1
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Travis CR, Kean KM, Albanese KI, Henriksen HC, Treacy JW, Chao EY, Houk KN, Waters ML. Trimethyllysine Reader Proteins Exhibit Widespread Charge-Agnostic Binding via Different Mechanisms to Cationic and Neutral Ligands. J Am Chem Soc 2024; 146:3086-3093. [PMID: 38266163 PMCID: PMC11140585 DOI: 10.1021/jacs.3c10031] [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] [Indexed: 01/26/2024]
Abstract
In the last 40 years, cation-π interactions have become part of the lexicon of noncovalent forces that drive protein binding. Indeed, tetraalkylammoniums are universally bound by aromatic cages in proteins, suggesting that cation-π interactions are a privileged mechanism for binding these ligands. A prominent example is the recognition of histone trimethyllysine (Kme3) by the conserved aromatic cage of reader proteins, dictating gene expression. However, two proteins have recently been suggested as possible exceptions to the conventional understanding of tetraalkylammonium recognition. To broadly interrogate the role of cation-π interactions in protein binding interactions, we report the first large-scale comparative evaluation of reader proteins for a neutral Kme3 isostere, experimental and computational mechanistic studies, and structural analysis. We find unexpected widespread binding of readers to a neutral isostere with the first examples of readers that bind the neutral isostere more tightly than Kme3. We find that no single factor dictates the charge selectivity, demonstrating the challenge of predicting such interactions. Further, readers that bind both cationic and neutral ligands differ in mechanism: binding Kme3 via cation-π interactions and the neutral isostere through the hydrophobic effect in the same aromatic cage. This discovery explains apparently contradictory results in previous studies, challenges traditional understanding of molecular recognition of tetraalkylammoniums by aromatic cages in myriad protein-ligand interactions, and establishes a new framework for selective inhibitor design by exploiting differences in charge dependence.
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Affiliation(s)
- Christopher R. Travis
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kelsey M. Kean
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Katherine I. Albanese
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Hanne C. Henriksen
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Joseph W. Treacy
- Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095-1569, USA
| | - Elaine Y. Chao
- Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095-1569, USA
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095-1569, USA
| | - Marcey L. Waters
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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2
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Togo T, Tram L, Denton LG, ElHilali-Pollard X, Gu J, Jiang J, Liu C, Zhao Y, Zhao Y, Zheng Y, Zheng Y, Yang J, Fan P, Arkin MR, Härmä H, Sun D, Canan SS, Wheeler SE, Renslo AR. Systematic Study of Heteroarene Stacking Using a Congeneric Set of Molecular Glues for Procaspase-6. J Med Chem 2023; 66:9784-9796. [PMID: 37406165 PMCID: PMC10388292 DOI: 10.1021/acs.jmedchem.3c00590] [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: 04/02/2023] [Indexed: 07/07/2023]
Abstract
Heteroaromatic stacking interactions are important in drug binding, supramolecular chemistry, and materials science, making protein-ligand model systems of these interactions of considerable interest. Here we studied 30 congeneric ligands that each present a distinct heteroarene for stacking between tyrosine residues at the dimer interface of procaspase-6. Complex X-ray crystal structures of 10 analogs showed that stacking geometries were well conserved, while high-accuracy computations showed that heteroarene stacking energy was well correlated with predicted overall ligand binding energies. Empirically determined KD values in this system thus provide a useful measure of heteroarene stacking with tyrosine. Stacking energies are discussed in the context of torsional strain, the number and positioning of heteroatoms, tautomeric state, and coaxial orientation of heteroarene in the stack. Overall, this study provides an extensive data set of empirical and high-level computed binding energies in a versatile new protein-ligand system amenable to studies of other intermolecular interactions.
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Affiliation(s)
- Takaya Togo
- Department
of Pharmaceutical Chemistry, University
of California, 600 16th Street, San Francisco, California 94143, United States
| | - Linh Tram
- Department
of Pharmaceutical Chemistry, University
of California, 600 16th Street, San Francisco, California 94143, United States
| | - Laura G. Denton
- Department
of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Xochina ElHilali-Pollard
- Department
of Pharmaceutical Chemistry, University
of California, 600 16th Street, San Francisco, California 94143, United States
| | - Jun Gu
- Departments
of Chemistry and Biology, Viva Biotech, Pu Dong New Area, 201203 Shanghai, China
| | - Jinglei Jiang
- Departments
of Chemistry and Biology, Viva Biotech, Pu Dong New Area, 201203 Shanghai, China
| | - Chenglei Liu
- Departments
of Chemistry and Biology, Viva Biotech, Pu Dong New Area, 201203 Shanghai, China
| | - Yan Zhao
- Departments
of Chemistry and Biology, Viva Biotech, Pu Dong New Area, 201203 Shanghai, China
| | - Yanlong Zhao
- Departments
of Chemistry and Biology, Viva Biotech, Pu Dong New Area, 201203 Shanghai, China
| | - Yinzhe Zheng
- Departments
of Chemistry and Biology, Viva Biotech, Pu Dong New Area, 201203 Shanghai, China
| | - Yunping Zheng
- Departments
of Chemistry and Biology, Viva Biotech, Pu Dong New Area, 201203 Shanghai, China
| | - Jingjing Yang
- Departments
of Chemistry and Biology, Viva Biotech, Pu Dong New Area, 201203 Shanghai, China
| | - Panpan Fan
- Departments
of Chemistry and Biology, Viva Biotech, Pu Dong New Area, 201203 Shanghai, China
| | - Michelle R. Arkin
- Department
of Pharmaceutical Chemistry, University
of California, 600 16th Street, San Francisco, California 94143, United States
| | - Harri Härmä
- Department
of Chemistry, University of Turku, 20500 Turku, Finland
| | - Deqian Sun
- Departments
of Chemistry and Biology, Viva Biotech, Pu Dong New Area, 201203 Shanghai, China
| | - Stacie S. Canan
- Departments of Chemistry
and Structural Biology, Elgia Therapeutics, La Jolla, California 92037, United States
| | - Steven E. Wheeler
- Department
of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Adam R. Renslo
- Department
of Pharmaceutical Chemistry, University
of California, 600 16th Street, San Francisco, California 94143, United States
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3
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Shulga DA, Tserkovnikova NA, Tarasov DN, Tovbin DG. Investigation of the tight binding mechanism of a new anticoagulant DD217 to factor Xa by means of molecular docking and molecular dynamics. J Biomol Struct Dyn 2022:1-12. [PMID: 35532097 DOI: 10.1080/07391102.2022.2072387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
A new promising drug candidate DD217 has been proposed recently as a potent anticoagulant acting on factor Xa (fXa) target. It exhibits the lowest concentration of doubling the prothrombin time among the known anticoagulants. In order to explain the efficacy of DD217 in terms of molecular interactions with its target we studied the hypothesis of the tight binding mechanism by means of molecular dynamics simulations and statistical analysis of the trajectory. The conducted analysis confirms the significant contributions to the MM/GBSA estimated binding free energy of the S4 pocket residues as well the crucial role of establishing the hydrogen bonds between the ligand and the backbone amides of Gly216 and Gly218 of the target. The simulation results support the hypothesis of the tight binding mechanism of DD217 to fXa.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dmitry A Shulga
- Department of Chemistry, Moscow State University, Moscow, Russia
| | - Natalia A Tserkovnikova
- Department of Kinetics and Catalysis, Institute of Chemical Physics of Russian, Academy of Sciences, Moscow, Russia
| | - Dmitry N Tarasov
- Department of Kinetics and Catalysis, Institute of Chemical Physics of Russian, Academy of Sciences, Moscow, Russia.,PharmaDiall LLC, Moscow, Russia
| | - Dmitry G Tovbin
- Department of Kinetics and Catalysis, Institute of Chemical Physics of Russian, Academy of Sciences, Moscow, Russia.,PharmaDiall LLC, Moscow, Russia
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4
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Sorensen AB, Greisen PJ, Madsen JJ, Lund J, Andersen G, Wulff-Larsen PG, Pedersen AA, Gandhi PS, Overgaard MT, Østergaard H, Olsen OH. A systematic approach for evaluating the role of surface-exposed loops in trypsin-like serine proteases applied to the 170 loop in coagulation factor VIIa. Sci Rep 2022; 12:3747. [PMID: 35260627 PMCID: PMC8904457 DOI: 10.1038/s41598-022-07620-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/14/2022] [Indexed: 12/27/2022] Open
Abstract
Proteases play a major role in many vital physiological processes. Trypsin-like serine proteases (TLPs), in particular, are paramount in proteolytic cascade systems such as blood coagulation and complement activation. The structural topology of TLPs is highly conserved, with the trypsin fold comprising two β-barrels connected by a number of variable surface-exposed loops that provide a surprising capacity for functional diversity and substrate specificity. To expand our understanding of the roles these loops play in substrate and co-factor interactions, we employ a systematic methodology akin to the natural truncations and insertions observed through evolution of TLPs. The approach explores a larger deletion space than classical random or directed mutagenesis. Using FVIIa as a model system, deletions of 1–7 amino acids through the surface exposed 170 loop, a vital allosteric regulator, was introduced. All variants were extensively evaluated by established functional assays and computational loop modelling with Rosetta. The approach revealed detailed structural and functional insights recapitulation and expanding on the main findings in relation to 170 loop functions elucidated over several decades using more cumbersome crystallization and single deletion/mutation methodologies. The larger deletion space was key in capturing the most active variant, which unexpectedly had a six-amino acid truncation. This variant would have remained undiscovered if only 2–3 deletions were considered, supporting the usefulness of the methodology in general protease engineering approaches. Our findings shed further light on the complex role that surface-exposed loops play in TLP function and supports the important role of loop length in the regulation and fine-tunning of enzymatic function throughout evolution.
