1
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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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2
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Chiodi D, Ishihara Y. "Magic Chloro": Profound Effects of the Chlorine Atom in Drug Discovery. J Med Chem 2023; 66:5305-5331. [PMID: 37014977 DOI: 10.1021/acs.jmedchem.2c02015] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
Abstract
Chlorine is one of the most common atoms present in small-molecule drugs beyond carbon, hydrogen, nitrogen, and oxygen. There are currently more than 250 FDA-approved chlorine-containing drugs, yet the beneficial effect of the chloro substituent has not yet been reviewed. The seemingly simple substitution of a hydrogen atom (R = H) with a chlorine atom (R = Cl) can result in remarkable improvements in potency of up to 100,000-fold and can lead to profound effects on pharmacokinetic parameters including clearance, half-life, and drug exposure in vivo. Following the literature terminology of the "magic methyl effect" in drugs, the term "magic chloro effect" has been coined herein. Although reports of 500-fold or 1000-fold potency improvements are often serendipitous discoveries that can be considered "magical" rather than planned, hypotheses made to explain the magic chloro effect can lead to lessons that accelerate the cycle of drug discovery.
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Affiliation(s)
- Debora Chiodi
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yoshihiro Ishihara
- Department of Chemistry, Vividion Therapeutics, 5820 Nancy Ridge Drive, San Diego, California 92121, United States
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3
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Belle R, Kamps JJAG, Poater J, Kumar K, Pieters BJGE, Salah E, Claridge TDW, Paton RS, Bickelhaupt FM, Kawamura A, Schofield CJ, Mecinović J. Reading and erasing of the phosphonium analogue of trimethyllysine by epigenetic proteins. Commun Chem 2022; 5:10.1038/s42004-022-00640-4. [PMID: 36071790 PMCID: PMC7613515 DOI: 10.1038/s42004-022-00640-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 02/03/2022] [Indexed: 01/27/2023] Open
Abstract
N ε-Methylation of lysine residues in histones plays an essential role in the regulation of eukaryotic transcription. The 'highest' methylation mark, N ε-trimethyllysine, is specifically recognised by N ε-trimethyllysine binding 'reader' domains, and undergoes demethylation, as catalysed by 2-oxoglutarate dependent JmjC oxygenases. We report studies on the recognition of the closest positively charged N ε-trimethyllysine analogue, i.e. its trimethylphosphonium derivative (KPme3), by N ε-trimethyllysine histone binding proteins and Nε-trimethyllysine demethylases. Calorimetric and computational studies with histone binding proteins reveal that H3KP4me3 binds more tightly than the natural H3K4me3 substrate, though the relative differences in binding affinity vary. Studies with JmjC demethylases show that some, but not all, of them can accept the phosphonium analogue of their natural substrates and that the methylation state selectivity can be changed by substitution of nitrogen for phosphorus. The combined results reveal that very subtle changes, e.g. substitution of nitrogen for phosphorus, can substantially affect interactions between ligand and reader domains / demethylases, knowledge that we hope will inspire the development of highly selective small molecules modulating their activity.
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Affiliation(s)
- Roman Belle
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA UK
- Chemistry—School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
| | - Jos J. A. G. Kamps
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA UK
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Jordi Poater
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
- Departament de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - Kiran Kumar
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA UK
| | - Bas J. G. E. Pieters
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Eidarus Salah
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA UK
| | - Timothy D. W. Claridge
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA UK
| | - Robert S. Paton
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA UK
| | - F. Matthias Bickelhaupt
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
- Department of Theoretical Chemistry, Amsterdam Center for Multiscale Modeling, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Akane Kawamura
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA UK
- Chemistry—School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
| | - Christopher J. Schofield
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA UK
| | - Jasmin Mecinović
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
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4
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Xu M, Shen C, Yang J, Wang Q, Huang N. Systematic Investigation of Docking Failures in Large-Scale Structure-Based Virtual Screening. ACS OMEGA 2022; 7:39417-39428. [PMID: 36340123 PMCID: PMC9632257 DOI: 10.1021/acsomega.2c05826] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
In recent years, large-scale structure-based virtual screening has attracted increasing levels of interest for identification of novel compounds corresponding to potential drug targets. It is critical to understand the strengths and weaknesses of docking algorithms to increase the success rate in practical applications. Here, we systematically investigated the docking successes and failures of two representative docking programs: UCSF DOCK 3.7 and AutoDock Vina. DOCK 3.7 performed better in early enrichment on the Directory of Useful Decoys: Enhanced (DUD-E) data set, although both docking methods were roughly comparable in overall enrichment performance. DOCK 3.7 also showed superior computational efficiency. Intriguingly, the Vina scoring function showed a bias toward compounds with higher molecular weights. Both the tested docking approaches yielded incorrectly predicted ligand binding poses caused by the limitations of torsion sampling. Based on a careful analysis of docking results from six representative cases, we propose the reasons underlying docking failures; furthermore, we provide a few solutions, representing practical guidance for large-scale virtual screening campaigns and future docking algorithm development.
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Affiliation(s)
- Min Xu
- College
of Life Sciences, Beijing Normal University, No. 19 Xinjiekouwai Street, Beijing 100875, China
- National
Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science
Park, Beijing 102206, China
| | - Cheng Shen
- National
Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science
Park, Beijing 102206, China
- Graduate
School of Peking Union Medical College, Chinese Academy of Medical Sciences, No. 9, Dongdan Santiao, Dongcheng District, Beijing 100730, China
| | - Jincai Yang
- National
Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science
Park, Beijing 102206, China
| | - Qing Wang
- National
Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science
Park, Beijing 102206, China
- School
of Pharmaceutical Science and Technology, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Niu Huang
- National
Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science
Park, Beijing 102206, China
- Tsinghua
Institute of Multidisciplinary Biomedical Research, Tsinghua University, 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
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5
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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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6
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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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7
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Liu H, Fu H, Chipot C, Shao X, Cai W. Accuracy of Alternate Nonpolarizable Force Fields for the Determination of Protein-Ligand Binding Affinities Dominated by Cation-π Interactions. J Chem Theory Comput 2021; 17:3908-3915. [PMID: 34125530 DOI: 10.1021/acs.jctc.1c00219] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Modifying pair-specific Lennard-Jones parameters through the nonbonded FIX (NBFIX) feature of the CHARMM36 force field has proven cost-effective for improving the description of cation-π interactions in biological objects by means of pairwise additive potential energy functions. Here, two sets of newly optimized CHARMM36 force-field parameters including NBFIX corrections, coined CHARMM36m-NBF and CHARMM36-WYF, and the original force fields, namely CHARMM36m and Amber ff14SB, are used to determine the standard binding free energies of seven protein-ligand complexes containing cation-π interactions. Compared with precise experimental measurements, our results indicate that the uncorrected, original force fields significantly underestimate the binding free energies, with a mean error of 5.3 kcal/mol, while the mean errors of CHARMM36m-NBF and CHARMM36-WYF amount to 0.8 and 2.1 kcal/mol, respectively. The present study cogently demonstrates that the use of modified parameters jointly with NBFIX corrections dramatically increases the accuracy of the standard binding free energy of protein-ligand complexes dominated by cation-π interactions, most notably with CHARMM36m-NBF.
