1
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Owuocha LF, Mitchum MG, Beamer LJ. Structural insights into binding of polyglutamylated tetrahydrofolate by serine hydroxymethyltransferase 8 from soybean. FRONTIERS IN PLANT SCIENCE 2024; 15:1451839. [PMID: 39224855 PMCID: PMC11366715 DOI: 10.3389/fpls.2024.1451839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Accepted: 07/31/2024] [Indexed: 09/04/2024]
Abstract
Tetrahydrofolate and its derivatives participate in one-carbon transfer reactions in all organisms. The cellular form of tetrahydrofolate (THF) is modified by multiple glutamate residues and polyglutamylation plays a key role in organellar and cellular folate homeostasis. In addition, polyglutamylation of THF is known to increase the binding affinity to enzymes in the folate cycle, many of which can utilize polyglutamylated THF as a substrate. Here, we use X-ray crystallography to provide a high-resolution view of interactions between the enzyme serine hydroxymethyltransferase (SHMT), which provides one carbon precursors for the folate cycle, and a polyglutamylated form of THF. Our 1.7 Å crystal structure of soybean SHMT8 in complex with diglutamylated 5-formyl-THF reveals, for the first time, a structural rearrangement of a loop at the entrance to the folate binding site accompanied by the formation of novel specific interactions between the enzyme and the diglutamyl tail of the ligand. Biochemical assays show that additional glutamate moieties on the folate ligand increase both enzyme stability and binding affinity. Together these studies provide new information on SHMT structure and function and inform the design of anti-folate agents.
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Affiliation(s)
- Luckio F. Owuocha
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Melissa G. Mitchum
- Department of Plant Pathology and Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Athens, GA, United States
| | - Lesa J. Beamer
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
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2
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Monticelli M, Hay Mele B, Wright DM, Guerriero S, Andreotti G, Cubellis MV. Exploring ligand interactions with human phosphomannomutases using recombinant bacterial thermal shift assay and biochemical validation. Biochimie 2024; 222:123-131. [PMID: 38458414 DOI: 10.1016/j.biochi.2024.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 02/26/2024] [Indexed: 03/10/2024]
Abstract
PMM2-CDG, a disease caused by mutations in phosphomannomutase-2, is the most common congenital disorder of glycosylation. Yet, it still lacks a cure. Targeting phosphomannomutase-2 with pharmacological chaperones or inhibiting the phosphatase activity of phosphomannomutase-1 to enhance intracellular glucose-1,6-bisphosphate have been proposed as therapeutical approaches. We used Recombinant Bacterial Thermal Shift Assay to assess the binding of a substrate analog to phosphomannomutase-2 and the specific binding to phosphomannomutase-1 of an FDA-approved drug - clodronate. We also deepened the clodronate binding by enzyme activity assays and in silico docking. Our results confirmed the selective binding of clodronate to phosphomannomutase-1 and shed light on such binding.
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Affiliation(s)
- Maria Monticelli
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078, Pozzuoli, Italy; Department of Biology, University of Napoli "Federico II", Complesso Universitario Monte Sant'Angelo, Via Cinthia, 80126, Napoli, Italy
| | - Bruno Hay Mele
- Department of Biology, University of Napoli "Federico II", Complesso Universitario Monte Sant'Angelo, Via Cinthia, 80126, Napoli, Italy
| | - Demi Marie Wright
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078, Pozzuoli, Italy; Institute of Chemistry and Biochemistry, Freie Universität Berlin, D-14195, Berlin, Germany
| | - Simone Guerriero
- Department of Biology, University of Napoli "Federico II", Complesso Universitario Monte Sant'Angelo, Via Cinthia, 80126, Napoli, Italy
| | - Giuseppina Andreotti
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078, Pozzuoli, Italy.
| | - Maria Vittoria Cubellis
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078, Pozzuoli, Italy; Department of Biology, University of Napoli "Federico II", Complesso Universitario Monte Sant'Angelo, Via Cinthia, 80126, Napoli, Italy; Stazione Zoologica "Anton Dohrn", Villa Comunale, Naples, Italy
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3
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Monticelli M, Wright DM, Cubellis MV, Andreotti G. ReBaTSA: A simplified CeTSA protocol for studying recombinant mutant proteins in bacterial extracts. Biochim Biophys Acta Gen Subj 2024; 1868:130526. [PMID: 38049040 DOI: 10.1016/j.bbagen.2023.130526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/15/2023] [Accepted: 11/27/2023] [Indexed: 12/06/2023]
Abstract
INTRODUCTION The study of protein stability is crucial to biochemistry and relies on different methodologies. Recently, the Cellular Thermal Shift Assay has been introduced to study protein stability in whole cells. METHODS We report a novel application of CeTSA named ReBaTSA. This Recombinant Bacterial TSA was performed using clear extracts from bacteria expressing a recombinant protein, incubated at different temperatures, centrifuged and analyzed via SDS-PAGE. RESULTS AND CONCLUSIONS We demonstrated the feasibility and reliability of this simplified approach. We validated the method using the protein phosphomannomutase-2 and its common mutants, which were compared in the presence or the absence of a known ligand.
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Affiliation(s)
- Maria Monticelli
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy; Department of Biology, University of Napoli "Federico II", Complesso Universitario Monte Sant'Angelo, Via Cinthia, 80126 Napoli, Italy
| | - Demi Marie Wright
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy; Institute of Chemistry and Biochemistry, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Maria Vittoria Cubellis
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy; Department of Biology, University of Napoli "Federico II", Complesso Universitario Monte Sant'Angelo, Via Cinthia, 80126 Napoli, Italy; Stazione Zoologica "Anton Dohrn", Villa Comunale, Naples, Italy.
| | - Giuseppina Andreotti
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy.
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4
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Malakoutikhah M, Mahran R, Gooran N, Masoumi A, Lundell K, Liljeblad A, Guiley K, Dai S, Zheng Q, Zhu L, Shokat KM, Kopra K, Härmä H. Nanomolar Protein Thermal Profiling with Modified Cyanine Dyes. Anal Chem 2023; 95:18344-18351. [PMID: 38060502 PMCID: PMC10733900 DOI: 10.1021/acs.analchem.3c02844] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 11/15/2023] [Accepted: 11/17/2023] [Indexed: 12/20/2023]
Abstract
Protein properties and interactions have been widely investigated by using external labels. However, the micromolar sensitivity of the current dyes limits their applicability due to the high material consumption and assay cost. In response to this challenge, we synthesized a series of cyanine5 (Cy5) dye-based quencher molecules to develop an external dye technique to probe proteins at the nanomolar protein level in a high-throughput one-step assay format. Several families of Cy5 dye-based quenchers with ring and/or side-chain modifications were designed and synthesized by introducing organic small molecules or peptides. Our results showed that steric hindrance and electrostatic interactions are more important than hydrophobicity in the interaction between the luminescent negatively charged europium-chelate-labeled peptide (Eu-probe) and the quencher molecules. The presence of substituents on the quencher indolenine rings reduces their quenching property, whereas the increased positive charge on the indolenine side chain improved the interaction between the quenchers and the luminescent compound. The designed quencher structures entirely altered the dynamics of the Eu-probe (protein-probe) for studying protein stability and interactions, as we were able to reduce the quencher concentration 100-fold. Moreover, the new quencher molecules allowed us to conduct the experiments using neutral buffer conditions, known as the peptide-probe assay. These improvements enabled us to apply the method in a one-step format for nanomolar protein-ligand interaction and protein profiling studies instead of the previously developed two-step protocol. These improvements provide a faster and simpler method with lower material consumption.
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Affiliation(s)
| | - Randa Mahran
- Department
of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland
| | - Negin Gooran
- Department
of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland
| | - Ahmadreza Masoumi
- Department
of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland
| | - Katri Lundell
- Laboratory
of Synthetic Drug Chemistry, Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, FI-20520 Turku, Finland
| | - Arto Liljeblad
- Laboratory
of Synthetic Drug Chemistry, Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, FI-20520 Turku, Finland
| | - Keelan Guiley
- Department
of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, California 94158, United States
- Current
address: Rezo Therapeutics, Inc., San Francisco, California 94158, United States
| | - Shizhong Dai
- Department
of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, California 94158, United States
- Current
address: Department of Genetics, Stanford
University, Stanford, California 94305, United States
| | - Qinheng Zheng
- Department
of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, California 94158, United States
| | - Lawrence Zhu
- Department
of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, California 94158, United States
| | - Kevan M. Shokat
- Department
of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, California 94158, United States
| | - Kari Kopra
- Department
of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland
| | - Harri Härmä
- Department
of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland
- Department
of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, California 94158, United States
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Yu J, Yuan H, Guo J, Dong Z, Li S, Fu Q, Aode B, Baoyin S, Bao L, Wu L. Combining multi-omics analysis to identify host-targeted targets for the control of Brucella infection. Microb Biotechnol 2023; 16:2345-2366. [PMID: 37882474 PMCID: PMC10686141 DOI: 10.1111/1751-7915.14307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 02/15/2023] [Accepted: 06/20/2023] [Indexed: 10/27/2023] Open
Abstract
Human infections caused by Brucella (called brucellosis) are among the most common zoonoses worldwide with an estimated 500,000 cases each year. Since chronic Brucella infections are extremely difficult to treat, there is an urgent need for more effective therapeutics. As a facultative intracellular bacterium, Brucella is strictly parasitic in the host cell. Here, we performed proteomic and transcriptomic and metabolomic analyses on Brucella infected patients, mice and cells that provided an extensive "map" of physiological changes in brucellosis patients and characterized the metabolic pathways essential to the response to infection, as well as the associated cellular response and molecular mechanisms. This is the first report utilizing multi-omics analysis to investigate the global response of proteins and metabolites associated with Brucella infection, and the data can provide a comprehensive insight to understand the mechanism of Brucella infection. We demonstrated that Brucella increased nucleotide synthesis in the host, consistent with increased biomass requirement. We also identified IMPDH2, a key regulatory complex that controls nucleotide synthesis during Brucella infection. Pharmacological targeting of IMPDH2, the rate-limiting enzyme in guanine nucleotide biosynthesis, efficiently inhibits B. abortus growth both in vitro and in vivo. Through screening a library of natural products, we identified oxymatrine, an alkaloid obtained primarily from Sophora roots, is a novel and selective IMPDH2 inhibitor. In further in vitro bacterial inhibition assays, oxymatrine effectively inhibited the growth of B. abortus, which was impaired by exogenous supplementation of guanosine, a salvage pathway of purine nucleotides. This moderately potent, structurally novel compound may provide clues for further design and development of efficient IMPDH2 inhibitors and also demonstrates the potential of natural compounds from plants against Brucella.
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Affiliation(s)
- Jiuwang Yu
- TCM Hospital of Mongolian Medicine in HohhotHohhotChina
| | - Hongwei Yuan
- Department of PathologyAffiliated Hospital of Inner Mongolia Medical UniversityHohhotChina
| | - Jiarong Guo
- TCM Hospital of Mongolian Medicine in HohhotHohhotChina
| | - Zhiheng Dong
- Department of PharmacyAffiliated Hospital of Inner Mongolia Medical UniversityHohhotChina
| | - Sha Li
- Department of PharmacyAffiliated Hospital of Inner Mongolia Medical UniversityHohhotChina
| | - Quan Fu
- Department of LaboratoryAffiliated Hospital of Inner Mongolia Medical UniversityHohhotChina
| | - Bilige Aode
- Department of Mongolian MedicineInner Mongolia Xilin Gol League Mongolian Medical HospitalXilinhaoteChina
| | - Sachula Baoyin
- Mongolia Medical SchoolInner Mongolia Medical UniversityHohhotChina
| | - Lidao Bao
- TCM Hospital of Mongolian Medicine in HohhotHohhotChina
| | - Lan Wu
- TCM Hospital of Mongolian Medicine in HohhotHohhotChina
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6
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Gao X, McFadden WM, Wen X, Emanuelli A, Lorson ZC, Zheng H, Kirby KA, Sarafianos SG. Use of TSAR, Thermal Shift Analysis in R, to identify Folic Acid as a Molecule that Interacts with HIV-1 Capsid. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.29.569293. [PMID: 38076946 PMCID: PMC10705415 DOI: 10.1101/2023.11.29.569293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Thermal shift assay (TSA) is a versatile biophysical technique for studying protein interactions. Here, we report a free, open-source software tool TSAR (Thermal Shift Analysis in R) to expedite and automate the analysis of thermal shift data derived either from individual experiments or large screens of chemical libraries. The TSAR package incorporates multiple, dynamic workflows to facilitate the analysis of TSA data and returns publication-ready graphics or processed results. Further, the package includes a graphic user interface (GUI) that enables easy use by non-programmers, aiming to simplify TSA analysis while diversifying visualization. To exemplify the utility of TSAR we screened a chemical library of vitamins to identify molecules that interact with the capsid protein (CA) of human immunodeficiency virus type 1 (HIV-1). Our data show that hexameric CA interacts with folic acid in vitro.
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Affiliation(s)
- X. Gao
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
- Children’s Healthcare of Atlanta, Atlanta, GA
| | - W. M. McFadden
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
- Children’s Healthcare of Atlanta, Atlanta, GA
| | - X. Wen
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
- Children’s Healthcare of Atlanta, Atlanta, GA
| | - A. Emanuelli
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
- Children’s Healthcare of Atlanta, Atlanta, GA
| | - Z. C. Lorson
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
- Children’s Healthcare of Atlanta, Atlanta, GA
| | - H. Zheng
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
- Children’s Healthcare of Atlanta, Atlanta, GA
| | - K. A. Kirby
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
- Children’s Healthcare of Atlanta, Atlanta, GA
| | - S. G. Sarafianos
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
- Children’s Healthcare of Atlanta, Atlanta, GA
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7
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Anding A, Kinton S, Baranowski K, Brezzani A, De Busser H, Dufault MR, Finn P, Keefe K, Tetrault T, Li Y, Qiu W, Raes K, Vitse O, Zhang M, Ziegler R, Sardi SP, Hunter B, George K. Increasing Enzyme Mannose-6-Phosphate Levels but Not Miglustat Coadministration Enhances the Efficacy of Enzyme Replacement Therapy in Pompe Mice. J Pharmacol Exp Ther 2023; 387:188-203. [PMID: 37679046 DOI: 10.1124/jpet.123.001593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/17/2023] [Accepted: 06/01/2023] [Indexed: 09/09/2023] Open
Abstract
Pompe disease is a rare glycogen storage disorder caused by a deficiency in the lysosomal enzyme acid α-glucosidase, which leads to muscle weakness, cardiac and respiratory failure, and early mortality. Alglucosidase alfa, a recombinant human acid α-glucosidase, was the first approved treatment of Pompe disease, but its uptake into skeletal muscle via the cation-independent mannose-6-phosphate (M6P) receptor (CIMPR) is limited. Avalglucosidase alfa has received marketing authorization in several countries for infantile-onset and/or late-onset Pompe disease. This recently approved enzyme replacement therapy (ERT) was glycoengineered to maximize CIMPR binding through high-affinity interactions with ∼7 bis-M6P moieties. Recently, small molecules like the glucosylceramide synthase inhibitor miglustat were reported to increase the stability of recombinant human acid α-glucosidase, and it was suggested that an increased serum half-life would result in better glycogen clearance. Here, the effects of miglustat on alglucosidase alfa and avalglucosidase alfa stability, activity, and efficacy in Pompe mice were evaluated. Although miglustat increased the stability of both enzymes in fluorescent protein thermal shift assays and when incubated in neutral pH buffer over time, it reduced their enzymatic activity by ∼50%. Improvement in tissue glycogen clearance and transcriptional dysregulation in Pompe mice correlated with M6P levels but not with miglustat coadministration. These results further substantiate the crucial role of CIMPR binding in lysosomal targeting of ERTs. SIGNIFICANCE STATEMENT: This work describes important new insights into the treatment of Pompe disease using currently approved enzyme replacement therapies (ERTs) coadministered with miglustat. Although miglustat increased the stability of ERTs in vitro, there was no positive impact to glycogen clearance and transcriptional correction in Pompe mice. However, increasing mannose-6-phosphate levels resulted in increased cell uptake in vitro and increased glycogen clearance and transcriptional correction in Pompe mice, further underscoring the crucial role of cation-independent mannose-6-phosphate receptor-mediated lysosomal targeting for ERTs.