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Affiliation(s)
- Anders B Sorensen
- Global Research, Novo Nordisk A/S, 2760, Måløv, Denmark.,Department of Chemistry and Bioscience, Aalborg University, 9220, Ålborg, Denmark
| | | | - Jesper J Madsen
- Global and Planetary Health, College of Public Health, University of South Florida, Tampa, FL, 33612, USA.,Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Jacob Lund
- Global Research, Novo Nordisk A/S, 2760, Måløv, Denmark
| | - Gorm Andersen
- Global Research, Novo Nordisk A/S, 2760, Måløv, Denmark
| | | | | | | | - Michael T Overgaard
- Department of Chemistry and Bioscience, Aalborg University, 9220, Ålborg, Denmark
| | | | - Ole H Olsen
- Global Research, Novo Nordisk A/S, 2760, Måløv, Denmark. .,Novo Nordisk Foundation Center for Basic Metabolic Research, Section for Metabolic Receptology, University of Copenhagen, Blegdamsvej 3b, 2200, Copenhagen, Denmark.
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5
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Latypova DK, Shmakov SV, Pechkovskaya SA, Filatov AS, Stepakov AV, Knyazev NA, Boitsov VM. Identification of Spiro-Fused Pyrrolo[3,4- a]pyrrolizines and Tryptanthrines as Potential Antitumor Agents: Synthesis and In Vitro Evaluation. Int J Mol Sci 2021; 22:ijms222111997. [PMID: 34769424 PMCID: PMC8584944 DOI: 10.3390/ijms222111997] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/31/2021] [Accepted: 11/02/2021] [Indexed: 01/01/2023] Open
Abstract
A series of heterocyclic compounds containing a spiro-fused pyrrolo[3,4-a]pyrrolizine and tryptanthrin framework have been synthesized and studied as potential antitumor agents. Cytotoxicity of products was screened against human erythroleukemia (K562) and human cervical carcinoma (HeLa) cell lines. Among the screened compounds. 4a, 4b and 5a were active against human erythroleukemia (K562) cell line, while 4a and 5a were active against cervical carcinoma (HeLa) cell line. In agreement with the DNA cytometry studies, the tested compounds have achieved significant cell-cycle perturbation with higher accumulation of cells in G2/M phase and induced apoptosis. Using confocal microscopy, we found that with 4a and 5a treatment of HeLa cells, actin filaments disappeared, and granular actin was distributed diffusely in the cytoplasm in 76–91% of cells. We discovered that HeLa cells after treatment with compounds 4a and 5a significantly reduced the number of cells with filopodium-like membrane protrusions (from 63 % in control cells to 29% after treatment) and a decrease in cell motility.
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Affiliation(s)
- Diana K. Latypova
- Saint-Petersburg National Research Academic University of the Russian Academy of Sciences, 194021 Saint-Petersburg, Russia; (D.K.L.); (S.V.S.)
| | - Stanislav V. Shmakov
- Saint-Petersburg National Research Academic University of the Russian Academy of Sciences, 194021 Saint-Petersburg, Russia; (D.K.L.); (S.V.S.)
| | - Sofya A. Pechkovskaya
- Institute of Cytology, Russian Academy of Sciences, 194064 Saint-Petersburg, Russia;
| | - Alexander S. Filatov
- Department of Chemistry, Saint-Petersburg State University, 199034 Saint Petersburg, Russia; (A.S.F.); (A.V.S.)
| | - Alexander V. Stepakov
- Department of Chemistry, Saint-Petersburg State University, 199034 Saint Petersburg, Russia; (A.S.F.); (A.V.S.)
- Department of Organic Chemistry, Saint Petersburg State Institute of Technology, 190013 Saint-Petersburg, Russia
| | - Nickolay A. Knyazev
- Institute of Cytology, Russian Academy of Sciences, 194064 Saint-Petersburg, Russia;
- Saint-Petersburg Clinical Scientific and Practical Center for Specialized Types of Medical Care (Oncological), 197758 Saint-Petersburg, Russia
- Correspondence: (N.A.K.); (V.M.B.)
| | - Vitali M. Boitsov
- Saint-Petersburg National Research Academic University of the Russian Academy of Sciences, 194021 Saint-Petersburg, Russia; (D.K.L.); (S.V.S.)
- Correspondence: (N.A.K.); (V.M.B.)
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6
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Santana AG, Díaz-Casado L, Montalvillo L, Jiménez-Moreno E, Mann E, Asensio JL. Aromatic interactions in Glycochemistry: from molecular recognition to catalysis. Curr Med Chem 2021; 29:1208-1218. [PMID: 34254906 DOI: 10.2174/0929867328666210709120216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/05/2021] [Accepted: 05/13/2021] [Indexed: 11/22/2022]
Abstract
Aromatic platforms are ubiquitous recognition motifs occurring in protein carbohydrate binding domains (CBDs), RNA receptors and enzymes. They stabilize the glycoside/receptor complexes by participating in stacking CH/π interactions with either the α- or β- face of the corresponding pyranose units. In addition, the role played by aromatic units in the stabilization of glycoside cationic transition states has started being recognized in recent years. Extensive studies carried out during the last decade have allowed to dissect the main contributing forces that stabilize the carbohydrate/aromatic complexes, while helping delineate not only the standing relationship between the glycoside/aromatic chemical structures and the strength of this interaction, but also their potential influence on glycoside reactivity.
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Affiliation(s)
| | | | | | | | - Enrique Mann
- Instituto de Química Orgánica General (IQOG-CSIC), Madrid, Spain
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7
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Bitencourt-Ferreira G, Rizzotto C, de Azevedo Junior WF. Machine Learning-Based Scoring Functions, Development and Applications with SAnDReS. Curr Med Chem 2021; 28:1746-1756. [PMID: 32410551 DOI: 10.2174/0929867327666200515101820] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/06/2020] [Accepted: 04/07/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Analysis of atomic coordinates of protein-ligand complexes can provide three-dimensional data to generate computational models to evaluate binding affinity and thermodynamic state functions. Application of machine learning techniques can create models to assess protein-ligand potential energy and binding affinity. These methods show superior predictive performance when compared with classical scoring functions available in docking programs. OBJECTIVE Our purpose here is to review the development and application of the program SAnDReS. We describe the creation of machine learning models to assess the binding affinity of protein-ligand complexes. METHODS SAnDReS implements machine learning methods available in the scikit-learn library. This program is available for download at https://github.com/azevedolab/sandres. SAnDReS uses crystallographic structures, binding and thermodynamic data to create targeted scoring functions. RESULTS Recent applications of the program SAnDReS to drug targets such as Coagulation factor Xa, cyclin-dependent kinases and HIV-1 protease were able to create targeted scoring functions to predict inhibition of these proteins. These targeted models outperform classical scoring functions. CONCLUSION Here, we reviewed the development of machine learning scoring functions to predict binding affinity through the application of the program SAnDReS. Our studies show the superior predictive performance of the SAnDReS-developed models when compared with classical scoring functions available in the programs such as AutoDock4, Molegro Virtual Docker and AutoDock Vina.
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Affiliation(s)
| | - Camila Rizzotto
- Pontifical Catholic University of Rio Grande do Sul - PUCRS, Porto Alegre-RS, Brazil
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8
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Li J, Moumbock AFA, Günther S. Exploring Cocrystallized Aromatic Cage Binders to Target Histone Methylation Reader Proteins. J Chem Inf Model 2020; 60:5225-5233. [DOI: 10.1021/acs.jcim.0c00765] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Jianyu Li
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Straße 9, D-79104 Freiburg, Germany
| | - Aurélien F. A. Moumbock
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Straße 9, D-79104 Freiburg, Germany
| | - Stefan Günther
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Straße 9, D-79104 Freiburg, Germany
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9
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Mora Lagares L, Minovski N, Caballero Alfonso AY, Benfenati E, Wellens S, Culot M, Gosselet F, Novič M. Homology Modeling of the Human P-glycoprotein (ABCB1) and Insights into Ligand Binding through Molecular Docking Studies. Int J Mol Sci 2020; 21:ijms21114058. [PMID: 32517082 PMCID: PMC7312539 DOI: 10.3390/ijms21114058] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/28/2020] [Accepted: 06/02/2020] [Indexed: 12/12/2022] Open
Abstract
The ABCB1 transporter also known as P-glycoprotein (P-gp) is a transmembrane protein belonging to the ATP binding cassette super-family of transporters; it is a xenobiotic efflux pump that limits intracellular drug accumulation by pumping the compounds out of cells. P-gp contributes to a decrease of toxicity and possesses broad substrate specificity. It is involved in the failure of numerous anticancer and antiviral chemotherapies due to the multidrug resistance (MDR) phenomenon, where it removes the chemotherapeutics out of the targeted cells. Understanding the details of the ligand–P-gp interaction is therefore crucial for the development of drugs that might overcome the MRD phenomenon and for obtaining a more effective prediction of the toxicity of certain compounds. In this work, an in silico modeling was performed using homology modeling and molecular docking methods with the aim of better understanding the ligand–P-gp interactions. Based on different mouse P-gp structural templates from the PDB repository, a 3D model of the human P-gp (hP-gp) was constructed by means of protein homology modeling. The homology model was then used to perform molecular docking calculations on a set of thirteen compounds, including some well-known compounds that interact with P-gp as substrates, inhibitors, or both. The sum of ranking differences (SRD) was employed for the comparison of the different scoring functions used in the docking calculations. A consensus-ranking scheme was employed for the selection of the top-ranked pose for each docked ligand. The docking results showed that a high number of π interactions, mainly π–sigma, π–alkyl, and π–π type of interactions, together with the simultaneous presence of hydrogen bond interactions contribute to the stability of the ligand–protein complex in the binding site. It was also observed that some interacting residues in hP-gp are the same when compared to those observed in a co-crystallized ligand (PBDE-100) with mouse P-gp (PDB ID: 4XWK). Our in silico approach is consistent with available experimental results regarding P-gp efflux transport assay; therefore it could be useful in the prediction of the role of new compounds in systemic toxicity.