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Affiliation(s)
- Han Liu
- Research Center for Analytical Sciences, College of Chemistry, and Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
| | - Haohao Fu
- Research Center for Analytical Sciences, College of Chemistry, and Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
| | - Christophe Chipot
- Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, UMR No. 7019, Université de Lorraine, BP 70239, F-54506 Vandœuvre-lès-Nancy, France.,Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - Xueguang Shao
- Research Center for Analytical Sciences, College of Chemistry, and Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
| | - Wensheng Cai
- Research Center for Analytical Sciences, College of Chemistry, and Key Laboratory of Biosensing and Molecular Recognition, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
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8
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Kumar S, Kim MH. SMPLIP-Score: predicting ligand binding affinity from simple and interpretable on-the-fly interaction fingerprint pattern descriptors. J Cheminform 2021; 13:28. [PMID: 33766140 PMCID: PMC7993508 DOI: 10.1186/s13321-021-00507-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 03/16/2021] [Indexed: 12/13/2022] Open
Abstract
In drug discovery, rapid and accurate prediction of protein–ligand binding affinities is a pivotal task for lead optimization with acceptable on-target potency as well as pharmacological efficacy. Furthermore, researchers hope for a high correlation between docking score and pose with key interactive residues, although scoring functions as free energy surrogates of protein–ligand complexes have failed to provide collinearity. Recently, various machine learning or deep learning methods have been proposed to overcome the drawbacks of scoring functions. Despite being highly accurate, their featurization process is complex and the meaning of the embedded features cannot directly be interpreted by human recognition without an additional feature analysis. Here, we propose SMPLIP-Score (Substructural Molecular and Protein–Ligand Interaction Pattern Score), a direct interpretable predictor of absolute binding affinity. Our simple featurization embeds the interaction fingerprint pattern on the ligand-binding site environment and molecular fragments of ligands into an input vectorized matrix for learning layers (random forest or deep neural network). Despite their less complex features than other state-of-the-art models, SMPLIP-Score achieved comparable performance, a Pearson’s correlation coefficient up to 0.80, and a root mean square error up to 1.18 in pK units with several benchmark datasets (PDBbind v.2015, Astex Diverse Set, CSAR NRC HiQ, FEP, PDBbind NMR, and CASF-2016). For this model, generality, predictive power, ranking power, and robustness were examined using direct interpretation of feature matrices for specific targets. ![]()
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Affiliation(s)
- Surendra Kumar
- Gachon Institute of Pharmaceutical Science & Department of Pharmacy, College of Pharmacy, Gachon University, 191 Hambakmoeiro, Yeonsu-gu, Incheon, Republic of Korea
| | - Mi-Hyun Kim
- Gachon Institute of Pharmaceutical Science & Department of Pharmacy, College of Pharmacy, Gachon University, 191 Hambakmoeiro, Yeonsu-gu, Incheon, Republic of Korea.
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9
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Denesyuk AI, Permyakov SE, Johnson MS, Denessiouk K, Permyakov EA. System Approach for Building of Calcium-Binding Sites in Proteins. Biomolecules 2020; 10:biom10040588. [PMID: 32290360 PMCID: PMC7226230 DOI: 10.3390/biom10040588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/08/2020] [Accepted: 04/09/2020] [Indexed: 11/16/2022] Open
Abstract
We introduce five new local metal cation (first of all, Ca2+) recognition units in proteins: Clampn,(n−2), Clampn,(n−1), Clampn,n, Clampn,(n+1) and Clampn,(n+2). In these units, the backbone oxygen atom of a residue in position “n” of an amino acid sequence and side-chain oxygen atom of a residue in position “n + i” (i = −2 to +2) directly interact with a metal cation. An analysis of the known “Ca2+-bound niches” in proteins has shown that a system approach based on the simultaneous use of the Clamp units and earlier proposed One-Residue (OR)/Three-Residue (TR) units significantly improves the results of constructing metal cation-binding sites in proteins.
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Affiliation(s)
- Alexander I. Denesyuk
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino 142290, Russia; (S.E.P.); (E.A.P.)
- Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, Turku 20520, Finland; (M.S.J.); (K.D.)
- Correspondence: ; Tel.: +358-2-215-4006
| | - Sergei E. Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino 142290, Russia; (S.E.P.); (E.A.P.)
| | - Mark S. Johnson
- Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, Turku 20520, Finland; (M.S.J.); (K.D.)
| | - Konstantin Denessiouk
- Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, Turku 20520, Finland; (M.S.J.); (K.D.)
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, Turku 20520, Finland
| | - Eugene A. Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino 142290, Russia; (S.E.P.); (E.A.P.)
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10
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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: 10] [Impact Index Per Article: 2.5] [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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11
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Jarvis A, Ouvry G. Essential ingredients for rational drug design. Bioorg Med Chem Lett 2019; 29:126674. [PMID: 31521476 DOI: 10.1016/j.bmcl.2019.126674] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/03/2019] [Accepted: 09/04/2019] [Indexed: 01/09/2023]
Abstract
This short review focuses on three aspects of rational drug design that we consider of utmost importance: the conformation of small molecules in solid form, the conformation of small molecules in solution and lesser studied interactions in protein-ligand complexes. Using examples from recent literature, we will illustrate these different aspects and how they have contributed to the discovery of potent modulators.
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Affiliation(s)
- Ashley Jarvis
- Evotec (U.K.) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Gilles Ouvry
- Evotec (U.K.) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom.
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12
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Abstract
Predicting the strength of stacking interactions involving heterocycles is vital for several fields, including structure-based drug design. While quantum chemical computations can provide accurate stacking interaction energies, these come at a steep computational cost. To address this challenge, we recently developed quantitative predictive models of stacking interactions between druglike heterocycles and the aromatic amino acids Phe, Tyr, and Trp (DOI: 10.1021/jacs.9b00936 ). These models depend on heterocycle descriptors derived from electrostatic potentials (ESPs) computed using density functional theory and provide accurate stacking interactions without the need for expensive computations on stacked dimers. Herein, we show that these ESP-based descriptors can be reliably evaluated directly from the atom connectivity of the heterocycle, providing a means of predicting both the descriptors and the potential for a given heterocycle to engage in stacking interactions without resorting to any quantum chemical computations. This enables the rapid conversion of simple molecular representations (e.g., SMILES) directly into accurate stacking interaction energies using a freely available online tool, thereby providing a way to rank the stacking abilities of large sets of heterocycles.
