büşra Ertaş
- Department of Pharmacology, Faculty of Pharmacy, Marmara University, Istanbul, Turkey.
| | - Ahmet Doğan
- Department of Pharmaceutical Botany, Faculty of Pharmacy, Marmara University, Istanbul, Turkey.
| | - Leyla Bitiş
- Department of Pharmacognosy, Faculty of Pharmacy, Marmara University, Istanbul, Turkey.
| | - Göksel Şener
- Department of Pharmacology, Faculty of Pharmacy, Fenerbahce University, Istanbul, 34758, Turkey.
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Demirci F, Teralı K, Karadağ AE, Biltekin SN, Ak Sakallı E, Demirci B, Koşar M, Başer KHC. In Vitro and In Silico Evaluation of ACE2 and LOX Inhibitory Activity of Origanum Essential Oils and Carvacrol. PLANTA MEDICA 2022. [PMID: 35439836 DOI: 10.1055/a-1828-2479] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Origanum spp. are used both for culinary purposes and for their biological activities. In this study, commercial Origanum majorana, Origanum minutiflorum, Origanum vulgare, and Origanum onites essential oils and their prominent constituent carvacrol were evaluated for their in vitro and in silico angiotensin-converting enzyme 2 and lipoxygenase enzyme inhibitory potentials. The essential oils were analysed by gas chromatography-flame ionisation detection and gas chromatography-mass spectrometry, where carvacrol was identified as the major component (62 - 81%), confirming the quality. In vitro enzyme inhibition assays were conducted both with the essential oils (20 µg/mL) and with carvacrol (5 µg/mL). The comparative values of angiotensin-converting enzyme 2 percent inhibition for O. majorana, O. minutiflorum, O. vulgare, and O. onites essential oils were determined as 85.5, 79.1, 74.3, and 42.8%, respectively. As a result of the enzyme assays, carvacrol showed 90.7% in vitro angiotensin-converting enzyme 2 inhibitory activity. The in vitro lipoxygenase inhibition of the essential oils (in the same order) was 89.4, 78.9, 81.1, and 73.5%, respectively, where carvacrol showed 74.8% inhibition. In addition, protein-ligand docking and interaction profiling was used to gain structural and mechanistic insights into the angiotensin-converting enzyme 2 and lipoxygenase inhibitory potentials of major Origanum essential oil constituents. The in silico findings agreed with the significant enzyme inhibition activity observed in vitro. Further in vivo studies are suggested to confirm the safety and efficacy of the oils.
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Affiliation(s)
- Fatih Demirci
- Department of Pharmacognosy, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey
- Faculty of Pharmacy, Eastern Mediterranean University, Famagusta, N. Cyprus, Mersin 10, Turkey
| | - Kerem Teralı
- Department of Medical Biochemistry, Faculty of Medicine, Girne American University, Kyrenia, Mersin 10, Turkey
| | - Ayşe Esra Karadağ
- Department of Pharmacognosy, School of Pharmacy, Istanbul Medipol University, Beykoz, Istanbul, Turkey
- Graduate School of Health Sciences, Anadolu University, Eskişehir, Turkey
| | - Sevde Nur Biltekin
- Department of Pharmaceutical Microbiology, School of Pharmacy, Istanbul Medipol University, Beykoz, Istanbul, Turkey
- Institute of Sciences, Istanbul University, Istanbul, Turkey
| | - Ezgi Ak Sakallı
- Faculty of Pharmacy, Eastern Mediterranean University, Famagusta, N. Cyprus, Mersin 10, Turkey
| | - Betül Demirci
- Department of Pharmacognosy, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey
| | - Müberra Koşar
- Faculty of Pharmacy, Eastern Mediterranean University, Famagusta, N. Cyprus, Mersin 10, Turkey
| | - K Hüsnü Can Başer
- Department of Pharmacognosy, Faculty of Pharmacy, Near East University, Nicosia, N. Cyprus, Mersin 10, Turkey
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Faria AVS, Fonseca EMB, Fernandes-Oliveira PDS, de Lima TI, Clerici SP, Justo GZ, Silveira LR, Durán N, Ferreira-Halder CV. Violacein switches off low molecular weight tyrosine phosphatase and rewires mitochondria in colorectal cancer cells. Bioorg Chem 2022; 127:106000. [PMID: 35853296 DOI: 10.1016/j.bioorg.2022.106000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 11/26/2022]
Abstract