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Affiliation(s)
- Liadys Mora Lagares
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, 1000 Ljubljana, Slovenia;
- Jožef Stefan International Postgraduate School, 1000 Ljubljana, Slovenia;
- Correspondence: (L.M.L.); (M.N.); Tel.: +386-01-476-0253 (L.M.L. & M.N.)
| | - Nikola Minovski
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, 1000 Ljubljana, Slovenia;
| | - Ana Yisel Caballero Alfonso
- Jožef Stefan International Postgraduate School, 1000 Ljubljana, Slovenia;
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche “Mario Negri”—IRCCS, 20156 Milano, Italy;
| | - Emilio Benfenati
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche “Mario Negri”—IRCCS, 20156 Milano, Italy;
| | - Sara Wellens
- Laboratoire de la Barrière Hémato-Encéphalique (LBHE), University Artois, UR 2465, F-62300 Lens, France; (S.W.); (M.C.); (F.G.)
| | - Maxime Culot
- Laboratoire de la Barrière Hémato-Encéphalique (LBHE), University Artois, UR 2465, F-62300 Lens, France; (S.W.); (M.C.); (F.G.)
| | - Fabien Gosselet
- Laboratoire de la Barrière Hémato-Encéphalique (LBHE), University Artois, UR 2465, F-62300 Lens, France; (S.W.); (M.C.); (F.G.)
| | - Marjana Novič
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, 1000 Ljubljana, Slovenia;
- Correspondence: (L.M.L.); (M.N.); Tel.: +386-01-476-0253 (L.M.L. & M.N.)
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10
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Acharyya A, Shin D, Troxler T, Gai F. Can glycine betaine denature proteins? Phys Chem Chem Phys 2020; 22:7794-7802. [PMID: 32242578 DOI: 10.1039/d0cp00397b] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Glycine betaine (GB) is a naturally occurring osmolyte that has been widely recognized as a protein protectant. Since GB consists of a methylated ammonium moiety, it can engage in strong cation-π interactions with aromatic amino acid sidechains. We hypothesize that such specific binding interactions would allow GB to decrease the stability of proteins that are predominantly stabilized by a cluster of aromatic amino acids. To test this hypothesis, we investigate the effect of GB on the stability of two β-hairpins (or mini-proteins) that contain such a cluster. We find that for both systems the stability of the folded state first decreases and then increases with increasing GB concentration. Such non-monotonic dependence not only confirms that GB can act as a protein denaturant, but also underscores the complex interplay between GB's stabilizing and destabilizing forces toward a given protein. While stabilizing osmolytes all have the tendency to be excluded from the protein surface which is the action underlying their stabilizing effect, our results suggest that in order to quantitatively assess the effect of GB on the stability of any given protein, specific cation-π binding interactions need to be explicitly considered. Moreover, our results show, consistent with other studies, that cation methylation can strengthen the respective cation-π interactions. Taken together, these findings provide new insight into the mechanism by which amino acid-based osmolytes interact with proteins.
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Affiliation(s)
- Arusha Acharyya
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, USA.
| | - Dayoung Shin
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, USA.
| | - Thomas Troxler
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, USA.
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, USA.
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11
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Raghunathan S, Jaganade T, Priyakumar UD. Urea-aromatic interactions in biology. Biophys Rev 2020; 12:65-84. [PMID: 32067192 PMCID: PMC7040157 DOI: 10.1007/s12551-020-00620-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 01/08/2020] [Indexed: 02/06/2023] Open
Abstract
Noncovalent interactions are key determinants in both chemical and biological processes. Among such processes, the hydrophobic interactions play an eminent role in folding of proteins, nucleic acids, formation of membranes, protein-ligand recognition, etc.. Though this interaction is mediated through the aqueous solvent, the stability of the above biomolecules can be highly sensitive to any small external perturbations, such as temperature, pressure, pH, or even cosolvent additives, like, urea-a highly soluble small organic molecule utilized by various living organisms to regulate osmotic pressure. A plethora of detailed studies exist covering both experimental and theoretical regimes, to understand how urea modulates the stability of biological macromolecules. While experimentalists have been primarily focusing on the thermodynamic and kinetic aspects, theoretical modeling predominantly involves mechanistic information at the molecular level, calculating atomistic details applying the force field approach to the high level electronic details using the quantum mechanical methods. The review focuses mainly on examples with biological relevance, such as (1) urea-assisted protein unfolding, (2) urea-assisted RNA unfolding, (3) urea lesion interaction within damaged DNA, (4) urea conduction through membrane proteins, and (5) protein-ligand interactions those explicitly address the vitality of hydrophobic interactions involving exclusively the urea-aromatic moiety.
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Affiliation(s)
- Shampa Raghunathan
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, 500032, India
| | - Tanashree Jaganade
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, 500032, India
| | - U Deva Priyakumar
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, 500032, India.
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12
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Characterization of the enzymatic activity of the serine protease domain of Factor VII activating protease (FSAP). Sci Rep 2019; 9:18990. [PMID: 31831842 PMCID: PMC6908674 DOI: 10.1038/s41598-019-55531-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 11/30/2019] [Indexed: 12/18/2022] Open
Abstract
Factor VII (FVII) activating protease (FSAP) is a circulating serine protease. Human genetic studies, based on the Marburg I (MI) (Gly221Glu, chymotrypsin numbering system) polymorphism, implicate FSAP in the pathogenesis of many diseases. Here, we describe the molecular and functional changes caused by the Gly221Glu substitution in the 220 loop using recombinant proteins expressed in E. coli. The serine protease domain (SPD) of wild type (WT) FSAP displayed auto-catalytic activation whereas the MI isoform displayed very low autocatalytic activation and low proteolytic activity against the chromogenic substrate S-2288, Factor VII, tissue factor pathway inhibitor as well as pro-urokinase. Introduction of a thermolysin cleavage site in the activation position (Arg15Gln) led to cleavage of both WT- and MI-SPD and the resulting WT-SPD, but not the MI-SPD, was active. Mutating the Gly221 position to Asp, Gln and Leu led to a loss of activity whereas the Ala substitution was partially active. These results suggest a disturbance of the active site, or non-accessibility of the substrate to the active site in MI-SPD. With respect to regulation with metal ions, calcium, more than sodium, increased the enzymatic activity of WT-SPD. Thus, we describe a novel method for the production of recombinant FSAP-SPD to understand the role of the MI-single nucleotide polymorphism (SNP) in the regulation of its activity.
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13
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Hao X, Zuo X, Kang D, Zhang J, Song Y, Liu X, Zhan P. Contemporary medicinal-chemistry strategies for discovery of blood coagulation factor Xa inhibitors. Expert Opin Drug Discov 2019; 14:915-931. [DOI: 10.1080/17460441.2019.1626821] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Xia Hao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Ji’nan, Shandong, PR China
| | - Xiaofang Zuo
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Ji’nan, Shandong, PR China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Ji’nan, Shandong, PR China
| | - Jian Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Ji’nan, Shandong, PR China
| | - Yuning Song
- Department of Clinical Pharmacy, Qilu Hospital of Shandong University, Jinan, China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Ji’nan, Shandong, PR China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Ji’nan, Shandong, PR China
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14
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DeFrees K, Kemp MT, ElHilali-Pollard X, Zhang X, Mohamed A, Chen Y, Renslo AR. An Empirical Study of Amide-Heteroarene π-Stacking Interactions Using Reversible Inhibitors of a Bacterial Serine Hydrolase. Org Chem Front 2019; 6:1749-1756. [PMID: 32774871 DOI: 10.1039/c9qo00342h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Compared to aryl-aryl π-stacking interactions, the analogous stacking of heteroarenes on amide π systems is less well understood and vastly underutilized in structure-based drug design. Recent theoretical studies have delineated the important geometric coordinates of the interaction, some of which have been confirmed with synthetic model systems based on Rebek imides. Unfortunately, a broadly useful and tractable protein-ligand model system of this interaction has remained elusive. Here we employed a known inhibitor scaffold to study π-stacking of diverse heteroarene substituents on the amide face of Gly238 in the cephalosporinases CTX-M-14 and CTX-M-27. Biochemical inhibition constants (K i) and biophysical binding constants (K d) were determined for nineteen new analogues against both enzymes, while multiple high-resolution co-crystal structures revealed remarkably consistent placement of the probe heteroarene on Gly238. The data presented support the predicted importance of opposing dipoles in amide-heteroarene interactions and should be useful for evaluating other theoretical predictions concerning these interactions.