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Affiliation(s)
- Andrea N Bootsma
- Center for Computational Quantum Chemistry, Department of Chemistry , University of Georgia , Athens , Georgia 30602 , United States
| | - Steven E Wheeler
- Center for Computational Quantum Chemistry, Department of Chemistry , University of Georgia , Athens , Georgia 30602 , United States
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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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Ilin I, Lipets E, Sulimov A, Kutov D, Shikhaliev K, Potapov A, Krysin M, Zubkov F, Sapronova L, Ataullakhanov F, Sulimov V. New factor Xa inhibitors based on 1,2,3,4-tetrahydroquinoline developed by molecular modelling. J Mol Graph Model 2019; 89:215-224. [PMID: 30913501 DOI: 10.1016/j.jmgm.2019.03.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 03/11/2019] [Accepted: 03/13/2019] [Indexed: 10/27/2022]
Abstract
Factor Xa is a serine protease representing a crucial element in the coagulation process and an attractive target for anticoagulant therapy. At the present time there are several chemical classes of factor Xa inhibitors with proven activity. Furthermore, three factor Xa inhibitors have been approved for the medical use to date. However, therapy with these medications is accompanied by substantial adverse effects. In this background, the structure-based computational approach combining molecular docking and semiempirical quantum chemical calculations was applied for a search for new effective factor Xa inhibitors. We have undertaken a few virtual screening procedures to select potential candidates for synthesis and subsequent testing. The first screen of the focused library resulted in identifying 20 compounds among which 7 compounds showed the noticeable inhibition of factor Xa at maximal concentrations, allowed by solubility. The subsequent additional screens identified 20 additional candidates. Of these, 5 substances were shown to be capable of inhibiting factor Xa at 5 μM. The best two found 1,2,3,4-tetrahydroquinoline derivatives identified by means of modelling have demonstrated IC50 values in the micromolar range. One of them turned out to be selective factor Xa inhibitor over trypsin, factors IIa, IXa and XIa.
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Affiliation(s)
- Ivan Ilin
- Research Computer Center, Moscow State University, Leninskie Gory 1, Building 4, Moscow, 119992, Russia; Dimonta, Ltd, Nagornaya Street 15, Building 8, Moscow, 17186, Russia.
| | - Elena Lipets
- Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, 1 Samory Mashela Str., Moscow, 117997, Russia; Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences Kosygina Str. 4, Moscow, 119334, Russia
| | - Alexey Sulimov
- Research Computer Center, Moscow State University, Leninskie Gory 1, Building 4, Moscow, 119992, Russia; Dimonta, Ltd, Nagornaya Street 15, Building 8, Moscow, 17186, Russia
| | - Danil Kutov
- Research Computer Center, Moscow State University, Leninskie Gory 1, Building 4, Moscow, 119992, Russia; Dimonta, Ltd, Nagornaya Street 15, Building 8, Moscow, 17186, Russia
| | - Khidmet Shikhaliev
- Voronezh State University, Universitetskaya Sq. 1, Voronezh, 394018, Russia
| | - Andrey Potapov
- Voronezh State University, Universitetskaya Sq. 1, Voronezh, 394018, Russia
| | - Michael Krysin
- Voronezh State University, Universitetskaya Sq. 1, Voronezh, 394018, Russia
| | - Fedor Zubkov
- Department of Organic Chemistry, Peoples' Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya St., Moscow, Russia
| | - Lyudmila Sapronova
- Department of Organic Chemistry, Peoples' Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya St., Moscow, Russia
| | - Fazoyl Ataullakhanov
- Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, 1 Samory Mashela Str., Moscow, 117997, Russia; Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences Kosygina Str. 4, Moscow, 119334, Russia
| | - Vladimir Sulimov
- Research Computer Center, Moscow State University, Leninskie Gory 1, Building 4, Moscow, 119992, Russia; Dimonta, Ltd, Nagornaya Street 15, Building 8, Moscow, 17186, Russia
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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: 59] [Impact Index Per Article: 11.8] [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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Jing L, Wu G, Kang D, Zhou Z, Song Y, Liu X, Zhan P. Contemporary medicinal-chemistry strategies for the discovery of selective butyrylcholinesterase inhibitors. Drug Discov Today 2018; 24:629-635. [PMID: 30503804 DOI: 10.1016/j.drudis.2018.11.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 10/25/2018] [Accepted: 11/15/2018] [Indexed: 01/02/2023]
Abstract
Butyrylcholinesterase (BChE) is considered a promising drug target for the treatment of moderate to severe Alzheimer's disease (AD). Here, we review medicinal-chemistry strategies that are currently available for the discovery of selective BChE inhibitors.
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Affiliation(s)
- Lanlan Jing
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Ji'nan, Shandong 250012, PR China
| | - Gaochan Wu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Ji'nan, Shandong 250012, PR China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Ji'nan, Shandong 250012, PR China
| | - Zhongxia Zhou
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Ji'nan, Shandong 250012, PR China
| | - Yuning Song
- Department of Clinical Pharmacy, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Ji'nan, Shandong 250012, PR China.
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Ji'nan, Shandong 250012, PR China.
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18
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Gunaratne R, Kumar S, Frederiksen JW, Stayrook S, Lohrmann JL, Perry K, Bompiani KM, Chabata CV, Thalji NK, Ho MD, Arepally G, Camire RM, Krishnaswamy S, Sullenger BA. Combination of aptamer and drug for reversible anticoagulation in cardiopulmonary bypass. Nat Biotechnol 2018; 36:606-613. [PMID: 29863725 PMCID: PMC6349032 DOI: 10.1038/nbt.4153] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 03/27/2018] [Indexed: 02/05/2023]
Abstract
Unfractionated heparin (UFH), the standard anticoagulant for cardiopulmonary bypass (CPB) surgery, carries a risk of post-operative bleeding and is potentially harmful in patients with heparin-induced thrombocytopenia-associated antibodies. To improve the activity of an alternative anticoagulant, the RNA aptamer 11F7t, we solved X-ray crystal structures of the aptamer bound to factor Xa (FXa). The finding that 11F7t did not bind the catalytic site suggested that it could complement small-molecule FXa inhibitors. We demonstrate that combinations of 11F7t and catalytic-site FXa inhibitors enhance anticoagulation in purified reaction mixtures and plasma. Aptamer-drug combinations prevented clot formation as effectively as UFH in human blood circulated in an extracorporeal oxygenator circuit that mimicked CPB, while avoiding side effects of UFH. An antidote could promptly neutralize the anticoagulant effects of both FXa inhibitors. Our results suggest that drugs and aptamers with shared targets can be combined to exert more specific and potent effects than either agent alone.