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Affiliation(s)
- Allyson Anding
- Metabolic and Lysosomal Storage Disease Research, Rare and Neurologic Diseases Therapeutic Area (A.A., S.K., K.B., A.B., P.F., K.K., T.T., R.Z., S.P.S., B.H., K.G.), Precision Medicine and Computational Biology (M.R.D., M.Z.), and Nonclinical Efficacy and Safety (W.Q.), Sanofi, Cambridge, Massachusetts; Manufacturing Sciences, Analytics, and Technology (MSAT), Sanofi, Geel, Belgium (H.D.B., K.R.); Medicinal Chemistry, Integrated Drug Discovery, Sanofi, Waltham, Massachusetts (Y.L.); and Pharmacokinetics Dynamics and Metabolism, Sanofi, Montpellier, France (O.V.)
| | - Sofia Kinton
- Metabolic and Lysosomal Storage Disease Research, Rare and Neurologic Diseases Therapeutic Area (A.A., S.K., K.B., A.B., P.F., K.K., T.T., R.Z., S.P.S., B.H., K.G.), Precision Medicine and Computational Biology (M.R.D., M.Z.), and Nonclinical Efficacy and Safety (W.Q.), Sanofi, Cambridge, Massachusetts; Manufacturing Sciences, Analytics, and Technology (MSAT), Sanofi, Geel, Belgium (H.D.B., K.R.); Medicinal Chemistry, Integrated Drug Discovery, Sanofi, Waltham, Massachusetts (Y.L.); and Pharmacokinetics Dynamics and Metabolism, Sanofi, Montpellier, France (O.V.)
| | - Kaitlyn Baranowski
- Metabolic and Lysosomal Storage Disease Research, Rare and Neurologic Diseases Therapeutic Area (A.A., S.K., K.B., A.B., P.F., K.K., T.T., R.Z., S.P.S., B.H., K.G.), Precision Medicine and Computational Biology (M.R.D., M.Z.), and Nonclinical Efficacy and Safety (W.Q.), Sanofi, Cambridge, Massachusetts; Manufacturing Sciences, Analytics, and Technology (MSAT), Sanofi, Geel, Belgium (H.D.B., K.R.); Medicinal Chemistry, Integrated Drug Discovery, Sanofi, Waltham, Massachusetts (Y.L.); and Pharmacokinetics Dynamics and Metabolism, Sanofi, Montpellier, France (O.V.)
| | - Alexander Brezzani
- Metabolic and Lysosomal Storage Disease Research, Rare and Neurologic Diseases Therapeutic Area (A.A., S.K., K.B., A.B., P.F., K.K., T.T., R.Z., S.P.S., B.H., K.G.), Precision Medicine and Computational Biology (M.R.D., M.Z.), and Nonclinical Efficacy and Safety (W.Q.), Sanofi, Cambridge, Massachusetts; Manufacturing Sciences, Analytics, and Technology (MSAT), Sanofi, Geel, Belgium (H.D.B., K.R.); Medicinal Chemistry, Integrated Drug Discovery, Sanofi, Waltham, Massachusetts (Y.L.); and Pharmacokinetics Dynamics and Metabolism, Sanofi, Montpellier, France (O.V.)
| | - Hilde De Busser
- Metabolic and Lysosomal Storage Disease Research, Rare and Neurologic Diseases Therapeutic Area (A.A., S.K., K.B., A.B., P.F., K.K., T.T., R.Z., S.P.S., B.H., K.G.), Precision Medicine and Computational Biology (M.R.D., M.Z.), and Nonclinical Efficacy and Safety (W.Q.), Sanofi, Cambridge, Massachusetts; Manufacturing Sciences, Analytics, and Technology (MSAT), Sanofi, Geel, Belgium (H.D.B., K.R.); Medicinal Chemistry, Integrated Drug Discovery, Sanofi, Waltham, Massachusetts (Y.L.); and Pharmacokinetics Dynamics and Metabolism, Sanofi, Montpellier, France (O.V.)
| | - Michael R Dufault
- Metabolic and Lysosomal Storage Disease Research, Rare and Neurologic Diseases Therapeutic Area (A.A., S.K., K.B., A.B., P.F., K.K., T.T., R.Z., S.P.S., B.H., K.G.), Precision Medicine and Computational Biology (M.R.D., M.Z.), and Nonclinical Efficacy and Safety (W.Q.), Sanofi, Cambridge, Massachusetts; Manufacturing Sciences, Analytics, and Technology (MSAT), Sanofi, Geel, Belgium (H.D.B., K.R.); Medicinal Chemistry, Integrated Drug Discovery, Sanofi, Waltham, Massachusetts (Y.L.); and Pharmacokinetics Dynamics and Metabolism, Sanofi, Montpellier, France (O.V.)
| | - Patrick Finn
- Metabolic and Lysosomal Storage Disease Research, Rare and Neurologic Diseases Therapeutic Area (A.A., S.K., K.B., A.B., P.F., K.K., T.T., R.Z., S.P.S., B.H., K.G.), Precision Medicine and Computational Biology (M.R.D., M.Z.), and Nonclinical Efficacy and Safety (W.Q.), Sanofi, Cambridge, Massachusetts; Manufacturing Sciences, Analytics, and Technology (MSAT), Sanofi, Geel, Belgium (H.D.B., K.R.); Medicinal Chemistry, Integrated Drug Discovery, Sanofi, Waltham, Massachusetts (Y.L.); and Pharmacokinetics Dynamics and Metabolism, Sanofi, Montpellier, France (O.V.)
| | - Kelly Keefe
- Metabolic and Lysosomal Storage Disease Research, Rare and Neurologic Diseases Therapeutic Area (A.A., S.K., K.B., A.B., P.F., K.K., T.T., R.Z., S.P.S., B.H., K.G.), Precision Medicine and Computational Biology (M.R.D., M.Z.), and Nonclinical Efficacy and Safety (W.Q.), Sanofi, Cambridge, Massachusetts; Manufacturing Sciences, Analytics, and Technology (MSAT), Sanofi, Geel, Belgium (H.D.B., K.R.); Medicinal Chemistry, Integrated Drug Discovery, Sanofi, Waltham, Massachusetts (Y.L.); and Pharmacokinetics Dynamics and Metabolism, Sanofi, Montpellier, France (O.V.)
| | - Tanya Tetrault
- Metabolic and Lysosomal Storage Disease Research, Rare and Neurologic Diseases Therapeutic Area (A.A., S.K., K.B., A.B., P.F., K.K., T.T., R.Z., S.P.S., B.H., K.G.), Precision Medicine and Computational Biology (M.R.D., M.Z.), and Nonclinical Efficacy and Safety (W.Q.), Sanofi, Cambridge, Massachusetts; Manufacturing Sciences, Analytics, and Technology (MSAT), Sanofi, Geel, Belgium (H.D.B., K.R.); Medicinal Chemistry, Integrated Drug Discovery, Sanofi, Waltham, Massachusetts (Y.L.); and Pharmacokinetics Dynamics and Metabolism, Sanofi, Montpellier, France (O.V.)
| | - Yi Li
- Metabolic and Lysosomal Storage Disease Research, Rare and Neurologic Diseases Therapeutic Area (A.A., S.K., K.B., A.B., P.F., K.K., T.T., R.Z., S.P.S., B.H., K.G.), Precision Medicine and Computational Biology (M.R.D., M.Z.), and Nonclinical Efficacy and Safety (W.Q.), Sanofi, Cambridge, Massachusetts; Manufacturing Sciences, Analytics, and Technology (MSAT), Sanofi, Geel, Belgium (H.D.B., K.R.); Medicinal Chemistry, Integrated Drug Discovery, Sanofi, Waltham, Massachusetts (Y.L.); and Pharmacokinetics Dynamics and Metabolism, Sanofi, Montpellier, France (O.V.)
| | - Weiliang Qiu
- Metabolic and Lysosomal Storage Disease Research, Rare and Neurologic Diseases Therapeutic Area (A.A., S.K., K.B., A.B., P.F., K.K., T.T., R.Z., S.P.S., B.H., K.G.), Precision Medicine and Computational Biology (M.R.D., M.Z.), and Nonclinical Efficacy and Safety (W.Q.), Sanofi, Cambridge, Massachusetts; Manufacturing Sciences, Analytics, and Technology (MSAT), Sanofi, Geel, Belgium (H.D.B., K.R.); Medicinal Chemistry, Integrated Drug Discovery, Sanofi, Waltham, Massachusetts (Y.L.); and Pharmacokinetics Dynamics and Metabolism, Sanofi, Montpellier, France (O.V.)
| | - Katrien Raes
- Metabolic and Lysosomal Storage Disease Research, Rare and Neurologic Diseases Therapeutic Area (A.A., S.K., K.B., A.B., P.F., K.K., T.T., R.Z., S.P.S., B.H., K.G.), Precision Medicine and Computational Biology (M.R.D., M.Z.), and Nonclinical Efficacy and Safety (W.Q.), Sanofi, Cambridge, Massachusetts; Manufacturing Sciences, Analytics, and Technology (MSAT), Sanofi, Geel, Belgium (H.D.B., K.R.); Medicinal Chemistry, Integrated Drug Discovery, Sanofi, Waltham, Massachusetts (Y.L.); and Pharmacokinetics Dynamics and Metabolism, Sanofi, Montpellier, France (O.V.)
| | - Olivier Vitse
- Metabolic and Lysosomal Storage Disease Research, Rare and Neurologic Diseases Therapeutic Area (A.A., S.K., K.B., A.B., P.F., K.K., T.T., R.Z., S.P.S., B.H., K.G.), Precision Medicine and Computational Biology (M.R.D., M.Z.), and Nonclinical Efficacy and Safety (W.Q.), Sanofi, Cambridge, Massachusetts; Manufacturing Sciences, Analytics, and Technology (MSAT), Sanofi, Geel, Belgium (H.D.B., K.R.); Medicinal Chemistry, Integrated Drug Discovery, Sanofi, Waltham, Massachusetts (Y.L.); and Pharmacokinetics Dynamics and Metabolism, Sanofi, Montpellier, France (O.V.)
| | - Mindy Zhang
- Metabolic and Lysosomal Storage Disease Research, Rare and Neurologic Diseases Therapeutic Area (A.A., S.K., K.B., A.B., P.F., K.K., T.T., R.Z., S.P.S., B.H., K.G.), Precision Medicine and Computational Biology (M.R.D., M.Z.), and Nonclinical Efficacy and Safety (W.Q.), Sanofi, Cambridge, Massachusetts; Manufacturing Sciences, Analytics, and Technology (MSAT), Sanofi, Geel, Belgium (H.D.B., K.R.); Medicinal Chemistry, Integrated Drug Discovery, Sanofi, Waltham, Massachusetts (Y.L.); and Pharmacokinetics Dynamics and Metabolism, Sanofi, Montpellier, France (O.V.)
| | - Robin Ziegler
- Metabolic and Lysosomal Storage Disease Research, Rare and Neurologic Diseases Therapeutic Area (A.A., S.K., K.B., A.B., P.F., K.K., T.T., R.Z., S.P.S., B.H., K.G.), Precision Medicine and Computational Biology (M.R.D., M.Z.), and Nonclinical Efficacy and Safety (W.Q.), Sanofi, Cambridge, Massachusetts; Manufacturing Sciences, Analytics, and Technology (MSAT), Sanofi, Geel, Belgium (H.D.B., K.R.); Medicinal Chemistry, Integrated Drug Discovery, Sanofi, Waltham, Massachusetts (Y.L.); and Pharmacokinetics Dynamics and Metabolism, Sanofi, Montpellier, France (O.V.)
| | - S Pablo Sardi
- Metabolic and Lysosomal Storage Disease Research, Rare and Neurologic Diseases Therapeutic Area (A.A., S.K., K.B., A.B., P.F., K.K., T.T., R.Z., S.P.S., B.H., K.G.), Precision Medicine and Computational Biology (M.R.D., M.Z.), and Nonclinical Efficacy and Safety (W.Q.), Sanofi, Cambridge, Massachusetts; Manufacturing Sciences, Analytics, and Technology (MSAT), Sanofi, Geel, Belgium (H.D.B., K.R.); Medicinal Chemistry, Integrated Drug Discovery, Sanofi, Waltham, Massachusetts (Y.L.); and Pharmacokinetics Dynamics and Metabolism, Sanofi, Montpellier, France (O.V.)
| | - Bridge Hunter
- Metabolic and Lysosomal Storage Disease Research, Rare and Neurologic Diseases Therapeutic Area (A.A., S.K., K.B., A.B., P.F., K.K., T.T., R.Z., S.P.S., B.H., K.G.), Precision Medicine and Computational Biology (M.R.D., M.Z.), and Nonclinical Efficacy and Safety (W.Q.), Sanofi, Cambridge, Massachusetts; Manufacturing Sciences, Analytics, and Technology (MSAT), Sanofi, Geel, Belgium (H.D.B., K.R.); Medicinal Chemistry, Integrated Drug Discovery, Sanofi, Waltham, Massachusetts (Y.L.); and Pharmacokinetics Dynamics and Metabolism, Sanofi, Montpellier, France (O.V.)
| | - Kelly George
- Metabolic and Lysosomal Storage Disease Research, Rare and Neurologic Diseases Therapeutic Area (A.A., S.K., K.B., A.B., P.F., K.K., T.T., R.Z., S.P.S., B.H., K.G.), Precision Medicine and Computational Biology (M.R.D., M.Z.), and Nonclinical Efficacy and Safety (W.Q.), Sanofi, Cambridge, Massachusetts; Manufacturing Sciences, Analytics, and Technology (MSAT), Sanofi, Geel, Belgium (H.D.B., K.R.); Medicinal Chemistry, Integrated Drug Discovery, Sanofi, Waltham, Massachusetts (Y.L.); and Pharmacokinetics Dynamics and Metabolism, Sanofi, Montpellier, France (O.V.)
