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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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Repurposing α-Adrenoreceptor Blockers as Promising Anti-Virulence Agents in Gram-Negative Bacteria. Antibiotics (Basel) 2022; 11:antibiotics11020178. [PMID: 35203781 PMCID: PMC8868568 DOI: 10.3390/antibiotics11020178] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/16/2022] [Accepted: 01/25/2022] [Indexed: 12/12/2022] Open
Abstract
Antimicrobial resistance is among the world’s most urgent public health problems. Diminishing of the virulence of bacteria is a promising approach to decrease the development of bacterial resistance. Quorum sensing (QS) systems orchestrate the bacterial virulence in inducer–receptors manner. Bacteria can spy on the cells of the host by sensing adrenergic hormones and other neurotransmitters, and in turn, these neurotransmitters can induce bacterial pathogenesis. In this direction, α-adrenergic blockers were proposed as an anti-virulence agents through inhibiting the bacterial espionage. The current study aimed to explore the α-blockers’ anti-QS activities. Within comprehensive in silico investigation, the binding affinities of seven α-adrenoreceptor blockers were evaluated towards structurally different QS receptors. From the best docked α-blockers into QS receptors, terazosin was nominated to be subjected for further in vivo and in vitro anti-QS and anti-virulence activities against Chromobacterium violaceum and Pseudomonas aeruginosa. Terazosin showed a significant ability to diminish the QS-controlled pigment production in C. violaceum. Moreover, Terazosin decreased the P. aeruginosa biofilm formation and down-regulated its QS-encoding genes. Terazosin protected mice from the P. aeruginosa pathogenesis. In conclusion, α-adrenergic blockers are proposed as promising anti-virulence agents as they hinder QS receptors and inhibit bacterial espionage.
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Buendia-Atencio C, Pieffet GP, Montoya-Vargas S, Martínez Bernal JA, Rangel HR, Muñoz AL, Losada-Barragán M, Segura NA, Torres OA, Bello F, Suárez A, Rodríguez AK. Inverse Molecular Docking Study of NS3-Helicase and NS5-RNA Polymerase of Zika Virus as Possible Therapeutic Targets of Ligands Derived from Marcetia taxifolia and Its Implications to Dengue Virus. ACS OMEGA 2021; 6:6134-6143. [PMID: 33718704 PMCID: PMC7948243 DOI: 10.1021/acsomega.0c04719] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/29/2021] [Indexed: 06/01/2023]
Abstract
Dengue and Zika are two mosquito-borne diseases of great impact on public health around the world in tropical and subtropical countries. DENV and ZIKV belong to the Flaviviridae family and the Flavivirus genus. Currently, there are no effective therapeutic agents to treat or prevent these pathologies. The main objective of this work was to evaluate potential inhibitors from active compounds obtained from Marcetia taxifolia by performing inverse molecular docking on ZIKV-NS3-helicase and ZIKV-NS5-RNA polymerase as targets. This computational strategy is based on renormalizing the binding scores of the compounds to these two proteins, allowing a direct comparison of the results across the proteins. The crystallographic structures of the ZIKV-NS3-helicase and ZIKV-NS5-RNA-polymerase proteins share a great similarity with DENV homologous proteins. The P-loop active site of the crystallographic structure of ZIKV-NS3-helicase presents a high percentage of homology with the four dengue serotypes. It was found that most ligands of the active compounds (5,3'-dihydroxy-3,6,7,8,4'-pentamethoxyflavone (5DP); 5-hydroxy-3,6,7,8,3',4'-hexamethoxyflavone (5HH); myricetin-3-O-rhamnoside (M3OR)) from Marcetia taxifolia had a better affinity for ZIKV-NS3-helicase than for ZIKV-NS5-RNA polymerase, as indicated by the negative multiple active site correction (MASC) score, except for M3RG that showed a higher affinity for ZIKV-NS5-RNA polymerase. On the other hand, the AutoDock Vina scores showed that M3OR had the highest score value (-9.60 kcal/mol) and the highest normalized score (1.13) against ZIKV-NS3-helicase. These results in silico demonstrated that the nonstructural proteins NS3-helicase and NS5-RNA polymerase, which share similar molecular structures between the selected viruses, could become therapeutic targets for some bioactive compounds derived from Marcetia taxifolia.