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Affiliation(s)
- Ruwan Gunaratne
- Duke University, Department of Pharmacology and Cancer Biology, Durham, NC 27710
- Duke University, Medical Scientist Training Program, Durham, NC 27710
| | - Shekhar Kumar
- Research Institute, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | | | - Steven Stayrook
- Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19104
| | | | - Kay Perry
- Northeastern Collaborative Access Team (NE-CAT) and Departments of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, IL 60439
| | | | - Charlene V. Chabata
- Duke University, Department of Pharmacology and Cancer Biology, Durham, NC 27710
| | - Nabil K. Thalji
- Research Institute, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19104
| | - Michelle D. Ho
- Research Institute, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | | | - Rodney M. Camire
- Research Institute, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19104
| | - Sriram Krishnaswamy
- Research Institute, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19104
| | - Bruce A. Sullenger
- Duke University, Department of Pharmacology and Cancer Biology, Durham, NC 27710
- Duke University, Department of Surgery, Durham, NC 27710
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19
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Kim PY, Yeh CH, Dale BJ, Leslie BA, Stafford AR, Fredenburgh JC, Hirsh J, Weitz JI. Mechanistic Basis for the Differential Effects of Rivaroxaban and Apixaban on Global Tests of Coagulation. TH OPEN 2018; 2:e190-e201. [PMID: 31249942 PMCID: PMC6524873 DOI: 10.1055/s-0038-1649507] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 03/26/2018] [Indexed: 02/07/2023] Open
Abstract
Rivaroxaban and apixaban are both small molecules that reversibly inhibit factor Xa. Compared with rivaroxaban, apixaban has minimal effects on the prothrombin time and activated partial thromboplastin time. To investigate this phenomenon, we used a factor Xa-directed substrate in a buffer system. Although rivaroxaban and apixaban inhibited factor Xa with similar K i values at equilibrium, kinetic measurements revealed that rivaroxaban inhibited factor Xa up to 4-fold faster than apixaban ( p < 0.001). Using a discontinuous chromogenic assay to monitor thrombin production by prothrombinase in a purified system, rivaroxaban was 4-fold more potent than apixaban (K i values of 0.7 ± 0.3 and 2.9 ± 0.5 nM, respectively; p = 0.02). Likewise, in thrombin generation assays in plasma, rivaroxaban prolonged the lag time and suppressed endogenous thrombin potential to a greater extent than apixaban. To characterize how the two inhibitors differ in recognizing factor Xa, inhibition of prothrombinase was monitored in real-time using a fluorescent probe for thrombin. The data were fit using a mixed-inhibition model and the individual association and dissociation rate constants were determined. The association rates for the binding of rivaroxaban to either free factor Xa or factor Xa incorporated into the prothrombinase complex were 10- and 1,193-fold faster than those for apixaban, respectively, whereas dissociation rates were about 3-fold faster. Collectively, these findings suggest that rivaroxaban and apixaban differ in their capacity to inhibit factor Xa and provide a plausible explanation for the observation that rivaroxaban has a greater effect on global tests of coagulation than apixaban.
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Affiliation(s)
- Paul Y Kim
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada.,Thrombosis and Atherosclerosis Research Institute, Hamilton, Ontario, Canada
| | - Calvin H Yeh
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada.,Thrombosis and Atherosclerosis Research Institute, Hamilton, Ontario, Canada.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Brian J Dale
- Thrombosis and Atherosclerosis Research Institute, Hamilton, Ontario, Canada.,School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia
| | - Beverly A Leslie
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada.,Thrombosis and Atherosclerosis Research Institute, Hamilton, Ontario, Canada
| | - Alan R Stafford
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada.,Thrombosis and Atherosclerosis Research Institute, Hamilton, Ontario, Canada
| | - James C Fredenburgh
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada.,Thrombosis and Atherosclerosis Research Institute, Hamilton, Ontario, Canada
| | - Jack Hirsh
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Jeffrey I Weitz
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada.,Thrombosis and Atherosclerosis Research Institute, Hamilton, Ontario, Canada.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
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20
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Bootsma AN, Wheeler SE. Stacking Interactions of Heterocyclic Drug Fragments with Protein Amide Backbones. ChemMedChem 2018; 13:835-841. [PMID: 29451739 DOI: 10.1002/cmdc.201700721] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 01/18/2018] [Indexed: 12/25/2022]
Abstract
Stacking interactions can be important enthalpic contributors to drug binding. Among the less well-studied stacking interactions are those occurring between an arene and the π-face of an amide group. Given the ubiquity of heterocycles in drugs, combined with the abundance of amides in the protein backbone, optimizing these noncovalent interactions can provide a potential route to enhanced drug binding. Previously, Diederich et al. (ChemMedChem 2013, 8, 397-404) studied stacked dimers of a model amide with a set of 18 heterocycles, showing that computed interaction energies correlate with the dipole moments of the heterocycles and providing guidelines for the optimization of these interactions. We considered stacked dimers of the same model amide with a larger set of 28 heterocycles common in pharmaceuticals, by using more robust ab initio methods. While the overall trends in these new data corroborate many of the results of Diederich et al., these data provide a more refined view of the nature of amide stacking interactions. We present a robust scoring function for amide stacking interaction energies based on the molecular dipole moment and strength of the electric field above the arene.
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Affiliation(s)
- Andrea N Bootsma
- Center for Computational Quantum Chemistry, Department of Chemistry, University of Georgia, Athens, GA, 30602, USA.,Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Steven E Wheeler
- Center for Computational Quantum Chemistry, Department of Chemistry, University of Georgia, Athens, GA, 30602, USA
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21
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Denesyuk AI, Permyakov SE, Johnson MS, Permyakov EA, Denessiouk K. Building kit for metal cation binding sites in proteins. Biochem Biophys Res Commun 2017; 494:311-317. [PMID: 29017922 DOI: 10.1016/j.bbrc.2017.10.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 10/06/2017] [Indexed: 11/17/2022]
Abstract
Starting with conformations of calcium-binding sites in parvalbumin and integrin (representative structures of EF-hand and calcium blade zones, respectively) we introduce four new different local Ca2+-recognition units in proteins: a one-residue unit type I (ORI); a three-residue unit type I (TRI); a one-residue unit type II (ORII) and a three-residue unit type II (TRII). Based on the amount and nature of variable atoms, the type I and II units theoretically can have four and twelve variants, respectively. Analysis of known "Ca2+-bound functional niches" in proteins revealed presence of almost all possible variants of Ca2+-recognition units in actual structures. Parvalbumin, integrin alpha-IIb and sixteen other proteins with different Ca2+-bound functional niches contain various consecutively joined combinations of OR(I/II) and TR(I/II) units. Such a OR(I/II)+TR(I/II) joint unit forms a tripeptide, which uses three main-chain atoms for metal binding: nitrogenn (Donor), oxygenn (Acceptor) and nitrogenn+2 (Donor). Thus, taken together, the described ORI, TRI, ORII and TRII units can serve as elementary blocks to construct more complex calcium recognizing substructures in a variety of calcium binding sites of unrelated proteins.