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8
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Enzyme Replacement Therapy for FABRY Disease: Possible Strategies to Improve Its Efficacy. Int J Mol Sci 2023; 24:ijms24054548. [PMID: 36901983 PMCID: PMC10003632 DOI: 10.3390/ijms24054548] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/20/2023] [Accepted: 02/23/2023] [Indexed: 03/02/2023] Open
Abstract
Enzyme replacement therapy is the only therapeutic option for Fabry patients with completely absent AGAL activity. However, the treatment has side effects, is costly, and requires conspicuous amounts of recombinant human protein (rh-AGAL). Thus, its optimization would benefit patients and welfare/health services (i.e., society at large). In this brief report, we describe preliminary results paving the way for two possible approaches: i. the combination of enzyme replacement therapy with pharmacological chaperones; and ii. the identification of AGAL interactors as possible therapeutic targets on which to act. We first showed that galactose, a low-affinity pharmacological chaperone, can prolong AGAL half-life in patient-derived cells treated with rh-AGAL. Then, we analyzed the interactomes of intracellular AGAL on patient-derived AGAL-defective fibroblasts treated with the two rh-AGALs approved for therapeutic purposes and compared the obtained interactomes to the one associated with endogenously produced AGAL (data available as PXD039168 on ProteomeXchange). Common interactors were aggregated and screened for sensitivity to known drugs. Such an interactor-drug list represents a starting point to deeply screen approved drugs and identify those that can affect (positively or negatively) enzyme replacement therapy.
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9
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Zane G, Silveria M, Meyer N, White T, Duan R, Zou X, Chapman M. Cryo-EM structure of adeno-associated virus 4 at 2.2 Å resolution. Acta Crystallogr D Struct Biol 2023; 79:140-153. [PMID: 36762860 PMCID: PMC9912921 DOI: 10.1107/s2059798322012190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 12/26/2022] [Indexed: 01/21/2023] Open
Abstract
Adeno-associated virus (AAV) is the vector of choice for several approved gene-therapy treatments and is the basis for many ongoing clinical trials. Various strains of AAV exist (referred to as serotypes), each with their own transfection characteristics. Here, a high-resolution cryo-electron microscopy structure (2.2 Å) of AAV serotype 4 (AAV4) is presented. The receptor responsible for transduction of the AAV4 clade of AAV viruses (including AAV11, AAV12 and AAVrh32.33) is unknown. Other AAVs interact with the same cell receptor, adeno-associated virus receptor (AAVR), in one of two different ways. AAV5-like viruses interact exclusively with the polycystic kidney disease-like 1 (PKD1) domain of AAVR, while most other AAVs interact primarily with the PKD2 domain. A comparison of the present AAV4 structure with prior corresponding structures of AAV5, AAV2 and AAV1 in complex with AAVR provides a foundation for understanding why the AAV4-like clade is unable to interact with either PKD1 or PKD2 of AAVR. The conformation of the AAV4 capsid in variable regions I, III, IV and V on the viral surface appears to be sufficiently different from AAV2 to ablate binding with PKD2. Differences between AAV4 and AAV5 in variable region VII appear to be sufficient to exclude binding with PKD1.
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Affiliation(s)
- Grant Zane
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Mark Silveria
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Nancy Meyer
- Center for Spatial Systems Biomedicine, Oregon Health Sciences University, Portland, Oregon, USA
| | - Tommi White
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
- Bayer Crop Science, Bayer (United States), Chesterfield, MO 63017, USA
- Electron Microscopy Core, University of Missouri, Columbia, MO 65211, USA
| | - Rui Duan
- Dalton Cardiovascular Center, University of Missouri, Columbia, MO 65211, USA
| | - Xiaoqin Zou
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
- Dalton Cardiovascular Center, University of Missouri, Columbia, MO 65211, USA
- Department of Physics, University of Missouri, Columbia, MO 65211, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Michael Chapman
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
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10
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Li HY, Lee NC, Chiu YT, Chang YW, Lin CC, Chou CL, Chien YH, Hwu WL, Cheng WC. Harnessing polyhydroxylated pyrrolidines as a stabilizer of acid alpha-glucosidase (GAA) to enhance the efficacy of enzyme replacement therapy in Pompe disease. Bioorg Med Chem 2023; 78:117129. [PMID: 36542959 DOI: 10.1016/j.bmc.2022.117129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/29/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022]
Abstract
To discover small molecules as acid alpha-glucosidase (GAA) stabilizers for potential benefits of the exogenous enzyme treatment toward Pompe disease cells, we started from the initial screening of the unique chemical space, consisting of sixteen stereoisomers of 2-aminomethyl polyhydroxylated pyrrolidines (ADMDPs) to find out two primary stabilizers 17 and 18. Further external or internal structural modifications of 17 and 18 were performed to increase structural diversity, followed by the protein thermal shift study to evaluate the GAA stabilizing ability. Fortunately, pyrrolidine 21, possessing an l-arabino-typed configuration pattern, was identified as a specific potent rh-GAA stabilizer, enabling the suppression of rh-GAA protein denaturation. In a cell-based Pompe model, co-administration of 21 with rh-GAA protein significantly improved enzymatic activity (up to 5-fold) compared to administration of enzyme alone. Potentially, pyrrolidine 21 enables the direct increase of ERT (enzyme replacement therapy) efficacy in cellulo and in vivo.
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Affiliation(s)
- Huang-Yi Li
- Genomics Research Center, Academia Sinica, 128, Academia Road, Section 2, Nankang, Taipei 11529, Taiwan; Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, 1001, University Road, Hsinchu 300, Taiwan
| | - Ni-Chung Lee
- Department of Pediatrics and Medical Genetics, National Taiwan University Hospital, 8 Chung-Shan South Road, Taipei 10041, Taiwan
| | - Yu-Ting Chiu
- Genomics Research Center, Academia Sinica, 128, Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Yu-Wen Chang
- Genomics Research Center, Academia Sinica, 128, Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Chu-Chung Lin
- AnHorn Medicines Co., Ltd. National Biotechnology Research Park C522, 99, Lane 130, Academia Road, Section 1, Nankang, Taipei 11529, Taiwan
| | - Cheng-Li Chou
- AnHorn Medicines Co., Ltd. National Biotechnology Research Park C522, 99, Lane 130, Academia Road, Section 1, Nankang, Taipei 11529, Taiwan
| | - Yin-Hsiu Chien
- Department of Pediatrics and Medical Genetics, National Taiwan University Hospital, 8 Chung-Shan South Road, Taipei 10041, Taiwan
| | - Wuh-Liang Hwu
- Department of Pediatrics and Medical Genetics, National Taiwan University Hospital, 8 Chung-Shan South Road, Taipei 10041, Taiwan.
| | - Wei-Chieh Cheng
- Genomics Research Center, Academia Sinica, 128, Academia Road, Section 2, Nankang, Taipei 11529, Taiwan; Department of Chemistry, National Cheng Kung University, 1, University Road, Tainan 70101, Taiwan; Department of Chemistry, National University of Kaohsiung, 700, Kaohsiung University Road, Nanzih District, Kaohsiung 81148, Taiwan; Department of Chemistry, National Chiayi University, 300, Syuefu Road, Chiayi 60004, Taiwan.
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11
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Monticelli M, Hay Mele B, Allocca M, Liguori L, Lukas J, Monti MC, Morretta E, Cubellis MV, Andreotti G. Curcumin Has Beneficial Effects on Lysosomal Alpha-Galactosidase: Potential Implications for the Cure of Fabry Disease. Int J Mol Sci 2023; 24:ijms24021095. [PMID: 36674610 PMCID: PMC9863837 DOI: 10.3390/ijms24021095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/28/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023] Open
Abstract
Fabry disease is a lysosomal storage disease caused by mutations in the GLA gene that encodes alpha-galactosidase (AGAL). The disease causes abnormal globotriaosylceramide (Gb3) storage in the lysosomes. Variants responsible for the genotypic spectrum of Fabry disease include mutations that abolish enzymatic activity and those that cause protein instability. The latter can be successfully treated with small molecules that either bind and stabilize AGAL or indirectly improve its cellular activity. This paper describes the first attempt to reposition curcumin, a nutraceutical, to treat Fabry disease. We tested the efficacy of curcumin in a cell model and found an improvement in AGAL activity for 80% of the tested mutant genotypes (four out of five tested). The fold-increase was dependent on the mutant and ranged from 1.4 to 2.2. We produced evidence that supports a co-chaperone role for curcumin when administered with AGAL pharmacological chaperones (1-deoxygalactonojirimycin and galactose). The combined treatment with curcumin and either pharmacological chaperone was beneficial for four out of five tested mutants and showed fold-increases ranging from 1.1 to 2.3 for DGJ and from 1.1 to 2.8 for galactose. Finally, we tested a long-term treatment on one mutant (L300F) and detected an improvement in Gb3 clearance and lysosomal markers (LAMP-1 and GAA). Altogether, our findings confirmed the necessity of personalized therapies for Fabry patients and paved the way to further studies and trials of treatments for Fabry disease.
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Affiliation(s)
- Maria Monticelli
- Department of Biology, University of Napoli “Federico II”, Complesso Universitario Monte Sant’Angelo, Via Cinthia, 80126 Napoli, Italy
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy
- Department of Environmental, Biological, and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Bruno Hay Mele
- Department of Biology, University of Napoli “Federico II”, Complesso Universitario Monte Sant’Angelo, Via Cinthia, 80126 Napoli, Italy
| | - Mariateresa Allocca
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy
- Department of Environmental, Biological, and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Ludovica Liguori
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy
- Department of Environmental, Biological, and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Jan Lukas
- Translational Neurodegeneration Section “Albrecht-Kossel”, Department of Neurology, University Medical Center Rostock, 18147 Rostock, Germany
- Center for Transdisciplinary Neurosciences Rostock (CTNR), University Medical Center Rostock, 18147 Rostock, Germany
| | - Maria Chiara Monti
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy
| | - Elva Morretta
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy
| | - Maria Vittoria Cubellis
- Department of Biology, University of Napoli “Federico II”, Complesso Universitario Monte Sant’Angelo, Via Cinthia, 80126 Napoli, Italy
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy
- Correspondence: ; Tel.: +39-081-679-152
| | - Giuseppina Andreotti
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy
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12
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Engrola FSS, Paquete-Ferreira J, Santos-Silva T, Correia MAS, Leisico F, Santos MFA. Screening of Buffers and Additives for Protein Stabilization by Thermal Shift Assay: A Practical Approach. Methods Mol Biol 2023; 2652:199-213. [PMID: 37093477 DOI: 10.1007/978-1-0716-3147-8_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Thermal shift assay (TSA), also commonly designed by differential scanning fluorimetry (DSF) or ThermoFluor, is a technique relatively easy to implement and perform, useful in a myriad of applications. In addition to versatility, it is also rather inexpensive, making it suitable for high-throughput approaches. TSA uses a fluorescent dye to monitor the thermal denaturation of the protein under study and determine its melting temperature (Tm). One of its main applications is to identify the best buffers and additives that enhance protein stability.Understanding the TSA operating mode and the main methodological steps is a central key to designing effective experiments and retrieving meaningful conclusions. This chapter intends to present a straightforward TSA protocol, with different troubleshooting tips, to screen effective protein stabilizers such as buffers and additives, as well as data treatment and analysis. TSA results provide conditions in which the protein of interest is stable and therefore suitable to carry out further biophysical and structural characterization.
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Affiliation(s)
- Filipa S S Engrola
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - João Paquete-Ferreira
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Teresa Santos-Silva
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Márcia A S Correia
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
- UCIBIO, Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
| | - Francisco Leisico
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
- UCIBIO, Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
- Institut de Biologie Structurale, UMR 5075, University Grenoble Alpes, CNRS, CEA, Grenoble, France.
| | - Marino F A Santos
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
- UCIBIO, Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
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13
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Kato A, Nakagome I, Yoshimura K, Kanekiyo U, Kishida M, Shinzawa K, Lu TT, Li YX, Nash RJ, Fleet GWJ, Tanaka N, Yu CY. Introduction of C-alkyl branches to L-iminosugars changes their active site binding orientation. Org Biomol Chem 2022; 20:7250-7260. [PMID: 35838176 DOI: 10.1039/d2ob01099b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
L-ido-Deoxynojirimycin (L-ido-DNJ) itself showed no affinity for human lysosomal acid α-glucosidase (GAA), whereas 5-C-methyl-L-ido-DNJ showed a strong affinity for GAA, comparable to the glucose analog DNJ, with a Ki value of 0.060 μM. This excellent affinity for GAA and enzyme stabilization was observed only when methyl and ethyl groups were introduced. Docking simulation analysis revealed that the alkyl chains of 5-C-alkyl-L-ido-DNJs were stored in three different pockets, depending on their length, thereby the molecular orientation was changed. Comparison of the binding poses of DNJ and 5-C-methyl-L-ido-DNJ showed that they formed a common ionic interaction with Asp404, Asp518, and Asp616, but both the binding orientation and the distance between the ligand and each amino acid residue were different. 5-C-Methyl-L-ido-DNJ dose-dependently increased intracellular GAA activity in Pompe patient fibroblasts with the M519V mutation and also promoted enzyme transport to lysosomes. This study provides the first example of a strategy to design high-affinity ligands by introducing alkyl branches into rare sugars and L-sugar-type iminosugars to change the orientation of binding.
