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Avadanei M, Brunchi CE. Wheat gliadin/xanthan gum intermolecular complexes: Interaction mechanism and structural characterization. Food Chem 2024; 460:140619. [PMID: 39067426 DOI: 10.1016/j.foodchem.2024.140619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 07/10/2024] [Accepted: 07/22/2024] [Indexed: 07/30/2024]
Abstract
In this study, the interactions between wheat gliadin (GL) and xanthan gum (XG) were investigated to design new systems with potential applications as a gluten-free substitute product. Combining spectral with morphological and molecular docking methods allowed the establishment of the complexation mechanism between globular hydrophobic GL and the hydrophilic XG with an extended and partially disordered backbone. GL maintains intact its hydrophobic core even at high GL/XG ratios and organizes into small aggregate-type assemblies. The stable and uniform complexes have a low GL content, based on intermolecular hydrogen bonds and hydrophobic interactions. The GL/XG combining ratio influences the size, structure and interaction mechanism of the microparticles. The preferred sites of interaction and the binding affinities were determined by molecular docking on GL libraries and XG models. This research may provide significant knowledge for the development of low-GL wheat food products using a dietary fiber polysaccharide as a functional compound.
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Affiliation(s)
- Mihaela Avadanei
- "Petru Poni" Institute of Macromolecular Chemistry, 41A, Grigore Ghica Voda Alley, 700487, Iasi, Romania
| | - Cristina-Eliza Brunchi
- "Petru Poni" Institute of Macromolecular Chemistry, 41A, Grigore Ghica Voda Alley, 700487, Iasi, Romania.
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2
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Wongprasert T, Mathatheeranan P, Siripitakpong P, Vilaivan T, Suriya U, Rungrotmongkol T, Cadwallader K, Suppavorasatit I. Effect of functional groups in strawberry flavoring on pea protein-flavor interactions: Potential applicable in flavor formulation for plant-based protein aqueous foods. Food Chem X 2024; 23:101702. [PMID: 39184319 PMCID: PMC11342753 DOI: 10.1016/j.fochx.2024.101702] [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: 04/25/2024] [Revised: 07/23/2024] [Accepted: 07/24/2024] [Indexed: 08/27/2024] Open
Abstract
This research aimed to explore binding interactions between pea protein isolate (PPI) and selected strawberry flavorings including vanillin, γ-decalactone, furaneol, and (Z)-3-hexen-1-ol within an aqueous system. The results showed that binding affinities of PPI with all various functional group of flavor compounds decreased as temperature increased from 5 °C to 25 °C. Notably, at 25 °C, γ-decalactone displayed the highest binding affinity, followed by vanillin, (Z)-3-hexen-1-ol, and furaneol. Lowest binding was observed for furaneol, explained by its greater lipophilicity (lower partition coefficient values or LogP value) and molecular structure in each functional group in the flavor compounds. Thermodynamically, the interaction between PPI and each selected flavor compound was spontaneous, with evidence suggesting primary forces being hydrophobic interactions or hydrogen bonding/van der Waals forces. Computational molecular docking further confirmed these interaction types. This research provides insights into the interactions between PPI and strawberry flavorings, aiding in the selection of optimal flavor compound proportion for protein-rich products.
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Affiliation(s)
- Thanakorn Wongprasert
- Department of Food Technology, Faculty of Science, Chulalongkorn University, Phayathai Road, Wangmai, Pathumwan, Bangkok 10330, Thailand
| | - Pakavit Mathatheeranan
- Department of Food Technology, Faculty of Science, Chulalongkorn University, Phayathai Road, Wangmai, Pathumwan, Bangkok 10330, Thailand
| | - Panatthida Siripitakpong
- Department of Food Technology, Faculty of Science, Chulalongkorn University, Phayathai Road, Wangmai, Pathumwan, Bangkok 10330, Thailand
| | - Tirayut Vilaivan
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Utid Suriya
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Thanyada Rungrotmongkol
- Center of Excellence in Biocatalyst and Sustainable Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
| | - Keith Cadwallader
- Department of Food Science and Human Nutrition, University of Illinois, 1302 W Pennsylvania Ave, Urbana, IL 61801, United States
| | - Inthawoot Suppavorasatit
- Department of Food Technology, Faculty of Science, Chulalongkorn University, Phayathai Road, Wangmai, Pathumwan, Bangkok 10330, Thailand
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3
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Li W, Luo R, Liu Z, Li X, Zhang C, Huang J, Wang Z, Chen J, Ding H, Zhou X, Liu B. Anti-inflammatory effects of resveratrol in treating interstitial cystitis/bladder pain syndrome: a multi-faceted approach integrating network pharmacology, molecular docking, and experimental validation. Mol Divers 2024:10.1007/s11030-024-11004-6. [PMID: 39400868 DOI: 10.1007/s11030-024-11004-6] [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: 07/05/2024] [Accepted: 09/27/2024] [Indexed: 10/15/2024]
Abstract
This study aims to investigate the anti-inflammatory effects of Resveratrol (RES) in the treatment of Interstitial Cystitis/Bladder Pain Syndrome (IC/BPS) by integrating network pharmacology, molecular docking, and experimental validation. Potential targets of RES were identified using DrugBank and SwissTargetPrediction, while IC/BPS-related targets were obtained from DisGeNET and Genecards. Molecular docking was performed using UCSF Chimera and SwissDock to validate the binding affinity of RES to key targets. Experimental validation involved treating TNF-α induced urothelial cells with RES, followed by assessments using RT-qPCR, ELISA, and Western blotting. A total of 86 drug targets and 211 disease targets were analyzed, leading to the identification of 8 key therapeutic targets for RES in IC/BPS treatment. Molecular docking revealed a strong affinity of RES for ESR2, with notable interactions also observed with SHBG, PTGS2, PPARG, KIT, PI3KCA, and AKT1. In vitro experiments confirmed that RES significantly alleviated the inflammatory response in TNF-α-induced urothelial cells, normalizing the expression levels of ESR2, SHBG, PPARG, and AKT1. RES can modulate critical pathways involving ESR2, SHBG, PPARG, and AKT1, highlighting its potential as a therapeutic agent for IC/BPS. This study provides a theoretical foundation for the clinical application of RES in treating IC/BPS.
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Grants
- 82170786 and 81670688 to Xiangfu Zhou, 81800666 to Bolong Liu, 82100816 to Chi Zhang National Natural Science Foundation of China
- 82170786 and 81670688 to Xiangfu Zhou, 81800666 to Bolong Liu, 82100816 to Chi Zhang National Natural Science Foundation of China
- 82170786 and 81670688 to Xiangfu Zhou, 81800666 to Bolong Liu, 82100816 to Chi Zhang National Natural Science Foundation of China
- 2023A1515010422 to Bolong Liu, 2024A1515010461 and 2022A1515010250 to Xiangfu Zhou Natural Science Foundation of Guangdong Province
- 2023A1515010422 to Bolong Liu, 2024A1515010461 and 2022A1515010250 to Xiangfu Zhou Natural Science Foundation of Guangdong Province
- 202301-323 to Xiangfu Zhou Open Research Funds from Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital
- 2023A03J0201 to Bolong Liu Guangzhou Municipal Science and Technology Project
- 20231063 to Bolong Liu Scientific Research Project of Traditional Chinese Medicine Bureau of Guangdong Province
- 2024GZRPYMS03 to Bolong Liu Cultivation Special Project Foundation of The Third Affiliated Hospital of Sun Yat-Sen University
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Affiliation(s)
- Wenshuang Li
- Department of Urology, The Third Affiliated Hospital, Sun Yat-Sen University, 600 Tianhe Road, Guangzhou, 510630, People's Republic of China
| | - Ruixiang Luo
- Department of Urology, The Third Affiliated Hospital, Sun Yat-Sen University, 600 Tianhe Road, Guangzhou, 510630, People's Republic of China
| | - Zheng Liu
- Department of Urology, The Third Affiliated Hospital, Sun Yat-Sen University, 600 Tianhe Road, Guangzhou, 510630, People's Republic of China
| | - Xiaoyang Li
- Department of Urology, The Third Affiliated Hospital, Sun Yat-Sen University, 600 Tianhe Road, Guangzhou, 510630, People's Republic of China
| | - Chi Zhang
- Department of Urology, The Third Affiliated Hospital, Sun Yat-Sen University, 600 Tianhe Road, Guangzhou, 510630, People's Republic of China
| | - Junlong Huang
- Department of Urology, The Third Affiliated Hospital, Sun Yat-Sen University, 600 Tianhe Road, Guangzhou, 510630, People's Republic of China
| | - Ziqiao Wang
- Department of Urology, The Third Affiliated Hospital, Sun Yat-Sen University, 600 Tianhe Road, Guangzhou, 510630, People's Republic of China
| | - Jialiang Chen
- Department of Urology, The Third Affiliated Hospital, Sun Yat-Sen University, 600 Tianhe Road, Guangzhou, 510630, People's Republic of China
| | - Honglu Ding
- Department of Urology, The Third Affiliated Hospital, Sun Yat-Sen University, 600 Tianhe Road, Guangzhou, 510630, People's Republic of China
| | - Xiangfu Zhou
- Department of Urology, The Third Affiliated Hospital, Sun Yat-Sen University, 600 Tianhe Road, Guangzhou, 510630, People's Republic of China.
- Department of Urology, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511500, People's Republic of China.
| | - Bolong Liu
- Department of Urology, The Third Affiliated Hospital, Sun Yat-Sen University, 600 Tianhe Road, Guangzhou, 510630, People's Republic of China.
- Department of Urology, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, 511500, People's Republic of China.
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4
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Uba AI. Computer-Aided Design of VEGFR-2 Inhibitors as Anticancer Agents: A Review. J Mol Recognit 2024:e3104. [PMID: 39389566 DOI: 10.1002/jmr.3104] [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: 06/21/2024] [Revised: 08/01/2024] [Accepted: 09/03/2024] [Indexed: 10/12/2024]
Abstract
Due to its intricate molecular and structural characteristics, vascular endothelial growth factor receptor 2 (VEGFR-2) is essential for the development of new blood vessels in various pathological processes and conditions, especially in cancers. VEGFR-2 inhibitors have demonstrated significant anticancer effects by blocking many signaling pathways linked to tumor growth, metastasis, and angiogenesis. Several small compounds, including the well-tolerated sunitinib and sorafenib, have been approved as VEGFR-2 inhibitors. However, the widespread side effects linked to these VEGFR-2 inhibitors-hypertension, epistaxis, proteinuria, and upper respiratory infection-motivate researchers to search for new VEGFR-2 inhibitors with better pharmacokinetic profiles. The key molecular interactions required for the interaction of the small molecules with the protein target to produce the desired pharmacological effects are identified using computer-aided drug design (CADD) methods such as pharmacophore and QSAR modeling, structure-based virtual screening, molecular docking, molecular dynamics (MD) simulation coupled with MM/PB(GB)SA, and other computational strategies. This review discusses the applications of these methods for VEGFR-2 inhibitor design. Future VEGFR-2 inhibitor designs may be influenced by this review, which focuses on the current trends of using multiple screening layers to design better inhibitors.
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Affiliation(s)
- Abdullahi Ibrahim Uba
- Department of Molecular Biology and Genetics, Istanbul AREL University, Istanbul, Turkey
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5
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Abbott GW, Manville RW. Discovery of a potent, Kv7.3-selective potassium channel opener from a Polynesian traditional botanical anticonvulsant. Commun Chem 2024; 7:233. [PMID: 39390220 PMCID: PMC11467302 DOI: 10.1038/s42004-024-01318-9] [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: 06/05/2024] [Accepted: 10/01/2024] [Indexed: 10/12/2024] Open
Abstract
Plants remain an important source of biologically active small molecules with high therapeutic potential. The voltage-gated potassium (Kv) channel formed by Kv7.2/3 (KCNQ2/3) heteromers is a major target for anticonvulsant drug development. Here, we screened 1444 extracts primarily from plants collected in California and the US Virgin Islands, for their ability to activate Kv7.2/3 but not inhibit Kv1.3, to select against tannic acid being the active component. We validated the 7 strongest hits, identified Thespesia populnea (miro, milo, portia tree) as the most promising, then discovered its primary active metabolite to be gentisic acid (GA). GA highly potently activated Kv7.2/3 (EC50, 2.8 nM). GA is, uniquely to our knowledge, 100% selective for Kv7.3 versus other Kv7 homomers; it requires S5 residue Kv7.3-W265 for Kv7.2/3 activation, and it ameliorates pentylenetetrazole-induced seizures in mice. Structure-activity studies revealed that the FDA-approved vasoprotective drug calcium dobesilate, a GA analog, is a previously unrecognized Kv7.2/3 channel opener. Also an active aspirin metabolite, GA provides a molecular rationale for the use of T. populnea as an anticonvulsant in Polynesian indigenous medicine and presents novel pharmacological prospects for potent, isoform-selective, therapeutic Kv7 channel activation.
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Affiliation(s)
- Geoffrey W Abbott
- Bioelectricity Laboratory, Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, USA.
| | - Rían W Manville
- Bioelectricity Laboratory, Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, USA
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6
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Ryan EM, Norinskiy MA, Bracken AK, Lueders EE, Chen X, Fu Q, Anderson ET, Zhang S, Abbasov ME. Activity-Based Acylome Profiling with N-(Cyanomethyl)- N-(phenylsulfonyl)amides for Targeted Lysine Acylation and Post-Translational Control of Protein Function in Cells. J Am Chem Soc 2024; 146:27622-27643. [PMID: 39348182 DOI: 10.1021/jacs.4c09073] [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: 10/01/2024]
Abstract
Lysine acylations are ubiquitous and structurally diverse post-translational modifications that vastly expand the functional heterogeneity of the human proteome. Hence, the targeted acylation of lysine residues has emerged as a strategic approach to exert biomimetic control over the protein function. However, existing strategies for targeted lysine acylation in cells often rely on genetic intervention, recruitment of endogenous acylation machinery, or nonspecific acylating agents and lack methods to quantify the magnitude of specific acylations on a global level. In this study, we develop activity-based acylome profiling (ABAP), a chemoproteomic strategy that exploits elaborate N-(cyanomethyl)-N-(phenylsulfonyl)amides and lysine-centric probes for site-specific introduction and proteome-wide mapping of posttranslational lysine acylations in human cells. Harnessing this framework, we quantify various artificial acylations and rediscover numerous endogenous lysine acylations. We validate site-specific acetylation of target lysines and establish a structure-activity relationship for N-(cyanomethyl)-N-(phenylsulfonyl)amides in proteins from diverse structural and functional classes. We identify paralog-selective chemical probes that acetylate conserved lysines within interferon-stimulated antiviral RNA-binding proteins, generating de novo proteoforms with obstructed RNA interactions. We further demonstrate that targeted acetylation of a key enzyme in retinoid metabolism engenders a proteoform with a conformational change in the protein structure, leading to a gain-of-function phenotype and reduced drug potency. These findings underscore the versatility of our strategy in biomimetic control over protein function through targeted delivery and global profiling of endogenous and artificial lysine acylations, potentially advancing therapeutic modalities and our understanding of biological processes orchestrated by these post-translational modifications.
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Affiliation(s)
- Elizabeth M Ryan
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Michael A Norinskiy
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Amy K Bracken
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Emma E Lueders
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Xueer Chen
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Qin Fu
- Proteomics and Metabolomics Facility, Cornell University, Ithaca, New York 14853, United States
| | - Elizabeth T Anderson
- Proteomics and Metabolomics Facility, Cornell University, Ithaca, New York 14853, United States
| | - Sheng Zhang
- Proteomics and Metabolomics Facility, Cornell University, Ithaca, New York 14853, United States
| | - Mikail E Abbasov
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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7
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Shen L, Peraglie C, Podlesainski D, Stracke C, Ojha RS, Caliebe F, Kaiser M, Forchhammer K, Hagemann M, Gutekunst K, Snoep JL, Bräsen C, Siebers B. Structure function analysis of ADP-dependent cyanobacterial phosphofructokinase reveals new phylogenetic grouping in the PFK-A family. J Biol Chem 2024:107868. [PMID: 39393572 DOI: 10.1016/j.jbc.2024.107868] [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: 06/12/2024] [Revised: 09/19/2024] [Accepted: 10/01/2024] [Indexed: 10/13/2024] Open
Abstract
Dependent on the light conditions, photosynthetic organisms switch between carbohydrate synthesis or breakdown, for which the reversibility of carbohydrate metabolism, including glycolysis, is essential. Kinetic regulation of phosphofructokinase (PFK), a key-control point in glycolysis, was studied in the cyanobacterium Synechocystis sp. PCC 6803. The two PFK iso-enzymes (PFK- A1, PFK-A2), were found to use ADP instead of ATP, and have similar kinetic characteristics, but differ in their allosteric regulation. PFK-A1 is inhibited by 3- phosphoglycerate, a product of the Calvin-Benson-Bassham cycle, while PFK-A2 is inhibited by ATP, which is provided by photosynthesis. This regulation enables cyanobacteria to switch PFK off in light, and on in darkness. ADP dependence has not been reported before for the PFK-A enzyme family, and was thought to be restricted to the PFK-B ribokinase superfamily. Phosphate donor specificity within the PFK-A family could be related to specific binding motifs in ATP-, ADP-, and PPi-dependent PFK-As. Phylogenetic analysis revealed a distribution of ADP-PFK-As in cyanobacteria and in a few alphaproteobacteria, which was confirmed in enzymatic studies.
