1
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Pahil KS, Gilman MSA, Baidin V, Clairfeuille T, Mattei P, Bieniossek C, Dey F, Muri D, Baettig R, Lobritz M, Bradley K, Kruse AC, Kahne D. A new antibiotic traps lipopolysaccharide in its intermembrane transporter. Nature 2024; 625:572-577. [PMID: 38172635 PMCID: PMC10794137 DOI: 10.1038/s41586-023-06799-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 10/30/2023] [Indexed: 01/05/2024]
Abstract
Gram-negative bacteria are extraordinarily difficult to kill because their cytoplasmic membrane is surrounded by an outer membrane that blocks the entry of most antibiotics. The impenetrable nature of the outer membrane is due to the presence of a large, amphipathic glycolipid called lipopolysaccharide (LPS) in its outer leaflet1. Assembly of the outer membrane requires transport of LPS across a protein bridge that spans from the cytoplasmic membrane to the cell surface. Maintaining outer membrane integrity is essential for bacterial cell viability, and its disruption can increase susceptibility to other antibiotics2-6. Thus, inhibitors of the seven lipopolysaccharide transport (Lpt) proteins that form this transenvelope transporter have long been sought. A new class of antibiotics that targets the LPS transport machine in Acinetobacter was recently identified. Here, using structural, biochemical and genetic approaches, we show that these antibiotics trap a substrate-bound conformation of the LPS transporter that stalls this machine. The inhibitors accomplish this by recognizing a composite binding site made up of both the Lpt transporter and its LPS substrate. Collectively, our findings identify an unusual mechanism of lipid transport inhibition, reveal a druggable conformation of the Lpt transporter and provide the foundation for extending this class of antibiotics to other Gram-negative pathogens.
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Affiliation(s)
- Karanbir S Pahil
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Morgan S A Gilman
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Vadim Baidin
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Thomas Clairfeuille
- Departments of Immunology, Infectious Disease and Ophthalmology (I2O), Medicinal Chemistry and Lead Discovery, Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Patrizio Mattei
- Departments of Immunology, Infectious Disease and Ophthalmology (I2O), Medicinal Chemistry and Lead Discovery, Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Christoph Bieniossek
- Departments of Immunology, Infectious Disease and Ophthalmology (I2O), Medicinal Chemistry and Lead Discovery, Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Fabian Dey
- Departments of Immunology, Infectious Disease and Ophthalmology (I2O), Medicinal Chemistry and Lead Discovery, Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Dieter Muri
- Departments of Immunology, Infectious Disease and Ophthalmology (I2O), Medicinal Chemistry and Lead Discovery, Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Remo Baettig
- Departments of Immunology, Infectious Disease and Ophthalmology (I2O), Medicinal Chemistry and Lead Discovery, Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Michael Lobritz
- Departments of Immunology, Infectious Disease and Ophthalmology (I2O), Medicinal Chemistry and Lead Discovery, Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Kenneth Bradley
- Departments of Immunology, Infectious Disease and Ophthalmology (I2O), Medicinal Chemistry and Lead Discovery, Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Andrew C Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
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2
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Anang S, Zhang S, Fritschi C, Chiu TJ, Yang D, Smith III AB, Madani N, Sodroski J. V3 tip determinants of susceptibility to inhibition by CD4-mimetic compounds in natural clade A human immunodeficiency virus (HIV-1) envelope glycoproteins. J Virol 2023; 97:e0117123. [PMID: 37888980 PMCID: PMC10688366 DOI: 10.1128/jvi.01171-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE CD4-mimetic compounds (CD4mcs) are small-molecule inhibitors of human immunodeficiency virus (HIV-1) entry into host cells. CD4mcs target a pocket on the viral envelope glycoprotein (Env) spike that is used for binding to the receptor, CD4, and is highly conserved among HIV-1 strains. Nonetheless, naturally occurring HIV-1 strains exhibit a wide range of sensitivities to CD4mcs. Our study identifies changes distant from the binding pocket that can influence the susceptibility of natural HIV-1 strains to the antiviral effects of multiple CD4mcs. We relate the antiviral potency of the CD4mc against this panel of HIV-1 variants to the ability of the CD4mc to activate entry-related changes in Env conformation prematurely. These findings will guide efforts to improve the potency and breadth of CD4mcs against natural HIV-1 variants.
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Affiliation(s)
- Saumya Anang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Shijian Zhang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Christopher Fritschi
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ta-Jung Chiu
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Derek Yang
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Amos B. Smith III
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Navid Madani
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
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3
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Duan Y, Zhou H, Liu X, Iketani S, Lin M, Zhang X, Bian Q, Wang H, Sun H, Hong SJ, Culbertson B, Mohri H, Luck MI, Zhu Y, Liu X, Lu Y, Yang X, Yang K, Sabo Y, Chavez A, Goff SP, Rao Z, Ho DD, Yang H. Molecular mechanisms of SARS-CoV-2 resistance to nirmatrelvir. Nature 2023; 622:376-382. [PMID: 37696289 DOI: 10.1038/s41586-023-06609-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 09/05/2023] [Indexed: 09/13/2023]
Abstract
Nirmatrelvir is a specific antiviral drug that targets the main protease (Mpro) of SARS-CoV-2 and has been approved to treat COVID-191,2. As an RNA virus characterized by high mutation rates, whether SARS-CoV-2 will develop resistance to nirmatrelvir is a question of concern. Our previous studies have shown that several mutational pathways confer resistance to nirmatrelvir, but some result in a loss of viral replicative fitness, which is then compensated for by additional alterations3. The molecular mechanisms for this observed resistance are unknown. Here we combined biochemical and structural methods to demonstrate that alterations at the substrate-binding pocket of Mpro can allow SARS-CoV-2 to develop resistance to nirmatrelvir in two distinct ways. Comprehensive studies of the structures of 14 Mpro mutants in complex with drugs or substrate revealed that alterations at the S1 and S4 subsites substantially decreased the level of inhibitor binding, whereas alterations at the S2 and S4' subsites unexpectedly increased protease activity. Both mechanisms contributed to nirmatrelvir resistance, with the latter compensating for the loss in enzymatic activity of the former, which in turn accounted for the restoration of viral replicative fitness, as observed previously3. Such a profile was also observed for ensitrelvir, another clinically relevant Mpro inhibitor. These results shed light on the mechanisms by which SARS-CoV-2 evolves to develop resistance to the current generation of protease inhibitors and provide the basis for the design of next-generation Mpro inhibitors.
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Affiliation(s)
- Yinkai Duan
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Clinical Research and Trial Center, Shanghai, China
| | - Hao Zhou
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Clinical Research and Trial Center, Shanghai, China
| | - Xiang Liu
- College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Sho Iketani
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Mengmeng Lin
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Xiaoyu Zhang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Clinical Research and Trial Center, Shanghai, China
- Lingang Laboratory, Shanghai, China
| | - Qucheng Bian
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Clinical Research and Trial Center, Shanghai, China
| | - Haofeng Wang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Clinical Research and Trial Center, Shanghai, China
| | - Haoran Sun
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Clinical Research and Trial Center, Shanghai, China
| | - Seo Jung Hong
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Bruce Culbertson
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Medical Scientist Training Program, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Hiroshi Mohri
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Maria I Luck
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Yan Zhu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Clinical Research and Trial Center, Shanghai, China
| | - Xiaoce Liu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Clinical Research and Trial Center, Shanghai, China
| | - Yuchi Lu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Clinical Research and Trial Center, Shanghai, China
- Lingang Laboratory, Shanghai, China
| | - Xiuna Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Clinical Research and Trial Center, Shanghai, China
| | - Kailin Yang
- Taussig Cancer Center, Cleveland Clinic, Cleveland, OH, USA
| | - Yosef Sabo
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Alejandro Chavez
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Stephen P Goff
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Zihe Rao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China
- Innovation Center for Pathogen Research, Guangzhou Laboratory, Guangzhou, China
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences and College of Pharmacy, Nankai University, Tianjin, China
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
| | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Shanghai Clinical Research and Trial Center, Shanghai, China.
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4
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Abstract
Type A γ-aminobutyric acid receptors (GABAARs) are the principal inhibitory receptors in the brain and the target of a wide range of clinical agents, including anaesthetics, sedatives, hypnotics and antidepressants1-3. However, our understanding of GABAAR pharmacology has been hindered by the vast number of pentameric assemblies that can be derived from 19 different subunits4 and the lack of structural knowledge of clinically relevant receptors. Here, we isolate native murine GABAAR assemblies containing the widely expressed α1 subunit and elucidate their structures in complex with drugs used to treat insomnia (zolpidem (ZOL) and flurazepam) and postpartum depression (the neurosteroid allopregnanolone (APG)). Using cryo-electron microscopy (cryo-EM) analysis and single-molecule photobleaching experiments, we uncover three major structural populations in the brain: the canonical α1β2γ2 receptor containing two α1 subunits, and two assemblies containing one α1 and either an α2 or α3 subunit, in which the single α1-containing receptors feature a more compact arrangement between the transmembrane and extracellular domains. Interestingly, APG is bound at the transmembrane α/β subunit interface, even when not added to the sample, revealing an important role for endogenous neurosteroids in modulating native GABAARs. Together with structurally engaged lipids, neurosteroids produce global conformational changes throughout the receptor that modify the ion channel pore and the binding sites for GABA and insomnia medications. Our data reveal the major α1-containing GABAAR assemblies, bound with endogenous neurosteroid, thus defining a structural landscape from which subtype-specific drugs can be developed.
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Affiliation(s)
- Chang Sun
- Vollum Institute, Oregon Health and Science University, Portland, OR, USA
| | - Hongtao Zhu
- Vollum Institute, Oregon Health and Science University, Portland, OR, USA
- Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Sarah Clark
- Vollum Institute, Oregon Health and Science University, Portland, OR, USA
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Eric Gouaux
- Vollum Institute, Oregon Health and Science University, Portland, OR, USA.
- Howard Hughes Medical Institute, Oregon Health and Science University, Portland, OR, USA.
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5
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Yang KB, Cameranesi M, Gowder M, Martinez C, Shamovsky Y, Epshtein V, Hao Z, Nguyen T, Nirenstein E, Shamovsky I, Rasouly A, Nudler E. High-resolution landscape of an antibiotic binding site. Nature 2023; 622:180-187. [PMID: 37648864 PMCID: PMC10550828 DOI: 10.1038/s41586-023-06495-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 07/28/2023] [Indexed: 09/01/2023]
Abstract
Antibiotic binding sites are located in important domains of essential enzymes and have been extensively studied in the context of resistance mutations; however, their study is limited by positive selection. Using multiplex genome engineering1 to overcome this constraint, we generate and characterize a collection of 760 single-residue mutants encompassing the entire rifampicin binding site of Escherichia coli RNA polymerase (RNAP). By genetically mapping drug-enzyme interactions, we identify an alpha helix where mutations considerably enhance or disrupt rifampicin binding. We find mutations in this region that prolong antibiotic binding, converting rifampicin from a bacteriostatic to bactericidal drug by inducing lethal DNA breaks. The latter are replication dependent, indicating that rifampicin kills by causing detrimental transcription-replication conflicts at promoters. We also identify additional binding site mutations that greatly increase the speed of RNAP.Fast RNAP depletes the cell of nucleotides, alters cell sensitivity to different antibiotics and provides a cold growth advantage. Finally, by mapping natural rpoB sequence diversity, we discover that functional rifampicin binding site mutations that alter RNAP properties or confer drug resistance occur frequently in nature.
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Affiliation(s)
- Kevin B Yang
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Maria Cameranesi
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Manjunath Gowder
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Criseyda Martinez
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Yosef Shamovsky
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Vitaliy Epshtein
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Zhitai Hao
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Thao Nguyen
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Eric Nirenstein
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Ilya Shamovsky
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Aviram Rasouly
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA.
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, USA.
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA.
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, USA.
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6
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Kher G, Sabin C, Lun JH, Devant JM, Ruoff K, Koromyslova AD, von Itzstein M, Pancera M, Hansman GS. Direct Blockade of the Norovirus Histo-Blood Group Antigen Binding Pocket by Nanobodies. J Virol 2023; 97:e0183322. [PMID: 36971561 PMCID: PMC10134814 DOI: 10.1128/jvi.01833-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 03/29/2023] Open
Abstract
Noroviruses are the leading cause of outbreaks of acute gastroenteritis. These viruses usually interact with histo-blood group antigens (HBGAs), which are considered essential cofactors for norovirus infection. This study structurally characterizes nanobodies developed against the clinically important GII.4 and GII.17 noroviruses with a focus on the identification of novel nanobodies that efficiently block the HBGA binding site. Using X-ray crystallography, we have characterized nine different nanobodies that bound to the top, side, or bottom of the P domain. The eight nanobodies that bound to the top or side of the P domain were mainly genotype specific, while one nanobody that bound to the bottom cross-reacted against several genotypes and showed HBGA blocking potential. The four nanobodies that bound to the top of the P domain also inhibited HBGA binding, and structural analysis revealed that these nanobodies interacted with several GII.4 and GII.17 P domain residues that commonly engaged HBGAs. Moreover, these nanobody complementarity-determining regions (CDRs) extended completely into the cofactor pockets and would likely impede HBGA engagement. The atomic level information for these nanobodies and their corresponding binding sites provide a valuable template for the discovery of additional "designer" nanobodies. These next-generation nanobodies would be designed to target other important genotypes and variants, while maintaining cofactor interference. Finally, our results clearly demonstrate for the first time that nanobodies directly targeting the HBGA binding site can function as potent norovirus inhibitors. IMPORTANCE Human noroviruses are highly contagious and a major problem in closed institutions, such as schools, hospitals, and cruise ships. Reducing norovirus infections is challenging on multiple levels and includes the frequent emergence of antigenic variants, which complicates designing effective, broadly reactive capsid therapeutics. We successfully developed and characterized four norovirus nanobodies that bound at the HBGA pockets. Compared with previously developed norovirus nanobodies that inhibited HBGA through disrupted particle stability, these four novel nanobodies directly inhibited HBGA engagement and interacted with HBGA binding residues. Importantly, these new nanobodies specifically target two genotypes that have caused the majority of outbreaks worldwide and consequently would have an enormous benefit if they could be further developed as norovirus therapeutics. To date, we have structurally characterized 16 different GII nanobody complexes, a number of which block HBGA binding. These structural data could be used to design multivalent nanobody constructs with improved inhibition properties.
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Affiliation(s)
- Gargi Kher
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Charles Sabin
- Schaller Research Group, University of Heidelberg, DKFZ, Heidelberg, Germany
- Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany
| | - Jennifer H. Lun
- Schaller Research Group, University of Heidelberg, DKFZ, Heidelberg, Germany
- Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany
| | - Jessica M. Devant
- Schaller Research Group, University of Heidelberg, DKFZ, Heidelberg, Germany
- Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany
| | - Kerstin Ruoff
- Schaller Research Group, University of Heidelberg, DKFZ, Heidelberg, Germany
- Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany
| | - Anna D. Koromyslova
- Schaller Research Group, University of Heidelberg, DKFZ, Heidelberg, Germany
- Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany
| | - Mark von Itzstein
- Institute for Glycomics, Griffith University, Gold Coast Campus, Gold Coast, Queensland, Australia
| | - Marie Pancera
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Grant S. Hansman
- Schaller Research Group, University of Heidelberg, DKFZ, Heidelberg, Germany
- Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany
- Institute for Glycomics, Griffith University, Gold Coast Campus, Gold Coast, Queensland, Australia
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7
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Perner F, Stein EM, Wenge DV, Singh S, Kim J, Apazidis A, Rahnamoun H, Anand D, Marinaccio C, Hatton C, Wen Y, Stone RM, Schaller D, Mowla S, Xiao W, Gamlen HA, Stonestrom AJ, Persaud S, Ener E, Cutler JA, Doench JG, McGeehan GM, Volkamer A, Chodera JD, Nowak RP, Fischer ES, Levine RL, Armstrong SA, Cai SF. MEN1 mutations mediate clinical resistance to menin inhibition. Nature 2023; 615:913-919. [PMID: 36922589 PMCID: PMC10157896 DOI: 10.1038/s41586-023-05755-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 01/24/2023] [Indexed: 03/17/2023]
Abstract
Chromatin-binding proteins are critical regulators of cell state in haematopoiesis1,2. Acute leukaemias driven by rearrangement of the mixed lineage leukaemia 1 gene (KMT2Ar) or mutation of the nucleophosmin gene (NPM1) require the chromatin adapter protein menin, encoded by the MEN1 gene, to sustain aberrant leukaemogenic gene expression programs3-5. In a phase 1 first-in-human clinical trial, the menin inhibitor revumenib, which is designed to disrupt the menin-MLL1 interaction, induced clinical responses in patients with leukaemia with KMT2Ar or mutated NPM1 (ref. 6). Here we identified somatic mutations in MEN1 at the revumenib-menin interface in patients with acquired resistance to menin inhibition. Consistent with the genetic data in patients, inhibitor-menin interface mutations represent a conserved mechanism of therapeutic resistance in xenograft models and in an unbiased base-editor screen. These mutants attenuate drug-target binding by generating structural perturbations that impact small-molecule binding but not the interaction with the natural ligand MLL1, and prevent inhibitor-induced eviction of menin and MLL1 from chromatin. To our knowledge, this study is the first to demonstrate that a chromatin-targeting therapeutic drug exerts sufficient selection pressure in patients to drive the evolution of escape mutants that lead to sustained chromatin occupancy, suggesting a common mechanism of therapeutic resistance.