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Affiliation(s)
- Atsushi Kato
- Department of Hospital Pharmacy, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan.
| | - Izumi Nakagome
- School of Pharmaceutical Sciences, Kitasato University, Tokyo 108-8641, Japan
| | - Kosuke Yoshimura
- Department of Hospital Pharmacy, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan.
| | - Uta Kanekiyo
- Department of Hospital Pharmacy, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan.
| | - Mana Kishida
- Department of Hospital Pharmacy, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan.
| | - Kenta Shinzawa
- Department of Hospital Pharmacy, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan.
| | - Tian-Tian Lu
- Beijing National Laboratory for Molecular Science (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China. .,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi-Xian Li
- Beijing National Laboratory for Molecular Science (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China. .,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Robert J Nash
- Institute of Biological, Environmental and Rural Sciences/Phytoquest Limited, Plas Gogerddan, Aberystwyth, Ceredigion, SY23 3EB, UK
| | - George W J Fleet
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
| | - Nobutada Tanaka
- School of Pharmaceutical Sciences, Kitasato University, Tokyo 108-8641, Japan
| | - Chu-Yi Yu
- Beijing National Laboratory for Molecular Science (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China. .,University of Chinese Academy of Sciences, Beijing 100049, China
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14
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Xu Y, Zeng P, Wang H, Han K, Qiu G, Wei Y, Chen R, Wang L, Liu X. Novel matrinic acid derivatives bearing 2-anilinothiazole structure for non-small cell lung cancer treatment with improved Hsp90 targeting effect. Drug Dev Res 2022; 83:1434-1454. [PMID: 35841121 DOI: 10.1002/ddr.21974] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 06/03/2022] [Accepted: 06/22/2022] [Indexed: 11/09/2022]
Abstract
Involved in mediating the folding and maturation of more than 300 client proteins, many of which are oncoproteins, Hsp90 has emerged as a promising drug target for cancer therapy. In particular, inhibiting Hsp90 plays a vital role in the treatment of non-small cell lung cancer. Owing to undesirable outcomes of Hsp90 inhibitors in clinical trials, a series of matrinic acid compounds bearing 2-anilinothiazole moiety were designed based on the structural features allocation shared among Hsp90 inhibitors within the ATP-binding pocket. Most of the compounds showed potent anticancer activities validated by MTT assay. Among them, the most potent compound C4 (IC50 < 10 μM against four cell lines) was chosen for further mechanism study. Notably, C4 showed a better safety profile than 17AAG with a higher SI value. Thermal shift assay data indicated C4 exhibited a strong binding affinity with Hsp90 (-18.85 ± 0.56°C) comparable to radicicol. Mechanism studies verified that C4 significantly inhibited proliferation and migration activities of A549 cells. Besides, C4 can induce a prolonged G1-phase and cell apoptosis. Western blot analysis results indicated C4 could moderately suppress Hsp90 and upregulate Hsp70 expression. Furthermore, the downregulated trend of the client proteins of Hsp90, such as β-Catenin and Bcl-2, were consistent with the cellular effect of C4, suggesting that C4 could exert anticancer activity via targeting Hsp90. In the xenograft model in vivo, C4 effectively inhibited lung cancer growth without obvious side effects. Collectively, C4 could be a promising therapeutic agent for lung cancer and the novel scaffold provided new insights into the design of Hsp90 inhibitors.
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Affiliation(s)
- Yiming Xu
- Medical College, Guangxi University, Nanning, China.,Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Panke Zeng
- Medical College, Guangxi University, Nanning, China
| | - Haodong Wang
- Medical College, Guangxi University, Nanning, China
| | - Keyan Han
- Medical College, Guangxi University, Nanning, China
| | - Gan Qiu
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, China
| | - Yongquan Wei
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, China
| | - Rui Chen
- Guangxi University of Chinese Medicine, Nanning, China
| | - Lisheng Wang
- Medical College, Guangxi University, Nanning, China
| | - Xu Liu
- Medical College, Guangxi University, Nanning, China
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15
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Cao Y, Aimaiti A, Zhu Z, Zhou L, Ye D. Discovery of Novel 3-Hydroxyquinazoline-2,4(1 H,3 H)-Dione Derivatives: A Series of Metal Ion Chelators with Potent Anti-HCV Activities. Int J Mol Sci 2022; 23:ijms23115930. [PMID: 35682608 PMCID: PMC9180926 DOI: 10.3390/ijms23115930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 05/21/2022] [Accepted: 05/24/2022] [Indexed: 11/16/2022] Open
Abstract
Millions of people worldwide suffer from acute or chronic liver inflammation caused by the hepatitis C virus (HCV). Metal ion chelators have achieved widespread success in the development of antiviral drugs. Some inhibitors with metal ion chelating structures have been proven to have good inhibitory activities on non-structural protein 5B (NS5B) polymerase. However, most of the reported metal ion chelators showed poor anti-HCV potency at the cellular level. Hence, we designed and synthesized a series of 3-hydroxyquinazoline-2,4(1H,3H)-dione derivatives with novel metal ion chelating structures. Typical compounds such as 21h, 21k, and 21t showed better anti-HCV activities than ribavirin with EC50 values less than 10 μM. 21t is currently known as one of the metal ion chelators with the best anti-HCV potency (EC50 = 2.0 μM) at the cellular level and has a better therapeutic index (TI > 25) as compared to ribavirin and the reported compound 6. In the thermal shift assay, the representative compounds 21e and 21k increased the melting temperature (Tm) of NS5B protein solution by 1.6 °C and 2.1 °C, respectively, at the test concentration, indicating that these compounds may exert an anti-HCV effect by targeting NS5B. This speculation was also supported by our molecular docking studies and ultraviolet-visible (UV-Vis) spectrophotometry assay, in which the possibility of binding of 3-hydroxyquinazoline-2,4(1H,3H)-diones with Mg2+ in the NS5B catalytic center was observed.
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Affiliation(s)
- Yang Cao
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Rd, Shanghai 201203, China; (Y.C.); (Z.Z.)
| | - Abudumijiti Aimaiti
- Shanghai Medical College, Fudan University, 130 Dongan Rd, Shanghai 200032, China;
| | - Zeyun Zhu
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Rd, Shanghai 201203, China; (Y.C.); (Z.Z.)
| | - Lu Zhou
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Rd, Shanghai 201203, China; (Y.C.); (Z.Z.)
- Correspondence: (L.Z.); (D.Y.)
| | - Deyong Ye
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Rd, Shanghai 201203, China; (Y.C.); (Z.Z.)
- Correspondence: (L.Z.); (D.Y.)
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16
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Monticelli M, Liguori L, Allocca M, Bosso A, Andreotti G, Lukas J, Monti MC, Morretta E, Cubellis MV, Hay Mele B. Drug Repositioning for Fabry Disease: Acetylsalicylic Acid Potentiates the Stabilization of Lysosomal Alpha-Galactosidase by Pharmacological Chaperones. Int J Mol Sci 2022; 23:ijms23095105. [PMID: 35563496 PMCID: PMC9105905 DOI: 10.3390/ijms23095105] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/01/2022] [Accepted: 05/02/2022] [Indexed: 12/10/2022] Open
Abstract
Fabry disease is caused by a deficiency of lysosomal alpha galactosidase and has a very large genotypic and phenotypic spectrum. Some patients who carry hypomorphic mutations can benefit from oral therapy with a pharmacological chaperone. The drug requires a very precise regimen because it is a reversible inhibitor of alpha-galactosidase. We looked for molecules that can potentiate this pharmacological chaperone, among drugs that have already been approved for other diseases. We tested candidate molecules in fibroblasts derived from a patient carrying a large deletion in the gene GLA, which were stably transfected with a plasmid expressing hypomorphic mutants. In our cell model, three drugs were able to potentiate the action of the pharmacological chaperone. We focused our attention on one of them, acetylsalicylic acid. We expect that acetylsalicylic acid can be used in synergy with the Fabry disease pharmacological chaperone and prolong its stabilizing effect on alpha-galactosidase.
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Affiliation(s)
- Maria Monticelli
- Department Biology, University of Napoli « Federico II », Complesso Universitario Monte Sant’Angelo, Via Cinthia, 80126 Napoli, Italy; (M.M.); (A.B.); (B.H.M.)
- Department Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy; (L.L.); (M.A.)
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy;
| | - Ludovica Liguori
- Department Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy; (L.L.); (M.A.)
| | - Mariateresa Allocca
- Department Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy; (L.L.); (M.A.)
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy;
| | - Andrea Bosso
- Department Biology, University of Napoli « Federico II », Complesso Universitario Monte Sant’Angelo, Via Cinthia, 80126 Napoli, Italy; (M.M.); (A.B.); (B.H.M.)
- Institute of Biochemistry and Cellular Biology, National Research Council, Via Pietro Castellino 111, 80131 Napoli, Italy
| | - Giuseppina Andreotti
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy;
| | - Jan Lukas
- Translational Neurodegeneration Section “Albrecht-Kossel”, Department of Neurology, University Medical Center Rostock, 18147 Rostock, Germany;
- Center for Transdisciplinary Neurosciences Rostock (CTNR), University Medical Center Rostock, 18147 Rostock, Germany
| | - Maria Chiara Monti
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy; (M.C.M.); (E.M.)
| | - Elva Morretta
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy; (M.C.M.); (E.M.)
| | - Maria Vittoria Cubellis
- Department Biology, University of Napoli « Federico II », Complesso Universitario Monte Sant’Angelo, Via Cinthia, 80126 Napoli, Italy; (M.M.); (A.B.); (B.H.M.)
- Institute of Biomolecular Chemistry ICB, CNR, Via Campi Flegrei 34, 80078 Pozzuoli, Italy;
- Correspondence: ; Tel.: +39-081-679152
| | - Bruno Hay Mele
- Department Biology, University of Napoli « Federico II », Complesso Universitario Monte Sant’Angelo, Via Cinthia, 80126 Napoli, Italy; (M.M.); (A.B.); (B.H.M.)
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17
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Mechanistic Insight into the Mode of Action of Acid β-Glucosidase Enhancer Ambroxol. Int J Mol Sci 2022; 23:ijms23073536. [PMID: 35408914 PMCID: PMC8998264 DOI: 10.3390/ijms23073536] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 01/27/2023] Open
Abstract
Ambroxol (ABX) is a mucolytic agent used for the treatment of respiratory diseases. Bioactivity has been demonstrated as an enhancement effect on lysosomal acid β-glucosidase (β-Glu) activity in Gaucher disease (GD). The positive effects observed have been attributed to a mechanism of action similar to pharmacological chaperones (PCs), but an exact mechanistic description is still pending. The current study uses cell culture and in vitro assays to study the effects of ABX on β-Glu activity, processing, and stability upon ligand binding. Structural analogues bromohexine, 4-hydroxybromohexine, and norbromohexine were screened for chaperone efficacy, and in silico docking was performed. The sugar mimetic isofagomine (IFG) strongly inhibits β-Glu, while ABX exerts its inhibitory effect in the micromolar range. In GD patient fibroblasts, IFG and ABX increase mutant β-Glu activity to identical levels. However, the characteristics of the banding patterns of Endoglycosidase-H (Endo-H)-digested enzyme and a substantially lower half-life of ABX-treated β-Glu suggest different intracellular processing. In line with this observation, IFG efficiently stabilizes recombinant β-Glu against thermal denaturation in vitro, whereas ABX exerts no significant effect. Additional β-Glu enzyme activity testing using Bromohexine (BHX) and two related structures unexpectedly revealed that ABX alone can refunctionalize β-Glu in cellula. Taken together, our data indicate that ABX has little in vitro ability to act as PC, so the mode of action requires further clarification.
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18
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He CX, Lv Y, Guo M, Zhou H, Qin W, Zhao D, Li HJ, Xing L, Zhou X, Li PQ, Yu F, He JH, Cao HL. Complex Crystal Structure Determination of Hsp90 N-NVP-AUY922 and In Vitro Anti-NSCLC Activity of NVP-AUY922. Front Oncol 2022; 12:847556. [PMID: 35280745 PMCID: PMC8907572 DOI: 10.3389/fonc.2022.847556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
New targeted chemotherapy agents greatly improved five-year survival in NSCLC patients, but which were susceptible to drug resistance. NVP-AUY922, terminated in phase II clinical trials, exhibited promising anti-NSCLC (non-small-cell lung cancer) activity targeting to Hsp90N (heat shock protein), which demonstrated advantages in overcoming drug resistance as a broad-spectrum anti-cancer target. It was expected to develop novel anti-NSCLC drugs to overcome drug resistance by the structural optimization of NVP-AUY922. However, the absence of high-resolution complex crystal structure of Hsp90N-NVP-AUY922 blocked the way. Herein, 1.59 Å-resolution complex crystal structure of Hsp90N-NVP-AUY922 (PDB ID 6LTI) was successfully determined by X-ray diffraction. Meanwhile, there was a strong binding capability between NVP-AUY922 and its target Hsp90N verified by TSA (ΔTm, -15.56 ± 1.78°C) and ITC (K d, 5.10 ± 2.10 nM). Results by the complex crystal structure, TSA and ITC verified that NVP-AUY922 well accommodated in the ATP-binding pocket of Hsp90N to disable the molecular chaperone activity of Hsp90. Therefore, NVP-AUY922 exhibited approving inhibitory activity on NSCLC cell line H1299 (IC50, 2.85 ± 0.06 μM) by inhibiting cell proliferation, inducing cell cycle arrest and promoting cell apoptosis. At the basis of the complex crystal structure and molecular interaction analysis, thirty-two new NVP-AUY922 derivatives were further designed, and among which twenty-eight new ones display enhanced binding force with Hsp90N by molecular docking evaluation. The results would promote anti-NSCLC new drug development to overcome drug resistance based on the lead compound NVP-AUY922.
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Affiliation(s)
- Chun-Xia He
- Xi'an Key Laboratory of Basic and Translation of Cardiovascular Metabolic Disease, Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Institute of Basic & Translational Medicine, Xi'an Medical University, Xi'an, China
| | - You Lv
- College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science & Technology, Xi'an, China
| | - Meng Guo
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Huan Zhou
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Wei Qin
- Xi'an Key Laboratory of Basic and Translation of Cardiovascular Metabolic Disease, Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Institute of Basic & Translational Medicine, Xi'an Medical University, Xi'an, China
| | - Dong Zhao
- Xi'an Key Laboratory of Basic and Translation of Cardiovascular Metabolic Disease, Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Institute of Basic & Translational Medicine, Xi'an Medical University, Xi'an, China
| | - Hui-Jin Li
- Xi'an Key Laboratory of Basic and Translation of Cardiovascular Metabolic Disease, Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Institute of Basic & Translational Medicine, Xi'an Medical University, Xi'an, China
| | - Lu Xing
- Xi'an Key Laboratory of Basic and Translation of Cardiovascular Metabolic Disease, Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Institute of Basic & Translational Medicine, Xi'an Medical University, Xi'an, China
| | - Xin Zhou
- Xi'an Key Laboratory of Basic and Translation of Cardiovascular Metabolic Disease, Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Institute of Basic & Translational Medicine, Xi'an Medical University, Xi'an, China
| | - Peng-Quan Li
- Xi'an Key Laboratory of Basic and Translation of Cardiovascular Metabolic Disease, Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Institute of Basic & Translational Medicine, Xi'an Medical University, Xi'an, China
| | - Feng Yu
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Jian-Hua He
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China.,Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Hui-Ling Cao
- Xi'an Key Laboratory of Basic and Translation of Cardiovascular Metabolic Disease, Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Institute of Basic & Translational Medicine, Xi'an Medical University, Xi'an, China.,College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, China
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19
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Kato A, Nakagome I, Kanekiyo U, Lu TT, Li YX, Yoshimura K, Kishida M, Shinzawa K, Yoshida T, Tanaka N, Jia YM, Nash RJ, Fleet GWJ, Yu CY. 5-C-Branched Deoxynojirimycin: Strategy for Designing a 1-Deoxynojirimycin-Based Pharmacological Chaperone with a Nanomolar Affinity for Pompe Disease. J Med Chem 2022; 65:2329-2341. [DOI: 10.1021/acs.jmedchem.1c01673] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Atsushi Kato
- Department of Hospital Pharmacy, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Izumi Nakagome
- School of Pharmacy, Kitasato University, Tokyo 108-8641, Japan
| | - Uta Kanekiyo
- Department of Hospital Pharmacy, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Tian-Tian Lu
- Beijing National Laboratory for Molecular Science (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi-Xian Li
- Beijing National Laboratory for Molecular Science (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kosuke Yoshimura
- Department of Hospital Pharmacy, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Mana Kishida
- Department of Hospital Pharmacy, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Kenta Shinzawa
- Department of Hospital Pharmacy, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Tomoki Yoshida
- School of Pharmacy, Kitasato University, Tokyo 108-8641, Japan
| | - Nobutada Tanaka
- School of Pharmacy, Kitasato University, Tokyo 108-8641, Japan
| | - Yue-Mei Jia
- Beijing National Laboratory for Molecular Science (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Robert J. Nash
- Institute of Biological, Environmental and Rural Sciences / Phytoquest Limited, Plas Gogerddan, Aberystwyth, Ceredigion SY23 3EB, U.K
| | - George W. J. Fleet
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, U.K
| | - Chu-Yi Yu
- Beijing National Laboratory for Molecular Science (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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20
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Quelhas D, Carneiro J, Lopes-Marques M, Jaeken J, Martins E, Rocha JF, Teixeira Carla SS, Ferreira CR, Sousa SF, Azevedo L. Assessing the effects of PMM2 variants on protein stability. Mol Genet Metab 2021; 134:344-352. [PMID: 34863624 DOI: 10.1016/j.ymgme.2021.11.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/30/2021] [Accepted: 11/02/2021] [Indexed: 11/16/2022]
Abstract
Phosphomannomutase 2 deficiency, PMM2-CDG, is the most frequent disorder of protein N-glycosylation. It is an autosomal recessive disease with a broad clinical and biochemical phenotype. Trying to predict the impact of novel variants is often a challenge due to the high number of variants and the difficulty to establish solid genotype-phenotype correlations. A potential useful strategy is to use computational chemistry calculations as a tool from which relevant information on the structural impact of novel variants may be deduced. Here we present our analyses based on four well-known PMM2 deleterious variants (p.(Leu32Arg), p.(Asp65Tyr), p.(Phe119Leu), p.(Arg141His)) and the polymorphic p.(Glu197Ala) for which we have predicted the effect on protein stability. Our work predicts the effect of different amino acid residues on the conformation and stability of PMM2. These computational simulations are, therefore, an extremely useful methodology which, in combination with routinely used in silico methods of pathogenicity prediction, may help to reveal the structural impact of novel variants at the protein level, potentially leading to a better understanding of target biological molecules.
