1
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Fuchs DI, Serio LD, Balaji S, Sprenger KG. Investigating how HIV-1 antiretrovirals differentially behave as substrates and inhibitors of P-glycoprotein via molecular dynamics simulations. Comput Struct Biotechnol J 2024; 23:2669-2679. [PMID: 39027651 PMCID: PMC11254953 DOI: 10.1016/j.csbj.2024.06.025] [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: 04/15/2024] [Revised: 06/18/2024] [Accepted: 06/18/2024] [Indexed: 07/20/2024] Open
Abstract
HIV-1 can rapidly infect the brain upon initial infection, establishing latent reservoirs that induce neuronal damage and/or death, resulting in HIV-Associated Neurocognitive Disorder. Though anti-HIV-1 antiretrovirals (ARVs) suppress viral load, the blood-brain barrier limits drug access to the brain, largely because of highly expressed efflux proteins like P-glycoprotein (P-gp). While no FDA-approved P-gp inhibitor currently exists, HIV-1 protease inhibitors show promise as partial P-gp inhibitors, potentially enhancing drug delivery to the brain. Herein, we employed docking and molecular dynamics simulations to elucidate key differences in P-gp's interactions with several antiretrovirals, including protease inhibitors, with known inhibitory or substrate-like behaviors towards P-gp. Our results led us to hypothesize new mechanistic details of small-molecule efflux by and inhibition of P-gp, where the "Lower Pocket" in P-gp's transmembrane domain serves as the primary initial site for small-molecule binding. Subsequently, this pocket merges with the more traditionally studied drug binding site-the "Upper Pocket"-thus funneling small-molecule drugs, such as ARVs, towards the Upper Pocket for efflux. Furthermore, our results reinforce the understanding that both binding energetics and changes in protein dynamics are crucial in discerning small molecules as non-substrates, substrates, or inhibitors of P-gp. Our findings indicate that interactions between P-gp and inhibitory ARVs induce bridging of transmembrane domain helices, impeding P-gp conformational changes and contributing to the inhibitory behavior of these ARVs. Overall, insights gained in this study could serve to guide the design of future P-gp-targeting therapeutics for a wide range of pathological conditions and diseases, including HIV-1.
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Affiliation(s)
- Daisy I. Fuchs
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Lauren D. Serio
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Sahana Balaji
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Kayla G. Sprenger
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80303, USA
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2
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Fuentes-Martín R, Ayuda-Durán P, Hanes R, Gallego-Yerga L, Wolterinck L, Enserink JM, Álvarez R, Peláez R. Promising anti-proliferative indolic benzenesulfonamides alter mechanisms with sulfonamide nitrogen substituents. Eur J Med Chem 2024; 275:116617. [PMID: 38959729 DOI: 10.1016/j.ejmech.2024.116617] [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: 05/14/2024] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 07/05/2024]
Abstract
Agents that cause apoptotic cell death by interfering with tubulin dynamics, such as vinblastine and paclitaxel, are an important class of chemotherapeutics. Unfortunately, these compounds are substrates for multidrug resistance (MDR) pumps, allowing cancer cells to gain resistance to these chemotherapeutics. The indolesulfonamide family of tubulin inhibitors are not excluded by MDR pumps and have a promising activity profile, although their high lipophilicity is a pharmacokinetic limitation for their clinical use. Here we present a new family of N-indolyl-3,4,5-trimethoxybenzenesulfonamide derivatives with modifications on the indole system at positions 1 and 3 and on the sulfonamide nitrogen. We synthesized and screened against HeLa cells 34 novel indolic benzenesulfonamides. The most potent derivatives (1.7-109 nM) were tested against a broad panel of cancer cell lines, which revealed that substituted benzenesulfonamides analogs had highest potency. Importantly, these compounds were only moderately toxic to non-tumorigenic cells, suggesting the presence of a therapeutic index. Consistent with known clinical anti-tubulin agents, these compounds arrested the cell cycle at G2/M phase. Mechanistically, they induced apoptosis via caspase 3/7 activation, which occurred during M arrest. The substituents on the sulfonamide nitrogen appeared to determine different mechanistic results and cell fates. These results suggest that the compounds act differently depending on the bridge substituents, thus making them very interesting as mechanistic probes as well as potential drugs for further development.
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Affiliation(s)
- Raúl Fuentes-Martín
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, E-37007, Salamanca, Spain; Instituto de Investigación Biomédica de Salamanca (IBSAL), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, E-37007, Salamanca, Spain; Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS). Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, E-37007, Salamanca, Spain
| | - Pilar Ayuda-Durán
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Robert Hanes
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Section for Biochemistry and Molecular Biology, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Laura Gallego-Yerga
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, E-37007, Salamanca, Spain; Instituto de Investigación Biomédica de Salamanca (IBSAL), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, E-37007, Salamanca, Spain; Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS). Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, E-37007, Salamanca, Spain
| | - Lisanne Wolterinck
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; HAN University of Applied Sciences, Nijmegen, the Netherlands
| | - Jorrit M Enserink
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Section for Biochemistry and Molecular Biology, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Raquel Álvarez
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, E-37007, Salamanca, Spain; Instituto de Investigación Biomédica de Salamanca (IBSAL), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, E-37007, Salamanca, Spain; Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS). Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, E-37007, Salamanca, Spain
| | - Rafael Peláez
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Universidad de Salamanca, Campus Miguel de Unamuno, E-37007, Salamanca, Spain; Instituto de Investigación Biomédica de Salamanca (IBSAL), Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, E-37007, Salamanca, Spain; Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS). Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, E-37007, Salamanca, Spain.
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3
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Kabier M, Gambacorta N, Trisciuzzi D, Kumar S, Nicolotti O, Mathew B. MzDOCK: A free ready-to-use GUI-based pipeline for molecular docking simulations. J Comput Chem 2024; 45:1980-1986. [PMID: 38703357 DOI: 10.1002/jcc.27390] [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: 03/01/2024] [Revised: 04/12/2024] [Accepted: 04/19/2024] [Indexed: 05/06/2024]
Abstract
Molecular docking is by far the most preferred approach in structure-based drug design for its effectiveness to predict the scoring and posing of a given bioactive small molecule into the binding site of its pharmacological target. Herein, we present MzDOCK, a new GUI-based pipeline for Windows operating system, designed with the intent of making molecular docking easier to use and higher reproducible even for inexperienced people. By harmonic integration of python and batch scripts, which employs various open source packages such as Smina (docking engine), OpenBabel (file conversion) and PLIP (analysis), MzDOCK includes many practical options such as: binding site configuration based on co-crystallized ligands; generation of enantiomers from SMILES input; application of different force fields (MMFF94, MMFF94s, UFF, GAFF, Ghemical) for energy minimization; retention of selectable ions and cofactors; sidechain flexibility of selectable binding site residues; multiple input file format (SMILES, PDB, SDF, Mol2, Mol); generation of reports and of pictures for interactive visualization. Users can download for free MzDOCK at the following link: https://github.com/Muzatheking12/MzDOCK.
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Affiliation(s)
- Muzammil Kabier
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, India
| | - Nicola Gambacorta
- Division of Medical Genetics, IRCSS Foundation-Casa Sollievo della Sofferenza, San Giovanni Rotondo (Foggia), Foggia, Italy
| | - Daniela Trisciuzzi
- Dipartimento di Farmacia - Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", Bari, Italy
| | - Sunil Kumar
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, India
| | - Orazio Nicolotti
- Dipartimento di Farmacia - Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", Bari, Italy
| | - Bijo Mathew
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi, India
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4
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Zăgrean-Tuza C, Matei A, Silaghi-Dumitrescu R. A biomimetic assay for antioxidant reactivity, based on liposomes and myoglobin. J Inorg Biochem 2024; 258:112613. [PMID: 38815361 DOI: 10.1016/j.jinorgbio.2024.112613] [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: 04/02/2024] [Revised: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 06/01/2024]
Abstract
Antioxidant assays are typically based on non-physiologically relevant reagents. We describe here a quantitative assay based on the inhibition of the liposome autooxidation in the presence of myoglobin (ILA-Mb), an oxidative process with direct biomedical relevance. Additional advantages of the assay include the use of standard and readily available reagents (lecithin and myoglobin) and the applicability to lipophilic antioxidants. The ILA-Mb assay is based on previously reported qualitative or semi-quantitative ones that employed cytochrome c instead of myoglobin. A number of antioxidants are tested, and their IC50 parameters are discussed and interpreted to involve direct interaction with both myoglobin and the liposomes.
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Affiliation(s)
- Cezara Zăgrean-Tuza
- Department of Chemistry, Babeș-Bolyai University, 11 Arany Janos, 400028 Cluj-Napoca, Romania
| | - Alina Matei
- Department of Chemistry, Babeș-Bolyai University, 11 Arany Janos, 400028 Cluj-Napoca, Romania
| | - Radu Silaghi-Dumitrescu
- Department of Chemistry, Babeș-Bolyai University, 11 Arany Janos, 400028 Cluj-Napoca, Romania.
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5
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Yang J, Duan YF, Liu L. Crystal structure of the iron-sulfur cluster transfer protein ApbC from Escherichia coli. Biochem Biophys Res Commun 2024; 722:150167. [PMID: 38797154 DOI: 10.1016/j.bbrc.2024.150167] [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: 05/21/2024] [Accepted: 05/22/2024] [Indexed: 05/29/2024]
Abstract
Iron-sulfur (Fe-S) clusters are ubiquitous and are necessary to sustain basic life processes. The intracellular Fe-S clusters do not form spontaneously and many proteins are required for their biosynthesis and delivery. The bacterial P-loop NTPase family protein ApbC participates in Fe-S cluster assembly and transfers the cluster into apoproteins, with the Walker A motif and CxxC motif being essential for functionality of ApbC in Fe-S protein biogenesis. However, the structural basis underlying the ApbC activity and the motifs' role remains unclear. Here, we report the crystal structure of Escherichia coli ApbC at 2.8 Å resolution. The dimeric structure is in a W shape and the active site is located in the 2-fold center. The function of the motifs can be annotated by structural analyses. ApbC has an additional N-terminal domain that differs from other P-loop NTPases, possibly conferring its inherent specificity in vivo.
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Affiliation(s)
- Jingyu Yang
- School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China.
| | - Ya-Fei Duan
- School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China
| | - Lin Liu
- School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China
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6
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Vicari HP, Gomes RDC, Lima K, Rossini NDO, Rodrigues Junior MT, de Miranda LBL, Dias MVB, Costa-Lotufo LV, Coelho F, Machado-Neto JA. Cyclopenta[b]indoles as novel antimicrotubule agents with antileukemia activity. Toxicol In Vitro 2024; 99:105856. [PMID: 38821378 DOI: 10.1016/j.tiv.2024.105856] [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: 04/02/2024] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 06/02/2024]
Abstract
Acute leukemias present therapeutic challenges despite advances in treatments. Microtubule inhibitors have played a pivotal role in cancer therapy, inspiring exploration into novel compounds like C2E1 from the cyclopenta[b]indole class. In the present study, we investigated C2E1's potential as a therapeutic agent for acute leukemia at molecular, cellular, and genetic levels. C2E1 demonstrated tubulin depolarization activity, significantly reducing leukemia cell viability. Its impact involved multifaceted mechanisms: inducing apoptosis, arrest of cell cycle progression, and inhibition of clonogenicity and migration in leukemia cells. At a molecular level, C2E1 triggered DNA damage, antiproliferative, and apoptosis markers and altered gene expression related to cytoskeletal regulation, disrupting essential cellular processes crucial for leukemia cell survival and proliferation. These findings highlight C2E1's promise as a potential candidate for novel anti-cancer therapies. Notably, its distinct mode of action from conventional microtubule-targeting drugs suggests the potential to bypass common resistance mechanisms encountered with existing treatments. In summary, C2E1 emerges as a compelling compound with diverse effects on leukemia cells, showcasing promising antineoplastic properties. Its ability to disrupt critical cellular functions selective to leukemia cells positions it as a candidate for future therapeutic development.
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Affiliation(s)
- Hugo Passos Vicari
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Ralph da Costa Gomes
- Department of Organic Chemistry, Institute of Chemistry, State University of Campinas, Campinas, São Paulo, Brazil
| | - Keli Lima
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; Laboratory of Medical Investigation in Pathogenesis and Targeted Therapy in Onco-Immuno-Hematology (LIM-31), Department of Internal Medicine, Hematology Division, Faculdade de Medicina, University of São Paulo, São Paulo, Brazil
| | | | | | | | | | - Leticia Veras Costa-Lotufo
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Fernando Coelho
- Department of Organic Chemistry, Institute of Chemistry, State University of Campinas, Campinas, São Paulo, Brazil.
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7
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Zhang W, Zhuang X, Wu C, Jin Y, Xing J, Hou M, Yang W, Feng Q, Wang H. Apigenin inhibits tumor angiogenesis by hindering microvesicle biogenesis via ARHGEF1. Cancer Lett 2024; 596:216961. [PMID: 38823764 DOI: 10.1016/j.canlet.2024.216961] [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: 02/14/2024] [Revised: 05/11/2024] [Accepted: 05/13/2024] [Indexed: 06/03/2024]
Abstract
Extracellular vesicles are essential for intercellular communication and are involved in tumor progression. Inhibiting the direct release of extracellular vesicles seems to be an effective strategy in inhibiting tumor progression, but lacks of investigation. Here, we report a natural flavonoid compound, apigenin, could significantly inhibit the growth of hepatocellular carcinoma by preventing microvesicle secretion. Mechanistically, apigenin primarily targets the guanine nucleotide exchange factor ARHGEF1, inhibiting the activity of small G protein Cdc42, which is essential in regulating the release of microvesicles from tumor cells. In turn, this inhibits tumor angiogenesis related to VEGF90K transported on microvesicles, ultimately impeding tumor progression. Collectively, these findings highlight the therapeutic potential of apigenin and shed light on its anticancer mechanisms through inhibiting microvesicle biogenesis, providing a solid foundation for the refinement and practical application of apigenin.
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Affiliation(s)
- Wanying Zhang
- Cancer Research Center, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230036, China
| | - XiangJin Zhuang
- Cancer Research Center, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230036, China
| | - Chenlong Wu
- Cancer Research Center, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230036, China
| | - Yong Jin
- Cancer Research Center, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230036, China
| | - Jiayu Xing
- Cancer Research Center, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230036, China
| | - Mei Hou
- Cancer Research Center, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230036, China
| | - Wen Yang
- Cancer Research Center, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230036, China; International Co-operation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Naval Medical University (Second Military Medical University), Shanghai, 200438, China; National Center for Liver Cancer, Naval Medical University (Second Military Medical University), Shanghai, 201805, China; Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer, Ministry of Education, Shanghai, 200438, China.
| | - Qiyu Feng
- Cancer Research Center, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230036, China; Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer, Ministry of Education, Shanghai, 200438, China.
| | - Hongyang Wang
- Cancer Research Center, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230036, China; International Co-operation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Naval Medical University (Second Military Medical University), Shanghai, 200438, China; National Center for Liver Cancer, Naval Medical University (Second Military Medical University), Shanghai, 201805, China; Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer, Ministry of Education, Shanghai, 200438, China.
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8
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Campos-Fernández E, Alqualo NO, Vaz ER, Rodrigues CM, Alonso-Goulart V. Unveiling the characteristics of D4 and R4 aptamers for their future use in prostate cancer clinical practice. Biophys Chem 2024; 311:107259. [PMID: 38763045 DOI: 10.1016/j.bpc.2024.107259] [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: 02/25/2024] [Revised: 04/24/2024] [Accepted: 05/12/2024] [Indexed: 05/21/2024]
Abstract
The DNA and RNA aptamers D4 and R4, respectively, emerged from the modification of PC-3 cell-binding aptamer A4. Our objective was to characterize the aptamers in silico and in vitro and begin to identify their target molecules. We represented their structures using computational algorithms; evaluated their binding to several prostate cell lines and their effects on the viability and migration of these cells; and determined their dissociation constant by flow cytometry. We analyzed circulating prostate tumor cells from patients using D4, R4, anti-CD133 and anti-CD44. Finally, the target proteins of both aptamers were precipitated and identified by mass spectrometry to simulate their in silico docking. The aptamers presented similar structures and bound to prostate tumor cells without modifying the cellular parameters studied, but with different affinities. The ligand cells for both aptamers were CD44+, indicating that they could identify cells in the mesenchymal stage of the metastatic process. The possible target proteins NXPE1, ADAM30, and MUC6 need to be further studied to better understand their interaction with the aptamers. These results support the development of new assays to determine the clinical applications of D4 and R4 aptamers in prostate cancer.
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Affiliation(s)
- Esther Campos-Fernández
- Laboratory of Nanobiotechnology Prof. Dr. Luiz Ricardo Goulart Filho, Institute of Biotechnology, Universidade Federal de Uberlândia, Uberlândia, MG, Brazil
| | - Nathalia Oliveira Alqualo
- Laboratory of Nanobiotechnology Prof. Dr. Luiz Ricardo Goulart Filho, Institute of Biotechnology, Universidade Federal de Uberlândia, Uberlândia, MG, Brazil
| | - Emília Rezende Vaz
- Laboratory of Nanobiotechnology Prof. Dr. Luiz Ricardo Goulart Filho, Institute of Biotechnology, Universidade Federal de Uberlândia, Uberlândia, MG, Brazil
| | - Cláudia Mendonça Rodrigues
- Laboratory of Nanobiotechnology Prof. Dr. Luiz Ricardo Goulart Filho, Institute of Biotechnology, Universidade Federal de Uberlândia, Uberlândia, MG, Brazil
| | - Vivian Alonso-Goulart
- Laboratory of Nanobiotechnology Prof. Dr. Luiz Ricardo Goulart Filho, Institute of Biotechnology, Universidade Federal de Uberlândia, Uberlândia, MG, Brazil.