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Affiliation(s)
- Florian Perner
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Internal Medicine C, University Medicine Greifswald, Greifswald, Germany
| | - Eytan M Stein
- Leukemia Service, Department of Medicine, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniela V Wenge
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Sukrit Singh
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jeonghyeon Kim
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Athina Apazidis
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Homa Rahnamoun
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Disha Anand
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Internal Medicine C, University Medicine Greifswald, Greifswald, Germany
| | - Christian Marinaccio
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Charlie Hatton
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Yanhe Wen
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Richard M Stone
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David Schaller
- In silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Shoron Mowla
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wenbin Xiao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Hematopathology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Holly A Gamlen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Aaron J Stonestrom
- Leukemia Service, Department of Medicine, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sonali Persaud
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elizabeth Ener
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jevon A Cutler
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - John G Doench
- Genetic Perturbation Platform, Broad Institute, Cambridge, MA, USA
| | | | - Andrea Volkamer
- In silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - John D Chodera
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Radosław P Nowak
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Ross L Levine
- Leukemia Service, Department of Medicine, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Scott A Armstrong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Sheng F Cai
- Leukemia Service, Department of Medicine, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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8
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Shen Z, Ratia K, Cooper L, Kong D, Lee H, Kwon Y, Li Y, Alqarni S, Huang F, Dubrovskyi O, Rong L, Thatcher G, Xiong R. Design of SARS-CoV-2 PLpro Inhibitors for COVID-19 Antiviral Therapy Leveraging Binding Cooperativity. J Med Chem 2022; 65:2940-2955. [PMID: 34665619 PMCID: PMC8547495 DOI: 10.1021/acs.jmedchem.1c01307] [Citation(s) in RCA: 81] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Indexed: 12/29/2022]
Abstract
Antiviral agents that complement vaccination are urgently needed to end the COVID-19 pandemic. The SARS-CoV-2 papain-like protease (PLpro), one of only two essential cysteine proteases that regulate viral replication, also dysregulates host immune sensing by binding and deubiquitination of host protein substrates. PLpro is a promising therapeutic target, albeit challenging owing to featureless P1 and P2 sites recognizing glycine. To overcome this challenge, we leveraged the cooperativity of multiple shallow binding sites on the PLpro surface, yielding novel 2-phenylthiophenes with nanomolar inhibitory potency. New cocrystal structures confirmed that ligand binding induces new interactions with PLpro: by closing of the BL2 loop of PLpro forming a novel "BL2 groove" and by mimicking the binding interaction of ubiquitin with Glu167 of PLpro. Together, this binding cooperativity translates to the most potent PLpro inhibitors reported to date, with slow off-rates, improved binding affinities, and low micromolar antiviral potency in SARS-CoV-2-infected human cells.
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Affiliation(s)
- Zhengnan Shen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
- UICentre (Drug Discovery @ UIC), University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
- Department of Pharmacology & Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ, 85721, USA
| | - Kiira Ratia
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
- Research Resources Center, University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
| | - Laura Cooper
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
- Department of Microbiology, College of Medicine, University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
| | - Deyu Kong
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
- UICentre (Drug Discovery @ UIC), University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
| | - Hyun Lee
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
- Research Resources Center, University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
| | - Youngjin Kwon
- Research Resources Center, University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
| | - Yangfeng Li
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
- UICentre (Drug Discovery @ UIC), University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
| | - Saad Alqarni
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
| | - Fei Huang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
- UICentre (Drug Discovery @ UIC), University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
| | - Oleksii Dubrovskyi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
- UICentre (Drug Discovery @ UIC), University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
| | - Lijun Rong
- Department of Microbiology, College of Medicine, University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
| | - Gregory Thatcher
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
- Department of Pharmacology & Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ, 85721, USA
| | - Rui Xiong
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
- UICentre (Drug Discovery @ UIC), University of Illinois at Chicago (UIC), Chicago, IL, 60612, USA
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9
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O’Connor S, Le Bihan YV, Westwood IM, Liu M, Mak OW, Zazeri G, Povinelli APR, Jones AM, van Montfort R, Reynisson J, Collins I. Discovery and Characterization of a Cryptic Secondary Binding Site in the Molecular Chaperone HSP70. Molecules 2022; 27:817. [PMID: 35164081 PMCID: PMC8839746 DOI: 10.3390/molecules27030817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/19/2022] [Accepted: 01/24/2022] [Indexed: 12/23/2022] Open
Abstract
Heat Shock Protein 70s (HSP70s) are key molecular chaperones that are overexpressed in many cancers and often associated with metastasis and poor prognosis. It has proven difficult to develop ATP-competitive, drug-like small molecule inhibitors of HSP70s due to the flexible and hydrophilic nature of the HSP70 ATP-binding site and its high affinity for endogenous nucleotides. The aim of this study was to explore the potential for the inhibition of HSP70 through alternative binding sites using fragment-based approaches. A surface plasmon resonance (SPR) fragment screen designed to detect secondary binding sites in HSP70 led to the identification by X-ray crystallography of a cryptic binding site in the nucleotide-binding domain (NBD) of HSP70 adjacent to the ATP-binding site. Fragment binding was confirmed and characterized as ATP-competitive using SPR and ligand-observed NMR methods. Molecular dynamics simulations were applied to understand the interactions with the protein upon ligand binding, and local secondary structure changes consistent with interconversion between the observed crystal structures with and without the cryptic pocket were detected. A virtual high-throughput screen (vHTS) against the cryptic pocket was conducted, and five compounds with diverse chemical scaffolds were confirmed to bind to HSP70 with micromolar affinity by SPR. These results identified and characterized a new targetable site on HSP70. While targeting HSP70 remains challenging, the new site may provide opportunities to develop allosteric ATP-competitive inhibitors with differentiated physicochemical properties from current series.
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Affiliation(s)
- Suzanne O’Connor
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, UK; (S.O.); (Y.-V.L.B.); (I.M.W.); (M.L.); (R.v.M.)
| | - Yann-Vaï Le Bihan
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, UK; (S.O.); (Y.-V.L.B.); (I.M.W.); (M.L.); (R.v.M.)
| | - Isaac M. Westwood
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, UK; (S.O.); (Y.-V.L.B.); (I.M.W.); (M.L.); (R.v.M.)
| | - Manjuan Liu
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, UK; (S.O.); (Y.-V.L.B.); (I.M.W.); (M.L.); (R.v.M.)
| | - Oi Wei Mak
- School of Pharmacy and Bioengineering, Keele University, Keele ST5 5BG, UK; (O.W.M.); (J.R.)
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Gabriel Zazeri
- School of Pharmacy, Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; (G.Z.); (A.P.R.P.); (A.M.J.)
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas (IBILCE), UNESP, Rua Cristovão Colombo 2265, São José do Rio Preto 15054-000, Brazil
| | - Ana P. R. Povinelli
- School of Pharmacy, Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; (G.Z.); (A.P.R.P.); (A.M.J.)
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas (IBILCE), UNESP, Rua Cristovão Colombo 2265, São José do Rio Preto 15054-000, Brazil
| | - Alan M. Jones
- School of Pharmacy, Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; (G.Z.); (A.P.R.P.); (A.M.J.)
| | - Rob van Montfort
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, UK; (S.O.); (Y.-V.L.B.); (I.M.W.); (M.L.); (R.v.M.)
| | - Jóhannes Reynisson
- School of Pharmacy and Bioengineering, Keele University, Keele ST5 5BG, UK; (O.W.M.); (J.R.)
| | - Ian Collins
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, UK; (S.O.); (Y.-V.L.B.); (I.M.W.); (M.L.); (R.v.M.)
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10
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Bienstein M, Minond D, Schwaneberg U, Davari MD, Yildiz D. In Silico and Experimental ADAM17 Kinetic Modeling as Basis for Future Screening System for Modulators. Int J Mol Sci 2022; 23:ijms23031368. [PMID: 35163294 PMCID: PMC8835787 DOI: 10.3390/ijms23031368] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/12/2022] [Accepted: 01/23/2022] [Indexed: 11/21/2022] Open
Abstract
Understanding the mechanisms of modulators’ action on enzymes is crucial for optimizing and designing pharmaceutical substances. The acute inflammatory response, in particular, is regulated mainly by a disintegrin and metalloproteinase (ADAM) 17. ADAM17 processes several disease mediators such as TNFα and APP, releasing their soluble ectodomains (shedding). A malfunction of this process leads to a disturbed inflammatory response. Chemical protease inhibitors such as TAPI-1 were used in the past to inhibit ADAM17 proteolytic activity. However, due to ADAM17′s broad expression and activity profile, the development of active-site-directed ADAM17 inhibitor was discontinued. New ‘exosite’ (secondary substrate binding site) inhibitors with substrate selectivity raised the hope of a substrate-selective modulation as a promising approach for inflammatory disease therapy. This work aimed to develop a high-throughput screen for potential ADAM17 modulators as therapeutic drugs. By combining experimental and in silico methods (structural modeling and docking), we modeled the kinetics of ADAM17 inhibitor. The results explain ADAM17 inhibition mechanisms and give a methodology for studying selective inhibition towards the design of pharmaceutical substances with higher selectivity.
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Affiliation(s)
- Marian Bienstein
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany; (M.B.); (U.S.)
| | - Dmitriy Minond
- College of Pharmacy, Nova Southeastern University, Fort Lauderdale, FL 33314, USA;
- Rumbaugh-Goodwin Institute for Cancer Research, Nova Southeastern University, Fort Lauderdale, FL 33314, USA
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany; (M.B.); (U.S.)
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52056 Aachen, Germany
| | - Mehdi D. Davari
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
- Correspondence: (M.D.D.); (D.Y.)
| | - Daniela Yildiz
- Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Center for Human and Molecular Biology (ZHMB), University of Saarland, Kirrbergerstr., 66421 Homburg, Germany
- Correspondence: (M.D.D.); (D.Y.)
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11
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Muchiri RN, Kibitel J, Redick MA, van Breemen RB. Advances in Magnetic Microbead Affinity Selection Screening: Discovery of Natural Ligands to the SARS-CoV-2 Spike Protein. J Am Soc Mass Spectrom 2022; 33:181-188. [PMID: 34939787 PMCID: PMC9429804 DOI: 10.1021/jasms.1c00318] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Affinity selection-mass spectrometry, which includes magnetic microbead affinity selection-screening (MagMASS), is ideal for the discovery of ligands in complex mixtures that bind to pharmacological targets. Therapeutic agents are needed to prevent or treat COVID-19, which is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Infection of human cells by SARS-CoV-2 involves binding of the virus spike protein subunit 1 (S1) to the human cell receptor angiotensin converting enzyme-2 (ACE2). Like antibodies, small molecules have the potential to block the interaction of the viral S1 protein with human ACE2 and prevent SARS-CoV-2 infection. Therefore, a MagMASS assay was developed for the discovery of ligands to the S1 protein. Unlike previous MagMASS approaches, this new assay used robotics for 5-fold enhancement of throughput and sensitivity. The assay was validated using the SBP-1 peptide, which is identical to the ACE2 amino acid sequence recognized by the S1 protein, and then applied to the discovery of natural ligands from botanical extracts. Small molecule ligands to the S1 protein were discovered in extracts of the licorice species, Glycyrrhiza inflata. In particular, the licorice ligand licochalcone A was identified through dereplication and comparison with standards using HPLC with high-resolution tandem mass spectrometry.
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Affiliation(s)
- Ruth N. Muchiri
- Linus Pauling Institute and College of Pharmacy, Oregon State University, Corvallis, OR 97331 USA
| | | | - Margaret A. Redick
- Linus Pauling Institute and College of Pharmacy, Oregon State University, Corvallis, OR 97331 USA
| | - Richard B. van Breemen
- Linus Pauling Institute and College of Pharmacy, Oregon State University, Corvallis, OR 97331 USA
- Corresponding author: 373 Linus Pauling Science Center, Corvallis, OR 97331 USA, TEL: 541-737-5080,
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12
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Pinos D, Wang Y, Hernández-Martínez P, He K, Ferré J. Alteration of a Cry1A Shared Binding Site in a Cry1Ab-Selected Colony of Ostrinia furnacalis. Toxins (Basel) 2022; 14:toxins14010032. [PMID: 35051009 PMCID: PMC8779817 DOI: 10.3390/toxins14010032] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/15/2021] [Accepted: 12/24/2021] [Indexed: 12/10/2022] Open
Abstract
The Asian corn borer, Ostrinia furnacalis (Guenée, 1854), is a highly damaging pest in Asia and the Pacific islands, and larvae feed mainly from corn crops. To determine the suitability of Bt-corn technology for the future control of this pest, understanding the potential to develop resistance to Cry1Ab and the basis of cross-resistance to other Cry1 proteins is of great interest. Here, we have explored the binding of Cry1A proteins to brush border membrane vesicles from two O. furnacalis colonies, one susceptible (ACB-BtS) and one laboratory-selected with Cry1Ab (ACB-AbR). The insects developed resistance to Cry1Ab and showed cross-resistance to Cry1Aa, Cry1Ac, and Cry1F. Binding assays with radiolabeled Cry1Ab and brush border membrane vesicles from susceptible insects showed that Cry1A proteins shared binding sites, though the results were not conclusive for Cry1F. The results were confirmed using radiolabeled Cry1Aa. The resistant insects showed a reduction of the specific binding of both Cry1Ab and Cry1Aa, suggesting that part of the binding sites were lost or altered. Competition binding assays showed full competition between Cry1Ab and Cry1Aa proteins in the susceptible colony but only partial competition in resistant insects, confirming the alteration of some, but not all, binding sites for these two proteins. The binding site model for Cry1A proteins in O. furnacalis is in agreement with the occurrence of multiple membrane receptors for these proteins.
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Affiliation(s)
- Daniel Pinos
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Deparment of Genetics, Universitat de València, 46100 Burjassot, Spain; (D.P.); (P.H.-M.)
| | - Yueqin Wang
- The State Key Laboratory for Biology of Plant Diseas and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Y.W.); (K.H.)
| | - Patricia Hernández-Martínez
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Deparment of Genetics, Universitat de València, 46100 Burjassot, Spain; (D.P.); (P.H.-M.)
| | - Kanglai He
- The State Key Laboratory for Biology of Plant Diseas and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Y.W.); (K.H.)
| | - Juan Ferré
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Deparment of Genetics, Universitat de València, 46100 Burjassot, Spain; (D.P.); (P.H.-M.)
- Correspondence:
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13
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Pang JP, Shen C, Zhou WF, Wang YX, Shan LH, Chai X, Shao Y, Hu XP, Zhu F, Zhu DY, Xiao L, Xu L, Xu XH, Li D, Hou TJ. Discovery of novel antagonists targeting the DNA binding domain of androgen receptor by integrated docking-based virtual screening and bioassays. Acta Pharmacol Sin 2022; 43:229-239. [PMID: 33767381 PMCID: PMC8724294 DOI: 10.1038/s41401-021-00632-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/24/2021] [Indexed: 02/01/2023] Open
Abstract
Androgen receptor (AR), a ligand-activated transcription factor, is a master regulator in the development and progress of prostate cancer (PCa). A major challenge for the clinically used AR antagonists is the rapid emergence of resistance induced by the mutations at AR ligand binding domain (LBD), and therefore the discovery of novel anti-AR therapeutics that can combat mutation-induced resistance is quite demanding. Therein, blocking the interaction between AR and DNA represents an innovative strategy. However, the hits confirmed targeting on it so far are all structurally based on a sole chemical scaffold. In this study, an integrated docking-based virtual screening (VS) strategy based on the crystal structure of the DNA binding domain (DBD) of AR was conducted to search for novel AR antagonists with new scaffolds and 2-(2-butyl-1,3-dioxoisoindoline-5-carboxamido)-4,5-dimethoxybenzoicacid (Cpd39) was identified as a potential hit, which was competent to block the binding of AR DBD to DNA and showed decent potency against AR transcriptional activity. Furthermore, Cpd39 was safe and capable of effectively inhibiting the proliferation of PCa cell lines (i.e., LNCaP, PC3, DU145, and 22RV1) and reducing the expression of the genes regulated by not only the full-length AR but also the splice variant AR-V7. The novel AR DBD-ARE blocker Cpd39 could serve as a starting point for the development of new therapeutics for castration-resistant PCa.
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Affiliation(s)
- Jin-Ping Pang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chao Shen
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Wen-Fang Zhou
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yun-Xia Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Lu-Hu Shan
- Institute of Cancer Research and Basic Medical Sciences of Chinese Academy of Sciences, Cancer Hospital of University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, 310022, China
| | - Xin Chai
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ying Shao
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xue-Ping Hu
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Feng Zhu
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Dan-Yan Zhu
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Li Xiao
- School of Life Science, Huzhou University, Huzhou, 313000, China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, 213001, China
| | - Xiao-Hong Xu
- Institute of Cancer Research and Basic Medical Sciences of Chinese Academy of Sciences, Cancer Hospital of University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, 310022, China
| | - Dan Li
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Ting-Jun Hou
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
- State Key Lab of CAD & CG, Zhejiang University, Hangzhou, 310058, China.