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Affiliation(s)
- D Quelhas
- Unidade de Bioquímica Genética, Centro de Genética Médica, Centro Hospitalar Universitário do Porto, Porto, Portugal; Unit for Multidisciplinary Research in Biomedicine, ICBAS, UP, Porto, Portugal; Centro Referência Doenças Hereditárias do Metabolismo, Centro Hospitalar Universitário do Porto, Porto, Portugal.
| | - J Carneiro
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, Matosinhos, Portugal
| | - M Lopes-Marques
- i3S- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal; IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal; FCUP-Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - J Jaeken
- Center for Metabolic Diseases, KU Leuven, Leuven, Belgium
| | - E Martins
- Unit for Multidisciplinary Research in Biomedicine, ICBAS, UP, Porto, Portugal; Centro Referência Doenças Hereditárias do Metabolismo, Centro Hospitalar Universitário do Porto, Porto, Portugal
| | - J F Rocha
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal; UCIBIO - Applied Molecular Biosciences Unit, BioSIM - Department of Biomedicine, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
| | - S S Teixeira Carla
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal; UCIBIO - Applied Molecular Biosciences Unit, BioSIM - Department of Biomedicine, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
| | - C R Ferreira
- Skeletal Genomics Unit, Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - S F Sousa
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal; UCIBIO - Applied Molecular Biosciences Unit, BioSIM - Department of Biomedicine, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
| | - L Azevedo
- i3S- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal; IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal; FCUP-Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
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21
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Campbell AC, Prater AR, Bogner AN, Quinn TP, Gates KS, Becker DF, Tanner JJ. Photoinduced Covalent Irreversible Inactivation of Proline Dehydrogenase by S-Heterocycles. ACS Chem Biol 2021; 16:2268-2279. [PMID: 34542291 DOI: 10.1021/acschembio.1c00427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Proline dehydrogenase (PRODH) is a flavoenzyme that catalyzes the first step of proline catabolism, the oxidation of l-proline to Δ1-pyrroline-5-carboxylate. PRODH has emerged as a cancer therapy target because of its involvement in the metabolic reprogramming of cancer cells. Here, we report the discovery of a new class of PRODH inactivator, which covalently and irreversibly modifies the FAD in a light-dependent manner. Two examples, 1,3-dithiolane-2-carboxylate and tetrahydrothiophene-2-carboxylate, have been characterized using X-ray crystallography (1.52-1.85 Å resolution), absorbance spectroscopy, and enzyme kinetics. The structures reveal that in the dark, these compounds function as classical reversible, proline analogue inhibitors. However, exposure of enzyme-inhibitor cocrystals to bright white light induces decarboxylation of the inhibitor and covalent attachment of the residual S-heterocycle to the FAD N5 atom, locking the cofactor into a reduced, inactive state. Spectroscopic measurements of the inactivation process in solution confirm the requirement for light and show that blue light is preferred. Enzyme activity assays show that the rate of inactivation is enhanced by light and that the inactivation is irreversible. We also demonstrate the photosensitivity of cancer cells to one of these compounds. A possible mechanism is proposed involving photoexcitation of the FAD, while the inhibitor is noncovalently bound in the active site, followed by electron transfer, decarboxylation, and radical combination steps. Our results could lead to the development of photopharmacological drugs targeting PRODH.
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Affiliation(s)
- Ashley C. Campbell
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Austin R. Prater
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Alexandra N. Bogner
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Thomas P. Quinn
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Kent S. Gates
- Department of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Donald F. Becker
- Department of Biochemistry, Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588, United States
| | - John J. Tanner
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
- Department of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
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22
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Zhao D, Xu YM, Cao LQ, Yu F, Zhou H, Qin W, Li HJ, He CX, Xing L, Zhou X, Li PQ, Jin X, He Y, He JH, Cao HL. Complex Crystal Structure Determination and in vitro Anti-non-small Cell Lung Cancer Activity of Hsp90 N Inhibitor SNX-2112. Front Cell Dev Biol 2021; 9:650106. [PMID: 33855025 PMCID: PMC8039390 DOI: 10.3389/fcell.2021.650106] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 02/23/2021] [Indexed: 11/13/2022] Open
Abstract
SNX-2112, as a promising anticancer lead compound targeting heat shock protein 90 (Hsp90), absence of complex crystal structure of Hsp90N-SNX-2112 hindered further structural optimization and understanding on molecular interaction mechanism. Herein, a high-resolution complex crystal structure of Hsp90N-SNX-2112 was successfully determined by X-ray diffraction, resolution limit, 2.14 Å, PDB ID 6LTK, and their molecular interaction was analyzed in detail, which suggested that SNX-2112 was well accommodated in the ATP-binding pocket to disable molecular chaperone activity of Hsp90, therefore exhibiting favorable inhibiting activity on three non–small cell lung cancer (NSCLC) cell lines (IC50, 0.50 ± 0.01 μM for A549, 1.14 ± 1.11 μM for H1299, 2.36 ± 0.82 μM for H1975) by inhibited proliferation, induced cell cycle arrest, and aggravated cell apoptosis. SNX-2112 exhibited high affinity and beneficial thermodynamic changes during the binding process with its target Hsp90N confirmed by thermal shift assay (TSA, ΔTm, and −9.51 ± 1.00°C) and isothermal titration calorimetry (Kd, 14.10 ± 1.60 nM). Based on the complex crystal structure and molecular interaction analysis, 32 novel SNX-2112 derivatives were designed, and 25 new ones displayed increased binding force with the target Hsp90N verified by molecular docking evaluation. The results would provide new references and guides for anti-NSCLC new drug development based on the lead compound SNX-2112.
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Affiliation(s)
- Dong Zhao
- Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Institute of Basic & Translational Medicine, Xi'an Medical University, Xi'an, China
| | - Yi-Ming Xu
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA, United States
| | - Lu-Qi Cao
- Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Institute of Basic & Translational Medicine, Xi'an Medical University, Xi'an, China
| | - Feng Yu
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Huan Zhou
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Wei Qin
- Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Institute of Basic & Translational Medicine, Xi'an Medical University, Xi'an, China
| | - Hui-Jin Li
- Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Institute of Basic & Translational Medicine, Xi'an Medical University, Xi'an, China
| | - Chun-Xia He
- Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Institute of Basic & Translational Medicine, Xi'an Medical University, Xi'an, China
| | - Lu Xing
- Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Institute of Basic & Translational Medicine, Xi'an Medical University, Xi'an, China
| | - Xin Zhou
- Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Institute of Basic & Translational Medicine, Xi'an Medical University, Xi'an, China
| | - Peng-Quan Li
- Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Institute of Basic & Translational Medicine, Xi'an Medical University, Xi'an, China
| | - Xin Jin
- Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Institute of Basic & Translational Medicine, Xi'an Medical University, Xi'an, China
| | - Yuan He
- College of Chemistry and Materials Science, Key Laboratory of Synthetic and Natural Functional Molecule, Ministry of Education, Northwest University, Xi'an, China
| | - Jian-Hua He
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China.,Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Hui-Ling Cao
- Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Institute of Basic & Translational Medicine, Xi'an Medical University, Xi'an, China.,College of Chemistry and Materials Science, Key Laboratory of Synthetic and Natural Functional Molecule, Ministry of Education, Northwest University, Xi'an, China
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23
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Du A, Zheng R, Disoma C, Li S, Chen Z, Li S, Liu P, Zhou Y, Shen Y, Liu S, Zhang Y, Dong Z, Yang Q, Alsaadawe M, Razzaq A, Peng Y, Chen X, Hu L, Peng J, Zhang Q, Jiang T, Mo L, Li S, Xia Z. Epigallocatechin-3-gallate, an active ingredient of Traditional Chinese Medicines, inhibits the 3CLpro activity of SARS-CoV-2. Int J Biol Macromol 2021; 176:1-12. [PMID: 33548314 PMCID: PMC7859723 DOI: 10.1016/j.ijbiomac.2021.02.012] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/30/2021] [Accepted: 02/01/2021] [Indexed: 12/12/2022]
Abstract
SARS-CoV-2 is the etiological agent responsible for the ongoing pandemic of coronavirus disease 2019 (COVID-19). The main protease of SARS-CoV-2, 3CLpro, is an attractive target for antiviral inhibitors due to its indispensable role in viral replication and gene expression of viral proteins. The search of compounds that can effectively inhibit the crucial activity of 3CLpro, which results to interference of the virus life cycle, is now widely pursued. Here, we report that epigallocatechin-3-gallate (EGCG), an active ingredient of Chinese herbal medicine (CHM), is a potent inhibitor of 3CLpro with half-maximum inhibitory concentration (IC50) of 0.874 ± 0.005 μM. In the study, we retrospectively analyzed the clinical data of 123 cases of COVID-19 patients, and found three effective Traditional Chinese Medicines (TCM) prescriptions. Multiple strategies were performed to screen potent inhibitors of SARS-CoV-2 3CLpro from the active ingredients of TCMs, including network pharmacology, molecular docking, surface plasmon resonance (SPR) binding assay and fluorescence resonance energy transfer (FRET)-based inhibition assay. The SPR assay showed good interaction between EGCG and 3CLpro with KD ~6.17 μM, suggesting a relatively high affinity of EGCG with SARS-CoV-2 3CLpro. Our results provide critical insights into the mechanism of action of EGCG as a potential therapeutic agent against COVID-19.
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Affiliation(s)
- Ashuai Du
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha 410013, China; Department of Infectious Diseases, Guizhou Provincial People's Hospital, Guizhou 550000, China
| | - Rong Zheng
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha 410013, China
| | - Cyrollah Disoma
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha 410013, China
| | - Shiqin Li
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha 410013, China
| | - Zongpeng Chen
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha 410013, China
| | - Sijia Li
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha 410013, China
| | - Pinjia Liu
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha 410013, China
| | - Yuzheng Zhou
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha 410013, China
| | - Yilun Shen
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha 410013, China
| | - Sixu Liu
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha 410013, China
| | - Yongxing Zhang
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha 410013, China
| | - Zijun Dong
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha 410013, China
| | - Qinglong Yang
- Department of General Surgery, Guizhou Provincial People's Hospital, Guizhou 550000, China
| | - Moyed Alsaadawe
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha 410013, China
| | - Aroona Razzaq
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha 410013, China
| | - Yuyang Peng
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha 410013, China
| | - Xuan Chen
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha 410013, China
| | - Liqiang Hu
- The First Hospital of Changsha, University of South China, Changsha 410201, China
| | - Jian Peng
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Qianjun Zhang
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha 410013, China
| | - Taijiao Jiang
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Long Mo
- Department of Cardiology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Shanni Li
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha 410013, China.
| | - Zanxian Xia
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha 410013, China; Hunan Key Laboratory of Animal Models for Human Diseases, Hunan Key Laboratory of Medical Genetics & Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410013, China.
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24
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Han L, Xu D, Xi Z, Wu M, Nik Nabil WN, Zhang J, Sui H, Fu W, Zhou H, Lao Y, Xu G, Guo C, Xu H. The Natural Compound Oblongifolin C Exhibits Anticancer Activity by Inhibiting HSPA8 and Cathepsin B In Vitro. Front Pharmacol 2021; 11:564833. [PMID: 33390942 PMCID: PMC7773843 DOI: 10.3389/fphar.2020.564833] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 10/19/2020] [Indexed: 11/13/2022] Open
Abstract
PPAPs (Polycyclic polyprenylated acylphloroglucinols) are a class of compounds with diverse bioactivities, including anticancer effects. Oblongifolin C (OC) is a PPAP isolated from the plant of Garcinia yunnanensis Hu. We previously discovered that OC induces apoptosis, inhibits autophagic flux, and attenuates metastasis in cancer cells. However, the protein targets and the detailed mechanism of action of OC remain unclear. To identify protein targets of OC, a non-labeled protein fishing assay was performed, and it was found that OC may interact with several proteins, including the heat shock 70 kDa protein 8 (HSPA8). Expanding on our previous studies on protein cathepsin B, this current study applied Surface Plasmon Resonance (SPR) and Isothermal Titration Calorimetry (ITC) to confirm the potential binding affinity between OC and two protein targets. This study highlights the inhibitory effect of OC on HSPA8 in cancer cells under heat shock stress, by specifically inhibiting the translocation of HSPA8. OC also enhanced the interaction between HSPA8, HSP90, and p53, upregulated the expression of p53 and significantly promoted apoptosis in cisplatin-treated cells. Additionally, a flow cytometry assay detected that OC sped up the apoptosis rate in HSPA8 knockdown A549 cells, while overexpression of HSPA8 delayed the OC-induced apoptosis rate. In summary, our results reveal that OC potentially interacts with HSPA8 and cathepsin B and inhibits HSPA8 nuclear translocation and cathepsin B activities, altogether suggesting the potential of OC to be developed as an anticancer drug.