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9
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Sosa MB, Leeman JT, Washington LJ, Scheller HV, Chang MCY. Biosynthesis of Strained Amino Acids by a PLP-Dependent Enzyme through Cryptic Halogenation. Angew Chem Int Ed Engl 2024; 63:e202319344. [PMID: 38519422 DOI: 10.1002/anie.202319344] [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: 12/14/2023] [Revised: 03/02/2024] [Accepted: 03/18/2024] [Indexed: 03/24/2024]
Abstract
Amino acids (AAs) are modular building blocks which nature uses to synthesize both macromolecules, such as proteins, and small molecule natural products, such as alkaloids and non-ribosomal peptides. While the 20 main proteinogenic AAs display relatively limited side chain diversity, a wide range of non-canonical amino acids (ncAAs) exist that are not used by the ribosome for protein synthesis, but contain a broad array of structural features and functional groups. In this communication, we report the discovery of the biosynthetic pathway for a new ncAA, pazamine, which contains a cyclopropane ring formed in two steps. In the first step, a chlorine is added onto the C4 position of lysine by a radical halogenase, PazA. The cyclopropane ring is then formed in the next step by a pyridoxal-5'-phosphate-dependent enzyme, PazB, via an SN2-like attack at C4 to eliminate chloride. Genetic studies of this pathway in the native host, Pseudomonas azotoformans, show that pazamine potentially inhibits ethylene biosynthesis in growing plants based on alterations in the root phenotype of Arabidopsis thaliana seedlings. We further show that PazB can be utilized to make an alternative cyclobutane-containing AA. These discoveries may lead to advances in biocatalytic production of specialty chemicals and agricultural biotechnology.
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Affiliation(s)
- Max B Sosa
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720-1460, USA
| | - Jacob T Leeman
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720-1460, USA
| | - Lorenzo J Washington
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720-3102, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Henrik V Scheller
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720-3102, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Michelle C Y Chang
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720-1460, USA
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720-1462, USA
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
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10
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Dhanasekaran S, Selvadoss PP, Manoharan SS, Jeyabalan S, Yaraguppi DA, Choudhury AA, Rajeswari VD, Ramanathan G, Thamaraikani T, Sekar M, Subramaniyan V, Shing WL. Regulation of NS5B Polymerase Activity of Hepatitis C Virus by Target Specific Phytotherapeutics: An In-Silico Molecular Dynamics Approach. Cell Biochem Biophys 2024:10.1007/s12013-024-01359-w. [PMID: 39042185 DOI: 10.1007/s12013-024-01359-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2024] [Indexed: 07/24/2024]
Abstract
Chronic hepatitis caused by the hepatitis C virus (HCV) is closely linked with the advancement of liver disease. The research hypothesis suggests that the NS5B enzyme (non-structural 5B protein) of HCV plays a pivotal role in facilitating viral replication within host cells. Hence, the objective of the present investigation is to identify the binding interactions between the structurally diverse phytotherapeutics and those of the catalytic residue of the target NS5B polymerase protein. Results of our docking simulations reveal that compounds such as arjunolic acid, sesamin, arjungenin, astragalin, piperic acid, piperidine, piperine, acalyphin, adhatodine, amyrin, anisotine, apigenin, cuminaldehyde, and curcumin exhibit a maximum of three interactions with the catalytic residues (Asp 220, Asp 318, and Asp 319) present on the Hepatitis C virus NS5B polymerase of HCV. Molecular dynamic simulation, particularly focusing on the best binding lead compound, arjunolic acid (-8.78 kcal/mol), was further extensively analyzed using RMSD, RMSF, Rg, and SASA techniques. The results of the MD simulation confirm that the NS5B-arjunolic acid complex becomes increasingly stable from 20 to 100 ns. The orientation of both arjunolic acid and sofosbuvir triphosphate (standard) within the active site was investigated through DCCM, PCA, and FEL analysis, indicating highly stable interactions of the lead arjunolic acid with the catalytic region of the NS5B enzyme. The findings of our current investigation suggest that bioactive therapeutics like arjunolic acid could serve as promising candidates for limiting the NS5B polymerase activity of the hepatitis C virus, offering hope for the future of HCV treatment.
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Affiliation(s)
- Sivaraman Dhanasekaran
- Department of Biotechnology, School of Energy Technology, Pandit Deendayal Energy University, Knowledge Corridor, Raisan Village, PDPU Road, Gandhinagar, Gujarat, 382426, India.
| | - Pradeep Pushparaj Selvadoss
- Department of Biotechnology, School of Energy Technology, Pandit Deendayal Energy University, Knowledge Corridor, Raisan Village, PDPU Road, Gandhinagar, Gujarat, 382426, India
| | - Solomon Sundar Manoharan
- Department of Biotechnology, School of Energy Technology, Pandit Deendayal Energy University, Knowledge Corridor, Raisan Village, PDPU Road, Gandhinagar, Gujarat, 382426, India
| | - Srikanth Jeyabalan
- Sri Ramachandra Institute of Higher Education and Research, Chennai, Tamil Nadu, 600116, India
| | | | | | - V Devi Rajeswari
- Vellore Institute of Technology, Vellore, 632014, Tamil Nadu, India
| | | | | | - Mahendran Sekar
- Monash University, Bandar Sunway, Subang Jaya, Selangor, 47500, Malaysia
| | | | - Wong Ling Shing
- INTI International University, Nilai, Negeri Sembilan, 71800, Malaysia
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11
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Khanal M, Acharya A, Maharjan R, Gyawali K, Adhikari R, Mulmi DD, Lamichhane TR, Lamichhane HP. Identification of potent inhibitors of HDAC2 from herbal products for the treatment of colon cancer: Molecular docking, molecular dynamics simulation, MM/GBSA calculations, DFT studies, and pharmacokinetic analysis. PLoS One 2024; 19:e0307501. [PMID: 39037973 DOI: 10.1371/journal.pone.0307501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 07/06/2024] [Indexed: 07/24/2024] Open
Abstract
The histone deacetylase 2 (HDAC2), an enzyme involved in gene regulation, is a potent drug target for the treatment of colon cancer. Phytocompounds having anticancer properties show the ability to interact with HDAC2 enzyme. Among the compounds, docking scores of caffeic acid (CA) and p-coumaric acid (pCA) with HDAC2 showed good binding efficacy of -5.46 kcal/mol and -5.16 kcal/mol, respectively, with small inhibition constants. The higher binding efficacy of CA compared to pCA can be credited to the presence of an extra oxygen atom in the CA molecule, which forms an additional hydrogen bond with Tyr297. The HDAC2 in complex with these molecules was found to be stable by analyzing RMSD, RMSF, Rg, and SASA values obtained through MD simulations. Furthermore, CA and pCA exhibited low MM/GBSA free energies of -16.32 ± 2.62 kcal/mol and -17.01 ± 2.87 kcal/mol, respectively. The HOMO and LUMO energy gaps, dipole moments, global reactivity descriptor values, and MEP surfaces showed the reactivity of the molecules. The favourable physicochemical and pharmacokinetic properties, along with absence of toxicity of the molecules determined using ADMET analysis, suggested both the acids to be regarded as effective drugs in the treatment of colon cancer.
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Affiliation(s)
- Madan Khanal
- Central Department of Physics, Tribhuvan University, Kathmandu, Nepal
| | - Arjun Acharya
- Central Department of Physics, Tribhuvan University, Kathmandu, Nepal
| | - Rajesh Maharjan
- Central Department of Physics, Tribhuvan University, Kathmandu, Nepal
| | - Kalpana Gyawali
- Central Department of Physics, Tribhuvan University, Kathmandu, Nepal
| | - Rameshwar Adhikari
- Central Department of Chemistry, Tribhuvan University, Kathmandu, Nepal
- Research Center for Applied Science and Technology (RECAST), Tribhuvan University, Kathmandu, Nepal
| | - Deependra Das Mulmi
- Nanomaterials Research Laboratory, Nepal Academy of Science and Technology (NAST), Lalitpur, Nepal
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12
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Gao P, Tambe M, Chen CZ, Huang W, Tawa GJ, Hirschhorn T, Stockwell BR, Zheng W, Shen M. Identification of Potent ADCK3 Inhibitors through Structure-Based Virtual Screening. J Chem Inf Model 2024. [PMID: 39025788 DOI: 10.1021/acs.jcim.4c00530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
ADCK3 is a member of the UbiB family of atypical protein kinases in humans, with homologues in archaea, bacteria, and eukaryotes. In lieu of protein kinase activity, ADCK3 plays a role in the biosynthesis of coenzyme Q10 (CoQ10), and inactivating mutations can cause a CoQ10 deficiency and ataxia. However, the exact functions of ADCK3 are still unclear, and small-molecule inhibitors could be useful as chemical probes to elucidate its molecular mechanisms. In this study, we applied structure-based virtual screening (VS) to discover a novel chemical series of ADCK3 inhibitors. Through extensive structural analysis of the active-site residues, we developed a pharmacophore model and applied it to a large-scale VS. Out of ∼170,000 compounds virtually screened, 800 top-ranking candidate compounds were selected and tested in both ADCK3 and p38 biochemical assays for hit validation. In total, 129 compounds were confirmed as ADCK3 inhibitors, and among them, 114 compounds are selective against p38, which was used as a counter-target. Molecular dynamics (MD) simulations were then conducted to predict the binding modes of the most potent compounds within the ADCK3 active site. Through metadynamics analysis, we successfully detected the key amino acid residues that govern intermolecular interactions. The findings provided in this study can serve as a promising starting point for drug development.
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Affiliation(s)
- Peng Gao
- Therapeutics Development Branch, Division of Preclinical Innovation, National Center for Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
| | - Mitali Tambe
- Therapeutics Development Branch, Division of Preclinical Innovation, National Center for Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
| | - Catherine Z Chen
- Therapeutics Development Branch, Division of Preclinical Innovation, National Center for Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
| | - Wenwei Huang
- Therapeutics Development Branch, Division of Preclinical Innovation, National Center for Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
| | - Gregory J Tawa
- Therapeutics Development Branch, Division of Preclinical Innovation, National Center for Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
| | - Tal Hirschhorn
- Department of Biological Sciences, Department of Chemistry and Department of Pathology and Cell Biology, Columbia University, 550 West 120th Street MC 4846, 1208 Northwest Corner Building, New York, New York 10027, United States
| | - Brent R Stockwell
- Department of Biological Sciences, Department of Chemistry and Department of Pathology and Cell Biology, Columbia University, 550 West 120th Street MC 4846, 1208 Northwest Corner Building, New York, New York 10027, United States
| | - Wei Zheng
- Therapeutics Development Branch, Division of Preclinical Innovation, National Center for Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
| | - Min Shen
- Early Translation Branch, Division of Preclinical Innovation, National Center for Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
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13
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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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14
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Mao T, Chen B, Wei W, Chen G, Liu Z, Wu L, Li X, Pathak JL, Li J. AutoDock and molecular dynamics-based therapeutic potential prediction of flavonoids for primary Sjögren's syndrome. Heliyon 2024; 10:e33860. [PMID: 39027572 PMCID: PMC11255588 DOI: 10.1016/j.heliyon.2024.e33860] [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: 02/21/2024] [Revised: 06/27/2024] [Accepted: 06/27/2024] [Indexed: 07/20/2024] Open
Abstract
Primary Sjögren's Syndrome (pSS) is a systemic autoimmune disease that leads to reduced saliva production, primarily affecting women due to estrogen deficiency. The estrogen receptor α (ERα) plays a crucial role in mediating the expression of the aquaporin 5 (AQP5) gene through the estrogen response element-dependent signaling pathway, making ERα a key drug target for pSS. Several flavonoids have been reported to have the potential to treat pSS. This study aimed to screen and compare flavonoids binding to ERα using AutoDock, providing a basis for treating pSS with flavonoids. The estrogenic potential of six representative flavonoids was examined in this study. Molecular docking revealed that the binding energy of all six flavonoids to ERα was less than -5.6 kcal/mol. Apigenin, naringenin, and daidzein were the top three flavonoids with even lower binding energies of -7.8, -8.09, and -8.59 kcal/mol, respectively. Similar to the positive control estradiol, apigenin, naringenin, and daidzein showed hydrogen bond interactions with GLU353, GLY521, and HIS524 at the active site. The results of luciferase reporter assays demonstrated that apigenin, naringenin, and daidzein significantly enhanced the transcription of estrogen receptor element (ERE) in the PGL3/AQP5 promoter. Furthermore, molecular dynamics simulations using GROMACS for a time scale of 100 ns revealed relatively stable binding of apigenin-ERα, naringenin-ERα, and daidzein-ERα. Mechanistically, homology modeling indicated that GLU353, GLY521, and HIS524 were the key residues of ERα exerting an estrogenic effect. The therapeutic effect of apigenin on dry mouth in pSS models was further validated. In conclusion, these results indicate the estrogenic and pSS therapeutic potential of apigenin, naringenin, and daidzein.
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Affiliation(s)
- Tianjiao Mao
- School and Hospital of Stomatology, Guangdong Engineering Research Center of Oral Restoration and Reconstruction, Guangzhou Medical University, Guangzhou, 510140, China
| | - Bo Chen
- School and Hospital of Stomatology, Guangdong Engineering Research Center of Oral Restoration and Reconstruction, Guangzhou Medical University, Guangzhou, 510140, China
| | - Wei Wei
- Department of Prosthodontics, School and Hospital of Stomatology, Jilin University, Changchun, 130012, China
| | - Guiping Chen
- School and Hospital of Stomatology, Guangdong Engineering Research Center of Oral Restoration and Reconstruction, Guangzhou Medical University, Guangzhou, 510140, China
| | - Zhuoyuan Liu
- School and Hospital of Stomatology, Guangdong Engineering Research Center of Oral Restoration and Reconstruction, Guangzhou Medical University, Guangzhou, 510140, China
| | - Lihong Wu
- School and Hospital of Stomatology, Guangdong Engineering Research Center of Oral Restoration and Reconstruction, Guangzhou Medical University, Guangzhou, 510140, China
| | - Xiaomeng Li
- KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, 510140, China
| | - Janak L. Pathak
- School and Hospital of Stomatology, Guangdong Engineering Research Center of Oral Restoration and Reconstruction, Guangzhou Medical University, Guangzhou, 510140, China
| | - Jiang Li
- School and Hospital of Stomatology, Guangdong Engineering Research Center of Oral Restoration and Reconstruction, Guangzhou Medical University, Guangzhou, 510140, China
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15
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Monticone G, Huang Z, Hewins P, Cook T, Mirzalieva O, King B, Larter K, Miller-Ensminger T, Sanchez-Pino MD, Foster TP, Nichols OV, Ramsay AJ, Majumder S, Wyczechowska D, Tauzier D, Gravois E, Crabtree JS, Garai J, Li L, Zabaleta J, Barbier MT, Del Valle L, Jurado KA, Miele L. Novel immunomodulatory properties of adenosine analogs promote their antiviral activity against SARS-CoV-2. EMBO Rep 2024:10.1038/s44319-024-00189-4. [PMID: 39009832 DOI: 10.1038/s44319-024-00189-4] [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: 07/26/2023] [Revised: 04/30/2024] [Accepted: 06/14/2024] [Indexed: 07/17/2024] Open
Abstract
The COVID-19 pandemic reminded us of the urgent need for new antivirals to control emerging infectious diseases and potential future pandemics. Immunotherapy has revolutionized oncology and could complement the use of antivirals, but its application to infectious diseases remains largely unexplored. Nucleoside analogs are a class of agents widely used as antiviral and anti-neoplastic drugs. Their antiviral activity is generally based on interference with viral nucleic acid replication or transcription. Based on our previous work and computer modeling, we hypothesize that antiviral adenosine analogs, like remdesivir, have previously unrecognized immunomodulatory properties which contribute to their therapeutic activity. In the case of remdesivir, we here show that these properties are due to its metabolite, GS-441524, acting as an Adenosine A2A Receptor antagonist. Our findings support a new rationale for the design of next-generation antiviral agents with dual - immunomodulatory and intrinsic - antiviral properties. These compounds could represent game-changing therapies to control emerging viral diseases and future pandemics.
