1
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Afantitis A. Nanoinformatics: Artificial Intelligence and Nanotechnology in the New Decade. Comb Chem High Throughput Screen 2021; 23:4-5. [PMID: 32189589 DOI: 10.2174/138620732301200316112000] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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2
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Kim SY, Ahn G, Kim HS, Je JG, Kim KN, Jeon YJ. Diphlorethohydroxycarmalol (DPHC) Isolated from the Brown Alga Ishige okamurae Acts on Inflammatory Myopathy as an Inhibitory Agent of TNF-α. Mar Drugs 2020; 18:E529. [PMID: 33114618 PMCID: PMC7692396 DOI: 10.3390/md18110529] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/22/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022] Open
Abstract
Inflammation affects various organs of the human body, including skeletal muscle. Phlorotannins are natural biologically active substances found in marine brown algae and exhibit anti-inflammatory activities. In this study, we focused on the effects of phlorotannins on anti-inflammatory activity and skeletal muscle cell proliferation activity to identify the protective effects on the inflammatory myopathy. First, the five species of marine brown algal extracts dramatically inhibited nitric oxide (NO) production in lipopolysaccharide (LPS)-induced RAW 264.7 cells without toxicity at all the concentrations tested. Moreover, the extracts collected from Ishige okamurae (I. okamurae) significantly increased cell proliferation of C2C12 myoblasts compared to the non-treated cells with non-toxicity. In addition, as a result of finding a potential tumor necrosis factor (TNF)-α inhibitor that regulates the signaling pathway of muscle degradation in I. okamurae-derived natural bioactive compounds, Diphlorethohydroxycarmalol (DPHC) is favorably docked to the TNF-α with the lowest binding energy and docking interaction energy value. Moreover, DPHC down-regulated the mRNA expression level of pro-inflammatory cytokines and suppressed the muscle RING-finger protein (MuRF)-1 and Muscle Atrophy F-box (MAFbx)/Atrgoin-1, which are the key protein muscle atrophy via nuclear factor-κB (NF-κB), and mitogen-activated protein kinase (MAPKs) signaling pathways in TNF-α-stimulated C2C12 myotubes. Therefore, it is expected that DPHC isolated from IO would be developed as a TNF-α inhibitor against inflammatory myopathy.
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Affiliation(s)
- Seo-Young Kim
- Department of Marine Life Science, Jeju National University, Jeju 63243, Korea; (S.-Y.K.); (H.-S.K.); (J.-G.J.)
- Chuncheon Center, Korea Basic Science Institute (KBSI), Chuncheon 24341, Korea;
| | - Ginnae Ahn
- Department of Food Technology and Nutrition, Chonnam National University, Yeosu 59626, Korea;
| | - Hyun-Soo Kim
- Department of Marine Life Science, Jeju National University, Jeju 63243, Korea; (S.-Y.K.); (H.-S.K.); (J.-G.J.)
- Department of Applied Research, National Marine Biodiversity Institute of Korea, 75, Jangsan-ro 101-gil, Janghang-eup, Seocheon 33662, Korea
| | - Jun-Geon Je
- Department of Marine Life Science, Jeju National University, Jeju 63243, Korea; (S.-Y.K.); (H.-S.K.); (J.-G.J.)
| | - Kil-Nam Kim
- Chuncheon Center, Korea Basic Science Institute (KBSI), Chuncheon 24341, Korea;
| | - You-Jin Jeon
- Department of Marine Life Science, Jeju National University, Jeju 63243, Korea; (S.-Y.K.); (H.-S.K.); (J.-G.J.)
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3
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Jade DD, Pandey R, Kumar R, Gupta D. Ligand-based pharmacophore modeling of TNF-α to design novel inhibitors using virtual screening and molecular dynamics. J Biomol Struct Dyn 2020; 40:1702-1718. [PMID: 33034255 DOI: 10.1080/07391102.2020.1831962] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Tumor necrosis factor-α (TNF-α) is one of the promising targets for treating inflammatory (Crohn disease, psoriasis, psoriatic arthritis, rheumatoid arthritis) and various other diseases. Commercially available TNF-α inhibitors are associated with several risks and limitations. In the present study, we have identified small TNF-α inhibitors using in silico approaches, namely pharmacophore modeling, virtual screening, molecular docking, molecular dynamics simulation and free binding energy calculations. The study yielded better and potent hits that bind to TNF-α with significant affinity. The best pharmacophore model generated using LigandScout has an efficient hit rate and Area Under the operating Curve. High throughput virtual screening of SPECS database molecules against crystal structure of TNF-α protein, coupled with physicochemical filtration, PAINS test. Virtual hit compounds used for molecular docking enabled the identification of 20 compounds with better binding energies when compared with previously known TNF-α inhibitors. MD simulation analysis on 20 virtual identified hits showed that ligand binding with TNF-α protein is stable and protein-ligand conformation remains unchanged. Further, 16 compounds passed ADMET analysis suggesting these identified hit compounds are suitable for designing a future class of potent TNF-α inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dhananjay D Jade
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Rajan Pandey
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Rakesh Kumar
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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4