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Affiliation(s)
- Kyle DeFrees
- Department of Pharmaceutical Chemistry, University of California San Francisco, 600 16th St., San Francisco, California 94158, United States
| | - M Trent Kemp
- Department of Molecular Medicine, University of South Florida College of Medicine, 12901, Bruce B. Downs Blvd, MDC 3522, Tampa, Florida 33612, United States
| | - Xochina ElHilali-Pollard
- Department of Pharmaceutical Chemistry, University of California San Francisco, 600 16th St., San Francisco, California 94158, United States
| | - Xiujun Zhang
- Department of Molecular Medicine, University of South Florida College of Medicine, 12901, Bruce B. Downs Blvd, MDC 3522, Tampa, Florida 33612, United States
| | - Ahmed Mohamed
- Department of Pharmaceutical Chemistry, University of California San Francisco, 600 16th St., San Francisco, California 94158, United States
| | - Yu Chen
- Department of Molecular Medicine, University of South Florida College of Medicine, 12901, Bruce B. Downs Blvd, MDC 3522, Tampa, Florida 33612, United States
| | - Adam R Renslo
- Department of Pharmaceutical Chemistry, University of California San Francisco, 600 16th St., San Francisco, California 94158, United States
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15
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Vadivel K, Schreuder HA, Liesum A, Schmidt AE, Goldsmith G, Bajaj SP. Sodium-site in serine protease domain of human coagulation factor IXa: evidence from the crystal structure and molecular dynamics simulations study. J Thromb Haemost 2019; 17:574-584. [PMID: 30725510 PMCID: PMC6443445 DOI: 10.1111/jth.14401] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 01/24/2019] [Indexed: 01/03/2023]
Abstract
Essentials Consensus sequence and biochemical data suggest a Na+ -site in the factor (F) IXa protease domain. X-ray structure of the FIXa EGF2/protease domain at 1.37 Å reveals a Na+ -site not observed earlier. Molecular dynamics simulations data support that Na+ ± Ca2+ promote FIXa protease domain stability. Sulfate ions found in the protease domain mimic heparin sulfate binding mode in FIXa. SUMMARY: Background Activated coagulation factor IX (FIXa) consists of a γ-carboxyglutamic acid domain, two epidermal growth factor-like (EGF) domains, and a C-terminal protease domain. Consensus sequence and biochemical data support the existence of a Na+ -site in the FIXa protease domain. However, soaking experiments or crystals grown in high concentration of ammonium sulfate did not reveal a Na+ -site in wild-type or mutant FIXa EGF2/protease domain structure. Objective Determine the structure of the FIXa EGF2/protease domain in the presence of Na+ ; perform molecular dynamics (MD) simulations to explore the role of Na+ in stabilizing FIXa structure. Methods Crystallography, MD simulations, and modeling heparin binding to FIXa. Results Crystal structure at 1.37-Å resolution revealed that Na+ is coordinated to carbonyl groups of residues 184A, 185, 221A, and 224 in the FIXa protease domain. The Na+ -site in FIXa is similar to that of FXa and is linked to the Asp189 S1-site. In MD simulations, Na+ reduced fluctuations in residues 217-225 (Na+ -loop) and 70-80 (Ca2+ -loop), whereas Ca2+ reduced fluctuations only in residues of the Ca2+ -loop. Ca2+ and Na+ together reduced fluctuations in residues of the Ca2+ -loop and Na+ -loop (residues 70-80, 183-194, and 217-225). Moreover, we observed four sulfate ions that make salt bridges with FIXa protease domain Arg/Lys residues, which have been implicated in heparin binding. Based upon locations of the sulfate ions, we modeled heparin binding to FIXa, which is similar to the heparin binding in thrombin. Conclusions The FIXa Na+ -site in association with Ca2+ contributes to stabilization of the FIXa protease domain. The heparin binding mode in FIXa is similar to that in thrombin.
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Affiliation(s)
- Kanagasabai Vadivel
- Department of Orthopaedic Surgery, University of California, Los Angeles, CA, USA
| | | | - Alexander Liesum
- Sanofi-Aventis Pharma Deutschland GmbH, Frankfurt am Main, Germany
| | - Amy E Schmidt
- Department of Orthopaedic Surgery, University of California, Los Angeles, CA, USA
| | | | - S Paul Bajaj
- Department of Orthopaedic Surgery, University of California, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, CA, USA
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16
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Itoh Y, Nakashima Y, Tsukamoto S, Kurohara T, Suzuki M, Sakae Y, Oda M, Okamoto Y, Suzuki T. N +-C-H···O Hydrogen bonds in protein-ligand complexes. Sci Rep 2019; 9:767. [PMID: 30683882 PMCID: PMC6347603 DOI: 10.1038/s41598-018-36987-9] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 11/28/2018] [Indexed: 12/03/2022] Open
Abstract
In the context of drug design, C-H···O hydrogen bonds have received little attention so far, mostly because they are considered weak relative to other noncovalent interactions such as O-H···O hydrogen bonds, π/π interactions, and van der Waals interactions. Herein, we demonstrate the significance of hydrogen bonds between C-H groups adjacent to an ammonium cation and an oxygen atom (N+-C-H···O hydrogen bonds) in protein-ligand complexes. Quantum chemical calculations revealed details on the strength and geometrical requirements of these N+-C-H···O hydrogen bonds, and a subsequent survey of the Protein Data Bank (PDB) based on these criteria suggested that numerous protein-ligand complexes contain such N+-C-H···O hydrogen bonds. An ensuing experimental investigation into the G9a-like protein (GLP)-inhibitor complex demonstrated that N+-C-H···O hydrogen bonds affect the activity of the inhibitors against the target enzyme. These results should provide the basis for the use of N+-C-H···O hydrogen bonds in drug discovery.
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Affiliation(s)
- Yukihiro Itoh
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan
| | - Yusuke Nakashima
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan
| | - Shuichiro Tsukamoto
- Department of Physics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Takashi Kurohara
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan
| | - Miki Suzuki
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan
| | - Yoshitake Sakae
- Department of Physics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Masayuki Oda
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-8522, Japan
| | - Yuko Okamoto
- Department of Physics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan.,CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Takayoshi Suzuki
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan. .,CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.
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17
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Affiliation(s)
- Shinji Yamada
- Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
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18
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Ko K, Kim HJ, Ho PS, Lee SO, Lee JE, Min CR, Kim YC, Yoon JH, Park EJ, Kwon YJ, Yun JH, Yoon DO, Kim JS, Park WS, Oh SS, Song YM, Cho WK, Morikawa K, Lee KJ, Park CH. Discovery of a Novel Highly Selective Histamine H4 Receptor Antagonist for the Treatment of Atopic Dermatitis. J Med Chem 2018; 61:2949-2961. [PMID: 29579390 DOI: 10.1021/acs.jmedchem.7b01855] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The histamine H4 receptor (H4R), a member of the G-protein coupled receptor family, has been considered as a potential therapeutic target for treating atopic dermatitis (AD). A large number of H4R antagonists have been disclosed, but no efficient agents controlling both pruritus and inflammation in AD have been developed yet. Here, we have discovered a novel class of orally available H4R antagonists showing strong anti-itching and anti-inflammation activity as well as excellent selectivity against off-targets. A pharmacophore-based virtual screening system constructed in-house successfully identified initial hit compound 9, and the subsequent homology model-guided optimization efficiently led us to discover pyrido[2,3- e]tetrazolo[1,5- a]pyrazine analogue 48 as a novel chemotype of a potent and highly selective H4R antagonist. Importantly, orally administered compound 48 exhibits remarkable efficacy on antipruritus and anti-inflammation with a favorable pharmacokinetic (PK) profile in several mouse models of AD. Thus, these data strongly suggest that our compound 48 is a promising clinical candidate for treatment of AD.