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Affiliation(s)
- Lu Shen
- Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), University of Duisburg-Essen, Universitätsstr. 5, Essen, 45141, State, Germany
| | - Carmen Peraglie
- Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), University of Duisburg-Essen, Universitätsstr. 5, Essen, 45141, State, Germany
| | - David Podlesainski
- Chemical Biology, Centre of Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany
| | - Christina Stracke
- Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), University of Duisburg-Essen, Universitätsstr. 5, Essen, 45141, State, Germany
| | - Ravi Shankar Ojha
- Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), University of Duisburg-Essen, Universitätsstr. 5, Essen, 45141, State, Germany
| | - Frauke Caliebe
- Molekulare Pflanzenphysiologie, University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - Markus Kaiser
- Chemical Biology, Centre of Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany
| | - Karl Forchhammer
- Microbiology, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Martin Hagemann
- Plant Physiology, University of Rostock, Albert-Einstein-Str. 3, 18059 Rostock, Germany
| | - Kirstin Gutekunst
- Molekulare Pflanzenphysiologie, University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - Jacky L Snoep
- Biochemistry, University of Stellenbosch, Private Bag X1, 7600 Stellenbosch, South Africa; Molecular Cell Biology, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Christopher Bräsen
- Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), University of Duisburg-Essen, Universitätsstr. 5, Essen, 45141, State, Germany.
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), University of Duisburg-Essen, Universitätsstr. 5, Essen, 45141, State, Germany.
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8
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Huynh DTN, Nguyen HT, Hsieh CM. Taiwan Chingguan Yihau may improve post-COVID-19 respiratory complications through PI3K/AKT, HIF-1, and TNF signaling pathways revealed by network pharmacology analysis. Mol Divers 2024:10.1007/s11030-024-10993-8. [PMID: 39382736 DOI: 10.1007/s11030-024-10993-8] [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: 06/08/2024] [Accepted: 09/14/2024] [Indexed: 10/10/2024]
Abstract
The emergence of new SARS-CoV-2 variants with a higher contagious capability and faster transmissible speed has imposed an incessant menace on global health and the economy. The SARS-CoV-2 infection might reoccur and last much longer than expected. Thence, there is a high possibility that COVID-19 can cause long-term health problems. This condition needs to be investigated thoroughly, especially the post-COVID-19 complications. Respiratory tract disorders are common and typical complications after recovery. Until now, there has been a lack of data on specialized therapeutic medicine for post-COVID-19 complications. The clinical efficacy of NRICM101 has been demonstrated in hospitalized COVID-19 patients. This herbal medicine may also be a promising therapy for post-COVID-19 complications, thanks to its phytochemical constituents. The potential pharmacological mechanisms of NRICM101 in treating post-COVID-19 respiratory complications were investigated using network pharmacology combined with molecular docking, and the results revealed that NRICM101 may exert a beneficial effect through the three primary pathways: PI3K/AKT, HIF-1, and TNF signaling pathways. Flavonoids (especially quercetin) have a predominant role and synergize with other active compounds to produce therapeutic effectiveness. Most of the main active compounds exist in three chief herbal ingredients, including Liquorice root (Glycyrrhiza glabra), Scutellaria root (Scutellaria baicalensis), and Mulberry leaf (Morus alba). To our knowledge, this is the first study of the NRICM101 effect on post-COVID-19 respiratory complications. Our findings may provide a better understanding of the potential mechanisms of NRICM101 in treating SARS-CoV-2 infection and regulating the immunoinflammatory response to improve post-COVID-19 respiratory complications.
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Affiliation(s)
- Dung Tam Nguyen Huynh
- College of Pharmacy, Taipei Medical University, Taipei, 11031, Taiwan
- Can Tho University of Medicine and Pharmacy, Can Tho City, 94117, Vietnam
| | - Hien Thi Nguyen
- Department of Nutrition and Food Safety, Faculty of Public Health, Can Tho University of Medicine and Pharmacy, Can Tho City, 94117, Vietnam
| | - Chien-Ming Hsieh
- College of Pharmacy, Taipei Medical University, Taipei, 11031, Taiwan.
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9
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Papadopoulos MGE, Perhal AF, Medel-Lacruz B, Ladurner A, Selent J, Dirsch VM, Kolb P. Discovery and characterization of small-molecule TGR5 ligands with agonistic activity. Eur J Med Chem 2024; 276:116616. [PMID: 38996653 DOI: 10.1016/j.ejmech.2024.116616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/15/2024] [Accepted: 06/20/2024] [Indexed: 07/14/2024]
Abstract
The Takeda G protein-coupled receptor 5 (TGR5) is activated endogenously by primary and secondary bile acids. This receptor is considered a candidate target for addressing inflammatory and metabolic disorders. We have targeted TGR5 with structure-based methods for ligand finding using the recently solved experimental structures, as well as structures obtained from molecular dynamics simulations. Through addressing the orthosteric as well as a putative allosteric site, we identified agonists and positive allosteric modulators. While the predicted binding locations were not in line with their efficacy, our work contributes activating small-molecule ligands that we have thoroughly characterized in vitro.
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Affiliation(s)
| | - Alexander F Perhal
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Brian Medel-Lacruz
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Hospital del Mar Medical Research Institute (IMIM), Pompeu Fabra University (UPF), Barcelona, Spain
| | - Angela Ladurner
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Jana Selent
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Hospital del Mar Medical Research Institute (IMIM), Pompeu Fabra University (UPF), Barcelona, Spain
| | - Verena M Dirsch
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Peter Kolb
- Department of Pharmaceutical Chemistry, University of Marburg, Marburg, Germany.
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10
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Vela-Corcia D, Hierrezuelo J, Pérez-Lorente AI, Stincone P, Pakkir Shah AK, Grélard A, Zi-Long Y, de Vicente A, Pérez García A, Bai L, Loquet A, Petras D, Romero D. Cyclo(Pro-Tyr) elicits conserved cellular damage in fungi by targeting the [H +]ATPase Pma1 in plasma membrane domains. Commun Biol 2024; 7:1253. [PMID: 39362977 PMCID: PMC11449911 DOI: 10.1038/s42003-024-06947-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 09/24/2024] [Indexed: 10/05/2024] Open
Abstract
Bioactive metabolites play a crucial role in shaping interactions among diverse organisms. In this study, we identified cyclo(Pro-Tyr), a metabolite produced by Bacillus velezensis, as a potent inhibitor of Botrytis cinerea and Caenorhabditis elegans, two potential cohabitant eukaryotic organisms. Based on our investigation, cyclo(Pro-Tyr) disrupts plasma membrane polarization, induces oxidative stress and increases membrane fluidity, which compromises fungal membrane integrity. These cytological and physiological changes induced by cyclo(Pro-Tyr) may be triggered by the destabilization of membrane microdomains containing the [H+]ATPase Pma1. In response to cyclo(Pro-Tyr) stress, fungal cells activate a transcriptomic and metabolomic response, which primarily involves lipid metabolism and Reactive Oxygen Species (ROS) detoxification, to mitigate membrane damage. This similar response occurs in the nematode C. elegans, indicating that cyclo(Pro-Tyr) targets eukaryotic cellular membranes.
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Affiliation(s)
- D Vela-Corcia
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - J Hierrezuelo
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - A I Pérez-Lorente
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - P Stincone
- University of Tuebingen, CMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Infection Medicine, Tuebingen, Germany
- University of Tuebingen, Center for Plant Molecular Biology, Tuebingen, Germany
| | - A K Pakkir Shah
- University of Tuebingen, CMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Infection Medicine, Tuebingen, Germany
| | - A Grélard
- L'Institut de Chimie et Biologie des Membranes et des Nano-Objets (CBMN), Unité Mixte de Recherche (UMR) 5248, Centre National de la Recherche (CNRS), University of Bordeaux, Pessac, France
| | - Y Zi-Long
- Department of Biophysics, School of Basic Medical Sciences, Peking University, Beijing, China
| | - A de Vicente
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - A Pérez García
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - L Bai
- Department of Biophysics, School of Basic Medical Sciences, Peking University, Beijing, China
| | - A Loquet
- L'Institut de Chimie et Biologie des Membranes et des Nano-Objets (CBMN), Unité Mixte de Recherche (UMR) 5248, Centre National de la Recherche (CNRS), University of Bordeaux, Pessac, France
| | - D Petras
- University of Tuebingen, CMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Infection Medicine, Tuebingen, Germany
- University of California Riverside, Department of Biochemistry, Riverside, USA
| | - D Romero
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Málaga, Spain.
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11
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Mehta N, Meng Y, Zare R, Kamenetsky-Goldstein R, Sattely E. A developmental gradient reveals biosynthetic pathways to eukaryotic toxins in monocot geophytes. Cell 2024; 187:5620-5637.e10. [PMID: 39276773 DOI: 10.1016/j.cell.2024.08.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 01/23/2024] [Accepted: 08/13/2024] [Indexed: 09/17/2024]
Abstract
Numerous eukaryotic toxins that accumulate in geophytic plants are valuable in the clinic, yet their biosynthetic pathways have remained elusive. A notable example is the >150 Amaryllidaceae alkaloids (AmAs), including galantamine, an FDA-approved treatment for Alzheimer's disease. We show that while AmAs accumulate to high levels in many daffodil tissues, biosynthesis is localized to nascent, growing tissue at the leaf base. A similar trend is found in the production of steroidal alkaloids (e.g., cyclopamine) in corn lily. This model of active biosynthesis enabled the elucidation of a complete set of biosynthetic genes that can be used to produce AmAs. Taken together, our work sheds light on the developmental and enzymatic logic of diverse alkaloid biosynthesis in daffodils. More broadly, it suggests a paradigm for biosynthesis regulation in monocot geophytes, where plants are protected from herbivory through active charging of newly formed cells with eukaryotic toxins that persist as above-ground tissue develops.
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Affiliation(s)
- Niraj Mehta
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Yifan Meng
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Richard Zare
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | | | - Elizabeth Sattely
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA; HHMI, Stanford University, Stanford, CA 94305, USA.
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12
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Frempong KEB, He G, Kuang M, Xue M, Wang J, Wei Y, Zhou J. Sulfonated cottonseed hydrolysates with adjustable amphiphilicity as environmental -Stress stable emulsifiers. Food Chem 2024; 454:139787. [PMID: 38795628 DOI: 10.1016/j.foodchem.2024.139787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 05/28/2024]
Abstract
Cottonseed protein isolate (CPI) is a valuable agro-industrial waste with potential biotechnological applications. However, inadequate stability in water due to its characteristic hinders its widespread use. Therefore, a new sulfonation modification approach was developed to improve the amphiphilicity and structural flexibility of CPI. Structural characterizations confirmed the successful incorporation of sulfonate groups with structural and conformational changes. This significantly unfolded molecular-chain, and improved amphiphilicity, flexibility, and surface-hydrophobicity while reducing pI (5.1-1.7), and molecular-weight (5745-2089 g/mol). The modified samples exhibited improved emulsification with higher amounts of absorbed proteins on the droplet interface, smaller droplet size, and a higher zeta-potential. Additionally, they possessed good emulsification ability under acidic conditions. The nano-emulsions exhibited long-term stability (≥70 days) under different environmental conditions, with excellent fluidity. This study contributes to understanding sulfonation as a viable approach for improving protein properties, thus, opening up new possibilities for their application and maximizing their economic benefits.
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Affiliation(s)
- Kwame Eduam Baiden Frempong
- Engineering Research Center of Biomass Materials, Ministry of Education, School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010, PR China
| | - Guiqiang He
- Engineering Research Center of Biomass Materials, Ministry of Education, School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010, PR China
| | - Meng Kuang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang, Henan 455000, PR China.
| | - Min Xue
- Institute of Feed Research, Chinese Academy of Agricultural Sciences, 100081 Beijing, PR China
| | - Jie Wang
- Institute of Feed Research, Chinese Academy of Agricultural Sciences, 100081 Beijing, PR China
| | - Yanxia Wei
- Engineering Research Center of Biomass Materials, Ministry of Education, School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010, PR China.
| | - Jian Zhou
- Engineering Research Center of Biomass Materials, Ministry of Education, School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010, PR China.
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13
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Liu J, Jiang B, Xu W, Liu Q, Huang H, Chang X, Ma G, Xu X, Zhou L, Xiao GG, Guo J. Targeted inhibition of CHKα and mTOR in models of pancreatic ductal adenocarcinoma: A novel regimen for metastasis. Cancer Lett 2024; 605:217280. [PMID: 39343354 DOI: 10.1016/j.canlet.2024.217280] [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: 07/16/2024] [Revised: 09/17/2024] [Accepted: 09/24/2024] [Indexed: 10/01/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly metastatic malignancy for which there are currently no effective anti-metastatic therapies. Herein, we employed single-cell RNA sequencing and metabolomics analysis to demonstrate that metastatic cells highly express focal adhesion kinase (FAK), which promotes metastasis by remodeling choline kinase α (CHKα)-dependent choline metabolism. We designed a novel CHKα inhibitor, CHKI-03, and verified its efficacy in inhibiting metastasis in multiple preclinical models. Classical and newly synthesized small-molecule inhibitors have previously been used to assess the therapeutic potential of targeting mTOR and CHKα in various animal models. Mechanistically, FAK activated mTOR and its downstream HIF-1α, thereby elevating CHKα expression and promoting the proliferation, migration, and invasion of PDAC cells, as well as tumor growth and metastasis. Consistently, high expression levels of both FAK and CHKα are correlated with poor prognosis in patients with PDAC. Notably, CHK1-03 inhibited CHKα expression and also suppressed mTORC1 phosphorylation, disrupting the mTORC1-CHKα positive feedback loop. In addition, the combination of CHKI-03 and the mTORC1 inhibitor rapamycin synergistically inhibited tumor growth and metastasis in PDX models. The combination of CHKI-03 and rapamycin demonstrates considerable therapeutic efficacy in PDO models resistant to gemcitabine. Our findings reveal a pivotal mechanism underlying PDAC metastasis regulated by mTORC1-CHKα loop-dependent choline metabolism reprogramming, highlighting the therapeutic potential of this novel regimen for treating PDAC metastasis.
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Affiliation(s)
- Jianzhou Liu
- Department of General Surgery, Key Laboratory of Research in Pancreatic Tumor, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China; Institute of Clinical Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Bolun Jiang
- Department of Colorectal Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 31003, China
| | - Wenchao Xu
- Department of General Surgery, Key Laboratory of Research in Pancreatic Tumor, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Qiaofei Liu
- Department of General Surgery, Key Laboratory of Research in Pancreatic Tumor, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Haoran Huang
- Department of General Surgery, Key Laboratory of Research in Pancreatic Tumor, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Xiaoyan Chang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Guoxu Ma
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Key Laboratory of New Drug Discovery Based on Classic Chinese Medicine Prescription, Chinese Academy of Medical Sciences, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - Xudong Xu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Key Laboratory of New Drug Discovery Based on Classic Chinese Medicine Prescription, Chinese Academy of Medical Sciences, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - Li Zhou
- Department of General Surgery, Key Laboratory of Research in Pancreatic Tumor, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Gary Guishan Xiao
- Functional Genomics and Proteomics Center, Creighton University Medical Center, 601N 30th ST, Omaha, NE, 68131, USA
| | - Junchao Guo
- Department of General Surgery, Key Laboratory of Research in Pancreatic Tumor, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
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14
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Hwang W, Austin SL, Blondel A, Boittier ED, Boresch S, Buck M, Buckner J, Caflisch A, Chang HT, Cheng X, Choi YK, Chu JW, Crowley MF, Cui Q, Damjanovic A, Deng Y, Devereux M, Ding X, Feig MF, Gao J, Glowacki DR, Gonzales JE, Hamaneh MB, Harder ED, Hayes RL, Huang J, Huang Y, Hudson PS, Im W, Islam SM, Jiang W, Jones MR, Käser S, Kearns FL, Kern NR, Klauda JB, Lazaridis T, Lee J, Lemkul JA, Liu X, Luo Y, MacKerell AD, Major DT, Meuwly M, Nam K, Nilsson L, Ovchinnikov V, Paci E, Park S, Pastor RW, Pittman AR, Post CB, Prasad S, Pu J, Qi Y, Rathinavelan T, Roe DR, Roux B, Rowley CN, Shen J, Simmonett AC, Sodt AJ, Töpfer K, Upadhyay M, van der Vaart A, Vazquez-Salazar LI, Venable RM, Warrensford LC, Woodcock HL, Wu Y, Brooks CL, Brooks BR, Karplus M. CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed. J Phys Chem B 2024. [PMID: 39303207 DOI: 10.1021/acs.jpcb.4c04100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
Since its inception nearly a half century ago, CHARMM has been playing a central role in computational biochemistry and biophysics. Commensurate with the developments in experimental research and advances in computer hardware, the range of methods and applicability of CHARMM have also grown. This review summarizes major developments that occurred after 2009 when the last review of CHARMM was published. They include the following: new faster simulation engines, accessible user interfaces for convenient workflows, and a vast array of simulation and analysis methods that encompass quantum mechanical, atomistic, and coarse-grained levels, as well as extensive coverage of force fields. In addition to providing the current snapshot of the CHARMM development, this review may serve as a starting point for exploring relevant theories and computational methods for tackling contemporary and emerging problems in biomolecular systems. CHARMM is freely available for academic and nonprofit research at https://academiccharmm.org/program.