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Affiliation(s)
- Alexander I Denesyuk
- Faculty of Science and Engineering, Åbo Akademi University, Turku 20500, Finland; Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino 142290, Russia.
| | - Sergei E Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino 142290, Russia
| | - Mark S Johnson
- Faculty of Science and Engineering, Åbo Akademi University, Turku 20500, Finland
| | - Eugene A Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino 142290, Russia
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22
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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: 232] [Impact Index Per Article: 33.1] [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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23
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Simó Padial J, Poater J, Nguyen DT, Tinnemans P, Bickelhaupt FM, Mecinović J. Stabilization of 2,6-Diarylanilinum Cation by Through-Space Cation-π Interactions. J Org Chem 2017; 82:9418-9424. [PMID: 28836782 PMCID: PMC5603827 DOI: 10.1021/acs.joc.7b01406] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
![]()
Energetically
favorable cation−π interactions play
important roles in numerous molecular recognition processes in chemistry
and biology. Herein, we present synergistic experimental and computational
physical–organic chemistry studies on 2,6-diarylanilines that
contain flanking meta/para-substituted
aromatic rings adjacent to the central anilinium ion. A combination
of measurements of pKa values, structural
analyses of 2,6-diarylanilinium cations, and quantum chemical analyses
based on the quantitative molecular orbital theory and a canonical
energy decomposition analysis (EDA) scheme reveal that through-space
cation−π interactions essentially contribute to observed
trends in proton affinities and pKa values
of 2,6-diarylanilines.
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Affiliation(s)
- Joan Simó Padial
- Institute for Molecules and Materials, Radboud University , Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Jordi Poater
- Catalan Institution for Research and Advanced Studies (ICREA) , Passeig Lluís Companys 23, 08010 Barcelona, Spain.,Departament de Química Inorgànica i Orgànica and IQTCUB, Universitat de Barcelona , Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - D Thao Nguyen
- Institute for Molecules and Materials, Radboud University , Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Paul Tinnemans
- Institute for Molecules and Materials, Radboud University , Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - F Matthias Bickelhaupt
- Institute for Molecules and Materials, Radboud University , Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.,Department of Theoretical Chemistry, Amsterdam Center for Multiscale Modeling, Vrije Universiteit Amsterdam , De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Jasmin Mecinović
- Institute for Molecules and Materials, Radboud University , Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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24
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Shen X, Liu X, Wang J, Dai J, Zhu J. Synthesis of an Epoxy Monomer from Bio-Based 2,5-Furandimethanol and Its Toughening via Diels–Alder Reaction. Ind Eng Chem Res 2017. [DOI: 10.1021/acs.iecr.7b01624] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xiaobin Shen
- Ningbo
Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315201, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Xiaoqing Liu
- Ningbo
Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315201, P. R. China
| | - Jinggang Wang
- Ningbo
Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315201, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jinyue Dai
- Ningbo
Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315201, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jin Zhu
- Ningbo
Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315201, P. R. China
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25
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Parrish RM, Sitkoff DF, Cheney DL, Sherrill CD. The Surprising Importance of Peptide Bond Contacts in Drug–Protein Interactions. Chemistry 2017; 23:7887-7890. [DOI: 10.1002/chem.201701031] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Indexed: 01/08/2023]
Affiliation(s)
- Robert M. Parrish
- Center for Computational Molecular Science and Technology School of Chemistry and Biochemistry School of Computational Science and Engineering Georgia Institute of Technology Atlanta GA 30332-0400 USA
| | - Doree F. Sitkoff
- Molecular Structure and Design Bristol-Myers Squibb Company 311 Pennington-Rocky Hill Road Pennington NJ 08534 USA
| | - Daniel L. Cheney
- Molecular Structure and Design Bristol-Myers Squibb Company 311 Pennington-Rocky Hill Road Pennington NJ 08534 USA
| | - C. David Sherrill
- Center for Computational Molecular Science and Technology School of Chemistry and Biochemistry School of Computational Science and Engineering Georgia Institute of Technology Atlanta GA 30332-0400 USA
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26
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Giroud M, Ivkovic J, Martignoni M, Fleuti M, Trapp N, Haap W, Kuglstatter A, Benz J, Kuhn B, Schirmeister T, Diederich F. Inhibition of the Cysteine Protease Human Cathepsin L by Triazine Nitriles: Amide⋅⋅⋅Heteroarene π-Stacking Interactions and Chalcogen Bonding in the S3 Pocket. ChemMedChem 2017; 12:257-270. [DOI: 10.1002/cmdc.201600563] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 12/19/2016] [Indexed: 12/29/2022]
Affiliation(s)
- Maude Giroud
- Laboratorium für Organische Chemie; ETH Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Jakov Ivkovic
- Laboratorium für Organische Chemie; ETH Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Mara Martignoni
- Laboratorium für Organische Chemie; ETH Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Marianne Fleuti
- Laboratorium für Organische Chemie; ETH Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Nils Trapp
- Laboratorium für Organische Chemie; ETH Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Wolfgang Haap
- F. Hoffmann-La Roche Ltd.; Pharma Research and Early Development (pRED); Therapeutic Modalities; Roche Innovation Center Basel; Grenzacherstrasse 124 4070 Basel Switzerland
| | - Andreas Kuglstatter
- F. Hoffmann-La Roche Ltd.; Pharma Research and Early Development (pRED); Therapeutic Modalities; Roche Innovation Center Basel; Grenzacherstrasse 124 4070 Basel Switzerland
| | - Jörg Benz
- F. Hoffmann-La Roche Ltd.; Pharma Research and Early Development (pRED); Therapeutic Modalities; Roche Innovation Center Basel; Grenzacherstrasse 124 4070 Basel Switzerland
| | - Bernd Kuhn
- F. Hoffmann-La Roche Ltd.; Pharma Research and Early Development (pRED); Therapeutic Modalities; Roche Innovation Center Basel; Grenzacherstrasse 124 4070 Basel Switzerland
| | - Tanja Schirmeister
- Institut für Pharmazie und Biochemie; Johannes Gutenberg-Universität Mainz; Staudinger Weg 5 55128 Mainz Germany
| | - François Diederich
- Laboratorium für Organische Chemie; ETH Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
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27
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A Synopsis of the Properties and Applications of Heteroaromatic Rings in Medicinal Chemistry. ADVANCES IN HETEROCYCLIC CHEMISTRY 2017. [DOI: 10.1016/bs.aihch.2016.11.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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28
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Releasing the brakes in coagulation Factor IXa by co-operative maturation of the substrate-binding site. Biochem J 2016; 473:2395-411. [DOI: 10.1042/bcj20160336] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 05/19/2016] [Indexed: 01/27/2023]
Abstract
Coagulation Factor IX is positioned at the merging point of the intrinsic and extrinsic blood coagulation cascades. Factor IXa (activated Factor IX) serves as the trigger for amplification of coagulation through formation of the so-called Xase complex, which is a ternary complex of Factor IXa, its substrate Factor X and the cofactor Factor VIIIa on the surface of activated platelets. Within the Xase complex the substrate turnover by Factor IXa is enhanced 200000-fold; however, the mechanistic and structural basis for this dramatic enhancement remains only partly understood. A multifaceted approach using enzymatic, biophysical and crystallographic methods to evaluate a key set of activity-enhanced Factor IXa variants has demonstrated a delicately balanced bidirectional network. Essential molecular interactions across multiple regions of the Factor IXa molecule co-operate in the maturation of the active site. This maturation is specifically facilitated by long-range communication through the Ile212–Ile213 motif unique to Factor IXa and a flexibility of the 170-loop that is further dependent on the conformation in the Cys168–Cys182 disulfide bond. Ultimately, the network consists of compensatory brakes (Val16 and Ile213) and accelerators (Tyr99 and Phe174) that together allow for a subtle fine-tuning of enzymatic activity.