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Affiliation(s)
- Kwangseok Ko
- C&C Research Laboratories, DRC, Sungkyunkwan University , 2066, Seobu-ro, Jangan-gu, Suwon-si , Gyeonggi-do , 16419 , Korea
| | - Hye-Jung Kim
- C&C Research Laboratories, DRC, Sungkyunkwan University , 2066, Seobu-ro, Jangan-gu, Suwon-si , Gyeonggi-do , 16419 , Korea
| | - Pil-Su Ho
- JW Pharmaceutical Co., Ltd ., 2477, Nambusunhwan-ro, Seocho-gu , Seoul , 06725 , Korea
| | - Soon Ok Lee
- C&C Research Laboratories, DRC, Sungkyunkwan University , 2066, Seobu-ro, Jangan-gu, Suwon-si , Gyeonggi-do , 16419 , Korea
| | - Ji-Eun Lee
- C&C Research Laboratories, DRC, Sungkyunkwan University , 2066, Seobu-ro, Jangan-gu, Suwon-si , Gyeonggi-do , 16419 , Korea
| | - Cho-Rong Min
- C&C Research Laboratories, DRC, Sungkyunkwan University , 2066, Seobu-ro, Jangan-gu, Suwon-si , Gyeonggi-do , 16419 , Korea
| | - Yu Chul Kim
- C&C Research Laboratories, DRC, Sungkyunkwan University , 2066, Seobu-ro, Jangan-gu, Suwon-si , Gyeonggi-do , 16419 , Korea
| | - Ju-Han Yoon
- C&C Research Laboratories, DRC, Sungkyunkwan University , 2066, Seobu-ro, Jangan-gu, Suwon-si , Gyeonggi-do , 16419 , Korea
| | - Eun-Jung Park
- C&C Research Laboratories, DRC, Sungkyunkwan University , 2066, Seobu-ro, Jangan-gu, Suwon-si , Gyeonggi-do , 16419 , Korea
| | - Young-Jin Kwon
- C&C Research Laboratories, DRC, Sungkyunkwan University , 2066, Seobu-ro, Jangan-gu, Suwon-si , Gyeonggi-do , 16419 , Korea
| | - Jee-Hun Yun
- C&C Research Laboratories, DRC, Sungkyunkwan University , 2066, Seobu-ro, Jangan-gu, Suwon-si , Gyeonggi-do , 16419 , Korea
| | - Dong-Oh Yoon
- C&C Research Laboratories, DRC, Sungkyunkwan University , 2066, Seobu-ro, Jangan-gu, Suwon-si , Gyeonggi-do , 16419 , Korea
| | - Jung-Sook Kim
- C&C Research Laboratories, DRC, Sungkyunkwan University , 2066, Seobu-ro, Jangan-gu, Suwon-si , Gyeonggi-do , 16419 , Korea
| | - Woul-Seong Park
- C&C Research Laboratories, DRC, Sungkyunkwan University , 2066, Seobu-ro, Jangan-gu, Suwon-si , Gyeonggi-do , 16419 , Korea
| | - Seung-Su Oh
- C&C Research Laboratories, DRC, Sungkyunkwan University , 2066, Seobu-ro, Jangan-gu, Suwon-si , Gyeonggi-do , 16419 , Korea
| | - Yu-Mi Song
- C&C Research Laboratories, DRC, Sungkyunkwan University , 2066, Seobu-ro, Jangan-gu, Suwon-si , Gyeonggi-do , 16419 , Korea
| | - Woon-Ki Cho
- C&C Research Laboratories, DRC, Sungkyunkwan University , 2066, Seobu-ro, Jangan-gu, Suwon-si , Gyeonggi-do , 16419 , Korea
| | - Kazumi Morikawa
- Chugai Pharmaceutical Co., Ltd., Fuji Gotemba Research Laboratories , 1-135 Komakado, Gotemba , Shizuoka , 412-8513 , Japan
| | - Kyoung-June Lee
- JW Pharmaceutical Co., Ltd ., 2477, Nambusunhwan-ro, Seocho-gu , Seoul , 06725 , Korea
| | - Chan-Hee Park
- C&C Research Laboratories, DRC, Sungkyunkwan University , 2066, Seobu-ro, Jangan-gu, Suwon-si , Gyeonggi-do , 16419 , Korea
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19
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Gropp C, Quigley BL, Diederich F. Molecular Recognition with Resorcin[4]arene Cavitands: Switching, Halogen-Bonded Capsules, and Enantioselective Complexation. J Am Chem Soc 2018; 140:2705-2717. [DOI: 10.1021/jacs.7b12894] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Cornelius Gropp
- Laboratory of Organic Chemistry,
Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg
3, 8093 Zürich, Switzerland
| | - Brendan L. Quigley
- Laboratory of Organic Chemistry,
Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg
3, 8093 Zürich, Switzerland
| | - François Diederich
- Laboratory of Organic Chemistry,
Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg
3, 8093 Zürich, Switzerland
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20
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Al Temimi AHK, Belle R, Kumar K, Poater J, Betlem P, Pieters BJGE, Paton RS, Bickelhaupt FM, Mecinović J. Recognition of shorter and longer trimethyllysine analogues by epigenetic reader proteins. Chem Commun (Camb) 2018; 54:2409-2412. [DOI: 10.1039/c8cc01009a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Combined thermodynamic data, molecular dynamics simulations, and quantum chemical studies reveal that epigenetic reader proteins efficiently bind trimethylornithine and trimethylhomolysine.
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Affiliation(s)
- Abbas H. K. Al Temimi
- Institute for Molecules and Materials
- Radboud University
- Nijmegen 6525 AJ
- The Netherlands
| | - Roman Belle
- Institute for Molecules and Materials
- Radboud University
- Nijmegen 6525 AJ
- The Netherlands
| | - Kiran Kumar
- Chemistry Research Laboratory
- University of Oxford
- Oxford OX1 3TA
- UK
| | - Jordi Poater
- ICREA
- Barcelona 08010
- Spain
- Departament de Química Inorgànica i Orgànica & IQTCUB
- Universitat de Barcelona
| | - Peter Betlem
- Institute for Molecules and Materials
- Radboud University
- Nijmegen 6525 AJ
- The Netherlands
| | - Bas J. G. E. Pieters
- Institute for Molecules and Materials
- Radboud University
- Nijmegen 6525 AJ
- The Netherlands
| | - Robert S. Paton
- Chemistry Research Laboratory
- University of Oxford
- Oxford OX1 3TA
- UK
| | - F. Matthias Bickelhaupt
- Institute for Molecules and Materials
- Radboud University
- Nijmegen 6525 AJ
- The Netherlands
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM)
| | - Jasmin Mecinović
- Institute for Molecules and Materials
- Radboud University
- Nijmegen 6525 AJ
- The Netherlands
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21
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Ferreira de Freitas R, Schapira M. A systematic analysis of atomic protein-ligand interactions in the PDB. MEDCHEMCOMM 2017; 8:1970-1981. [PMID: 29308120 PMCID: PMC5708362 DOI: 10.1039/c7md00381a] [Citation(s) in RCA: 251] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 09/15/2017] [Indexed: 12/20/2022]
Abstract
As the protein databank (PDB) recently passed the cap of 123 456 structures, it stands more than ever as an important resource not only to analyze structural features of specific biological systems, but also to study the prevalence of structural patterns observed in a large body of unrelated structures, that may reflect rules governing protein folding or molecular recognition. Here, we compiled a list of 11 016 unique structures of small-molecule ligands bound to proteins - 6444 of which have experimental binding affinity - representing 750 873 protein-ligand atomic interactions, and analyzed the frequency, geometry and impact of each interaction type. We find that hydrophobic interactions are generally enriched in high-efficiency ligands, but polar interactions are over-represented in fragment inhibitors. While most observations extracted from the PDB will be familiar to seasoned medicinal chemists, less expected findings, such as the high number of C-H···O hydrogen bonds or the relatively frequent amide-π stacking between the backbone amide of proteins and aromatic rings of ligands, uncover underused ligand design strategies.
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Affiliation(s)
| | - Matthieu Schapira
- Structural Genomics Consortium , University of Toronto , Toronto , ON M5G 1L7 , Canada .
- Department of Pharmacology and Toxicology , University of Toronto , Toronto , ON M5S 1A8 , Canada
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22
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Lee ECY, Steeno G, Wassermann AM, Zhang L, Shah F, Price DA. Amine promiscuity and toxicology analysis. Bioorg Med Chem Lett 2016; 27:653-657. [PMID: 28011216 DOI: 10.1016/j.bmcl.2016.11.085] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 11/27/2016] [Accepted: 11/28/2016] [Indexed: 12/22/2022]
Abstract
Drug discovery programs often face challenges to obtain sufficient duration of action of the drug (i.e. seek longer half-lives). If the pharmacodynamic response is driven by free plasma concentration of the drug then extending the plasma drug concentration is a valid approach. Half-life is dependent on the volume of distribution, which in turn can be dependent upon the ionization state of the molecule. Basic compounds tend to have a higher volume of distribution leading to longer half-lives. However, it has been shown that bases may also have higher promiscuity. In this work, we describe an analysis of in vitro pharmacological profiling and toxicology data investigating the role of primary, secondary, and tertiary amines in imparting promiscuity and thus off-target toxicity. Primary amines are found to be less promiscuous in in vitro assays and have improved profiles in in vivo toxicology studies compared to secondary and tertiary amines.
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Affiliation(s)
- Esther C Y Lee
- Medicine Design, Pfizer Worldwide Research & Development, Cambridge, MA 02139, United States.
| | - Gregory Steeno
- Research Statistics, Pfizer Worldwide Research & Development, Groton, CT 06340, United States
| | | | - Liying Zhang
- Computational Sciences, Pfizer Worldwide Research & Development, Cambridge, MA 02139, United States
| | - Falgun Shah
- Computational Sciences, Pfizer Worldwide Research & Development, Cambridge, MA 02139, United States
| | - David A Price
- Medicine Design, Pfizer Worldwide Research & Development, Cambridge, MA 02139, United States
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23
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Medvedeva SM, Shikhaliev KS. (3+2) Cycloaddition reactions in the synthesis of C(4)–N(5)-condensed tetrahydropyrrolo[3,4-c]pyrrole-1,3-diones (microreview). Chem Heterocycl Compd (N Y) 2016. [DOI: 10.1007/s10593-016-1949-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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24
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Abstract
On the basis of many literature measurements, a critical overview is given on essential noncovalent interactions in synthetic supramolecular complexes, accompanied by analyses with selected proteins. The methods, which can be applied to derive binding increments for single noncovalent interactions, start with the evaluation of consistency and additivity with a sufficiently large number of different host-guest complexes by applying linear free energy relations. Other strategies involve the use of double mutant cycles, of molecular balances, of dynamic combinatorial libraries, and of crystal structures. Promises and limitations of these strategies are discussed. Most of the analyses stem from solution studies, but a few also from gas phase. The empirically derived interactions are then presented on the basis of selected complexes with respect to ion pairing, hydrogen bonding, electrostatic contributions, halogen bonding, π-π-stacking, dispersive forces, cation-π and anion-π interactions, and contributions from the hydrophobic effect. Cooperativity in host-guest complexes as well as in self-assembly, and entropy factors are briefly highlighted. Tables with typical values for single noncovalent free energies and polarity parameters are in the Supporting Information.