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Affiliation(s)
- Giulia Monticone
- Department of Genetics, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, USA.
| | - Zhi Huang
- Department of Genetics, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Peter Hewins
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Thomasina Cook
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Oygul Mirzalieva
- Department of Biochemistry and Molecular Biology, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Brionna King
- Department of Genetics, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Kristina Larter
- Department of Genetics, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Taylor Miller-Ensminger
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Maria D Sanchez-Pino
- Department of Genetics, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, USA
- Department of Interdisciplinary Oncology, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Timothy P Foster
- Department of Microbiology, Immunology & Parasitology, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Olga V Nichols
- Department of Microbiology, Immunology & Parasitology, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Alistair J Ramsay
- Department of Microbiology, Immunology & Parasitology, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Samarpan Majumder
- Department of Genetics, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Dorota Wyczechowska
- Department of Interdisciplinary Oncology, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Darlene Tauzier
- Precision Medicine Program, Louisiana State University Health Sciences Center, New Orleans, LA, USA
- Department of Pathology, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Elizabeth Gravois
- Precision Medicine Program, Louisiana State University Health Sciences Center, New Orleans, LA, USA
- Department of Pathology, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Judy S Crabtree
- Department of Genetics, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, USA
- Precision Medicine Program, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Jone Garai
- Department of Interdisciplinary Oncology, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Li Li
- Department of Interdisciplinary Oncology, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Jovanny Zabaleta
- Department of Interdisciplinary Oncology, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Mallory T Barbier
- Department of Interdisciplinary Oncology, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Luis Del Valle
- Department of Interdisciplinary Oncology, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, USA
- Department of Pathology, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Kellie A Jurado
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lucio Miele
- Department of Genetics, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, USA
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16
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Zhu S, Zhu W, Zhao K, Yu J, Lu W, Zhou R, Fan S, Kong W, Yang F, Shan P. Discovery of a novel hybrid coumarin-hydroxamate conjugate targeting the HDAC1-Sp1-FOSL2 signaling axis for breast cancer therapy. Cell Commun Signal 2024; 22:361. [PMID: 39010083 PMCID: PMC11247895 DOI: 10.1186/s12964-024-01733-4] [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: 03/27/2024] [Accepted: 07/02/2024] [Indexed: 07/17/2024] Open
Abstract
BACKGROUND Breast cancer is one of the most lethal cancers in women. Despite significant advances in the diagnosis and treatment of breast cancer, many patients still succumb to this disease, and thus, novel effective treatments are urgently needed. Natural product coumarin has been broadly investigated since it reveals various biological properties in the medicinal field. Accumulating evidence indicates that histone deacetylase inhibitors (HDACIs) are promising novel anti-breast cancer agents. However, most current HDACIs exhibit only moderate effects against solid tumors and are associated with severe side effects. Thus, to develop more effective HDACIs for breast cancer therapy, hydroxamate of HDACIs was linked to coumarin core, and coumarin-hydroxamate hybrids were designed and synthesized. METHODS A substituted coumarin moiety was incorporated into the classic hydroxamate HDACIs by the pharmacophore fusion strategy. ZN444B was identified by using the HDACI screening kit and cell viability assay. Molecular docking was performed to explore the binding mode of ZN444B with HDAC1. Western blot, immunofluorescent staining, cell viability, colony formation and cell migration and flow cytometry assays were used to analyze the anti-breast cancer effects of ZN444B in vitro. Orthotopic studies in mouse models were applied for preclinical evaluation of efficacy and toxicity in vivo. Proteomic analysis, dual-luciferase reporter assay, chromatin immunoprecipitation, co-immunoprecipitation, immunofluorescent staining assays along with immunohistochemical (IHC) analysis were used to elucidate the molecular basis of the actions of ZN444B. RESULTS We synthesized and identified a novel coumarin-hydroxamate conjugate, ZN444B which possesses promising anti-breast cancer activity both in vitro and in vivo. A molecular docking model showed that ZN444B binds to HDAC1 with high affinity. Further mechanistic studies revealed that ZN444B specifically decreases FOS-like antigen 2 (FOSL2) mRNA levels by inhibiting the deacetylase activity of HDAC1 on Sp1 at K703 and abrogates the binding ability of Sp1 to the FOSL2 promoter. Furthermore, FOSL2 expression positively correlates with breast cancer progression and metastasis. Silencing FOSL2 expression decreases the sensitivity of breast cancer cells to ZN444B treatment. In addition, ZN444B shows no systemic toxicity in mice. CONCLUSIONS Our findings highlight the potential of FOSL2 as a new biomarker and therapeutic target for breast cancer and that targeting the HDAC1-Sp1-FOSL2 signaling axis with ZN444B may be a promising therapeutic strategy for breast cancer.
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Affiliation(s)
- Sujie Zhu
- Institute of Translational Medicine, College of Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266021, China
| | - Wenjing Zhu
- Clinical Research Center, Qingdao Municipal Hospital, Qingdao, 266071, China
| | - Kaihua Zhao
- Qingdao Central Hospital, University of Health and Rehabilitation Sciences (Qingdao Central Hospital), Qingdao, 266042, China
| | - Jie Yu
- Qingdao Central Hospital, University of Health and Rehabilitation Sciences (Qingdao Central Hospital), Qingdao, 266042, China
| | - Wenxia Lu
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Rui Zhou
- Department of Marine Bio-Pharmacology, College of Food Science and Technology, Shanghai Ocean University, Shanghai, 201306, China
| | - Shule Fan
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Weikaixin Kong
- Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University Health Science Center, Beijing, 100191, China.
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, 00250, Finland.
- Institute Sanqu Technology (Hangzhou) Co., Ltd., Hangzhou, China.
| | - Feifei Yang
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China.
| | - Peipei Shan
- Institute of Translational Medicine, College of Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266021, China.
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17
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Tang W, Ma J, Chen K, Wang K, Chen Z, Chen C, Li X, Wang Y, Shu Y, Zhang W, Yuan X, Shi G, Chen T, Wang P, Chen Y. Berbamine ameliorates DSS-induced colitis by inhibiting peptidyl-arginine deiminase 4-dependent neutrophil extracellular traps formation. Eur J Pharmacol 2024; 975:176634. [PMID: 38710356 DOI: 10.1016/j.ejphar.2024.176634] [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: 12/25/2023] [Revised: 03/29/2024] [Accepted: 05/03/2024] [Indexed: 05/08/2024]
Abstract
Ulcerative colitis (UC) is a chronic inflammatory bowel disease with immune dysregulation affecting colon inflammatory response. Recent studies have highlighted that neutrophil extracellular traps (NETs) play an important role in the pathogenesis of UC. Berbamine (BBM), one of the bioactive ingredients extracted from Chinese herbal medicine Berberis vulgaris L, has attracted intensive attentions due to its significant anti-inflammatory activity and a marketing drug for treating leukemia in China. However, the exact role and potential molecular mechanism of BBM against UC remains elusive. In the present study, our results showed that BBM could markedly improve the pathological phenotype and the colon inflammation in mice with dextran sulfate sodium (DSS)-induced colitis. Then, comprehensive approaches combining network pharmacology and molecular docking analyses were employed to predict the therapeutic potential of BBM in treating UC by peptidyl-arginine deiminase 4 (PAD4), a crucial molecule involved in NETs formation. The molecular docking results showed BBM had a high affinity for PAD4 with a binding energy of -9.3 kcal/mol Moreover, PAD4 expression and NETs productions, including citrullination of histone H3 (Cit-H3), neutrophil elastase (NE), myeloperoxidase (MPO) in both neutrophils and colonic tissue were reduced after BBM administration. However, in the mice with DSS-induced colitis pretreated with GSK484, a PAD4-specific inhibitor, BBM could not further reduce disease related indexes, expression of PAD4 and NETs productions. Above all, the identification of PAD4 as a potential target for BBM to inhibit NETs formation in colitis provides novel insights into the development of BBM-derived drugs for the clinical management of UC.
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Affiliation(s)
- Wenwen Tang
- Department of Colorectal Surgery, Jiangsu Province Hospital of Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China; Jiangsu Province Key Laboratory of Tumor Systems Biology and Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China
| | - Jiaze Ma
- Department of Colorectal Surgery, Jiangsu Province Hospital of Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China; Jiangsu Province Key Laboratory of Tumor Systems Biology and Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China
| | - Kaidi Chen
- Department of Colorectal Surgery, Jiangsu Province Hospital of Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China; Jiangsu Province Key Laboratory of Tumor Systems Biology and Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China
| | - Kuiling Wang
- Department of Colorectal Surgery, Jiangsu Province Hospital of Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China; Jiangsu Province Key Laboratory of Tumor Systems Biology and Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China
| | - Zepeng Chen
- Department of Colorectal Surgery, Jiangsu Province Hospital of Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China; Jiangsu Province Key Laboratory of Tumor Systems Biology and Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China
| | - Chen Chen
- Department of Colorectal Surgery, Jiangsu Province Hospital of Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China; Jiangsu Province Key Laboratory of Tumor Systems Biology and Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China
| | - Xun Li
- Institute for Molecular Bioscience, the University of Queensland, Brisbane, 4702, Australia
| | - Yuji Wang
- Department of Colorectal Surgery, Jiangsu Province Hospital of Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China; Jiangsu Province Key Laboratory of Tumor Systems Biology and Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China
| | - Yi Shu
- Department of Colorectal Surgery, Jiangsu Province Hospital of Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China; Jiangsu Province Key Laboratory of Tumor Systems Biology and Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China
| | - Wei Zhang
- Department of Colorectal Surgery, Jiangsu Province Hospital of Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China; Jiangsu Province Key Laboratory of Tumor Systems Biology and Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China
| | - Xiaomin Yuan
- Department of Colorectal Surgery, Jiangsu Province Hospital of Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China; Jiangsu Province Key Laboratory of Tumor Systems Biology and Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China
| | - Guoping Shi
- Department of Colorectal Surgery, Jiangsu Province Hospital of Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China; Jiangsu Province Key Laboratory of Tumor Systems Biology and Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China
| | - Tuo Chen
- Jiangsu Province Key Laboratory of Tumor Systems Biology and Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China; Department of Orthopedics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China; Department of Orthopedics, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, PR China; Institute for Molecular Bioscience, the University of Queensland, Brisbane, 4702, Australia.
| | - Peimin Wang
- Department of Orthopedics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China; Department of Orthopedics, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, PR China.
| | - Yugen Chen
- Department of Colorectal Surgery, Jiangsu Province Hospital of Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China; Jiangsu Province Key Laboratory of Tumor Systems Biology and Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China; Jiangsu Collaborative Innovation Center of Chinese Medicine in Prevention and Treatment of Tumor, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, PR China.
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18
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Jagtap YA, Kumar P, Dubey AR, Kinger S, Choudhary A, Karmakar S, Lal G, Kumar A, Kumar A, Prasad A, Mishra A. Acetaminophen induces mitochondrial apoptosis through proteasome dysfunctions. Life Sci 2024; 349:122732. [PMID: 38768775 DOI: 10.1016/j.lfs.2024.122732] [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: 11/15/2023] [Revised: 03/12/2024] [Accepted: 05/15/2024] [Indexed: 05/22/2024]
Abstract
Acetaminophen is a known antipyretic and non-opioid analgesic for mild pain and fever. Numerous studies uncover their hidden chemotherapeutics applications, including chronic cancer pain management. Acetaminophen also represents an anti-proliferative effect in some cancer cells. Few studies also suggest that the use of Acetaminophen can trigger apoptosis and impede cellular growth. However, Acetaminophen's molecular potential and precise mechanism against improper cellular proliferation and use as an effective anti-proliferative agent still need to be better understood. Here, our current findings show that Acetaminophen induces proteasomal dysfunctions, resulting in aberrant protein accumulation and mitochondrial abnormalities, and consequently induces cell apoptosis. We observed that the Acetaminophen treatment leads to improper aggregation of ubiquitylated expanded polyglutamine proteins, which may be due to the dysfunctions of proteasome activities. Our in-silico analysis suggests the interaction of Acetaminophen and proteasome. Furthermore, we demonstrated the accumulation of proteasome substrates and the depletion of proteasome activities after treating Acetaminophen in cells. Acetaminophen induces proteasome dysfunctions and mitochondrial abnormalities, leading to pro-apoptotic morphological changes and apoptosis successively. These results suggest that Acetaminophen can induce cell death and may retain a promising anti-proliferative effect. These observations can open new possible molecular strategies in the near future for developing and designing specific and effective proteasome inhibitors, which can be helpful in conjugation with other anti-tumor drugs for their better efficiency.
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Affiliation(s)
- Yuvraj Anandrao Jagtap
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, 342037, India
| | - Prashant Kumar
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, 342037, India
| | - Ankur Rakesh Dubey
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, 342037, India
| | - Sumit Kinger
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, 342037, India
| | - Akash Choudhary
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, 342037, India
| | - Surojit Karmakar
- National Centre for Cell Science (NCCS), Ganeshkhind, Pune, Maharashtra, 411007, India
| | - Girdhari Lal
- National Centre for Cell Science (NCCS), Ganeshkhind, Pune, Maharashtra, 411007, India
| | - Awanish Kumar
- Department of Biotechnology, National Institute of Technology, Raipur, Chhattisgarh, 492010, India
| | - Amit Kumar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, Madhya Pradesh, 453552, India
| | - Amit Prasad
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh, 175005, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, 342037, India.
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19
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Zhou X, Wang G, Tian C, Du L, Prochownik EV, Li Y. Inhibition of DUSP18 impairs cholesterol biosynthesis and promotes anti-tumor immunity in colorectal cancer. Nat Commun 2024; 15:5851. [PMID: 38992029 PMCID: PMC11239938 DOI: 10.1038/s41467-024-50138-x] [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: 02/05/2024] [Accepted: 07/02/2024] [Indexed: 07/13/2024] Open
Abstract
Tumor cells reprogram their metabolism to produce specialized metabolites that both fuel their own growth and license tumor immune evasion. However, the relationships between these functions remain poorly understood. Here, we report CRISPR screens in a mouse model of colo-rectal cancer (CRC) that implicates the dual specificity phosphatase 18 (DUSP18) in the establishment of tumor-directed immune evasion. Dusp18 inhibition reduces CRC growth rates, which correlate with high levels of CD8+ T cell activation. Mechanistically, DUSP18 dephosphorylates and stabilizes the USF1 bHLH-ZIP transcription factor. In turn, USF1 induces the SREBF2 gene, which allows cells to accumulate the cholesterol biosynthesis intermediate lanosterol and release it into the tumor microenvironment (TME). There, lanosterol uptake by CD8+ T cells suppresses the mevalonate pathway and reduces KRAS protein prenylation and function, which in turn inhibits their activation and establishes a molecular basis for tumor cell immune escape. Finally, the combination of an anti-PD-1 antibody and Lumacaftor, an FDA-approved small molecule inhibitor of DUSP18, inhibits CRC growth in mice and synergistically enhances anti-tumor immunity. Collectively, our findings support the idea that a combination of immune checkpoint and metabolic blockade represents a rationally-designed, mechanistically-based and potential therapy for CRC.
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Affiliation(s)
- Xiaojun Zhou
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
| | - Genxin Wang
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
| | - Chenhui Tian
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
| | - Lin Du
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China
| | - Edward V Prochownik
- Division of Hematology/Oncology, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, 15224, USA
- Department of Microbiology and Molecular Genetics of UPMC, Pittsburgh, PA, 15224, USA
- The Pittsburgh Liver Research Center, The Hillman Cancer Institute of UPMC, Pittsburgh, PA, 15224, USA
| | - Youjun Li
- Department of Colorectal and Anal Surgery, Zhongnan Hospital of Wuhan University, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China.
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, 430071, China.
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20
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Fallon MA, Tadfie H, Watson AP, Dyke MM, Flores C, Cook N, Fei Z, Holland CK. Molecular basis of one-step methyl anthranilate biosynthesis in grapes, sweet orange, and maize. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38976445 DOI: 10.1111/tpj.16922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 06/26/2024] [Indexed: 07/10/2024]
Abstract
Plants synthesize an array of volatile compounds, many of which serve ecological roles in attracting pollinators, deterring herbivores, and communicating with their surroundings. Methyl anthranilate (MeAA) is an anti-herbivory defensive volatile responsible for grape aroma that is emitted by several agriculturally relevant plants, including citrus, grapes, and maize. Unlike maize, which uses a one-step anthranilate methyltransferase (AAMT), grapes have been thought to use a two-step pathway for MeAA biosynthesis. By mining available transcriptomics data, we identified two AAMTs in Vitis vinifera (wine grape), as well as one ortholog in "Concord" grape. Many angiosperms methylate the plant hormone salicylic acid (SA) to produce methyl salicylate, which acts as a plant-to-plant communication molecule. Because the Citrus sinensis (sweet orange) SA methyltransferase can methylate both anthranilate (AA) and SA, we used this enzyme to examine the molecular basis of AA activity by introducing rational mutations, which identified several active site residues that increase activity with AA. Reversing this approach, we introduced mutations that imparted activity with SA in the maize AAMT, which uncovered different active site residues from those in the citrus enzyme. Sequence and phylogenetic analysis revealed that one of the Vitis AAMTs shares an ancestor with jasmonic acid methyltransferases, similar to the AAMT from strawberry (Frageria sp.). Collectively, these data demonstrate the molecular mechanisms underpinning AA activity across methyltransferases and identify one-step enzymes by which grapes synthesize MeAA.