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29
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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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30
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Kamps JJAG, Khan A, Choi H, Lesniak RK, Brem J, Rydzik AM, McDonough MA, Schofield CJ, Claridge TDW, Mecinović J. Cation-π Interactions Contribute to Substrate Recognition in γ-Butyrobetaine Hydroxylase Catalysis. Chemistry 2015; 22:1270-6. [PMID: 26660433 PMCID: PMC4736438 DOI: 10.1002/chem.201503761] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Indexed: 11/08/2022]
Abstract
γ-Butyrobetaine hydroxylase (BBOX) is a non-heme Fe(II) - and 2-oxoglutarate-dependent oxygenase that catalyzes the stereoselective hydroxylation of an unactivated C-H bond of γ-butyrobetaine (γBB) in the final step of carnitine biosynthesis. BBOX contains an aromatic cage for the recognition of the positively charged trimethylammonium group of the γBB substrate. Enzyme binding and kinetic analyses on substrate analogues with P and As substituting for N in the trimethylammonium group show that the analogues are good BBOX substrates, which follow the efficiency trend N(+) >P(+) >As(+). The results reveal that an uncharged carbon analogue of γBB is not a BBOX substrate, thus highlighting the importance of the energetically favorable cation-π interactions in productive substrate recognition.
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Affiliation(s)
- Jos J A G Kamps
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Amjad Khan
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Hwanho Choi
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Robert K Lesniak
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Jürgen Brem
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Anna M Rydzik
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Michael A McDonough
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Timothy D W Claridge
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Jasmin Mecinović
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
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31
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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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32
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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: 412] [Impact Index Per Article: 45.8] [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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33
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Abdel-Azeim S, Oliva R, Chermak E, De Cristofaro R, Cavallo L. Molecular Dynamics Characterization of Five Pathogenic Factor X Mutants Associated with Decreased Catalytic Activity. Biochemistry 2014; 53:6992-7001. [DOI: 10.1021/bi500770p] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Safwat Abdel-Azeim
- Kaust
Catalysis Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Romina Oliva
- Department
of Sciences and Technologies, University “Parthenope” of Naples, Centro Direzionale Isola C4, 80133 Naples, Italy
| | - Edrisse Chermak
- Kaust
Catalysis Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Raimondo De Cristofaro
- Hemostasis
Research Centre, Institute of Internal Medicine and Geriatrics, Catholic University School of Medicine, Rome, Italy
| | - Luigi Cavallo
- Kaust
Catalysis Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
- Dipartimento
di Chimica e Biologia, University of Salerno, Via Papa Giovanni Paolo II, I-84084 Fisciano, Italy
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34
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Myslinski JM, Clements JH, Martin SF. Protein-ligand interactions: probing the energetics of a putative cation-π interaction. Bioorg Med Chem Lett 2014; 24:3164-7. [PMID: 24856058 DOI: 10.1016/j.bmcl.2014.04.114] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 04/25/2014] [Accepted: 04/28/2014] [Indexed: 01/01/2023]
Abstract
In order to probe the energetics associated with a putative cation-π interaction, thermodynamic parameters are determined for complex formation between the Grb2 SH2 domain and tripeptide derivatives of RCO-pTyr-Ac6c-Asn wherein the R group is varied to include different alkyl, cycloalkyl, and aryl groups. Although an indole ring is reputed to have the strongest interaction with a guanidinium ion, binding free energies, ΔG°, for derivatives of RCO-pTyr-Ac6c-Asn bearing cyclohexyl and phenyl groups were slightly more favorable than their indolyl analog. Crystallographic analysis of two complexes reveals that test ligands bind in similar poses with the notable exception of the relative orientation and proximity of the phenyl and indolyl rings relative to an arginine residue of the domain. These spatial orientations are consistent with those observed in other cation-π interactions, but there is no net energetic benefit to such an interaction in this biological system. Accordingly, although cation-π interactions are well documented as important noncovalent forces in molecular recognition, the energetics of such interactions may be mitigated by other nonbonded interactions and solvation effects in protein-ligand associations.
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Affiliation(s)
- James M Myslinski
- The Department of Chemistry, The Institute of Cellular and Molecular Biology, and the Texas Institute of Drug and Diagnostic Development, The University of Texas, Austin, TX 78712, USA
| | - John H Clements
- The Department of Chemistry, The Institute of Cellular and Molecular Biology, and the Texas Institute of Drug and Diagnostic Development, The University of Texas, Austin, TX 78712, USA
| | - Stephen F Martin
- The Department of Chemistry, The Institute of Cellular and Molecular Biology, and the Texas Institute of Drug and Diagnostic Development, The University of Texas, Austin, TX 78712, USA.