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Affiliation(s)
- Frank Biedermann
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT) , Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Hans-Jörg Schneider
- FR Organische Chemie der Universität des Saarlandes , D-66041 Saarbrücken, Germany
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25
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Chen D, Oezguen N, Urvil P, Ferguson C, Dann SM, Savidge TC. Regulation of protein-ligand binding affinity by hydrogen bond pairing. SCIENCE ADVANCES 2016; 2:e1501240. [PMID: 27051863 PMCID: PMC4820369 DOI: 10.1126/sciadv.1501240] [Citation(s) in RCA: 360] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 02/05/2016] [Indexed: 05/20/2023]
Abstract
Hydrogen (H)-bonds potentiate diverse cellular functions by facilitating molecular interactions. The mechanism and the extent to which H-bonds regulate molecular interactions are a largely unresolved problem in biology because the H-bonding process continuously competes with bulk water. This interference may significantly alter our understanding of molecular function, for example, in the elucidation of the origin of enzymatic catalytic power. We advance this concept by showing that H-bonds regulate molecular interactions via a hitherto unappreciated donor-acceptor pairing mechanism that minimizes competition with water. On the basis of theoretical and experimental correlations between H-bond pairings and their effects on ligand binding affinity, we demonstrate that H-bonds enhance receptor-ligand interactions when both the donor and acceptor have either significantly stronger or significantly weaker H-bonding capabilities than the hydrogen and oxygen atoms in water. By contrast, mixed strong-weak H-bond pairings decrease ligand binding affinity due to interference with bulk water, offering mechanistic insight into why indiscriminate strengthening of receptor-ligand H-bonds correlates poorly with experimental binding affinity. Further support for the H-bond pairing principle is provided by the discovery and optimization of lead compounds targeting dietary melamine and Clostridium difficile toxins, which are not realized by traditional drug design methods. Synergistic H-bond pairings have therefore evolved in the natural design of high-affinity binding and provide a new conceptual framework to evaluate the H-bonding process in biological systems. Our findings may also guide wider applications of competing H-bond pairings in lead compound design and in determining the origin of enzymatic catalytic power.
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Affiliation(s)
- Deliang Chen
- Key Laboratory of Organo-Pharmaceutical Chemistry of Jiangxi Province, Chemistry and Chemical Engineering College, Gannan Normal University, Ganzhou, Jiangxi 341000, P. R. China
| | - Numan Oezguen
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Microbiome Center, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Petri Urvil
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Microbiome Center, Texas Children’s Hospital, Houston, TX 77030, USA
| | | | - Sara M. Dann
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Tor C. Savidge
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Microbiome Center, Texas Children’s Hospital, Houston, TX 77030, USA
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26
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Waldner BJ, Fuchs JE, Huber RG, von Grafenstein S, Schauperl M, Kramer C, Liedl KR. Quantitative Correlation of Conformational Binding Enthalpy with Substrate Specificity of Serine Proteases. J Phys Chem B 2016; 120:299-308. [PMID: 26709959 PMCID: PMC4724848 DOI: 10.1021/acs.jpcb.5b10637] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
![]()
Members of the same protease family
show different substrate specificity,
even if they share identical folds, depending on the physiological
processes they are part of. Here, we investigate the key factors for
subpocket and global specificity of factor Xa, elastase, and granzyme
B which despite all being serine proteases and sharing the chymotrypsin-fold
show distinct substrate specificity profiles. We determined subpocket
interaction potentials with GRID for static X-ray structures and an in silico generated ensemble of conformations. Subpocket
interaction potentials determined for static X-ray structures turned
out to be insufficient to explain serine protease specificity for
all subpockets. Therefore, we generated conformational ensembles using
molecular dynamics simulations. We identified representative binding
site conformations using distance-based hierarchical agglomerative
clustering and determined subpocket interaction potentials for each
representative conformation of the binding site. Considering the differences
in subpocket interaction potentials for these representative conformations
as well as their abundance allowed us to quantitatively explain subpocket
specificity for the nonprime side for all three example proteases
on a molecular level. The methods to identify key regions determining
subpocket specificity introduced in this study are directly applicable
to other serine proteases, and the results provide starting points
for new strategies in rational drug design.
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Affiliation(s)
- Birgit J Waldner
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck , Innrain 82, 6020 Innsbruck, Austria
| | - Julian E Fuchs
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck , Innrain 82, 6020 Innsbruck, Austria.,Centre for Molecular Informatics, Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Roland G Huber
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck , Innrain 82, 6020 Innsbruck, Austria.,Bioinformatics Institute (BII), Agency of Science, Technology and Research (A* STAR) , 30 Biopolis Street, Matrix#07-01, 138671 Singapore
| | - Susanne von Grafenstein
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck , Innrain 82, 6020 Innsbruck, Austria
| | - Michael Schauperl
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck , Innrain 82, 6020 Innsbruck, Austria
| | - Christian Kramer
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck , Innrain 82, 6020 Innsbruck, Austria
| | - Klaus R Liedl
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck , Innrain 82, 6020 Innsbruck, Austria
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27
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Korb O, Kuhn B, Hert J, Taylor N, Cole J, Groom C, Stahl M. Interactive and Versatile Navigation of Structural Databases. J Med Chem 2016; 59:4257-66. [DOI: 10.1021/acs.jmedchem.5b01756] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Oliver Korb
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, U.K
| | - Bernd Kuhn
- Roche
Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, CH-4070 Basel, Switzerland
| | - Jérôme Hert
- Roche
Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, CH-4070 Basel, Switzerland
| | - Neil Taylor
- Desert Scientific Software Pty Ltd., Level 5 Nexus Building, Norwest Business Park, 4 Columbia Court, Baulkham Hills, NSW 2153, Australia
| | - Jason Cole
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, U.K
| | - Colin Groom
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, U.K
| | - Martin Stahl
- Roche
Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, CH-4070 Basel, Switzerland
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28
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Sorensen AB, Madsen JJ, Svensson LA, Pedersen AA, Østergaard H, Overgaard MT, Olsen OH, Gandhi PS. Molecular Basis of Enhanced Activity in Factor VIIa-Trypsin Variants Conveys Insights into Tissue Factor-mediated Allosteric Regulation of Factor VIIa Activity. J Biol Chem 2015; 291:4671-83. [PMID: 26694616 DOI: 10.1074/jbc.m115.698613] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Indexed: 11/06/2022] Open
Abstract
The complex of coagulation factor VIIa (FVIIa), a trypsin-like serine protease, and membrane-bound tissue factor (TF) initiates blood coagulation upon vascular injury. Binding of TF to FVIIa promotes allosteric conformational changes in the FVIIa protease domain and improves its catalytic properties. Extensive studies have revealed two putative pathways for this allosteric communication. Here we provide further details of this allosteric communication by investigating FVIIa loop swap variants containing the 170 loop of trypsin that display TF-independent enhanced activity. Using x-ray crystallography, we show that the introduced 170 loop from trypsin directly interacts with the FVIIa active site, stabilizing segment 215-217 and activation loop 3, leading to enhanced activity. Molecular dynamics simulations and novel fluorescence quenching studies support that segment 215-217 conformation is pivotal to the enhanced activity of the FVIIa variants. We speculate that the allosteric regulation of FVIIa activity by TF binding follows a similar path in conjunction with protease domain N terminus insertion, suggesting a more complete molecular basis of TF-mediated allosteric enhancement of FVIIa activity.
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Affiliation(s)
- Anders B Sorensen
- From Global Research, Novo Nordisk A/S, 2760 Måløv, Denmark, Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark, and
| | - Jesper J Madsen
- From Global Research, Novo Nordisk A/S, 2760 Måløv, Denmark, Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | | | | | | | - Michael T Overgaard
- Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark, and
| | - Ole H Olsen
- From Global Research, Novo Nordisk A/S, 2760 Måløv, Denmark
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29
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New Infestin-4 Mutants with Increased Selectivity against Factor XIIa. PLoS One 2015; 10:e0144940. [PMID: 26670620 PMCID: PMC4684401 DOI: 10.1371/journal.pone.0144940] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/25/2015] [Indexed: 01/21/2023] Open
Abstract
Factor XIIa (fXIIa) is a serine protease that triggers the coagulation contact pathway and plays a role in thrombosis. Because it interferes with coagulation testing, the need to inhibit fXIIa exists in many cases. Infestin-4 (Inf4) is a Kazal-type inhibitor of fXIIa. Its specificity for fXIIa can be enhanced by point mutations in the protease-binding loop. We attempted to adapt Inf4 for the selective repression of the contact pathway under various in vitro conditions, e.g., during blood collection and in ‘global’ assays of tissue factor (TF)-dependent coagulation. First, we designed a set of new Inf4 mutants that, in contrast to wt-Inf4, had stabilized canonical conformations during molecular dynamics simulation. Off-target activities against factor Xa (fXa), plasmin, and other coagulation proteases were either reduced or eliminated in these recombinant mutants, as demonstrated by chromogenic assays. Interactions with fXIIa and fXa were also analyzed using protein-protein docking. Next, Mutant B, one of the most potent mutants (its Ki for fXIIa is 0.7 nM) was tested in plasma. At concentrations 5–20 μM, this mutant delayed the contact-activated generation of thrombin, as well as clotting in thromboelastography and thrombodynamics assays. In these assays, Mutant B did not affect coagulation initiated by TF, thus demonstrating sufficient selectivity and its potential practical significance as a reagent for coagulation diagnostics.