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Affiliation(s)
- Wonmuk Hwang
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, United States
- Department of Materials Science and Engineering, Texas A&M University, College Station, Texas 77843, United States
- Department of Physics and Astronomy, Texas A&M University, College Station, Texas 77843, United States
- Center for AI and Natural Sciences, Korea Institute for Advanced Study, Seoul 02455, Republic of Korea
| | - Steven L Austin
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Arnaud Blondel
- Institut Pasteur, Université Paris Cité, CNRS UMR3825, Structural Bioinformatics Unit, 28 rue du Dr. Roux F-75015 Paris, France
| | - Eric D Boittier
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Stefan Boresch
- Faculty of Chemistry, Department of Computational Biological Chemistry, University of Vienna, Wahringerstrasse 17, 1090 Vienna, Austria
| | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106, United States
| | - Joshua Buckner
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zürich, CH-8057 Zürich, Switzerland
| | - Hao-Ting Chang
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan, ROC
| | - Xi Cheng
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yeol Kyo Choi
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Jhih-Wei Chu
- Institute of Bioinformatics and Systems Biology, Department of Biological Science and Technology, Institute of Molecular Medicine and Bioengineering, and Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan, ROC
| | - Michael F Crowley
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Qiang Cui
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts 02215, United States
| | - Ana Damjanovic
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Physics and Astronomy, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Yuqing Deng
- Shanghai R&D Center, DP Technology, Ltd., Shanghai 201210, China
| | - Mike Devereux
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Xinqiang Ding
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Michael F Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jiali Gao
- School of Chemical Biology & Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, China
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518055, China
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - David R Glowacki
- CiTIUS Centro Singular de Investigación en Tecnoloxías Intelixentes da USC, 15705 Santiago de Compostela, Spain
| | - James E Gonzales
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, United States
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Mehdi Bagerhi Hamaneh
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106, United States
| | | | - Ryan L Hayes
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697, United States
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697, United States
| | - Jing Huang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
| | - Yandong Huang
- College of Computer Engineering, Jimei University, Xiamen 361021, China
| | - Phillip S Hudson
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
- Medicine Design, Pfizer Inc., Cambridge, Massachusetts 02139, United States
| | - Wonpil Im
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Shahidul M Islam
- Department of Chemistry, Delaware State University, Dover, Delaware 19901, United States
| | - Wei Jiang
- Computational Science Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Michael R Jones
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Silvan Käser
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Fiona L Kearns
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Nathan R Kern
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering, Institute for Physical Science and Technology, Biophysics Program, University of Maryland, College Park, Maryland 20742, United States
| | - Themis Lazaridis
- Department of Chemistry, City College of New York, New York, New York 10031, United States
| | - Jinhyuk Lee
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34141, Republic of Korea
| | - Justin A Lemkul
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Xiaorong Liu
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yun Luo
- Department of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, California 91766, United States
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Dan T Major
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Kwangho Nam
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States
| | - Lennart Nilsson
- Karolinska Institutet, Department of Biosciences and Nutrition, SE-14183 Huddinge, Sweden
| | - Victor Ovchinnikov
- Harvard University, Department of Chemistry and Chemical Biology, Cambridge, Massachusetts 02138, United States
| | - Emanuele Paci
- Dipartimento di Fisica e Astronomia, Universitá di Bologna, Bologna 40127, Italy
| | - Soohyung Park
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Amanda R Pittman
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Carol Beth Post
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Samarjeet Prasad
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Jingzhi Pu
- Department of Chemistry and Chemical Biology, Indiana University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Yifei Qi
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | | | - Daniel R Roe
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Benoit Roux
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | | | - Jana Shen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Andrew C Simmonett
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Alexander J Sodt
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Kai Töpfer
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Meenu Upadhyay
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Arjan van der Vaart
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | | | - Richard M Venable
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Luke C Warrensford
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - H Lee Woodcock
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Yujin Wu
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Charles L Brooks
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Martin Karplus
- Harvard University, Department of Chemistry and Chemical Biology, Cambridge, Massachusetts 02138, United States
- Laboratoire de Chimie Biophysique, ISIS, Université de Strasbourg, 67000 Strasbourg, France
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15
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Huyen NTT, Phuc BV, Huyen TT, Hong TT, Nguyen H, Nguyen VH, Nguyen MT, Hung TQ, Dinh CP, Dang TT. Design and Synthesis of Novel β-Carboline-Bisindole Hybrids as Potential Anticancer Agents. ChemMedChem 2024; 19:e202400316. [PMID: 38856518 DOI: 10.1002/cmdc.202400316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 06/04/2024] [Accepted: 06/05/2024] [Indexed: 06/11/2024]
Abstract
We are reporting a short and convenient pathway for the synthesis of novel β-carboline-bisindole hybrid compounds from relatively cheap and commercially available chemicals such as tryptamine, dialdehydes and indoles. These newly designed compounds can also be prepared in high yields with the tolerance of many functional groups under mild conditions. Notably, these β-carboline-bisindole hybrid compounds exhibited some promising applications as anticancer agents against the three common cancer cell lines MCF-7 (breast cancer), SK-LU-1 (lung cancer), and HepG2 (liver cancer). The two best compounds 5 b and 5 g inhibited the aforementioned cell lines with the same IC50 range of the reference Ellipticine at less than 2 μM. A molecular docking study to gain more information about the interactions between the synthesized molecules and the kinase domain of the EGFR was performed. Therefore, this finding can have significant impacts on the development of future research in medicinal chemistry and drug discovery.
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Affiliation(s)
- Nguyen Thi Thanh Huyen
- Faculty of Chemistry, VNU-Ha Noi University of Science, 19 Le Thanh Tong, Phan Chu Trinh, Hoan Kiem, Hanoi, Vietnam
| | - Ban Van Phuc
- Institute of Chemistry, Vietnamese Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Hanoi, Vietnam
| | - Tran Thi Huyen
- Faculty of Chemistry, VNU-Ha Noi University of Science, 19 Le Thanh Tong, Phan Chu Trinh, Hoan Kiem, Hanoi, Vietnam
| | - Tran Thi Hong
- Faculty of Chemistry, VNU-Ha Noi University of Science, 19 Le Thanh Tong, Phan Chu Trinh, Hoan Kiem, Hanoi, Vietnam
| | - Hien Nguyen
- Faculty of Chemistry, Hanoi National University of Education (HNUE), Vietnam
| | - Van Ha Nguyen
- Faculty of Chemistry, VNU-Ha Noi University of Science, 19 Le Thanh Tong, Phan Chu Trinh, Hoan Kiem, Hanoi, Vietnam
| | - Minh Tho Nguyen
- Faculty of Applied Technology, School of Technology, Van Lang University, Ho Chi Minh City, 70000, Vietnam
| | - Tran Quang Hung
- Institute of Chemistry, Vietnamese Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Vietnam
| | - Chau Phi Dinh
- NuChem Sciences, a Sygnature Discovery Business, 480 rue Perreault, Lévis, QC, G6 W 7 V6, Canada
| | - Tuan Thanh Dang
- Faculty of Chemistry, VNU-Ha Noi University of Science, 19 Le Thanh Tong, Phan Chu Trinh, Hoan Kiem, Hanoi, Vietnam
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16
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Staudt S, Nikolka F, Perl M, Franz J, Leblay N, Yuan XK, Warmuth L, Fantes MA, Skorupskaitė A, Fei T, Bromberg M, Martin-Uriz PS, Rodriguez-Madoz JR, Ziegler-Martin K, Gholam NA, Benz P, Tran PH, Freitag F, Riester Z, Stein-Thoeringer C, Schmitt M, Kleigrewe K, Weber J, Mangold K, Einsele H, Prosper F, Ellmeier W, Busch D, Visekruna A, Slingerland J, Shouval R, Hiller K, van den Brink M, Pausch P, Neri P, Hudecek M, Poeck H, Luu M. Microbial metabolite-guided CAR T cell engineering enhances anti-tumor immunity via epigenetic-metabolic crosstalk. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.19.608538. [PMID: 39314273 PMCID: PMC11418944 DOI: 10.1101/2024.08.19.608538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Emerging data have highlighted a correlation between microbiome composition and cancer immunotherapy outcome. While commensal bacteria and their metabolites are known to modulate the host environment, contradictory effects and a lack of mechanistic understanding impede the translation of microbiome-based therapies into the clinic. In this study, we demonstrate that abundance of the commensal metabolite pentanoate is predictive for survival of chimeric antigen receptor (CAR) T cell patients in two independent cohorts. Its implementation in the CAR T cell manufacturing workflow overcomes solid tumor microenvironments in immunocompetent cancer models by hijacking the epigenetic-metabolic crosstalk, reducing exhaustion and promoting naive-like differentiation. While synergy of clinically relevant drugs mimicked the phenotype of pentanoate-engineered CAR T cells in vitro, in vivo challenge showed inferior tumor control. Metabolic tracing of 13C-pentanoate revealed citrate generation in the TCA cycle via the acetyl- and succinyl-CoA entry points as a unique feature of the C5 aliphatic chain. Inhibition of the ATP-citrate lyase, which links metabolic output and histone acetylation, led to accumulation of pentanoate-derived citrate from the succinyl-CoA route and decreased functionality of SCFA-engineered CAR T cells. Our data demonstrate that microbial metabolites are incorporated as epigenetic imprints and implementation into CAR T cell production might serve as embodiment of the microbiome-host axis benefits for clinical applications.
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Affiliation(s)
- Sarah Staudt
- Lehrstuhl für Zelluläre Immuntherapie, Medizinische Klinik und Poliklinik II, Universitätsklinikum Würzburg, Würzburg, Germany
| | - Fabian Nikolka
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Markus Perl
- University Hospital Regensburg, Department of Internal Medicine III, Hematology & Internal Oncology, Regensburg, Germany
| | - Julia Franz
- Lehrstuhl für Zelluläre Immuntherapie, Medizinische Klinik und Poliklinik II, Universitätsklinikum Würzburg, Würzburg, Germany
| | - Noémi Leblay
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
| | - Xiaoli-Kat Yuan
- Precision Oncology Hub, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
| | - Linda Warmuth
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Munich, Germany
| | - Matthias A. Fantes
- University Hospital Regensburg, Department of Internal Medicine III, Hematology & Internal Oncology, Regensburg, Germany
| | - Aistė Skorupskaitė
- Life Sciences Center - European Molecular Biology Laboratory (LSC-EMBL) Partnership for Genome Editing Technologies, Vilnius University - Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Teng Fei
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria Bromberg
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Patxi San Martin-Uriz
- Hemato-Oncology Program, Cima Universidad de Navarra, Centro de Investigacion Biomedica en Red de Cancer (CIBERONC), Cancer Center Clinica Universidad de Navarra (CCUN), IdiSNA, Pamplona, Spain
| | - Juan Roberto Rodriguez-Madoz
- Hemato-Oncology Program, Cima Universidad de Navarra, Centro de Investigacion Biomedica en Red de Cancer (CIBERONC), Cancer Center Clinica Universidad de Navarra (CCUN), IdiSNA, Pamplona, Spain
| | - Kai Ziegler-Martin
- Lehrstuhl für Zelluläre Immuntherapie, Medizinische Klinik und Poliklinik II, Universitätsklinikum Würzburg, Würzburg, Germany
| | - Nazdar Adil Gholam
- Lehrstuhl für Zelluläre Immuntherapie, Medizinische Klinik und Poliklinik II, Universitätsklinikum Würzburg, Würzburg, Germany
| | - Pascal Benz
- Lehrstuhl für Zelluläre Immuntherapie, Medizinische Klinik und Poliklinik II, Universitätsklinikum Würzburg, Würzburg, Germany
| | - Phuc-Huu Tran
- Medical University of Vienna, Center for Pathophysiology, Infectiology and Immunology, Institute of Immunology, Vienna, Austria
| | - Fabian Freitag
- Lehrstuhl für Zelluläre Immuntherapie, Medizinische Klinik und Poliklinik II, Universitätsklinikum Würzburg, Würzburg, Germany
| | - Zeno Riester
- Lehrstuhl für Zelluläre Immuntherapie, Medizinische Klinik und Poliklinik II, Universitätsklinikum Würzburg, Würzburg, Germany
- Mildred Scheel Early Career Center, University Hospital of Würzburg, Würzburg, Germany
| | | | - Michael Schmitt
- Department of Hematology, Oncology and Rheumatology, University Clinic Heidelberg, Heidelberg, Germany
| | - Karin Kleigrewe
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany
| | - Justus Weber
- Lehrstuhl für Zelluläre Immuntherapie, Medizinische Klinik und Poliklinik II, Universitätsklinikum Würzburg, Würzburg, Germany
| | - Kira Mangold
- Lehrstuhl für Zelluläre Immuntherapie, Medizinische Klinik und Poliklinik II, Universitätsklinikum Würzburg, Würzburg, Germany
- Institute for Medical Microbiology and Hygiene, Philipps-University Marburg, Marburg, Germany
| | - Hermann Einsele
- Medizinische Klinik und Poliklinik II, Universitätsklinikum Würzburg, Würzburg, Germany
| | - Felipe Prosper
- Hematology and Cell Therapy Department, Clinica Universidad de Navarra (CUN), Hemato-Oncology Program, Cima Universidad de Navarra. Centro de Investigacion Biomedica en Red de Cancer (CIBERONC), Cancer Center Clinica Universidad de Navarra (CCUN), IdiSNA, Pamplona, Spain
| | - Wilfried Ellmeier
- Medical University of Vienna, Center for Pathophysiology, Infectiology and Immunology, Institute of Immunology, Vienna, Austria
| | - Dirk Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Munich, Germany
| | - Alexander Visekruna
- Institute for Medical Microbiology and Hygiene, Philipps-University Marburg, Marburg, Germany
| | | | - Roni Shouval
- Adult Bone Marrow Transplantation Service and Cellular Therapy Service, Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
| | - Karsten Hiller
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | | | - Patrick Pausch
- Life Sciences Center - European Molecular Biology Laboratory (LSC-EMBL) Partnership for Genome Editing Technologies, Vilnius University - Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Paola Neri
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
| | - Michael Hudecek
- Lehrstuhl für Zelluläre Immuntherapie, Medizinische Klinik und Poliklinik II, Universitätsklinikum Würzburg, Würzburg, Germany
- Bavarian Cancer Research Center (BZKF), Regensburg & Würzburg, Germany
| | - Hendrik Poeck
- University Hospital Regensburg, Department of Internal Medicine III, Hematology & Internal Oncology, Regensburg, Germany
- Bavarian Cancer Research Center (BZKF), Regensburg & Würzburg, Germany
- Leibniz Institute for Immunotherapy (LIT), Regensburg, Germany
| | - Maik Luu
- Lehrstuhl für Zelluläre Immuntherapie, Medizinische Klinik und Poliklinik II, Universitätsklinikum Würzburg, Würzburg, Germany
- Leibniz Institute for Immunotherapy (LIT), Regensburg, Germany
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17
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Del Favero G, Bergen J, Palm L, Fellinger C, Matlaeva M, Szabadi A, Fernandes AS, Saraiva N, Schröder C, Marko D. Short-Term Exposure to Foodborne Xenoestrogens Affects Breast Cancer Cell Morphology and Motility Relevant for Metastatic Behavior In Vitro. Chem Res Toxicol 2024. [PMID: 39262136 DOI: 10.1021/acs.chemrestox.4c00061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
Abstract
Breast cancer is highly susceptible to metastasis formation. During the time of disease progression, tumor pathophysiology can be impacted by endogenous factors, like hormonal status, as well as by environmental exposures, such as those related to diet and lifestyle. New lines of evidence point toward a potential role for foodborne endocrine disruptive chemicals in this respect; however, mechanistic understanding remains limited. At the molecular level, crucial steps toward metastasis formation include cell structural changes, alteration of adhesion, and reorganization of cytoskeletal proteins involved in motility. Hence, this study investigates the potential of dietary xenoestrogens to impact selected aspects of breast cancer cell mechanotransduction. Taking the onset of the metastatic cascade as a model, experiments focused on cell-matrix adhesion, single-cell migration, and adaptation of cell morphology. Dietary mycoestrogens alternariol (AOH, 1 μM) and α-zearalenol (α-ZEL, 10 nM), soy isoflavone genistein (GEN, 1 μM), and food packaging plasticizer bisphenol A (BPA, 10 nM) were applied as single compounds or in mixtures. Pursuing the hypothesis that endocrine active molecules could affect cell functions beyond the estrogen receptor-dependent cascade, experiments were performed comparing the MCF-7 cell line to the triple negative breast cancer cells MDA MB-231. Indeed, the four compounds functionally affected the motility and the adhesion of both cell types. These responses were coherent with rearrangements of the actin cytoskeleton and with the modulation of the expression of integrin β1 and cathepsin D. Mechanistically, molecular dynamics simulations confirmed a potential interaction with fragments of the α1 and β1 integrin subunits. In sum, dietary xenoestrogens proved effective in modifying the motility and adhesion of breast cancer cells, as predictive end points for metastatic behavior in vitro. These effects were measurable after short incubation times (1 or 8 h) and contribute to shed novel light on the activity of compounds with hormonal mimicry potential in breast cancer progression.
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Affiliation(s)
- Giorgia Del Favero
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
- Core Facility Multimodal Imaging, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
| | - Janice Bergen
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
- Core Facility Multimodal Imaging, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Str. 42, Vienna 1090, Austria
| | - Lena Palm
- Computational Biological Chemistry Department, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
| | - Christian Fellinger
- Computational Biological Chemistry Department, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
- Department of Pharmaceutical Sciences, Faculty of Life Sciences, University of Vienna, Vienna 1090, Austria
- Christian Doppler Laboratory for Molecular Informatics in the Biosciences, Department for Pharmaceutical Sciences, University of Vienna, Vienna 1090, Austria
| | - Maria Matlaeva
- Computational Biological Chemistry Department, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
| | - András Szabadi
- Computational Biological Chemistry Department, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
| | - Ana Sofia Fernandes
- CBIOS, Universidade Lusófona's Research Center for Biosciences & Health Technologies, Lisboa 1749-024, Portugal
| | - Nuno Saraiva
- CBIOS, Universidade Lusófona's Research Center for Biosciences & Health Technologies, Lisboa 1749-024, Portugal
| | - Christian Schröder
- Computational Biological Chemistry Department, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
| | - Doris Marko
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
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18
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Wan X, Shahrear S, Chew SW, Vilaplana F, Mäkelä MR. Discovery of alkaline laccases from basidiomycete fungi through machine learning-based approach. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:120. [PMID: 39261970 PMCID: PMC11391777 DOI: 10.1186/s13068-024-02566-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Accepted: 09/02/2024] [Indexed: 09/13/2024]
Abstract
BACKGROUND Laccases can oxidize a broad spectrum of substrates, offering promising applications in various sectors, such as bioremediation, biomass fractionation in future biorefineries, and synthesis of biochemicals and biopolymers. However, laccase discovery and optimization with a desirable pH optimum remains a challenge due to the labor-intensive and time-consuming nature of the traditional laboratory methods. RESULTS This study presents a machine learning (ML)-integrated approach for predicting pH optima of basidiomycete fungal laccases, utilizing a small, curated dataset against a vast metagenomic data. Comparative computational analyses unveiled the structural and pH-dependent solubility differences between acidic and neutral-alkaline laccases, helping us understand the molecular bases of enzyme pH optimum. The pH profiling of the two ML-predicted alkaline laccase candidates from the basidiomycete fungus Lepista nuda further validated our computational approach, showing the accuracy of this comprehensive method. CONCLUSIONS This study uncovers the efficacy of ML in the prediction of enzyme pH optimum from minimal datasets, marking a significant step towards harnessing computational tools for systematic screening of enzymes for biotechnology applications.