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14
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Choi J, Tark D, Lim YS, Hwang SB. Identification of African Swine Fever Virus Inhibitors through High Performance Virtual Screening Using Machine Learning. Int J Mol Sci 2021; 22:ijms222413414. [PMID: 34948216 PMCID: PMC8703626 DOI: 10.3390/ijms222413414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/08/2021] [Accepted: 12/10/2021] [Indexed: 11/21/2022] Open
Abstract
African swine fever virus (ASFV) is a highly contagious virus that causes severe hemorrhagic viral disease resulting in high mortality in domestic and wild pigs, until few antiviral agents can inhibit ASFV infections. Thus, new anti-ASFV drugs need to be urgently identified. Recently, we identified pentagastrin as a potential antiviral drug against ASFVs using molecular docking and machine learning models. However, the scoring functions are easily influenced by properties of protein pockets, resulting in a scoring bias. Here, we employed the 5′-P binding pocket of AsfvPolX as a potential binding site to identify antiviral drugs and classified 13 AsfvPolX structures into three classes based on pocket parameters calculated by the SiteMap module. We then applied principal component analysis to eliminate this scoring bias, which was effective in making the SP Glide score more balanced between 13 AsfvPolX structures in the dataset. As a result, we identified cangrelor and fostamatinib as potential antiviral drugs against ASFVs. Furthermore, the classification of the pocket properties of AsfvPolX protein can provide an alternative approach to identify novel antiviral drugs by optimizing the scoring function of the docking programs. Here, we report a machine learning-based novel approach to generate high binding affinity compounds that are individually matched to the available classification of the pocket properties of AsfvPolX protein.
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Affiliation(s)
- Jiwon Choi
- College of Pharmacy, Dongduk Women’s University, Seoul 02748, Korea
- Correspondence: (J.C.); (Y.-S.L.); Tel.: +82-2-940-4516 (J.C.); +82-63-900-4076 (Y.-S.L.); Fax: +82-2-940-4195 (J.C.); +82-63-900-4012 (Y.-S.L.)
| | - Dongseob Tark
- Laboratory for Infectious Disease Prevention, Korea Zoonosis Research Institute, Jeonbuk National University, Iksan 54596, Korea;
| | - Yun-Sook Lim
- Laboratory of RNA Viral Diseases, Korea Zoonosis Research Institute, Jeonbuk National University, Iksan 54596, Korea;
- Correspondence: (J.C.); (Y.-S.L.); Tel.: +82-2-940-4516 (J.C.); +82-63-900-4076 (Y.-S.L.); Fax: +82-2-940-4195 (J.C.); +82-63-900-4012 (Y.-S.L.)
| | - Soon B. Hwang
- Laboratory of RNA Viral Diseases, Korea Zoonosis Research Institute, Jeonbuk National University, Iksan 54596, Korea;
- Ilsong Institute of Life Science, Hallym University, Seoul 07247, Korea
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15
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Wang H, Nie X, You W, Huang W, Chen G, Gao F, Xia L, Zhang L, Wang L, Shen AZ, Wu KL, Ding SG, You YZ. Tug-of-War between Covalent Binding and Electrostatic Interaction Effectively Killing E. coli without Detectable Resistance. ACS Appl Mater Interfaces 2021; 13:56838-56849. [PMID: 34816709 DOI: 10.1021/acsami.1c15868] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Antimicrobial resistance in Gram-negative bacteria has become one of the leading causes of morbidity and mortality and a serious worldwide public health concern due to the fact that Gram-negative bacteria have an additional outer membrane protecting them from an unwanted compound invading. It is still very difficult for antimicrobials to reach intracellular targets and very challenging to treat Gram-negative bacteria with the current strategies. Here, we found that (o-(bromomethyl)phenyl)boronic acid was incorporated into poly((2-N,N-diethyl)aminoethyl acrylate) (PDEA), forming a copolymer (poly(o-Bn-DEA)) having both phenylboronic acid (B) and ((2-N,N-diethyl)amino) (DEA) units. Poly(o-Bn-DEA) exhibits very strong intramolecular B-N coordination, which could highly promote the covalent binding of phenylboronic acid with lipopolysaccharide (LPS) on the outer membrane of E. coli and lodge poly(o-Bn-DEA) on the LPS layer on the surface of E. coli. Meanwhile, the strong electrostatic interaction between poly(o-Bn-DEA) and the negatively charged lipid preferred tugging the poly(o-Bn-DEA) into the lipid bilayer of E. coli. The combating interactions between covalent binding and electrostatic interaction form a tug-of-war action, which could trigger the lysis of the outer membrane, thereby killing Gram-negative E. coli effectively without detectable resistance.
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Affiliation(s)
- Haili Wang
- The Department of Pharmacy, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xuan Nie
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Wei You
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Weiqiang Huang
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Guang Chen
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Fan Gao
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Lei Xia
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Lei Zhang
- The Department of Pharmacy, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
| | - Longhai Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Ai-Zong Shen
- The Department of Pharmacy, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
| | - Kai-Le Wu
- Department of Otolaryngology Head & Neck Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China
| | - Sheng-Gang Ding
- Department of Pediatrics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China
| | - Ye-Zi You
- The Department of Pharmacy, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
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Zloh M, Gupta M, Parish T, Brucoli F. Novel C-3-(N-alkyl-aryl)-aminomethyl rifamycin SV derivatives exhibit activity against rifampicin-resistant Mycobacterium tuberculosis RpoB S522L strain and display a different binding mode at the RNAP β-subunit site compared to rifampicin. Eur J Med Chem 2021; 225:113734. [PMID: 34418786 DOI: 10.1016/j.ejmech.2021.113734] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 07/26/2021] [Accepted: 07/28/2021] [Indexed: 11/16/2022]
Abstract
Antimicrobial resistance is a main concern in tuberculosis treatment and is often associated with the emergence of Mycobacterium tuberculosis strains resistant to rifampicin (RIF), which is one of the cornerstones of tuberculosis chemotherapy. In this study, aminoalkyl-aromatic ring tails were appended to the C3 position of rifamycin core to assess the role of C3 substitutions to the anti-mycobacterial activity of the rifamycin antibiotics. The typical hydrazone unit of RIF was replaced by an amino-alkyl linkage to connect the aromatic ring tails with the rifamycin naphthoquinone core. Eight novel C3-(N-alkyl-aryl)-aminoalkyl analogues of rifamycin SV were synthesised and screened in vitro against wild-type HR37Rv and "hypervirulent" HN-878 strains, and a panel of rifampicin-resistant M. tuberculosis clinical isolates carrying mutations at the 522, 531 and 455 positions of the rpoB gene (RpoBS522L, RpoBS531L and RpoBH455D strains). The analogues exhibited anti-tubercular activity against H37Rv and HN-878 at submicromolar or nanomolar concentrations, and against clinical H37Rv isolates bearing the S522L mutations at low micromolar concentration. Benzylamine moiety-including analogue 8 was as active as rifampicin against HN-878 with a MIC90 value of 0.02 μM, whereas 14 and 15, which included tryptamine and para-methyl-sulfonylbenzylamine C3-substituents, respectively, showed higher anti-tubercular activity (MIC90 = 3 μM) compared to rifampicin against the S522L mutated H37Rv strain. Detailed in silico analysis of different RNAP molecular systems predicted a distinct, possibly novel, binding mode for the new rifamycin analogues. These were found to occupy a different space in the binding pockets of both wild type and mutated RNAP proteins compared to that of rifampicin. Moreover, the molecular modelling experiments investigated the ability of the novel analogues aromatic tails to establish key interactions at the RNAP binding site. These interesting findings might pave the way for generating rifamycin analogues that can overcome anti-microbial resistance in M. tuberculosis.
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Affiliation(s)
- Mire Zloh
- Faculty of Pharmacy, University Business Academy, Novi Sad, 2100, Serbia; UCL School of Pharmacy, UCL, London, WC1N 1AX, UK
| | - Megha Gupta
- Infectious Disease Research Institute, 1616 Eastlake Ave E, Suite 400, Seattle, WA, 98102, USA
| | - Tanya Parish
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, USA
| | - Federico Brucoli
- Leicester School of Pharmacy, De Montfort University, Leicester, LE1 9BH, UK.
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Gu W, Martinez S, Singh AK, Nguyen H, Rozenski J, Schols D, Herdewijn P, Das K, De Jonghe S. Exploring the dNTP -binding site of HIV-1 reverse transcriptase for inhibitor design. Eur J Med Chem 2021; 225:113785. [PMID: 34425311 DOI: 10.1016/j.ejmech.2021.113785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/13/2021] [Accepted: 08/14/2021] [Indexed: 11/17/2022]
Abstract
HIV-1 reverse transcriptase (RT) plays a central role in the viral life cycle, and roughly half of the FDA-approved anti-HIV drugs are targeting RT. Nucleoside analogs (NRTIs) require cellular phosphorylation for binding to RT, and to bypass this rate-limiting path, we designed a new series of acyclic nucleoside phosphonate analogs as nucleoside triphosphate mimics, aiming at the chelation of the catalytic Mg2+ ions via a phosphonate and/or a carboxylic acid group. Novel synthetic procedures were developed to access these nucleoside phosphonate analogs. X-ray structures in complex with HIV-1 RT/dsDNA demonstrated that their binding modes are distinct from that of our previously reported compound series. The impact of chain length, chirality and linker atom have been discussed. The detailed structural understanding of these new compounds provides opportunities for designing new class of HIV-1 RT inhibitors.
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Affiliation(s)
- Weijie Gu
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, 3000, Leuven, Belgium; KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Laboratory of Medicinal Chemistry, Herestraat 49, 3000, Leuven, Belgium
| | - Sergio Martinez
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, 3000, Leuven, Belgium
| | - Abhimanyu K Singh
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, 3000, Leuven, Belgium
| | - Hoai Nguyen
- KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Laboratory of Medicinal Chemistry, Herestraat 49, 3000, Leuven, Belgium
| | - Jef Rozenski
- KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Laboratory of Medicinal Chemistry, Herestraat 49, 3000, Leuven, Belgium
| | - Dominique Schols
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, 3000, Leuven, Belgium
| | - Piet Herdewijn
- KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Laboratory of Medicinal Chemistry, Herestraat 49, 3000, Leuven, Belgium
| | - Kalyan Das
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, 3000, Leuven, Belgium.
| | - Steven De Jonghe
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, 3000, Leuven, Belgium.
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Sohraby F, Aryapour H. Reconstruction of the binding pathway of an anti-HIV drug, Indinavir, in complex with the HTLV-1 protease using unaggregated unbiased molecular dynamics simulation. Comput Biol Chem 2021; 96:107616. [PMID: 34883394 DOI: 10.1016/j.compbiolchem.2021.107616] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 11/16/2021] [Accepted: 12/02/2021] [Indexed: 12/13/2022]
Abstract
Retroviruses are a growing concern for the health of human beings, and one of the dangerous members of this family is the Human T-cell Leukemia Virus 1 (HTLV-1) virus. It has affected more than 20 million people so far, and since there are no registered treatments against it yet, urgent treatment solutions are needed. One of the most promising drug targets to fight this virus is the protease enzyme of the virus's protein machinery. In this study, by utilizing a computational method called Unaggregated Unbiased Molecular Dynamics (UUMD), we reconstructed the binding pathway of a HTLV-1 protease inhibitor, Indinavir, to find the details of the binding pathway, the influential residues, and also the stable states of the binding pathway. We achieved the native conformation of the inhibitor in 6 rounds, 360 replicas by performing over 4 micro-seconds of UMD simulations. We found 3 Intermediate states between the solvated state and the native conformation state in the binding pathway. We also discovered that aromatic residues such as Trp98 and Trp98', catalytic residues Asp32 and Asp32', and the flap region's residues have the most influential roles in the binding pathway and also have the most contribution to the total interaction energies. We believe that the details found in this study would be a great guide for developing new treatment solutions against the HTLV-1 virus by inhibiting the HTLV-1 protease.
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Affiliation(s)
- Farzin Sohraby
- Department of Biology, Faculty of Science, Golestan University, Gorgan, Iran
| | - Hassan Aryapour
- Department of Biology, Faculty of Science, Golestan University, Gorgan, Iran.
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Cornejo A, Caballero J, Simirgiotis M, Torres V, Sánchez L, Díaz N, Guimaraes M, Hernández M, Areche C, Alfaro S, Caballero L, Melo F. Dammarane triterpenes targeting α-synuclein: biological activity and evaluation of binding sites by molecular docking. J Enzyme Inhib Med Chem 2021; 36:154-162. [PMID: 33307873 PMCID: PMC7738290 DOI: 10.1080/14756366.2020.1851216] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 01/09/2023] Open
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder that affects adult people whose treatment is palliative. Thus, we decided to test three dammarane triterpenes 1, 1a, 1b, and we determined that 1 and 1a inhibit β-aggregation through thioflavine T rather than 1b. Since compound 1 was most active, we determined the interaction between α-synuclein and 1 at 50 µM (Kd) through microscale thermophoresis. Also, we observed differences in height and diameter of aggregates, and α-synuclein remains unfolded in the presence of 1. Also, aggregates treated with 1 do not provoke neurites' retraction in N2a cells previously induced by retinoic acid. Finally, we studied the potential sites of interaction between 1 with α-synuclein fibrils using molecular modelling. Docking experiments suggest that 1 preferably interact with the site 2 of α-synuclein through hydrogen bonds with residues Y39 and T44.
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Affiliation(s)
- Alberto Cornejo
- Escuela de Tecnología Médica, Facultad de Medicina, Universidad Andres Bello, Laboratorio Catem V, Santiago, Chile
| | - Julio Caballero
- Departamento de Bioinformática, Facultad de Ingeniería, Centro de Bioinformática, Simulación y Modelado (CBSM), Universidad de Talca, Talca, Chile
| | - Mario Simirgiotis
- Facultad de Ciencias, Instituto de Farmacia, Universidad Austral de Chile, Valdivia, Chile
| | - Vanessa Torres
- Escuela de Tecnología Médica, Facultad de Medicina, Universidad Andres Bello, Laboratorio Catem V, Santiago, Chile
| | - Luisa Sánchez
- Escuela de Tecnología Médica, Facultad de Medicina, Universidad Andres Bello, Laboratorio Catem V, Santiago, Chile
| | - Nicolás Díaz
- Escuela de Tecnología Médica, Facultad de Medicina, Universidad Andres Bello, Laboratorio Catem V, Santiago, Chile
| | - Marcela Guimaraes
- Department of Science and Technology, Federal University of São Paulo, São José dos Campos, Brazil
| | - Marcos Hernández
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Carlos Areche
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Sergio Alfaro
- Doctorado en Ciencias, mención Modelado de Sistemas Químicos y Biológicos, Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, Talca, Chile
| | - Leonardo Caballero
- Departamento de Física and Soft Matter Research Center, SMAT-C, Universidad de Santiago, Santiago, Chile
| | - Francisco Melo
- Departamento de Física and Soft Matter Research Center, SMAT-C, Universidad de Santiago, Santiago, Chile
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Hagras M, El Deeb MA, Elzahabi HSA, Elkaeed EB, Mehany ABM, Eissa IH. Discovery of new quinolines as potent colchicine binding site inhibitors: design, synthesis, docking studies, and anti-proliferative evaluation. J Enzyme Inhib Med Chem 2021; 36:640-658. [PMID: 33588683 PMCID: PMC7889231 DOI: 10.1080/14756366.2021.1883598] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 12/26/2020] [Accepted: 01/25/2021] [Indexed: 01/03/2023] Open
Abstract
Discovering of new anticancer agents with potential activity against tubulin polymerisation is still a promising approach. Colchicine binding site inhibitors are the most relevant anti-tubulin polymerisation agents. Thus, new quinoline derivatives have been designed and synthesised to possess the same essential pharmacophoric features of colchicine binding site inhibitors. The synthesised compounds were tested in vitro against a panel of three human cancer cell lines (HepG-2, HCT-116, and MCF-7) using colchicine as a positive control. Comparing to colchicine (IC50 = 7.40, 9.32, and 10.41 µM against HepG-2, HCT-116, and MCF-7, respectively), compounds 20, 21, 22, 23, 24, 25, 26, and 28 exhibited superior cytotoxic activities with IC50 values ranging from 1.78 to 9.19 µM. In order to sightsee the proposed mechanism of anti-proliferative activity, the most active members were further evaluated in vitro for their inhibitory activities against tubulin polymerisation. Compounds 21 and 32 exhibited the highest tubulin polymerisation inhibitory effect with IC50 values of 9.11 and 10.5 nM, respectively. Such members showed activities higher than that of colchicine (IC50 = 10.6 nM) and CA-4 (IC50 = 13.2 nM). The impact of the most promising compound 25 on cell cycle distribution was assessed. The results revealed that compound 25 can arrest the cell cycle at G2/M phase. Annexin V and PI double staining assay was carried out to explore the apoptotic effect of the synthesised compounds. Compound 25 induced apoptotic effect on HepG-2 thirteen times more than the control cells. To examine the binding pattern of the target compounds against the tubulin heterodimers active site, molecular docking studies were carried out.
