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Li Z, Lee JE, Cho N, Yoo HM. Anti-viral effect of usenamine a using SARS-CoV-2 pseudo-typed viruses. Heliyon 2023; 9:e21742. [PMID: 38027904 PMCID: PMC10656252 DOI: 10.1016/j.heliyon.2023.e21742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 09/09/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023] Open
Abstract
The escalating pandemic brought about by the novel SARS-CoV-2 virus is threatening global health, and thus, it is necessary to develop effective antiviral drugs. Usenamine A is a dibenzo-furan derivative separated from lichen Usnea diffracta showing broad-spectrum activity against different viruses. We evaluate that usenamine A has antiviral effects against novel SARS-CoV-2 Delta variant pseudotyped viruses (PVs) in A549 cells. In addition, usenamine A significantly suppresses SARS-CoV-2 PV-induced mitochondrial depolarization, elevated reactive oxygen species (ROS) levels, apoptosis, and inflammation. Usenamine A also causes the SARS-CoV-2 spike protein to become less stable. Thus, usenamine A shows potential as an antiviral drug that can provide protection against COVID-19.
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Affiliation(s)
- Zijun Li
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, South Korea
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Chonnam National University, Gwangju 61186, South Korea
| | - Joo-Eun Lee
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Chonnam National University, Gwangju 61186, South Korea
| | - Namki Cho
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Chonnam National University, Gwangju 61186, South Korea
| | - Hee Min Yoo
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, South Korea
- Department of Precision Measurement, University of Science and Technology (UST), Daejeon 34113, South Korea
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Hetmann M, Langner C, Durmaz V, Cespugli M, Köchl K, Krassnigg A, Blaschitz K, Groiss S, Loibner M, Ruau D, Zatloukal K, Gruber K, Steinkellner G, Gruber CC. Identification and validation of fusidic acid and flufenamic acid as inhibitors of SARS-CoV-2 replication using DrugSolver CavitomiX. Sci Rep 2023; 13:11783. [PMID: 37479788 PMCID: PMC10362000 DOI: 10.1038/s41598-023-39071-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/19/2023] [Indexed: 07/23/2023] Open
Abstract
In this work, we present DrugSolver CavitomiX, a novel computational pipeline for drug repurposing and identifying ligands and inhibitors of target enzymes. The pipeline is based on cavity point clouds representing physico-chemical properties of the cavity induced solely by the protein. To test the pipeline's ability to identify inhibitors, we chose enzymes essential for SARS-CoV-2 replication as a test system. The active-site cavities of the viral enzymes main protease (Mpro) and papain-like protease (Plpro), as well as of the human transmembrane serine protease 2 (TMPRSS2), were selected as target cavities. Using active-site point-cloud comparisons, it was possible to identify two compounds-flufenamic acid and fusidic acid-which show strong inhibition of viral replication. The complexes from which fusidic acid and flufenamic acid were derived would not have been identified using classical sequence- and structure-based methods as they show very little structural (TM-score: 0.1 and 0.09, respectively) and very low sequence (~ 5%) identity to Mpro and TMPRSS2, respectively. Furthermore, a cavity-based off-target screening was performed using acetylcholinesterase (AChE) as an example. Using cavity comparisons, the human carboxylesterase was successfully identified, which is a described off-target for AChE inhibitors.
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Affiliation(s)
- M Hetmann
- Innophore, San Francisco, CA, USA
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- Austrian Centre of Industrial Biotechnology, Graz, Austria
| | - C Langner
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - V Durmaz
- Innophore, San Francisco, CA, USA
| | | | - K Köchl
- Innophore, San Francisco, CA, USA
| | | | | | - S Groiss
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - M Loibner
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - D Ruau
- NVIDIA, Santa Clara, CA, USA
| | - K Zatloukal
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - K Gruber
- Innophore, San Francisco, CA, USA
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- Austrian Centre of Industrial Biotechnology, Graz, Austria
- Field of Excellence BioHealth - University of Graz, Graz, Austria
| | - G Steinkellner
- Innophore, San Francisco, CA, USA
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- Field of Excellence BioHealth - University of Graz, Graz, Austria
| | - C C Gruber
- Innophore, San Francisco, CA, USA.