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Affiliation(s)
- Xing Wan
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Biocenter 1, Viikinkaari 9, 00790, Helsinki, Finland.
| | - Sazzad Shahrear
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Biocenter 1, Viikinkaari 9, 00790, Helsinki, Finland
| | - Shea Wen Chew
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Biocenter 1, Viikinkaari 9, 00790, Helsinki, Finland
| | - Francisco Vilaplana
- Division of Glycoscience, Department of Chemistry, School of Engineering Science in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, Roslagstullbacken 21, 11421, Stockholm, Sweden
| | - Miia R Mäkelä
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Biocenter 1, Viikinkaari 9, 00790, Helsinki, Finland.
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 02150, Espoo, Finland.
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19
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Biswal S, Mallick B. Unlocking the potential of signature-based drug repurposing for anticancer drug discovery. Arch Biochem Biophys 2024; 761:110150. [PMID: 39265695 DOI: 10.1016/j.abb.2024.110150] [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: 04/21/2024] [Revised: 08/01/2024] [Accepted: 09/09/2024] [Indexed: 09/14/2024]
Abstract
Cancer is the leading cause of death worldwide and is often associated with tumor relapse even after chemotherapeutics. This reveals malignancy is a complex process, and high-throughput omics strategies in recent years have contributed significantly in decoding the molecular mechanisms of these complex events in cancer. Further, the omics studies yield a large volume of cancer-specific molecular signatures that promote the discovery of cancer therapy drugs by a method termed signature-based drug repurposing. The drug repurposing method identifies new uses for approved drugs beyond their intended initial therapeutic use, and there are several approaches to it. In this review, we discuss signature-based drug repurposing in cancer, how cancer omics have revolutionized this method of drug discovery, and how one can use the cancer signature data for repurposed drug identification by providing a step-by-step procedural handout. This modern approach maximizes the use of existing therapeutic agents for cancer therapy or combination therapy to overcome chemotherapeutics resistance, making it a pragmatic and efficient alternative to traditional resource-intensive and time-consuming methods.
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Affiliation(s)
- Sruti Biswal
- RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology Rourkela, Rourkela-769008, Odisha, India
| | - Bibekanand Mallick
- RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology Rourkela, Rourkela-769008, Odisha, India.
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20
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Kihn KC, Purdy O, Lowe V, Slachtova L, Smith AK, Shapiro P, Deredge DJ. Integration of Hydrogen-Deuterium Exchange Mass Spectrometry with Molecular Dynamics Simulations and Ensemble Reweighting Enables High Resolution Protein-Ligand Modeling. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024. [PMID: 39254669 DOI: 10.1021/jasms.4c00202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Hydrogen-Deuterium exchange mass spectrometry's (HDX-MS) utility in identifying and characterizing protein-small molecule interaction sites has been established. The regions that are seen to be protected from exchange upon ligand binding indicate regions that may be interacting with the ligand, giving a qualitative understanding of the ligand binding pocket. However, quantitatively deriving an accurate high-resolution structure of the protein-ligand complex from the HDX-MS data remains a challenge, often limiting its use in applications such as small molecule drug design. Recent efforts have focused on the development of methods to quantitatively model Hydrogen-Deuterium exchange (HDX) data from computationally modeled structures to garner atomic level insights from peptide-level resolution HDX-MS. One such method, HDX ensemble reweighting (HDXer), employs maximum entropy reweighting of simulated HDX data to experimental HDX-MS to model structural ensembles. In this study, we implement and validate a workflow which quantitatively leverages HDX-MS data to accurately model protein-small molecule ligand interactions. To that end, we employ a strategy combining computational protein-ligand docking, molecular dynamics simulations, HDXer, and dimensional reduction and clustering approaches to extract high-resolution drug binding poses that most accurately conform with HDX-MS data. We apply this workflow to model the interaction of ERK2 and FosA with small molecule compounds and inhibitors they are known to bind. In five out of six of the protein-ligand pairs tested, the HDX derived protein-ligand complexes result in a ligand root-mean-square deviation (RMSD) within 2.5 Å of the known crystal structure ligand.
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Affiliation(s)
- Kyle C Kihn
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States
| | - Olivia Purdy
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States
| | - Vincent Lowe
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States
| | - Lenka Slachtova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague, Prague 116 36, Czech Republic
| | - Ally K Smith
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States
| | - Paul Shapiro
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States
| | - Daniel J Deredge
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States
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21
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Chingizova EA, Chingizov AR, Menchinskaya ES, Pislyagin EA, Kuzmich AS, Leshchenko EV, Borkunov GV, Guzhova IV, Aminin DL, Yurchenko EA. The influence of marine fungal meroterpenoid meroantarctine A toward HaCaT keratinocytes infected with Staphylococcus aureus. J Antibiot (Tokyo) 2024:10.1038/s41429-024-00771-x. [PMID: 39256545 DOI: 10.1038/s41429-024-00771-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 08/17/2024] [Accepted: 08/29/2024] [Indexed: 09/12/2024]
Abstract
A new biological activity was discovered for marine fungal meroterpenoid meroantarctine A with unique 6/5/6/6 polycyclic system. It was found that meroantarctine A can significantly reduce biofilm formation by Staphylococcus aureus with an IC50 of 9.2 µM via inhibition of sortase A activity. Co-cultivation of HaCaT keratinocytes with a S. aureus suspension was used as an in vitro model of skin infection. Treatment of S. aureus-infected HaCaT cells with meroantarctine A at 10 µM caused a reduction in the production of TNF-α, IL-18, NO, and ROS, as well as LDH release and caspase 1 activation in these cells and, finally, recovered the proliferation and migration of HaCaT cells in an in vitro wound healing assay up to the control level. Thus, meroantarctine A is a new promising antibiofilm compound which can effective against S. aureus caused skin infection.
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Affiliation(s)
- Ekaterina A Chingizova
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry FEB RAS, 690022, Vladivostok, Russia.
| | - Artur R Chingizov
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry FEB RAS, 690022, Vladivostok, Russia
| | | | - Evgeny A Pislyagin
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry FEB RAS, 690022, Vladivostok, Russia
| | - Aleksandra S Kuzmich
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry FEB RAS, 690022, Vladivostok, Russia
| | - Elena V Leshchenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry FEB RAS, 690022, Vladivostok, Russia
| | - Gleb V Borkunov
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry FEB RAS, 690022, Vladivostok, Russia
| | | | - Dmitry L Aminin
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry FEB RAS, 690022, Vladivostok, Russia
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, 80708, Kaohsiung, Taiwan
| | - Ekaterina A Yurchenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry FEB RAS, 690022, Vladivostok, Russia.
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22
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Arabestani MR, Saadat M, Taherkhani A. Antibiotic resistance challenge: evaluating anthraquinones as rifampicin monooxygenase inhibitors through integrated bioinformatics analysis. Genomics Inform 2024; 22:13. [PMID: 39232833 PMCID: PMC11375879 DOI: 10.1186/s44342-024-00015-2] [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: 07/09/2024] [Accepted: 07/23/2024] [Indexed: 09/06/2024] Open
Abstract
OBJECTIVE Antibiotic resistance poses a pressing and crucial global public health challenge, leading to significant clinical and health-related consequences. Substantial evidence highlights the pivotal involvement of rifampicin monooxygenase (RIFMO) in the context of antibiotic resistance. Hence, inhibiting RIFMO could offer potential in the treatment of various infections. Anthraquinones, a group of organic compounds, have shown promise in addressing tuberculosis. This study employed integrated bioinformatics approaches to evaluate the potential inhibitory effects of a selection of anthraquinones on RIFMO. The findings were subsequently compared with those of rifampicin (RIF), serving as a positive control inhibitor. METHODS The AutoDock 4.0 tool assessed the binding free energy between 21 anthraquinones and the RIFMO catalytic cleft. The ligands were ranked based on the most favorable scores derived from ΔGbinding. The docking analyses for the highest-ranked anthraquinone and RIF underwent a cross-validation process. This validation procedure utilized the SwissDock server and the Schrödinger Maestro docking software. Molecular dynamics simulations were conducted to scrutinize the stability of the backbone atoms in free RIFMO, RIFMO-RIF, and RIFMO complexed with the top-ranked anthraquinone throughout a 100-ns computer simulation. The Discovery Studio Visualizer tool visualized interactions between RIFMO residues and ligands. An evaluation of the pharmacokinetics and toxicity profiles of the tested compounds was also conducted. RESULTS Five anthraquinones were indicated with ΔGbinding scores less than - 10 kcal/mol. Hypericin emerged as the most potent RIFMO inhibitor, boasting a ΔGbinding score and inhibition constant value of - 12.11 kcal/mol and 798.99 pM, respectively. The agreement across AutoDock 4.0, SwissDock, and Schrödinger Maestro results highlighted hypericin's notable binding affinity to the RIFMO catalytic cleft. The RIFMO-hypericin complex achieved stability after a 70-ns computer simulation, exhibiting a root-mean-square deviation of 0.55 nm. Oral bioavailability analysis revealed that all anthraquinones except hypericin, sennidin A, and sennidin B may be suitable for oral administration. Furthermore, the carcinogenicity prediction analysis indicated a favorable safety profile for all examined anthraquinones. CONCLUSION Inhibiting RIFMO, particularly with anthraquinones such as hypericin, holds promise as a potential therapeutic strategy for infectious diseases.
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Affiliation(s)
- Mohammad Reza Arabestani
- Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Masoumeh Saadat
- Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Amir Taherkhani
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.
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23
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Khazravi L, Hamedi J, Attar H, Ardjmand M. Nymphaea alba leaf powder effectiveness in removing nisin from fermentation broth using docking and experimental analysis. Sci Rep 2024; 14:20645. [PMID: 39232102 PMCID: PMC11375215 DOI: 10.1038/s41598-024-71513-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 08/28/2024] [Indexed: 09/06/2024] Open
Abstract
The accumulation of nisin in the fermentation medium can reduce the process's productivity. This research studied the potential of Nymphaea alba leaf powder (NALP) as a hydrophobic biosorbent for efficient in-situ nisin adsorption from the fermentation medium by docking and experimental analysis. Molecular docking analysis showed that di-galloyl ellagic acid, a phytochemical compound found in N. alba, had the highest affinity towards nisin. Enhancements in nisin adsorption were seen following pre-treatment of NAPL with HCl and MgCl2. A logistic growth model was employed to evaluate the growth dynamics of the biosorption capacity, offering valuable insights for process scalability. Furthermore, optimization through Response Surface Methodology elucidated optimal nisin desorption conditions by Liebig's law of the minimum, which posits that the scarcest resource governs production efficiency. Fourier Transform Infrared (FTIR) spectroscopy pinpointed vital functional groups involved in biosorption. Scanning electron microscopy revealed the changing physical characteristics of the biosorbent after exposure to nisin. The findings designate NALP as a feasible adsorbent for nisin removal from the fermentation broth, thus facilitating its application in the purification of other biotechnological products based on growth and production optimization principles.
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Affiliation(s)
- Leila Khazravi
- Department of Petroleum Engineering, Faculty of Petroleum and Chemical Engineering, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Javad Hamedi
- Department of Microbial Biotechnology, School of Biology, College of Science, University of Tehran, Tehran, Iran.
| | - Hossein Attar
- Department of Petroleum Engineering, Faculty of Petroleum and Chemical Engineering, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mehdi Ardjmand
- Chemical Engineering Department, Islamic Azad University, South Tehran Branch, Tehran, Iran
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24
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Zhou ZH, Stevens A, Kashyap S, Crofut E, Wang S, Muratore K, Johnson P. Structures of Native Doublet Microtubules from Trichomonas vaginalis Reveal Parasite-Specific Proteins as Potential Drug Targets. RESEARCH SQUARE 2024:rs.3.rs-4632384. [PMID: 39281863 PMCID: PMC11398567 DOI: 10.21203/rs.3.rs-4632384/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/18/2024]
Abstract
Doublet microtubules (DMTs) are flagellar components required for the protist Trichomonas vaginalis (Tv) to swim through the human genitourinary tract to cause trichomoniasis, the most common non-viral sexually transmitted disease. Lack of DMT structures has prevented structure-guided drug design to manage Tv infection. Here, we determined the cryo-EM structure of native Tv-DMTs, identifying 29 unique proteins, including 18 microtubule inner proteins and 9 microtubule outer proteins. While the A-tubule is simplistic compared to DMTs of other organisms, the B-tubule features specialized, parasite-specific proteins, such as TvFAP40 and TvFAP35 that form filaments near the inner and outer junctions, respectively, to stabilize DMTs and enable Tv locomotion. Notably, a small molecule, assigned as IP6, is coordinated within a pocket of TvFAP40 and has characteristics of a drug molecule. This first atomic model of the Tv-DMT highlights the diversity of eukaryotic motility machinery and provides a structural framework to inform rational design of therapeutics.
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25
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Ezzemani W, Altawalah H, Windisch M, Ouladlahsen A, Saile R, Kettani A, Ezzikouri S. Identification of Zika virus NS2B-NS3 protease and NS5 polymerase inhibitors by structure-based virtual screening of FDA-approved drugs. J Biomol Struct Dyn 2024; 42:8073-8088. [PMID: 37528667 DOI: 10.1080/07391102.2023.2242963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 07/26/2023] [Indexed: 08/03/2023]
Abstract
Zika virus (ZIKV) is a mosquito-borne human flavivirus responsible that causing emergency outbreaks in Brazil. ZIKV is suspected of causing Guillain-Barre syndrome in adults and microcephaly. The NS2B-NS3 protease and NS5 RNA-dependent RNA polymerase (RdRp), central to ZIKV multiplication, have been identified as attractive molecular targets for drugs. We performed a structure-based virtual screening of 2,659 FDA-approved small molecule drugs in the DrugBank database using AutoDock Vina in PyRx v0.8. Accordingly, 15 potential drugs were selected as ZIKV inhibitors because of their high values (binding affinity - binding energy) and we analyzed the molecular interactions between the active site amino acids and the compounds. Among these drugs, tamsulosin was found to interact most efficiently with NS2B/NS3 protease, as indicated by the lowest binding energy value (-8.27 kJ/mol), the highest binding affinity (-5.7 Kcal/mol), and formed H-bonds with amino acid residues TYRB130, SERB135, TYRB150. Furthermore, biotin was found to interact most efficiently with NS5 RdRp with a binding energy of -150.624 kJ/mol, a binding affinity of -5.6 Kcal/mol, and formed H-bonds with the amino acid residues ASPA665 and ASPA540. In vitro, in vivo, and clinical studies are needed to demonstrate anti-ZIKV safety and the efficacy of these FDA-approved drug candidates.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Wahiba Ezzemani
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
- Laboratoire de Biologie et Santé (URAC34), Départment de Biologie, Faculté des Sciences Ben Msik, Hassan II University of Casablanca, Morocco
| | - Haya Altawalah
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait
- Virology Unit, Yacoub Behbehani Center, Sabah Hospital, Ministry of Health, Kuwait
| | - Marc Windisch
- Applied Molecular Virology Laboratory, Discovery Biology Department, Institut Pasteur Korea, Gyeonggi-do, South Korea
| | - Ahd Ouladlahsen
- Faculté de médecine et de pharmacie, Université Hassan II, Casablanca, Morocco
- Service des maladies Infectieuses, CHU Ibn Rochd, Casablanca, Morocco
| | - Rachid Saile
- Laboratoire de Biologie et Santé (URAC34), Départment de Biologie, Faculté des Sciences Ben Msik, Hassan II University of Casablanca, Morocco
| | - Anass Kettani
- Laboratoire de Biologie et Santé (URAC34), Départment de Biologie, Faculté des Sciences Ben Msik, Hassan II University of Casablanca, Morocco
| | - Sayeh Ezzikouri
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
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Gayathiri E, Prakash P, Ahamed M, Pandiaraj S, Venkidasamy B, Dayalan H, Thangaraj P, Selvam K, Chaudhari SY, Govindasamy R, Thiruvengadam M. Multitargeted pharmacokinetics, molecular docking and network pharmacology-based identification of effective phytocompounds from Sauropus androgynus (L.) Merr for inflammation and cancer treatment. J Biomol Struct Dyn 2024; 42:7883-7896. [PMID: 37534448 DOI: 10.1080/07391102.2023.2243335] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 07/23/2023] [Indexed: 08/04/2023]
Abstract
According to worldwide health data, cancer, and inflammatory illnesses are on the rise and are among the most common causes of death. Across the world, these types of health problems are now considered top priorities for government health organizations. Hence, this study aimed to investigate medicinal plants' potential for treating cancer and inflammatory disorders. This network pharmacology analysis aims to learn more about the potential targets and mechanisms of action for the bioactive ingredients in Sauropus androgynus (L.) Merr L. The compound-target network and protein-protein interaction analysis were built using the STRING database. Using Network Analyst, Gene Ontology, and Kyoto Encyclopaedia of Genes and Genomes, pathway enrichment was performed on the hub genes. 1-hexadecanol was shown to inhibit drug-metabolizing enzymes in a pharmacokinetic investigation. Those samples of 1-hexadecanol were found to be 1-hexadecanol (BBB 0.783), GI High, Pgp Substrate Yes, CYP2C19 Inhibitor Yes, CYP2D6 Yes, and HI -89.803. The intermolecular binding energies for 1-hexadecanol (4-DRI, -8.2 kcal/mol) are evaluated. These results from a study on S. androgynus used molecular docking and network pharmacology to gain insight into the prime target genes and potential mechanisms identified for AKT1, mTOR, AR, PPID, FKBP5, and NR3C1. The PI3K-Akt signalling pathway has become an important regulatory node in various pathological processes requiring coordinated actions. Stability and favourable conformations have been resolved by considering nonbonding interactions such as electrostatic and hydrogen bonds in MD simulations of the perfect molecules using the Desmond package. Thus, using an appropriate platform of network pharmacology, molecular docking, and in vitro experiments, this study provides for the first time a clearer knowledge of the anti-cancer and anti-inflammatory molecular bioactivities of S. androgynus. Further in vitro and in vivo confirmations are strongly needed to determine the efficacy and therapeutic effects of 1-hexadecanol in the biological process.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ekambaram Gayathiri
- Department of Plant Biology and Plant Biotechnology, Guru Nanak College (Autonomous), Chennai, India
| | | | - Maqusood Ahamed
- Department of Physics and Astronomy, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Saravanan Pandiaraj
- Department of Self-Development Skills, King Saud University, Riyadh, Saudi Arabia
| | - Baskar Venkidasamy
- Department of Oral and Maxillofacial Surgery, Saveetha Dental College and Hospitals, Saveetha University, Chennai, India
| | - Haripriya Dayalan
- Department of Biotechnology, Rajalakshmi Engineering College (Affiliated to Anna University), Thandalam, Chennai, India
| | - Pratheep Thangaraj
- Department of Biotechnology, Rathinam College of Arts and Science, Coimbatore, India
| | | | - Somdatta Y Chaudhari
- Department of Pharmaceutical Chemistry, Modern College of Pharmacy, Nigdi, India
| | - Rajakumar Govindasamy
- Department of Orthodontics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
| | - Muthu Thiruvengadam
- Department of Applied Bioscience, College of Life and Environmental Science, Konkuk University, Seoul, South Korea
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Luan Y, Ding X, Zhang L, Huang S, Yang C, Tang Y, Xing L, Zhang H, Liu Z. Identification of Dalbergiae Odoriferae Lignum active ingredients and potential mechanisms in the treatment of adriamycin-induced cardiotoxicity based on network pharmacology and experimental verification. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:6661-6675. [PMID: 38498061 DOI: 10.1007/s00210-024-03016-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 02/15/2024] [Indexed: 03/19/2024]
Abstract
The purpose of this study is to investigate the ingredients and mechanisms through which Dalbergiae Odoriferae Lignum (DOL) reduces adriamycin-induced cardiotoxicity. DOL's ingredients and drug targets were acquired from Traditional Chinese Medicine System Pharmacology Database and Analysis Platform (TCMSP), and adriamycin-induced cardiotoxicity disease targets were gathered from GeneCards and National Center for Biotechnology Information (NCBI). The therapeutic targets of DOL against adriamycin-induced cardiotoxicity were identified by intersecting drug and disease targets. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) were conducted using R. Subsequently, core targets were determined and used for molecular docking with DOL ingredients. In vitro and in vivo experiments validated DOL's primary ingredients against adriamycin-induced cardiotoxicity efficacy. Western blot and immunohistochemistry verified its impact on target protein. After intersecting 530 drug targets and 51 disease targets, 19 therapeutic targets for DOL alleviated adriamycin-induced cardiotoxicity were received. Molecular docking demonstrated that DOL primary ingredient formononetin had a robust binding affinity for nitric oxide synthase 3 (NOS3). Experimental results showed that formononetin effectively mitigated adriamycin-induced cardiotoxicity. Additionally, western blot and immunohistochemistry showed that formononetin improved NOS3 expression. The network pharmacology and experimentation suggest that the primary ingredient of DOL, formononetin, may target NOS3 to act as a therapeutic agent for adriamycin-induced cardiotoxicity.