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Affiliation(s)
- Li Han
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Pharmacy, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Danqing Xu
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zhichao Xi
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Man Wu
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Wan Najbah Nik Nabil
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Juan Zhang
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Hua Sui
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Wenwei Fu
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hua Zhou
- Institute of Cardiovascular Disease of Integrated Traditional Chinese and Western Medicine, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yuanzhi Lao
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Gang Xu
- State Key Laboratory of Phytochemistry and Plant Resources in West China and Yunnan Key Laboratory of National Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Cheng Guo
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Pharmacy, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Hongxi Xu
- Institute of Cardiovascular Disease of Integrated Traditional Chinese and Western Medicine, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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25
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Qin W, Yu F, Zhou H, Li P, Zhou F, Li HJ, He CX, Xing L, Zhou X, Zhao D, Li PQ, Jin X, Wang QS, He JH, Cao HL. Complex crystal structure determination and anti-non-small-cell lung cancer activity of the Hsp90 N inhibitor Debio0932. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2021; 77:86-97. [PMID: 33404528 DOI: 10.1107/s2059798320014990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 11/10/2020] [Indexed: 12/24/2022]
Abstract
Debio0932 is a promising lead compound in phase I clinical trials targeting the N-terminal ATP-binding pocket of the molecular chaperone heat-shock protein 90 (Hsp90N). The absence of a crystal structure of the Hsp90N-Debio0932 complex, however, has impeded further structural optimization of Debio0932 and understanding of the molecular-interaction mechanism. Here, a high-resolution crystal structure of the Hsp90N-Debio0932 complex was successfully determined (resolution limit 2.20 Å; PDB entry 6lr9) by X-ray diffraction and the molecular-interaction mechanism was analysed in detail, which suggested that Debio0932 suppresses cancer cells by accommodating itself in the ATP-binding pocket of Hsp90N, disabling its molecular-chaperone capability. The results of a thermal shift assay (ΔTm = 8.83 ± 0.90°C) and isothermal titration calorimetry (Kd = 15.50 ± 1.30 nM) indicated strong binding and favourable thermodynamic changes in the binding of Hsp90N and Debio0932. Based on the crystal structure of the complex and on molecular-interaction analysis, 30 new Debio0932 derivatives were designed and nine new derivatives exhibited increased binding to Hsp90N, as determined by molecular-docking evaluation. Additionally, Debio0932 suppressed cell proliferation (IC50 values of 3.26 ± 2.82 µM for A549, 20.33 ± 5.39 µM for H1299 and 3.16 ± 1.04 µM for H1975), induced cell-cycle arrest and promoted apoptosis in three non-small-cell lung cancer (NSCLC) cell lines. These results provide novel perspectives and guidance for the development of new anti-NSCLC drugs based on the lead compound Debio0932.
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Affiliation(s)
- Wei Qin
- Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Shaanxi Key Laboratory of Brain Disorders, Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an 710021, People's Republic of China
| | - Feng Yu
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China
| | - Huan Zhou
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China
| | - Ping Li
- Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Shaanxi Key Laboratory of Brain Disorders, Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an 710021, People's Republic of China
| | - Fang Zhou
- Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Shaanxi Key Laboratory of Brain Disorders, Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an 710021, People's Republic of China
| | - Hui Jin Li
- Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Shaanxi Key Laboratory of Brain Disorders, Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an 710021, People's Republic of China
| | - Chun Xia He
- Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Shaanxi Key Laboratory of Brain Disorders, Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an 710021, People's Republic of China
| | - Lu Xing
- Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Shaanxi Key Laboratory of Brain Disorders, Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an 710021, People's Republic of China
| | - Xin Zhou
- Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Shaanxi Key Laboratory of Brain Disorders, Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an 710021, People's Republic of China
| | - Dong Zhao
- Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Shaanxi Key Laboratory of Brain Disorders, Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an 710021, People's Republic of China
| | - Peng Quan Li
- Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Shaanxi Key Laboratory of Brain Disorders, Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an 710021, People's Republic of China
| | - Xi Jin
- Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Shaanxi Key Laboratory of Brain Disorders, Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an 710021, People's Republic of China
| | - Qi Sheng Wang
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China
| | - Jian Hua He
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China
| | - Hui Ling Cao
- Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Shaanxi Key Laboratory of Brain Disorders, Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an 710021, People's Republic of China
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26
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Campbell AC, Bogner AN, Mao Y, Becker DF, Tanner JJ. Structural analysis of prolines and hydroxyprolines binding to the l-glutamate-γ-semialdehyde dehydrogenase active site of bifunctional proline utilization A. Arch Biochem Biophys 2020; 698:108727. [PMID: 33333077 DOI: 10.1016/j.abb.2020.108727] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/11/2020] [Accepted: 12/12/2020] [Indexed: 01/31/2023]
Abstract
Proline utilization A (PutA) proteins are bifunctional proline catabolic enzymes that catalyze the 4-electron oxidation of l-proline to l-glutamate using spatially-separated proline dehydrogenase and l-glutamate-γ-semialdehyde dehydrogenase (GSALDH, a.k.a. ALDH4A1) active sites. The observation that l-proline inhibits both the GSALDH activity of PutA and monofunctional GSALDHs motivated us to study the inhibition of PutA by proline stereoisomers and analogs. Here we report five high-resolution crystal structures of PutA with the following ligands bound in the GSALDH active site: d-proline, trans-4-hydroxy-d-proline, cis-4-hydroxy-d-proline, l-proline, and trans-4-hydroxy-l-proline. Three of the structures are of ternary complexes of the enzyme with an inhibitor and either NAD+ or NADH. To our knowledge, the NADH complex is the first for any GSALDH. The structures reveal a conserved mode of recognition of the inhibitor carboxylate, which results in the pyrrolidine rings of the d- and l-isomers having different orientations and different hydrogen bonding environments. Activity assays show that the compounds are weak inhibitors with millimolar inhibition constants. Curiously, although the inhibitors occupy the aldehyde binding site, kinetic measurements show the inhibition is uncompetitive. Uncompetitive inhibition may involve proline binding to a remote site or to the enzyme-NADH complex. Together, the structural and kinetic data expand our understanding of how proline-like molecules interact with GSALDH, reveal insight into the relationship between stereochemistry and inhibitor affinity, and demonstrate the pitfalls of inferring the mechanism of inhibition from crystal structures alone.
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Affiliation(s)
- Ashley C Campbell
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, United States
| | - Alexandra N Bogner
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, United States
| | - Yizi Mao
- Department of Biochemistry, Redox Biology Center, University of Nebraska, Lincoln, NE, 68588, United States
| | - Donald F Becker
- Department of Biochemistry, Redox Biology Center, University of Nebraska, Lincoln, NE, 68588, United States
| | - John J Tanner
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, United States; Department of Chemistry, University of Missouri, Columbia, MO, 65211, United States.
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27
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Stiers KM, Hansen RP, Daghlas BA, Mason KN, Zhu JS, Jakeman DL, Beamer LJ. A missense variant remote from the active site impairs stability of human phosphoglucomutase 1. J Inherit Metab Dis 2020; 43:861-870. [PMID: 32057119 DOI: 10.1002/jimd.12222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 02/04/2020] [Accepted: 02/10/2020] [Indexed: 12/18/2022]
Abstract
Missense variants of human phosphoglucomutase 1 (PGM1) cause the inherited metabolic disease known as PGM1 deficiency. This condition is categorised as both a glycogen storage disease and a congenital disorder of glycosylation. Approximately 20 missense variants of PGM1 are linked to PGM1 deficiency, and biochemical studies have suggested that they fall into two general categories: those affecting the active site and catalytic efficiency, and those that appear to impair protein folding and/or stability. In this study, we characterise a novel variant of Arg422, a residue distal from the active site of PGM1 and the site of a previously identified disease-related variant (Arg422Trp). In prior studies, the R422W variant was found to produce insoluble protein in a recombinant expression system, precluding further in vitro characterisation. Here we investigate an alternative variant of this residue, Arg422Gln, which is amenable to experimental characterisation presumably due to its more conservative physicochemical substitution. Biochemical, crystallographic, and computational studies of R422Q establish that this variant causes only minor changes in catalytic efficiency and 3D structure, but is nonetheless dramatically reduced in stability. Unexpectedly, binding of a substrate analog is found to further destabilise the protein, in contrast to its stabilising effect on wild-type PGM1 and several other missense variants. This work establishes Arg422 as a lynchpin residue for the stability of PGM1 and supports the impairment of protein stability as a pathomechanism for variants that cause PGM1 deficiency. SYNOPSIS: Biochemical and structural studies of a missense variant far from the active site of human PGM1 identify a residue with a key role in enzyme stability.
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Affiliation(s)
- Kyle M Stiers
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Reed P Hansen
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Bana A Daghlas
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Kelly N Mason
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Jian-She Zhu
- College of Pharmacy, Dalhousie University, Halifax, Nova Scotia, Canada
| | - David L Jakeman
- College of Pharmacy, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Lesa J Beamer
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
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28
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Senarisoy M, Barette C, Lacroix F, De Bonis S, Stelter M, Hans F, Kleman JP, Fauvarque MO, Timmins J. Förster Resonance Energy Transfer Based Biosensor for Targeting the hNTH1-YB1 Interface as a Potential Anticancer Drug Target. ACS Chem Biol 2020; 15:990-1003. [PMID: 32125823 DOI: 10.1021/acschembio.9b01023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The Y-box binding protein 1 (YB1) is an established metastatic marker: high expression and nuclear localization of YB1 correlate with tumor aggressiveness, drug resistance, and poor patient survival in various tumors. In the nucleus, YB1 interacts with and regulates the activities of several nuclear proteins, including the DNA glycosylase, human endonuclease III (hNTH1). In the present study, we used Förster resonance energy transfer (FRET) and AlphaLISA technologies to further characterize this interaction and define the minimal regions of hNTH1 and YB1 required for complex formation. This work led us to design an original and cost-effective FRET-based biosensor for the rapid in vitro high-throughput screening for potential inhibitors of the hNTH1-YB1 complex. Two pilot screens were carried out, allowing the selection of several promising compounds exhibiting IC50 values in the low micromolar range. Interestingly, two of these compounds bind to YB1 and sensitize drug-resistant breast tumor cells to the chemotherapeutic agent, cisplatin. Taken together, these findings demonstrate that the hNTH1-YB1 interface is a druggable target for the development of new therapeutic strategies for the treatment of drug-resistant tumors. Moreover, beyond this study, the simple design of our biosensor defines an innovative and efficient strategy for the screening of inhibitors of therapeutically relevant protein-protein interfaces.
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Affiliation(s)
- Muge Senarisoy
- Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Caroline Barette
- Univ. Grenoble Alpes, CEA, INSERM, BGE, F-38000 Grenoble, France
| | | | | | - Meike Stelter
- Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Fabienne Hans
- Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
| | | | | | - Joanna Timmins
- Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
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29
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Liguori L, Monticelli M, Allocca M, Hay Mele B, Lukas J, Cubellis MV, Andreotti G. Pharmacological Chaperones: A Therapeutic Approach for Diseases Caused by Destabilizing Missense Mutations. Int J Mol Sci 2020; 21:ijms21020489. [PMID: 31940970 PMCID: PMC7014102 DOI: 10.3390/ijms21020489] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/08/2020] [Accepted: 01/09/2020] [Indexed: 02/07/2023] Open
Abstract
The term “pharmacological chaperone” was introduced 20 years ago. Since then the approach with this type of drug has been proposed for several diseases, lysosomal storage disorders representing the most popular targets. The hallmark of a pharmacological chaperone is its ability to bind a protein specifically and stabilize it. This property can be beneficial for curing diseases that are associated with protein mutants that are intrinsically active but unstable. The total activity of the affected proteins in the cell is lower than normal because they are cleared by the quality control system. Although most pharmacological chaperones are reversible competitive inhibitors or antagonists of their target proteins, the inhibitory activity is neither required nor desirable. This issue is well documented by specific examples among which those concerning Fabry disease. Direct specific binding is not the only mechanism by which small molecules can rescue mutant proteins in the cell. These drugs and the properly defined pharmacological chaperones can work together with different and possibly synergistic modes of action to revert a disease phenotype caused by an unstable protein.
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Affiliation(s)
- Ludovica Liguori
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy; (L.L.); (M.A.)
- Istituto di Chimica Biomolecolare–CNR, 80078 Pozzuoli, Italy;
| | - Maria Monticelli
- Dipartimento di Biologia, Università Federico II, 80126 Napoli, Italy;
| | - Mariateresa Allocca
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy; (L.L.); (M.A.)
- Istituto di Chimica Biomolecolare–CNR, 80078 Pozzuoli, Italy;
| | - Bruno Hay Mele
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy;
| | - Jan Lukas
- Translational Neurodegeneration Section “Albrecht-Kossel”, Department of Neurology, University Medical Center Rostock, University of Rostock, 18147 Rostock, Germany;
- Center for Transdisciplinary Neurosciences Rostock (CTNR), University Medical Center Rostock, University of Rostock, 18147 Rostock, Germany
| | - Maria Vittoria Cubellis
- Istituto di Chimica Biomolecolare–CNR, 80078 Pozzuoli, Italy;
- Dipartimento di Biologia, Università Federico II, 80126 Napoli, Italy;
- Correspondence: ; Tel.: +39-081-679118; Fax: +39-081-679233
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30
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Xu Y, Jing D, Zhao D, Wu Y, Xing L, Ur Rashid H, Wang H, Wang L, Cao H. New modification strategy of matrine as Hsp90 inhibitors based on its specific L conformation for cancer treatment. Bioorg Med Chem 2020; 28:115305. [PMID: 31928863 DOI: 10.1016/j.bmc.2020.115305] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 12/22/2019] [Accepted: 01/02/2020] [Indexed: 10/25/2022]
Abstract
The similarity of spatial structure between radicicol and matrine urged us to perform conformation modification of matrine, followed by L-shaped matrine derivatives, 6, 12, 21a-h and 22a-h were originally designed, synthesized and evaluated for Hsp90N inhibitors as anticancer agents. TSA (Thermal Shift Assay) results indicated that 21e, 22a-c and 22e-g exhibited strong binding force against Hsp90N with∣ΔTm∣ > 3, meanwhile, MTT assay also revealed these compounds displayed potent anticancer activity with IC50 values below 25 μM against HepG2, HeLa and MDA-MB-231 cells lines. Then, compound 22g with a high ΔTm = 10.92 was chosen as a representative to perform further mechanism study. It can induce cell apoptosis, arrest the cell cycle at the S phase and decrease the expression level of Hsp90 in Hela cell. These results originally provided targeted modification strategy for matrine derivatives to serve as Hsp90 inhibitors for cancer therapy.
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Affiliation(s)
- Yiming Xu
- Medicinal College, Guangxi University, Nanning 530004, China; School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Dewang Jing
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Dong Zhao
- Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Institute of Basic Translational Medicine, Xi'an Medical University, Xi'an 710021, China
| | - Yongji Wu
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Lu Xing
- Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Institute of Basic Translational Medicine, Xi'an Medical University, Xi'an 710021, China
| | - Haroon Ur Rashid
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China; Department of Chemistry, Sarhad University of Science & Information Technology, Peshawar, Khyber Pakhtunkhwa 25120, Pakistan
| | - Haodong Wang
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Lisheng Wang
- Medicinal College, Guangxi University, Nanning 530004, China.
| | - Huiling Cao
- Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Institute of Basic Translational Medicine, Xi'an Medical University, Xi'an 710021, China.