In the last decade, emerging evidence has shown that low molecular weight protein tyrosine phosphatase (LMWPTP) not only contributes to the progression of cancer but is associated with prostate low survival rate and colorectal cancer metastasis. We report that LMWPTP favors the glycolytic profile in some tumors. Therefore, the focus of the present study was to identify metabolic enzymes that correlate with LMWPTP expression in patient samples. Exploratory data analysis from RNA-seq, proteomics, and histology staining, confirmed the higher expression of LMWPTP in CRC. Our descriptive statistical analyses indicate a positive expression correlation between LMWPTP and energy metabolism enzymes such as acetyl-CoA carboxylase (ACC) and fatty acid synthase (FASN). In addition, we examine the potential of violacein to reprogram energetic metabolism and LMWPTP activity. Violacein treatment induced a shift of glycolytic to oxidative metabolism associated with alteration in mitochondrial efficiency, as indicated by higher oxygen consumption rate. Particularly, violacein treated cells displayed higher proton leak and ATP-linked oxygen consumption rate (OCR) as an indicator of the OXPHOS preference. Notably, violacein is able to bind and inhibit LMWPTP. Since the LMWPTP acts as a hub of signaling pathways that offer tumor cells invasive advantages, such as survival and the ability to migrate, our findings highlight an unexplored potential of violacein in circumventing the metabolic plasticity of tumor cells.
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Affiliation(s)
- Alessandra V S Faria
- Department of Biochemistry and Tissue Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Emanuella M B Fonseca
- Department of Biochemistry and Tissue Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil; Federal Institute of Education, Science and Technology of São Paulo (IFSP), São Roque, São Paulo, Brazil
| | | | - Tanes I de Lima
- Department of Structural and Functional Biology, University of Campinas, (UNICAMP), Campinas, SP, Brazil
| | - Stefano P Clerici
- Department of Biochemistry and Tissue Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Giselle Z Justo
- Department of Pharmaceutical Sciences and Department of Biochemistry, Federal University of São Paulo (UNIFESP), São Paulo, SP, Brazil
| | - Leonardo R Silveira
- Department of Structural and Functional Biology, University of Campinas, (UNICAMP), Campinas, SP, Brazil
| | - Nelson Durán
- Laboratory of Urogenital Carcinogenesis and Immunotherapy, Department of Structural and Functional Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil; Nanomedicine Research Unit (Nanomed), Center for Natural and Human Sciences (CCNH), Federal University of ABC (UFABC), Santo André, Brazil
| | - Carmen V Ferreira-Halder
- Department of Biochemistry and Tissue Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil.
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Anti-Virulence Activity of 3,3′-Diindolylmethane (DIM): A Bioactive Cruciferous Phytochemical with Accelerated Wound Healing Benefits. Pharmaceutics 2022; 14:pharmaceutics14050967. [PMID: 35631553 PMCID: PMC9144697 DOI: 10.3390/pharmaceutics14050967] [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: 03/25/2022] [Revised: 04/24/2022] [Accepted: 04/28/2022] [Indexed: 01/27/2023] Open
Abstract
Antimicrobial resistance is among the top global health problems with antibacterial resistance currently representing the major threat both in terms of occurrence and complexity. One reason current treatments of bacterial diseases are ineffective is the occurrence of protective and resistant biofilm structures. Phytochemicals are currently being reviewed for newer anti-virulence agents. In the present study, we aimed to investigate the anti-virulence activity of 3,3′-diindolylmethane (DIM), a bioactive cruciferous phytochemical. Using a series of in vitro assays on major Gram-negative pathogens, including transcriptomic analysis, and in vivo porcine wound studies as well as in silico experiments, we show that DIM has anti-biofilm activity. Following DIM treatment, our findings show that biofilm formation of two of the most prioritized bacterial pathogens Acinetobacter baumannii and Pseudomonas aeruginosa was inhibited respectively by 65% and 70%. Combining the antibiotic tobramycin with DIM enabled a high inhibition (94%) of P. aeruginosa biofilm. A DIM-based formulation, evaluated for its wound-healing efficacy on P. aeruginosa-infected wounds, showed a reduction in its bacterial bioburden, and wound size. RNA-seq was used to evaluate the molecular mechanism underlying the bacterial response to DIM. The gene expression profile encompassed shifts in virulence and biofilm-associated genes. A network regulation analysis showed the downregulation of 14 virulence-associated super-regulators. Quantitative real-time PCR verified and supported the transcriptomic results. Molecular docking and interaction profiling indicate that DIM can be accommodated in the autoinducer- or DNA-binding pockets of the virulence regulators making multiple non-covalent interactions with the key residues that are involved in ligand binding. DIM treatment prevented biofilm formation and destroyed existing biofilm without affecting microbial death rates. This study provides evidence for bacterial virulence attenuation by DIM.