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Affiliation(s)
- Yuling Luan
- Institute of Cardiovascular Translational Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, No. 164 Lanxi Road, Putuo District, Shanghai, China
| | - Xinyue Ding
- Institute of Cardiovascular Translational Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, No. 164 Lanxi Road, Putuo District, Shanghai, China
| | - Lingxiao Zhang
- Institute of Cardiovascular Translational Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, No. 164 Lanxi Road, Putuo District, Shanghai, China
| | - Shuyan Huang
- Institute of Cardiovascular Translational Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, No. 164 Lanxi Road, Putuo District, Shanghai, China
| | - Chenghao Yang
- Institute of Cardiovascular Translational Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, No. 164 Lanxi Road, Putuo District, Shanghai, China
| | - Yueer Tang
- Institute of Cardiovascular Translational Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, No. 164 Lanxi Road, Putuo District, Shanghai, China
| | - Lina Xing
- Institute of Cardiovascular Translational Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, No. 164 Lanxi Road, Putuo District, Shanghai, China
| | - Hui Zhang
- Institute of Cardiovascular Translational Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, No. 164 Lanxi Road, Putuo District, Shanghai, China.
| | - Zongjun Liu
- Institute of Cardiovascular Translational Medicine, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, No. 164 Lanxi Road, Putuo District, Shanghai, China.
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Tabakmakher KM, Makarieva TN, Sabutski YE, Kokoulin MS, Menshov AS, Popov RS, Guzii AG, Shubina LK, Chingizova EA, Chingizov AR, Yurchenko EA, Fedorov SN, Grebnev BB, von Amsberg G, Dyshlovoy SA, Ivanchina NV, Dmitrenok PS. Stonikacidin A, an Antimicrobial 4-Bromopyrrole Alkaloid Containing L-Idonic Acid Core from the Northwestern Pacific Marine Sponge Lissodendoryx papillosa. Mar Drugs 2024; 22:396. [PMID: 39330277 PMCID: PMC11432817 DOI: 10.3390/md22090396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Revised: 08/27/2024] [Accepted: 08/28/2024] [Indexed: 09/28/2024] Open
Abstract
Stonikacidin A (1), the first representative of a new class of 4-bromopyrrole alkaloids containing an aldonic acid core, was isolated from the marine sponge Lissodendoryx papillosa. The compound is named in honor of Prof. Valentin A. Stonik, who is one of the outstanding investigators in the field of marine natural chemistry. The structure of 1 was determined using NMR, MS analysis, and chemical correlations. The L-idonic acid core was established by the comparison of GC, NMR, MS, and optical rotation data of methyl-pentaacetyl-aldonates obtained from the hydrolysis products of 1 and standard hexoses. The L-form of the idonic acid residue in 1 was confirmed by GC analysis of pentaacetate of (S)-2-butyl ester of the hydrolysis product from 1 and compared with corresponding derivatives of L- and D-idonic acids. The biosynthetic pathway for stonikacidin A (1) was proposed. The alkaloid 1 inhibited the growth of Staphylococcus aureus and Escherichia coli test strains, as well as affected the formation of S. aureus and E. coli biofilms. Compound 1 inhibited the activity of sortase A. Molecular docking data showed that stonikacidin A (1) can bind with sortase A due to the interactions between its bromine atoms and some amino acid residues of the enzyme.
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Affiliation(s)
- Kseniya M. Tabakmakher
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-let Vladivostoku 159, 690022 Vladivostok, Russia; (K.M.T.); (Y.E.S.); (M.S.K.); (A.S.M.); (R.S.P.); (A.G.G.); (L.K.S.); (E.A.C.); (A.R.C.); (E.A.Y.); (S.N.F.); (B.B.G.); (N.V.I.); (P.S.D.)
| | - Tatyana N. Makarieva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-let Vladivostoku 159, 690022 Vladivostok, Russia; (K.M.T.); (Y.E.S.); (M.S.K.); (A.S.M.); (R.S.P.); (A.G.G.); (L.K.S.); (E.A.C.); (A.R.C.); (E.A.Y.); (S.N.F.); (B.B.G.); (N.V.I.); (P.S.D.)
| | - Yuri E. Sabutski
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-let Vladivostoku 159, 690022 Vladivostok, Russia; (K.M.T.); (Y.E.S.); (M.S.K.); (A.S.M.); (R.S.P.); (A.G.G.); (L.K.S.); (E.A.C.); (A.R.C.); (E.A.Y.); (S.N.F.); (B.B.G.); (N.V.I.); (P.S.D.)
| | - Maxim S. Kokoulin
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-let Vladivostoku 159, 690022 Vladivostok, Russia; (K.M.T.); (Y.E.S.); (M.S.K.); (A.S.M.); (R.S.P.); (A.G.G.); (L.K.S.); (E.A.C.); (A.R.C.); (E.A.Y.); (S.N.F.); (B.B.G.); (N.V.I.); (P.S.D.)
| | - Alexander S. Menshov
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-let Vladivostoku 159, 690022 Vladivostok, Russia; (K.M.T.); (Y.E.S.); (M.S.K.); (A.S.M.); (R.S.P.); (A.G.G.); (L.K.S.); (E.A.C.); (A.R.C.); (E.A.Y.); (S.N.F.); (B.B.G.); (N.V.I.); (P.S.D.)
| | - Roman S. Popov
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-let Vladivostoku 159, 690022 Vladivostok, Russia; (K.M.T.); (Y.E.S.); (M.S.K.); (A.S.M.); (R.S.P.); (A.G.G.); (L.K.S.); (E.A.C.); (A.R.C.); (E.A.Y.); (S.N.F.); (B.B.G.); (N.V.I.); (P.S.D.)
| | - Alla G. Guzii
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-let Vladivostoku 159, 690022 Vladivostok, Russia; (K.M.T.); (Y.E.S.); (M.S.K.); (A.S.M.); (R.S.P.); (A.G.G.); (L.K.S.); (E.A.C.); (A.R.C.); (E.A.Y.); (S.N.F.); (B.B.G.); (N.V.I.); (P.S.D.)
| | - Larisa K. Shubina
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-let Vladivostoku 159, 690022 Vladivostok, Russia; (K.M.T.); (Y.E.S.); (M.S.K.); (A.S.M.); (R.S.P.); (A.G.G.); (L.K.S.); (E.A.C.); (A.R.C.); (E.A.Y.); (S.N.F.); (B.B.G.); (N.V.I.); (P.S.D.)
| | - Ekaterina A. Chingizova
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-let Vladivostoku 159, 690022 Vladivostok, Russia; (K.M.T.); (Y.E.S.); (M.S.K.); (A.S.M.); (R.S.P.); (A.G.G.); (L.K.S.); (E.A.C.); (A.R.C.); (E.A.Y.); (S.N.F.); (B.B.G.); (N.V.I.); (P.S.D.)
| | - Artur R. Chingizov
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-let Vladivostoku 159, 690022 Vladivostok, Russia; (K.M.T.); (Y.E.S.); (M.S.K.); (A.S.M.); (R.S.P.); (A.G.G.); (L.K.S.); (E.A.C.); (A.R.C.); (E.A.Y.); (S.N.F.); (B.B.G.); (N.V.I.); (P.S.D.)
| | - Ekaterina A. Yurchenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-let Vladivostoku 159, 690022 Vladivostok, Russia; (K.M.T.); (Y.E.S.); (M.S.K.); (A.S.M.); (R.S.P.); (A.G.G.); (L.K.S.); (E.A.C.); (A.R.C.); (E.A.Y.); (S.N.F.); (B.B.G.); (N.V.I.); (P.S.D.)
| | - Sergey N. Fedorov
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-let Vladivostoku 159, 690022 Vladivostok, Russia; (K.M.T.); (Y.E.S.); (M.S.K.); (A.S.M.); (R.S.P.); (A.G.G.); (L.K.S.); (E.A.C.); (A.R.C.); (E.A.Y.); (S.N.F.); (B.B.G.); (N.V.I.); (P.S.D.)
| | - Boris B. Grebnev
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-let Vladivostoku 159, 690022 Vladivostok, Russia; (K.M.T.); (Y.E.S.); (M.S.K.); (A.S.M.); (R.S.P.); (A.G.G.); (L.K.S.); (E.A.C.); (A.R.C.); (E.A.Y.); (S.N.F.); (B.B.G.); (N.V.I.); (P.S.D.)
| | - Gunhild von Amsberg
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald Tumorzentrum–University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany; (G.v.A.); (S.A.D.)
- Martini-Klinik, Prostate Cancer Center, University Hospital Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Sergey A. Dyshlovoy
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald Tumorzentrum–University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany; (G.v.A.); (S.A.D.)
| | - Natalia V. Ivanchina
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-let Vladivostoku 159, 690022 Vladivostok, Russia; (K.M.T.); (Y.E.S.); (M.S.K.); (A.S.M.); (R.S.P.); (A.G.G.); (L.K.S.); (E.A.C.); (A.R.C.); (E.A.Y.); (S.N.F.); (B.B.G.); (N.V.I.); (P.S.D.)
| | - Pavel S. Dmitrenok
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Pr. 100-let Vladivostoku 159, 690022 Vladivostok, Russia; (K.M.T.); (Y.E.S.); (M.S.K.); (A.S.M.); (R.S.P.); (A.G.G.); (L.K.S.); (E.A.C.); (A.R.C.); (E.A.Y.); (S.N.F.); (B.B.G.); (N.V.I.); (P.S.D.)
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29
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Höfmann S, Schmerling C, Stracke C, Niemeyer F, Schaller T, Snoep JL, Bräsen C, Siebers B. The archaeal family 3 polyphosphate kinase reveals a function of polyphosphate as energy buffer under low energy charge. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.28.610084. [PMID: 39257778 PMCID: PMC11383997 DOI: 10.1101/2024.08.28.610084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
Inorganic polyphosphate, a linear polymer of orthophosphate residues linked by phosphoanhydride bonds, occurs in all three domains of life and plays a diverse and prominent role in metabolism and cellular regulation. While the polyphosphate metabolism and its physiological significance have been well studied in bacteria and eukaryotes including human, there are only few studies in archaea available so far. In Crenarchaeota including members of Sulfolobaceae , the presence of polyphosphate and degradation via exopolyphosphatase has been reported and there is some evidence for a functional role in metal ion chelation, biofilm formation, adhesion and motility, however, the nature of the crenarchaeal polyphosphate kinase is still unknown. Here we used the crenarchaeal model organism Sulfolobus acidocaldarius to study the enzymes involved in polyphosphate synthesis. The two genes annotated as thymidylate kinase ( saci_2019 and saci_2020 ), localized downstream of the exopolyphosphatase, were identified as the missing polyphosphate kinase in S. acidocaldarius ( Sa PPK3). Thymidylate kinase activity was confirmed for Saci_0893. Notably Saci_2020 showed no polyphosphate kinase activity on its own but served as regulatory subunit (rPPK3) and was able to enhance polyphosphate kinase activity of the catalytically active subunit Saci_2019 (cPPK3). Heteromeric polyphosphate kinase activity is reversible and shows a clear preference for polyP-dependent nucleotide kinase activity, i.e. polyP-dependent formation of ATP from ADP (12.4 U/mg) and to a lower extent of GDP to GTP whereas AMP does not serve as substrate. PPK activity in the direction of ATP-dependent polyP synthesis is rather low (0.25 U/mg); GTP was not used as phosphoryl donor. A combined experimental modelling approach using quantitative 31 P NMR allowed to follow the reversible enzyme reaction for both ATP and polyP synthesis. PolyP synthesis was only observed when the ATP/ADP ratio was kept high, using an ATP recycling system. In absence of such a recycling system, all incubations with polyP and PPK would reach an equilibrium state with an ATP/ADP ratio between 3 and 4, independent of the initial conditions. Structural and sequence comparisons as well as phylogenetic analysis reveal that the S. acidocaldarius PPK is a member of a new PPK family, named PPK3, within the thymidylate kinase family of the P-loop kinase superfamily, clearly separated from PPK2. Our studies show that polyP, in addition to its function as phosphate storage, has a special importance for the energy homeostasis of S. acidocaldarius and due to its reversibility serves as energy buffer under low energy charge enabling a quick response to changes in cellular demand.
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Sharma P, Sethi RS. In Vivo Exposure of Deltamethrin Dysregulates the NFAT Signalling Pathway and Induces Lung Damage. J Toxicol 2024; 2024:5261994. [PMID: 39239465 PMCID: PMC11377118 DOI: 10.1155/2024/5261994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 07/23/2024] [Accepted: 08/10/2024] [Indexed: 09/07/2024] Open
Abstract
Deltamethrin is an insecticide used to control harmful agricultural insects that otherwise damage crops and to control vector-borne diseases. Long-term exposure to deltamethrin results in the inflammation of the lungs. The present study elucidates the molecular mechanism underlying the deltamethrin-induced lung damage. The lung samples were extracted from the Swiss albino mice following the treatment of low (2.5 mg/kg) and high (5 mg/kg) doses of deltamethrin. The mRNA expression of TCR, IL-4, and IL-13 showed upregulation, while the expression of NFAT and FOS was downregulated following a low dose of deltamethrin. Moreover, the expression of TCR was downregulated with the exposure of a high dose of deltamethrin. Furthermore, the immunohistochemistry data confirmed the pattern of protein expression for TCR, FOS, IL-4, and IL-13 following a low dose of deltamethrin exposure. However, no change was seen in the TCR, NFAT, FOS, JUN, IL-4, and IL-13 immunopositive cells of the high-dose treatment group. Also, ELISA results showed increased expression of IL-13 in the BAL fluid of animals exposed to low doses of deltamethrin. Overall, the present study showed that deltamethrin exposure induces lung damage and immune dysregulation via dysregulating the NFAT signalling pathway.