- Institute of Molecular Biosciences, University of Graz, Graz, Austria.
- Austrian Centre of Industrial Biotechnology, Graz, Austria.
- Field of Excellence BioHealth - University of Graz, Graz, Austria.
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Kumbhar N, Nimal S, Patil D, Kaiser VF, Haupt J, Gacche RN. Repurposing of neprilysin inhibitor 'sacubitrilat' as an anti-cancer drug by modulating epigenetic and apoptotic regulators. Sci Rep 2023; 13:9952. [PMID: 37336927 DOI: 10.1038/s41598-023-36872-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 06/12/2023] [Indexed: 06/21/2023] Open
Abstract
Modifications in the epigenetic landscape have been considered a hallmark of cancer. Histone deacetylation is one of the crucial epigenetic modulations associated with the aggressive progression of various cancer subtypes. Herein, we have repurposed the neprilysin inhibitor sacubitrilat as a potent anticancer agent using in-silico protein-ligand interaction profiler (PLIP) analysis, molecular docking, and in vitro studies. The screening of PLIP profiles between vorinostat/panobinostat and HDACs/LTA4H followed by molecular docking resulted in five (Sacubitrilat, B65, BDS, BIR, and NPV) FDA-approved, experimental and investigational drugs. Sacubitrilat has demonstrated promising anticancer activity against colorectal cancer (SW-480) and triple-negative breast cancer (MDA-MB-231) cells, with IC50 values of 14.07 μg/mL and 23.02 μg/mL, respectively. FACS analysis revealed that sacubitrilat arrests the cell cycle at the G0/G1 phase and induces apoptotic-mediated cell death in SW-480 cells. In addition, sacubitrilat inhibited HDAC isoforms at the transcriptomic level by 0.7-0.9 fold and at the proteomic level by 0.5-0.6 fold as compared to the control. Sacubitrilat increased the protein expression of tumor-suppressor (p53) and pro-apoptotic makers (Bax and Bid) by 0.2-2.5 fold while decreasing the expression of anti-apoptotic Bcl2 and Nrf2 proteins by 0.2-0.5 fold with respect to control. The observed cleaved PARP product indicates that sacubitrilat induces apoptotic-mediated cell death. This study may pave the way to identify the anticancer potential of sacubitrilat and can be explored in human clinical trials.
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Affiliation(s)
- Navanath Kumbhar
- Department of Biotechnology, Savitribai Phule Pune University, Pune, Maharashtra (MS), 411007, India
| | - Snehal Nimal
- Department of Biotechnology, Savitribai Phule Pune University, Pune, Maharashtra (MS), 411007, India
| | - Deeksha Patil
- Department of Microbiology, Savitribai Phule Pune University, Pune, Maharashtra (MS), 411007, India
| | | | | | - Rajesh N Gacche
- Department of Biotechnology, Savitribai Phule Pune University, Pune, Maharashtra (MS), 411007, India.
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Abstract
Major histocompatibility complex (MHC) proteins are the most polymorphic and polygenic proteins in humans. They bind peptides, derived from cleavage of different pathogenic antigens, and are responsible for presenting them to T cells. The peptides recognized by the T cell receptors are denoted as epitopes and they trigger an immune response.In this chapter, we describe a docking protocol for predicting the peptide binding to a given MHC protein using the software tool GOLD. The protocol starts with the construction of a combinatorial peptide library used in the docking and ends with the derivation of a quantitative matrix (QM) accounting for the contribution of each amino acid at each peptide position.