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Affiliation(s)
- Mohamed Hagras
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
| | - Moshira A. El Deeb
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
| | - Heba S. A. Elzahabi
- Department of Pharmaceutical Medicinal Chemistry & Drug Design, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
| | - Eslam B. Elkaeed
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
- Department of Pharmaceutical Sciences, College of Pharmacy, AlMaarefa University, Ad Diriyah, Riyadh, Saudi Arabia
| | - Ahmed B. M. Mehany
- Department of Zoology, Faculty of Science, Al-Azhar University, Cairo, Egypt
| | - Ibrahim H. Eissa
- Department of Pharmaceutical Medicinal Chemistry & Drug Design, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
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21
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Teng YN, Huang BH, Huang SY, Wu IT, Wu TS, Lee TE, Hung CC. Cinnamophilin overcomes cancer multi-drug resistance via allosterically modulating human P-glycoprotein on both drug binding sites and ATPase binding sites. Biomed Pharmacother 2021; 144:112379. [PMID: 34794239 DOI: 10.1016/j.biopha.2021.112379] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/20/2021] [Accepted: 10/25/2021] [Indexed: 11/17/2022] Open
Abstract
Cancer multi-drug resistance (MDR) caused by P-glycoprotein (P-gp) efflux is a critical unresolved clinical concern. The present study analyzed the effect of cinnamophilin on P-gp inhibition and MDR reversion. The effect of cinnamophilin on P-gp was investigated through drug efflux assay, ATPase assay, MDR1 shift assay, and molecular docking. The cancer MDR-reversing ability and mechanisms were analyzed through cytotoxicity and combination index (CI), cell cycle, and apoptosis experiments. P-gp efflux function was significantly inhibited by cinnamophilin without influencing the drug's expression or conformation. Cinnamophilin uncompetitively inhibited the efflux of doxorubicin and rhodamine 123 and exhibited a distinct binding behavior compared with verapamil, the P-gp standard inhibitor. The half maximal inhibitory concentration of cinnamophilin for doxorubicin and rhodamine 123 efflux was 12.47 and 11.59 μM, respectively. In regard to P-gp energy consumption, verapamil-stimulated ATPase activity was further enhanced by cinnamophilin at concentrations of 0.1, 1, 10, and 20 μM. In terms of MDR reversion, cinnamophilin demonstrated synergistic cytotoxic effects when combined with docetaxel, vincristine, or paclitaxel. The CI was < 0.7 in all experimental combination treatments. The present study showed that cinnamophilin possesses P-gp-modulating effects and cancer MDR resensitizing ability.
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Affiliation(s)
- Yu-Ning Teng
- School of Medicine, College of Medicine, I-Shou University, 8 Yida Road, Kaohsiung 82445, Taiwan, ROC.
| | - Bo-Hau Huang
- Department of Pharmacy, China Medical University Hsinchu Hospital, No. 199, Section1, Xinglong Rd., Zhubei City, Hsinchu Country 302056, Taiwan, ROC.
| | - Shih-Ya Huang
- Department of Pharmacy, College of Pharmacy, China Medical University, 100, Section 1, Jingmao Rd., Beitun Dist., Taichung City 406040, Taiwan, ROC.
| | - I-Ting Wu
- Department of Pharmacy, College of Pharmacy, China Medical University, 100, Section 1, Jingmao Rd., Beitun Dist., Taichung City 406040, Taiwan, ROC.
| | - Tian-Shung Wu
- School of Pharmacy, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan, ROC; Department of Pharmacy, College of Pharmacy and Health Care, Tajen University, Pingtung 907, Taiwan, ROC.
| | - Tsui-Er Lee
- Office of Physical Education, Asia University, 500, Lioufeng Rd., Wufeng, Taichung 41354, Taiwan, ROC.
| | - Chin-Chuan Hung
- Department of Pharmacy, College of Pharmacy, China Medical University, 100, Section 1, Jingmao Rd., Beitun Dist., Taichung City 406040, Taiwan, ROC; Department of Pharmacy, China Medical University Hospital, 2 Yude Road, Taichung 40447, Taiwan, ROC; Department of Healthcare Administration, Asia University, 500, Lioufeng Rd., Wufeng, Taichung 41354, Taiwan, ROC.
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Kumar A, Paul M, Panda M, Jayaram S, Kalidindi N, Sale H, Vetrichelvan M, Gupta A, Mathur A, Beno B, Regueiro-Ren A, Cheng D, Ramarao M, Ghosh K. Molecular mechanism of interspecies differences in the binding affinity of TD139 to Galectin-3. Glycobiology 2021; 31:1390-1400. [PMID: 34228782 DOI: 10.1093/glycob/cwab072] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/26/2021] [Accepted: 06/29/2021] [Indexed: 01/07/2023] Open
Abstract
Galectin-3 (Gal-3), a β-galactoside-binding lectin, has been implicated in a plethora of pathological disorders including fibrosis, inflammation, cancer and metabolic diseases. TD139-a thio-digalactoside inhibitor developed by Galecto Biotech as a potential therapeutic for idiopathic pulmonary fibrosis-is the most advanced small-molecule Gal-3 inhibitor in clinical studies. It binds to human Gal-3 with high affinity but has lower affinity towards mouse and rat homologs, which is also manifested in the differential inhibition of Gal-3 function. Using biophysical methods and high-resolution X-ray co-crystal structures of TD139 and Gal-3 proteins, we demonstrate that a single amino acid change corresponding to A146 in human Gal-3 is sufficient for the observed reduction in the binding affinity of TD139 in rodents. Site-directed mutagenesis of A146V (in human Gal-3) and V160A (in mouse Gal-3) was sufficient to interchange the affinities, mainly by affecting the off rates of the inhibitor binding. In addition, molecular dynamics simulations of both wild-type and mutant structures revealed the sustained favorable noncovalent interactions between the fluorophenyl ring and the active site A146 (human Gal-3 and mouse V160A) that corroborate the finding from biophysical studies. Current findings have ramifications in the context of optimization of drug candidates against Gal-3.
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Affiliation(s)
- Amit Kumar
- Discovery Biology and Translational Medicine, Biocon Bristol-Myers Squibb R&D Center, Bristol-Myers Squibb India Pvt. Ltd, Bangalore 560099, India
| | - Marilyn Paul
- Discovery Biology and Translational Medicine, Biocon Bristol-Myers Squibb R&D Center, Bristol-Myers Squibb India Pvt. Ltd, Bangalore 560099, India
| | - Manoranjan Panda
- Medicinal Chemistry, Biocon Bristol-Myers Squibb R&D Center, Bristol-Myers Squibb India Pvt. Ltd, Bangalore 560099, India
| | - Shruthi Jayaram
- Discovery Biology and Translational Medicine, Biocon Bristol-Myers Squibb R&D Center, Bristol-Myers Squibb India Pvt. Ltd, Bangalore 560099, India
| | - Narasimharaju Kalidindi
- Discovery Biology and Translational Medicine, Biocon Bristol-Myers Squibb R&D Center, Bristol-Myers Squibb India Pvt. Ltd, Bangalore 560099, India
| | - Harinath Sale
- Discovery Biology and Translational Medicine, Biocon Bristol-Myers Squibb R&D Center, Bristol-Myers Squibb India Pvt. Ltd, Bangalore 560099, India
| | - Muthalagu Vetrichelvan
- Department of Discovery Synthesis, Biocon Bristol-Myers Squibb R&D Center, Bristol-Myers Squibb India Pvt. Ltd, Bangalore 560099, India
| | - Anuradha Gupta
- Department of Discovery Synthesis, Biocon Bristol-Myers Squibb R&D Center, Bristol-Myers Squibb India Pvt. Ltd, Bangalore 560099, India
| | - Arvind Mathur
- Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543, USA
| | - Brett Beno
- Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543, USA
| | - Alicia Regueiro-Ren
- Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543, USA
| | - Dong Cheng
- Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543, USA
| | - Manjunath Ramarao
- Discovery Biology and Translational Medicine, Biocon Bristol-Myers Squibb R&D Center, Bristol-Myers Squibb India Pvt. Ltd, Bangalore 560099, India
| | - Kaushik Ghosh
- Discovery Biology and Translational Medicine, Biocon Bristol-Myers Squibb R&D Center, Bristol-Myers Squibb India Pvt. Ltd, Bangalore 560099, India
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23
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Shreevatsa B, Dharmashekara C, Swamy VH, Gowda MV, Achar RR, Kameshwar VH, Thimmulappa RK, Syed A, Elgorban AM, Al-Rejaie SS, Ortega-Castro J, Frau J, Flores-Holguín N, Shivamallu C, Kollur SP, Glossman-Mitnik D. Virtual Screening for Potential Phytobioactives as Therapeutic Leads to Inhibit NQO1 for Selective Anticancer Therapy. Molecules 2021; 26:molecules26226863. [PMID: 34833955 PMCID: PMC8622762 DOI: 10.3390/molecules26226863] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/04/2021] [Accepted: 11/08/2021] [Indexed: 11/16/2022] Open
Abstract
NAD(P)H:quinone acceptor oxidoreductase-1 (NQO1) is a ubiquitous flavin adenine dinucleotide-dependent flavoprotein that promotes obligatory two-electron reductions of quinones, quinonimines, nitroaromatics, and azo dyes. NQO1 is a multifunctional antioxidant enzyme whose expression and deletion are linked to reduced and increased oxidative stress susceptibilities. NQO1 acts as both a tumor suppressor and tumor promoter; thus, the inhibition of NQO1 results in less tumor burden. In addition, the high expression of NQO1 is associated with a shorter survival time of cancer patients. Inhibiting NQO1 also enables certain anticancer agents to evade the detoxification process. In this study, a series of phytobioactives were screened based on their chemical classes such as coumarins, flavonoids, and triterpenoids for their action on NQO1. The in silico evaluations were conducted using PyRx virtual screening tools, where the flavone compound, Orientin showed a better binding affinity score of −8.18 when compared with standard inhibitor Dicumarol with favorable ADME properties. An MD simulation study found that the Orientin binding to NQO1 away from the substrate-binding site induces a potential conformational change in the substrate-binding site, thereby inhibiting substrate accessibility towards the FAD-binding domain. Furthermore, with this computational approach we are offering a scope for validation of the new therapeutic components for their in vitro and in vivo efficacy against NQO1.
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Affiliation(s)
- Bhargav Shreevatsa
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru 570015, India; (B.S.); (C.D.)
| | - Chandan Dharmashekara
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru 570015, India; (B.S.); (C.D.)
| | - Vikas Halasumane Swamy
- Division of Biochemistry, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru 570015, India; (V.H.S.); (M.V.G.)
| | - Meghana V. Gowda
- Division of Biochemistry, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru 570015, India; (V.H.S.); (M.V.G.)
| | - Raghu Ram Achar
- Division of Biochemistry, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru 570015, India; (V.H.S.); (M.V.G.)
- Correspondence: (R.R.A.); (C.S.); (S.P.K.); (D.G.-M.)
| | - Vivek Hamse Kameshwar
- School of Natural Science, Adichunchanagiri University, B.G. Nagara, Nagamangala, Mandya 571448, India;
| | - Rajesh Kumar Thimmulappa
- Department of Biochemistry, JSS Medical College, JSS Academy of Higher Education and Research, Mysuru 570015, India;
| | - Asad Syed
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (A.S.); (A.M.E.)
| | - Abdallah M. Elgorban
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (A.S.); (A.M.E.)
| | - Salim S. Al-Rejaie
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 55760, Riyadh 11451, Saudi Arabia;
| | - Joaquín Ortega-Castro
- Departament de Química, Universitat de les Illes Balears, 07122 Palma de Malllorca, Spain; (J.O.-C.); (J.F.)
| | - Juan Frau
- Departament de Química, Universitat de les Illes Balears, 07122 Palma de Malllorca, Spain; (J.O.-C.); (J.F.)
| | - Norma Flores-Holguín
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chihuahua 31136, Mexico;
| | - Chandan Shivamallu
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru 570015, India; (B.S.); (C.D.)
- Correspondence: (R.R.A.); (C.S.); (S.P.K.); (D.G.-M.)
| | - Shiva Prasad Kollur
- Department of Sciences, Mysuru Campus, Amrita School of Arts and Sciences, Amrita Vishwa Vidyapeetham, Mysuru 570026, India
- Correspondence: (R.R.A.); (C.S.); (S.P.K.); (D.G.-M.)
| | - Daniel Glossman-Mitnik
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chihuahua 31136, Mexico;
- Correspondence: (R.R.A.); (C.S.); (S.P.K.); (D.G.-M.)
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Xu J, Chen Y, Li X, Lei Y, Shu C, Luo Q, Chen L, Li X. Reconstruction of a Demineralized Dentin Matrix via Rapid Deposition of CaF 2 Nanoparticles In Situ Promotes Dentin Bonding. ACS Appl Mater Interfaces 2021; 13:51775-51789. [PMID: 34693718 DOI: 10.1021/acsami.1c15787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Dentin bonding based on a wet-bonding technique is the fundamental technique used daily in clinics for tooth-restoration fixation and clinical treatment of tooth-related diseases. Limited bonding durability led by insufficient adhesive infiltration in the demineralized dentin (DD) matrix is the biggest concern in contemporary adhesive dentistry. This study proposes that the highly hydrated noncollagenous protein (NCP)-formed interfacial microenvironment of the DD matrix is the root cause of this problem. Meanwhile, the endogenous phosphate groups of the NCPs are used as pseudonuclei to rapidly induce the formation of amorphous CaF2 nanoparticles in situ in the interfacial microenvironment. The DD matrix is thus reconstructed into a novel porous structure. It markedly facilitates the infiltration of dentin adhesives in the DD matrix and also endows the DD matrix with anticollapsing capability when water evaporates. Whether using a wet-bonding or air-drying mode, the bonding effectiveness is greatly promoted, with the 12 month bonding strength being about twice that of the corresponding control groups. This suggests that the nanoreinforced DD matrix eliminates the dependence of bonding effectiveness on the moisture status of the DD surface controlled only by experiences of dentists. Consequently, this bonding strategy not only greatly improves bonding durability but also overcomes the technical sensitivity of bonding operations of the total-etched bonding pattern. This exhibits the potential to promote dentin bonding and is of great significance to dentistry.
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Affiliation(s)
- Jiajia Xu
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Hangzhou 310006, P. R. China
- Zhejiang Provincial Clinical Research Center for Oral Disease, Hangzhou 310006, P. R. China
- Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou 310006, P. R. China
| | - Yadong Chen
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Hangzhou 310006, P. R. China
- Zhejiang Provincial Clinical Research Center for Oral Disease, Hangzhou 310006, P. R. China
- Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou 310006, P. R. China
| | - Xiaojun Li
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Hangzhou 310006, P. R. China
- Zhejiang Provincial Clinical Research Center for Oral Disease, Hangzhou 310006, P. R. China
- Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou 310006, P. R. China
| | - Yuqing Lei
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Hangzhou 310006, P. R. China
- Zhejiang Provincial Clinical Research Center for Oral Disease, Hangzhou 310006, P. R. China
- Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou 310006, P. R. China
| | - Chang Shu
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Hangzhou 310006, P. R. China
- Zhejiang Provincial Clinical Research Center for Oral Disease, Hangzhou 310006, P. R. China
- Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou 310006, P. R. China
| | - Qiaojie Luo
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Hangzhou 310006, P. R. China
- Zhejiang Provincial Clinical Research Center for Oral Disease, Hangzhou 310006, P. R. China
- Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou 310006, P. R. China
| | - Lili Chen
- Union Hospital, Tongji Medical College, Department of Stomatology, Huazhong University Science & Technology, 1277 Jiefang Ave., Wuhan 430022, Peoples R. China
| | - Xiaodong Li
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Hangzhou 310006, P. R. China
- Zhejiang Provincial Clinical Research Center for Oral Disease, Hangzhou 310006, P. R. China
- Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou 310006, P. R. China
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Li XP, Harijan RK, Cao B, Kahn JN, Pierce M, Tsymbal AM, Roberge JY, Augeri D, Tumer NE. Synthesis and Structural Characterization of Ricin Inhibitors Targeting Ribosome Binding Using Fragment-Based Methods and Structure-Based Design. J Med Chem 2021; 64:15334-15348. [PMID: 34648707 PMCID: PMC10704857 DOI: 10.1021/acs.jmedchem.1c01370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ricin toxin A subunit (RTA) is the catalytic subunit of ricin, which depurinates an adenine from the sarcin/ricin loop in eukaryotic ribosomes. There are no approved inhibitors against ricin. We used a new strategy to disrupt RTA-ribosome interactions by fragment screening using surface plasmon resonance. Here, using a structure-guided approach, we improved the affinity and inhibitory activity of small-molecular-weight lead compounds and obtained improved compounds with over an order of magnitude higher efficiency. Four advanced compounds were characterized by X-ray crystallography. They bind at the RTA-ribosome binding site as the original compound but in a distinctive manner. These inhibitors bind remotely from the catalytic site and cause local conformational changes with no alteration of the catalytic site geometry. Yet they inhibit depurination by ricin holotoxin and inhibit the cytotoxicity of ricin in mammalian cells. They are the first agents that protect against ricin holotoxin by acting directly on RTA.
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Affiliation(s)
- Xiao-Ping Li
- Department of Plant Biology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, New Jersey 08901, United States
| | - Rajesh K Harijan
- Department of Biochemistry, Albert Einstein College of Medicine, Jack and Pearl Resnick Campus, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Bin Cao
- Molecular Design and Synthesis Core, Rutgers University Biomolecular Innovations Cores, Office for Research, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - Jennifer N Kahn
- Department of Plant Biology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, New Jersey 08901, United States
| | - Michael Pierce
- Department of Plant Biology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, New Jersey 08901, United States
| | - Anastasiia M Tsymbal
- Molecular Design and Synthesis Core, Rutgers University Biomolecular Innovations Cores, Office for Research, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - Jacques Y Roberge
- Molecular Design and Synthesis Core, Rutgers University Biomolecular Innovations Cores, Office for Research, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - David Augeri
- Molecular Design and Synthesis Core, Rutgers University Biomolecular Innovations Cores, Office for Research, Rutgers University, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - Nilgun E Tumer
- Department of Plant Biology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, New Jersey 08901, United States
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Almalki FA, Shawky AM, Abdalla AN, Gouda AM. Icotinib, Almonertinib, and Olmutinib: A 2D Similarity/Docking-Based Study to Predict the Potential Binding Modes and Interactions into EGFR. Molecules 2021; 26:molecules26216423. [PMID: 34770832 PMCID: PMC8588130 DOI: 10.3390/molecules26216423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 11/16/2022] Open
Abstract
In the current study, a 2D similarity/docking-based study was used to predict the potential binding modes of icotinib, almonertinib, and olmutinib into EGFR. The similarity search of icotinib, almonertinib, and olmutinib against a database of 154 EGFR ligands revealed the highest similarity scores with erlotinib (0.9333), osimertinib (0.9487), and WZ4003 (0.8421), respectively. In addition, the results of the docking study of the three drugs into EGFR revealed high binding free energies (ΔGb = −6.32 to −8.42 kcal/mol) compared to the co-crystallized ligands (ΔGb = −7.03 to −8.07 kcal/mol). Analysis of the top-scoring poses of the three drugs was done to identify their potential binding modes. The distances between Cys797 in EGFR and the Michael acceptor sites in almonertinib and olmutinib were determined. In conclusion, the results could provide insights into the potential binding characteristics of the three drugs into EGFR which could help in the design of new more potent analogs.