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Schöning-Stierand K, Diedrich K, Ehrt C, Flachsenberg F, Graef J, Sieg J, Penner P, Poppinga M, Ungethüm A, Rarey M. ProteinsPlus: a comprehensive collection of web-based molecular modeling tools. Nucleic Acids Res 2022; 50:W611-W615. [PMID: 35489057 PMCID: PMC9252762 DOI: 10.1093/nar/gkac305] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 04/05/2022] [Accepted: 04/19/2022] [Indexed: 12/21/2022] Open
Abstract
Upon the ever-increasing number of publicly available experimentally determined and predicted protein and nucleic acid structures, the demand for easy-to-use tools to investigate these structural models is higher than ever before. The ProteinsPlus web server (https://proteins.plus) comprises a growing collection of molecular modeling tools focusing on protein–ligand interactions. It enables quick access to structural investigations ranging from structure analytics and search methods to molecular docking. It is by now well-established in the community and constantly extended. The server gives easy access not only to experts but also to students and occasional users from the field of life sciences. Here, we describe its recently added new features and tools, beyond them a novel method for on-the-fly molecular docking and a search method for single-residue substitutions in local regions of a protein structure throughout the whole Protein Data Bank. Finally, we provide a glimpse into new avenues for the annotation of AlphaFold structures which are directly accessible via a RESTful service on the ProteinsPlus web server.
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Affiliation(s)
| | | | | | | | | | | | - Patrick Penner
- Universität Hamburg, ZBH - Center for Bioinformatics, Bundesstraße 43, 20146 Hamburg, Germany
| | - Martin Poppinga
- Universität Hamburg, ZBH - Center for Bioinformatics, Bundesstraße 43, 20146 Hamburg, Germany
- Universität Hamburg, Department of Informatics, Vogt-Kölln-Straße 30, 22527 Hamburg, Germany
| | - Annett Ungethüm
- Universität Hamburg, Center for Data and Computing in Natural Sciences (CDCS), Notkestraße 11, 22607 Hamburg, Germany
| | - Matthias Rarey
- To whom correspondence should be addressed. Tel: +49 40 428387350; Fax: +49 40 428387352;
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8
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Aykac A, Teralı K, Özbeyli D, Ede S, Albayrak Ö, Başer KHC, Şener G. A multi-parameter evaluation of the neuroprotective and cognitive-enhancing effects of Origanum onites L. (Turkish Oregano) essential oil on scopolamine-induced amnestic rats. Metab Brain Dis 2022; 37:1041-1055. [PMID: 35201555 DOI: 10.1007/s11011-022-00933-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/09/2022] [Indexed: 10/19/2022]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder characterized by progressive deterioration of cognitive functions (dementia) and represents a growing public health concern since the population in the age groups at risk is increasing. The latter raises an urgent need to translate research findings in the basic brain and behavioral sciences into anti-AD drugs and disease-modifying therapies. Origanum onites (L.), also called Turkish oregano, is a perennial and herbaceous plant species grown for centuries for medicinal, cosmetic and culinary purposes. This is the first study to investigate the putative neuroprotective and pro-cognitive activities of O. onites essential oil (OOEO) against scopolamine-induced amnesia of AD-type in Wistar albino rats. The results of behavioral tests revealed that OOEO administration was able to significantly alleviate learning and memory impairments induced by scopolamine in vivo. The observed effects could be attributed to inhibition of acetylcholinesterase activity, attenuation of oxidative stress and prevention of neuronal apoptosis in the hippocampus and frontal cortex of AD rats. Modulation of pro-inflammatory enzymes, including cyclooxygenase-2, inducible nitric oxide synthase and myeloperoxidase, might further contribute to the neuroprotective properties of OEOO, as predicted by our in silico models. These findings offer novel insights into the therapeutic potential of OEOO in patients with AD.