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Qaiser H, Saeed M, Nerukh D, Ul-Haq Z. Structural insight into TNF-α inhibitors through combining pharmacophore-based virtual screening and molecular dynamic simulation. J Biomol Struct Dyn 2020; 39:5920-5939. [PMID: 32705954 DOI: 10.1080/07391102.2020.1796794] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Tumor Necrosis Factor-alpha (TNF-α), a multifunctional cytokine responsible for providing resistance against infections, inflammation, and cancers. TNF-α has emerged as a promising drug target against several autoimmune and inflammatory disorders. Several synthetic antibodies (Infliximab, Etanercept, and Adalimumab) are available, but their potential to cause severe side effects has prompted them to develop alternative small molecules-based therapies for inhibition of TNF-α. In the present study, combined in silico approaches based on pharmacophore modeling, virtual screening, molecular docking, and molecular dynamics studies were employed to understand significant direct interactions between TNF-α protein and small molecule inhibitors. Initially, four different small molecule libraries (∼17.5 million molecules) were virtually screened against the selected pharmacophore model. The identified hits were further subjected to molecular docking studies. The three potent lead compounds (ZINC05848961, ZINC09402309, ZINC04502991) were further subjected to 100 ns molecular dynamic studies to examine their stability. Our docking and molecular dynamic analysis revealed that the selected lead compounds target the TNF receptor (TNFR) and efficiently block the production of TNF. Moreover, in silico ADMET (Absorption, Distribution, Metabolism, Excretion and Toxicity) analysis revealed that all the predicted compounds have good pharmacokinetic properties with high gastrointestinal absorption and a decent bioavailability score. Furthermore, toxicity profiles further evidenced that these compounds have no risk of being mutagenic, tumorigenic, reproductive and irritant except ZINC11915498. In conclusion, the present study could serve as the starting point to develop new therapeutic regimens to treat various TNF- related diseases. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hina Qaiser
- Dr. Panjwani Center for Molecular Medicine and Drug Research, ICCBS, University of Karachi, Karachi, Pakistan.,Department of Mathematics, Aston University, Birmingham, United Kingdom
| | - Maria Saeed
- Dr. Panjwani Center for Molecular Medicine and Drug Research, ICCBS, University of Karachi, Karachi, Pakistan
| | - Dmitry Nerukh
- Department of Mathematics, Aston University, Birmingham, United Kingdom
| | - Zaheer Ul-Haq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, ICCBS, University of Karachi, Karachi, Pakistan
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5
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Li G, Boyle JW, Ko CN, Zeng W, Wong VKW, Wan JB, Chan PWH, Ma DL, Leung CH. Aurone derivatives as Vps34 inhibitors that modulate autophagy. Acta Pharm Sin B 2019; 9:537-544. [PMID: 31193773 PMCID: PMC6543056 DOI: 10.1016/j.apsb.2019.01.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 01/19/2019] [Accepted: 01/23/2019] [Indexed: 12/14/2022] Open
Abstract
We report in this study the identification of a natural product-like antagonist (1a) of Vps34 as a potent autophagy modulator via structure-based virtual screening. Aurone derivative 1a strongly inhibited Vps34 activity in cell-free and cell-based assays. Significantly, 1a prevents autophagy in human cells induced either by starvation or by an mTOR inhibitor. In silico modeling and kinetic data revealed that 1a could function as an ATP-competitive inhibitor of Vps34. Moreover, it suppressed autophagy in vivo and without inducing heart or liver damage in mice. 1a could be utilized as a new motif for more selective and efficacious antagonists of Vps34 for the potential treatment of autophagy-related human diseases.
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Key Words
- Aurone derivative
- Autophagy
- CETSA, cellular thermal shift assay
- Co-IP, co-immunoprecipitation
- DMEM, Dulbecco׳s modified Eagle׳s medium
- DMSO, dimethyl sulfoxide
- EBSS, Earle׳s balanced salt solution
- ELISA, enzyme-linked immunosorbent assay
- FBS, fetal bovine serum
- Heart or liver damage
- Inhibitor
- Natural products
- PE, phosphatidylethanolamine
- PI, phosphatidylinositol
- PI3K, phosphoinositide 3-kinase
- PI3P, phosphatidylinositol 3-phosphate
- PS, phosphatidylserine
- Structure-based virtual screening
- Vesicle trafficking
- Vps34
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6
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Melagraki G, Ntougkos E, Papadopoulou D, Rinotas V, Leonis G, Douni E, Afantitis A, Kollias G. In Silico Discovery of Plant-Origin Natural Product Inhibitors of Tumor Necrosis Factor (TNF) and Receptor Activator of NF-κB Ligand (RANKL). Front Pharmacol 2018; 9:800. [PMID: 30090063 PMCID: PMC6068282 DOI: 10.3389/fphar.2018.00800] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 07/03/2018] [Indexed: 01/08/2023] Open
Abstract
An in silico drug discovery pipeline for the virtual screening of plant-origin natural products (NPs) was developed to explore new direct inhibitors of TNF and its close relative receptor activator of nuclear factor kappa-B ligand (RANKL), both representing attractive therapeutic targets for many chronic inflammatory conditions. Direct TNF inhibition through identification of potent small molecules is a highly desired goal; however, it is often hampered by severe limitations. Our approach yielded a priority list of 15 NPs as potential direct TNF inhibitors that were subsequently tested in vitro against TNF and RANKL. We thus identified two potent direct inhibitors of TNF function with low micromolar IC50 values and minimal toxicity even at high concentrations. Most importantly, one of them (A11) was proved to be a dual inhibitor of both TNF and RANKL. Extended molecular dynamics simulations with the fully automated EnalosMD suite rationalized the mode of action of the compounds at the molecular level. To our knowledge, these compounds constitute the first NP TNF inhibitors, one of which being the first NP small-molecule dual inhibitor of TNF and RANKL, and could serve as lead compounds for the development of novel treatments for inflammatory and autoimmune diseases.