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Affiliation(s)
- Faisal A. Almalki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia;
| | - Ahmed M. Shawky
- Science and Technology Unit (STU), Umm Al-Qura University, Makkah 21955, Saudi Arabia;
- Central Laboratory for Micro-analysis, Minia University, Minia 61519, Egypt
| | - Ashraf N. Abdalla
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia;
- Department of Pharmacology and Toxicology, Medicinal And Aromatic Plants Research Institute, National Center for Research, Khartoum 2404, Sudan
| | - Ahmed M. Gouda
- Medicinal Chemistry Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt
- Correspondence: or ; Tel.: +20-1126897483; Fax: +20-822162133
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Franco Pinto J, Fillion A, Duchambon P, Bombard S, Granzhan A. Acridine-O 6-benzylguanine hybrids: Synthesis, DNA binding, MGMT inhibition and antiproliferative activity. Eur J Med Chem 2021; 227:113909. [PMID: 34731767 DOI: 10.1016/j.ejmech.2021.113909] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/24/2021] [Accepted: 10/06/2021] [Indexed: 12/13/2022]
Abstract
O6-Methylguanine-DNA-methyltransferase (MGMT) is a key DNA repair enzyme involved in chemoresistance to DNA-alkylating anti-cancer drugs such as Temozolomide (TMZ) through direct repair of drug-induced O6-methylguanine residues in DNA. MGMT substrate analogues, such as O6-benzylguanine (BG), efficiently inactivate MGMT in vitro and in cells; however, these drugs failed to reach the clinic due to adverse side effects. Here, we designed hybrid drugs combining a BG residue covalently linked to a DNA-interacting moiety (6-chloro-2-methoxy-9-aminoacridine). Specifically, two series of hybrids, encompassing three compounds each, were obtained by varying the position of the attachment point of BG (N9 of guanine vs. the benzyl group) and the length and nature of the linker. UV/vis absorption and fluorescence data indicate that all six hybrids adopt an intramolecularly stacked conformation in aqueous solutions in a wide range of temperatures. All hybrids interact with double-stranded DNA, as clearly evidenced by spectrophotometric titrations, without intercalation of the acridine ring and do not induce thermal stabilization of the duplex. All hybrids, as well as the reference DNA intercalator (6-chloro-2-methoxy-9-aminoacridine 8), irreversibly inhibit MGMT in vitro with variable efficiency, comparable to that of BG. In a multidrug-resistant glioblastoma cell line T98G, benzyl-linked hybrids 7a-c and the N9-linked hybrid 19b are moderately cytotoxic (GI50 ≥ 15 μM after 96 h), while N9-linked hybrids 19a and 19c are strongly cytotoxic (GI50 = 1-2 μM), similarly to acridine 8 (GI50 = 0.6 μM). Among all compounds, hybrids 19a and 19c, similarly to BG, display synergic cytotoxic effect upon co-treatment with subtoxic doses of TMZ, with combination index (CI) values as low as 0.2-0.3. In agreement with in vitro results, compound 19a inactivates cellular MGMT but, unlike BG, does not induce significant levels of DNA damage, either alone or in combination with TMZ, as indicated by the results of γH2AX immunostaining experiments. Instead, and unlike BG, compound 19a alone induces significant apoptosis of T98G cells, which is not further increased in a combination with TMZ. These results indicate that molecular mechanisms underlying the cytotoxicity of 19a and its combination with TMZ are distinct from that of BG. The strongly synergic properties of this combination represent an interesting therapeutic opportunity in treating TMZ-resistant cancers.
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Affiliation(s)
- Jaime Franco Pinto
- CNRS UMR9187, Inserm U1196, Institut Curie, PSL Research University, 91405, Orsay, France; CNRS UMR9187, Inserm U1196, Université Paris Saclay, 91405, Orsay, France
| | - Alexandra Fillion
- CNRS UMR9187, Inserm U1196, Institut Curie, PSL Research University, 91405, Orsay, France; CNRS UMR9187, Inserm U1196, Université Paris Saclay, 91405, Orsay, France
| | - Patricia Duchambon
- CNRS UMR9187, Inserm U1196, Institut Curie, PSL Research University, 91405, Orsay, France; CNRS UMR9187, Inserm U1196, Université Paris Saclay, 91405, Orsay, France
| | - Sophie Bombard
- CNRS UMR9187, Inserm U1196, Institut Curie, PSL Research University, 91405, Orsay, France; CNRS UMR9187, Inserm U1196, Université Paris Saclay, 91405, Orsay, France.
| | - Anton Granzhan
- CNRS UMR9187, Inserm U1196, Institut Curie, PSL Research University, 91405, Orsay, France; CNRS UMR9187, Inserm U1196, Université Paris Saclay, 91405, Orsay, France.
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Ramos CIV, Monteiro AR, Moura NMM, Faustino MAF, Trindade T, Neves MGPMS. The Interactions of H 2TMPyP, Analogues and Its Metal Complexes with DNA G-Quadruplexes-An Overview. Biomolecules 2021; 11:biom11101404. [PMID: 34680037 PMCID: PMC8533071 DOI: 10.3390/biom11101404] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 09/16/2021] [Accepted: 09/22/2021] [Indexed: 12/26/2022] Open
Abstract
The evidence that telomerase is overexpressed in almost 90% of human cancers justifies the proposal of this enzyme as a potential target for anticancer drug design. The inhibition of telomerase by quadruplex stabilizing ligands is being considered a useful approach in anticancer drug design proposals. Several aromatic ligands, including porphyrins, were exploited for telomerase inhibition by adduct formation with G-Quadruplex (GQ). 5,10,15,20-Tetrakis(N-methyl-4-pyridinium)porphyrin (H2TMPyP) is one of the most studied porphyrins in this field, and although reported as presenting high affinity to GQ, its poor selectivity for GQ over duplex structures is recognized. To increase the desired selectivity, porphyrin modifications either at the peripheral positions or at the inner core through the coordination with different metals have been handled. Herein, studies involving the interactions of TMPyP and analogs with different DNA sequences able to form GQ and duplex structures using different experimental conditions and approaches are reviewed. Some considerations concerning the structural diversity and recognition modes of G-quadruplexes will be presented first to facilitate the comprehension of the studies reviewed. Additionally, considering the diversity of experimental conditions reported, we decided to complement this review with a screening where the behavior of H2TMPyP and of some of the reviewed metal complexes were evaluated under the same experimental conditions and using the same DNA sequences. In this comparison under unified conditions, we also evaluated, for the first time, the behavior of the AgII complex of H2TMPyP. In general, all derivatives showed good affinity for GQ DNA structures with binding constants in the range of 106–107 M−1 and ligand-GQ stoichiometric ratios of 3:1 and 4:1. A promising pattern of selectivity was also identified for the new AgII derivative.
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Affiliation(s)
- Catarina I. V. Ramos
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; (A.R.M.); (N.M.M.M.); (M.A.F.F.); (M.G.P.M.S.N.)
- Correspondence: ; Tel.: +351-234-370-692
| | - Ana R. Monteiro
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; (A.R.M.); (N.M.M.M.); (M.A.F.F.); (M.G.P.M.S.N.)
- CICECO-Aveiro, Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Nuno M. M. Moura
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; (A.R.M.); (N.M.M.M.); (M.A.F.F.); (M.G.P.M.S.N.)
| | - Maria Amparo F. Faustino
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; (A.R.M.); (N.M.M.M.); (M.A.F.F.); (M.G.P.M.S.N.)
| | - Tito Trindade
- CICECO-Aveiro, Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Maria Graça P. M. S. Neves
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; (A.R.M.); (N.M.M.M.); (M.A.F.F.); (M.G.P.M.S.N.)
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Papadopoulou D, Drakopoulos A, Lagarias P, Melagraki G, Kollias G, Afantitis A. In Silico Identification and Evaluation of Natural Products as Potential Tumor Necrosis Factor Function Inhibitors Using Advanced Enalos Asclepios KNIME Nodes. Int J Mol Sci 2021; 22:10220. [PMID: 34638561 PMCID: PMC8508374 DOI: 10.3390/ijms221910220] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/10/2021] [Accepted: 09/17/2021] [Indexed: 12/26/2022] Open
Abstract
Tumor necrosis factor (TNF) is a regulator of several chronic inflammatory diseases, such as rheumatoid arthritis. Although anti-TNF biologics have been used in clinic, they render several drawbacks, such as patients' progressive immunodeficiency and loss of response, high cost, and intravenous administration. In order to find new potential anti-TNF small molecule inhibitors, we employed an in silico approach, aiming to find natural products, analogs of Ampelopsin H, a compound that blocks the formation of TNF active trimer. Two out of nine commercially available compounds tested, Nepalensinol B and Miyabenol A, efficiently reduced TNF-induced cytotoxicity in L929 cells and production of chemokines in mice joints' synovial fibroblasts, while Nepalensinol B also abolished TNF-TNFR1 binding in non-toxic concentrations. The binding mode of the compounds was further investigated by molecular dynamics and free energy calculation studies, using and advancing the Enalos Asclepios pipeline. Conclusively, we propose that Nepalensinol B, characterized by the lowest free energy of binding and by a higher number of hydrogen bonds with TNF, qualifies as a potential lead compound for TNF inhibitors' drug development. Finally, the upgraded Enalos Asclepios pipeline can be used for improved identification of new therapeutics against TNF-mediated chronic inflammatory diseases, providing state-of-the-art insight on their binding mode.
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Affiliation(s)
- Dimitra Papadopoulou
- Biomedical Sciences Research Center "Alexander Fleming", Institute for Bioinnovation, 16672 Vari, Greece
- Department of Physiology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | | | | | - Georgia Melagraki
- Division of Physical Sciences and Applications, Hellenic Military Academy, 16673 Vari, Greece
| | - George Kollias
- Biomedical Sciences Research Center "Alexander Fleming", Institute for Bioinnovation, 16672 Vari, Greece
- Department of Physiology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
- Center of New Biotechnologies & Precision Medicine, National and Kapodistrian University of Athens Medical School, 11527 Athens, Greece
- Joint Rheumatology Program, National and Kapodistrian University of Athens Medical School, 11527 Athens, Greece
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30
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Qiao S, Zhang H, Sun F, Jiang Z. Molecular Basis of Artemisinin Derivatives Inhibition of Myeloid Differentiation Protein 2 by Combined in Silico and Experimental Study. Molecules 2021; 26:molecules26185698. [PMID: 34577169 PMCID: PMC8469597 DOI: 10.3390/molecules26185698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 12/11/2022] Open
Abstract
Artemisinin (also known as Qinghaosu), an active component of the Qinghao extract, is widely used as antimalarial drug. Previous studies reveal that artemisinin and its derivatives also have effective anti-inflammatory and immunomodulatory properties, but the direct molecular target remains unknown. Recently, several reports mentioned that myeloid differentiation factor 2 (MD-2, also known as lymphocyte antigen 96) may be the endogenous target of artemisinin in the inhibition of lipopolysaccharide signaling. However, the exact interaction between artemisinin and MD-2 is still not fully understood. Here, experimental and computational methods were employed to elucidate the relationship between the artemisinin and its inhibition mechanism. Experimental results showed that artemether exhibit higher anti-inflammatory activity performance than artemisinin and artesunate. Molecular docking results showed that artemisinin, artesunate, and artemether had similar binding poses, and all complexes remained stable throughout the whole molecular dynamics simulations, whereas the binding of artemisinin and its derivatives to MD-2 decreased the TLR4(Toll-Like Receptor 4)/MD-2 stability. Moreover, artemether exhibited lower binding energy as compared to artemisinin and artesunate, which is in good agreement with the experimental results. Leu61, Leu78, and Ile117 are indeed key residues that contribute to the binding free energy. Binding free energy analysis further confirmed that hydrophobic interactions were critical to maintain the binding mode of artemisinin and its derivatives with MD-2.
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Affiliation(s)
- Sennan Qiao
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China;
| | - Hansi Zhang
- College of Basic Medical Sciences, Jilin University, Changchun 130021, China;
| | - Fei Sun
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China;
- Correspondence: (F.S.); (Z.J.)
| | - Zhenyan Jiang
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China;
- Correspondence: (F.S.); (Z.J.)
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31
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Mammoli A, Riccio A, Bianconi E, Coletti A, Camaioni E, Macchiarulo A. One Key and Multiple Locks: Substrate Binding in Structures of Tryptophan Dioxygenases and Hydroxylases. ChemMedChem 2021; 16:2732-2743. [PMID: 34137184 PMCID: PMC8518741 DOI: 10.1002/cmdc.202100312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 06/14/2021] [Indexed: 12/18/2022]
Abstract
Since its discovery at the beginning of the past century, the essential nutrient l-Tryptophan (l-Trp) and its catabolic pathways have acquired an increasing interest in an ever wider scientific community for their pivotal roles in underlying many important physiological functions and associated pathological conditions. As a consequence, enzymes catalyzing rate limiting steps along l-Trp catabolic pathways - including IDO1, TDO, TPH1 and TPH2 - have turned to be interesting drug targets for the design and development of novel therapeutic agents for different disorders such as carcinoid syndrome, cancer and autoimmune diseases. This article provides a fresh comparative overview on the most recent advancements that crystallographic studies, biophysical and computational works have brought on structural aspects and molecular recognition patterns of these enzymes toward l-Trp. Finally, a conformational analysis of l-Trp is also discussed as part of the molecular recognition process governing the binding of a substrate to its cognate enzymes.
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Affiliation(s)
- Andrea Mammoli
- Department of Pharmaceutical SciencesUniversity of PerugiaVia del Liceo N. 106123PerugiaItaly
| | - Alessandra Riccio
- Department of Pharmaceutical SciencesUniversity of PerugiaVia del Liceo N. 106123PerugiaItaly
| | - Elisa Bianconi
- Department of Pharmaceutical SciencesUniversity of PerugiaVia del Liceo N. 106123PerugiaItaly
| | - Alice Coletti
- Department of Medicine and SurgeryUniversity of PerugiaP. le Gambuli06132PerugiaItaly
| | - Emidio Camaioni
- Department of Pharmaceutical SciencesUniversity of PerugiaVia del Liceo N. 106123PerugiaItaly
| | - Antonio Macchiarulo
- Department of Pharmaceutical SciencesUniversity of PerugiaVia del Liceo N. 106123PerugiaItaly
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32
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Parise A, Romeo I, Russo N, Marino T. The Se-S Bond Formation in the Covalent Inhibition Mechanism of SARS-CoV-2 Main Protease by Ebselen-like Inhibitors: A Computational Study. Int J Mol Sci 2021; 22:9792. [PMID: 34575955 PMCID: PMC8467846 DOI: 10.3390/ijms22189792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/03/2021] [Accepted: 09/07/2021] [Indexed: 12/20/2022] Open
Abstract
The inhibition mechanism of the main protease (Mpro) of SARS-CoV-2 by ebselen (EBS) and its analog with a hydroxyl group at position 2 of the benzisoselenazol-3(2H)-one ring (EBS-OH) was studied by using a density functional level of theory. Preliminary molecular dynamics simulations on the apo form of Mpro were performed taking into account both the hydrogen donor and acceptor natures of the Nδ and Nε of His41, a member of the catalytic dyad. The potential energy surfaces for the formation of the Se-S covalent bond mediated by EBS and EBS-OH on Mpro are discussed in detail. The EBS-OH shows a distinctive behavior with respect to EBS in the formation of the noncovalent complex. Due to the presence of canonical H-bonds and noncanonical ones involving less electronegative atoms, such as sulfur and selenium, the influence on the energy barriers and reaction energy of the Minnesota hybrid meta-GGA functionals M06, M06-2X and M08HX, and the more recent range-separated hybrid functional wB97X were also considered. The knowledge of the inhibition mechanism of Mpro by the small protease inhibitors EBS or EBS-OH can enlarge the possibilities for designing more potent and selective inhibitor-based drugs to be used in combination with other antiviral therapies.
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Affiliation(s)
- Angela Parise
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via Pietro Bucci, 87036 Arcavacata di Rende, CS, Italy; (A.P.); (I.R.); (N.R.)
- Institut de Chimie Physique UMR8000, Université Paris-Saclay, CNRS, 91405 Orsay, France
| | - Isabella Romeo
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via Pietro Bucci, 87036 Arcavacata di Rende, CS, Italy; (A.P.); (I.R.); (N.R.)
| | - Nino Russo
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via Pietro Bucci, 87036 Arcavacata di Rende, CS, Italy; (A.P.); (I.R.); (N.R.)
| | - Tiziana Marino
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via Pietro Bucci, 87036 Arcavacata di Rende, CS, Italy; (A.P.); (I.R.); (N.R.)