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30
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Carrazana-García JA, Cabaleiro-Lago EM, Campo-Cacharrón A, Rodríguez-Otero J. A theoretical study of ternary indole-cation-anion complexes. Org Biomol Chem 2015; 12:9145-56. [PMID: 25296040 DOI: 10.1039/c4ob01879f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The simultaneous interactions of an anion and a cation with a π system were investigated by MP2 and M06-2X theoretical calculations. Indole was chosen as a model π system for its relevance in biological environments. Two different orientations of the anion, interacting with the N-H and with the C-H groups of indole, were considered. The four cations (Na(+), NH4(+), C(NH2)3(+) and N(CH3)4(+)) and the four anions (Cl(-), NO3(-), HCOO(-) and BF4(-)) included in the study are of biological interest. The total interaction energy of the ternary complexes was calculated and separated into its two- and three-body components and all of them are further divided into their electrostatic, exchange, repulsion, polarization and dispersion contributions using the local molecular orbital-energy decomposition analysis (LMO-EDA) methodology. The binding energy of the indole-cation-anion complexes depends on both ions, with the cation having the strongest effect. The intense cation-anion attraction determines the geometric and energetic features in all ternary complexes. These structures, with both ions on the same side of the π system, show an anti-cooperative interaction. However, the interaction is not only determined by electrostatics, but also the polarization contribution is important. Specific interactions like the one established between the anion and the N-H group of indole or the proton transfer between an acidic cation and a basic anion play a significant role in the energetics and the structure of particular complexes. The presence of the polar solvent as modelled with the polarizable continuum model (PCM) does not seem to have a significant effect on the geometry of the ternary complexes, but drastically weakens the interaction energy. Also, the strength of the interaction is reduced at a faster rate when the anion is pushed away, compared to the results obtained in the gas phase. The combination of PCM with the addition of one water molecule indicates that the PCM method properly reproduces the main energetic and geometrical changes, even at the quantitative level, but the explicit hydration allows refining the solvent effect and detecting cases that do not follow the general trend.
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Affiliation(s)
- Jorge A Carrazana-García
- Departamento de Química Física, Facultade de Ciencias, Universidade de Santiago de Compostela, Campus de Lugo, Avenida Alfonso X El Sabio s/n, Lugo 27002, Lugo, Spain.
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31
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Tziridis A, Rauh D, Neumann P, Kolenko P, Menzel A, Bräuer U, Ursel C, Steinmetzer P, Stürzebecher J, Schweinitz A, Steinmetzer T, Stubbs MT. Correlating structure and ligand affinity in drug discovery: a cautionary tale involving second shell residues. Biol Chem 2015; 395:891-903. [PMID: 25003390 DOI: 10.1515/hsz-2014-0158] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 04/24/2014] [Indexed: 11/15/2022]
Abstract
A high-resolution crystallographic structure determination of a protein-ligand complex is generally accepted as the 'gold standard' for structure-based drug design, yet the relationship between structure and affinity is neither obvious nor straightforward. Here we analyze the interactions of a series of serine proteinase inhibitors with trypsin variants onto which the ligand-binding site of factor Xa has been grafted. Despite conservative mutations of only two residues not immediately in contact with ligands (second shell residues), significant differences in the affinity profiles of the variants are observed. Structural analyses demonstrate that these are due to multiple effects, including differences in the structure of the binding site, differences in target flexibility and differences in inhibitor binding modes. The data presented here highlight the myriad competing microscopic processes that contribute to protein-ligand interactions and emphasize the difficulties in predicting affinity from structure.
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32
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Belskaya NP, Lesogorova SG, Subbotina JO, Koksharov AV, Slepukhin PA, Dehaen W, Bakulev VA. 1,3-Dipolar cycloaddition of 3-alkylsulfanyl-2-arylazo-3-(tert-cycloalkylamino)acrylonitriles with N-methyl- and N-phenylmaleimides. Tetrahedron 2015. [DOI: 10.1016/j.tet.2014.12.087] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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33
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Persch E, Dumele O, Diederich F. Molekulare Erkennung in chemischen und biologischen Systemen. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201408487] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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34
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Persch E, Dumele O, Diederich F. Molecular recognition in chemical and biological systems. Angew Chem Int Ed Engl 2015; 54:3290-327. [PMID: 25630692 DOI: 10.1002/anie.201408487] [Citation(s) in RCA: 424] [Impact Index Per Article: 47.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Indexed: 12/13/2022]
Abstract
Structure-based ligand design in medicinal chemistry and crop protection relies on the identification and quantification of weak noncovalent interactions and understanding the role of water. Small-molecule and protein structural database searches are important tools to retrieve existing knowledge. Thermodynamic profiling, combined with X-ray structural and computational studies, is the key to elucidate the energetics of the replacement of water by ligands. Biological receptor sites vary greatly in shape, conformational dynamics, and polarity, and require different ligand-design strategies, as shown for various case studies. Interactions between dipoles have become a central theme of molecular recognition. Orthogonal interactions, halogen bonding, and amide⋅⋅⋅π stacking provide new tools for innovative lead optimization. The combination of synthetic models and biological complexation studies is required to gather reliable information on weak noncovalent interactions and the role of water.
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Affiliation(s)
- Elke Persch
- Laboratorium für Organische Chemie, Departement Chemie und Angewandte Biowissenschaften, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich (Switzerland)
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35
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Zhou C, Deng L, Yao F, Xu L, Zhou J, Fu GD. A Well-Defined Amphiphilic Polymer Conetwork from Sequence Control of the Cross-Linking in Polymer Chains. Ind Eng Chem Res 2014. [DOI: 10.1021/ie503649t] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Chao Zhou
- School
of Chemistry and Chemical Engineering, Southeast University, Nanjing, Jiangsu Province 211189, P. R. China
| | - Linhong Deng
- Institute
of Biomedical Engineering and Health Sciences, Changzhou University, Changzhou, Jiangsu Province 213164, P. R. China
| | - Fang Yao
- School
of Chemistry and Chemical Engineering, Southeast University, Nanjing, Jiangsu Province 211189, P. R. China
| | - Liqun Xu
- Institute of Clean Energy & Advanced Materials, Southwest University, Chongqing, 400715, P. R. China
| | - Jian Zhou
- School
of Materials and Engineering, Jiangsu University of Technology, Changzhou, Jiangsu Province 213001, P. R. China
| | - Guo Dong Fu
- School
of Chemistry and Chemical Engineering, Southeast University, Nanjing, Jiangsu Province 211189, P. R. China
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36
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Belviso BD, Caliandro R, de Candia M, Zaetta G, Lopopolo G, Incampo F, Colucci M, Altomare CD. How a β-d-Glucoside Side Chain Enhances Binding Affinity to Thrombin of Inhibitors Bearing 2-Chlorothiophene as P1 Moiety: Crystallography, Fragment Deconstruction Study, and Evaluation of Antithrombotic Properties. J Med Chem 2014; 57:8563-75. [DOI: 10.1021/jm5010754] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Benny D. Belviso
- Institute
of Crystallography, Consiglio Nazionale delle Ricerche, Via Amendola
122/o, 70126 Bari, Italy
| | - Rocco Caliandro
- Institute
of Crystallography, Consiglio Nazionale delle Ricerche, Via Amendola
122/o, 70126 Bari, Italy
| | - Modesto de Candia
- Department
of Pharmacy—Drug Sciences, University of Bari ‘‘Aldo Moro’’, Via E. Orabona 4, 70125 Bari, Italy
| | - Giorgia Zaetta
- Department
of Pharmacy—Drug Sciences, University of Bari ‘‘Aldo Moro’’, Via E. Orabona 4, 70125 Bari, Italy
| | - Gianfranco Lopopolo
- Department
of Pharmacy—Drug Sciences, University of Bari ‘‘Aldo Moro’’, Via E. Orabona 4, 70125 Bari, Italy
| | - Francesca Incampo
- Department
of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, Piazza Giulio Cesare 11, 70124 Bari, Italy
| | - Mario Colucci
- Department
of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, Piazza Giulio Cesare 11, 70124 Bari, Italy
| | - Cosimo D. Altomare
- Department
of Pharmacy—Drug Sciences, University of Bari ‘‘Aldo Moro’’, Via E. Orabona 4, 70125 Bari, Italy
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37
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Rooney TPC, Filippakopoulos P, Fedorov O, Picaud S, Cortopassi WA, Hay DA, Martin S, Tumber A, Rogers CM, Philpott M, Wang M, Thompson AL, Heightman TD, Pryde DC, Cook A, Paton RS, Müller S, Knapp S, Brennan PE, Conway SJ. A Series of Potent CREBBP Bromodomain Ligands Reveals an Induced-Fit Pocket Stabilized by a Cation-π Interaction. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402750] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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38
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Rooney TPC, Filippakopoulos P, Fedorov O, Picaud S, Cortopassi WA, Hay DA, Martin S, Tumber A, Rogers CM, Philpott M, Wang M, Thompson AL, Heightman TD, Pryde DC, Cook A, Paton RS, Müller S, Knapp S, Brennan PE, Conway SJ. A series of potent CREBBP bromodomain ligands reveals an induced-fit pocket stabilized by a cation-π interaction. Angew Chem Int Ed Engl 2014; 53:6126-30. [PMID: 24821300 PMCID: PMC4298791 DOI: 10.1002/anie.201402750] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Indexed: 12/04/2022]
Abstract
The benzoxazinone and dihydroquinoxalinone fragments were employed as novel acetyl lysine mimics in the development of CREBBP bromodomain ligands. While the benzoxazinone series showed low affinity for the CREBBP bromodomain, expansion of the dihydroquinoxalinone series resulted in the first potent inhibitors of a bromodomain outside the BET family. Structural and computational studies reveal that an internal hydrogen bond stabilizes the protein-bound conformation of the dihydroquinoxalinone series. The side chain of this series binds in an induced-fit pocket forming a cation–π interaction with R1173 of CREBBP. The most potent compound inhibits binding of CREBBP to chromatin in U2OS cells.