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Affiliation(s)
| | - Evangelos Ntougkos
- Division of Immunology Biomedical Sciences Research Center "Alexander Fleming,", Vari, Greece
| | - Dimitra Papadopoulou
- Division of Immunology Biomedical Sciences Research Center "Alexander Fleming,", Vari, Greece.,Department of Experimental Physiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Vagelis Rinotas
- Division of Immunology Biomedical Sciences Research Center "Alexander Fleming,", Vari, Greece.,Department of Biotechnology, Agricultural University of Athens, Athens, Greece
| | | | - Eleni Douni
- Division of Immunology Biomedical Sciences Research Center "Alexander Fleming,", Vari, Greece.,Department of Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Antreas Afantitis
- Division of Immunology Biomedical Sciences Research Center "Alexander Fleming,", Vari, Greece.,NovaMechanics Ltd., Nicosia, Cyprus
| | - George Kollias
- Division of Immunology Biomedical Sciences Research Center "Alexander Fleming,", Vari, Greece.,Department of Experimental Physiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
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7
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Deng X, Zhang X, Tang B, Liu H, Shen Q, Liu Y, Lai L. Design, Synthesis, and Evaluation of Dihydrobenzo[ cd]indole-6-sulfonamide as TNF-α Inhibitors. Front Chem 2018; 6:98. [PMID: 29670876 PMCID: PMC5893771 DOI: 10.3389/fchem.2018.00098] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 03/20/2018] [Indexed: 11/26/2022] Open
Abstract
Tumor necrosis factor-α (TNF-α) plays a pivotal role in inflammatory response. Dysregulation of TNF can lead to a variety of disastrous pathological effects, including auto-inflammatory diseases. Antibodies that directly targeting TNF-α have been proven effective in suppressing symptoms of these disorders. Compared to protein drugs, small molecule drugs are normally orally available and less expensive. Till now, peptide and small molecule TNF-α inhibitors are still in the early stage of development, and much more efforts should be made. In a previously study, we reported a TNF-α inhibitor, EJMC-1 with modest activity. Here, we optimized this compound by shape screen and rational design. In the first round, we screened commercial compound library for EJMC-1 analogs based on shape similarity. Out of the 68 compounds tested, 20 compounds showed better binding affinity than EJMC-1 in the SPR competitive binding assay. These 20 compounds were tested in cell assay and the most potent compound was 2-oxo-N-phenyl-1,2-dihydrobenzo[cd]indole-6-sulfonamide (S10) with an IC50 of 14 μM, which was 2.2-fold stronger than EJMC-1. Based on the docking analysis of S10 and EJMC-1 binding with TNF-α, in the second round, we designed S10 analogs, purchased seven of them, and synthesized seven new compounds. The best compound, 4e showed an IC50-value of 3 μM in cell assay, which was 14-fold stronger than EJMC-1. 4e was among the most potent TNF-α organic compound inhibitors reported so far. Our study demonstrated that 2-oxo-N-phenyl-1,2-dihydrobenzo[cd]indole-6-sulfonamide analogs could be developed as potent TNF-α inhibitors. 4e can be further optimized for its activity and properties. Our study provides insights into designing small molecule inhibitors directly targeting TNF-α and for protein–protein interaction inhibitor design.
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Affiliation(s)
- Xiaobing Deng
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Xiaoling Zhang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Bo Tang
- BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Hongbo Liu
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Qi Shen
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Ying Liu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.,BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Luhua Lai
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.,BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
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8
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Wu KJ, Zhong HJ, Yang G, Wu C, Huang JM, Li G, Ma DL, Leung CH. Small Molecule Pin1 Inhibitor Blocking NF-κB Signaling in Prostate Cancer Cells. Chem Asian J 2018; 13:275-279. [DOI: 10.1002/asia.201701216] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 12/24/2017] [Indexed: 01/27/2023]
Affiliation(s)
- Ke-Jia Wu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences; University of Macau; Macao China
| | - Hai-Jing Zhong
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences; University of Macau; Macao China
| | - Guanjun Yang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences; University of Macau; Macao China
| | - Chun Wu
- Department of Chemistry; Hong Kong Baptist University; Kowloon Tong Hong Kong China
| | - Jie-Min Huang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences; University of Macau; Macao China
| | - Guodong Li
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences; University of Macau; Macao China
| | - Dik-Lung Ma
- Department of Chemistry; Hong Kong Baptist University; Kowloon Tong Hong Kong China
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences; University of Macau; Macao China
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9
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Thiopurine Drugs Repositioned as Tyrosinase Inhibitors. Int J Mol Sci 2017; 19:ijms19010077. [PMID: 29283382 PMCID: PMC5796027 DOI: 10.3390/ijms19010077] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Revised: 12/14/2017] [Accepted: 12/26/2017] [Indexed: 02/06/2023] Open
Abstract
Drug repositioning is the application of the existing drugs to new uses and has the potential to reduce the time and cost required for the typical drug discovery process. In this study, we repositioned thiopurine drugs used for the treatment of acute leukaemia as new tyrosinase inhibitors. Tyrosinase catalyses two successive oxidations in melanin biosynthesis: the conversions of tyrosine to dihydroxyphenylalanine (DOPA) and DOPA to dopaquinone. Continuous efforts are underway to discover small molecule inhibitors of tyrosinase for therapeutic and cosmetic purposes. Structure-based virtual screening predicted inhibitor candidates from the US Food and Drug Administration (FDA)-approved drugs. Enzyme assays confirmed the thiopurine leukaemia drug, thioguanine, as a tyrosinase inhibitor with the inhibitory constant of 52 μM. Two other thiopurine drugs, mercaptopurine and azathioprine, were also evaluated for their tyrosinase inhibition; mercaptopurine caused stronger inhibition than thioguanine did, whereas azathioprine was a poor inhibitor. The inhibitory constant of mercaptopurine (16 μM) was comparable to that of the well-known inhibitor kojic acid (13 μM). The cell-based assay using B16F10 melanoma cells confirmed that the compounds inhibit mammalian tyrosinase. Particularly, 50 μM thioguanine reduced the melanin content by 57%, without apparent cytotoxicity. Cheminformatics showed that the thiopurine drugs shared little chemical similarity with the known tyrosinase inhibitors.