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Affiliation(s)
- Asli Aykac
- Department of Biophysics, Near East University, Near East Boulevard, 99138, Nicosia, Cyprus.
| | - Kerem Teralı
- Department of Medical Biochemistry, Faculty of Medicine, Girne American University, Kyrenia, Cyprus
| | - Dilek Özbeyli
- Department of Medical Pathology Techniques, Vocational School of Health Services, Marmara University, Istanbul, Turkey
| | - Seren Ede
- Department of Pharmacology, Faculty of Pharmacy, Marmara University, Istanbul, Turkey
| | - Ömercan Albayrak
- Department of Pharmacology, Faculty of Pharmacy, Marmara University, Istanbul, Turkey
| | - Kemal Hüsnü Can Başer
- Department of Pharmacognosy, Faculty of Pharmacy, Near East University, Nicosia, Cyprus
| | - Göksel Şener
- Department of Pharmacology, Fenerbahce University, Istanbul, Turkey
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Isolation, Characterization and In Silico Studies of Secondary Metabolites from the Whole Plant of Polygala inexpectata Peşmen & Erik. Molecules 2022; 27:molecules27030684. [PMID: 35163950 PMCID: PMC8838668 DOI: 10.3390/molecules27030684] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/13/2022] [Accepted: 01/15/2022] [Indexed: 02/06/2023] Open
Abstract
Polygala species are frequently used worldwide in the treatment of various diseases, such as inflammatory and autoimmune disorders as well as metabolic and neurodegenerative diseases, due to the large number of secondary metabolites they contain. The present study was performed on Polygala inexpectata, which is a narrow endemic species for the flora of Turkey, and resulted in the isolation of nine known compounds, 6,3'-disinapoyl-sucrose (1), 6-O-sinapoyl,3'-O-trimethoxy-cinnamoyl-sucrose (tenuifoliside C) (2), 3'-O-(O-methyl-feruloyl)-sucrose (3), 3'-O-(sinapoyl)-sucrose (4), 3'-O-trimethoxy-cinnamoyl-sucrose (glomeratose) (5), 3'-O-feruloyl-sucrose (sibiricose A5) (6), sinapyl alcohol 4-O-glucoside (syringin or eleutheroside B) (7), liriodendrin (8), and 7,4'-di-O-methylquercetin-3-O-β-rutinoside (ombuin 3-O-rutinoside or ombuoside) (9). The structures of the compounds were determined by the spectroscopic methods including 1D-NMR (1H NMR, 13C NMR, DEPT-135), 2D-NMR (COSY, NOESY, HSQC, HMBC), and HRMS. The isolated compounds were shown in an in silico setting to be accommodated well within the inhibitor-binding pockets of myeloperoxidase and inducible nitric oxide synthase and anchored mainly through hydrogen-bonding interactions and π-effects. It is therefore plausible to suggest that the previously established anti-inflammatory properties of some Polygala-derived phytochemicals may be due, in part, to the modulation of pro-inflammatory enzyme activities.