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Affiliation(s)
- Timothy P C Rooney
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA (UK) http://conway.chem.ox.ac.uk/
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39
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Rapp C, Goldberger E, Tishbi N, Kirshenbaum R. Cation-π interactions of methylated ammonium ions: a quantum mechanical study. Proteins 2014; 82:1494-502. [PMID: 24464782 DOI: 10.1002/prot.24519] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 01/12/2014] [Accepted: 01/16/2014] [Indexed: 11/05/2022]
Abstract
Cation-π interactions of methylated ammonium ions play a key role in a broad range of biochemical systems. These include methyl-lysine binding proteins which bind to methylated sites on histone proteins, lysine demethylase enzymes which demethylate these sites, and neurotransmitter receptor complexes which bind choline-derived ligands. Recognition in these systems is achieved through an 'aromatic cage' motif in the binding site. Here we use high-level quantum mechanical calculations to address how cation-π interactions of methylated ammonium ions are modulated by a change in methylation state and interaction geometry. We survey methyl-lysine and choline-derived complexes in the Protein Databank to validate our results against available structural data. A quantitative description of cation-π interactions of methylated ammonium systems is critical to structure-based efforts to target methyl-lysine binding proteins and demethylase enzymes in the treatment of unregulated transcriptional control, and neurotransmitter receptors in the treatment of neurological disease. It is our hope that our work will serve as a benchmark for the development of physical chemistry based force fields that can accurately model the contribution of cation-π interactions to binding and specificity in these systems.
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Affiliation(s)
- Chaya Rapp
- Department of Chemistry and Biochemistry, Stern College for Women, Yeshiva University, New York, New York
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40
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41
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Zhou C, Qian S, Zhang A, Xu L, Zhu J, Cheng Z, Kang ET, Yao F, Fu GD. A well-defined amphiphilic polymer co-network from precise control of the end-functional groups of linear RAFT polymers. RSC Adv 2014. [DOI: 10.1039/c3ra47939k] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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42
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Müller MP, Albers MF, Itzen A, Hedberg C. Exploring Adenylylation and Phosphocholination as Post-Translational Modifications. Chembiochem 2013; 15:19-26. [DOI: 10.1002/cbic.201300508] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Indexed: 01/07/2023]
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43
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Suresh CH, Sayyed FB. Resonance Enhancement via Imidazole Substitution Predicts New Cation Receptors. J Phys Chem A 2013; 117:10455-61. [DOI: 10.1021/jp406041x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Cherumuttathu H. Suresh
- Chemical Sciences and
Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum 695019, India
| | - Fareed Bhasha Sayyed
- Chemical Sciences and
Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum 695019, India
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44
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Diehl RC, Guinn EJ, Capp MW, Tsodikov OV, Record MT. Quantifying additive interactions of the osmolyte proline with individual functional groups of proteins: comparisons with urea and glycine betaine, interpretation of m-values. Biochemistry 2013; 52:5997-6010. [PMID: 23909383 DOI: 10.1021/bi400683y] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
To quantify interactions of the osmolyte l-proline with protein functional groups and predict their effects on protein processes, we use vapor pressure osmometry to determine chemical potential derivatives dμ2/dm3 = μ23, quantifying the preferential interactions of proline (component 3) with 21 solutes (component 2) selected to display different combinations of aliphatic or aromatic C, amide, carboxylate, phosphate or hydroxyl O, and amide or cationic N surface. Solubility data yield μ23 values for four less-soluble solutes. Values of μ23 are dissected using an ASA-based analysis to test the hypothesis of additivity and obtain α-values (proline interaction potentials) for these eight surface types and three inorganic ions. Values of μ23 predicted from these α-values agree with the experiment, demonstrating additivity. Molecular interpretation of α-values using the solute partitioning model yields partition coefficients (Kp) quantifying the local accumulation or exclusion of proline in the hydration water of each functional group. Interactions of proline with native protein surfaces and effects of proline on protein unfolding are predicted from α-values and ASA information and compared with experimental data, with results for glycine betaine and urea, and with predictions from transfer free energy analysis. We conclude that proline stabilizes proteins because of its unfavorable interactions with (exclusion from) amide oxygens and aliphatic hydrocarbon surfaces exposed in unfolding and that proline is an effective in vivo osmolyte because of the osmolality increase resulting from its unfavorable interactions with anionic (carboxylate and phosphate) and amide oxygens and aliphatic hydrocarbon groups on the surface of cytoplasmic proteins and nucleic acids.
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Affiliation(s)
- Roger C Diehl
- Department of Biochemistry and ‡Department of Chemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
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45
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Manley PW, Blasco F, Mestan J, Aichholz R. The kinetic deuterium isotope effect as applied to metabolic deactivation of imatinib to the des-methyl metabolite, CGP74588. Bioorg Med Chem 2013; 21:3231-9. [DOI: 10.1016/j.bmc.2013.03.038] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 03/01/2013] [Accepted: 03/11/2013] [Indexed: 01/11/2023]
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46
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Zhou D, Lobo YA, Batista IFC, Marques-Porto R, Gustchina A, Oliva MLV, Wlodawer A. Crystal structures of a plant trypsin inhibitor from Enterolobium contortisiliquum (EcTI) and of its complex with bovine trypsin. PLoS One 2013; 8:e62252. [PMID: 23626794 PMCID: PMC3633903 DOI: 10.1371/journal.pone.0062252] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 03/19/2013] [Indexed: 12/03/2022] Open
Abstract
A serine protease inhibitor from Enterolobium contortisiliquum (EcTI) belongs to the Kunitz family of plant inhibitors, common in plant seeds. It was shown that EcTI inhibits the invasion of gastric cancer cells through alterations in integrin-dependent cell signaling pathway. We determined high-resolution crystal structures of free EcTI (at 1.75 Å) and complexed with bovine trypsin (at 2 Å). High quality of the resulting electron density maps and the redundancy of structural information indicated that the sequence of the crystallized isoform contained 176 residues and differed from the one published previously. The structure of the complex confirmed the standard inhibitory mechanism in which the reactive loop of the inhibitor is docked into trypsin active site with the side chains of Arg64 and Ile65 occupying the S1 and S1′ pockets, respectively. The overall conformation of the reactive loop undergoes only minor adjustments upon binding to trypsin. Larger deviations are seen in the vicinity of Arg64, driven by the needs to satisfy specificity requirements. A comparison of the EcTI-trypsin complex with the complexes of related Kunitz inhibitors has shown that rigid body rotation of the inhibitors by as much as 15° is required for accurate juxtaposition of the reactive loop with the active site while preserving its conformation. Modeling of the putative complexes of EcTI with several serine proteases and a comparison with equivalent models for other Kunitz inhibitors elucidated the structural basis for the fine differences in their specificity, providing tools that might allow modification of their potency towards the individual enzymes.
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Affiliation(s)
- Dongwen Zhou
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
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Mahadevi AS, Sastry GN. Cation-π interaction: its role and relevance in chemistry, biology, and material science. Chem Rev 2012; 113:2100-38. [PMID: 23145968 DOI: 10.1021/cr300222d] [Citation(s) in RCA: 731] [Impact Index Per Article: 60.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- A Subha Mahadevi
- Molecular Modeling Group, CSIR-Indian Institute of Chemical Technology Tarnaka, Hyderabad 500 607, Andhra Pradesh, India
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Rueda-Zubiaurre A, Herrero-García N, del Rosario Torres M, Fernández I, Osío Barcina J. Rational Design of a Nonbasic Molecular Receptor for Selective NH4+/K+Complexation in the Gas Phase. Chemistry 2012; 18:16884-9. [DOI: 10.1002/chem.201201642] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 09/16/2012] [Indexed: 11/08/2022]
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Shrestha TB, Kalita M, Pokhrel MR, Liu Y, Troyer DL, Turro C, Bossmann SH, Dürr H. Maleimide-functionalized photochromic spirodihydroindolizines. J Org Chem 2012; 78:1903-9. [PMID: 23095100 DOI: 10.1021/jo301894s] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Two photochromic spirodihydroindolizine/betaine systems for tethering to peptides and proteins via a maleimide function have been prepared. The absorption spectra of the betaines are in the red region of the visible spectrum and in the near-IR spectral domain, which are suitable energies of light for future in vivo applications. The half-times of cyclization have been determined for both DHI/betaine systems. The findings are consistent with a thermal barrier of varying size between the transoid and cisoid conformers of the betaines.
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Affiliation(s)
- Tej B Shrestha
- Department of Anatomy & Physiology, Kansas State University, Coles 130, Manhattan, Kansas 66506, United States.
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Lopopolo G, de Candia M, Panza L, Romano MR, Lograno MD, Campagna F, Altomare C. β-D-Glucosyl Conjugates of Highly Potent Inhibitors of Blood Coagulation Factor Xa Bearing 2-Chorothiophene as a P1 Motif. ChemMedChem 2012; 7:1669-77. [DOI: 10.1002/cmdc.201200224] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Revised: 07/11/2012] [Indexed: 11/08/2022]
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