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10
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Wu KJ, Zhong HJ, Li G, Liu C, Wang HMD, Ma DL, Leung CH. Structure-based identification of a NEDD8-activating enzyme inhibitor via drug repurposing. Eur J Med Chem 2017; 143:1021-1027. [PMID: 29232579 DOI: 10.1016/j.ejmech.2017.11.101] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 11/27/2017] [Accepted: 11/29/2017] [Indexed: 10/18/2022]
Abstract
NEDD8-activating enzyme (NAE) is an essential player of the NEDD8 conjugation pathway that regulates protein degradation. Meanwhile, drug repurposing is a cost-efficient strategy to identify new therapeutic uses for existing scaffolds. In this report, mitoxantrone (1) was repurposed as an inhibitor of NAE by virtual screening of an FDA-approved drug database. Compound 1 inhibited NAE activity in cell-free and cell-based systems with high selectivity and was competitive with ATP. Furthermore, compound 1 induced apoptosis of colorectal adenocarcinoma cancer cells through inhibiting the degradation of the neddylation substrate p53.
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Affiliation(s)
- Ke-Jia Wu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Hai-Jing Zhong
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Guodong Li
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Chenfu Liu
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Hui-Min David Wang
- Graduate Institute of Biomedical Engineering, National Chung Hsing University, Taichung, 402, Taiwan
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China.
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China.
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11
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Identification of an in vivo orally active dual-binding protein-protein interaction inhibitor targeting TNFα through combined in silico/in vitro/in vivo screening. Sci Rep 2017; 7:3424. [PMID: 28611375 PMCID: PMC5469758 DOI: 10.1038/s41598-017-03427-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 04/28/2017] [Indexed: 12/31/2022] Open
Abstract
TNFα is a homotrimeric pro-inflammatory cytokine, whose direct targeting by protein biotherapies has been an undeniable success for the treatment of chronic inflammatory diseases. Despite many efforts, no orally active drug targeting TNFα has been identified so far. In the present work, we identified through combined in silico/in vitro/in vivo approaches a TNFα direct inhibitor, compound 1, displaying nanomolar and micromolar range bindings to TNFα. Compound 1 inhibits the binding of TNFα with both its receptors TNFRI and TNFRII. Compound 1 inhibits the TNFα induced apoptosis on L929 cells and the TNFα induced NF-κB activation in HEK cells. In vivo, oral administration of compound 1 displays a significant protection in a murine TNFα-dependent hepatic shock model. This work illustrates the ability of low-cost combined in silico/in vitro/in vivo screening approaches to identify orally available small-molecules targeting challenging protein-protein interactions such as homotrimeric TNFα.
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12
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Cheminformatics-aided discovery of small-molecule Protein-Protein Interaction (PPI) dual inhibitors of Tumor Necrosis Factor (TNF) and Receptor Activator of NF-κB Ligand (RANKL). PLoS Comput Biol 2017; 13:e1005372. [PMID: 28426652 PMCID: PMC5398486 DOI: 10.1371/journal.pcbi.1005372] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 01/17/2017] [Indexed: 12/20/2022] Open
Abstract
We present an in silico drug discovery pipeline developed and applied for the identification and virtual screening of small-molecule Protein-Protein Interaction (PPI) compounds that act as dual inhibitors of TNF and RANKL through the trimerization interface. The cheminformatics part of the pipeline was developed by combining structure-based with ligand-based modeling using the largest available set of known TNF inhibitors in the literature (2481 small molecules). To facilitate virtual screening, the consensus predictive model was made freely available at: http://enalos.insilicotox.com/TNFPubChem/. We thus generated a priority list of nine small molecules as candidates for direct TNF function inhibition. In vitro evaluation of these compounds led to the selection of two small molecules that act as potent direct inhibitors of TNF function, with IC50 values comparable to those of a previously-described direct inhibitor (SPD304), but with significantly reduced toxicity. These molecules were also identified as RANKL inhibitors and validated in vitro with respect to this second functionality. Direct binding of the two compounds was confirmed both for TNF and RANKL, as well as their ability to inhibit the biologically-active trimer forms. Molecular dynamics calculations were also carried out for the two small molecules in each protein to offer additional insight into the interactions that govern TNF and RANKL complex formation. To our knowledge, these compounds, namely T8 and T23, constitute the second and third published examples of dual small-molecule direct function inhibitors of TNF and RANKL, and could serve as lead compounds for the development of novel treatments for inflammatory and autoimmune diseases.