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Assessing the Molecular Targets and Mode of Action of Furanone C-30 on Pseudomonas aeruginosa Quorum Sensing. Molecules 2021; 26:molecules26061620. [PMID: 33803983 PMCID: PMC7998126 DOI: 10.3390/molecules26061620] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/11/2021] [Accepted: 03/13/2021] [Indexed: 11/17/2022] Open
Abstract
Quorum sensing (QS), a sophisticated system of bacterial communication that depends on population density, is employed by many pathogenic bacteria to regulate virulence. In view of the current reality of antibiotic resistance, it is expected that interfering with QS can address bacterial pathogenicity without stimulating the incidence of resistance. Thus, harnessing QS inhibitors has been considered a promising approach to overriding bacterial infections and combating antibiotic resistance that has become a major threat to public healthcare around the globe. Pseudomonas aeruginosa is one of the most frequent multidrug-resistant bacteria that utilize QS to control virulence. Many natural compounds, including furanones, have demonstrated strong inhibitory effects on several pathogens via blocking or attenuating QS. While the natural furanones show no activity against P. aeruginosa, furanone C-30, a brominated derivative of natural furanone compounds, has been reported to be a potent inhibitor of the QS system of the notorious opportunistic pathogen. In the present study, we assess the molecular targets and mode of action of furanone C-30 on P. aeruginosa QS system. Our results suggest that furanone C-30 binds to LasR at the ligand-binding site but fails to establish interactions with the residues crucial for the protein's productive conformational changes and folding, thus rendering the protein dysfunctional. We also show that furanone C-30 inhibits RhlR, independent of LasR, suggesting a complex mechanism for the agent beyond what is known to date.
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Flachsenberg F, Meyder A, Sommer K, Penner P, Rarey M. A Consistent Scheme for Gradient-Based Optimization of Protein -Ligand Poses. J Chem Inf Model 2020; 60:6502-6522. [PMID: 33258376 DOI: 10.1021/acs.jcim.0c01095] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Scoring and numerical optimization of protein-ligand poses is an integral part of docking tools. Although many scoring functions exist, many of them are not continuously differentiable and they are rarely explicitly analyzed with respect to their numerical optimization behavior. Here, we present a consistent scheme for pose scoring and gradient-based pose optimization. It consists of a novel variant of the BFGS algorithm enabling step-length control, named LSL-BFGS (limited step length BFGS), and the empirical JAMDA scoring function designed for pose prediction and good numerical optimizability. The JAMDA scoring function shows a high pose prediction performance in the CASF-2016 docking power benchmark, top-ranking a pose with an RMSD of ≤2 Å in about 89% of the cases. The combination of JAMDA scoring with the LSL-BFGS algorithm shows a significantly higher optimization locality (i.e., no excessive movement of poses) than with the classical BFGS algorithm while retaining the characteristically low number of scoring function evaluations. The JAMDA scoring and optimization scheme is freely available for noncommercial use and academic research.
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Affiliation(s)
- Florian Flachsenberg
- ZBH - Center for Bioinformatics, Universität Hamburg, Bundesstraβe 43, 20146 Hamburg, Germany
| | - Agnes Meyder
- ZBH - Center for Bioinformatics, Universität Hamburg, Bundesstraβe 43, 20146 Hamburg, Germany
| | - Kai Sommer
- ZBH - Center for Bioinformatics, Universität Hamburg, Bundesstraβe 43, 20146 Hamburg, Germany
| | - Patrick Penner
- ZBH - Center for Bioinformatics, Universität Hamburg, Bundesstraβe 43, 20146 Hamburg, Germany
| | - Matthias Rarey
- ZBH - Center for Bioinformatics, Universität Hamburg, Bundesstraβe 43, 20146 Hamburg, Germany
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von Behren MM, Rarey M. Ligand-based virtual screening under partial shape constraints. J Comput Aided Mol Des 2017; 31:335-347. [PMID: 28315995 DOI: 10.1007/s10822-017-0011-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 02/16/2017] [Indexed: 01/26/2023]
Abstract
Ligand-based virtual screening has proven to be a viable technology during the search for new lead structures in drug discovery. Despite the rapidly increasing number of published methods, meaningful shape matching as well as ligand and target flexibility still remain open challenges. In this work, we analyze the influence of knowledge-based sterical constraints on the performance of the recently published ligand-based virtual screening method mRAISE. We introduce the concept of partial shape matching enabling a more differentiated view on chemical structure. The new method is integrated into the LBVS tool mRAISE providing multiple options for such constraints. The applied constraints can either be derived automatically from a protein-ligand complex structure or by manual selection of ligand atoms. In this way, the descriptor directly encodes the fit of a ligand into the binding site. Furthermore, the conservation of close contacts between the binding site surface and the query ligand can be enforced. We validated our new method on the DUD and DUD-E datasets. Although the statistical performance remains on the same level, detailed analysis reveal that for certain and especially very flexible targets a significant improvement can be achieved. This is further highlighted looking at the quality of calculated molecular alignments using the recently introduced mRAISE dataset. The new partial shape constraints improved the overall quality of molecular alignments especially for difficult targets with highly flexible or different sized molecules. The software tool mRAISE is freely available on Linux operating systems for evaluation purposes and academic use (see http://www.zbh.uni-hamburg.de/raise ).