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Sagulkoo P, Suratanee A, Plaimas K. Immune-Related Protein Interaction Network in Severe COVID-19 Patients toward the Identification of Key Proteins and Drug Repurposing. Biomolecules 2022; 12:biom12050690. [PMID: 35625619 PMCID: PMC9138873 DOI: 10.3390/biom12050690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/07/2022] [Accepted: 05/09/2022] [Indexed: 02/05/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is still an active global public health issue. Although vaccines and therapeutic options are available, some patients experience severe conditions and need critical care support. Hence, identifying key genes or proteins involved in immune-related severe COVID-19 is necessary to find or develop the targeted therapies. This study proposed a novel construction of an immune-related protein interaction network (IPIN) in severe cases with the use of a network diffusion technique on a human interactome network and transcriptomic data. Enrichment analysis revealed that the IPIN was mainly associated with antiviral, innate immune, apoptosis, cell division, and cell cycle regulation signaling pathways. Twenty-three proteins were identified as key proteins to find associated drugs. Finally, poly (I:C), mitomycin C, decitabine, gemcitabine, hydroxyurea, tamoxifen, and curcumin were the potential drugs interacting with the key proteins to heal severe COVID-19. In conclusion, IPIN can be a good representative network for the immune system that integrates the protein interaction network and transcriptomic data. Thus, the key proteins and target drugs in IPIN help to find a new treatment with the use of existing drugs to treat the disease apart from vaccination and conventional antiviral therapy.
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Affiliation(s)
- Pakorn Sagulkoo
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand;
- Center of Biomedical Informatics, Department of Family Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Apichat Suratanee
- Department of Mathematics, Faculty of Applied Science, King Mongkut’s University of Technology North Bangkok, Bangkok 10800, Thailand;
- Intelligent and Nonlinear Dynamics Innovations Research Center, Science and Technology Research Institute, King Mongkut’s University of Technology North Bangkok, Bangkok 10800, Thailand
| | - Kitiporn Plaimas
- Advance Virtual and Intelligent Computing (AVIC) Center, Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Omics Science and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Correspondence:
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Kores K, Kolenc Z, Furlan V, Bren U. Inverse Molecular Docking Elucidating the Anticarcinogenic Potential of the Hop Natural Product Xanthohumol and Its Metabolites. Foods 2022; 11:foods11091253. [PMID: 35563976 PMCID: PMC9104229 DOI: 10.3390/foods11091253] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/19/2022] [Accepted: 04/25/2022] [Indexed: 01/27/2023] Open
Abstract
Natural products from plants exert a promising potential to act as antioxidants, antimicrobials, anti-inflammatory, and anticarcinogenic agents. Xanthohumol, a natural compound from hops, is indeed known for its anticarcinogenic properties. Xanthohumol is converted into three metabolites: isoxanthohumol (non-enzymatically) as well as 8- and 6-prenylnaringenin (enzymatically). An inverse molecular docking approach was applied to xanthohumol and its three metabolites to discern their potential protein targets. The aim of our study was to disclose the potential protein targets of xanthohumol and its metabolites in order to expound on the potential anticarcinogenic mechanisms of xanthohumol based on the found target proteins. The investigated compounds were docked into the predicted binding sites of all human protein structures from the Protein Data Bank, and the best docking poses were examined. Top scoring human protein targets with successfully docked compounds were identified, and their experimental connection with the anticarcinogenic function or cancer was investigated. The obtained results were carefully checked against the existing experimental findings from the scientific literature as well as further validated using retrospective metrics. More than half of the human protein targets of xanthohumol with the highest docking scores have already been connected with the anticarcinogenic function, and four of them (including two important representatives of the matrix metalloproteinase family, MMP-2 and MMP-9) also have a known experimental correlation with xanthohumol. Another important protein target is acyl-protein thioesterase 2, to which xanthohumol, isoxanthohumol, and 6-prenylnaringenin were successfully docked with the lowest docking scores. Moreover, the results for the metabolites show that their most promising protein targets are connected with the anticarcinogenic function as well. We firmly believe that our study can help to elucidate the anticarcinogenic mechanisms of xanthohumol and its metabolites as after consumption, all four compounds can be simultaneously present in the organism.