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31
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Monticelli M, Liguori L, Allocca M, Andreotti G, Cubellis MV. β-Glucose-1,6-Bisphosphate Stabilizes Pathological Phophomannomutase2 Mutants In Vitro and Represents a Lead Compound to Develop Pharmacological Chaperones for the Most Common Disorder of Glycosylation, PMM2-CDG. Int J Mol Sci 2019; 20:E4164. [PMID: 31454904 PMCID: PMC6747070 DOI: 10.3390/ijms20174164] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/13/2019] [Accepted: 08/22/2019] [Indexed: 12/13/2022] Open
Abstract
A large number of mutations causing PMM2-CDG, which is the most frequent disorder of glycosylation, destabilize phosphomannomutase2. We looked for a pharmacological chaperone to cure PMM2-CDG, starting from the structure of a natural ligand of phosphomannomutase2, α-glucose-1,6-bisphosphate. The compound, β-glucose-1,6-bisphosphate, was synthesized and characterized via 31P-NMR. β-glucose-1,6-bisphosphate binds its target enzyme in silico. The binding induces a large conformational change that was predicted by the program PELE and validated in vitro by limited proteolysis. The ability of the compound to stabilize wild type phosphomannomutase2, as well as frequently encountered pathogenic mutants, was measured using thermal shift assay. β-glucose-1,6-bisphosphate is relatively resistant to the enzyme that specifically hydrolyses natural esose-bisphosphates.
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Affiliation(s)
- Maria Monticelli
- Dipartimento di Biologia, Università Federico II, 80126 Napoli, Italy
| | - Ludovica Liguori
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università degli Studi della Campania "Luigi Vanvitelli", 81100 Caserta, Italy
- Istituto di Chimica Biomolecolare-CNR, 80078 Pozzuoli, Italy
| | - Mariateresa Allocca
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università degli Studi della Campania "Luigi Vanvitelli", 81100 Caserta, Italy
- Istituto di Chimica Biomolecolare-CNR, 80078 Pozzuoli, Italy
| | | | - Maria Vittoria Cubellis
- Dipartimento di Biologia, Università Federico II, 80126 Napoli, Italy
- Istituto di Chimica Biomolecolare-CNR, 80078 Pozzuoli, Italy
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32
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Genomic Identification of the TOR Signaling Pathway as a Target of the Plant Alkaloid Antofine in the Phytopathogen Fusarium graminearum. mBio 2019; 10:mBio.00792-19. [PMID: 31186319 PMCID: PMC6561021 DOI: 10.1128/mbio.00792-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Fusarium head blight caused by the fungal pathogen Fusarium graminearum is a devastating disease of cereal crops worldwide, with limited effective chemical treatments available. Here we show that the natural alkaloid compound antofine can inhibit fusarium head blight in wheat. Using yeast genomic screening, we identified the TOR pathway component RRD2 as a target of antofine that is also required for F. graminearum pathogenicity. Antofine, a phenanthroindolizidine alkaloid, is a bioactive natural product isolated from milkweeds that exhibits numerous biological activities, including anticancer, antimicrobial, antiviral, and anti-inflammatory properties. However, the direct targets and mode of action of antofine have not been determined. In this report, we show that antofine displays antifungal properties against the phytopathogen Fusarium graminearum, the cause of Fusarium head blight disease (FHB). FHB does devastating damage to agriculture, causing billions of dollars in economic losses annually. We therefore sought to understand the mode of action of antofine in F. graminearum using insights from yeast chemical genomic screens. We used haploinsufficiency profiling (HIP) to identify putative targets of antofine in yeast and identified three candidate targets, two of which had homologs in F. graminearum. The Fusarium homologues of two targets, glutamate dehydrogenase (FgGDH) and resistance to rapamycin deletion 2 (FgRRD2), can bind antofine. Of the two genes, only the Fgrrd2 knockout displayed a loss of virulence in wheat, indicating that RRD2 is an antivirulence target of antofine in F. graminearum. Mechanistically, we demonstrate that antofine disrupts the interaction between FgRRD2 and FgTap42, which is part of the Tap42-phosphatase complex in the target of rapamycin (TOR) signaling pathway, a central regulator of cell growth in eukaryotes and a pathway of extensive study for controlling numerous pathologies.
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SN-38, the active metabolite of irinotecan, inhibits the acute inflammatory response by targeting toll-like receptor 4. Cancer Chemother Pharmacol 2019; 84:287-298. [DOI: 10.1007/s00280-019-03844-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 04/16/2019] [Indexed: 12/27/2022]
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Samuels ER, Sevrioukova I. Structure-Activity Relationships of Rationally Designed Ritonavir Analogues: Impact of Side-Group Stereochemistry, Headgroup Spacing, and Backbone Composition on the Interaction with CYP3A4. Biochemistry 2019; 58:2077-2087. [PMID: 30912932 DOI: 10.1021/acs.biochem.9b00156] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In a continuing effort to identify structural attributes required for strong binding and potent inhibition of human drug-metabolizing CYP3A4, we designed ten ritonavir-like analogues differing in the side-group stereochemistry, backbone atomic composition, and headgroup spacing. All analogues had pyridine and tert-butyloxycarbonyl (Boc) as the heme-ligating head and tail groups, respectively, phenyl side groups, and either a methyl- or ethyl-pyridyl linker. Each linker subseries had S/ R, R/ S, R/ R, and S/S side-group conformers (4a-d and 4e-h, respectively), and one S/S stereoisomer with the backbone S-to-N-heteroatom substitution (6a and 6b). To elucidate structure-activity relationships, ligand-dependent changes in optical spectra, dissociation constant ( Ks), inhibitory potency (IC50), thermostability, and heme ligation and reduction kinetics were analyzed. Comparison of the subseries and individual compounds showed that CYP3A4 only weakly discriminates between side-group configurations, associates more tightly with the pyridyl-ethyl-linker analogues, and strongly disfavors the N-containing backbone. Ks and IC50 for the pyridyl-ethyl R/ R conformer, 4g, were the lowest and close to those for ritonavir: 0.04 and 0.31 μM versus 0.02 and 0.13 μM, respectively. Determination of the X-ray structures of the inhibitory complexes was critical for experimental data interpretation, especially for the uniquely oriented 4a and 4e. Based on structural analysis, we conclude that, for this series of analogues, the ligand-mediated interactions near the heme are dominant and define the binding mode and that fine-tuning of these interactions as well as the backbone spacing could further improve the affinity and inhibitory strength.
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Stiers KM, Beamer LJ. A Hotspot for Disease-Associated Variants of Human PGM1 Is Associated with Impaired Ligand Binding and Loop Dynamics. Structure 2018; 26:1337-1345.e3. [PMID: 30122451 DOI: 10.1016/j.str.2018.07.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/18/2018] [Accepted: 07/21/2018] [Indexed: 12/20/2022]
Abstract
Human phosphoglucomutase 1 (PGM1) plays a central role in cellular glucose homeostasis, catalyzing the conversion of glucose 1-phosphate and glucose 6-phosphate. Recently, missense variants of this enzyme were identified as causing an inborn error of metabolism, PGM1 deficiency, with features of a glycogen storage disease and a congenital disorder of glycosylation. Previous studies of selected PGM1 variants have revealed various mechanisms for enzyme dysfunction, including regions of structural disorder and side-chain rearrangements within the active site. Here, we examine variants within a substrate-binding loop in domain 4 (D4) of PGM1 that cause extreme impairment of activity. Biochemical, structural, and computational studies demonstrate multiple detrimental impacts resulting from these variants, including loss of conserved ligand-binding interactions and reduced mobility of the D4 loop, due to perturbation of its conformational ensemble. These potentially synergistic effects make this conserved ligand-binding loop a hotspot for disease-related variants in PGM1 and related enzymes.
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Affiliation(s)
- Kyle M Stiers
- Biochemistry Department, University of Missouri, 117 Schweitzer Hall, Columbia, MO 65211, USA
| | - Lesa J Beamer
- Biochemistry Department, University of Missouri, 117 Schweitzer Hall, Columbia, MO 65211, USA.
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The Analysis of Variants in the General Population Reveals That PMM2 Is Extremely Tolerant to Missense Mutations and That Diagnosis of PMM2-CDG Can Benefit from the Identification of Modifiers. Int J Mol Sci 2018; 19:ijms19082218. [PMID: 30061496 PMCID: PMC6121245 DOI: 10.3390/ijms19082218] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 07/19/2018] [Accepted: 07/26/2018] [Indexed: 12/11/2022] Open
Abstract
Type I disorders of glycosylation (CDG), the most frequent of which is phosphomannomutase 2 (PMM2-CDG), are a group of diseases causing the incomplete N-glycosylation of proteins. PMM2-CDG is an autosomal recessive disease with a large phenotypic spectrum, and is associated with mutations in the PMM2 gene. The biochemical analysis of mutants does not allow a precise genotype⁻phenotype correlation for PMM2-CDG. PMM2 is very tolerant to missense and loss of function mutations, suggesting that a partial deficiency of activity might be beneficial under certain circumstances. The patient phenotype might be influenced by variants in other genes associated with the type I disorders of glycosylation in the general population.
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Citro V, Cimmaruta C, Liguori L, Viscido G, Cubellis MV, Andreotti G. A mutant of phosphomannomutase1 retains full enzymatic activity, but is not activated by IMP: Possible implications for the disease PMM2-CDG. PLoS One 2017; 12:e0189629. [PMID: 29261720 PMCID: PMC5736207 DOI: 10.1371/journal.pone.0189629] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 11/29/2017] [Indexed: 11/18/2022] Open
Abstract
The most frequent disorder of glycosylation, PMM2-CDG, is caused by a deficiency of phosphomannomutase activity. In humans two paralogous enzymes exist, both of them require mannose 1,6-bis-phosphate or glucose 1,6-bis-phosphate as activators, but only phospho-mannomutase1 hydrolyzes bis-phosphate hexoses. Mutations in the gene encoding phosphomannomutase2 are responsible for PMM2-CDG. Although not directly causative of the disease, the role of the paralogous enzyme in the disease should be clarified. Phosphomannomutase1 could have a beneficial effect, contributing to mannose 6-phosphate isomerization, or a detrimental effect, hydrolyzing the bis-phosphate hexose activator. A pivotal role in regulating mannose-1phosphate production and ultimately protein glycosylation might be played by inosine monophosphate that enhances the phosphatase activity of phosphomannomutase1. In this paper we analyzed human phosphomannomutases by conventional enzymatic assays as well as by novel techniques such as 31P-NMR and thermal shift assay. We characterized a triple mutant of phospomannomutase1 that retains mutase and phosphatase activity, but is unable to bind inosine monophosphate.
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Affiliation(s)
- Valentina Citro
- Dipartimento di Biologia, Università Federico II, Napoli, Italy
| | | | - Ludovica Liguori
- Istituto di Chimica Biomolecolare–CNR, Pozzuoli, Italy
- Dipartimento di scienze e tecnologie ambientali, biologiche e farmaceutiche, Università della Campania "Luigi Vanvitelli", Caserta, Italy
| | - Gaetano Viscido
- Dipartimento di Biologia, Università Federico II, Napoli, Italy
| | - Maria Vittoria Cubellis
- Dipartimento di Biologia, Università Federico II, Napoli, Italy
- Istituto di Chimica Biomolecolare–CNR, Pozzuoli, Italy
- * E-mail:
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Abstract
Sphingolipidoses are genetically inherited diseases in which genetic mutations lead to functional deficiencies in the enzymes needed for lysosomal degradation of sphingolipid substrates. As a consequence, nondegradable lipids enrich in the lysosomes and lead to fatal pathological phenotypes in affected individuals. In this review, different drug-based treatment strategies including enzyme replacement therapy and substrate reduction therapy are discussed. A special focus is on the concept of pharmacological chaperones, one of which recently acquired clinical approval within the EU. On the basis of the different limitations for each approach, possible future directions of research are discussed.
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Korasick DA, Gamage TT, Christgen S, Stiers KM, Beamer LJ, Henzl MT, Becker DF, Tanner JJ. Structure and characterization of a class 3B proline utilization A: Ligand-induced dimerization and importance of the C-terminal domain for catalysis. J Biol Chem 2017; 292:9652-9665. [PMID: 28420730 PMCID: PMC5465489 DOI: 10.1074/jbc.m117.786855] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Revised: 04/12/2017] [Indexed: 12/23/2022] Open
Abstract
The bifunctional flavoenzyme proline utilization A (PutA) catalyzes the two-step oxidation of proline to glutamate using separate proline dehydrogenase (PRODH) and l-glutamate-γ-semialdehyde dehydrogenase active sites. Because PutAs catalyze sequential reactions, they are good systems for studying how metabolic enzymes communicate via substrate channeling. Although mechanistically similar, PutAs vary widely in domain architecture, oligomeric state, and quaternary structure, and these variations represent different structural solutions to the problem of sequestering a reactive metabolite. Here, we studied PutA from Corynebacterium freiburgense (CfPutA), which belongs to the uncharacterized 3B class of PutAs. A 2.7 Å resolution crystal structure showed the canonical arrangement of PRODH, l-glutamate-γ-semialdehyde dehydrogenase, and C-terminal domains, including an extended interdomain tunnel associated with substrate channeling. The structure unexpectedly revealed a novel open conformation of the PRODH active site, which is interpreted to represent the non-activated conformation, an elusive form of PutA that exhibits suboptimal channeling. Nevertheless, CfPutA exhibited normal substrate-channeling activity, indicating that it isomerizes into the active state under assay conditions. Sedimentation-velocity experiments provided insight into the isomerization process, showing that CfPutA dimerizes in the presence of a proline analog and NAD+ These results are consistent with the morpheein model of enzyme hysteresis, in which substrate binding induces conformational changes that promote assembly of a high-activity oligomer. Finally, we used domain deletion analysis to investigate the function of the C-terminal domain. Although this domain contains neither catalytic residues nor substrate sites, its removal impaired both catalytic activities, suggesting that it may be essential for active-site integrity.