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Affiliation(s)
- Michael A Fallon
- Department of Biology, Williams College, Williamstown, Massachusetts, 01267, USA
| | - Hisham Tadfie
- Department of Biology, Williams College, Williamstown, Massachusetts, 01267, USA
| | - Aracely P Watson
- Department of Biology, Williams College, Williamstown, Massachusetts, 01267, USA
| | - Madeline M Dyke
- Department of Biology, Williams College, Williamstown, Massachusetts, 01267, USA
| | - Christopher Flores
- Department of Biology, Williams College, Williamstown, Massachusetts, 01267, USA
| | - Nathan Cook
- Department of Chemistry, Williams College, Williamstown, Massachusetts, 01267, USA
| | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, New York, 14850, USA
| | - Cynthia K Holland
- Department of Biology, Williams College, Williamstown, Massachusetts, 01267, USA
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21
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Xue H, Nie H, Huang Z, Lu B, Wei M, Xu H, Ji L. 2,3,5,4'-tetrahydroxy-stilbene-2-O-β-D-glucoside promotes liver regeneration after partial hepatectomy in mice: The potential involvement of PPARα-mediated fatty acid metabolism. JOURNAL OF ETHNOPHARMACOLOGY 2024; 334:118513. [PMID: 38969151 DOI: 10.1016/j.jep.2024.118513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 06/19/2024] [Accepted: 06/30/2024] [Indexed: 07/07/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE 2,3,5,4'-tetrahydroxy-stilbene-2-O-β-D-glucoside (TSG) is the principal bioactive compound contained in Polygonum multiflorum Thunb. (PMT), which is traditionally recorded to possess tonic and anti-aging efficacy. AIM OF THE STUDY To identify the TSG-provided promotion on liver regeneration (LR) following partial hepatectomy (PHx) in mice and to explicate its involved mechanism. MATERIALS AND METHODS The promotion of TSG on LR was evaluated by hematoxylin and eosin (H&E), 5-bromodeoxyuridinc (BrdU) and Ki-67 staining, and measuring the level of proliferating cell nuclear antigen (PCNA) and Cyclin D1 in mice with PHx at different time points. Gene Expression Omnibus (GEO, GSE15239) database and the label-free quantitative proteomics from liver of mice at 24 h after PHx were integrated to identify potential involved critical proteins, which were verified by Western-blot, Real-time polymerase chain reaction (RT-PCR), molecular docking and luciferase activity assay. Primary hepatocytes isolated from mice were used to investigate the TSG-provided promotion on proliferation in vitro. RESULTS TSG (20 mg/kg) promoted LR in mice after PHx. Results from RNA expression data from clinical samples and proteomic analysis from liver tissues indicated that peroxisome proliferator-activated receptor α (PPARα)-mediated fatty acid metabolism pathway were crucially associated with the TSG-provided promotion on LR. TSG enhanced the nuclear translocation of PPARα and the mRNA expression of a series of PPARα-regulated downstream genes. In addition, TSG lowered hepatic triglyceride (TG) and non-esterified fatty acid (NEFA) amounts and increased hepatic adenosine triphosphate (ATP) level in mice after PHx. TSG up-regulated the transcriptional activity of PPARα in vitro. Next results displayed that TSG promoted cell proliferation as well as ATP level in mice primary hepatocytes, which were abolished when PPARα was suppressed. Meanwhile, the cell viability was also elevated in mice primary hepatocytes treated with ATP. CONCLUSION Activating PPARα-mediated fatty acid β-oxidation (FAO) pathway led to the production of ATP, which contributed to the TSG-provided promotion on LR after PHx in mice.
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Affiliation(s)
- Haoyu Xue
- The MOE Key Laboratory for Standardization of Chinese Medicines, Shanghai Key Laboratory of Compound Chinese Medicines and The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Huizhong Nie
- Department of TCM Chemistry, School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Zhenlin Huang
- The MOE Key Laboratory for Standardization of Chinese Medicines, Shanghai Key Laboratory of Compound Chinese Medicines and The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Bin Lu
- The MOE Key Laboratory for Standardization of Chinese Medicines, Shanghai Key Laboratory of Compound Chinese Medicines and The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Mengjuan Wei
- The MOE Key Laboratory for Standardization of Chinese Medicines, Shanghai Key Laboratory of Compound Chinese Medicines and The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Hong Xu
- The MOE Key Laboratory for Standardization of Chinese Medicines, Shanghai Key Laboratory of Compound Chinese Medicines and The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Lili Ji
- The MOE Key Laboratory for Standardization of Chinese Medicines, Shanghai Key Laboratory of Compound Chinese Medicines and The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
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22
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Du C, Chen Z, Liu S, Liu J, Zhan J, Zou J, Liao J, Huang W, Lei Y. Lubricin-Inspired Nanozymes Reconstruct Cartilage Lubrication System with an "In-Out" Strategy. SMALL METHODS 2024:e2400757. [PMID: 38962862 DOI: 10.1002/smtd.202400757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 06/25/2024] [Indexed: 07/05/2024]
Abstract
Lubricin, secreted primarily by chondrocytes, plays a critical role in maintaining the function of the cartilage lubrication system. However, both external factors such as friction and internal factors like oxidative stress can disrupt this system, leading to osteoarthritis. Inspired by lubricin, a lubricating nanozyme, that is, Poly-2-acrylamide-2-methylpropanesulfonic acid sodium salt-grafted aminofullerene, is developed to restore the cartilage lubrication system using an "In-Out" strategy. The "Out" aspect involves reducing friction through a combination of hydration lubrication and ball-bearing lubrication. Simultaneously, the "In" aspect aims to mitigate oxidative stress by reducing free radical, increasing autophagy, and improving the mitochondrial respiratory chain. This results in reduced chondrocyte senescence and increased lubricin production, enhancing the natural lubrication ability of cartilage. Transcriptome sequencing and Western blot results demonstrate that it enhances the functionality of mitochondrial respiratory chain complexes I, III, and V, thereby improving mitochondrial function in chondrocytes. In vitro and in vivo experiments show that the lubricating nanozymes reduce cartilage wear, improve chondrocyte senescence, and mitigate oxidative stress damage, thereby mitigating the progression of osteoarthritis. These findings provide novel insights into treating diseases associated with oxidative stress and frictional damage, such as osteoarthritis, and set the stage for future research and development of therapeutic interventions.
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Affiliation(s)
- Chengcheng Du
- Department of Orthopedics, Orthopedic Laboratory of Chongqing Medical University, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Zhuolin Chen
- Department of Orthopedics, Orthopedic Laboratory of Chongqing Medical University, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Senrui Liu
- Department of Orthopedics, Orthopedic Laboratory of Chongqing Medical University, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Jiacheng Liu
- Department of Orthopedics, Orthopedic Laboratory of Chongqing Medical University, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Jingdi Zhan
- Department of Orthopedics, Orthopedic Laboratory of Chongqing Medical University, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Jing Zou
- Department of Orthopedics, Orthopedic Laboratory of Chongqing Medical University, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Junyi Liao
- Department of Orthopedics, Orthopedic Laboratory of Chongqing Medical University, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Wei Huang
- Department of Orthopedics, Orthopedic Laboratory of Chongqing Medical University, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Yiting Lei
- Department of Orthopedics, Orthopedic Laboratory of Chongqing Medical University, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
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23
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Govada GV, Pal S, Panjacharam P, Bhatt HS, Kumar S, Lin CC, Wang SK, Reddy SR. Pd(II)-Catalyzed Site-Selective Cross Coupling Reaction: Synthesis of Highly Fluorescent Aryl-Formyl-Chromenes and its Iminoantipyrine Analogues as Selective AChE Inhibitors. Chem Biodivers 2024:e202400719. [PMID: 38958461 DOI: 10.1002/cbdv.202400719] [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: 03/29/2024] [Accepted: 05/21/2024] [Indexed: 07/04/2024]
Abstract
A versatile and efficient chemo selective synthesis of 4-aryl-3-formyl-2H-chromenes (AFC) was undertaken using Pd-catalyzed cross-coupling conditions. The key oxidative transmetalation was successfully applied to a significant range of substitutions on the chromene moiety and aryl ring in Ar(BOH)3, accommodating both electron-rich and electron-deficient groups. These π-extended scaffolds exhibited green-yellow fluorescence with a large Stokes shift and high quantum yield. Measurement of photophysical properties revealed that the compound with methoxy substitution in the chromene ring, 3t, caused a significant bathochromic shift. The AFCs obtained from this method can be transformed into biologically active 4-aryl-3-iminoantipyrine-2H-chromenes (AAC) through functionalization of the formyl chromenes. The AFCs and AACs with methoxy substitutions (3t and 4e) were docked against AChE inhibition, and compound 4e had the lowest binding energy of -11.20 kcal/mol. DFT calculations performed on representative compounds revealed that compound 4e is more reactive than 3t, which is in accordance with the docking studies.
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Affiliation(s)
- Grace Victoria Govada
- Advanced Catalysis laboratory, Vellore Institute of Technology (VIT), Vellore, 632014, India
| | - Sanjivani Pal
- Advanced Catalysis laboratory, Vellore Institute of Technology (VIT), Vellore, 632014, India
| | - Paranimuthu Panjacharam
- Advanced Catalysis laboratory, Vellore Institute of Technology (VIT), Vellore, 632014, India
| | - Harshil Samir Bhatt
- Centre for Bio Separation Technology, Vellore Institute of Technology (VIT), Vellore, 632014, India
| | - Sanjit Kumar
- Department of Biotechnology, School of Interdisciplinary Education and Research, Guru Ghasidas Vishwavidyalaya (Central university), Bilaspur, India
| | - Chun-Cheng Lin
- Department of Chemistry, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Sheng-Kai Wang
- Department of Chemistry, National Tsing Hua University, Hsinchu, 300, Taiwan
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24
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Kehinde IO, Akawa O, Adewumi AT, Rabbad AH, Soliman MES. PCSK9 inhibitors as safer therapeutics for atherosclerotic cardiovascular disease (ASCVD): Pharmacophore design and molecular dynamics analysis. J Cell Biochem 2024; 125:e30581. [PMID: 38747499 DOI: 10.1002/jcb.30581] [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: 01/09/2024] [Revised: 04/30/2024] [Accepted: 05/05/2024] [Indexed: 07/12/2024]
Abstract
Cardiovascular disorders are still challenging and are among the deadly diseases. As a major risk factor for atherosclerotic cardiovascular disease, dyslipidemia, and high low-density lipoprotein cholesterol in particular, can be prevented primary and secondary by lipid-lowering medications. Therefore, insights are still needed into designing new drugs with minimal side effects. Proprotein convertase subtilisin/kexin 9 (PCSK9) enzyme catalyses protein-protein interactions with low-density lipoprotein, making it a critical target for designing promising inhibitors compared to statins. Therefore, we screened for potential compounds using a redesigned PCSK9 conformational behaviour to search for a significantly extensive chemical library and investigated the inhibitory mechanisms of the final compounds using integrated computational methods, from ligand essential functional group screening to all-atoms MD simulations and MMGBSA-based binding free energy. The inhibitory mechanisms of the screened compounds compared with the standard inhibitor. K31 and K34 molecules showed stronger interactions for PCSK9, having binding energy (kcal/mol) of -33.39 and -63.51, respectively, against -27.97 of control. The final molecules showed suitable drug-likeness, non-mutagenesis, permeability, and high solubility values. The C-α atoms root mean square deviation and root mean square fluctuation of the bound-PCSK9 complexes showed stable and lower fluctuations compared to apo PCSK9. The findings present a model that unravels the mechanism by which the final molecules proposedly inhibit the PCSK9 function and could further improve the design of novel drugs against cardiovascular diseases.
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Affiliation(s)
- Ibrahim O Kehinde
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, South Africa
- Department of Pharmaceutical and Medicinal Chemistry, College of Pharmacy, Afe Babalola University, Ado-Ekiti, Nigeria
| | - Oluwole Akawa
- Department of Pharmaceutical and Medicinal Chemistry, College of Pharmacy, Afe Babalola University, Ado-Ekiti, Nigeria
| | - Adeniyi T Adewumi
- Department of Life and Consumer Sciences, University of South Africa, Florida Campus, Johannesburg, South Africa
| | - Ali H Rabbad
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, South Africa
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25
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Li FR, Wang Q, Pan X, Xu HM, Dong LB. Discovery, Structure, and Engineering of a cis-Geranylfarnesyl Diphosphate Synthase. Angew Chem Int Ed Engl 2024; 63:e202401669. [PMID: 38651244 DOI: 10.1002/anie.202401669] [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: 01/24/2024] [Revised: 04/15/2024] [Accepted: 04/22/2024] [Indexed: 04/25/2024]
Abstract
cis-Prenyltransferases (cis-PTs) catalyze the sequential head-to-tail condensation of isopentenyl diphosphate (IPP) to allylic diphosphates, producing mixed E-Z prenyl diphosphates of varying lengths; however, the specific enzymes synthesizing cis-C25 prenyl diphosphates have not been identified. Herein, we present the discovery and characterization of a cis-geranylfarnesyl diphosphate synthase (ScGFPPS) from Streptomyces clavuligerus. This enzyme demonstrates high catalytic proficiency in generating six distinct cis-polyisoprenoids, including three C25 and three C20 variants. We determined the crystal structure of ScGFPPS. Additionally, we unveil the crystal structure of nerylneryl diphosphate synthase (NNPS), known for synthesizing an all-cis-C20 polyisoprenoid. Comparative structural analysis of ScGFPPS and NNPS has identified key differences that influence product specificity. Through site-directed mutagenesis, we have identified eight single mutations that significantly refine the selectivity of ScGFPPS for cis-polyisoprenoids. Our findings not only expand the functional spectrum of cis-PTs but also provide a structural comparison strategy in cis-PTs engineering.
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Affiliation(s)
- Fang-Ru Li
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Qingling Wang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Xingming Pan
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Hui-Min Xu
- The Public Laboratory Platform, China Pharmaceutical University, Nanjing, 211198, China
| | - Liao-Bin Dong
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
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26
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Wozniak JM, Li W, Governa P, Chen LY, Jadhav A, Dongre A, Forli S, Parker CG. Enhanced mapping of small-molecule binding sites in cells. Nat Chem Biol 2024; 20:823-834. [PMID: 38167919 PMCID: PMC11213684 DOI: 10.1038/s41589-023-01514-z] [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: 12/05/2022] [Accepted: 11/29/2023] [Indexed: 01/05/2024]
Abstract
Photoaffinity probes are routinely utilized to identify proteins that interact with small molecules. However, despite this common usage, resolving the specific sites of these interactions remains a challenge. Here we developed a chemoproteomic workflow to determine precise protein binding sites of photoaffinity probes in cells. Deconvolution of features unique to probe-modified peptides, such as their tendency to produce chimeric spectra, facilitated the development of predictive models to confidently determine labeled sites. This yielded an expansive map of small-molecule binding sites on endogenous proteins and enabled the integration with multiplexed quantitation, increasing the throughput and dimensionality of experiments. Finally, using structural information, we characterized diverse binding sites across the proteome, providing direct evidence of their tractability to small molecules. Together, our findings reveal new knowledge for the analysis of photoaffinity probes and provide a robust method for high-resolution mapping of reversible small-molecule interactions en masse in native systems.
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Affiliation(s)
- Jacob M Wozniak
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Weichao Li
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Paolo Governa
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Li-Yun Chen
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Appaso Jadhav
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Ashok Dongre
- Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
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27
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Bharadwaj KK, Ahmad I, Pati S, Ghosh A, Rabha B, Sarkar T, Bhattacharjya D, Patel H, Baishya D. Screening of Phytocompounds for Identification of Prospective Histone Deacetylase 1 (HDAC1) Inhibitor: An In Silico Molecular Docking, Molecular Dynamics Simulation, and MM-GBSA Approach. Appl Biochem Biotechnol 2024; 196:3747-3764. [PMID: 37776441 DOI: 10.1007/s12010-023-04731-3] [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] [Accepted: 09/15/2023] [Indexed: 10/02/2023]
Abstract
The upregulation of HDAC1 facilitate the induction of epigenetic repression of genes responsible for suppressing tumourigenesis, thereby triggering the development of cancer. HDAC1 inhibitors have thus emerged as possible therapeutic approaches against a variety of human malignancies, as they can inhibit the activity of certain HDACs, repair the overexpression of tumour suppressor genes, and induce cell differentiation, cell cycle arrest, and apoptosis. In this study, among 810 virtually screened compounds, Pinocembrin (PHUB000396) had a significant binding affinity (-7.99 kcal/mol). In molecular dynamics simulation (MD) studies for 200 ns time scale, the compound Pinocembrin effectively undergoes conformational optimization, thereby enabling its accommodation within the active site of the receptor. This outcome serves as a rational for the observed binding affinity. The optimal binding free energy calculations using the Molecular Mechanics Generalized Born Surface Area (MM-GBSA) (-35.86 ± 7.52 kcal/mol) showed the significant role of van der Waals forces and Coulomb interactions in the stability of the respective complex. The pharmacokinetic study showed its potential as a lead compound. The in-silico cytotoxicity prediction also confirmed its potential as an active anticancer phytocompound in lung and brain cancer. Therefore, it can be predicted that Pinocembrin could be a useful bioactive compound as an HDAC1 inhibitor and could be used in developing epigenetic therapy in cancer such as brain cancer and lung cancer to regulate gene expression.