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Affiliation(s)
- Katarina Kores
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty for Chemistry and Chemical Technology, University of Maribor, Smetanova 17, SI-2000 Maribor, Slovenia; (K.K.); (Z.K.); (V.F.)
| | - Zala Kolenc
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty for Chemistry and Chemical Technology, University of Maribor, Smetanova 17, SI-2000 Maribor, Slovenia; (K.K.); (Z.K.); (V.F.)
| | - Veronika Furlan
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty for Chemistry and Chemical Technology, University of Maribor, Smetanova 17, SI-2000 Maribor, Slovenia; (K.K.); (Z.K.); (V.F.)
| | - Urban Bren
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty for Chemistry and Chemical Technology, University of Maribor, Smetanova 17, SI-2000 Maribor, Slovenia; (K.K.); (Z.K.); (V.F.)
- Department of Applied Natural Sciences, Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, SI-6000 Koper, Slovenia
- Correspondence: ; Tel.: +386-2-229-4421
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Mohamed FF, Anhlan D, Schöfbänker M, Schreiber A, Classen N, Hensel A, Hempel G, Scholz W, Kühn J, Hrincius ER, Ludwig S. Hypericum perforatum and Its Ingredients Hypericin and Pseudohypericin Demonstrate an Antiviral Activity against SARS-CoV-2. Pharmaceuticals (Basel) 2022; 15:530. [PMID: 35631357 PMCID: PMC9146521 DOI: 10.3390/ph15050530] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/15/2022] [Accepted: 04/17/2022] [Indexed: 12/11/2022] Open
Abstract
For almost two years, the COVID-19 pandemic has constituted a major challenge to human health, particularly due to the lack of efficient antivirals to be used against the virus during routine treatment interventions. Multiple treatment options have been investigated for their potential inhibitory effect on SARS-CoV-2. Natural products, such as plant extracts, may be a promising option, as they have shown an antiviral activity against other viruses in the past. Here, a quantified extract of Hypericum perforatum was tested and found to possess a potent antiviral activity against SARS-CoV-2. The antiviral potency of the extract could be attributed to the naphtodianthrones hypericin and pseudohypericin, in contrast to other tested ingredients of the plant material, which did not show any antiviral activity. Hypericum perforatum and its main active ingredient hypericin were also effective against different SARS-CoV-2 variants (Alpha, Beta, Delta, and Omicron). Concerning its mechanism of action, evidence was obtained that Hypericum perforatum and hypericin may hold a direct virus-blocking effect against SARS-CoV-2 virus particles. Taken together, the presented data clearly emphasize the promising antiviral activity of Hypericum perforatum and its active ingredients against SARS-CoV-2 infections.
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Affiliation(s)
- Fakry F. Mohamed
- Institute of Virology Muenster, Center for Molecular Biology of Inflammation (ZMBE), University Hospital Muenster, 48149 Muenster, Germany; (F.F.M.); (D.A.); (M.S.); (A.S.); (E.R.H.)
- Department of Virology, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44511, Sharkia, Egypt
| | - Darisuren Anhlan
- Institute of Virology Muenster, Center for Molecular Biology of Inflammation (ZMBE), University Hospital Muenster, 48149 Muenster, Germany; (F.F.M.); (D.A.); (M.S.); (A.S.); (E.R.H.)
| | - Michael Schöfbänker
- Institute of Virology Muenster, Center for Molecular Biology of Inflammation (ZMBE), University Hospital Muenster, 48149 Muenster, Germany; (F.F.M.); (D.A.); (M.S.); (A.S.); (E.R.H.)
| | - André Schreiber
- Institute of Virology Muenster, Center for Molecular Biology of Inflammation (ZMBE), University Hospital Muenster, 48149 Muenster, Germany; (F.F.M.); (D.A.); (M.S.); (A.S.); (E.R.H.)
| | - Nica Classen
- Institute of Pharmaceutical Biology and Phytochemistry, University of Muenster, 48149 Muenster, Germany; (N.C.); (A.H.)
| | - Andreas Hensel
- Institute of Pharmaceutical Biology and Phytochemistry, University of Muenster, 48149 Muenster, Germany; (N.C.); (A.H.)