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Affiliation(s)
- Mathias M von Behren
- Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146, Hamburg, Germany
| | - Matthias Rarey
- Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146, Hamburg, Germany.
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von Behren MM, Bietz S, Nittinger E, Rarey M. mRAISE: an alternative algorithmic approach to ligand-based virtual screening. J Comput Aided Mol Des 2016; 30:583-94. [PMID: 27565795 DOI: 10.1007/s10822-016-9940-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 08/17/2016] [Indexed: 01/31/2023]
Abstract
Ligand-based virtual screening is a well established method to find new lead molecules in todays drug discovery process. In order to be applicable in day to day practice, such methods have to face multiple challenges. The most important part is the reliability of the results, which can be shown and compared in retrospective studies. Furthermore, in the case of 3D methods, they need to provide biologically relevant molecular alignments of the ligands, that can be further investigated by a medicinal chemist. Last but not least, they have to be able to screen large databases in reasonable time. Many algorithms for ligand-based virtual screening have been proposed in the past, most of them based on pairwise comparisons. Here, a new method is introduced called mRAISE. Based on structural alignments, it uses a descriptor-based bitmap search engine (RAISE) to achieve efficiency. Alignments created on the fly by the search engine get evaluated with an independent shape-based scoring function also used for ranking of compounds. The correct ranking as well as the alignment quality of the method are evaluated and compared to other state of the art methods. On the commonly used Directory of Useful Decoys dataset mRAISE achieves an average area under the ROC curve of 0.76, an average enrichment factor at 1 % of 20.2 and an average hit rate at 1 % of 55.5. With these results, mRAISE is always among the top performing methods with available data for comparison. To access the quality of the alignments calculated by ligand-based virtual screening methods, we introduce a new dataset containing 180 prealigned ligands for 11 diverse targets. Within the top ten ranked conformations, the alignment closest to X-ray structure calculated with mRAISE has a root-mean-square deviation of less than 2.0 Å for 80.8 % of alignment pairs and achieves a median of less than 2.0 Å for eight of the 11 cases. The dataset used to rate the quality of the calculated alignments is freely available at http://www.zbh.uni-hamburg.de/mraise-dataset.html . The table of all PDB codes contained in the ensembles can be found in the supplementary material. The software tool mRAISE is freely available for evaluation purposes and academic use (see http://www.zbh.uni-hamburg.de/raise ).
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Affiliation(s)
- Mathias M von Behren
- ZBH - Center for Bioinformatics, University of Hamburg, Bundesstraße 43, 20146, Hamburg, Germany
| | - Stefan Bietz
- ZBH - Center for Bioinformatics, University of Hamburg, Bundesstraße 43, 20146, Hamburg, Germany
| | - Eva Nittinger
- ZBH - Center for Bioinformatics, University of Hamburg, Bundesstraße 43, 20146, Hamburg, Germany
| | - Matthias Rarey
- ZBH - Center for Bioinformatics, University of Hamburg, Bundesstraße 43, 20146, Hamburg, Germany.
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