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Affiliation(s)
- Kaushik Kumar Bharadwaj
- Department of Bioengineering and Technology, Gauhati University, Guwahati, 781014, Assam, India
| | - Iqrar Ahmad
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, 425405, Maharashtra, India
| | - Siddhartha Pati
- Skills Innovation & Academic Network (SIAN) Institute-ABC, Balasore, 756001, Odisha, India
- NatNov Bioscience Private Limited, 756001, Balasore, Odisha, India
| | - Arabinda Ghosh
- Microbiology Division, Department of Botany, Gauhati University, Guwahati, Assam, India, 781014
| | - Bijuli Rabha
- Department of Bioengineering and Technology, Gauhati University, Guwahati, 781014, Assam, India
| | - Tanmay Sarkar
- Department of Food Processing Technology, Malda Polytechnic, West Bengal State Council of Technical Education, Government of West Bengal, Malda, 732102, West Bengal, India
| | - Dorothy Bhattacharjya
- Department of Bioengineering and Technology, Gauhati University, Guwahati, 781014, Assam, India
| | - Harun Patel
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, 425405, Maharashtra, India
| | - Debabrat Baishya
- Department of Bioengineering and Technology, Gauhati University, Guwahati, 781014, Assam, India.
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28
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Sun P, Zhao J, Sha G, Zhou Y, Zhao M, Li R, Kong X, Sun Q, Li Y, Li K, Bi R, Yang L, Qin Z, Huang W, Wang Y, Gao J, Chen G, Zhang H, Adnan M, Yang L, Zheng L, Chen XL, Wang G, Ishikawa T, Li Q, Xu JR, Li G. Inhibitor of cardiolipin biosynthesis-related enzyme MoGep4 confers broad-spectrum anti-fungal activity. PLANT, CELL & ENVIRONMENT 2024. [PMID: 38946254 DOI: 10.1111/pce.15021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/29/2024] [Accepted: 06/13/2024] [Indexed: 07/02/2024]
Abstract
Plant pathogens cause devastating diseases, leading to serious losses to agriculture. Mechanistic understanding of pathogenesis of plant pathogens lays the foundation for the development of fungicides for disease control. Mitophagy, a specific form of autophagy, is important for fungal virulence. The role of cardiolipin, mitochondrial signature phospholipid, in mitophagy and pathogenesis is largely unknown in plant pathogenic fungi. The functions of enzymes involved in cardiolipin biosynthesis and relevant inhibitors were assessed using a set of assays, including genetic deletion, plant infection, lipidomics, chemical-protein interaction, chemical inhibition, and field trials. Our results showed that the cardiolipin biosynthesis-related gene MoGEP4 of the rice blast fungus Magnaporthe oryzae regulates growth, conidiation, cardiolipin biosynthesis, and virulence. Mechanistically, MoGep4 regulated mitophagy and Mps1-MAPK phosphorylation, which are required for virulence. Chemical alexidine dihydrochloride (AXD) inhibited the enzyme activity of MoGep4, cardiolipin biosynthesis and mitophagy. Importantly, AXD efficiently inhibited the growth of 10 plant pathogens and controlled rice blast and Fusarium head blight in the field. Our study demonstrated that MoGep4 regulates mitophagy, Mps1 phosphorylation and pathogenesis in M. oryzae. In addition, we found that the MoGep4 inhibitor, AXD, displays broad-spectrum antifungal activity and is a promising candidate for fungicide development.
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Affiliation(s)
- Peng Sun
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, The Center of Crop Nanotechnology, Huazhong Agricultural University, Wuhan, China
| | - Juan Zhao
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, The Center of Crop Nanotechnology, Huazhong Agricultural University, Wuhan, China
| | - Gan Sha
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, The Center of Crop Nanotechnology, Huazhong Agricultural University, Wuhan, China
| | - Yaru Zhou
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, The Center of Crop Nanotechnology, Huazhong Agricultural University, Wuhan, China
| | - Mengfei Zhao
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, The Center of Crop Nanotechnology, Huazhong Agricultural University, Wuhan, China
| | - Renjian Li
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, The Center of Crop Nanotechnology, Huazhong Agricultural University, Wuhan, China
| | - Xiaojing Kong
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, The Center of Crop Nanotechnology, Huazhong Agricultural University, Wuhan, China
| | - Qiping Sun
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, The Center of Crop Nanotechnology, Huazhong Agricultural University, Wuhan, China
| | - Yun Li
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, The Center of Crop Nanotechnology, Huazhong Agricultural University, Wuhan, China
| | - Ke Li
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, The Center of Crop Nanotechnology, Huazhong Agricultural University, Wuhan, China
| | - Ruiqing Bi
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, The Center of Crop Nanotechnology, Huazhong Agricultural University, Wuhan, China
| | - Lei Yang
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, The Center of Crop Nanotechnology, Huazhong Agricultural University, Wuhan, China
| | - Ziting Qin
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, The Center of Crop Nanotechnology, Huazhong Agricultural University, Wuhan, China
| | - Wenzheng Huang
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, The Center of Crop Nanotechnology, Huazhong Agricultural University, Wuhan, China
| | - Yin Wang
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, The Center of Crop Nanotechnology, Huazhong Agricultural University, Wuhan, China
| | - Jie Gao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Guang Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Haifeng Zhang
- Department of Plant Pathology, Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Muhammad Adnan
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Long Yang
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, The Center of Crop Nanotechnology, Huazhong Agricultural University, Wuhan, China
| | - Lu Zheng
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, The Center of Crop Nanotechnology, Huazhong Agricultural University, Wuhan, China
| | - Xiao-Lin Chen
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, The Center of Crop Nanotechnology, Huazhong Agricultural University, Wuhan, China
| | - Guanghui Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Toshiki Ishikawa
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Qiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jin-Rong Xu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA
| | - Guotian Li
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, The Center of Crop Nanotechnology, Huazhong Agricultural University, Wuhan, China
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29
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Firoz A, Talwar P. Role of death-associated protein kinase 1 (DAPK1) in retinal degenerative diseases: an in-silico approach towards therapeutic intervention. J Biomol Struct Dyn 2024; 42:5686-5698. [PMID: 37387600 DOI: 10.1080/07391102.2023.2227720] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 06/15/2023] [Indexed: 07/01/2023]
Abstract
The Death-associated protein kinase 1 (DAPK1) has emerged as a crucial player in the pathogenesis of degenerative diseases. As a serine/threonine kinase family member, DAPK1 regulates critical signaling pathways, such as apoptosis and autophagy. In this study, we comprehensively analyzed DAPK1 interactors and enriched molecular functions, biological processes, phenotypic expression, disease associations, and aging signatures to elucidate the molecular networks of DAPK1. Furthermore, we employed a structure-based virtual screening approach using the PubChem database, which enabled the identification of potential bioactive compounds capable of inhibiting DAPK1, including caspase inhibitors and synthetic analogs. Three selected compounds, CID24602687, CID8843795, and CID110869998, exhibited high docking affinity and selectivity towards DAPK1, which were further investigated using molecular dynamics simulations to understand their binding patterns. Our findings establish a connection between DAPK1 and retinal degenerative diseases and highlight the potential of these selected compounds for the development of novel therapeutic strategies. This study provides valuable insights into the molecular mechanisms underlying DAPK1-related diseases, and offers new opportunities for the discovery of effective treatments for retinal degeneration.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Arman Firoz
- Apoptosis and Cell Survival Research Laboratory, 412G Pearl Research Park, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Priti Talwar
- Apoptosis and Cell Survival Research Laboratory, 412G Pearl Research Park, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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30
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Kumar P, Kinger S, Dubey AR, Jagtap YA, Choudhary A, Prasad A, Jha HC, Dhiman R, Gutti RK, Mishra A. Trehalose Promotes Clearance of Proteotoxic Aggregation of Neurodegenerative Disease-Associated Aberrant Proteins. Mol Neurobiol 2024; 61:4055-4073. [PMID: 38057642 DOI: 10.1007/s12035-023-03824-8] [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: 05/23/2023] [Accepted: 11/21/2023] [Indexed: 12/08/2023]
Abstract
Accumulation of misfolded proteins compromises overall cellular health and fitness. The failure to remove misfolded proteins is a critical reason for their unwanted aggregation in dense cellular protein pools. The accumulation of various inclusions serves as a clinical feature for neurodegenerative diseases. Previous findings suggest that different cellular compartments can store these abnormal inclusions. Studies of transgenic mice and cellular models of neurodegenerative diseases indicate that depleted chaperone capacity contributes to the aggregation of damaged or aberrant proteins, which consequently disturb proteostasis and cell viability. However, improving these abnormal proteins' selective elimination is yet to be well understood. Still, molecular strategies that can promote the effective degradation of abnormal proteins without compromising cellular viability are unclear. Here, we reported that the trehalose treatment elevates endogenous proteasome levels and enhances the activities of the proteasome. Trehalose-mediated proteasomal activation elevates the removal of both bona fide misfolded and various neurodegenerative disease-associated proteins. Our current study suggests that trehalose may retain a proteasome activation potential, which seems helpful in the solubilization of different mutant misfolded proteins, improving cell viability. These results reveal a possible molecular approach to reduce the overload of intracellular misfolded proteins, and such cytoprotective functions may play a critical role against protein conformational diseases.
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Affiliation(s)
- Prashant Kumar
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, 342037, India
| | - Sumit Kinger
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, 342037, India
| | - Ankur Rakesh Dubey
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, 342037, India
| | - Yuvraj Anandrao Jagtap
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, 342037, India
| | - Akash Choudhary
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, 342037, India
| | - Amit Prasad
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Mandi, India
| | - Hem Chandra Jha
- Infection Bioengineering Group, Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol, India
| | - Rohan Dhiman
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India
| | - Ravi Kumar Gutti
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, 342037, India.
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31
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Rathod S, Dey S, Pawar S, Dhavale R, Choudhari P, Rajakumara E, Mahuli D, Bhagwat D, Tamboli Y, Sankpal P, Mali S, More H. Identification of potential biogenic chalcones against antibiotic resistant efflux pump (AcrB) via computational study. J Biomol Struct Dyn 2024; 42:5178-5196. [PMID: 37340697 DOI: 10.1080/07391102.2023.2225099] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 06/09/2023] [Indexed: 06/22/2023]
Abstract
The cases of bacterial multidrug resistance are increasing every year and becoming a serious concern for human health. Multidrug efflux pumps are key players in the formation of antibiotic resistance, which transfer out a broad spectrum of drugs from the cell and convey resistance to the host. Efflux pumps have significantly reduced the efficacy of the previously available antibiotic armory, thereby increasing the frequency of therapeutic failures. In gram-negative bacteria, the AcrAB-TolC efflux pump is the principal transporter of the substrate and plays a major role in the formation of antibiotic resistance. In the current work, advanced computer-aided drug discovery approaches were utilized to find hit molecules from the library of biogenic chalcones against the bacterial AcrB efflux pump. The results of the performed computational studies via molecular docking, drug-likeness prediction, pharmacokinetic profiling, pharmacophore mapping, density functional theory, and molecular dynamics simulation study provided ZINC000004695648, ZINC000014762506, ZINC000014762510, ZINC000095099506, and ZINC000085510993 as stable hit molecules against the AcrB efflux pumps. Identified hits could successfully act against AcrB efflux pumps after optimization as lead molecules.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sanket Rathod
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Sreenath Dey
- Department of Biotechnology, Indian Institute of Technology, Hyderabad, Kandi, Sangareddy, Telangana, India
| | - Swaranjali Pawar
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Rakesh Dhavale
- Department of Pharmaceutics, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Prafulla Choudhari
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Eerappa Rajakumara
- Department of Biotechnology, Indian Institute of Technology, Hyderabad, Kandi, Sangareddy, Telangana, India
| | - Deepak Mahuli
- Department of Pharmacology, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Durgacharan Bhagwat
- Department of Pharmaceutics, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Yasinalli Tamboli
- King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
| | - Poournima Sankpal
- Department of Pharmaceutical Chemistry, Ashokrao Mane College of Pharmacy, Kolhapur, MS, India
| | - Sachin Mali
- Department of Pharmaceutics, Y. D. Mane College of Pharmacy, Kagal, MS, India Kolhapur
| | - Harinath More
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
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32
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Ngo VA. Insight into molecular basis and dynamics of full-length CRaf kinase in cellular signaling mechanisms. Biophys J 2024:S0006-3495(24)00438-7. [PMID: 38946141 DOI: 10.1016/j.bpj.2024.06.028] [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: 05/15/2024] [Accepted: 06/28/2024] [Indexed: 07/02/2024] Open
Abstract
Raf kinases play key roles in signal transduction in cells for regulating proliferation, differentiation, and survival. Despite decades of research into functions and dynamics of Raf kinases with respect to other cytosolic proteins, understanding Raf kinases is limited by the lack of their full-length structures at the atomic resolution. Here, we present the first model of the full-length CRaf kinase obtained from artificial intelligence/machine learning algorithms with a converging ensemble of structures simulated by large-scale temperature replica exchange simulations. Our model is validated by comparing simulated structures with the latest cryo-EM structure detailing close contacts among three key domains and regions of the CRaf. Our simulations identify potentially new epitopes of intramolecule interactions within the CRaf and reveal a dynamical nature of CRaf kinases, in which the three domains can move back and forth relative to each other for regulatory dynamics. The dynamic conformations are then used in a docking algorithm to shed insight into the paradoxical effect caused by vemurafenib in comparison with a paradox breaker PLX7904. We propose a model of Raf-heterodimer/KRas-dimer as a signalosome based on the dynamics of the full-length CRaf.
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Affiliation(s)
- Van A Ngo
- Advanced Computing for Life Sciences and Engineering, Science Engagement Section, Computing and Computational Sciences, National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee.
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33
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Dan J, Wei W, Ou W, Gao G, Song W, Ye L, Liang H, Guo X, Tan L, Jiang J. Excavation of Biomarker Candidates for the Diagnosis of Talaromyces marneffei Infection via Genome-Wide Prediction and Functional Annotation of Secreted Proteins. ACS OMEGA 2024; 9:27093-27103. [PMID: 38947822 PMCID: PMC11209904 DOI: 10.1021/acsomega.4c00571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 05/28/2024] [Accepted: 06/05/2024] [Indexed: 07/02/2024]
Abstract
Talaromyces marneffei is the third most common infectious pathogen in AIDS patients and leads to the highest death rate in Guangxi, China. The lack of reliable biomarkers is one of the major obstacles in current clinical diagnosis, which largely contributes to this high mortality. Here, we present a study that aimed at identifying diagnostic biomarker candidates through genome-wide prediction and functional annotation of Talaromyces marneffei secreted proteins. A total of 584 secreted proteins then emerged, including 382 classical and 202 nonclassical ones. Among them, there were 87 newly obtained functional annotations in this study. The annotated proteins were further evaluated by combining RNA profiling and a homology comparison. Three proteins were ultimately highlighted as biomarker candidates with robust expression and remarkable specificity. The predicted phosphoinositide phospholipase C and the galactomannoprotein were suggested to play an interactive immune game through metabolism of arachidonic acid. Therefore, they hold promise in developing new tools for clinical diagnosis of Talaromyces marneffei and also possibly serve as molecular targets for future therapy.
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Affiliation(s)
- Jing Dan
- Collaborative
Innovation Centre of Regenerative Medicine and Medical BioResource
Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning, Guangxi 530021, China
- Guangxi
Key Laboratory of AIDS Prevention and Treatment & Biosafety III
Laboratory, Guangxi Medical University, Nanning, Guangxi 530021, China
- Center
for Energy Metabolism and Reproduction, Institute of Biomedicine and
Biotechnology, Shenzhen Institute of Advanced
Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Wudi Wei
- Guangxi
Key Laboratory of AIDS Prevention and Treatment & Biosafety III
Laboratory, Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Weijie Ou
- Center
for Energy Metabolism and Reproduction, Institute of Biomedicine and
Biotechnology, Shenzhen Institute of Advanced
Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Guangshi Gao
- Geekgene
Technology Co. Ltd., Beijing 100091, China
| | - Wanjun Song
- Geekgene
Technology Co. Ltd., Beijing 100091, China
| | - Li Ye
- Guangxi
Key Laboratory of AIDS Prevention and Treatment & Biosafety III
Laboratory, Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Hao Liang
- Collaborative
Innovation Centre of Regenerative Medicine and Medical BioResource
Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning, Guangxi 530021, China
- Guangxi
Key Laboratory of AIDS Prevention and Treatment & Biosafety III
Laboratory, Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Xuzhen Guo
- Center
for Energy Metabolism and Reproduction, Institute of Biomedicine and
Biotechnology, Shenzhen Institute of Advanced
Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Lei Tan
- Center
for Energy Metabolism and Reproduction, Institute of Biomedicine and
Biotechnology, Shenzhen Institute of Advanced
Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- College
of Life Sciences, University of Chinese
Academy of Sciences, Beijing 100049, China
- Department
of Cardiology, Shenzhen Guangming District
People’s Hospital, Shenzhen 518055, China
| | - Junjun Jiang
- Collaborative
Innovation Centre of Regenerative Medicine and Medical BioResource
Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning, Guangxi 530021, China
- Guangxi
Key Laboratory of AIDS Prevention and Treatment & Biosafety III
Laboratory, Guangxi Medical University, Nanning, Guangxi 530021, China
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34
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Wang Y, Lin Q, Liu Y, Li C, Liu Z, Yu X, Wang KN. Lighting Up Nucleolus To Report Mitochondria Damage Using a Mitochondria-to-Nucleolus Migration Probe. Anal Chem 2024; 96:9808-9816. [PMID: 38833718 DOI: 10.1021/acs.analchem.3c05629] [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: 06/06/2024]
Abstract
Visualization of the mitochondrial state is crucial for tracking cell life processes and diagnosing disease, while fluorescent probes that can accurately assess mitochondrial status are currently scarce. Herein, a fluorescent probe named "SYN" was designed and prepared, which can target mitochondria via the mitochondrial membrane potential. Upon pathology or external stimulation, SYN can be released from the mitochondria and accumulate in the nucleolus to monitor the status of mitochondria. During this process, the brightness of the nucleolus can then serve as an indicator of mitochondrial damage. SYN has demonstrated excellent photostability in live cells as well as an extremely inert fluorescence response to bioactive molecules and the physiological pH environment of live cells. Spectroscopic titration and molecular docking studies have revealed that SYN can be lit up in nucleoli due to the high viscosity of the nucleus and the strong electrostatic interaction with the phosphate backbone of RNA. This probe is expected to be an exceptional tool based on its excellent imaging properties for tracking mitochondrial state in live cells.