| | - Georg Hempel
- Division of Clinical Pharmacy, Institute of Pharmaceutical and Medical Chemistry, University of Muenster, 48149 Muenster, Germany;
| | | | - Joachim Kühn
- Division of Clinical Virology, Institute of Virology, University Hospital Muenster, 48151 Muenster, Germany;
| | - Eike R. Hrincius
- Institute of Virology Muenster, Center for Molecular Biology of Inflammation (ZMBE), University Hospital Muenster, 48149 Muenster, Germany; (F.F.M.); (D.A.); (M.S.); (A.S.); (E.R.H.)
| | - Stephan Ludwig
- Institute of Virology Muenster, Center for Molecular Biology of Inflammation (ZMBE), University Hospital Muenster, 48149 Muenster, Germany; (F.F.M.); (D.A.); (M.S.); (A.S.); (E.R.H.)
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Sukmarini L. Antiviral Peptides (AVPs) of Marine Origin as Propitious Therapeutic Drug Candidates for the Treatment of Human Viruses. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27092619. [PMID: 35565968 PMCID: PMC9101517 DOI: 10.3390/molecules27092619] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/03/2022] [Accepted: 04/18/2022] [Indexed: 12/13/2022]
Abstract
The marine environment presents a favorable avenue for potential therapeutic agents as a reservoir of new bioactive natural products. Due to their numerous potential pharmacological effects, marine-derived natural products—particularly marine peptides—have gained considerable attention. These peptides have shown a broad spectrum of biological functions, such as antimicrobial, antiviral, cytotoxic, immunomodulatory, and analgesic effects. The emergence of new virus strains and viral resistance leads to continuing efforts to develop more effective antiviral drugs. Interestingly, antimicrobial peptides (AMPs) that possess antiviral properties and are alternatively regarded as antiviral peptides (AVPs) demonstrate vast potential as alternative peptide-based drug candidates available for viral infection treatments. Hence, AVPs obtained from various marine organisms have been evaluated. This brief review features recent updates of marine-derived AVPs from 2011 to 2021. Moreover, the biosynthesis of this class of compounds and their possible mechanisms of action are also discussed. Selected peptides from various marine organisms possessing antiviral activities against important human viruses—such as human immunodeficiency viruses, herpes simplex viruses, influenza viruses, hepatitis C virus, and coronaviruses—are highlighted herein.
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Affiliation(s)
- Linda Sukmarini
- Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), Jl. Raya Bogor Km. 46, Cibinong 16911, West Java, Indonesia
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Lešnik S, Bren U. Mechanistic Insights into Biological Activities of Polyphenolic Compounds from Rosemary Obtained by Inverse Molecular Docking. Foods 2021; 11:67. [PMID: 35010191 PMCID: PMC8750736 DOI: 10.3390/foods11010067] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/23/2021] [Accepted: 12/24/2021] [Indexed: 01/18/2023] Open
Abstract
Rosemary (Rosmarinus officinalis L.) represents a medicinal plant known for its various health-promoting properties. Its extracts and essential oils exhibit antioxidative, anti-inflammatory, anticarcinogenic, and antimicrobial activities. The main compounds responsible for these effects are the diterpenes carnosic acid, carnosol, and rosmanol, as well as the phenolic acid ester rosmarinic acid. However, surprisingly little is known about the molecular mechanisms responsible for the pharmacological activities of rosemary and its compounds. To discern these mechanisms, we performed a large-scale inverse molecular docking study to identify their potential protein targets. Listed compounds were separately docked into predicted binding sites of all non-redundant holo proteins from the Protein Data Bank and those with the top scores were further examined. We focused on proteins directly related to human health, including human and mammalian proteins as well as proteins from pathogenic bacteria, viruses, and parasites. The observed interactions of rosemary compounds indeed confirm the beforementioned activities, whereas we also identified their potential for anticoagulant and antiparasitic actions. The obtained results were carefully checked against the existing experimental findings from the scientific literature as well as further validated using both redocking procedures and retrospective metrics.
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Affiliation(s)
- Samo Lešnik
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova 17, SI-2000 Maribor, Slovenia;
| | - Urban Bren
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova 17, SI-2000 Maribor, Slovenia;
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, SI-6000 Koper, Slovenia
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