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35
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Persch E, Bryson S, Todoroff NK, Eberle C, Thelemann J, Dirdjaja N, Kaiser M, Weber M, Derbani H, Brun R, Schneider G, Pai EF, Krauth-Siegel RL, Diederich F. Binding to large enzyme pockets: small-molecule inhibitors of trypanothione reductase. ChemMedChem 2014; 9:1880-91. [PMID: 24788386 DOI: 10.1002/cmdc.201402032] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Indexed: 01/16/2023]
Abstract
The causative agents of the parasitic disease human African trypanosomiasis belong to the family of trypanosomatids. These parasitic protozoa exhibit a unique thiol redox metabolism that is based on the flavoenzyme trypanothione reductase (TR). TR was identified as a potential drug target and features a large active site that allows a multitude of possible ligand orientations, which renders rational structure-based inhibitor design highly challenging. Herein we describe the synthesis, binding properties, and kinetic analysis of a new series of small-molecule inhibitors of TR. The conjunction of biological activities, mutation studies, and virtual ligand docking simulations led to the prediction of a binding mode that was confirmed by crystal structure analysis. The crystal structures revealed that the ligands bind to the hydrophobic wall of the so-called "mepacrine binding site". The binding conformation and potency of the inhibitors varied for TR from Trypanosoma brucei and T. cruzi.
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Affiliation(s)
- Elke Persch
- Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zurich (Switzerland)
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36
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Meanwell NA. The Influence of Bioisosteres in Drug Design: Tactical Applications to Address Developability Problems. TACTICS IN CONTEMPORARY DRUG DESIGN 2014; 9. [PMCID: PMC7416817 DOI: 10.1007/7355_2013_29] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The application of bioisosteres in drug discovery is a well-established design concept that has demonstrated utility as an approach to solving a range of problems that affect candidate optimization, progression, and durability. In this chapter, the application of isosteric substitution is explored in a fashion that focuses on the development of practical solutions to problems that are encountered in typical optimization campaigns. The role of bioisosteres to affect intrinsic potency and selectivity, influence conformation, solve problems associated with drug developability, including P-glycoprotein recognition, modulating basicity, solubility, and lipophilicity, and to address issues associated with metabolism and toxicity is used as the underlying theme to capture a spectrum of creative applications of structural emulation in the design of drug candidates.
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37
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Ehmke V, Winkler E, Banner DW, Haap W, Schweizer WB, Rottmann M, Kaiser M, Freymond C, Schirmeister T, Diederich F. Optimization of triazine nitriles as rhodesain inhibitors: structure-activity relationships, bioisosteric imidazopyridine nitriles, and X-ray crystal structure analysis with human cathepsin L. ChemMedChem 2013; 8:967-75. [PMID: 23658062 DOI: 10.1002/cmdc.201300112] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Indexed: 11/10/2022]
Abstract
The cysteine protease rhodesain of Trypanosoma brucei parasites causing African sleeping sickness has emerged as a target for the development of new drug candidates. Based on a triazine nitrile moiety as electrophilic headgroup, optimization studies on the substituents for the S1, S2, and S3 pockets of the enzyme were performed using structure-based design and resulted in inhibitors with inhibition constants in the single-digit nanomolar range. Comprehensive structure-activity relationships clarified the binding preferences of the individual pockets of the active site. The S1 pocket tolerates various substituents with a preference for flexible and basic side chains. Variation of the S2 substituent led to high-affinity ligands with inhibition constants down to 2 nM for compounds bearing cyclohexyl substituents. Systematic investigations on the S3 pocket revealed its potential to achieve high activities with aromatic vectors that undergo stacking interactions with the planar peptide backbone forming part of the pocket. X-ray crystal structure analysis with the structurally related enzyme human cathepsin L confirmed the binding mode of the triazine ligand series as proposed by molecular modeling. Sub-micromolar inhibition of the proliferation of cultured parasites was achieved for ligands decorated with the best substituents identified through the optimization cycles. In cell-based assays, the introduction of a basic side chain on the inhibitors resulted in a 35-fold increase in antitrypanosomal activity. Finally, bioisosteric imidazopyridine nitriles were studied in order to prevent off-target effects with unselective nucleophiles by decreasing the inherent electrophilicity of the triazine nitrile headgroup. Using this ligand, the stabilization by intramolecular hydrogen bonding of the thioimidate intermediate, formed upon attack of the catalytic cysteine residue, compensates for the lower reactivity of the headgroup. The imidazopyridine nitrile ligand showed excellent stability toward the thiol nucleophile glutathione in a quantitative in vitro assay and fourfold lower cytotoxicity than the parent triazine nitrile.
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Affiliation(s)
- Veronika Ehmke
- Laboratorium für Organische Chemie, ETH Zürich, Zürich, Switzerland
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38
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Hewings D, Fedorov O, Filippakopoulos P, Martin S, Picaud S, Tumber A, Wells C, Olcina MM, Freeman K, Gill A, Ritchie AJ, Sheppard DW, Russell AJ, Hammond EM, Knapp S, Brennan PE, Conway SJ. Optimization of 3,5-dimethylisoxazole derivatives as potent bromodomain ligands. J Med Chem 2013; 56:3217-27. [PMID: 23517011 PMCID: PMC3640414 DOI: 10.1021/jm301588r] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2012] [Indexed: 12/14/2022]
Abstract
The bromodomain protein module, which binds to acetylated lysine, is emerging as an important epigenetic therapeutic target. We report the structure-guided optimization of 3,5-dimethylisoxazole derivatives to develop potent inhibitors of the BET (bromodomain and extra terminal domain) bromodomain family with good ligand efficiency. X-ray crystal structures of the most potent compounds reveal key interactions required for high affinity at BRD4(1). Cellular studies demonstrate that the phenol and acetate derivatives of the lead compounds showed strong antiproliferative effects on MV4;11 acute myeloid leukemia cells, as shown for other BET bromodomain inhibitors and genetic BRD4 knockdown, whereas the reported compounds showed no general cytotoxicity in other cancer cell lines tested.