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Affiliation(s)
- Yumeng Wang
- State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China
| | - Qiaowen Lin
- State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China
| | - Yang Liu
- State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China
| | - Chi Li
- State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China
| | - Zhiqiang Liu
- State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China
- Shenzhen Research Institute of Shandong University, Shenzhen 518057, China
| | - Xiaoqiang Yu
- State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China
| | - Kang-Nan Wang
- State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China
- Shenzhen Research Institute of Shandong University, Shenzhen 518057, China
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35
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Premkumar T, Sajitha Lulu S. Targeting key players in Alzheimer's disease: bioactive compounds from Moringa oleifera, Desmodium gangeticum, and Centella asiatica as potential therapeutics. J Biomol Struct Dyn 2024:1-23. [PMID: 38887054 DOI: 10.1080/07391102.2024.2335300] [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: 12/23/2023] [Accepted: 03/20/2024] [Indexed: 06/20/2024]
Abstract
Alzheimer's Disease (AD) is one of the critical reasons for dementia around the world, with a huge number of cases being reported every year. The breakdown of Amyloid Precursor Protein (APP) plays a crucial role in AD development. The Beta-site APP Cleaving Enzyme 1 (BACE1) is a highly significant proteolytic enzyme found to be critically involved in the APP breakdown process and generates beta-amyloid plaques in the extracellular neuronal membrane. In this study, we have used natural compounds with cognitive and neuroprotective activities from three plants, Centella asiatica, Moringa oleifera, and Desmodium gangeticum to inhibit the activity of BACE1. We have identified nine compounds out of 73 compounds filtered out from the three plants showing high affinity with the catalytic dyad region of BACE1 through molecular docking studies. Interestingly, the 200 ns molecular dynamics simulation study further confirmed the stability of the complexes formed between 9 compounds and the BACE1 protein. Furthermore, the free energy calculations also revealed these complexes possess favorable energies. Astilbin, Delphinidin 3-glucoside, and kaempferol 7-O-glucoside showed good binding affinity and structural stability when compared to other compounds and the control CNP520. Following a preliminary screening, the Astilbin compound was chosen based on the grounds of binding affinity, ADMET Properties, Hbond formation, Molecular Dynamic simulation, and MM-PBSA studies. A subsequent 1microsecond molecular dynamics simulation was conducted for the Astilbin complex. Through microsecond simulation, it was found that Astilbin alters BACE1's behavior and induces conformational rearrangements. Thus, this study opens a gateway to inhibit the activity of BACE1 protein through Astilbin thereby disclosing the possibility of managing Alzheimer's Disease.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- T Premkumar
- Integrative Multiomics Laboratory, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - S Sajitha Lulu
- Integrative Multiomics Laboratory, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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Zhang H, Cheng Y, Qiu L, Zeng W, Hu T, Yang J, Wang J, Wang H, Gong W, Liang H. In situ electron generation through Fe/C supported sludge coupled with a counter-diffusion biofilm for electron-deficient wastewater treatment: Binding properties and catalytic competition mechanism of nitrate reductase. WATER RESEARCH 2024; 257:121688. [PMID: 38723349 DOI: 10.1016/j.watres.2024.121688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/15/2024] [Accepted: 04/27/2024] [Indexed: 05/29/2024]
Abstract
A membrane-aerated biofilm-coupled Fe/C supported sludge system (MABR-Fe/C) was constructed to achieve in situ electron production for NO3--N reduction enhancement in different Fe/C loadings (10 g and 200 g). The anoxic environment formed in the MABR-Fe/C promoted a continual Fe2+release of Fe/C in 120 d operation (average Fe2+concentrations is 1.18 and 2.95 mg/L in MABR-Fe/C10 and MABR-Fe/C200, respectively). Metagenomics results suggested that the electrons generated from ongoing Fe2+ oxidation were transferred via the Quinone pool to EC 1.7.5.1 rather than EC 1.9.6.1 to complete the process of NO3--N reduction to NO2--N in Acidovorax, Ottowia, and Polaromonas. In the absence of organic matter, the NO3--N removal in MABR-Fe/C10 and MABR-Fe/C200 increased by 11.99 and 12.52 mg/L, respectively, compared to that in MABR. In the further NO2--N reduction, even if the minimum binding free energy (MBFE) was low, NO2--N in Acidovorax and Dechloromonas preferentially bind the Gln-residues for dissimilatory nitrate reduction (DNR) in the presence of Fe/C. Increasing Fe/C loading (MABR-Fe/C200) caused the formation of different residue binding sites, further enhancing the already dominant DNR. When DNR in MABR-Fe/C200 intensified, the TN in the effluent increased by 3.75 mg/L although the effluent NO3--N concentration was lower than that in MABR-Fe/C10. This study demonstrated a new MABR-Fe/C system for in situ electron generation to enhance biological nitrogen removal and analyzed the NO3--N reduction pathway and metabolic mechanism, thus providing new ideas for nitrogen removal in electron-deficient wastewater.
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Affiliation(s)
- Han Zhang
- State Key Laboratory of Urban Water Resource and Environment (SKLUWRE), Harbin Institute of Technology, 73 Huanghe Road, Nangang District, Harbin, 150090, PR China
| | - Yufei Cheng
- State Key Laboratory of Urban Water Resource and Environment (SKLUWRE), Harbin Institute of Technology, 73 Huanghe Road, Nangang District, Harbin, 150090, PR China
| | - Linhong Qiu
- State Key Laboratory of Urban Water Resource and Environment (SKLUWRE), Harbin Institute of Technology, 73 Huanghe Road, Nangang District, Harbin, 150090, PR China
| | - Weichen Zeng
- State Key Laboratory of Urban Water Resource and Environment (SKLUWRE), Harbin Institute of Technology, 73 Huanghe Road, Nangang District, Harbin, 150090, PR China
| | - Tianyi Hu
- State Key Laboratory of Urban Water Resource and Environment (SKLUWRE), Harbin Institute of Technology, 73 Huanghe Road, Nangang District, Harbin, 150090, PR China
| | - Jiaxuan Yang
- State Key Laboratory of Urban Water Resource and Environment (SKLUWRE), Harbin Institute of Technology, 73 Huanghe Road, Nangang District, Harbin, 150090, PR China
| | - Jinlong Wang
- State Key Laboratory of Urban Water Resource and Environment (SKLUWRE), Harbin Institute of Technology, 73 Huanghe Road, Nangang District, Harbin, 150090, PR China
| | - Hesong Wang
- State Key Laboratory of Urban Water Resource and Environment (SKLUWRE), Harbin Institute of Technology, 73 Huanghe Road, Nangang District, Harbin, 150090, PR China
| | - Weijia Gong
- School of Engineering, Northeast Agricultural University, 600 Changjiang Street, Xiangfang District, Harbin, 150030, PR China
| | - Heng Liang
- State Key Laboratory of Urban Water Resource and Environment (SKLUWRE), Harbin Institute of Technology, 73 Huanghe Road, Nangang District, Harbin, 150090, PR China.
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Elsayed SA, Elnabky IM, Aboelnga MM, El-Hendawy AM. Palladium(ii), platinum(ii), and silver(i) complexes with 3-acetylcoumarin benzoylhydrazone Schiff base: Synthesis, characterization, biomolecular interactions, cytotoxic activity, and computational studies. RSC Adv 2024; 14:19512-19527. [PMID: 38895519 PMCID: PMC11184370 DOI: 10.1039/d4ra02738h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 06/02/2024] [Indexed: 06/21/2024] Open
Abstract
New Pd(ii) (C1), Pt(ii) (C2), and Ag(i) (C3) complexes derived from 3-acetylcoumarin benzoylhydrazone (HL) Schiff base were synthesized and characterized by FTIR, 1H NMR, UV-visible spectroscopies along with elemental analysis (C, H, N), magnetic, molar conductivity measurements, and DFT calculations. The obtained results suggested that the ligand had different behaviors in the complexes: mono-negative tridentate (C1) and neutral tridentate (C2) as an ONO-donor and neutral bidentate (C3) as an ON-donor. Quantum chemistry calculations were performed to validate the stability of the suggested geometries and indicated that all the complexes possess tetra-coordinated metal ions. The binding affinity of all the compounds toward calf thymus (ctDNA), yeast (tRNA), and bovine serum albumin (BSA) was evaluated by absorption/emission spectral titration studies, which revealed the intercalative binding to ctDNA and tRNA and static binding upon complex formation with BSA. Molecular insights into the binding affinity of the characterized complexes were provided through conducting molecular docking analysis. Moreover, the cytotoxic activity (in vitro) of the compounds was screened against human cancerous cell lines and a non-cancerous lung fibroblast (WI38) one using cis-platin as a reference drug. The IC50 and selective index (SI) values indicated the higher cytotoxic activity of all the metal complexes compared to their parent ligand. Among all the compounds, the complex C2 showed the highest activity. These results confirmed the improvement of the anticancer activity of the ligand by incorporating the metal ions. In addition, flow cytometry results showed that complexes C1 and C2 induced cell cycle arrest at S and G1/S, respectively.
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Affiliation(s)
- Shadia A Elsayed
- Chemistry Department, Faculty of Science, Damietta University New Damietta 34517 Egypt
| | - Islam M Elnabky
- Chemistry Department, Faculty of Science, Damietta University New Damietta 34517 Egypt
| | - Mohamed M Aboelnga
- Chemistry Department, Faculty of Science, Damietta University New Damietta 34517 Egypt
| | - Ahmed M El-Hendawy
- Chemistry Department, Faculty of Science, Damietta University New Damietta 34517 Egypt
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Gutkin E, Gusev F, Gentile F, Ban F, Koby SB, Narangoda C, Isayev O, Cherkasov A, Kurnikova MG. In silico screening of LRRK2 WDR domain inhibitors using deep docking and free energy simulations. Chem Sci 2024; 15:8800-8812. [PMID: 38873063 PMCID: PMC11168082 DOI: 10.1039/d3sc06880c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 04/10/2024] [Indexed: 06/15/2024] Open
Abstract
The Critical Assessment of Computational Hit-Finding Experiments (CACHE) Challenge series is focused on identifying small molecule inhibitors of protein targets using computational methods. Each challenge contains two phases, hit-finding and follow-up optimization, each of which is followed by experimental validation of the computational predictions. For the CACHE Challenge #1, the Leucine-Rich Repeat Kinase 2 (LRRK2) WD40 Repeat (WDR) domain was selected as the target for in silico hit-finding and optimization. Mutations in LRRK2 are the most common genetic cause of the familial form of Parkinson's disease. The LRRK2 WDR domain is an understudied drug target with no known molecular inhibitors. Herein we detail the first phase of our winning submission to the CACHE Challenge #1. We developed a framework for the high-throughput structure-based virtual screening of a chemically diverse small molecule space. Hit identification was performed using the large-scale Deep Docking (DD) protocol followed by absolute binding free energy (ABFE) simulations. ABFEs were computed using an automated molecular dynamics (MD)-based thermodynamic integration (TI) approach. 4.1 billion ligands from Enamine REAL were screened with DD followed by ABFEs computed by MD TI for 793 ligands. 76 ligands were prioritized for experimental validation, with 59 compounds successfully synthesized and 5 compounds identified as hits, yielding a 8.5% hit rate. Our results demonstrate the efficacy of the combined DD and ABFE approaches for hit identification for a target with no previously known hits. This approach is widely applicable for the efficient screening of ultra-large chemical libraries as well as rigorous protein-ligand binding affinity estimation leveraging modern computational resources.
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Affiliation(s)
- Evgeny Gutkin
- Department of Chemistry, Mellon College of Science, Carnegie Mellon University Pittsburgh PA 15213 USA
| | - Filipp Gusev
- Department of Chemistry, Mellon College of Science, Carnegie Mellon University Pittsburgh PA 15213 USA
- Computational Biology Department, School of Computer Science, Carnegie Mellon University Pittsburgh PA 15213 USA
| | - Francesco Gentile
- Department of Chemistry and Biomolecular Sciences, University of Ottawa Ottawa ON Canada
- Ottawa Institute of Systems Biology Ottawa ON Canada
| | - Fuqiang Ban
- Vancouver Prostate Centre, The University of British Columbia Vancouver BC Canada
| | - S Benjamin Koby
- Department of Chemistry, Mellon College of Science, Carnegie Mellon University Pittsburgh PA 15213 USA
| | - Chamali Narangoda
- Department of Chemistry, Mellon College of Science, Carnegie Mellon University Pittsburgh PA 15213 USA
| | - Olexandr Isayev
- Department of Chemistry, Mellon College of Science, Carnegie Mellon University Pittsburgh PA 15213 USA
- Computational Biology Department, School of Computer Science, Carnegie Mellon University Pittsburgh PA 15213 USA
| | - Artem Cherkasov
- Vancouver Prostate Centre, The University of British Columbia Vancouver BC Canada
| | - Maria G Kurnikova
- Department of Chemistry, Mellon College of Science, Carnegie Mellon University Pittsburgh PA 15213 USA
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Lindner C, Friemel A, Schwegler N, Timmermann L, Pham TL, Reusche V, Kovermann M, Thomas F. Thermostable WW-Domain Scaffold to Design Functional β-Sheet Miniproteins. J Am Chem Soc 2024. [PMID: 38853610 DOI: 10.1021/jacs.4c03498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
There has been a recent surge in the design of miniproteins for medicinal chemistry, biomaterial design, or synthetic biology. In particular, there is an interest in peptide scaffolds that fold reliably, predictably, and with solid stability. In this article, we present the design of a highly thermostable WW domain, a three-stranded β-sheet motif, with a superior melting temperature of about 90 °C to serve as a core scaffold onto which receptor-like properties can be grafted. We have performed specific rounds of sequence iteration on a WW-domain consensus sequence to decipher sequence positions that affect structural and, thus, thermal stability. We identified a sequence-structure relationship that yields a highly thermostable WW-domain scaffold. High-resolution NMR spectroscopy was applied, which enabled the identification of structural features at the atomic scale that contribute to this high thermostability. Finally, we grafted the binding motifs of the three WW-domain groups─Group I, Group II/III, and Group IV─and organophosphate and metal binding onto the highly thermostable WW-domain scaffold and obtained thermostable de novo WW domains that indeed display the different binding modes that were intended. The organophosphate-binding WW domains exhibit melting temperatures that are up to 34 K higher than previously reported top-down designs. These results impressively demonstrate that the highly thermostable WW-domain core scaffold is a solid platform for the design of discrete and reliably folding functional β-sheet peptide miniproteins, providing an essential addition to the toolbox of peptide scaffolds previously used in synthetic biology and material design.
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Affiliation(s)
- Christina Lindner
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Anke Friemel
- Physical Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Niklas Schwegler
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
- Institute for Molecular Systems Engineering and Advanced Materials, Heidelberg University, Im Neuenheimer Feld 225, 69120 Heidelberg, Germany
| | - Lisa Timmermann
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Truc Lam Pham
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Vanessa Reusche
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Michael Kovermann
- Physical Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Franziska Thomas
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
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Syed Zameer Ahmed S, Vetrivel M, Khader SZA, Ragunathan YT, Kumar SK, Prabhu P, Rajaram DLD. Exploring gene network and protein interaction analysis of neurotrophin signaling pathway in ameloblastoma. In Silico Pharmacol 2024; 12:56. [PMID: 38867766 PMCID: PMC11164846 DOI: 10.1007/s40203-024-00223-2] [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: 02/13/2024] [Accepted: 05/18/2024] [Indexed: 06/14/2024] Open
Abstract
Ameloblastoma is a non-cancerous but aggressive oral tumor emerging from odontogenic epithelial tissue involved during odontogenesis. Since there is lack in unravelling the complete molecular pathogenesis of ameloblastoma, chemotherapy is less attempted and a lot of disagreement over the optimal treatment option. Hence, till date, wide surgical resection is considered to be the reliable treatment for ameloblastoma. The Neurotrophin Signaling pathway plays an important role in neuron signaling and it is closely related with the MAPK pathway, which on the other hand regulated cell differentiation, apoptosis, proliferation, plasticity and survival. Protein- Protein Interaction analysis was analysed with STRING tool using WNL value, identified that CTNNB1, HRAS, NGFR, NGFR, and SORT1 having high interacting with BDNF, NT4, p75NTR, NGF, and NT3. The results of ontology analysis revealed that Neurotrophin signaling pathway is associated with Cell surface receptor signaling pathway, regulation of cell differentiation, regulation of development process, EGFR tyrosine kinase inhibitor resistance, MAPK signaling pathway, PI3K-Akt signaling pathway and Ras signaling pathway leading to pathogenesis involving genes. Further, clustering coefficient values of proteins BDNF, NT4, p75NTR, NGF & NT3 were identified as 0.627, 0.708, 0.367, 0.644 & 0.415. The results of molecular docking studies revealed among the selected ligands Methyl-ɣ-oresellinate, N-(4-Hydroxy-phenyl)-2-phenyl-N-phenylacetyl-acetamide, Atranorin and Oresellinate exhibited high binding affinity with selected protein. The key genes involved in Neurotrophin signaling pathway leading to ameloblastoma pathogenesis is revealed, which are closely associated with cell differentiation, cell proliferation, pro-apoptosis, and pro-survival regulations. Further it can be concluded that Neurotrophin signaling pathway could be one of the promising pathway to tailor the targeted drug therapy for Ameloblastoma treatment. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-024-00223-2.