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33
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Newman H, Krajnc A, Bellini D, Eyermann CJ, Boyle GA, Paterson NG, McAuley KE, Lesniak R, Gangar M, von Delft F, Brem J, Chibale K, Schofield CJ, Dowson CG. High-Throughput Crystallography Reveals Boron-Containing Inhibitors of a Penicillin-Binding Protein with Di- and Tricovalent Binding Modes. J Med Chem 2021; 64:11379-11394. [PMID: 34337941 PMCID: PMC9282634 DOI: 10.1021/acs.jmedchem.1c00717] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The effectiveness of β-lactam antibiotics is increasingly compromised by β-lactamases. Boron-containing inhibitors are potent serine-β-lactamase inhibitors, but the interactions of boron-based compounds with the penicillin-binding protein (PBP) β-lactam targets have not been extensively studied. We used high-throughput X-ray crystallography to explore reactions of a boron-containing fragment set with the Pseudomonas aeruginosa PBP3 (PaPBP3). Multiple crystal structures reveal that boronic acids react with PBPs to give tricovalently linked complexes bonded to Ser294, Ser349, and Lys484 of PaPBP3; benzoxaboroles react with PaPBP3 via reaction with two nucleophilic serines (Ser294 and Ser349) to give dicovalently linked complexes; and vaborbactam reacts to give a monocovalently linked complex. Modifications of the benzoxaborole scaffold resulted in a moderately potent inhibition of PaPBP3, though no antibacterial activity was observed. Overall, the results further evidence the potential for the development of new classes of boron-based antibiotics, which are not compromised by β-lactamase-driven resistance.
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Affiliation(s)
- Hector Newman
- School
of Life Sciences, University of Warwick, Coventry CV4 7AL, U.K.
- Diamond
Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, U.K.
| | - Alen Krajnc
- Department
of Chemistry and the Ineos Oxford Institute of Antimicrobial Research, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Dom Bellini
- School
of Life Sciences, University of Warwick, Coventry CV4 7AL, U.K.
| | - Charles J. Eyermann
- Drug
Discovery and Development Centre (H3D), University of Cape Town, Rondebosch 7701, South Africa
| | - Grant A. Boyle
- Drug
Discovery and Development Centre (H3D), University of Cape Town, Rondebosch 7701, South Africa
| | - Neil G. Paterson
- Diamond
Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, U.K.
| | - Katherine E. McAuley
- Diamond
Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, U.K.
| | - Robert Lesniak
- Department
of Chemistry and the Ineos Oxford Institute of Antimicrobial Research, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Mukesh Gangar
- Drug
Discovery and Development Centre (H3D), University of Cape Town, Rondebosch 7701, South Africa
| | - Frank von Delft
- Diamond
Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, U.K.
- Structural
Genomics Consortium (SGC), University of
Oxford, Oxford, U.K.
- Department
of Biochemistry, University of Johannesburg, Auckland Park 2006, South Africa
- Research
Complex at Harwell, Harwell
Science and Innovation Campus, Didcot OX11 0FA, U.K.
| | - Jürgen Brem
- Department
of Chemistry and the Ineos Oxford Institute of Antimicrobial Research, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Kelly Chibale
- Drug
Discovery and Development Centre (H3D), University of Cape Town, Rondebosch 7701, South Africa
- South
African Medical Research Council Drug Discovery and Development Research
Unit, Department of Chemistry and Institute of Infectious Disease
and Molecular Medicine, University of Cape
Town, Rondebosch 7701, South Africa
| | - Christopher J. Schofield
- Department
of Chemistry and the Ineos Oxford Institute of Antimicrobial Research, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K.
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34
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Dolejší E, Chetverikov N, Szánti-Pintér E, Nelic D, Randáková A, Doležal V, El-Fakahany EE, Kudová E, Jakubík J. Neuroactive steroids, WIN-compounds and cholesterol share a common binding site on muscarinic acetylcholine receptors. Biochem Pharmacol 2021; 192:114699. [PMID: 34324870 DOI: 10.1016/j.bcp.2021.114699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/20/2021] [Accepted: 07/20/2021] [Indexed: 02/06/2023]
Abstract
Endogenous neurosteroids and their synthetic analogues-neuroactive steroids-have been found to bind to muscarinic acetylcholine receptors and allosterically modulate acetylcholine binding and function. Using radioligand binding experiments we investigated their binding mode. We show that neuroactive steroids bind to two binding sites on muscarinic receptors. Their affinity for the high-affinity binding site is about 100 nM. Their affinity for the low-affinity binding site is about 10 µM. The high-affinity binding occurs at the same site as binding of steroid-based WIN-compounds that is different from the common allosteric binding site for alcuronium or gallamine that is located between the second and third extracellular loop of the receptor. This binding site is also different from the allosteric binding site for the structurally related aminosteroid-based myorelaxants pancuronium and rapacuronium. Membrane cholesterol competes with neurosteroids/neuroactive steroids binding to both high- and low-affinity binding site, indicating that both sites are oriented towards the cell membrane..
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Affiliation(s)
- Eva Dolejší
- Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic
| | | | - Eszter Szánti-Pintér
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Dominik Nelic
- Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Alena Randáková
- Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Vladimír Doležal
- Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Esam E El-Fakahany
- Department of Experimental and Clinical Pharmacology, University of Minnesota College of Pharmacy, Minneapolis, MN 55455, USA
| | - Eva Kudová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic.
| | - Jan Jakubík
- Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic.
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Teevan-Hanman C, O’Shea P. Candida albicans exhibit two classes of cell surface binding sites for serum albumin defined by their affinity, abundance and prospective role in interkingdom signalling. PLoS One 2021; 16:e0254593. [PMID: 34280221 PMCID: PMC8289007 DOI: 10.1371/journal.pone.0254593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 06/28/2021] [Indexed: 11/19/2022] Open
Abstract
Serum albumin binding to the yeast form of Candida albicans is described. Two populations of binding site are identified using two complementary spectroscopic techniques: an extrinsic fluorescent probe, 3-hexa-decanoyl-7-hydrocoumarin ([HEXCO) added to the C. albicans yeast cell surface that records the electrostatic surface potential and so responds to the surface binding of serum albumin and secondly a light scattering technique that reveals how albumin modulates aggregation of the yeast population. The albumin binding sites are found to possess different binding affinities and relative abundance leading to different total binding capacities. These are characterized as a receptor population with high affinity binding (Kd ~ 17 μM) but relatively low abundance and a separate population with high abundance but much lower affinity (Kd ~ 364 μM). The low-affinity binding sites are shown to be associated with the yeast cell aggregation. These values are found be dependent on the C. albicans strain and the nature of the culture media; some examples of these effects are explored. The possible physiological consequences of the presence of these sites are speculated in terms of evading the host's immune response, biofilm formation and possible interkingdom signaling processes.
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Affiliation(s)
- Claire Teevan-Hanman
- Faculty of Health & Medicine, Lancaster University, Lancaster, England, United Kingdom
| | - Paul O’Shea
- Faculty of Health & Medicine, Lancaster University, Lancaster, England, United Kingdom
- * E-mail:
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36
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Akaki T, Bessho Y, Ito T, Fujioka S, Ubukata M, Mori G, Yamanaka K, Orita T, Doi S, Iwanaga T, Ikegashira K, Hantani Y, Nakanishi I, Adachi T. Fragment-based lead discovery to identify novel inhibitors that target the ATP binding site of pyruvate dehydrogenase kinases. Bioorg Med Chem 2021; 44:116283. [PMID: 34274549 DOI: 10.1016/j.bmc.2021.116283] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/13/2021] [Accepted: 06/17/2021] [Indexed: 12/24/2022]
Abstract
A fragment-based lead discovery approach was applied to Pyruvate Dehydrogenase Kinases (PDHKs) to discover inhibitors against the ATP binding site with novel chemotypes. X-ray fragment screening toward PDHK4 provided a fragment hit 1 with a characteristic interaction in a deep pocket of the ATP binding site. While known inhibitors utilize several water molecules in a deep pocket to form water-mediated hydrogen bond interactions, the fragment hit binds deeper in the pocket with a hydrophobic group. Displacement of a remaining water molecule in the pocket led to the identification of lead compound 7 with a notable improvement in inhibition potency. This lead compound possessed high ligand efficiency (LE) and showed decent selectivity profile. Two additional lead compounds 10 and 13 with new scaffolds with tricyclic and bicyclic cores were generated by merging structural information of another fragment hit 2. The characteristic interaction of these novel inhibitors in a deep pocket provides new structural insights about PDHKs ATP binding site and opens a novel direction for the development of PDHKs inhibitors.
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Affiliation(s)
- Tatsuo Akaki
- Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc, 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan.
| | - Yuki Bessho
- Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc, 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Takashi Ito
- Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc, 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Shingo Fujioka
- Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc, 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Minoru Ubukata
- Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc, 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Genki Mori
- Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc, 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Kenji Yamanaka
- Biological/Pharmacological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc, 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Takuya Orita
- Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc, 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Satoki Doi
- Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc, 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Tomoko Iwanaga
- Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc, 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Kazutaka Ikegashira
- Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc, 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Yoshiji Hantani
- Biological/Pharmacological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc, 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Isao Nakanishi
- Computational Drug Design and Discovery, Department of Pharmaceutical Sciences, Kindai University, 3-4-1, Higashi-osaka, Osaka 577-8502, Japan
| | - Tsuyoshi Adachi
- Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc, 1-1, Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
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37
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Kłopotowski K, Czyżewska MM, Mozrzymas JW. Glycine substitution of α1F64 residue at the loop D of GABA A receptor impairs gating - Implications for importance of binding site-channel gate linker rigidity. Biochem Pharmacol 2021; 192:114668. [PMID: 34216603 DOI: 10.1016/j.bcp.2021.114668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/27/2021] [Accepted: 06/28/2021] [Indexed: 12/29/2022]
Abstract
GABAA receptors (GABAARs) play a crucial role in mediating inhibition in adult mammalian brains. In the recent years, an impressive progress in revealing the static structure of GABAARs was achieved but the molecular mechanisms underlying their conformational transitions remain elusive. Phenylalanine 64 (α1F64) is located at the loop D of the orthosteric binding site of GABAAR and was found to directly interact with GABA molecule. Mutations of α1F64 were demonstrated to affect not only binding but also some gating properties. Loop D is a rigid β strand which seems to be particularly suitable to convey activatory signaling from the ligand binding site (LBS) to the gate at the channel pore. To test this scenario, we have investigated the substitution of α1F64 with glycine, the smallest amino acid, widely recognized as a rigidity "reducer" of protein structures. To this end, we assessed the impact of the α1F64G mutation in the α1β2γ2L type of GABAARs on gating properties by analyzing both macroscopic responses to rapid agonist applications and single-channel currents. We found that this substitution dramatically altered all gating features of the receptor (opening/closing, preactivation and desensitization) which contrasts with markedly weaker effects of previously considered substitutions (α1F64L and α1F64A). In particular, α1F64G mutation practically abolished the desensitization process. At the same time, the α1F64G mutant maintained gating integrity manifested as single-channel activity in the form of clusters. We conclude that rigidity of the loop D plays a crucial role in conveying the activation signal from the LBS to the channel gate.
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Affiliation(s)
- Karol Kłopotowski
- Wroclaw Medical University, Department of Biophysics and Neuroscience, Chalubinskiego 3A, Wroclaw, Dolnośląskie PL 50-368, +48 71 784 15 51, Poland.
| | - Marta M Czyżewska
- Wroclaw Medical University, Department of Biophysics and Neuroscience, Chalubinskiego 3A, Wroclaw, Dolnośląskie PL 50-368, +48 71 784 15 51, Poland
| | - Jerzy W Mozrzymas
- Wroclaw Medical University, Department of Biophysics and Neuroscience, Chalubinskiego 3A, Wroclaw, Dolnośląskie PL 50-368, +48 71 784 15 51, Poland.
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38
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Partridge LJ, Urwin L, Nicklin MJH, James DC, Green LR, Monk PN. ACE2-Independent Interaction of SARS-CoV-2 Spike Protein with Human Epithelial Cells Is Inhibited by Unfractionated Heparin. Cells 2021; 10:cells10061419. [PMID: 34200372 DOI: 10.1101/2020.05.21.107870] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 05/26/2021] [Accepted: 06/04/2021] [Indexed: 05/23/2023] Open
Abstract
Coronaviruses such as SARS-CoV-2, which is responsible for COVID-19, depend on virus spike protein binding to host cell receptors to cause infection. The SARS-CoV-2 spike protein binds primarily to ACE2 on target cells and is then processed by membrane proteases, including TMPRSS2, leading to viral internalisation or fusion with the plasma membrane. It has been suggested, however, that receptors other than ACE2 may be involved in virus binding. We have investigated the interactions of recombinant versions of the spike protein with human epithelial cell lines that express low/very low levels of ACE2 and TMPRSS2 in a proxy assay for interaction with host cells. A tagged form of the spike protein containing the S1 and S2 regions bound in a temperature-dependent manner to all cell lines, whereas the S1 region alone and the receptor-binding domain (RBD) interacted only weakly. Spike protein associated with cells independently of ACE2 and TMPRSS2, while RBD required the presence of high levels of ACE2 for interaction. As the spike protein has previously been shown to bind heparin, a soluble glycosaminoglycan, we tested the effects of various heparins on ACE2-independent spike protein interaction with cells. Unfractionated heparin inhibited spike protein interaction with an IC50 value of <0.05 U/mL, whereas two low-molecular-weight heparins were less effective. A mutant form of the spike protein, lacking the arginine-rich putative furin cleavage site, interacted only weakly with cells and had a lower affinity for unfractionated and low-molecular-weight heparin than the wild-type spike protein. This suggests that the furin cleavage site might also be a heparin-binding site and potentially important for interactions with host cells. The glycosaminoglycans heparan sulphate and dermatan sulphate, but not chondroitin sulphate, also inhibited the binding of spike protein, indicating that it might bind to one or both of these glycosaminoglycans on the surface of target cells.
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Affiliation(s)
- Lynda J Partridge
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, UK
| | - Lucy Urwin
- Department of Infection, Immunity and Cardiovascular Disease, The University of Sheffield, Sheffield S10 2RX, UK
| | - Martin J H Nicklin
- Department of Infection, Immunity and Cardiovascular Disease, The University of Sheffield, Sheffield S10 2RX, UK
| | - David C James
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield S1 4NL, UK
| | - Luke R Green
- Department of Infection, Immunity and Cardiovascular Disease, The University of Sheffield, Sheffield S10 2RX, UK
| | - Peter N Monk
- Department of Infection, Immunity and Cardiovascular Disease, The University of Sheffield, Sheffield S10 2RX, UK
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39
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Partridge LJ, Urwin L, Nicklin MJH, James DC, Green LR, Monk PN. ACE2-Independent Interaction of SARS-CoV-2 Spike Protein with Human Epithelial Cells Is Inhibited by Unfractionated Heparin. Cells 2021; 10:1419. [PMID: 34200372 PMCID: PMC8229176 DOI: 10.3390/cells10061419] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 05/26/2021] [Accepted: 06/04/2021] [Indexed: 12/12/2022] Open
Abstract
Coronaviruses such as SARS-CoV-2, which is responsible for COVID-19, depend on virus spike protein binding to host cell receptors to cause infection. The SARS-CoV-2 spike protein binds primarily to ACE2 on target cells and is then processed by membrane proteases, including TMPRSS2, leading to viral internalisation or fusion with the plasma membrane. It has been suggested, however, that receptors other than ACE2 may be involved in virus binding. We have investigated the interactions of recombinant versions of the spike protein with human epithelial cell lines that express low/very low levels of ACE2 and TMPRSS2 in a proxy assay for interaction with host cells. A tagged form of the spike protein containing the S1 and S2 regions bound in a temperature-dependent manner to all cell lines, whereas the S1 region alone and the receptor-binding domain (RBD) interacted only weakly. Spike protein associated with cells independently of ACE2 and TMPRSS2, while RBD required the presence of high levels of ACE2 for interaction. As the spike protein has previously been shown to bind heparin, a soluble glycosaminoglycan, we tested the effects of various heparins on ACE2-independent spike protein interaction with cells. Unfractionated heparin inhibited spike protein interaction with an IC50 value of <0.05 U/mL, whereas two low-molecular-weight heparins were less effective. A mutant form of the spike protein, lacking the arginine-rich putative furin cleavage site, interacted only weakly with cells and had a lower affinity for unfractionated and low-molecular-weight heparin than the wild-type spike protein. This suggests that the furin cleavage site might also be a heparin-binding site and potentially important for interactions with host cells. The glycosaminoglycans heparan sulphate and dermatan sulphate, but not chondroitin sulphate, also inhibited the binding of spike protein, indicating that it might bind to one or both of these glycosaminoglycans on the surface of target cells.
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Affiliation(s)
- Lynda J. Partridge
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, UK;
| | - Lucy Urwin
- Department of Infection, Immunity and Cardiovascular Disease, The University of Sheffield, Sheffield S10 2RX, UK; (L.U.); (M.J.H.N.); (L.R.G.)
| | - Martin J. H. Nicklin
- Department of Infection, Immunity and Cardiovascular Disease, The University of Sheffield, Sheffield S10 2RX, UK; (L.U.); (M.J.H.N.); (L.R.G.)
| | - David C. James
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield S1 4NL, UK;
| | - Luke R. Green
- Department of Infection, Immunity and Cardiovascular Disease, The University of Sheffield, Sheffield S10 2RX, UK; (L.U.); (M.J.H.N.); (L.R.G.)
| | - Peter N. Monk
- Department of Infection, Immunity and Cardiovascular Disease, The University of Sheffield, Sheffield S10 2RX, UK; (L.U.); (M.J.H.N.); (L.R.G.)