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Affiliation(s)
| | | | - Shelbi Christgen
- Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588
| | | | | | | | - Donald F Becker
- Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588
| | - John J Tanner
- From the Departments of Biochemistry and
- Chemistry, University of Missouri, Columbia, Missouri 65211, and
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A rhodium(III)-based inhibitor of autotaxin with antiproliferative activity. Biochim Biophys Acta Gen Subj 2017; 1861:256-263. [DOI: 10.1016/j.bbagen.2016.11.032] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 11/09/2016] [Accepted: 11/21/2016] [Indexed: 12/17/2022]
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41
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Sánchez-Fernández EM, García Fernández JM, Mellet CO. Glycomimetic-based pharmacological chaperones for lysosomal storage disorders: lessons from Gaucher, GM1-gangliosidosis and Fabry diseases. Chem Commun (Camb) 2016; 52:5497-515. [PMID: 27043200 DOI: 10.1039/c6cc01564f] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Lysosomal storage disorders (LSDs) are often caused by mutations that destabilize native folding and impair the trafficking of enzymes, leading to premature endoplasmic reticulum (ER)-associated degradation, deficiencies of specific hydrolytic functions and aberrant storage of metabolites in the lysosomes. Enzyme replacement therapy (ERT) and substrate reduction therapy (SRT) are available for a few of these conditions, but most remain orphan. A main difficulty is that virtually all LSDs involve neurological decline and neither proteins nor the current SRT drugs can cross the blood-brain barrier. Twenty years ago a new therapeutic paradigm better suited for neuropathic LSDs was launched, namely pharmacological chaperone (PC) therapy. PCs are small molecules capable of binding to the mutant protein at the ER, inducing proper folding, restoring trafficking and increasing enzyme activity and substrate processing in the lysosome. In many LSDs the mutated protein is a glycosidase and the accumulated substrate is an oligo- or polysaccharide or a glycoconjugate, e.g. a glycosphingolipid. Although it might appear counterintuitive, substrate analogues (glycomimetics) behaving as competitive glycosidase inhibitors are good candidates to perform PC tasks. The advancements in the knowledge of the molecular basis of LSDs, including enzyme structures, binding modes, trafficking pathways and substrate processing mechanisms, have been put forward to optimize PC selectivity and efficacy. Moreover, the chemical versatility of glycomimetics and the variety of structures at hand allow simultaneous optimization of chaperone and pharmacokinetic properties. In this Feature Article we review the advancements made in this field in the last few years and the future outlook through the lessons taught by three archetypical LSDs: Gaucher disease, GM1-gangliosidosis and Fabry disease.
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Affiliation(s)
- Elena M Sánchez-Fernández
- Departamento de Química Orgánica, Facultad de Química, Universidad de Sevilla, Profesor García González 1, 41012, Sevilla, Spain.
| | - José M García Fernández
- Instituto de Investigaciones Químicas (IIQ), CSIC - Universidad de Sevilla, Avda. Américo Vespucio 49, 41092 Sevilla, Spain.
| | - Carmen Ortiz Mellet
- Departamento de Química Orgánica, Facultad de Química, Universidad de Sevilla, Profesor García González 1, 41012, Sevilla, Spain.
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Citro V, Cammisa M, Liguori L, Cimmaruta C, Lukas J, Cubellis MV, Andreotti G. The Large Phenotypic Spectrum of Fabry Disease Requires Graduated Diagnosis and Personalized Therapy: A Meta-Analysis Can Help to Differentiate Missense Mutations. Int J Mol Sci 2016; 17:ijms17122010. [PMID: 27916943 PMCID: PMC5187810 DOI: 10.3390/ijms17122010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 11/23/2016] [Accepted: 11/24/2016] [Indexed: 12/28/2022] Open
Abstract
Fabry disease is caused by mutations in the GLA gene and is characterized by a large genotypic and phenotypic spectrum. Missense mutations pose a special problem for graduating diagnosis and choosing a cost-effective therapy. Some mutants retain enzymatic activity, but are less stable than the wild type protein. These mutants can be stabilized by small molecules which are defined as pharmacological chaperones. The first chaperone to reach clinical trial is 1-deoxygalactonojirimycin, but others have been tested in vitro. Residual activity of GLA mutants has been measured in the presence or absence of pharmacological chaperones by several authors. Data obtained from transfected cells correlate with those obtained in cells derived from patients, regardless of whether 1-deoxygalactonojirimycin was present or not. The extent to which missense mutations respond to 1-deoxygalactonojirimycin is variable and a reference table of the results obtained by independent groups that is provided with this paper can facilitate the choice of eligible patients. A review of other pharmacological chaperones is provided as well. Frequent mutations can have residual activity as low as one-fourth of normal enzyme in vitro. The reference table with residual activity of the mutants facilitates the identification of non-pathological variants.
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Affiliation(s)
- Valentina Citro
- Dipartimento di Biologia, Università Federico II, 80126 Napoli, Italy.
| | - Marco Cammisa
- Istituto di Genetica e Biofisica 'A. Buzzati-Traverso', CNR, 80131 Napoli, Italy.
| | | | - Chiara Cimmaruta
- Dipartimento di Biologia, Università Federico II, 80126 Napoli, Italy.
- Istituto di Chimica Biomolecolare, CNR, 80078 Pozzuoli, Italy.
| | - Jan Lukas
- Albrecht-Kossel-Institute for Neuroregeneration, University Rostock Medical Center, 18147 Rostock, Germany.
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Citro V, Peña-García J, den-Haan H, Pérez-Sánchez H, Del Prete R, Liguori L, Cimmaruta C, Lukas J, Cubellis MV, Andreotti G. Identification of an Allosteric Binding Site on Human Lysosomal Alpha-Galactosidase Opens the Way to New Pharmacological Chaperones for Fabry Disease. PLoS One 2016; 11:e0165463. [PMID: 27788225 PMCID: PMC5082870 DOI: 10.1371/journal.pone.0165463] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 10/12/2016] [Indexed: 12/19/2022] Open
Abstract
Personalized therapies are required for Fabry disease due to its large phenotypic spectrum and numerous different genotypes. In principle, missense mutations that do not affect the active site could be rescued with pharmacological chaperones. At present pharmacological chaperones for Fabry disease bind the active site and couple a stabilizing effect, which is required, to an inhibitory effect, which is deleterious. By in silico docking we identified an allosteric hot-spot for ligand binding where a drug-like compound, 2,6-dithiopurine, binds preferentially. 2,6-dithiopurine stabilizes lysosomal alpha-galactosidase in vitro and rescues a mutant that is not responsive to a mono-therapy with previously described pharmacological chaperones, 1-deoxygalactonojirimycin and galactose in a cell based assay.
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Affiliation(s)
- Valentina Citro
- Dipartimento di Biologia, Università Federico II, Napoli, 80126, Italy
| | - Jorge Peña-García
- Bioinformatics and High Performance Computing Research Group (BIO-HPC), Computer Engineering Department, Universidad Católica San Antonio de Murcia (UCAM), Spain
| | - Helena den-Haan
- Bioinformatics and High Performance Computing Research Group (BIO-HPC), Computer Engineering Department, Universidad Católica San Antonio de Murcia (UCAM), Spain
| | - Horacio Pérez-Sánchez
- Bioinformatics and High Performance Computing Research Group (BIO-HPC), Computer Engineering Department, Universidad Católica San Antonio de Murcia (UCAM), Spain
- * E-mail: (MVC); (HPS)
| | - Rosita Del Prete
- Dipartimento di Biologia, Università Federico II, Napoli, 80126, Italy
| | - Ludovica Liguori
- Dipartimento di Biologia, Università Federico II, Napoli, 80126, Italy
- Istituto di Chimica Biomolecolare–CNR, Pozzuoli, 80078, Italy
| | - Chiara Cimmaruta
- Dipartimento di Biologia, Università Federico II, Napoli, 80126, Italy
- Istituto di Chimica Biomolecolare–CNR, Pozzuoli, 80078, Italy
| | - Jan Lukas
- Albrecht-Kossel-Institute for Neuroregeneration, Medical University Rostock, Rostock, Germany
| | - Maria Vittoria Cubellis
- Dipartimento di Biologia, Università Federico II, Napoli, 80126, Italy
- * E-mail: (MVC); (HPS)
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Ben Bdira F, Jiang J, Kallemeijn W, de Haan A, Florea BI, Bleijlevens B, Boot R, Overkleeft HS, Aerts JM, Ubbink M. Hydrophobic Interactions Contribute to Conformational Stabilization of Endoglycoceramidase II by Mechanism-Based Probes. Biochemistry 2016; 55:4823-35. [DOI: 10.1021/acs.biochem.6b00363] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Fredj Ben Bdira
- Department
of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg
55, 2333 CC Leiden, The Netherlands
| | - Jianbing Jiang
- Department
of Bio-organic Synthesis, Leiden Institute of Chemistry, Einsteinweg
55, 2333 CC Leiden, The Netherlands
| | - Wouter Kallemeijn
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333
CC Leiden, The Netherlands
| | - Annett de Haan
- Department of Medical Biochemistry, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Bogdan I. Florea
- Department
of Bio-organic Synthesis, Leiden Institute of Chemistry, Einsteinweg
55, 2333 CC Leiden, The Netherlands
| | - Boris Bleijlevens
- Department of Medical Biochemistry, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Rolf Boot
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333
CC Leiden, The Netherlands
| | - Herman S. Overkleeft
- Department
of Bio-organic Synthesis, Leiden Institute of Chemistry, Einsteinweg
55, 2333 CC Leiden, The Netherlands
| | - Johannes M. Aerts
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333
CC Leiden, The Netherlands
| | - Marcellus Ubbink
- Department
of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg
55, 2333 CC Leiden, The Netherlands
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Ca-asp bound X-ray structure and inhibition of Bacillus anthracis dihydroorotase (DHOase). Bioorg Med Chem 2016; 24:4536-4543. [PMID: 27499369 DOI: 10.1016/j.bmc.2016.07.055] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/22/2016] [Accepted: 07/25/2016] [Indexed: 01/01/2023]
Abstract
Dihydroorotase (DHOase) is the third enzyme in the de novo pyrimidine synthesis pathway and is responsible for the reversible cyclization of carbamyl-aspartate (Ca-asp) to dihydroorotate (DHO). DHOase is further divided into two classes based on several structural characteristics, one of which is the length of the flexible catalytic loop that interacts with the substrate, Ca-asp, regulating the enzyme activity. Here, we present the crystal structure of Class I Bacillus anthracis DHOase with Ca-asp in the active site, which shows the peptide backbone of glycine in the shorter loop forming the necessary hydrogen bonds with the substrate, in place of the two threonines found in Class II DHOases. Despite the differences in the catalytic loop, the structure confirms that the key interactions between the substrate and active site residues are similar between Class I and Class II DHOase enzymes, which we further validated by mutagenesis studies. B. anthracis DHOase is also a potential antibacterial drug target. In order to identify prospective inhibitors, we performed high-throughput screening against several libraries using a colorimetric enzymatic assay and an orthogonal fluorescence thermal binding assay. Surface plasmon resonance was used for determining binding affinity (KD) and competition analysis with Ca-asp. Our results highlight that the primary difference between Class I and Class II DHOase is the catalytic loop. We also identify several compounds that can potentially be further optimized as potential B. anthracis inhibitors.
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Simon RP, Robaa D, Alhalabi Z, Sippl W, Jung M. KATching-Up on Small Molecule Modulators of Lysine Acetyltransferases. J Med Chem 2016; 59:1249-70. [PMID: 26701186 DOI: 10.1021/acs.jmedchem.5b01502] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The reversible acetylation of lysines is one of the best characterized epigenetic modifications. Its involvement in many key physiological and pathological processes has been documented in numerous studies. Lysine deacetylases (KDACs) and acetyltransferases (KATs) maintain the acetylation equilibrium at histones but also many other proteins. Besides acetylation, also other acyl groups are reversibly installed at the side chain of lysines in proteins. Because of their involvement in disease, KDACs and KATs were proposed to be promising drug targets, and for KDACs, indeed, five inhibitors are now approved for human use. While there is a similar level of evidence for the potential of KATs as drug targets, no inhibitor is in clinical trials. Here, we review the evidence for the diverse roles of KATs in disease pathology, provide an overview of structural features and the available modulators, including those targeting the bromodomains of KATs, and present an outlook.
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Affiliation(s)
- Roman P Simon
- Institute of Pharmaceutical Sciences, University of Freiburg , Albertstraße 25, Freiburg 79104, Germany
| | - Dina Robaa
- Department of Pharmaceutical Chemistry, University Halle-Wittenberg , Halle/Saale 06120, Germany
| | - Zayan Alhalabi
- Department of Pharmaceutical Chemistry, University Halle-Wittenberg , Halle/Saale 06120, Germany
| | - Wolfgang Sippl
- Department of Pharmaceutical Chemistry, University Halle-Wittenberg , Halle/Saale 06120, Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, University of Freiburg , Albertstraße 25, Freiburg 79104, Germany
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47
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Andreotti G, Monti MC, Citro V, Cubellis MV. Heterodimerization of Two Pathological Mutants Enhances the Activity of Human Phosphomannomutase2. PLoS One 2015; 10:e0139882. [PMID: 26488408 PMCID: PMC4619449 DOI: 10.1371/journal.pone.0139882] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 09/18/2015] [Indexed: 12/04/2022] Open
Abstract
The most frequent disorder of glycosylation is due to mutations in the gene encoding phosphomannomutase2 (PMM2-CDG). For this disease, which is autosomal and recessive, there is no cure at present. Most patients are composite heterozygous and carry one allele encoding an inactive mutant, R141H, and one encoding a hypomorphic mutant. Phosphomannomutase2 is a dimer. We reproduced composite heterozygosity in vitro by mixing R141H either with the wild type protein or the most common hypomorphic mutant F119L and compared the quaternary structure, the activity and the stability of the heterodimeric enzymes. We demonstrated that the activity of R141H/F119L heterodimers in vitro, which reproduces the protein found in patients, has the same activity of wild type/R141H, which reproduces the protein found in healthy carriers. On the other hand the stability of R141H/F119L appears to be reduced both in vitro and in vivo. These findings suggest that a therapy designed to enhance protein stability such as those based on pharmacological chaperones or modulation of proteostasis could be beneficial for PMM2-CDG patients carrying R141H/F119L genotype as well as for other genotypes where protein stability rather than specific activity is affected by mutations.
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Affiliation(s)
| | - Maria Chiara Monti
- Dipartimento di Farmacia, Università degli Studi di Salerno, Fisciano, Italy
| | - Valentina Citro
- Dipartimento di Biologia, Università Federico II, Napoli, Italy
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Andreotti G, Monticelli M, Cubellis MV. Looking for protein stabilizing drugs with thermal shift assay. Drug Test Anal 2015; 7:831-4. [PMID: 25845367 PMCID: PMC6681132 DOI: 10.1002/dta.1798] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 03/03/2015] [Accepted: 03/06/2015] [Indexed: 11/11/2022]
Abstract
Thermal shift assay can be used for the high-throughput screening of pharmacological chaperones. These drugs are small molecules that bind a mutant protein and stabilize it. We demonstrated the robustness, reproducibility and versatility of the method using two molecules that are in clinical trial for Fabry or Pompe disease, Deoxygalactonojirimycin and N-Butyldeoxynojirimycin, and their target enzymes, lysosomal alpha-galactosidaseA and alpha-glucosidase, as test cases. We assessed the influence of solvents and of scanning rate on the measures. We showed that a value that is equivalent to the melting temperature can be obtained by the first derivatives of raw data. We discuss the advantages of the method and the precaution to be taken in running the experiments.
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Affiliation(s)
| | - Maria Monticelli
- Istituto di Chimica Biomolecolare -CNR, Pozzuoli, Italy.,Dipartimento di Biologia, Università Federico II, Napoli, Italy
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