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Yu CX, Tan JW, Rullah K, Imran S, Tham CL. Insight parameter drug design for human β-tryptase inhibition integrated molecular docking, QSAR, molecular dynamics simulation, and pharmacophore modelling studies of α-keto-[1,2,4]-oxadiazoles. J Biomol Struct Dyn 2023; 41:12978-12996. [PMID: 36709457 DOI: 10.1080/07391102.2023.2171131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 01/11/2023] [Indexed: 01/30/2023]
Abstract
Dengue hemorrhagic fever (DHF) is severe dengue with a hallmark of vascular leakage. β-tryptase has been found to promote vascular leakage in DHF patients, which could be a potential target for DHF treatment. This study aims to develop a theoretical background for designing and selecting human β-tryptase inhibitors through computational studies. Thirty-four α-keto-[1,2,3]-oxadiazoles scaffold-based compounds were used to generate 2D-QSAR models and for molecular docking studies with β-tryptase (PDB Code 4A6L). In addition, molecular dynamics (MD) simulation and molecular mechanics generalised born surface area (MM-GBSA) analysis on the binding of the reported most active compound, compound 11e, towards β-tryptase were performed. Finally, a structure-based pharmacophore model was generated. The selected 2D-QSAR models have statistically proven good models by internal and external validation as well as the y-randomization test. The docking results of compound 11e showed lower CDOCKER energy than the 4A6L co-crystallised ligand and a similar binding pattern as the 4A6L co-crystallised ligand. From molecular dynamics simulation, 4A6L in compound 11e bound state has RMSD below 2 Å throughout the 500 ns simulation, indicating the docked complex is stable. Besides, MM-GBSA analysis suggested the 4A6L-compound 11e docked complex (-66.04 Kcal/mol) is structurally as stable as the 4A6L-native ligand co-crystallized structure (-66.84 Kcal/mol). The best pharmacophore model identified features included hydrogen bond acceptor, ionic interaction, hydrophobic interaction, and aromatic ring, which contribute to the inhibitory potency of a compound. This study supplied insight and knowledge for developing novel chemical compounds with improved inhibition of β-tryptase.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Chai Xin Yu
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Jian Wei Tan
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Kamal Rullah
- Drug Discovery and Synthetic Chemistry Research Group, Department of Pharmaceutical Chemistry, Kulliyyah of Pharmacy, International Islamic University Malaysia, Kuantan, Pahang, Malaysia
| | - Syahrul Imran
- Atta-ur-Rahman Institute for Natural Product Discovery (AuRIns), Universiti Teknologi MARA Cawangan Selangor Kampus Puncak Alam, Puncak Alam, Selangor, Malaysia
- Faculty of Applied Science, Universiti Teknologi MARA (UiTM), Shah Alam, Selangor, Malaysia
| | - Chau Ling Tham
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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2
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Investigations on a novel biologically active organic molecule of 5-Chloro-1-(4-piperidyl)-2-benzimidazolinone by spectroscopic, molecular docking, and quantum chemical approach. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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3
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Karki RG, Powers J, Mainolfi N, Anderson K, Belanger DB, Liu D, Ji N, Jendza K, Gelin CF, Mac Sweeney A, Solovay C, Delgado O, Crowley M, Liao SM, Argikar UA, Flohr S, La Bonte LR, Lorthiois EL, Vulpetti A, Brown A, Long D, Prentiss M, Gradoux N, de Erkenez A, Cumin F, Adams C, Jaffee B, Mogi M. Design, Synthesis, and Preclinical Characterization of Selective Factor D Inhibitors Targeting the Alternative Complement Pathway. J Med Chem 2019; 62:4656-4668. [PMID: 30995036 DOI: 10.1021/acs.jmedchem.9b00271] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Complement factor D (FD), a highly specific S1 serine protease, plays a central role in the amplification of the alternative complement pathway (AP) of the innate immune system. Dysregulation of AP activity predisposes individuals to diverse disorders such as age-related macular degeneration, atypical hemolytic uremic syndrome, membranoproliferative glomerulonephritis type II, and paroxysmal nocturnal hemoglobinuria. Previously, we have reported the screening efforts and identification of reversible benzylamine-based FD inhibitors (1 and 2) binding to the open active conformation of FD. In continuation of our drug discovery program, we designed compounds applying structure-based approaches to improve interactions with FD and gain selectivity against S1 serine proteases. We report herein the design, synthesis, and medicinal chemistry optimization of the benzylamine series culminating in the discovery of 12, an orally bioavailable and selective FD inhibitor. 12 demonstrated systemic suppression of AP activation in a lipopolysaccharide-induced AP activation model as well as local ocular suppression in intravitreal injection-induced AP activation model in mice expressing human FD.