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Affiliation(s)
- Prakriti Sharma
- Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, India
| | - R S Sethi
- Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, India
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31
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Manville RW, Yoshimura RF, Yeromin AV, Hogenkamp D, van der Horst J, Zavala A, Chinedu S, Arena G, Lasky E, Fisher M, Tracy CR, Othy S, Jepps TA, Cahalan MD, Abbott GW. Polymodal K + channel modulation contributes to dual analgesic and anti-inflammatory actions of traditional botanical medicines. Commun Biol 2024; 7:1059. [PMID: 39198706 PMCID: PMC11358443 DOI: 10.1038/s42003-024-06752-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/19/2024] [Indexed: 09/01/2024] Open
Abstract
Pain and inflammation contribute immeasurably to reduced quality of life, yet modern analgesic and anti-inflammatory therapeutics can cause dependence and side effects. Here, we screened 1444 plant extracts, prepared primarily from native species in California and the United States Virgin Islands, against two voltage-gated K+ channels - T-cell expressed Kv1.3 and nociceptive-neuron expressed Kv7.2/7.3. A subset of extracts both inhibits Kv1.3 and activates Kv7.2/7.3 at hyperpolarized potentials, effects predicted to be anti-inflammatory and analgesic, respectively. Among the top dual hits are witch hazel and fireweed; polymodal modulation of multiple K+ channel types by hydrolysable tannins contributes to their dual anti-inflammatory, analgesic actions. In silico docking and mutagenesis data suggest pore-proximal extracellular linker sequence divergence underlies opposite effects of hydrolysable tannins on different Kv1 isoforms. The findings provide molecular insights into the enduring, widespread medicinal use of witch hazel and fireweed and demonstrate a screening strategy for discovering dual anti-inflammatory, analgesic small molecules.
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Affiliation(s)
- Rían W Manville
- Bioelectricity Laboratory, Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, USA
| | - Ryan F Yoshimura
- Bioelectricity Laboratory, Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, USA
| | - Andriy V Yeromin
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, USA
| | - Derk Hogenkamp
- Bioelectricity Laboratory, Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, USA
| | - Jennifer van der Horst
- Department of Biomedical Sciences, Vascular Biology Group, Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Angel Zavala
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, USA
| | - Sonia Chinedu
- Bioelectricity Laboratory, Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, USA
| | - Grey Arena
- Redwood Creek Vegetation Team, National Park Service, Sausalito, CA, USA
| | - Emma Lasky
- Redwood Creek Vegetation Team, National Park Service, Sausalito, CA, USA
| | - Mark Fisher
- Philip L. Boyd Deep Canyon Desert Research Center, University of California Natural Reserve System, Indian Wells, CA, USA
| | - Christopher R Tracy
- Philip L. Boyd Deep Canyon Desert Research Center, University of California Natural Reserve System, Indian Wells, CA, USA
| | - Shivashankar Othy
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, USA
| | - Thomas A Jepps
- Department of Biomedical Sciences, Vascular Biology Group, Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Michael D Cahalan
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, USA
| | - Geoffrey W Abbott
- Bioelectricity Laboratory, Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, USA.
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Nayak R, Mallick B. BMS345541 is predicted as a repurposed drug for the treatment of TMZ-resistant Glioblastoma using target gene expression and virtual drug screening. Cancer Genet 2024; 288-289:20-31. [PMID: 39213700 DOI: 10.1016/j.cancergen.2024.08.082] [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: 08/05/2024] [Revised: 08/21/2024] [Accepted: 08/23/2024] [Indexed: 09/04/2024]
Abstract
Glioblastoma (GBM) is one of the most aggressive and fatal cancers, for which Temozolomide (TMZ) chemo drug is commonly used for its treatment. However, patients gradually develop resistance to this drug, leading to tumor relapse. In our previous study, we have identified lncRNAs that regulate chemoresistance through the competing endogenous RNA (ceRNA) mechanism. In this study, we tried to find FDA-approved drugs against the target proteins of these ceRNA networks through drug repurposing using differential gene expression profiles, which could be used to nullify the effect of lncRNAs and promote the sensitivity of TMZ in GBM. We performed molecular docking and simulation studies of predicted repurposed drugs and their targets. Among the predicted repurposed drugs, we found BMS345541 has a higher binding affinity towards its target protein - FOXG1, making it a more stable complex with FOXG1-DNA. The ADMET analysis of this drug BMS345541 shows a higher half-life and lower cytotoxicity level than other predicted repurposed drugs. Hence, we conjecture that this could be a better drug for increasing the sensitivity of TMZ for treating GBM patients.
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Affiliation(s)
- Rojalin Nayak
- RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology Rourkela, Rourkela, Odisha 769008, India
| | - Bibekanand Mallick
- RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology Rourkela, Rourkela, Odisha 769008, India.
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Femi-Oloye OP, Sutton RT, Gordon HD, Ain Das A, Morenikeji GO, Odorisio MK, Francestscu OD, Myers RL, Oloye FF. An Assessment of Polycyclic Aromatic Hydrocarbons Using Estimation Programs. TOXICS 2024; 12:592. [PMID: 39195694 PMCID: PMC11360689 DOI: 10.3390/toxics12080592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 08/10/2024] [Accepted: 08/12/2024] [Indexed: 08/29/2024]
Abstract
In the environment, the class of chemicals known as polycyclic aromatic hydrocarbons (PAHs) behave somewhat differently. This review covers situations where PAHs can be 'labile' and where they can be persistent. The in-silico prediction of toxicity and the properties of selected 29 PAHs were estimated using programs developed by the U.S. Environmental Protection Agency (EPA), such as the Estimation Programs Interface (E.P.I.) and the Toxicity Estimation Software Tool (version 5.1.2) (TEST), with online software such as SwissADME and SwissDock. TEST was used to estimate the LC50 of the fathead minnow (with a range of 14.53 mg/L for 1-indanone and 2.14 × 10-2 mg/L for cyclopenta[c,d]pyrene), the LC50 of Daphnia magna (with a range of 14.95 mg/L for 1-indanone and 7.53 × 10-2 mg/L for coronene), the IGC50 of Tetrahymena pyriformis (with a range of 66.14 mg/L for 1-indanone and 0.36 mg/L for coronene), the bioconcentration factor (8.36 for 1,2-acenaphthylenedione and 910.1 for coronene), the developmental toxicity (0.30 (-) for 1,2-acenaphthylenedione and 0.82 (+) for 4-hydroxy-9-fluorenone), and the mutagenicity (0.25 (-) for 2-methyl-9-fluorenone and 1.09 (+) for coronene). The carbon chain and molecular weight have a significant effect on the properties of PAHs. Overall, it was found that PAHs with a lower molecular weight (LMW) have a higher water solubility and LC50 value and a smaller LogKow value, whereas the opposite is true for heavier PAHs, with TEST predicting that PAHs with an MW of over 168.2 g/mol, with a few exceptions, are mutagenic. Hence, LMW PAHs have a higher potential to be in the environment but are less toxic.
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Affiliation(s)
- Oluwabunmi P. Femi-Oloye
- Toxicology Center, University of Saskatchewan, Saskatoon, SK S7N 5B3, Canada;
- Division of Biological and Health Sciences, University of Pittsburgh at Bradford, Bradford, PA 16701, USA
| | - Ryen T. Sutton
- Department of Chemistry, Division of Physical and Computational Sciences, University of Pittsburgh at Bradford, Bradford, PA 16701, USA (H.D.G.); (R.L.M.)
| | - Heidi D. Gordon
- Department of Chemistry, Division of Physical and Computational Sciences, University of Pittsburgh at Bradford, Bradford, PA 16701, USA (H.D.G.); (R.L.M.)
| | - Ayush Ain Das
- Division of Biological and Health Sciences, University of Pittsburgh at Bradford, Bradford, PA 16701, USA
| | - Grace O. Morenikeji
- Division of Biological and Health Sciences, University of Pittsburgh at Bradford, Bradford, PA 16701, USA
| | - Melissa K. Odorisio
- Department of Chemistry, Division of Physical and Computational Sciences, University of Pittsburgh at Bradford, Bradford, PA 16701, USA (H.D.G.); (R.L.M.)
- Department of Environmental Science, Division of Physical and Computational Sciences, University of Pittsburgh at Bradford, Bradford, PA 16701, USA
| | - Ovidiu D. Francestscu
- Department of Environmental Science, Division of Physical and Computational Sciences, University of Pittsburgh at Bradford, Bradford, PA 16701, USA
| | - Ryan L. Myers
- Department of Chemistry, Division of Physical and Computational Sciences, University of Pittsburgh at Bradford, Bradford, PA 16701, USA (H.D.G.); (R.L.M.)
| | - Femi F. Oloye
- Department of Chemistry, Division of Physical and Computational Sciences, University of Pittsburgh at Bradford, Bradford, PA 16701, USA (H.D.G.); (R.L.M.)
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Panmanee J, Charoensutthivarakul S, Cheng CW, Promthep K, Mukda S, Prasertporn T, Nopparat C, Teerapo K, Supcharoen P, Petchyam N, Chetsawang B, Govitrapong P, Phanchana M. A Complex Interplay Between Melatonin and RORβ: RORβ is Unlikely a Putative Receptor for Melatonin as Revealed by Biophysical Assays. Mol Neurobiol 2024:10.1007/s12035-024-04395-y. [PMID: 39105871 DOI: 10.1007/s12035-024-04395-y] [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: 08/30/2022] [Accepted: 07/12/2024] [Indexed: 08/07/2024]
Abstract
A nuclear retinoic acid receptor (RAR)-related orphan receptor β (RORβ) is strictly expressed in the brain, particularly in the pineal gland where melatonin is primarily synthesized and concentrated. The controversial issues regarding the direct interaction of melatonin toward ROR receptors have prompted us to investigate the potential melatonin binding sites on different ROR isoforms. We adopted computational and biophysical approaches to investigate the potential of melatonin as the ligand for RORs, in particular RORβ. Herein, possible melatonin binding sites were predicted by molecular docking on human RORs. The results showed that melatonin might be able to bind within the ligand-binding domain (LBD) of all RORs, despite their difference in sequence homology. The predicted melatonin binding scores were comparable to binding energies with respect to those of melatonin interaction to the well-characterized membrane receptors, MT1 and MT2. Although the computational analyses suggested the binding potential of melatonin to the LBD of RORβ, biophysical validation failed to confirm the binding. Melatonin was unable to alter the stability of human RORβ as shown by the unaltered melting temperatures upon melatonin administration in differential scanning fluorometry (DSF). A thermodynamic isothermal titration calorimetry (ITC) profile showed that melatonin did not interact with human RORβ in solutions, even in the presence of SRC-1 co-activator peptide. Although the direct interaction between the LBD of RORβ could not be established, RORα and RORβ gene expressions were increased upon 24 h treatment with μM-range melatonin. Our data, thus, support the studies that the nuclear effects of melatonin may not be directly mediated via its interaction with the RORβ. These findings warrant further investigation on how melatonin interacts with ROR signaling and urge the melatonin research community for a paradigm shift in the direct interaction of melatonin toward RORs. The quest to identify nuclear receptors for melatonin in neuronal cells remains valid for the community to achieve.
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Affiliation(s)
- Jiraporn Panmanee
- Research Center for Neuroscience, Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Sitthivut Charoensutthivarakul
- Innovative Molecular Discovery Laboratory (iMOD), School of Bioinnovation and Bio-Based Product Intelligence, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
- Excellent Center for Drug Discovery (ECDD), Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
- Center for Neuroscience, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Chew Weng Cheng
- Leeds Institute of Cardiovascular and Metabolic Medicine, Faculty of Medicine and Health, University of Leeds, Leeds, LS2 9JT, UK
| | - Kornkanok Promthep
- Research Center for Neuroscience, Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Sujira Mukda
- Research Center for Neuroscience, Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Tanya Prasertporn
- Research Center for Neuroscience, Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Chutikorn Nopparat
- Innovative Learning Center, Srinakharinwirot University, Sukhumvit 23, Bangkok, 10110, Thailand
| | - Kittitat Teerapo
- Mahidol University-Frontier Research Facility (MU-FRF), Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Promsup Supcharoen
- Mahidol University-Frontier Research Facility (MU-FRF), Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Nopphon Petchyam
- Center for Advanced Therapeutics, Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Banthit Chetsawang
- Research Center for Neuroscience, Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Piyarat Govitrapong
- Chulabhorn Graduate Institute, Kamphaeng Phet 6 Road, Lak Si, Bangkok, 10210, Thailand
| | - Matthew Phanchana
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand.
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Briganti L, Manzine LR, de Mello Capetti CC, de Araújo EA, de Oliveira Arnoldi Pellegrini V, Guimaraes FEG, de Oliveira Neto M, Polikarpov I. Unravelling biochemical and structural features of Bacillus licheniformis GH5 mannanase using site-directed mutagenesis and high-resolution protein crystallography studies. Int J Biol Macromol 2024; 274:133182. [PMID: 38885857 DOI: 10.1016/j.ijbiomac.2024.133182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 05/20/2024] [Accepted: 06/13/2024] [Indexed: 06/20/2024]
Abstract
Glycoside hydrolase family 5 (GH5) encompasses enzymes with several different activities, including endo-1,4-β-mannosidases. These enzymes are involved in mannan degradation, and have a number of biotechnological applications, such as mannooligosaccharide prebiotics production, stain removal and dyes decolorization, to name a few. Despite the importance of GH5 enzymes, only a few members of subfamily 7 were structurally characterized. In the present work, biochemical and structural characterization of Bacillus licheniformis GH5 mannanase, BlMan5_7 were performed and the enzyme cleavage pattern was analyzed, showing that BlMan5_7 requires at least 5 occupied subsites to perform efficient hydrolysis. Additionally, crystallographic structure at 1.3 Å resolution was determined and mannoheptaose (M7) was docked into the active site to investigate the interactions between substrate and enzyme through molecular dynamic (MD) simulations, revealing the existence of a - 4 subsite, which might explain the generation of mannotetraose (M4) as an enzyme product. Biotechnological application of the enzyme in stain removal was investigated, demonstrating that BlMan5_7 addition to washing solution greatly improves mannan-based stain elimination.
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Affiliation(s)
- Lorenzo Briganti
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São Carlense 400 - Centro, São Carlos, SP 13560-970, Brazil
| | - Livia R Manzine
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São Carlense 400 - Centro, São Carlos, SP 13560-970, Brazil
| | - Caio Cesar de Mello Capetti
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São Carlense 400 - Centro, São Carlos, SP 13560-970, Brazil
| | - Evandro Ares de Araújo
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials, Campinas 13083-970, São Paulo, Brazil
| | | | - Francisco Eduardo Gontijo Guimaraes
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São Carlense 400 - Centro, São Carlos, SP 13560-970, Brazil
| | - Mario de Oliveira Neto
- Departamento de Física e Biofísica, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, Distrito de Rubião Jr. s/n, Botucatu 18618-000, SP, Brazil
| | - Igor Polikarpov
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São Carlense 400 - Centro, São Carlos, SP 13560-970, Brazil.
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Sastre D, Colomer-Molera M, de Benito-Bueno A, Valenzuela C, Fernández-Ballester G, Felipe A. KCNE4-dependent modulation of Kv1.3 pharmacology. Biochem Pharmacol 2024; 226:116368. [PMID: 38880360 DOI: 10.1016/j.bcp.2024.116368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 06/11/2024] [Accepted: 06/13/2024] [Indexed: 06/18/2024]
Abstract
The voltage-dependent potassium channel Kv1.3 is a promising therapeutic target for the treatment of autoimmune and chronic inflammatory disorders. Kv1.3 blockers are effective in treating multiple sclerosis (fampridine) and psoriasis (dalazatide). However, most Kv1.3 pharmacological antagonists are not specific enough, triggering potential side effects and limiting their therapeutic use. Functional Kv are oligomeric complexes in which the presence of ancillary subunits shapes their function and pharmacology. In leukocytes, Kv1.3 associates with KCNE4, which reduces the surface abundance and enhances the inactivation of the channel. This mechanism exerts profound consequences on Kv1.3-related physiological responses. Because KCNE peptides alter the pharmacology of Kv channels, we studied the effects of KCNE4 on Kv1.3 pharmacology to gain insights into pharmacological approaches. To that end, we used margatoxin, which binds the channel pore from the extracellular space, and Psora-4, which blocks the channel from the intracellular side. While KCNE4 apparently did not alter the affinity of either margatoxin or Psora-4, it slowed the inhibition kinetics of the latter in a stoichiometry-dependent manner. The results suggested changes in the Kv1.3 architecture in the presence of KCNE4. The data indicated that while the outer part of the channel mouth remains unaffected, KCNE4 disturbs the intracellular architecture of the complex. Various leukocyte types expressing different Kv1.3/KCNE4 configurations participate in the immune response. Our data provide evidence that the presence of these variable architectures, which affect both the structure of the complex and their pharmacology, should be considered when developing putative therapeutic approaches.
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Affiliation(s)
- Daniel Sastre
- Molecular Physiology Laboratory, Departament de Bioquímica i Biomedicina Molecular, Institut de Biomedicina (IBUB), Universitat de Barcelona, 08028 Barcelona, Spain; Department of Anesthesiology, Pharmacology and Therapeutics, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Magalí Colomer-Molera
- Molecular Physiology Laboratory, Departament de Bioquímica i Biomedicina Molecular, Institut de Biomedicina (IBUB), Universitat de Barcelona, 08028 Barcelona, Spain
| | | | - Carmen Valenzuela
- Instituto de Investigaciones Biomédicas Alberto Sols CSIC-UAM, 28029 Madrid, Spain
| | | | - Antonio Felipe
- Molecular Physiology Laboratory, Departament de Bioquímica i Biomedicina Molecular, Institut de Biomedicina (IBUB), Universitat de Barcelona, 08028 Barcelona, Spain.