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Affiliation(s)
| | - Gilles Paul Pieffet
- Faculty
of Science, Universidad Antonio Nariño
(UAN), Bogotá 110231, Colombia
| | | | | | - Héctor Rafael Rangel
- Laboratory
of Molecular Virology, Instituto Venezolano
de Investigaciones Científicas, Caracas 1204, Venezuela
| | - Ana Luisa Muñoz
- PhD
Program of Health Science, Universidad Antonio
Nariño (UAN), Bogotá 110231, Colombia
| | | | - Nidya Alexandra Segura
- Faculty
of Science, Universidad Pedagógica
y Tecnológica de Colombia, Tunja150003, Colombia
| | - Orlando A. Torres
- Faculty
of
Veterinary Medicine, Universidad Antonio
Nariño (UAN), Bogotá 110231, Colombia
| | - Felio Bello
- Faculty
of Agricultural and Livestock Sciences, Program of Veterinary Medicine, Universidad de La Salle, Bogotá 110131 Colombia
| | - Alírica
Isabel Suárez
- Natural
Products Laboratory, Faculty of Pharmacy, Universidad Central de Venezuela, Caracas 1050, Venezuela
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Carlesso A, Chintha C, Gorman AM, Samali A, Eriksson LA. Binding Analysis of the Inositol-Requiring Enzyme 1 Kinase Domain. ACS OMEGA 2018; 3:13313-13322. [PMID: 30411035 PMCID: PMC6217623 DOI: 10.1021/acsomega.8b01404] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 10/02/2018] [Indexed: 06/08/2023]
Abstract
Inositol-requiring enzyme 1 (IRE1) is an orchestrator of the unfolded protein response (UPR), the cellular response to endoplasmic reticulum (ER) stress that plays a crucial role in tumor development. IRE1 signaling is the most evolutionary conserved branch of the UPR. Under ER stress, the IRE1 luminal domain undergoes a conformational change to multimerize, resulting in trans-autophosphorylation and activation of the cytosolic kinase and endoribonuclease domain. Adenosine triphosphate-competitive inhibitors that bind to the IRE1 kinase site can modulate the activity of the RNase domain through an allosteric relationship between the IRE1 kinase and RNase domains. The current study aims at the investigation of available structural data of the IRE1 kinase domain and provides insights into the design of novel kinase inhibitors. To this end, a detailed analysis of IRE1 kinase active site and investigation of suitable structures for virtual screening studies were performed. The results indicate in silico target fishing as an appropriate strategy for the identification of novel IRE1 kinase binders, further validating the robustness of the in silico protocol. Importantly, the study highlights the kinase-inhibiting RNase attenuator (KIRA)-bound protein data bank 4U6R structure as the best protein structure to perform virtual screening to develop diverse and more potent KIRA-like IRE1 kinase inhibitors that are capable of allosterically affecting the RNase activity.
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Affiliation(s)
- Antonio Carlesso
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, 405 30 Göteborg, Sweden
| | - Chetan Chintha
- Apoptosis
Research Centre, National University of
Ireland Galway, H91 TK33 Galway, Ireland
| | - Adrienne M. Gorman
- Apoptosis
Research Centre, National University of
Ireland Galway, H91 TK33 Galway, Ireland
| | - Afshin Samali
- Apoptosis
Research Centre, National University of
Ireland Galway, H91 TK33 Galway, Ireland
| | - Leif A. Eriksson
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, 405 30 Göteborg, Sweden
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Abstract
Nowadays it is widely accepted that one compound can be able to hit several targets at once. This "magic shotgun" approach for drug development properly describes the mechanism of biomolecular recognition. The need to take into account the polypharmacology in structure-based drug design has led to the development of several computational tools. Here we present a computational protocol to identify promising compounds against several biological targets, a protocol known as inverse docking.
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Affiliation(s)
- Patricia Saenz-Méndez
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden. .,Computational Chemistry and Biology Group, Facultad de Química, UdelaR, Montevideo, Uruguay.
| | - Leif A Eriksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
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