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Affiliation(s)
- David
S. Hewings
- Department of Chemistry, Chemistry
Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
- Nuffield Department of Clinical
Medicine, Structural Genomics Consortium, University
of Oxford, Old Road Campus Research Building, Roosevelt
Drive, Oxford, OX3 3TA, U.K
| | - Oleg Fedorov
- Nuffield Department of Clinical
Medicine, Structural Genomics Consortium, University
of Oxford, Old Road Campus Research Building, Roosevelt
Drive, Oxford, OX3 3TA, U.K
| | - Panagis Filippakopoulos
- Nuffield Department of Clinical
Medicine, Structural Genomics Consortium, University
of Oxford, Old Road Campus Research Building, Roosevelt
Drive, Oxford, OX3 3TA, U.K
| | - Sarah Martin
- Nuffield Department of Clinical
Medicine, Structural Genomics Consortium, University
of Oxford, Old Road Campus Research Building, Roosevelt
Drive, Oxford, OX3 3TA, U.K
| | - Sarah Picaud
- Nuffield Department of Clinical
Medicine, Structural Genomics Consortium, University
of Oxford, Old Road Campus Research Building, Roosevelt
Drive, Oxford, OX3 3TA, U.K
| | - Anthony Tumber
- Nuffield Department of Clinical
Medicine, Structural Genomics Consortium, University
of Oxford, Old Road Campus Research Building, Roosevelt
Drive, Oxford, OX3 3TA, U.K
| | - Christopher Wells
- Nuffield Department of Clinical
Medicine, Structural Genomics Consortium, University
of Oxford, Old Road Campus Research Building, Roosevelt
Drive, Oxford, OX3 3TA, U.K
| | - Monica M. Olcina
- Department of Oncology, Cancer
Research UK/MRC Gray Institute for Radiation Oncology and Biology, University of Oxford, Old Road Campus Research Building,
Oxford, OX3 7DQ, U.K
| | - Katherine Freeman
- Department of Chemistry, Chemistry
Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Andrew Gill
- BioFocus, Chesterford Research Park, Saffron Walden,
Essex, CB10 1XL, U.K
| | - Alison J. Ritchie
- BioFocus, Chesterford Research Park, Saffron Walden,
Essex, CB10 1XL, U.K
| | - David W. Sheppard
- BioFocus, Chesterford Research Park, Saffron Walden,
Essex, CB10 1XL, U.K
| | - Angela J. Russell
- Department of Chemistry, Chemistry
Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Ester M. Hammond
- Department of Oncology, Cancer
Research UK/MRC Gray Institute for Radiation Oncology and Biology, University of Oxford, Old Road Campus Research Building,
Oxford, OX3 7DQ, U.K
| | - Stefan Knapp
- Nuffield Department of Clinical
Medicine, Structural Genomics Consortium, University
of Oxford, Old Road Campus Research Building, Roosevelt
Drive, Oxford, OX3 3TA, U.K
| | - Paul E. Brennan
- Nuffield Department of Clinical
Medicine, Structural Genomics Consortium, University
of Oxford, Old Road Campus Research Building, Roosevelt
Drive, Oxford, OX3 3TA, U.K
| | - Stuart J. Conway
- Department of Chemistry, Chemistry
Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
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Wireduaah S, Parker TM, Lewis M. Effects of the aromatic substitution pattern in cation-π sandwich complexes. J Phys Chem A 2013; 117:2598-604. [PMID: 23452189 DOI: 10.1021/jp309740r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A computational study investigating the effects of the aromatic substitution pattern on the structure and binding energies of cation-π sandwich complexes is reported. The correlation between the binding energies (Ebind) and Hammett substituent constants is approximately the same as what is observed for cation-π half-sandwich complexes. For cation-π sandwich complexes where both aromatics contain substituents the issue of relative conformation is a possible factor in the strength of the binding; however, the work presented here shows the Ebind values are approximately the same regardless of the relative conformation of the two substituted aromatics. Finally, recent computational work has shown conflicting results on whether cation-π sandwich Ebind values (Ebind,S) are approximately equal to twice the respective half-sandwich Ebind values (Ebind,HS), or if cation-π sandwich Ebind,S values are less than double the respective half-sandwich Ebind,HS values. The work presented here shows that for cation-π sandwich complexes involving substituted aromatics the Ebind,S values are less than twice the respective half-sandwich Ebind,HS values, and this is termed nonadditive. The extent to which the cation-π sandwich complexes investigated here are nonadditive is greater for B3LYP calculated values than for MP2 calculated values and for sandwich complexes with electron-donating substituents than those with electron-withdrawing groups.
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Affiliation(s)
- Selina Wireduaah
- Department of Chemistry, Saint Louis University, 3501 Laclede Avenue, Saint Louis, Missouri 63103, USA
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Harder M, Kuhn B, Diederich F. Efficient stacking on protein amide fragments. ChemMedChem 2013; 8:397-404. [PMID: 23355480 DOI: 10.1002/cmdc.201200512] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2012] [Revised: 01/07/2013] [Indexed: 11/07/2022]
Abstract
The less polar π-surface of protein amide groups is exposed in many receptor binding sites, either as part of the backbone or in Gln/Asn side chains. Using quantum chemical calculations and Protein Data Bank (PDB) searches on model systems, we investigate the energetics and geometric preferences for the stacking on amide groups of a large number of heteroarenes that are relevant to medicinal chemistry. From this study, we discern that the stacking energy of an aromatic ligand substituent can be improved by: 1) orienting the fragment dipole vector such that it is aligned in an antiparallel fashion with the dipole of the interacting protein amide group, 2) increasing its dipole moment, and 3) decreasing its π-electron density. These guidelines should be helpful to more rationally exploit this interaction type in future structure-based drug design.
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Affiliation(s)
- Michael Harder
- Laboratorium für Organische Chemie, ETH Zürich, Hönggerberg, HCI, 8093 Zürich, Switzerland
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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: 711] [Impact Index Per Article: 59.3] [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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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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The role of structural information in the discovery of direct thrombin and factor Xa inhibitors. Trends Pharmacol Sci 2012; 33:279-88. [PMID: 22503439 DOI: 10.1016/j.tips.2012.03.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Revised: 03/05/2012] [Accepted: 03/07/2012] [Indexed: 11/21/2022]
Abstract
The quest for novel medications to treat thromboembolic disorders such as venous thrombosis, pulmonary embolism and stroke received a boost when the 3D structures of two major players in the blood coagulation cascade were determined in 1989 and 1993. Structure-guided design of inhibitors of thrombin (factor IIa, fIIa) and factor Xa (fXa) eventually led to the discovery of potent, selective, efficacious, orally active and safe compounds that proved successful in clinical studies. In 2008, the direct thrombin inhibitor dabigatran etexilate developed by Boehringer Ingelheim became the first novel antithrombotic molecular entity to enter the market in 50 years. Additional compounds targeting factor Xa were subsequently granted marketing authorization or are in late-stage clinical studies. In this review, I use selected case studies to describe the discovery of novel fIIa and fXa inhibitors, with a particular emphasis on the pre-eminent role that structural information played in this process.
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Bunzen J, Iwasa J, Bonakdarzadeh P, Numata E, Rissanen K, Sato S, Fujita M. Self-Assembly of M24L48 Polyhedra Based on Empirical Prediction. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201108731] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Bunzen J, Iwasa J, Bonakdarzadeh P, Numata E, Rissanen K, Sato S, Fujita M. Self-Assembly of M24L48 Polyhedra Based on Empirical Prediction. Angew Chem Int Ed Engl 2012; 51:3161-3. [DOI: 10.1002/anie.201108731] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 01/05/2012] [Indexed: 11/08/2022]
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