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Krafčík D, Ištvánková E, Džatko Š, Víšková P, Foldynová-Trantírková S, Trantírek L. Towards Profiling of the G-Quadruplex Targeting Drugs in the Living Human Cells Using NMR Spectroscopy. Int J Mol Sci 2021; 22:6042. [PMID: 34205000 PMCID: PMC8199861 DOI: 10.3390/ijms22116042] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/26/2021] [Accepted: 05/31/2021] [Indexed: 12/11/2022] Open
Abstract
Recently, the 1H-detected in-cell NMR spectroscopy has emerged as a unique tool allowing the characterization of interactions between nucleic acid-based targets and drug-like molecules in living human cells. Here, we assess the application potential of 1H and 19F-detected in-cell NMR spectroscopy to profile drugs/ligands targeting DNA G-quadruplexes, arguably the most studied class of anti-cancer drugs targeting nucleic acids. We show that the extension of the original in-cell NMR approach is not straightforward. The severe signal broadening and overlap of 1H in-cell NMR spectra of polymorphic G-quadruplexes and their complexes complicate their quantitative interpretation. Nevertheless, the 1H in-cell NMR can be used to identify drugs that, despite strong interaction in vitro, lose their ability to bind G-quadruplexes in the native environment. The in-cell NMR approach is adjusted to a recently developed 3,5-bis(trifluoromethyl)phenyl probe to monitor the intracellular interaction with ligands using 19F-detected in-cell NMR. The probe allows dissecting polymorphic mixture in terms of number and relative populations of individual G-quadruplex species, including ligand-bound and unbound forms in vitro and in cellulo. Despite the probe's discussed limitations, the 19F-detected in-cell NMR appears to be a promising strategy to profile G-quadruplex-ligand interactions in the complex environment of living cells.
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Affiliation(s)
- Daniel Krafčík
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic; (D.K.); (E.I.); (Š.D.); (P.V.)
- National Centre for Biomolecular Research, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Eva Ištvánková
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic; (D.K.); (E.I.); (Š.D.); (P.V.)
- National Centre for Biomolecular Research, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Šimon Džatko
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic; (D.K.); (E.I.); (Š.D.); (P.V.)
- National Centre for Biomolecular Research, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Pavlína Víšková
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic; (D.K.); (E.I.); (Š.D.); (P.V.)
- National Centre for Biomolecular Research, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | | | - Lukáš Trantírek
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic; (D.K.); (E.I.); (Š.D.); (P.V.)
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Mulliri S, Laaksonen A, Spanu P, Farris R, Farci M, Mingoia F, Roviello GN, Mocci F. Spectroscopic and In Silico Studies on the Interaction of Substituted Pyrazolo[1,2-a]benzo[1,2,3,4]tetrazine-3-one Derivatives with c-Myc G4-DNA. Int J Mol Sci 2021; 22:6028. [PMID: 34199659 PMCID: PMC8199725 DOI: 10.3390/ijms22116028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/29/2021] [Accepted: 05/30/2021] [Indexed: 12/14/2022] Open
Abstract
Herein we describe a combined experimental and in silico study of the interaction of a series of pyrazolo[1,2-a]benzo[1,2,3,4]tetrazin-3-one derivatives (PBTs) with parallel G-quadruplex (GQ) DNA aimed at correlating their previously reported anticancer activities and the stabilizing effects observed by us on c-myc oncogene promoter GQ structure. Circular dichroism (CD) melting experiments were performed to characterize the effect of the studied PBTs on the GQ thermal stability. CD measurements indicate that two out of the eight compounds under investigation induced a slight stabilizing effect (2-4 °C) on GQ depending on the nature and position of the substituents. Molecular docking results allowed us to verify the modes of interaction of the ligands with the GQ and estimate the binding affinities. The highest binding affinity was observed for ligands with the experimental melting temperatures (Tms). However, both stabilizing and destabilizing ligands showed similar scores, whilst Molecular Dynamics (MD) simulations, performed across a wide range of temperatures on the GQ in water solution, either unliganded or complexed with two model PBT ligands with the opposite effect on the Tms, consistently confirmed their stabilizing or destabilizing ability ascertained by CD. Clues about a relation between the reported anticancer activity of some PBTs and their ability to stabilize the GQ structure of c-myc emerged from our study. Furthermore, Molecular Dynamics simulations at high temperatures are herein proposed for the first time as a means to verify the stabilizing or destabilizing effect of ligands on the GQ, also disclosing predictive potential in GQ-targeting drug discovery.
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Affiliation(s)
- Simone Mulliri
- Department of Chemical and Geological Sciences, University of Cagliari, I-09042 Monserrato, Italy; (S.M.); (R.F.); (M.F.)
| | - Aatto Laaksonen
- State Key Laboratory of Materials-Oriented and Chemical Engineering, Nanjing Tech University, Nanjing 210009, China
- Division of Physical Chemistry, Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, 10691 Stockholm, Sweden
- Centre of Advanced Research in Bionanoconjugates and Biopolymers, Petru Poni Institute of Macromolecular Chemistry, 700487 Iasi, Romania
- Department of Engineering Sciences and Mathematics, Division of Energy Science, Luleå University of Technology, SE-97187 Luleå, Sweden
| | - Pietro Spanu
- Istituto di Chimica Biomolecolare, ICB-CNR-Trav. La Crucca 3, 07100 Sassari, Italy;
| | - Riccardo Farris
- Department of Chemical and Geological Sciences, University of Cagliari, I-09042 Monserrato, Italy; (S.M.); (R.F.); (M.F.)
| | - Matteo Farci
- Department of Chemical and Geological Sciences, University of Cagliari, I-09042 Monserrato, Italy; (S.M.); (R.F.); (M.F.)
| | - Francesco Mingoia
- Istituto per lo Studio dei Materiali Nanostrutturati ISMN-CNR, Via U. La Malfa 153, I-90146 Palermo, Italy;
| | - Giovanni N. Roviello
- Istituto di Biostrutture e Bioimmagini, IBB-CNR, Via Mezzocannone 16, I-80134 Naples, Italy
| | - Francesca Mocci
- Department of Chemical and Geological Sciences, University of Cagliari, I-09042 Monserrato, Italy; (S.M.); (R.F.); (M.F.)
- Centre of Advanced Research in Bionanoconjugates and Biopolymers, Petru Poni Institute of Macromolecular Chemistry, 700487 Iasi, Romania
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Bertuzzi S, Gimeno A, Martinez-Castillo A, Lete MG, Delgado S, Airoldi C, Rodrigues Tavares M, Bláhová M, Chytil P, Křen V, Abrescia NGA, Ardá A, Bojarová P, Jiménez-Barbero J. Cross-Linking Effects Dictate the Preference of Galectins to Bind LacNAc-Decorated HPMA Copolymers. Int J Mol Sci 2021; 22:ijms22116000. [PMID: 34206141 PMCID: PMC8199549 DOI: 10.3390/ijms22116000] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 05/28/2021] [Accepted: 05/29/2021] [Indexed: 01/02/2023] Open
Abstract
The interaction of multi-LacNAc (Galβ1-4GlcNAc)-containing N-(2-hydroxypropyl) methacrylamide (HPMA) copolymers with human galectin-1 (Gal-1) and the carbohydrate recognition domain (CRD) of human galectin-3 (Gal-3) was analyzed using NMR methods in addition to cryo-electron-microscopy and dynamic light scattering (DLS) experiments. The interaction with individual LacNAc-containing components of the polymer was studied for comparison purposes. For Gal-3 CRD, the NMR data suggest a canonical interaction of the individual small-molecule bi- and trivalent ligands with the lectin binding site and better affinity for the trivalent arrangement due to statistical effects. For the glycopolymers, the interaction was stronger, although no evidence for forming a large supramolecule was obtained. In contrast, for Gal-1, the results indicate the formation of large cross-linked supramolecules in the presence of multivalent LacNAc entities for both the individual building blocks and the polymers. Interestingly, the bivalent and trivalent presentation of LacNAc in the polymer did not produce such an increase, indicating that the multivalency provided by the polymer is sufficient for triggering an efficient binding between the glycopolymer and Gal-1. This hypothesis was further demonstrated by electron microscopy and DLS methods.
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Affiliation(s)
- Sara Bertuzzi
- CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Bizkaia Technology Park, 48162 Derio, Bizkaia, Spain; (S.B.); (A.G.); (A.M.-C.); (M.G.L.); (S.D.); (N.G.A.A.); (A.A.)
- BioOrgNMR Lab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy;
| | - Ana Gimeno
- CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Bizkaia Technology Park, 48162 Derio, Bizkaia, Spain; (S.B.); (A.G.); (A.M.-C.); (M.G.L.); (S.D.); (N.G.A.A.); (A.A.)
| | - Ane Martinez-Castillo
- CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Bizkaia Technology Park, 48162 Derio, Bizkaia, Spain; (S.B.); (A.G.); (A.M.-C.); (M.G.L.); (S.D.); (N.G.A.A.); (A.A.)
| | - Marta G. Lete
- CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Bizkaia Technology Park, 48162 Derio, Bizkaia, Spain; (S.B.); (A.G.); (A.M.-C.); (M.G.L.); (S.D.); (N.G.A.A.); (A.A.)
| | - Sandra Delgado
- CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Bizkaia Technology Park, 48162 Derio, Bizkaia, Spain; (S.B.); (A.G.); (A.M.-C.); (M.G.L.); (S.D.); (N.G.A.A.); (A.A.)
| | - Cristina Airoldi
- BioOrgNMR Lab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy;
| | - Marina Rodrigues Tavares
- Institute of Macromolecular Chemistry of the Czech Academy of Sciences, Heyrovského Nám. 2, 16206 Prague, Czech Republic; (M.R.T.); (M.B.); (P.C.)
| | - Markéta Bláhová
- Institute of Macromolecular Chemistry of the Czech Academy of Sciences, Heyrovského Nám. 2, 16206 Prague, Czech Republic; (M.R.T.); (M.B.); (P.C.)
| | - Petr Chytil
- Institute of Macromolecular Chemistry of the Czech Academy of Sciences, Heyrovského Nám. 2, 16206 Prague, Czech Republic; (M.R.T.); (M.B.); (P.C.)
| | - Vladimír Křen
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic;
| | - Nicola G. A. Abrescia
- CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Bizkaia Technology Park, 48162 Derio, Bizkaia, Spain; (S.B.); (A.G.); (A.M.-C.); (M.G.L.); (S.D.); (N.G.A.A.); (A.A.)
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Bizkaia, Spain
| | - Ana Ardá
- CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Bizkaia Technology Park, 48162 Derio, Bizkaia, Spain; (S.B.); (A.G.); (A.M.-C.); (M.G.L.); (S.D.); (N.G.A.A.); (A.A.)
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Bizkaia, Spain
| | - Pavla Bojarová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic;
- Department of Health Care Disciplines and Population Protection, Faculty of Biomedical Engineering, Czech Technical University in Prague, Nám. Sítná, 27201 Kladno, Czech Republic
- Correspondence: (P.B.); (J.J.-B.)
| | - Jesús Jiménez-Barbero
- CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Bizkaia Technology Park, 48162 Derio, Bizkaia, Spain; (S.B.); (A.G.); (A.M.-C.); (M.G.L.); (S.D.); (N.G.A.A.); (A.A.)
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Bizkaia, Spain
- Department of Organic Chemistry II, University of the Basque Country UPV/EHU, 48940 Leioa, Bizkaia, Spain
- Correspondence: (P.B.); (J.J.-B.)
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Sohraby F, Aryapour H. Unraveling the unbinding pathways of SARS-CoV-2 Papain-like proteinase known inhibitors by Supervised Molecular Dynamics simulation. PLoS One 2021; 16:e0251910. [PMID: 34010326 PMCID: PMC8133426 DOI: 10.1371/journal.pone.0251910] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 05/05/2021] [Indexed: 12/20/2022] Open
Abstract
The COVID-19 disease has infected and killed countless people all over the world since its emergence at the end of 2019. No specific therapy for COVID-19 is not currently available, and urgent treatment solutions are needed. Recent studies have found several potential molecular targets, and one of the most critical proteins of the SARS-CoV-2 virus work machine is the Papain-like protease (Plpro). Potential inhibitors are available, and their X-ray crystallographic structures in complex with this enzyme have been determined recently. However, their activities against this enzyme are insufficient and need to be characterized and improved to be of clinical values. Therefore, in this work, by utilizing the Supervised Molecular Dynamics (SuMD) simulation method, we achieved multiple unbinding events of Plpro inhibitors, GRL0617, and its derivates, and captured and understood the details of the unbinding pathway. We found that residues of the BL2 loop, such as Tyr268 and Gln269, play major roles in the unbinding pathways, but the most important contributing factor is the natural movements and behavior of the BL2 loop, which can control the entire process. We believe that the details found in this study can be used to refine and optimize potential inhibitors like GRL0617 and design more efficacious inhibitors as a treatment for the SARS-CoV-2 virus.
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Affiliation(s)
- Farzin Sohraby
- Department of Biology, Faculty of Science, Golestan University, Gorgan, Iran
| | - Hassan Aryapour
- Department of Biology, Faculty of Science, Golestan University, Gorgan, Iran
- * E-mail:
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Park SH, Siddiqi H, Castro DV, De Angelis AA, Oom AL, Stoneham CA, Lewinski MK, Clark AE, Croker BA, Carlin AF, Guatelli J, Opella SJ. Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity. PLoS Pathog 2021; 17:e1009519. [PMID: 34003853 PMCID: PMC8184013 DOI: 10.1371/journal.ppat.1009519] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/07/2021] [Accepted: 04/29/2021] [Indexed: 11/24/2022] Open
Abstract
SARS-CoV-2 is the novel coronavirus that is the causative agent of COVID-19, a sometimes-lethal respiratory infection responsible for a world-wide pandemic. The envelope (E) protein, one of four structural proteins encoded in the viral genome, is a 75-residue integral membrane protein whose transmembrane domain exhibits ion channel activity and whose cytoplasmic domain participates in protein-protein interactions. These activities contribute to several aspects of the viral replication-cycle, including virion assembly, budding, release, and pathogenesis. Here, we describe the structure and dynamics of full-length SARS-CoV-2 E protein in hexadecylphosphocholine micelles by NMR spectroscopy. We also characterized its interactions with four putative ion channel inhibitors. The chemical shift index and dipolar wave plots establish that E protein consists of a long transmembrane helix (residues 8–43) and a short cytoplasmic helix (residues 53–60) connected by a complex linker that exhibits some internal mobility. The conformations of the N-terminal transmembrane domain and the C-terminal cytoplasmic domain are unaffected by truncation from the intact protein. The chemical shift perturbations of E protein spectra induced by the addition of the inhibitors demonstrate that the N-terminal region (residues 6–18) is the principal binding site. The binding affinity of the inhibitors to E protein in micelles correlates with their antiviral potency in Vero E6 cells: HMA ≈ EIPA > DMA >> Amiloride, suggesting that bulky hydrophobic groups in the 5’ position of the amiloride pyrazine ring play essential roles in binding to E protein and in antiviral activity. An N15A mutation increased the production of virus-like particles, induced significant chemical shift changes from residues in the inhibitor binding site, and abolished HMA binding, suggesting that Asn15 plays a key role in maintaining the protein conformation near the binding site. These studies provide the foundation for complete structure determination of E protein and for structure-based drug discovery targeting this protein. The novel coronavirus SARS-CoV-2, the causative agent of the world-wide pandemic of COVID-19, has become one of the greatest threats to human health. While rapid progress has been made in the development of vaccines, drug discovery has lagged, partly due to the lack of atomic-resolution structures of the free and drug-bound forms of the viral proteins. The SARS-CoV-2 envelope (E) protein, with its multiple activities that contribute to viral replication, is widely regarded as a potential target for COVID-19 treatment. As structural information is essential for drug discovery, we established an efficient sample preparation system for biochemical and structural studies of intact full-length SARS-CoV-2 E protein and characterized its structure and dynamics. We also characterized the interactions of amilorides with specific E protein residues and correlated this with their antiviral activity during viral replication. The binding affinity of the amilorides to E protein correlated with their antiviral potency, suggesting that E protein is indeed the likely target of their antiviral activity. We found that residue asparagine15 plays an important role in maintaining the conformation of the amiloride binding site, providing molecular guidance for the design of inhibitors targeting E protein.
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Affiliation(s)
- Sang Ho Park
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Haley Siddiqi
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Daniela V. Castro
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Anna A. De Angelis
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Aaron L. Oom
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Charlotte A. Stoneham
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Mary K. Lewinski
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Alex E. Clark
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Ben A. Croker
- Department of Pediatrics, University of California San Diego, La Jolla, California, United States of America
| | - Aaron F. Carlin
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - John Guatelli
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Stanley J. Opella
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
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Napoleon JV, Singh S, Rana S, Bendjennat M, Kumar V, Kizhake S, Palermo NY, Ouellette MM, Huxford T, Natarajan A. Small molecule binding to inhibitor of nuclear factor kappa-B kinase subunit beta in an ATP non-competitive manner. Chem Commun (Camb) 2021; 57:4678-4681. [PMID: 33977973 PMCID: PMC8162871 DOI: 10.1039/d1cc01245b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Inhibitor of nuclear factor kappa-B kinase subunit beta (IKKβ) is a key regulator of the cannonical NF-κB pathway. IKKβ has been validated as a drug target for pathological conditions, which include chronic inflammatory diseases and cancer. Pharmacological studies revealed that chronic administration of ATP-competitive IKKβ inhibitors resulted in unexpected toxicity. We previously reported the discovery of 13-197 as a non-toxic IKKβ inhibitor that reduced tumor growth. Here, we show that 13-197 inhibits IKKβ in a ATP non-competitive manner and an allosteric pocket at the interface of the kinase and ubiquitin like domains was identified as the potential binding site.