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13
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Ramakrishnan G, Chandra NR, Srinivasan N. Recognizing drug targets using evolutionary information: implications for repurposing FDA-approved drugs against Mycobacterium tuberculosis H37Rv. MOLECULAR BIOSYSTEMS 2016; 11:3316-31. [PMID: 26429199 DOI: 10.1039/c5mb00476d] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Drug repurposing to explore target space has been gaining pace over the past decade with the upsurge in the use of systematic approaches for computational drug discovery. Such a cost and time-saving approach gains immense importance for pathogens of special interest, such as Mycobacterium tuberculosis H37Rv. We report a comprehensive approach to repurpose drugs, based on the exploration of evolutionary relationships inferred from the comparative sequence and structural analyses between targets of FDA-approved drugs and the proteins of M. tuberculosis. This approach has facilitated the identification of several polypharmacological drugs that could potentially target unexploited M. tuberculosis proteins. A total of 130 FDA-approved drugs, originally intended against other diseases, could be repurposed against 78 potential targets in M. tuberculosis. Additionally, we have also made an attempt to augment the chemical space by recognizing compounds structurally similar to FDA-approved drugs. For three of the attractive cases we have investigated the probable binding modes of the drugs in their corresponding M. tuberculosis targets by means of structural modelling. Such prospective targets and small molecules could be prioritized for experimental endeavours, and could significantly influence drug-discovery and drug-development programmes for tuberculosis.
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Affiliation(s)
- Gayatri Ramakrishnan
- Indian Institute of Science Mathematics Initiative, Indian Institute of Science, Bangalore-560012, India and Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India.
| | - Nagasuma R Chandra
- Department of Biochemistry, Indian Institute of Science, Bangalore-560012, India
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14
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A novel coumarin, (+)-3'-angeloxyloxy-4'-keto-3',4'-dihydroseselin, isolated from Bupleurum malconense (Chaihu) inhibited NF-κB activity. Chin Med 2016; 11:5. [PMID: 26877763 PMCID: PMC4752810 DOI: 10.1186/s13020-016-0077-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 02/04/2016] [Indexed: 01/02/2023] Open
Abstract
Background This study aims to identify the major anti-inflammatory components in the petroleum ether extract of Bupleurummalconense (Chaihu), by bioassay-guided fractionation, and to investigate the anti-inflammatory mechanisms of active components in lipopolysaccharide (LPS)-stimulated murine macrophage RAW-Blue cells. Methods A QUANTI-Blue assay was used to guide fractionation of B.malconense root extract. The petroleum ether extract which exerted significant secreted embryonic alkaline phosphatase (SEAP) inhibition effect was purified by silica gel column chromatography and assisted with reverse phase HPLC. The major bioactive compound which significantly inhibited SEAP activity was obtained and its anti-inflammatory effects in LPS-induced RAW-Blue cells were measured by the overproduction of NO (Griess method), gene expression of Il-1β, Tnf-α and iNos (real-time PCR). In parallel, protein expressions of COX-2, iNOS and IκB-α were determined by western blot. Results In bioassay-guided fractionation using LPS-stimulated mouse macrophage RAW-Blue cells, (+)-3′-angeloxyloxy-4′-keto-3′,4′-dihydroseselin (Pd-Ib) was identified by MS and NMR spectral analyses. Pd-Ib (5, 10, 20 μg/mL) suppressed the gene expression of Il-1β (P < 0.0001, P < 0.0001, P < 0.0001 for three respective concentrations), Tnf-α (P = 0.006, P = 0.001, P < 0.0001 for three respective concentrations) and iNos (P = 0.009, P < 0.0001, P < 0.0001 for three respective concentrations) in LPS-stimulated macrophages. The production of cyclooxygenase-2 (P = 0.019, P = 0.002, P < 0.0001), iNOS (P < 0.0001, P < 0.0001, P < 0.0001 for three respective concentrations) and NO (P < 0.0001, P < 0.0001, P < 0.0001 for three respective concentrations) significantly decreased when macrophages were treated with Pd-Ib (5, 10, 20 μg/mL) in the presence of LPS. Pd-Ib (5, 10, 20 μg/mL) suppressed the nuclear activation of NF-κB while it up-regulated the IκB-α level (P = 0.028, P = 0.013, P = 0.005 for three respective concentrations) in LPS-stimulated macrophages. Conclusions Pd-Ib isolated from B.malconense suppressed LPS-induced inflammatory responses in macrophages by inhibiting NF-κB activity and reducing the expression of iNOS, COX-2 as well as pro-inflammatory cytokines. Electronic supplementary material The online version of this article (doi:10.1186/s13020-016-0077-x) contains supplementary material, which is available to authorized users.
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Papaneophytou C, Alexiou P, Papakyriakou A, Ntougkos E, Tsiliouka K, Maranti A, Liepouri F, Strongilos A, Mettou A, Couladouros E, Eliopoulos E, Douni E, Kollias G, Kontopidis G. Synthesis and biological evaluation of potential small moleculeinhibitors of tumor necrosis factor. MEDCHEMCOMM 2015. [DOI: 10.1039/c5md00023h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A series of 39 novel SPD-304 analogs were designed synthesized and evaluated as inhibitors of TNF.