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Affiliation(s)
- Sidhra Syed Zameer Ahmed
- Department of Biotechnology, K. S. Rangasamy College of Technology, K. S. R. Kalvinagar, Tiruchengode, Tamil Nadu 637 215 India
| | - Manimaran Vetrivel
- Department of Biotechnology, K. S. Rangasamy College of Technology, K. S. R. Kalvinagar, Tiruchengode, Tamil Nadu 637 215 India
| | - Syed Zameer Ahmed Khader
- Department of Biotechnology, K. S. Rangasamy College of Technology, K. S. R. Kalvinagar, Tiruchengode, Tamil Nadu 637 215 India
| | | | - SriChinthu Kenniyan Kumar
- Department of Oral & Maxillofacial Pathology and Microbiology, K. S. R. Institute of Dental Science and Research, Tiruchengode, Tamil Nadu India
| | - Puniethaa Prabhu
- Department of Biotechnology, K. S. Rangasamy College of Technology, K. S. R. Kalvinagar, Tiruchengode, Tamil Nadu 637 215 India
| | - Dharani Lakshmi Devi Rajaram
- Department of Biotechnology, K. S. Rangasamy College of Technology, K. S. R. Kalvinagar, Tiruchengode, Tamil Nadu 637 215 India
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Fakim A, Maatouk BI, Maiti B, Dey A, Alotaiby SH, Moosa BA, Lin W, Khashab NM. Flaring Inflammation and ER Stress by an Organelle-Specific Fluorescent Cage. Adv Healthc Mater 2024:e2401117. [PMID: 38848965 DOI: 10.1002/adhm.202401117] [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: 03/25/2024] [Revised: 05/21/2024] [Indexed: 06/09/2024]
Abstract
The endoplasmic reticulum (ER) plays an important role in protein synthesis and its disruption can cause protein unfolding and misfolding. Accumulation of such proteins leads to ER stress, which ultimately promotes many diseases. Routine screening of ER activity in immune cells can flag serious conditions at early stages, but the current clinically used bio-probes have limitations. Herein, an ER-specific fluorophore based on a biocompatible benzothiadiazole-imine cage (BTD-cage) with excellent photophysical properties is developed. The cage outperforms commercially available ER stains in long-term live cell imaging with no fading or photobleaching over time. The cage is responsive to different levels of ER stress where its fluorescence increases accordingly. Incorporating the bio-probe into an immune disorder model, a 6-, 21-, and 48-fold increase in intensity is shown in THP-1, Raw 246.7, and Jurkat cells, respectively (within 15 min). These results strongly support that this system can be used for rapid visual and selective detection of ER stress. It is envisaged that tailoring molecular interactions and molecular recognition using supramolecular improved fluorophores can expand the library of biological probes for enhanced selectivity and targetability toward cellular organelles.
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Affiliation(s)
- Aliyah Fakim
- Chemistry Program, Physical Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Batoul I Maatouk
- Chemistry Program, Physical Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Bappa Maiti
- Chemistry Program, Physical Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Avishek Dey
- Chemistry Program, Physical Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Shahad H Alotaiby
- Chemistry Program, Physical Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Basem A Moosa
- Chemistry Program, Physical Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Weibin Lin
- Chemistry Program, Physical Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Niveen M Khashab
- Chemistry Program, Physical Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
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Milon TI, Wang Y, Fontenot RL, Khajouie P, Villinger F, Raghavan V, Xu W. Development of a novel representation of drug 3D structures and enhancement of the TSR-based method for probing drug and target interactions. Comput Biol Chem 2024; 112:108117. [PMID: 38852360 DOI: 10.1016/j.compbiolchem.2024.108117] [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: 03/05/2024] [Revised: 05/13/2024] [Accepted: 05/31/2024] [Indexed: 06/11/2024]
Abstract
Understanding the mechanisms underlying interactions between drugs and target proteins is critical for drug discovery. In our earlier studies, we introduced the Triangular Spatial Relationship (TSR)-based algorithm, which enables the representation of a protein's 3D structure as a vector of integers (TSR keys). These TSR keys correspond to substructures of the 3D structure of a protein and are computed based on the triangles constructed by all possible triples of Cα atoms within the protein. In this study, we report on a new TSR-based algorithm for probing drug and target interactions. Specifically, we have extended the previous algorithm in three novel directions: TSR keys for representing the 3D structure of a drug or a ligand, cross TSR keys between drugs and their targets and intra-residual TSR keys for phosphorylated amino acids. The outcomes illustrate the key contributions as follows: (i) The TSR-based method, which uses the TSR keys as features, is unique in its capability to interpret hierarchical relationships of drugs as well as drug - target complexes using common and specific TSR keys. (ii) The method can distinguish not only the binding sites from the rest of the protein structures, but also the binding sites of primary targets from those of off-targets. (iii) The method has the potential to correlate the 3D structures of drugs with their functions. (iv) Representation of 3D structures by TSR keys has its unique advantage in terms of ease of making searching for similar substructures across structure datasets easier. In summary, this study presents a novel computational methodology, with significant advantages, for providing insights into the mechanism underlying drug and target interactions.
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Affiliation(s)
- Tarikul I Milon
- Department of Chemistry, University of Louisiana at Lafayette, P.O. Box 44370, Lafayette, LA 70504, USA
| | - Yuhong Wang
- National Center for Advancing Translational Sciences, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Ryan L Fontenot
- Department of Chemistry, University of Louisiana at Lafayette, P.O. Box 44370, Lafayette, LA 70504, USA
| | - Poorya Khajouie
- Department of Chemistry, University of Louisiana at Lafayette, P.O. Box 44370, Lafayette, LA 70504, USA; The Center for Advanced Computer Studies, University of Louisiana at Lafayette, LA 70504, USA
| | - Francois Villinger
- Department of Biology, University of Louisiana at Lafayette, New Iberia, LA 70560, USA
| | - Vijay Raghavan
- The Center for Advanced Computer Studies, University of Louisiana at Lafayette, LA 70504, USA
| | - Wu Xu
- Department of Chemistry, University of Louisiana at Lafayette, P.O. Box 44370, Lafayette, LA 70504, USA.
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Rehman AU, Zhao C, Wu Y, Zhu Q, Luo R. Targeting SHP2 Cryptic Allosteric Sites for Effective Cancer Therapy. Int J Mol Sci 2024; 25:6201. [PMID: 38892388 PMCID: PMC11172685 DOI: 10.3390/ijms25116201] [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: 04/17/2024] [Revised: 05/28/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
SHP2, a pivotal component downstream of both receptor and non-receptor tyrosine kinases, has been underscored in the progression of various human cancers and neurodevelopmental disorders. Allosteric inhibitors have been proposed to regulate its autoinhibition. However, oncogenic mutations, such as E76K, convert SHP2 into its open state, wherein the catalytic cleft becomes fully exposed to its ligands. This study elucidates the dynamic properties of SHP2 structures across different states, with a focus on the effects of oncogenic mutation on two known binding sites of allosteric inhibitors. Through extensive modeling and simulations, we further identified an alternative allosteric binding pocket in solution structures. Additional analysis provides insights into the dynamics and stability of the potential site. In addition, multi-tier screening was deployed to identify potential binders targeting the potential site. Our efforts to identify a new allosteric site contribute to community-wide initiatives developing therapies using multiple allosteric inhibitors to target distinct pockets on SHP2, in the hope of potentially inhibiting or slowing tumor growth associated with SHP2.
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Affiliation(s)
| | | | | | | | - Ray Luo
- Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, CA 92697, USA; (A.U.R.)
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Ming T, Lei J, Peng Y, Wang M, Liang Y, Tang S, Tao Q, Wang M, Tang X, He Z, Liu X, Xu H. Curcumin suppresses colorectal cancer by induction of ferroptosis via regulation of p53 and solute carrier family 7 member 11/glutathione/glutathione peroxidase 4 signaling axis. Phytother Res 2024. [PMID: 38837315 DOI: 10.1002/ptr.8258] [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: 11/07/2023] [Revised: 05/14/2024] [Accepted: 05/18/2024] [Indexed: 06/07/2024]
Abstract
Driven by iron-dependent lipid peroxidation, ferroptosis is regulated by p53 and solute carrier family 7 member 11 (SLC7A11)/glutathione/glutathione peroxidase 4 (GPX4) axis in colorectal cancer (CRC). This study aimed to investigate the influence of curcumin (CUR) on ferroptosis in CRC. The efficacies of CUR on the malignant phenotype of CRC cells were determined by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide, wound healing, and clonogenic assays. The effects of CUR on ferroptosis of CRC cells were evaluated by transmission electron microscopy, lactate dehydrogenase release assay, Fe2+ staining, and analyses of reactive oxygen species, lipid peroxide, malondialdehyde, and glutathione levels. CUR's targets in ferroptosis were predicted by network pharmacological study and molecular docking. With SW620 xenograft tumors, the efficacy of CUR on CRC was investigated, and the effects of CUR on ferroptosis were assessed by detection of Fe2+, malondialdehyde, and glutathione levels. The effects of CUR on expressions of p53, SLC7A11, and GPX4 in CRC cells and tumors were analyzed by quantitative reverse transcription-polymerase chain reaction, western blotting, and immunohistochemistry. CUR suppressed the proliferation, migration, and clonogenesis of CRC cells and xenograft tumor growth by causing ferroptosis, with enhanced lactate dehydrogenase release and Fe2+, reactive oxygen species, lipid peroxide, and malondialdehyde levels, but attenuated glutathione level in CRC. In silico study indicated that CUR may bind p53, SLC7A11, and GPX4, consolidated by that CUR heightened p53 but attenuated SLC7A11 and GPX4 mRNA and protein levels in CRC. CUR may exert an inhibitory effect on CRC by inducing ferroptosis via regulation of p53 and SLC7A11/glutathione/GPX4 axis.
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Affiliation(s)
- Tianqi Ming
- State Key Laboratory of Southwestern Chinese Medicine Resources, Department of Pharmacology, School of Pharmaceutical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jiarong Lei
- State Key Laboratory of Southwestern Chinese Medicine Resources, Department of Pharmacology, School of Pharmaceutical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yuhui Peng
- State Key Laboratory of Southwestern Chinese Medicine Resources, Department of Pharmacology, School of Pharmaceutical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Minmin Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Department of Pharmacology, School of Pharmaceutical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yuanjing Liang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Department of Pharmacology, School of Pharmaceutical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Shun Tang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Department of Pharmacology, School of Pharmaceutical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Qiu Tao
- State Key Laboratory of Southwestern Chinese Medicine Resources, Department of Pharmacology, School of Pharmaceutical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Muqing Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Department of Pharmacology, School of Pharmaceutical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xiaomeng Tang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Department of Pharmacology, School of Pharmaceutical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Ziyu He
- State Key Laboratory of Southwestern Chinese Medicine Resources, Department of Pharmacology, School of Pharmaceutical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xiaohong Liu
- State Key Laboratory of Southwestern Chinese Medicine Resources, Department of Pharmacology, School of Pharmaceutical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Haibo Xu
- State Key Laboratory of Southwestern Chinese Medicine Resources, Department of Pharmacology, School of Pharmaceutical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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Interlandi G. Exploring ligands that target von Willebrand factor selectively under oxidizing conditions through docking and molecular dynamics simulations. Proteins 2024. [PMID: 38829206 DOI: 10.1002/prot.26706] [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: 01/29/2024] [Revised: 04/25/2024] [Accepted: 05/13/2024] [Indexed: 06/05/2024]
Abstract
The blood protein von Willebrand factor (VWF) is a large multimeric protein that, when activated, binds to blood platelets, tethering them to the site of vascular injury and initiating blood coagulation. This process is critical for the normal hemostatic response, but especially under inflammatory conditions, it is thought to be a major player in pathological thrombus formation. For this reason, VWF has been the target for the development of anti-thrombotic therapeutics. However, it is challenging to prevent pathological thrombus formation while still allowing normal physiological blood coagulation, as currently available anti-thrombotic therapeutics are known to cause unwanted bleeding, in particular intracranial hemorrhage. This work explores the possibility of inhibiting VWF selectively under the inflammatory conditions present during pathological thrombus formation. In particular, the A2 domain of VWF is known to inhibit the neighboring A1 domain from binding to the platelet surface receptor GpIbα, and this auto-inhibitory mechanism has been shown to be removed by oxidizing agents released during inflammation. Hence, finding drug molecules that bind at the interface between A1 and A2 only under oxidizing conditions could restore such an auto-inhibitory mechanism. Here, by using a combination of computational docking, molecular dynamics simulations, and free energy perturbation calculations, a ligand from the ZINC15 database was identified that binds at the A1A2 interface, with the interaction being stronger under oxidizing conditions. The results provide a framework for the discovery of drug molecules that bind to a protein selectively in the presence of inflammatory conditions.
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Affiliation(s)
- Gianluca Interlandi
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
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Liu X, Luo M, Wang Z, Yang SJ, Su M, Wang Y, Wang W, Sun Z, Cai Y, Wu L, Zhou R, Xu M, Zhao Q, Chen L, Zuo W, Huang Y, Ren P, Huang X. Mind shift I: Fructus Aurantii - Rhizoma Chuanxiong synergistically anchors stress-induced depression-like behaviours and gastrointestinal dysmotility cluster by regulating psycho-immune-neuroendocrine network. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 128:155324. [PMID: 38552437 DOI: 10.1016/j.phymed.2023.155324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 12/14/2023] [Accepted: 12/26/2023] [Indexed: 05/01/2024]
Abstract
BACKGROUND Researchers have not studied the integrity, orderly correlation, and dynamic openness of complex organisms and explored the laws of systems from a global perspective. In the context of reductionism, antidepressant development formerly focused on advanced technology and molecular details, clear targets and mechanisms, but the clinical results were often unsatisfactory. PURPOSE MDD represents an aggregate of different and highly diverse disease subtypes. The co-occurrence of stress-induced nonrandom multimorbidity is widespread, whereas only a fraction of the potential clusters are well known, such as the MDD-FGID cluster. Mapping these clusters, and determining which are nonrandom, is vital for discovering new mechanisms, developing treatments, and reconfiguring services to better meet patient needs. STUDY DESIGN Acute stress 15-minute forced swimming (AFS) or CUMS protocols can induce the nonrandom MDD-FGID cluster. Multiple biological processes of rats with depression-like behaviours and gastrointestinal dysmobility will be captured under conditions of stress, and the Fructus Aurantii-Rhizoma Chuanxiong (ZQCX) decoction will be utilized to dock the MDD-FGID cluster. METHODS/RESULTS Here, Rhizoma Chuanxiong, one of the seven components of Chaihu-shugan-San, elicited the best antidepressant effect on CUMS rats, followed by Fructus Aurantii. ZQCX reversed AFS-induced depression-like behaviours and gastrointestinal dysmobility by regulating the glutamatergic system, AMPAR/BDNF/mTOR/synapsin I pathway, ghrelin signalling and gastrointestinal nitric oxide synthase. Based on the bioethnopharmacological analysis strategy, the determined meranzin hydrate (MH) and senkyunolide I (SI) by UPLC-PDA, simultaneously absorbed by the jejunum and hippocampus of rats, have been considered major absorbed bioactive compounds acting on behalf of ZQCX. Cotreatment with MH and SI at an equivalent dose in ZQCX synergistically replicated over 50.33 % efficacy of the parent formula in terms of antidepressant and prokinetic actions by modulating neuroinflammation and ghrelin signalling. CONCLUSION Brain-centric mind shifts require the integration of multiple central and peripheral systems and the elucidation of the underlying neurobiological mechanisms that ultimately contribute to novel therapeutic options. Ghrelin signalling and the immune system may partially underlie multimorbidity vulnerability, and ZQCX anchors stress-induced MDD-FGID clusters by docking them. Combining the results of micro details with the laws of the macro world may be more effective in finding treatments for MDD.