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Affiliation(s)
- John V Napoleon
- Eppley Institute for Research in Cancer and Allied Diseases, UNMC, USA.
| | - Sarbjit Singh
- Eppley Institute for Research in Cancer and Allied Diseases, UNMC, USA.
| | - Sandeep Rana
- Eppley Institute for Research in Cancer and Allied Diseases, UNMC, USA.
| | - Mourad Bendjennat
- Eppley Institute for Research in Cancer and Allied Diseases, UNMC, USA.
| | - Vikas Kumar
- Mass Spectrometry and Proteomics Core Facility, UNMC, USA
| | - Smitha Kizhake
- Eppley Institute for Research in Cancer and Allied Diseases, UNMC, USA.
| | - Nicholas Y Palermo
- Mass Spectrometry and Proteomics Core Facility, UNMC, USA and Computational Chemistry Core Facility, UNMC, USA
| | - Michel M Ouellette
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, UNMC, USA and Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska 68022, USA
| | - Tom Huxford
- Structural Biochemistry Laboratory, Department of Chemistry & Biochemistry, San Diego State University, San Diego, CA 92182, USA
| | - Amarnath Natarajan
- Eppley Institute for Research in Cancer and Allied Diseases, UNMC, USA. and Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska 68022, USA and Department of Pharmaceutical Sciences and Department of Genetics, Cell Biology and Anatomy, UNMC, USA
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Schmitz A, Weber A, Bayin M, Breuers S, Fieberg V, Famulok M, Mayer G. A SARS-CoV-2 Spike Binding DNA Aptamer that Inhibits Pseudovirus Infection by an RBD-Independent Mechanism*. Angew Chem Int Ed Engl 2021; 60:10279-10285. [PMID: 33683787 DOI: 10.1101/2020.12.23.424171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Indexed: 05/25/2023]
Abstract
The receptor binding domain (RBD) of the spike glycoprotein of the coronavirus SARS-CoV-2 (CoV2-S) binds to the human angiotensin-converting enzyme 2 (ACE2) representing the initial contact point for leveraging the infection cascade. We used an automated selection process and identified an aptamer that specifically interacts with CoV2-S. The aptamer does not bind to the RBD of CoV2-S and does not block the interaction of CoV2-S with ACE2. Nevertheless, infection studies revealed potent and specific inhibition of pseudoviral infection by the aptamer. The present study opens up new vistas in developing SARS-CoV2 infection inhibitors, independent of blocking the ACE2 interaction of the virus, and harnesses aptamers as potential drug candidates and tools to disentangle hitherto inaccessible infection modalities, which is of particular interest in light of the increasing number of escape mutants that are currently being reported.
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Affiliation(s)
- Anton Schmitz
- Life and Medical Sciences (LIMES), University of Bonn, Gerhard-Domagk-Str.1, 53121, Bonn, Germany
- Max Planck Fellow Chemical Biology, Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175, Bonn, Germany
| | - Anna Weber
- Life and Medical Sciences (LIMES), University of Bonn, Gerhard-Domagk-Str.1, 53121, Bonn, Germany
- Center of Aptamer Research & Development, University of Bonn, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany
| | - Mehtap Bayin
- Life and Medical Sciences (LIMES), University of Bonn, Gerhard-Domagk-Str.1, 53121, Bonn, Germany
- Max Planck Fellow Chemical Biology, Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175, Bonn, Germany
| | - Stefan Breuers
- Life and Medical Sciences (LIMES), University of Bonn, Gerhard-Domagk-Str.1, 53121, Bonn, Germany
- Center of Aptamer Research & Development, University of Bonn, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany
| | - Volkmar Fieberg
- Life and Medical Sciences (LIMES), University of Bonn, Gerhard-Domagk-Str.1, 53121, Bonn, Germany
- Max Planck Fellow Chemical Biology, Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175, Bonn, Germany
| | - Michael Famulok
- Life and Medical Sciences (LIMES), University of Bonn, Gerhard-Domagk-Str.1, 53121, Bonn, Germany
- Max Planck Fellow Chemical Biology, Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175, Bonn, Germany
- Center of Aptamer Research & Development, University of Bonn, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany
| | - Günter Mayer
- Life and Medical Sciences (LIMES), University of Bonn, Gerhard-Domagk-Str.1, 53121, Bonn, Germany
- Center of Aptamer Research & Development, University of Bonn, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany
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47
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Schmitz A, Weber A, Bayin M, Breuers S, Fieberg V, Famulok M, Mayer G. A SARS-CoV-2 Spike Binding DNA Aptamer that Inhibits Pseudovirus Infection by an RBD-Independent Mechanism*. Angew Chem Int Ed Engl 2021; 60:10279-10285. [PMID: 33683787 PMCID: PMC8251191 DOI: 10.1002/anie.202100316] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Indexed: 11/24/2022]
Abstract
The receptor binding domain (RBD) of the spike glycoprotein of the coronavirus SARS-CoV-2 (CoV2-S) binds to the human angiotensin-converting enzyme 2 (ACE2) representing the initial contact point for leveraging the infection cascade. We used an automated selection process and identified an aptamer that specifically interacts with CoV2-S. The aptamer does not bind to the RBD of CoV2-S and does not block the interaction of CoV2-S with ACE2. Nevertheless, infection studies revealed potent and specific inhibition of pseudoviral infection by the aptamer. The present study opens up new vistas in developing SARS-CoV2 infection inhibitors, independent of blocking the ACE2 interaction of the virus, and harnesses aptamers as potential drug candidates and tools to disentangle hitherto inaccessible infection modalities, which is of particular interest in light of the increasing number of escape mutants that are currently being reported.
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Affiliation(s)
- Anton Schmitz
- Life and Medical Sciences (LIMES)University of BonnGerhard-Domagk-Str.153121BonnGermany
- Max Planck Fellow Chemical BiologyCenter of Advanced European Studies and Research (caesar)Ludwig-Erhard-Allee 253175BonnGermany
| | - Anna Weber
- Life and Medical Sciences (LIMES)University of BonnGerhard-Domagk-Str.153121BonnGermany
- Center of Aptamer Research & DevelopmentUniversity of BonnGerhard-Domagk-Str. 153121BonnGermany
| | - Mehtap Bayin
- Life and Medical Sciences (LIMES)University of BonnGerhard-Domagk-Str.153121BonnGermany
- Max Planck Fellow Chemical BiologyCenter of Advanced European Studies and Research (caesar)Ludwig-Erhard-Allee 253175BonnGermany
| | - Stefan Breuers
- Life and Medical Sciences (LIMES)University of BonnGerhard-Domagk-Str.153121BonnGermany
- Center of Aptamer Research & DevelopmentUniversity of BonnGerhard-Domagk-Str. 153121BonnGermany
| | - Volkmar Fieberg
- Life and Medical Sciences (LIMES)University of BonnGerhard-Domagk-Str.153121BonnGermany
- Max Planck Fellow Chemical BiologyCenter of Advanced European Studies and Research (caesar)Ludwig-Erhard-Allee 253175BonnGermany
| | - Michael Famulok
- Life and Medical Sciences (LIMES)University of BonnGerhard-Domagk-Str.153121BonnGermany
- Max Planck Fellow Chemical BiologyCenter of Advanced European Studies and Research (caesar)Ludwig-Erhard-Allee 253175BonnGermany
- Center of Aptamer Research & DevelopmentUniversity of BonnGerhard-Domagk-Str. 153121BonnGermany
| | - Günter Mayer
- Life and Medical Sciences (LIMES)University of BonnGerhard-Domagk-Str.153121BonnGermany
- Center of Aptamer Research & DevelopmentUniversity of BonnGerhard-Domagk-Str. 153121BonnGermany
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Alomari A, Gowland R, Southwood C, Barrow J, Bentley Z, Calvin-Nelson J, Kaminski A, LeFevre M, Callaghan AJ, Vincent HA, Gowers DM. Identification of Novel Inhibitors of Escherichia coli DNA Ligase (LigA). Molecules 2021; 26:molecules26092508. [PMID: 33923034 PMCID: PMC8123306 DOI: 10.3390/molecules26092508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 11/16/2022] Open
Abstract
Present in all organisms, DNA ligases catalyse the formation of a phosphodiester bond between a 3' hydroxyl and a 5' phosphate, a reaction that is essential for maintaining genome integrity during replication and repair. Eubacterial DNA ligases use NAD+ as a cofactor and possess low sequence and structural homology relative to eukaryotic DNA ligases which use ATP as a cofactor. These key differences enable specific targeting of bacterial DNA ligases as an antibacterial strategy. In this study, four small molecule accessible sites within functionally important regions of Escherichia coli ligase (EC-LigA) were identified using in silico methods. Molecular docking was then used to screen for small molecules predicted to bind to these sites. Eight candidate inhibitors were then screened for inhibitory activity in an in vitro ligase assay. Five of these (geneticin, chlorhexidine, glutathione (reduced), imidazolidinyl urea and 2-(aminomethyl)imidazole) showed dose-dependent inhibition of EC-LigA with half maximal inhibitory concentrations (IC50) in the micromolar to millimolar range (11-2600 µM). Two (geneticin and chlorhexidine) were predicted to bind to a region of EC-LigA that has not been directly investigated previously, raising the possibility that there may be amino acids within this region that are important for EC-LigA activity or that the function of essential residues proximal to this region are impacted by inhibitor interactions with this region. We anticipate that the identified small molecule binding sites and inhibitors could be pursued as part of an antibacterial strategy targeting bacterial DNA ligases.
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Affiliation(s)
- Arqam Alomari
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK or (A.A.); (R.G.); (C.S.); (J.B.); (Z.B.); (J.C.-N.); (A.K.); (M.L.); (A.J.C.); (H.A.V.)
- Department of Basic Sciences, College of Agriculture and Forestry, University of Mosul, Mosul 41002, Iraq
| | - Robert Gowland
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK or (A.A.); (R.G.); (C.S.); (J.B.); (Z.B.); (J.C.-N.); (A.K.); (M.L.); (A.J.C.); (H.A.V.)
| | - Callum Southwood
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK or (A.A.); (R.G.); (C.S.); (J.B.); (Z.B.); (J.C.-N.); (A.K.); (M.L.); (A.J.C.); (H.A.V.)
| | - Jak Barrow
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK or (A.A.); (R.G.); (C.S.); (J.B.); (Z.B.); (J.C.-N.); (A.K.); (M.L.); (A.J.C.); (H.A.V.)
| | - Zoe Bentley
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK or (A.A.); (R.G.); (C.S.); (J.B.); (Z.B.); (J.C.-N.); (A.K.); (M.L.); (A.J.C.); (H.A.V.)
| | - Jashel Calvin-Nelson
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK or (A.A.); (R.G.); (C.S.); (J.B.); (Z.B.); (J.C.-N.); (A.K.); (M.L.); (A.J.C.); (H.A.V.)
| | - Alice Kaminski
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK or (A.A.); (R.G.); (C.S.); (J.B.); (Z.B.); (J.C.-N.); (A.K.); (M.L.); (A.J.C.); (H.A.V.)
| | - Matthew LeFevre
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK or (A.A.); (R.G.); (C.S.); (J.B.); (Z.B.); (J.C.-N.); (A.K.); (M.L.); (A.J.C.); (H.A.V.)
| | - Anastasia J. Callaghan
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK or (A.A.); (R.G.); (C.S.); (J.B.); (Z.B.); (J.C.-N.); (A.K.); (M.L.); (A.J.C.); (H.A.V.)
| | - Helen A. Vincent
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK or (A.A.); (R.G.); (C.S.); (J.B.); (Z.B.); (J.C.-N.); (A.K.); (M.L.); (A.J.C.); (H.A.V.)
| | - Darren M. Gowers
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK or (A.A.); (R.G.); (C.S.); (J.B.); (Z.B.); (J.C.-N.); (A.K.); (M.L.); (A.J.C.); (H.A.V.)
- Correspondence:
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49
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Alqarni MH, Foudah AI, Muharram MM, Labrou NE. The Interaction of Human Glutathione Transferase GSTA1-1 with Reactive Dyes. Molecules 2021; 26:molecules26082399. [PMID: 33924269 PMCID: PMC8074892 DOI: 10.3390/molecules26082399] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/05/2021] [Accepted: 04/16/2021] [Indexed: 11/16/2022] Open
Abstract
Human glutathione transferase A1-1 (hGSTA1-1) contributes to developing resistance to anticancer drugs and, therefore, is promising in terms of drug-design targets for coping with this phenomenon. In the present study, the interaction of anthraquinone and diazo dichlorotriazine dyes (DCTD) with hGSTA1-1 was investigated. The anthraquinone dye Procion blue MX-R (PBMX-R) appeared to interact with higher affinity and was selected for further study. The enzyme was specifically and irreversibly inactivated by PBMX-R, following a biphasic pseudo-first-order saturation kinetics, with approximately 1 mol of inhibitor per mol of the dimeric enzyme being incorporated. Molecular modeling and protein chemistry data suggested that the modified residue is the Cys112, which is located at the entrance of the solvent channel at the subunits interface. The results suggest that negative cooperativity exists upon PBMX-R binding, indicating a structural communication between the two subunits. Kinetic inhibition analysis showed that the dye is a competitive inhibitor towards glutathione (GSH) and mixed-type inhibitor towards 1-chloro-2,4-dinitrobenzene (CDNB). The present study results suggest that PBMX-R is a useful probe suitable for assessing by kinetic means the drugability of the enzyme in future drug-design efforts.
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Affiliation(s)
- Mohammed Hamed Alqarni
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Alkharj 11942, Saudi Arabia;
- Correspondence: (M.H.A.); (N.E.L.)
| | - Ahmed Ibrahim Foudah
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Alkharj 11942, Saudi Arabia;
| | - Magdy Mohamed Muharram
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Alkharj 11942, Saudi Arabia;
- Department of Microbiology, College of Science, Al-Azhar University, Nasr City, Cairo 11884, Egypt
| | - Nikolaos E. Labrou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, 75 Iera Odos Street, GR-11855 Athens, Greece
- Correspondence: (M.H.A.); (N.E.L.)
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50
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Jin F, Sun M, Fujii T, Yamada Y, Wang J, Maturana AD, Wada M, Su S, Ma J, Takeda H, Kusakizako T, Tomita A, Nakada-Nakura Y, Liu K, Uemura T, Nomura Y, Nomura N, Ito K, Nureki O, Namba K, Iwata S, Yu Y, Hattori M. The structure of MgtE in the absence of magnesium provides new insights into channel gating. PLoS Biol 2021; 19:e3001231. [PMID: 33905418 PMCID: PMC8104411 DOI: 10.1371/journal.pbio.3001231] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 05/07/2021] [Accepted: 04/12/2021] [Indexed: 12/15/2022] Open
Abstract
MgtE is a Mg2+ channel conserved in organisms ranging from prokaryotes to eukaryotes, including humans, and plays an important role in Mg2+ homeostasis. The previously determined MgtE structures in the Mg2+-bound, closed-state, and structure-based functional analyses of MgtE revealed that the binding of Mg2+ ions to the MgtE cytoplasmic domain induces channel inactivation to maintain Mg2+ homeostasis. There are no structures of the transmembrane (TM) domain for MgtE in Mg2+-free conditions, and the pore-opening mechanism has thus remained unclear. Here, we determined the cryo-electron microscopy (cryo-EM) structure of the MgtE-Fab complex in the absence of Mg2+ ions. The Mg2+-free MgtE TM domain structure and its comparison with the Mg2+-bound, closed-state structure, together with functional analyses, showed the Mg2+-dependent pore opening of MgtE on the cytoplasmic side and revealed the kink motions of the TM2 and TM5 helices at the glycine residues, which are important for channel activity. Overall, our work provides structure-based mechanistic insights into the channel gating of MgtE.
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Affiliation(s)
- Fei Jin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Key Laboratory of Bioactive Small Molecules, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai, China
| | - Minxuan Sun
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Key Laboratory of Bioactive Small Molecules, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai, China
| | - Takashi Fujii
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
- Riken Quantitative Biology Center, Osaka, Japan
| | - Yurika Yamada
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Jin Wang
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Andrés D. Maturana
- Department of Bioengineering Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Miki Wada
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Shichen Su
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Multiscale Research Institute for Complex Systems, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Multiscale Research Institute for Complex Systems, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai, China
| | - Hironori Takeda
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
| | - Tsukasa Kusakizako
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Atsuhiro Tomita
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Yoshiko Nakada-Nakura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kehong Liu
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tomoko Uemura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yayoi Nomura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Norimichi Nomura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Koichi Ito
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
- Riken Quantitative Biology Center, Osaka, Japan
| | - So Iwata
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- RIKEN SPring-8 Center, Kouto, Hyogo, Japan
| | - Ye Yu
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Motoyuki Hattori
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Key Laboratory of Bioactive Small Molecules, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai, China
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