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Affiliation(s)
| | - Polyxeni Alexiou
- Laboratory of General Chemistry
- Department of Science
- Agricultural University of Athens
- Athens 11855
- Greece
| | - Athanasios Papakyriakou
- Laboratory of Genetics
- Department of Biotechnology
- Agricultural University of Athens
- Athens 11855
- Greece
| | | | | | | | | | | | - Anthi Mettou
- Department of Biochemistry
- Veterinary School
- University of Thessaly
- Karditsa 43100
- Greece
| | - Elias Couladouros
- Laboratory of General Chemistry
- Department of Science
- Agricultural University of Athens
- Athens 11855
- Greece
| | - Elias Eliopoulos
- Laboratory of Genetics
- Department of Biotechnology
- Agricultural University of Athens
- Athens 11855
- Greece
| | - Eleni Douni
- Laboratory of Genetics
- Department of Biotechnology
- Agricultural University of Athens
- Athens 11855
- Greece
| | - George Kollias
- Biomedical Sciences Research Center “Alexander Fleming”
- Vari
- Greece
| | - George Kontopidis
- Department of Biochemistry
- Veterinary School
- University of Thessaly
- Karditsa 43100
- Greece
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Wang Y, Law WK, Hu JS, Lin HQ, Ip TM, Wan DCC. Discovery of FDA-approved drugs as inhibitors of fatty acid binding protein 4 using molecular docking screening. J Chem Inf Model 2014; 54:3046-50. [PMID: 25360897 DOI: 10.1021/ci500503b] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We first identified fluorescein, ketazolam, antrafenine, darifenacin, fosaprepitant, paliperidone, risperidone, pimozide, trovafloxacin, and levofloxacin as inhibitors of fatty acid binding protein 4 using molecular docking screening from FDA-approved drugs. Subsequently, the biochemical characterizations showed that levofloxacin directly inhibited FABP4 activity in both the in vitro ligand displacement assay and cell-based function assay. Furthermore, levofloxacin did not induce adipogenesis in adipocytes, which is the major adverse effect of FABP4 inhibitors.
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Affiliation(s)
- Yan Wang
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong , Shatin, Hong Kong SAR, China
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17
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Zhu GY, Bai LP, Liu L, Jiang ZH. Limonoids from the fruits of Melia toosendan and their NF-κB modulating activities. PHYTOCHEMISTRY 2014; 107:175-181. [PMID: 25189120 DOI: 10.1016/j.phytochem.2014.08.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 06/25/2014] [Accepted: 06/25/2014] [Indexed: 06/03/2023]
Abstract
Eight ring C-seco and ring-intact limonoids, and 25 known limonoids were isolated from the fruits of Melia toosendan (Meliaceae). Their structures were elucidated on the basis of extensive spectroscopic evidence including HRMS, 1D and 2D NMR spectroscopic data. A total of 29 isolated limonoids was evaluated for NF-κB activities. Among them, eight compounds significantly enhanced the TNFα-induced NF-κB luciferase activity at 10μM, while 10 compounds suppressed the NF-κB activation.
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Affiliation(s)
- Guo-Yuan Zhu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, China
| | - Li-Ping Bai
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, China
| | - Liang Liu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, China.
| | - Zhi-Hong Jiang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, China.
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18
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Discovery of deoxyvasicinone derivatives as inhibitors of NEDD8-activating enzyme. Methods 2014; 71:71-6. [PMID: 25196325 DOI: 10.1016/j.ymeth.2014.08.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Revised: 08/16/2014] [Accepted: 08/22/2014] [Indexed: 12/11/2022] Open
Abstract
NEDD8-activating enzyme (NAE) controls the specific degradation of proteins regulated by cullin-RING ubiquitin E3 ligases, and has been considered as an attractive molecular target for the development of drugs against cancer. A pharmacophore model constructed from a training set of deoxyvasicinone derivatives was used to screen 376 compounds from an analogue database. From the initial screening, the valine-linked deoxyvasicinone derivative 9 and the N-isopropyl-linked deoxyvasicinone derivative 10 emerged as the top scoring candidates. Compounds 9 and 10 showed micromolar potencies in both cell-free and cell-based systems, with selectivity for NAE over the related enzymes SAE and UAE. Molecular modelling analysis suggested that 9 and 10 may inhibit NAE by blocking the ATP-binding domain. Thus, these deoxyvasicinone derivatives could be considered as promising lead molecules for the development of more potent inhibitors of NAE.
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Discovery of a small-molecule inhibitor of STAT3 by ligand-based pharmacophore screening. Methods 2014; 71:38-43. [PMID: 25160651 DOI: 10.1016/j.ymeth.2014.07.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 07/19/2014] [Accepted: 07/21/2014] [Indexed: 12/16/2022] Open
Abstract
STAT3 modulates the transcription of a wide variety of regulatory genes involved in cell proliferation, differentiation, migration, apoptosis, and other critical cellular functions. Constitutive activation of STAT3 has been detected in a wide spectrum of human malignancies. A pharmacophore model constructed from a training set of STAT3 inhibitors binding to the SH2 domain was used to screen an in-house database of compounds, from which azepine 1 emerged as a top candidate. Compound 1 inhibited STAT3 DNA-binding activity in vitro and attenuated STAT3-directed transcription in cellulo with comparable potency to the well-known STAT3 inhibitor S3I-201. A fluorescence polarization assay revealed that compound 1 targeted the SH2 domain of STAT3. Furthermore, compound 1 inhibited STAT3 phosphorylation in cells without affecting the total expression of STAT3. This study also validates the use of pharmacophore modeling to identify inhibitors of protein-protein interactions.