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Affiliation(s)
- XiangFei Liu
- Institute of TCM-Related Comorbid Depression, Nanjing University of Chinese Medicine, No.138 XianLin Avenue, QiXia District, Nanjing, Jiangsu, China
| | - Min Luo
- Institute of TCM-Related Comorbid Depression, Nanjing University of Chinese Medicine, No.138 XianLin Avenue, QiXia District, Nanjing, Jiangsu, China; Laboratory of Ethnopharmacology, Xiangya Hospital, Central South University, 410008 Changsha, China
| | - Zheng Wang
- Institute of TCM-Related Comorbid Depression, Nanjing University of Chinese Medicine, No.138 XianLin Avenue, QiXia District, Nanjing, Jiangsu, China
| | - Shu Jie Yang
- Institute of TCM-Related Comorbid Depression, Nanjing University of Chinese Medicine, No.138 XianLin Avenue, QiXia District, Nanjing, Jiangsu, China
| | - Mengqing Su
- Institute of TCM-Related Comorbid Depression, Nanjing University of Chinese Medicine, No.138 XianLin Avenue, QiXia District, Nanjing, Jiangsu, China
| | - Yang Wang
- Laboratory of Ethnopharmacology, Xiangya Hospital, Central South University, 410008 Changsha, China
| | - Wenzhu Wang
- Laboratory of Ethnopharmacology, Xiangya Hospital, Central South University, 410008 Changsha, China
| | - ZhongHua Sun
- Institute of TCM-Related Comorbid Depression, Nanjing University of Chinese Medicine, No.138 XianLin Avenue, QiXia District, Nanjing, Jiangsu, China
| | - YaWen Cai
- Institute of TCM-Related Comorbid Depression, Nanjing University of Chinese Medicine, No.138 XianLin Avenue, QiXia District, Nanjing, Jiangsu, China
| | - Lei Wu
- Department of Pharmacy, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, China
| | - RunZe Zhou
- Institute of TCM-Related Comorbid Depression, Nanjing University of Chinese Medicine, No.138 XianLin Avenue, QiXia District, Nanjing, Jiangsu, China
| | - Min Xu
- Institute of TCM-Related Comorbid Depression, Nanjing University of Chinese Medicine, No.138 XianLin Avenue, QiXia District, Nanjing, Jiangsu, China
| | - QiuLong Zhao
- Institute of TCM-Related Comorbid Depression, Nanjing University of Chinese Medicine, No.138 XianLin Avenue, QiXia District, Nanjing, Jiangsu, China
| | - Li Chen
- Institute of TCM-Related Comorbid Depression, Nanjing University of Chinese Medicine, No.138 XianLin Avenue, QiXia District, Nanjing, Jiangsu, China
| | - WenTing Zuo
- Department of Reproductive Medicine, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - YunKe Huang
- Women's Hospital, Zhejiang University School of Medicine, China
| | - Ping Ren
- Institute of TCM-Related Comorbid Depression, Nanjing University of Chinese Medicine, No.138 XianLin Avenue, QiXia District, Nanjing, Jiangsu, China; Department of Geriatrics, Jiangsu Province Hospital of TCM, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xi Huang
- Institute of TCM-Related Comorbid Depression, Nanjing University of Chinese Medicine, No.138 XianLin Avenue, QiXia District, Nanjing, Jiangsu, China.
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Syaifie PH, Ibadillah D, Jauhar MM, Reninta R, Ningsih S, Ramadhan D, Arda AG, Ningrum DWC, Kaswati NMN, Rochman NT, Mardliyati E. Phytochemical Profile, Antioxidant, Enzyme Inhibition, Acute Toxicity, In Silico Molecular Docking and Dynamic Analysis of Apis Mellifera Propolis as Antidiabetic Supplement. Chem Biodivers 2024; 21:e202400433. [PMID: 38584139 DOI: 10.1002/cbdv.202400433] [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: 02/19/2024] [Revised: 03/31/2024] [Accepted: 04/04/2024] [Indexed: 04/09/2024]
Abstract
This study aims to identify the phytochemical profile of Apis mellifera propolis and explore the potential of its anti-diabetic activity through inhibition of α-amylase (α-AE), α-glucosidase(α-GE), as well as novel antidiabetic compounds of propolis. Apis mellifera propolis extract (AMPE) exhibited elevated polyphenol 33.26±0.17 (mg GAE/g) and flavonoid (15.45±0.13 mg RE/g). It also indicated moderate strong antioxidant activity (IC50 793.09±1.94 μg/ml). This study found that AMPE displayed promising α-AE and α-GE inhibition through in vitro study. Based on LC-MS/MS screening, 18 unique AMPE compounds were identified, with majorly belonging to anthraquinone and flavonoid compounds. Furthermore, in silico study determined that 8 compounds of AMPE exhibited strong binding to α-AE that specifically interacted with its catalytic residue of ASP197. Moreover, 2 compounds exhibit potential inhibition of α-GE, by interacting with crucial amino acids of ARG315, ASP352, and ASP69. Finally, we suggested that 2,7-Dihydroxy-1-(p-hydroxybenzyl)-4-methoxy-9,10-dihydrophenanthrene and 3(3-(3,4-Dihydroxybenzyl)-7-hydroxychroman-4-one as novel inhibitors of α-AE and α-GE. Notably, these compounds were initially discovered from Apis mellifera propolis in this study. The molecular dynamic analysis confirmed their stable binding with both enzymes over 100 ns simulations. The in vivo acute toxicity assay reveals AMPE as a practically non-toxic product with an LD50 value of 16,050 mg/kg. Therefore, this propolis may serve as a promising natural product for diabetes mellitus treatment.
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Affiliation(s)
- Putri Hawa Syaifie
- Center of Excellece Life Sciences, Nano Center Indonesia, Jl. PUSPIPTEK, South Tangerang, 15314, Banten, Indonesia
| | - Delfritama Ibadillah
- Center of Excellece Life Sciences, Nano Center Indonesia, Jl. PUSPIPTEK, South Tangerang, 15314, Banten, Indonesia
| | - Muhammad Miftah Jauhar
- Center of Excellece Life Sciences, Nano Center Indonesia, Jl. PUSPIPTEK, South Tangerang, 15314, Banten, Indonesia
- Biomedical Engineering, Graduate School of Universitas Gadjah Mada, Sleman, 55281, Yogyakarta, Indonesia
| | - Rikania Reninta
- Research Center for Applied Botany, National Research and Innovation Agency (BRIN), Cibinong, 16911, Indonesia
| | - Sri Ningsih
- Research Center for Pharmaceutical Ingredients and Traditional Medicine, National Research and Innovation Agency (BRIN), Cibinong, 16911, Indonesia
| | - Donny Ramadhan
- Center of Excellece Life Sciences, Nano Center Indonesia, Jl. PUSPIPTEK, South Tangerang, 15314, Banten, Indonesia
- Research Center for Pharmaceutical Ingredients and Traditional Medicine, National Research and Innovation Agency (BRIN), Cibinong, 16911, Indonesia
| | - Adzani Gaisani Arda
- Center of Excellece Life Sciences, Nano Center Indonesia, Jl. PUSPIPTEK, South Tangerang, 15314, Banten, Indonesia
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, H-4032, Hungary
| | - Dhecella Winy Cintya Ningrum
- Center of Excellece Life Sciences, Nano Center Indonesia, Jl. PUSPIPTEK, South Tangerang, 15314, Banten, Indonesia
| | - Nofa Mardia Ningsih Kaswati
- Center of Excellece Life Sciences, Nano Center Indonesia, Jl. PUSPIPTEK, South Tangerang, 15314, Banten, Indonesia
| | - Nurul Taufiqu Rochman
- Research Center for Advanced Materials, National Research and Innovation Agency (BRIN), South Tangerang, 15314, Indonesia
| | - Etik Mardliyati
- Research Center for Vaccine and Drugs, National Research and Innovation Agency (BRIN), Cibinong, 16911, Indonesia
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Naik S, Soumya V, Mamledesai SN, Manickavasagam M, Choudhari P, Rathod S. Discovery of Substituted 2-oxoquinolinylthiazolidin-4-one Analogues as Potential EGFRK Inhibitors in Lung Cancer Treatment. Drug Res (Stuttg) 2024; 74:227-240. [PMID: 38830371 DOI: 10.1055/a-2305-2789] [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: 06/05/2024]
Abstract
PURPOSE Cancer is the second leading cause of death globally and is responsible for an estimated 9.6 million deaths in 2018. Globally, about 1 in 6 deaths is due to cancer and the chemotherapeutic drugs available have high toxicity and have reported side effects hence, there is a need for the synthesis of novel drugs in the treatment of cancer. METHODS The current research work dealt with the synthesis of a series of 3-(3-acetyl-2-oxoquinolin-1-(2H)-yl-2-(substitutedphenyl)thiazolidin-4-one (Va-j) derivatives and evaluation of their in-vitro anticancer activity. All the synthesized compounds were satisfactorily characterized by IR and NMR data. Compounds were further evaluated for their in-vitro anticancer activity against A-549 (lung cancer) cell lines. The in-vitro anticancer activity was based upon the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazoliumbromide (MTT) assay method. RESULTS The synthesized compounds exhibited satisfactory anticancer properties against the A-549 cell line. The compound (VH): showed the highest potency amongst the tested derivatives against the A-549 cell line with IC50 values of 100 µg/ml respectively and was also found to be more potent than Imatinib (150 µg/ml) which was used as a standard drug. Molecular docking studies of the titled compounds (Va-j) were carried out using AutoDock Vina/PyRx software. The synthesized compounds exhibited well-conserved hydrogen bonds with one or more amino acid residues in the active pocket of the EGFRK tyrosine kinase domain (PDB 1m17). CONCLUSION Among all the synthesized analogues, the binding affinity of the compound (Vh) was found to be higher than other synthesized derivatives and a molecular dynamics simulation study explored the stability of the docked complex system.
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Affiliation(s)
- Soniya Naik
- Department of Pharmaceutical Chemistry, Sri Ramachandra Faculty of Pharmacy, Sri Ramachandra Institute of Higher Education and Research, Porur, Chennai, India
- Department of Pharmaceutical Chemistry, P.E.S's Rajaram and Tarabai Bandekar College of Pharmacy, Farmagudi, Ponda, Goa, India
| | - Vasu Soumya
- Department of Pharmaceutical Chemistry, Sri Ramachandra Faculty of Pharmacy, Sri Ramachandra Institute of Higher Education and Research, Porur, Chennai, India
| | - Shivlingrao N Mamledesai
- Department of Pharmaceutical Chemistry, P.E.S's Rajaram and Tarabai Bandekar College of Pharmacy, Farmagudi, Ponda, Goa, India
| | - M Manickavasagam
- Department of Oncology, SRMC & RI, Sri Ramachandra Institute of Higher Education and Research, Porur, Chennai, India
| | - Prafulla Choudhari
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, Maharashtra, India
| | - Sanket Rathod
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, Maharashtra, India
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Carton C, Safran J, Lemaire A, Domon JM, Poelmans W, Beeckman T, Ramos-Martín F, Antonietti V, Sonnet P, Sahraoui ALH, Lefebvre V, Pelloux J, Pau-Roblot C. Structural and biochemical characterization of SmoPG1, an exo-polygalacturonase from Selaginella moellendorffii. Int J Biol Macromol 2024; 269:131918. [PMID: 38697418 DOI: 10.1016/j.ijbiomac.2024.131918] [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: 12/20/2023] [Revised: 03/22/2024] [Accepted: 04/25/2024] [Indexed: 05/05/2024]
Abstract
Polygalacturonases (PGs) can modulate chemistry and mechanical properties of the plant cell wall through the degradation of pectins, one of its major constituents. PGs are largely used in food, beverage, textile, and paper industries to increase processes' performances. To improve the use of PGs, knowledge of their biochemical, structural and functional features is of prime importance. Our study aims at characterizing SmoPG1, a polygalacturonase from Selaginella moellendorffii, that belongs to the lycophytes. Transcription data showed that SmoPG1 was mainly expressed in S. moellendorffii shoots while phylogenetic analyses suggested that SmoPG1 is an exo-PG, which was confirmed by the biochemical characterization following its expression in heterologous system. Indeed, LC-MS/MS oligoprofiling using various pectic substrates identified galacturonic acid (GalA) as the main hydrolysis product. We found that SmoPG1 was most active on polygalacturonic acid (PGA) at pH 5, and that its activity could be modulated by different cations (Ca2+, Cu2+, Fe2+, Mg2+, Mn2+, Na2+, Zn2+). In addition, SmoPG1 was inhibited by green tea catechins, including (-)-epigallocatechin-3-gallate (EGCG). Docking analyses and MD simulations showed in detail amino acids responsible for the SmoPG1-EGCG interaction. Considering its expression yield and activity, SmoPG1 appears as a prime candidate for the industrial production of GalA.
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Affiliation(s)
- Camille Carton
- UMRT INRAE 1158 BioEcoAgro - Biologie des Plantes et Innovation, Université de Picardie Jules Verne, UFR des Sciences, 33 Rue St Leu, 80039 Amiens, France
| | - Josip Safran
- UMRT INRAE 1158 BioEcoAgro - Biologie des Plantes et Innovation, Université de Picardie Jules Verne, UFR des Sciences, 33 Rue St Leu, 80039 Amiens, France
| | - Adrien Lemaire
- UMRT INRAE 1158 BioEcoAgro - Biologie des Plantes et Innovation, Université de Picardie Jules Verne, UFR des Sciences, 33 Rue St Leu, 80039 Amiens, France
| | - Jean-Marc Domon
- UMRT INRAE 1158 BioEcoAgro - Biologie des Plantes et Innovation, Université de Picardie Jules Verne, UFR des Sciences, 33 Rue St Leu, 80039 Amiens, France
| | - Ward Poelmans
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium; Center for Plant Systems Biology, VIB-UGent, Ghent 9052, Belgium
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium; Center for Plant Systems Biology, VIB-UGent, Ghent 9052, Belgium
| | - Francisco Ramos-Martín
- Unité de Génie Enzymatique et Cellulaire UMR 7025 CNRS, Université de Picardie Jules Verne, F-80039 Amiens, France
| | - Viviane Antonietti
- Agents Infectieux, Resistance Et Chimiothérapie (AGIR), EA4294, Université de Picardie Jules Verne, UFR de Pharmacie, 1, rue des Louvels, 80037 Amiens, France
| | - Pascal Sonnet
- Agents Infectieux, Resistance Et Chimiothérapie (AGIR), EA4294, Université de Picardie Jules Verne, UFR de Pharmacie, 1, rue des Louvels, 80037 Amiens, France
| | - Anissa Lounès-Hadj Sahraoui
- Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV), Université du Littoral Côte d'Opale, 50, Rue Ferdinand Buisson, 62228 Calais Cedex, France
| | - Valérie Lefebvre
- UMRT INRAE 1158 BioEcoAgro - Biologie des Plantes et Innovation, Université de Picardie Jules Verne, UFR des Sciences, 33 Rue St Leu, 80039 Amiens, France
| | - Jérôme Pelloux
- UMRT INRAE 1158 BioEcoAgro - Biologie des Plantes et Innovation, Université de Picardie Jules Verne, UFR des Sciences, 33 Rue St Leu, 80039 Amiens, France
| | - Corinne Pau-Roblot
- UMRT INRAE 1158 BioEcoAgro - Biologie des Plantes et Innovation, Université de Picardie Jules Verne, UFR des Sciences, 33 Rue St Leu, 80039 Amiens, France.
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Liang B, Li W, Yang C, Su J. LGP2 Facilitates Bacterial Escape through Binding Peptidoglycan via EEK Motif and Suppressing NOD2-RIP2 Axis in Cyprinidae and Xenocyprididae Families. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:1791-1806. [PMID: 38629918 DOI: 10.4049/jimmunol.2300800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/14/2024] [Indexed: 05/22/2024]
Abstract
RIG-I-like receptors and NOD-like receptors play pivotal roles in recognizing microbe-associated molecular patterns and initiating immune responses. The LGP2 and NOD2 proteins are important members of the RIG-I-like receptor and NOD-like receptor families, recognizing viral RNA and bacterial peptidoglycan (PGN), respectively. However, in some instances bacterial infections can induce LPG2 expression via a mechanism that remains largely unknown. In the current study, we found that LGP2 can compete with NOD2 for PGN binding and inhibit antibacterial immunity by suppressing the NOD2-RIP2 axis. Recombinant CiLGP2 (Ctenopharyngodon idella LGP2) produced using either prokaryotic or eukaryotic expression platform can bind PGN and bacteria in pull-down and ELISA assays. Comparative protein structure models and intermolecular interaction prediction calculations as well as pull-down and colocalization experiments indicated that CiLGP2 binds PGN via its EEK motif with species and structural specificity. EEK deletion abolished PGN binding of CiLGP2, but insertion of the CiLGP2 EEK motif into zebrafish and mouse LGP2 did not confer PGN binding activity. CiLGP2 also facilitates bacterial replication by interacting with CiNOD2 to suppress expression of NOD2-RIP2 pathway genes. Sequence analysis and experimental verification demonstrated that LGP2 having EEK motif that can negatively regulate antibacterial immune function is present in Cyprinidae and Xenocyprididae families. These results show that LGP2 containing EEK motif competes with NOD2 for PGN binding and suppresses antibacterial immunity by inhibiting the NOD2-RIP2 axis, indicating that LGP2 plays a crucial negative role in antibacterial response beyond its classical regulatory function in antiviral immunity.
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Affiliation(s)
- Bo Liang
- Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University, Wuhan, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Wenqian Li
- Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Chunrong Yang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Jianguo Su
- Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University, Wuhan, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
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