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Wang J, Beyer D, Vaccarin C, He Y, Tanriver M, Benoit R, Deupi X, Mu L, Bode JW, Schibli R, Müller C. Development of radiofluorinated MLN-4760 derivatives for PET imaging of the SARS-CoV-2 entry receptor ACE2. Eur J Nucl Med Mol Imaging 2024:10.1007/s00259-024-06831-6. [PMID: 39066808 DOI: 10.1007/s00259-024-06831-6] [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: 03/23/2024] [Accepted: 07/01/2024] [Indexed: 07/30/2024]
Abstract
PURPOSE The angiotensin converting enzyme 2 (ACE2) plays a regulatory role in the cardiovascular system and serves SARS-CoV-2 as an entry receptor. The aim of this study was to synthesize and evaluate radiofluorinated derivatives of the ACE2 inhibitor MLN-4760. [18F]F-MLN-4760 and [18F]F-Aza-MLN-4760 were demonstrated to be suitable for non-invasive imaging of ACE2, potentially enabling a better understanding of its expression dynamics. METHODS Computational molecular modeling, based on the structures of human ACE2 (hACE2) and mouse ACE2 (mACE2), revealed that the ACE2-binding modes of F-MLN-4760 and F-Aza-MLN-4760 were similar to that of MLN-4760. Co-crystallization of the hACE2/F-MLN-4760 protein complex was performed for confirmation. Displacement experiments using [3H]MLN-4760 enabled the determination of the binding affinities of the synthesized F-MLN-4760 and F-Aza-MLN-4760 to hACE2 expressed in HEK-ACE2 cells. Aryl trimethylstannane-based and pyridine-based radiofluorination precursors were synthesized and used for the preparation of the respective radiotracers. [18F]F-MLN-4760 and [18F]F-Aza-MLN-4760 were evaluated with regard to the uptake in HEK-ACE2 and HEK-ACE cells and in vitro binding to tissue sections of HEK-ACE2 xenografts and normal organs of mice. Biodistribution and PET/CT imaging studies of [18F]F-MLN-4760 and [18F]F-Aza-MLN-4760 were performed using HEK-ACE2 and HEK-ACE xenografted nude mice. RESULTS Crystallography data revealed an equal hACE2-binding mode for F-MLN-4760 as previously found for MLN-4760. Moreover, computer-based modeling indicated that similar binding to hACE2 and mACE2 holds true for both, F-MLN-4760 and F-Aza-MLN-4760, as is the case for MLN-4760. The IC50 values were three-fold and seven-fold higher for F-MLN-4760 and F-Aza-MLN-4760, respectively, than for MLN-4760. [18F]F-MLN-4760 and [18F]F-Aza-MLN-4760 were obtained in 1.4 ± 0.3 GBq and 0.5 ± 0.1 GBq activity with > 99% radiochemical purity in a 5.3% and 1.2% radiochemical yield, respectively. Uptake in HEK-ACE2 cells was higher for [18F]F-MLN-4760 (67 ± 9%) than for [18F]F-Aza-MLN-4760 (37 ± 8%) after 3-h incubation while negligible uptake was seen in HEK-ACE cells (< 0.3%). [18F]F-MLN-4760 and [18F]F-Aza-MLN-4760 accumulated specifically in HEK-ACE2 xenografts of mice (13 ± 2% IA/g and 15 ± 2% IA/g at 1 h p.i.) with almost no uptake observed in HEK-ACE xenografts (< 0.3% IA/g). This was confirmed by PET/CT imaging, which also visualized unspecific accumulation in the gall bladder and intestinal tract. CONCLUSION Both radiotracers showed specific and selective binding to ACE2 in vitro and in vivo. [18F]F-MLN-4760 was, however, obtained in higher yields and the ACE2-binding affinity was superior over that of [18F]F-Aza-MLN-4760. [18F]F-MLN-4760 would, thus, be the candidate of choice for further development in view of its use for PET imaging of ACE2.
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Affiliation(s)
- Jinling Wang
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, 8093, Switzerland
| | - Darja Beyer
- Center for Radiopharmaceutical Sciences ETH-PSI, Paul Scherrer Institute, Villigen-PSI, 5232, Switzerland
| | - Christian Vaccarin
- Center for Radiopharmaceutical Sciences ETH-PSI, Paul Scherrer Institute, Villigen-PSI, 5232, Switzerland
| | - Yingfang He
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, 8093, Switzerland
| | - Matthias Tanriver
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, 8093, Switzerland
| | - Roger Benoit
- Laboratory of Nanoscale Biology, Paul Scherrer Institute, Villigen-PSI, 5232, Switzerland
| | - Xavier Deupi
- Condensed Matter Theory Group, Division of Scientific Computing, Theory, and Data, Paul Scherrer Institute, Villigen-PSI, 5232, Switzerland
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen-PSI, 5232, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Linjing Mu
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, 8093, Switzerland
| | - Jeffrey W Bode
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, 8093, Switzerland
| | - Roger Schibli
- Center for Radiopharmaceutical Sciences ETH-PSI, Paul Scherrer Institute, Villigen-PSI, 5232, Switzerland
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, 8093, Switzerland
| | - Cristina Müller
- Center for Radiopharmaceutical Sciences ETH-PSI, Paul Scherrer Institute, Villigen-PSI, 5232, Switzerland.
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, 8093, Switzerland.
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Crandall JG, Zhou X, Rokas A, Hittinger CT. Specialization restricts the evolutionary paths available to yeast sugar transporters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.22.604696. [PMID: 39091816 PMCID: PMC11291069 DOI: 10.1101/2024.07.22.604696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Functional innovation at the protein level is a key source of evolutionary novelties. The constraints on functional innovations are likely to be highly specific in different proteins, which are shaped by their unique histories and the extent of global epistasis that arises from their structures and biochemistries. These contextual nuances in the sequence-function relationship have implications both for a basic understanding of the evolutionary process and for engineering proteins with desirable properties. Here, we have investigated the molecular basis of novel function in a model member of an ancient, conserved, and biotechnologically relevant protein family. These Major Facilitator Superfamily sugar porters are a functionally diverse group of proteins that are thought to be highly plastic and evolvable. By dissecting a recent evolutionary innovation in an α-glucoside transporter from the yeast Saccharomyces eubayanus, we show that the ability to transport a novel substrate requires high-order interactions between many protein regions and numerous specific residues proximal to the transport channel. To reconcile the functional diversity of this family with the constrained evolution of this model protein, we generated new, state-of-the-art genome annotations for 332 Saccharomycotina yeast species spanning approximately 400 million years of evolution. By integrating phylogenetic and phenotypic analyses across these species, we show that the model yeast α-glucoside transporters likely evolved from a multifunctional ancestor and became subfunctionalized. The accumulation of additive and epistatic substitutions likely entrenched this subfunction, which made the simultaneous acquisition of multiple interacting substitutions the only reasonably accessible path to novelty.
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Affiliation(s)
- Johnathan G. Crandall
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Xiaofan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Antonis Rokas
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA
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Zhao Z, Tajkhorshid E. GOLEM: Automated and Robust Cryo-EM-Guided Ligand Docking with Explicit Water Molecules. J Chem Inf Model 2024; 64:5680-5690. [PMID: 38990699 DOI: 10.1021/acs.jcim.4c00917] [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: 07/13/2024]
Abstract
A detailed understanding of ligand-protein interaction is essential for developing rational drug-design strategies. In recent years, technological advances in cryo-electron microscopy (cryo-EM) brought a new era to the structural determination of biological macromolecules and assemblies at high resolution, marking cryo-EM as a promising tool for studying ligand-protein interactions. However, even in high-resolution cryo-EM results, the densities for the bound small-molecule ligands are often of lower quality due to their relatively dynamic and flexible nature, frustrating their accurate coordinate assignment. To address the challenge of ligand modeling in cryo-EM maps, here we report the development of GOLEM (Genetic Optimization of Ligands in Experimental Maps), an automated and robust ligand docking method that predicts a ligand's pose and conformation in cryo-EM maps. GOLEM employs a Lamarckian genetic algorithm to perform a hybrid global/local search for exploring the ligand's conformational, orientational, and positional space. As an important feature, GOLEM explicitly considers water molecules and places them at optimal positions and orientations. GOLEM takes into account both molecular energetics and the correlation with the cryo-EM maps in its scoring function to optimally place the ligand. We have validated GOLEM against multiple cryo-EM structures with a wide range of map resolutions and ligand types, returning ligand poses in excellent agreement with the densities. As a VMD plugin, GOLEM is free of charge and accessible to the community. With these features, GOLEM will provide a valuable tool for ligand modeling in cryo-EM efforts toward drug discovery.
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Affiliation(s)
- Zhiyu Zhao
- Theoretical and Computational Biophysics Group, NIH Resource Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Resource Center for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
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Zúñiga-Hernández SR, García-Iglesias T, Macías-Carballo M, Pérez-Larios A, Gutiérrez-Mercado YK, Camargo-Hernández G, Rodríguez-Razón CM. A Bioinformatic Assay of Quercetin in Gastric Cancer. Int J Mol Sci 2024; 25:7934. [PMID: 39063176 PMCID: PMC11277512 DOI: 10.3390/ijms25147934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 07/10/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
Gastric cancer (GC) remains a significant global health challenge, with high mortality rates, especially in developing countries. Current treatments are invasive and have considerable risks, necessitating the exploration of safer alternatives. Quercetin (QRC), a flavonoid present in various plants and foods, has demonstrated multiple health benefits, including anticancer properties. This study investigated the therapeutic potential of QRC in the treatment of GC. We utilized advanced molecular techniques to assess the impact of QRC on GC cells, examining its effects on cellular pathways and gene expression. Our findings indicate that QRC significantly inhibits GC cell proliferation and induces apoptosis, suggesting its potential as a safer therapeutic option for GC treatment. Further research is required to validate these results and explore the clinical applications of QRC in cancer therapy.
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Affiliation(s)
- Sergio Raúl Zúñiga-Hernández
- Departamento de Ciencias de la Salud, Centro Universitario de los Altos, Universidad de Guadalajara, Tepatitlán de Morelos 47620, Mexico
| | - Trinidad García-Iglesias
- Instituto de Investigación de Cáncer en la Infancia y Adolescencia, Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, Guadalajara 44340, Mexico;
| | - Monserrat Macías-Carballo
- Laboratorio de Biociencias, Departamento de Clínicas, Centro Universitario de los Altos, Tepatitlán de Morelos 47620, Mexico;
| | - Alejandro Pérez-Larios
- Laboratorio de Nanomateriales, Agua y Energia, Departamento de Ingenierias, Centro Universitario de los Altos, Tepatitlán de Morelos 47620, Mexico;
| | - Yanet Karina Gutiérrez-Mercado
- Laboratorio Biotecnológico de Investigación y Diagnóstico, Departamento de Clínicas, Centro Universitario de los Altos, Tepatitlán de Morelos 47620, Mexico;
| | - Gabriela Camargo-Hernández
- Instituto de Investigación en Ciencias Médicas, Centro Universitario de los Altos, Universidad de Guadalajara, Tepatitlán de Morelos 47620, Mexico;
| | - Christian Martín Rodríguez-Razón
- Laboratorio de Experimentación Animal (Bioterio), Departamento de Ciencias de la Salud, Centro Universitario de los Altos, Tepatitlán de Morelos 47620, Mexico
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Pérez-Beltrán YE, Wall-Medrano A, Valencia Estrada MA, Sánchez-Burgos JA, Blancas-Benítez FJ, Tovar J, Sáyago-Ayerdi SG. In Vivo Glycemic Response of Fruit-Based Mango ( Mangifera indica) and Pineapple ( Ananas comosus) Bars in In Vitro and In Silico Enzyme Inhibitory Effects Studies. Foods 2024; 13:2258. [PMID: 39063344 PMCID: PMC11276214 DOI: 10.3390/foods13142258] [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: 06/21/2024] [Revised: 07/09/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
The habitual consumption of snacks has the potential to enrich or harm the diet. They can contribute to excessive caloric intake and hyperglycemia. Thus, there is an increasing interest in snacks with health-promoting properties. This study aimed to demonstrate the beneficial effect of two fruit-based bars on glucose levels through in vitro, in vivo, and in silico assays. Mango (Mangifera indica L.) and pineapple (Ananas comosus L.) bars (MB and PB) were prepared, and chemical composition, postprandial glycemic response, glycemic index (GI), and glycemic load (GL) were evaluated. The inhibitory effect of fruit bar extracts on α-amylase and α-glucosidase activity and their respective molecular docking was assessed. MB and PB showed the lowest postprandial glycemic response vs. the control bar (p < 0.005), a lower GI (CB: 64.20, PB: 53.20, MB: 40.40), and a GL of 10.9 (CB), 7.9 (PB), and 6.1 (MB), (p < 0.05). MB and PB showed the highest inhibition % of α-amylase (61.44 and 59.37%, respectively) and α-glucosidase (64.97 and 64.57%). Naringenin (-1692.5985 and -2757.674 kcal/mol) and ferulic acid (-1692.8904 and -2760.3513 kcal/mol) exhibited more favorable interaction energies against α-amylase and α-glucosidase activity. The presence of polyphenols from the fruit influenced enzymatic inhibition. Likewise, the dietary fiber in the bars evaluated allowed us to observe a positive effect that favors glycemic control, making them a healthy alternative for snacking.
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Affiliation(s)
- Yolanda E. Pérez-Beltrán
- Laboratorio Integral de Investigación en Alimentos, Tecnológico Nacional de México/Instituto Tecnológico de Tepic, Nayarit 63175, Mexico; (Y.E.P.-B.); (M.A.V.E.); (J.A.S.-B.); (F.J.B.-B.)
| | - Abraham Wall-Medrano
- Instituto de Ciencias Biomédicas, Universidad Autónoma de Ciudad Juárez, Chihuahua 32310, Mexico;
| | - Monserrat A. Valencia Estrada
- Laboratorio Integral de Investigación en Alimentos, Tecnológico Nacional de México/Instituto Tecnológico de Tepic, Nayarit 63175, Mexico; (Y.E.P.-B.); (M.A.V.E.); (J.A.S.-B.); (F.J.B.-B.)
| | - Jorge A. Sánchez-Burgos
- Laboratorio Integral de Investigación en Alimentos, Tecnológico Nacional de México/Instituto Tecnológico de Tepic, Nayarit 63175, Mexico; (Y.E.P.-B.); (M.A.V.E.); (J.A.S.-B.); (F.J.B.-B.)
| | - Francisco Javier Blancas-Benítez
- Laboratorio Integral de Investigación en Alimentos, Tecnológico Nacional de México/Instituto Tecnológico de Tepic, Nayarit 63175, Mexico; (Y.E.P.-B.); (M.A.V.E.); (J.A.S.-B.); (F.J.B.-B.)
| | - Juscelino Tovar
- Division of Food and Pharma, Lund University, 22100 Lund, Sweden;
| | - Sonia G. Sáyago-Ayerdi
- Laboratorio Integral de Investigación en Alimentos, Tecnológico Nacional de México/Instituto Tecnológico de Tepic, Nayarit 63175, Mexico; (Y.E.P.-B.); (M.A.V.E.); (J.A.S.-B.); (F.J.B.-B.)
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Kataria A, Srivastava A, Singh DD, Haque S, Han I, Yadav DK. Systematic computational strategies for identifying protein targets and lead discovery. RSC Med Chem 2024; 15:2254-2269. [PMID: 39026640 PMCID: PMC11253860 DOI: 10.1039/d4md00223g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/10/2024] [Indexed: 07/20/2024] Open
Abstract
Computational algorithms and tools have retrenched the drug discovery and development timeline. The applicability of computational approaches has gained immense relevance owing to the dramatic surge in the structural information of biomacromolecules and their heteromolecular complexes. Computational methods are now extensively used in identifying new protein targets, druggability assessment, pharmacophore mapping, molecular docking, the virtual screening of lead molecules, bioactivity prediction, molecular dynamics of protein-ligand complexes, affinity prediction, and for designing better ligands. Herein, we provide an overview of salient components of recently reported computational drug-discovery workflows that includes algorithms, tools, and databases for protein target identification and optimized ligand selection.
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Affiliation(s)
- Arti Kataria
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH) Hamilton MT 59840 USA
| | - Ankit Srivastava
- Laboratory of Neurological Infections and Immunity, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH) Hamilton MT 59840 USA
| | - Desh Deepak Singh
- Amity Institute of Biotechnology, Amity University Rajasthan Jaipur India
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Health Sciences, Jazan University Jazan-45142 Saudi Arabia
| | - Ihn Han
- Plasma Bioscience Research Center, Applied Plasma Medicine Center, Department of Electrical & Biological Physics, Kwangwoon University Seoul 01897 Republic of Korea +82 32 820 4948
| | - Dharmendra Kumar Yadav
- Department of Biologics, College of Pharmacy, Gachon University Hambakmoeiro 191, Yeonsu-gu Incheon 21924 Republic of Korea
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Wei Y, Chen T, Song H, Wang S, Shen C, Wang X, Li Y, Wang J. Rapidly screening of pancreatic lipase inhibitors from Clematis tangutica using affinity ultrafiltration-HPLC-QTOFMS technique combined with targeted separation, in vitro validation, and molecular docking. PHYTOCHEMICAL ANALYSIS : PCA 2024. [PMID: 39009466 DOI: 10.1002/pca.3422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/27/2024] [Accepted: 07/01/2024] [Indexed: 07/17/2024]
Abstract
INTRODUCTION Screening of novel pancreatic lipase inhibitors from complex natural products is a meaningful task. OBJECTIVES Through accurately screening and separating pancreatic lipase inhibitors from Clematis tangutica (C. tangutica), to discover new leading compounds for slimming and accelerate the development and utilization of Tibetan medicine resources. METHODS An integrated strategy that combines affinity ultrafiltration and high-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (AU-HPLC-QTOFMS), targeted separation, in vitro validation, and molecular docking was developed to screen pancreatic lipase inhibitors from C. tangutica. The AU-HPLC-QTOFMS technique was performed to fish for the potential active substances. Macroporous resin, preparative liquid chromatography, and high-speed countercurrent chromatography were implemented for the accurate and targeted separation of active compounds. The inhibitory activities of target compounds to pancreatic lipase were detected by the inhibition experiments in vitro. The binding affinities and binding sites were analyzed using molecular docking. RESULTS A total of eleven kinds of pancreatic lipase inhibitory substances were screened from C. tangutica. Seven triterpenoid saponins were screened for the first time as lipase inhibitors and successfully prepared with purities higher than 97%. Tanguticoside B, clematangoticoside J, hederoside H1, and rutin showed stronger inhibitory effects with IC50 values of 1.539 ± 0.048, 1.661 ± 0.092, 1.793 ± 0.069, and 1.792 ± 0.094 mmol/l. Moreover, they have the lowest ΔG values of -10.84, -9.97, -10.87, and -9.39 kcal/mol to pancreatic lipase. CONCLUSION The integrated strategy using AU-HPLC-QTOFMS, targeted separation, in vitro validation, and molecular docking was feasible for rapidly screening and directionally isolating pancreatic lipase inhibitors from C. tangutica.