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Zhu GY, Chen G, Liu L, Bai LP, Jiang ZH. C-17 lactam-bearing limonoids from the twigs and leaves of Amoora tsangii. JOURNAL OF NATURAL PRODUCTS 2014; 77:983-989. [PMID: 24621263 DOI: 10.1021/np401089h] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Twelve new lactam-bearing limonoids, amooramides A-L (1-12), were isolated from the twigs and leaves of Amoora tsangii, and their structures fully elucidated by spectroscopic analysis. These compounds represent the first examples of rings A,B-seco-limonoids bearing unusual lactam side chains at C-17, including a 3-substituted 1,5-dihydro-2H-pyrrol-2-one moiety in 1-7 and a 4-substituted 1,5-dihydro-2H-pyrrol-2-one unit in 8-12. Compound 9 inhibited TNFα-induced NF-κB activity by 64% at a concentration of 10 μM.
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Affiliation(s)
- Guo-Yuan Zhu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology , Taipa, Macau, People's Republic of China
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21
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Parameswaran S, Saudagar P, Dubey VK, Patra S. Discovery of novel anti-leishmanial agents targeting LdLip3 lipase. J Mol Graph Model 2014; 49:68-79. [DOI: 10.1016/j.jmgm.2014.01.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Revised: 01/19/2014] [Accepted: 01/20/2014] [Indexed: 10/27/2022]
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22
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Zhong HJ, Liu LJ, Chan DSH, Wang HM, Chan PWH, Ma DL, Leung CH. Structure-based repurposing of FDA-approved drugs as inhibitors of NEDD8-activating enzyme. Biochimie 2014; 102:211-5. [PMID: 24657219 DOI: 10.1016/j.biochi.2014.03.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 03/10/2014] [Indexed: 11/30/2022]
Abstract
We report the discovery of an inhibitor of NEDD8-activating enzyme (NAE) by an integrated virtual screening approach. Piperacillin 1 inhibited NAE activity in cell-free and cell-based systems with high selectivity. Furthermore, piperacillin 1 was able to inhibit the degradation of the NAE downstream protein substrate p27(kip1). Our molecular modeling and kinetic studies suggested that this compound may act as a non-covalent ATP-competitive inhibitor of NAE.
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Affiliation(s)
- Hai-Jing Zhong
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Li-Juan Liu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Daniel Shiu-Hin Chan
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Hui-Min Wang
- Department of Fragrance and Cosmetic Science, Graduate Institute of Natural Products, Kaohsiung Medical University, Taiwan, ROC
| | - Philip Wai Hong Chan
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China.
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China.
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23
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24
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Lian W, Upadhyaya P, Rhodes CA, Liu Y, Pei D. Screening bicyclic peptide libraries for protein-protein interaction inhibitors: discovery of a tumor necrosis factor-α antagonist. J Am Chem Soc 2013; 135:11990-5. [PMID: 23865589 PMCID: PMC3856571 DOI: 10.1021/ja405106u] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Protein-protein interactions represent a new class of exciting but challenging drug targets, because their large, flat binding sites lack well-defined pockets for small molecules to bind. We report here a methodology for chemical synthesis and screening of large combinatorial libraries of bicyclic peptides displayed on rigid small-molecule scaffolds. With planar trimesic acid as the scaffold, the resulting bicyclic peptides are effective for binding to protein surfaces such as the interfaces of protein-protein interactions. Screening of a bicyclic peptide library against tumor necrosis factor-α (TNFα) identified a potent antagonist that inhibits the TNFα-TNFα receptor interaction and protects cells from TNFα-induced cell death. Bicyclic peptides of this type may provide a general solution for inhibition of protein-protein interactions.
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Affiliation(s)
- Wenlong Lian
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18 Avenue, Columbus, OH 43210, USA
| | - Punit Upadhyaya
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18 Avenue, Columbus, OH 43210, USA
| | - Curran A. Rhodes
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18 Avenue, Columbus, OH 43210, USA
| | - Yusen Liu
- Center for Perinatal Research, The Research Institute at Nationwide Children’s Hospital, Department of Pediatrics, The Ohio State University College of Medicine, 700 Children’s Drive, Columbus, OH 43205, USA
| | - Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18 Avenue, Columbus, OH 43210, USA
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Leung CH, Zhong HJ, Chan DSH, Ma DL. Bioactive iridium and rhodium complexes as therapeutic agents. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2013.01.034] [Citation(s) in RCA: 234] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Hit identification of IKKβ natural product inhibitor. BMC Pharmacol Toxicol 2013; 14:3. [PMID: 23294515 PMCID: PMC3583241 DOI: 10.1186/2050-6511-14-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Accepted: 12/21/2012] [Indexed: 12/27/2022] Open
Abstract
Background The nuclear factor-κB (NF-κB) proteins are a small group of heterodimeric transcription factors that play an important role in regulating the inflammatory, immune, and apoptotic responses. NF-κB activity is suppressed by association with the inhibitor IκB. Aberrant NF-κB signaling activity has been associated with the development of cancer, chronic inflammatory diseases and auto-immune diseases. The IKK protein complex is comprised of IKKα, IKKβ and NEMO subunits, with IKKβ thought to play the dominant role in modulating NF-κB activity. Therefore, the discovery of new IKKβ inhibitors may offer new therapeutic options for the treatment of cancer and inflammatory diseases. Results A structure-based molecular docking approach has been employed to discover novel IKKβ inhibitors from a natural product library of over 90,000 compounds. Preliminary screening of the 12 highest-scoring compounds using a luciferase reporter assay identified 4 promising candidates for further biological study. Among these, the benzoic acid derivative (1) showed the most promising activity at inhibiting IKKβ phosphorylation and TNF-α-induced NF-κB signaling in vitro. Conclusions In this study, we have successfully identified a benzoic acid derivative (1) as a novel IKKβ inhibitor via high-throughput molecular docking. Compound 1 was able to inhibit IKKβ phosphorylation activity in vitro, and block IκBα protein degradation and subsequent NF-κB activation in human cells. Further in silico optimization of the compound is currently being conducted in order to generate more potent analogues for biological tests.
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Ma DL, Chan DSH, Leung CH. Drug repositioning by structure-based virtual screening. Chem Soc Rev 2013; 42:2130-41. [PMID: 23288298 DOI: 10.1039/c2cs35357a] [Citation(s) in RCA: 159] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Approved drugs have favourable or validated pharmacokinetic properties and toxicological profiles, and the repositioning of existing drugs for new indications can potentially avoid expensive costs associated with early-stage testing of the hit compounds. In recent years, technological advances in virtual screening methodologies have allowed medicinal chemists to rapidly screen drug libraries for therapeutic activity against new biomolecular targets in a cost-effective manner. This review article outlines the basic principles and recent advances in structure-based virtual screening and highlights the powerful synergy of in silico techniques in drug repositioning as demonstrated in several recent reports.
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Affiliation(s)
- Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China.
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Yang H, Zhong HJ, Leung KH, Chan DSH, Ma VPY, Fu WC, Nanjunda R, Wilson WD, Ma DL, Leung CH. Structure-based design of flavone derivatives as c-myc oncogene down-regulators. Eur J Pharm Sci 2013; 48:130-41. [DOI: 10.1016/j.ejps.2012.10.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2011] [Revised: 09/19/2012] [Accepted: 10/02/2012] [Indexed: 12/21/2022]
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29
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Leung CH, Zhong HJ, Yang H, Cheng Z, Chan DSH, Ma VPY, Abagyan R, Wong CY, Ma DL. A metal-based inhibitor of tumor necrosis factor-α. Angew Chem Int Ed Engl 2012; 51:9010-4. [PMID: 22807261 DOI: 10.1002/anie.201202937] [Citation(s) in RCA: 144] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 06/08/2012] [Indexed: 01/01/2023]
Abstract
Staying in the pocket: A cyclometalated iridium(III) biquinoline complex targets the protein-protein interface (see picture; C yellow, N blue, Ir dark green) of the tumor necrosis factor-α (TNF-α) trimer. Molecular-modeling studies confirm the nature of this interaction. Both enantiomers of the iridium complex display comparable in vitro potency to the strongest small-molecule inhibitor of TNF-α.
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Affiliation(s)
- Chung-Hang Leung
- Institute of Chinese Medical Sciences and State Key Laboratory of Quality Research in Chinese Medicine, University of Macau, Macao, SAR China.
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Leung CH, Zhong HJ, Yang H, Cheng Z, Chan DSH, Ma VPY, Abagyan R, Wong CY, Ma DL. A Metal-Based Inhibitor of Tumor Necrosis Factor-α. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201202937] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Bohari MH, Sastry GN. FDA approved drugs complexed to their targets: evaluating pose prediction accuracy of docking protocols. J Mol Model 2012; 18:4263-74. [PMID: 22562231 DOI: 10.1007/s00894-012-1416-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Accepted: 03/26/2012] [Indexed: 11/29/2022]
Abstract
Efficient drug discovery programs can be designed by utilizing existing pools of knowledge from the already approved drugs. This can be achieved in one way by repositioning of drugs approved for some indications to newer indications. Complex of drug to its target gives fundamental insight into molecular recognition and a clear understanding of putative binding site. Five popular docking protocols, Glide, Gold, FlexX, Cdocker and LigandFit have been evaluated on a dataset of 199 FDA approved drug-target complexes for their accuracy in predicting the experimental pose. Performance for all the protocols is assessed at default settings, with root mean square deviation (RMSD) between the experimental ligand pose and the docked pose of less than 2.0 Å as the success criteria in predicting the pose. Glide (38.7 %) is found to be the most accurate in top ranked pose and Cdocker (58.8 %) in top RMSD pose. Ligand flexibility is a major bottleneck in failure of docking protocols to correctly predict the pose. Resolution of the crystal structure shows an inverse relationship with the performance of docking protocol. All the protocols perform optimally when a balanced type of hydrophilic and hydrophobic interaction or dominant hydrophilic interaction exists. Overall in 16 different target classes, hydrophobic interactions dominate in the binding site and maximum success is achieved for all the docking protocols in nuclear hormone receptor class while performance for the rest of the classes varied based on individual protocol.
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Affiliation(s)
- Mohammed H Bohari
- Molecular Modeling Group, Indian Institute of Chemical Technology, Hyderabad,, 500 607, Andhra Pradesh, India
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Chan DSH, Yang H, Kwan MHT, Cheng Z, Lee P, Bai LP, Jiang ZH, Wong CY, Fong WF, Leung CH, Ma DL. Structure-based optimization of FDA-approved drug methylene blue as a c-myc G-quadruplex DNA stabilizer. Biochimie 2011; 93:1055-64. [DOI: 10.1016/j.biochi.2011.02.013] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Accepted: 02/24/2011] [Indexed: 12/20/2022]
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