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Affiliation(s)
- Yangfei Wei
- Key Laboratory of Hexi Corridor Resources Utilization of Gansu, Hexi University, Zhangye, China
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Tao Chen
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Hai Song
- Key Laboratory of Hexi Corridor Resources Utilization of Gansu, Hexi University, Zhangye, China
| | - Shuo Wang
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Cheng Shen
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Xiaojun Wang
- Key Laboratory of Hexi Corridor Resources Utilization of Gansu, Hexi University, Zhangye, China
| | - Yulin Li
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Junke Wang
- Key Laboratory of Hexi Corridor Resources Utilization of Gansu, Hexi University, Zhangye, China
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Bugnon M, Röhrig UF, Goullieux M, Perez MS, Daina A, Michielin O, Zoete V. SwissDock 2024: major enhancements for small-molecule docking with Attracting Cavities and AutoDock Vina. Nucleic Acids Res 2024; 52:W324-W332. [PMID: 38686803 PMCID: PMC11223881 DOI: 10.1093/nar/gkae300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/19/2024] [Accepted: 04/19/2024] [Indexed: 05/02/2024] Open
Abstract
Drug discovery aims to identify potential therapeutic compounds capable of modulating the activity of specific biological targets. Molecular docking can efficiently support this process by predicting binding interactions between small molecules and macromolecular targets and potentially accelerating screening campaigns. SwissDock is a computational tool released in 2011 as part of the SwissDrugDesign project, providing a free web-based service for small-molecule docking after automatized preparation of ligands and targets. Here, we present the latest version of SwissDock, in which EADock DSS has been replaced by two state-of-the-art docking programs, i.e. Attracting Cavities and AutoDock Vina. AutoDock Vina provides faster docking predictions, while Attracting Cavities offers more accurate results. Ligands can be imported in various ways, including as files, SMILES notation or molecular sketches. Targets can be imported as PDB files or identified by their PDB ID. In addition, advanced search options are available both for ligands and targets, giving users automatized access to widely-used databases. The web interface has been completely redesigned for interactive submission and analysis of docking results. Moreover, we developed a user-friendly command-line access which, in addition to all options of the web site, also enables covalent ligand docking with Attracting Cavities. The new version of SwissDock is freely available at https://www.swissdock.ch/.
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Affiliation(s)
- Marine Bugnon
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Ute F Röhrig
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Mathilde Goullieux
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Marta A S Perez
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Antoine Daina
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Olivier Michielin
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
- Department of Oncology, Geneva University Hospital (HUG), CH-1205 Geneva, Switzerland
| | - Vincent Zoete
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
- Department of Oncology UNIL-CHUV, Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne, CH-1015 Lausanne, Switzerland
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Kochnev Y, Ahmed M, Maldonado A, Durrant J. MolModa: accessible and secure molecular docking in a web browser. Nucleic Acids Res 2024; 52:W498-W506. [PMID: 38783339 PMCID: PMC11223821 DOI: 10.1093/nar/gkae406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/14/2024] [Accepted: 05/01/2024] [Indexed: 05/25/2024] Open
Abstract
Molecular docking advances early-stage drug discovery by predicting the geometries and affinities of small-molecule compounds bound to drug-target receptors, predictions that researchers can leverage in prioritizing drug candidates for experimental testing. Unfortunately, existing docking tools often suffer from poor usability, data security, and maintainability, limiting broader adoption. Additionally, the complexity of the docking process, which requires users to execute a series of specialized steps, often poses a substantial barrier for non-expert users. Here, we introduce MolModa, a secure, accessible environment where users can perform molecular docking entirely in their web browsers. We provide two case studies that illustrate how MolModa provides valuable biological insights. We further compare MolModa to other docking tools to highlight its strengths and limitations. MolModa is available free of charge for academic and commercial use, without login or registration, at https://durrantlab.com/molmoda.
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Affiliation(s)
- Yuri Kochnev
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mayar Ahmed
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Alex M Maldonado
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jacob D Durrant
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
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Eletskaya BZ, Mironov AF, Fateev IV, Berzina MY, Antonov KV, Smirnova OS, Zatsepina AB, Arnautova AO, Abramchik YA, Paramonov AS, Kayushin AL, Khandazhinskaya AL, Matyugina ES, Kochetkov SN, Miroshnikov AI, Mikhailopulo IA, Esipov RS, Konstantinova ID. Enzymatic Transglycosylation Features in Synthesis of 8-Aza-7-Deazapurine Fleximer Nucleosides by Recombinant E. coli PNP: Synthesis and Structure Determination of Minor Products. Biomolecules 2024; 14:798. [PMID: 39062512 PMCID: PMC11275124 DOI: 10.3390/biom14070798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 06/30/2024] [Accepted: 07/01/2024] [Indexed: 07/28/2024] Open
Abstract
Enzymatic transglycosylation of the fleximer base 4-(4-aminopyridine-3-yl)-1H-pyrazole using recombinant E. coli purine nucleoside phosphorylase (PNP) resulted in the formation of "non-typical" minor products of the reaction. In addition to "typical" N1-pyrazole nucleosides, a 4-imino-pyridinium riboside and a N1-pyridinium-N1-pyrazole bis-ribose derivative were formed. N1-Pyrazole 2'-deoxyribonucleosides and a N1-pyridinium-N1-pyrazole bis-2'-deoxyriboside were formed. But 4-imino-pyridinium deoxyriboside was not formed in the reaction mixture. The role of thermodynamic parameters of key intermediates in the formation of reaction products was elucidated. To determine the mechanism of binding and activation of heterocyclic substrates in the E. coli PNP active site, molecular modeling of the fleximer base and reaction products in the enzyme active site was carried out. As for N1-pyridinium riboside, there are two possible locations for it in the PNP active site. The presence of a relatively large space in the area of amino acid residues Phe159, Val178, and Asp204 allows the ribose residue to fit into that space, and the heterocyclic base can occupy a position that is suitable for subsequent glycosylation. Perhaps it is this "upside down" arrangement that promotes secondary glycosylation and the formation of minor bis-riboside products.
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Affiliation(s)
- Barbara Z. Eletskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Anton F. Mironov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
- Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia Named after Patrice Lumumba, Miklukho-Maklaya St. 6, Moscow 117198, Russia
| | - Ilya V. Fateev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Maria Ya. Berzina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Konstantin V. Antonov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Olga S. Smirnova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Alexandra B. Zatsepina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Alexandra O. Arnautova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Yulia A. Abramchik
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Alexander S. Paramonov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Alexey L. Kayushin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Anastasia L. Khandazhinskaya
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russia; (A.L.K.); (E.S.M.); (S.N.K.)
| | - Elena S. Matyugina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russia; (A.L.K.); (E.S.M.); (S.N.K.)
| | - Sergey N. Kochetkov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russia; (A.L.K.); (E.S.M.); (S.N.K.)
| | - Anatoly I. Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Igor A. Mikhailopulo
- Institute of Bioorganic Chemistry, National Academy of Sciences, Acad. Kuprevicha 5/2, 220141 Minsk, Belarus;
| | - Roman S. Esipov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
| | - Irina D. Konstantinova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (B.Z.E.); (A.F.M.); (I.V.F.); (M.Y.B.); (O.S.S.); (A.B.Z.); (A.O.A.); (Y.A.A.); (A.S.P.); (A.L.K.); (R.S.E.)
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Shuvo MN, Halder SK, Alam N, Himel MK, Shil A. Developing phytocompound-based new drugs against multi-drug-resistant Staphylococcus aureus. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231475. [PMID: 39050719 PMCID: PMC11265916 DOI: 10.1098/rsos.231475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 05/28/2024] [Accepted: 06/13/2024] [Indexed: 07/27/2024]
Abstract
Staphylococcus aureus, a prevalent component of the human microbiota, is associated with skin infections to life-threatening diseases, presenting challenges in treatment options and necessitating the development of effective treatments. This study integrated computational and in vitro approaches to identify promising phytocompounds with therapeutic potential. Staphopain B emerged as a target protein for its role in immune evasion, exhibiting stability during molecular dynamic simulation (MDS) with a root mean square deviation value of 2.376 Å. Screening 115 phytocompounds with antibacterial properties from the PubChem database identified 12 with drug-like properties, nine of which showed superior binding affinity to Staphopain B compared to a commercial antibiotic, doxycycline (-7.8 kcal mol-1). Notably, epoxyazadiradione and nimbolide displayed higher estimated free energy of binding scores (-7.91 and -7.93 kcal mol-1, respectively), indicating strong protein-ligand interactions. The root mean square fluctuation values for epoxyazadiradione and nimbolide were 1.097 and 1.034 Å, respectively, which was confirmed through MDS. Crude ethanolic extracts (100% and 70%) of neem (Azadirachta indica) leaves demonstrated narrow inhibition against the bacteria in comparison to doxycycline in the disc-diffusion assay. This study underscores the potential of phytocompounds as therapeutic agents against S. aureus; however, further in vitro experiments and testing of the phytocompounds in vivo are required.
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Affiliation(s)
| | | | - Nuhu Alam
- Department of Botany, Jahangirnagar University, Savar, Dhaka1342, Bangladesh
| | - Mahbubul Kabir Himel
- Department of Botany, Jahangirnagar University, Savar, Dhaka1342, Bangladesh
- Padma Bioresearch, Dhaka1342, Bangladesh
| | - Aparna Shil
- Department of Botany, Jahangirnagar University, Savar, Dhaka1342, Bangladesh
- Padma Bioresearch, Dhaka1342, Bangladesh
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48
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Zeng T, Liu S, Zou P, Yao X, Chen Q, Wei L, Wang Q, Zhang C, Zheng Y, Yu R. Create artilysins from a recombinant library to serve as bactericidal and antibiofilm agents targeting Pseudomonas aeruginosa. Int J Biol Macromol 2024; 273:132990. [PMID: 38857719 DOI: 10.1016/j.ijbiomac.2024.132990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 05/11/2024] [Accepted: 06/05/2024] [Indexed: 06/12/2024]
Abstract
Pseudomonas aeruginosa is a critical pathogen and novel treatments are urgently needed. The out membrane of P. aeruginosa facilitates biofilm formation and antibiotic resistance, and hinders the exogenous application against Gram-negative bacteria of endolysins. Engineered endolysins are investigated for enhancing antimicrobial activity, exemplified by artilysins. Nevertheless, existing research predominantly relies on laborious and time-consuming approaches of individually artilysin identification. This study proposes a novel strategy for expedited artilysin discovery using a recombinant artilysin library comprising proteins derived from 38 antimicrobial peptides and 8 endolysins. In this library, 19 colonies exhibited growth inhibition against P. aeruginosa exceeding 50 %, and three colonies were designated as dutarlysin-1, dutarlysin-2 and dutarlysin-3. Remarkably, dutarlysin-1, dutarlysin-2 and dutarlysin-3 demonstrated rapid and enhanced antibacterial activity, even minimum inhibitory concentration of them killed approximately 4.93 lg units, 6.75 lg units and 5.36 lg units P. aeruginosa, respectively. Dutarlysins were highly refractory to P. aeruginosa resistance development. Furthermore, 2 μmol/L dutarlysin-1 and dutarlysin-3 effectively eradicated over 76 % of the mature biofilm. These dutarlysins exhibited potential broad-spectrum activity against hospital susceptible Gram-negative bacteria. These results supported the effectiveness of this artilysins discovery strategy and suggested dutarlysin-1 and dutarlysin-3 could be promising antimicrobial agents for combating P. aeruginosa.
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Affiliation(s)
- Ting Zeng
- Department of Biopharmaceutics, West China School of Pharmacy, Sichuan University, Chengdu 610041, PR China; Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, PR China
| | - Shuang Liu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, PR China
| | - Peixuan Zou
- Department of Biopharmaceutics, West China School of Pharmacy, Sichuan University, Chengdu 610041, PR China; Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, PR China
| | - Xin Yao
- Department of Biopharmaceutics, West China School of Pharmacy, Sichuan University, Chengdu 610041, PR China; Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, PR China
| | - Qiexin Chen
- Department of Biopharmaceutics, West China School of Pharmacy, Sichuan University, Chengdu 610041, PR China; Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, PR China
| | - Long Wei
- Department of Biopharmaceutics, West China School of Pharmacy, Sichuan University, Chengdu 610041, PR China; Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, PR China
| | - Qiantao Wang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, PR China
| | - Chun Zhang
- Department of Biopharmaceutics, West China School of Pharmacy, Sichuan University, Chengdu 610041, PR China; Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, PR China
| | - Yongxiang Zheng
- Department of Biopharmaceutics, West China School of Pharmacy, Sichuan University, Chengdu 610041, PR China; Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, PR China.
| | - Rong Yu
- Department of Biopharmaceutics, West China School of Pharmacy, Sichuan University, Chengdu 610041, PR China; Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, PR China.
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49
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Kuo CY, Tay RJ, Lin HC, Juan SC, Vidal-Diez de Ulzurrun G, Chang YC, Hoki J, Schroeder FC, Hsueh YP. The nematode-trapping fungus Arthrobotrys oligospora detects prey pheromones via G protein-coupled receptors. Nat Microbiol 2024; 9:1738-1751. [PMID: 38649409 DOI: 10.1038/s41564-024-01679-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 03/20/2024] [Indexed: 04/25/2024]
Abstract
The ability to sense prey-derived cues is essential for predatory lifestyles. Under low-nutrient conditions, Arthrobotrys oligospora and other nematode-trapping fungi develop dedicated structures for nematode capture when exposed to nematode-derived cues, including a conserved family of pheromones, the ascarosides. A. oligospora senses ascarosides via conserved MAPK and cAMP-PKA pathways; however, the upstream receptors remain unknown. Here, using genomic, transcriptomic and functional analyses, we identified two families of G protein-coupled receptors (GPCRs) involved in sensing distinct nematode-derived cues. GPCRs homologous to yeast glucose receptors are required for ascaroside sensing, whereas Pth11-like GPCRs contribute to ascaroside-independent nematode sensing. Both GPCR classes activate conserved cAMP-PKA signalling to trigger trap development. This work demonstrates that predatory fungi use multiple GPCRs to sense several distinct nematode-derived cues for prey recognition and to enable a switch to a predatory lifestyle. Identification of these receptors reveals the molecular mechanisms of cross-kingdom communication via conserved pheromones also sensed by plants and animals.
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Affiliation(s)
- Chih-Yen Kuo
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and Graduate Institute of Life Science, National Defense Medical Center, Taipei, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Rebecca J Tay
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Hung-Che Lin
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Sheng-Chian Juan
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and Graduate Institute of Life Science, National Defense Medical Center, Taipei, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | | | - Yu-Chu Chang
- Department of Biochemistry and Molecular Cell Biology, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Jason Hoki
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Frank C Schroeder
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Yen-Ping Hsueh
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and Graduate Institute of Life Science, National Defense Medical Center, Taipei, Taiwan.
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.
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50
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Yip YS, Jaafar NR, Rahman RA, Puspaningsih NNT, Jailani N, Illias RM. Improvement of combined cross-linked enzyme aggregates of cyclodextrin glucanotransferase and maltogenic amylase by functionalization of cross-linker for maltooligosaccharides synthesis. Int J Biol Macromol 2024; 273:133241. [PMID: 38897508 DOI: 10.1016/j.ijbiomac.2024.133241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/02/2024] [Accepted: 06/16/2024] [Indexed: 06/21/2024]
Abstract
Combined cross-linked enzyme aggregates of cyclodextrin glucanotransferase (CGTase) and maltogenic amylase (Mag1) from Bacillus lehensis G1 (Combi-CLEAs-CM) were successfully developed to synthesis maltooligosaccharides (MOS). Yet, the poor cross-linking performance between chitosan (cross-linker) and enzymes resulting low activity recovery and catalytic efficiency. In this study, we proposed the functionalization of cross-linkers with the integration of computational analysis to study the influences of different functional group on cross-linkers in combi-CLEAs development. From in-silico analysis, O-carboxymethyl chitosan (OCMCS) with the highest binding affinity toward both enzymes was chosen and showed alignment with the experimental result, in which OCMCS was synthesized as cross-linker to develop improved activity recovery of Combi-CLEAs-CM-ocmcs (74 %). The thermal stability and deactivation energy (205.86 kJ/mol) of Combi-CLEAs-CM-ocmcs were found to be higher than Combi-CLEAs-CM (192.59 kJ/mol). The introduction of longer side chain of carboxymethyl group led to a more flexible structure of Combi-CLEAs-CM-ocmcs. This alteration significantly reduced the Km value of Combi-CLEAs-CM-ocmcs by about 3.64-fold and resulted in a greater Kcat/Km (3.63-fold higher) as compared to Combi-CLEAs-CM. Moreover, Combi-CLEAs-CM-ocmcs improved the reusability with retained >50 % of activity while Combi-CLEAs-CM only 36.18 % after five cycles. Finally, maximum MOS production (777.46 mg/g) was obtained by Combi-CLEAs-CM-ocmcs after optimization using response surface methodology.
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Affiliation(s)
- Yee Seng Yip
- Faculty of Chemical and Energy Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Nardiah Rizwana Jaafar
- Faculty of Chemical and Energy Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Roshanida A Rahman
- Faculty of Chemical and Energy Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Ni Nyoman Tri Puspaningsih
- Laboratory of Proteomics, University-CoE Research Center for Bio-Molecule Engineering, Universitas Airlangga, Kampus C-UNAIR, Surabaya, East Java, Indonesia
| | - Nashriq Jailani
- Faculty of Chemical and Energy Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Rosli Md Illias
- Faculty of Chemical and Energy Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia; Institute of Bioproduct Development, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia.
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