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Affiliation(s)
- Rajeshri G Karki
- Novartis Institutes for BioMedical Research , Cambridge , Massachusetts 02139 , United States
| | - James Powers
- Novartis Institutes for BioMedical Research , Cambridge , Massachusetts 02139 , United States
| | - Nello Mainolfi
- Novartis Institutes for BioMedical Research , Cambridge , Massachusetts 02139 , United States
| | - Karen Anderson
- Novartis Institutes for BioMedical Research , Cambridge , Massachusetts 02139 , United States
| | - David B Belanger
- Novartis Institutes for BioMedical Research , Cambridge , Massachusetts 02139 , United States
| | - Donglei Liu
- Novartis Institutes for BioMedical Research , Cambridge , Massachusetts 02139 , United States
| | - Nan Ji
- Novartis Institutes for BioMedical Research , Cambridge , Massachusetts 02139 , United States
| | - Keith Jendza
- Novartis Institutes for BioMedical Research , Cambridge , Massachusetts 02139 , United States
| | - Christine F Gelin
- Novartis Institutes for BioMedical Research , Cambridge , Massachusetts 02139 , United States
| | - Aengus Mac Sweeney
- Novartis Institutes for BioMedical Research , Novartis Campus , CH-4056 Basel , Switzerland
| | - Catherine Solovay
- Novartis Institutes for BioMedical Research , Cambridge , Massachusetts 02139 , United States
| | - Omar Delgado
- Novartis Institutes for BioMedical Research , Cambridge , Massachusetts 02139 , United States
| | - Maura Crowley
- Novartis Institutes for BioMedical Research , Cambridge , Massachusetts 02139 , United States
| | - Sha-Mei Liao
- Novartis Institutes for BioMedical Research , Cambridge , Massachusetts 02139 , United States
| | - Upendra A Argikar
- Novartis Institutes for BioMedical Research , Cambridge , Massachusetts 02139 , United States
| | - Stefanie Flohr
- Novartis Institutes for BioMedical Research , Novartis Campus , CH-4056 Basel , Switzerland
| | - Laura R La Bonte
- Novartis Institutes for BioMedical Research , Cambridge , Massachusetts 02139 , United States
| | - Edwige L Lorthiois
- Novartis Institutes for BioMedical Research , Novartis Campus , CH-4056 Basel , Switzerland
| | - Anna Vulpetti
- Novartis Institutes for BioMedical Research , Novartis Campus , CH-4056 Basel , Switzerland
| | - Ann Brown
- Novartis Institutes for BioMedical Research , Cambridge , Massachusetts 02139 , United States
| | - Debby Long
- Novartis Institutes for BioMedical Research , Cambridge , Massachusetts 02139 , United States
| | - Melissa Prentiss
- Novartis Institutes for BioMedical Research , Cambridge , Massachusetts 02139 , United States
| | - Nathalie Gradoux
- Novartis Institutes for BioMedical Research , Novartis Campus , CH-4056 Basel , Switzerland
| | - Andrea de Erkenez
- Novartis Institutes for BioMedical Research , Cambridge , Massachusetts 02139 , United States
| | - Frederic Cumin
- Novartis Institutes for BioMedical Research , Novartis Campus , CH-4056 Basel , Switzerland
| | - Christopher Adams
- Novartis Institutes for BioMedical Research , Cambridge , Massachusetts 02139 , United States
| | - Bruce Jaffee
- Novartis Institutes for BioMedical Research , Cambridge , Massachusetts 02139 , United States
| | - Muneto Mogi
- Novartis Institutes for BioMedical Research , Cambridge , Massachusetts 02139 , United States
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4
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Searching for Chymase Inhibitors among Chamomile Compounds Using a Computational-Based Approach. Biomolecules 2018; 9:biom9010005. [PMID: 30583487 PMCID: PMC6358779 DOI: 10.3390/biom9010005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 12/14/2018] [Accepted: 12/17/2018] [Indexed: 01/06/2023] Open
Abstract
Inhibitors of chymase have good potential to provide a novel therapeutic approach for the treatment of cardiovascular diseases. We used a computational approach based on pharmacophore modeling, docking, and molecular dynamics simulations to evaluate the potential ability of 13 natural compounds from chamomile extracts to bind chymase enzyme. The results indicated that some chamomile compounds can bind to the active site of human chymase. In particular, chlorogenic acid had a predicted binding energy comparable or even better than that of some known chymase inhibitors, interacted stably with key amino acids in the chymase active site, and appeared to be more selective for chymase than other serine proteases. Therefore, chlorogenic acid is a promising starting point for developing new chymase inhibitors.
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5
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Bird MJ, Silvestri AP, Dawson PE. Expedient on-resin synthesis of peptidic benzimidazoles. Bioorg Med Chem Lett 2018; 28:2679-2681. [PMID: 29739642 DOI: 10.1016/j.bmcl.2018.04.062] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 04/25/2018] [Indexed: 12/13/2022]
Abstract
The benzimidazole moiety is a ubiquitous pharmacophore present in numerous anthelmintic, antibacterial, antiviral, antineoplastic, and antifungal drugs. While the polypharmacology of this heterocycle has spurred the development of numerous solution-phase syntheses, only a handful of disparate and inefficient methods detailing its synthesis on-resin have been reported. Here we report the concise and expedient syntheses of internal and C-terminal peptidic benzimidazoles - an emerging class of peptide deformylase (PDF)-inhibiting antimicrobials. This method benefits from being performed wholly on solid-phase at room temperature resulting in minimal purification and tolerance of temperature-sensitive functionality.
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Affiliation(s)
- Michael J Bird
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
| | - Anthony P Silvestri
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
| | - Philip E Dawson
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States.
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6
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Maun HR, Liu PS, Franke Y, Eigenbrot C, Forrest WF, Schwartz LB, Lazarus RA. Dual functionality of β-tryptase protomers as both proteases and cofactors in the active tetramer. J Biol Chem 2018; 293:9614-9628. [PMID: 29661938 DOI: 10.1074/jbc.m117.812016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 04/05/2018] [Indexed: 01/07/2023] Open
Abstract
Human β-tryptase, a tetrameric trypsin-like serine protease, is an important mediator of the allergic inflammatory responses in asthma. During acute hypersensitivity reactions, mast cells degranulate, releasing active tetramer as a complex with proteoglycans. Extensive efforts have focused on developing therapeutic β-tryptase inhibitors, but its unique activation mechanism is less well-explored. Tryptase is active only after proteolytic removal of the pro-domain followed by tetramer formation via two distinct symmetry-related interfaces. We show that the cleaved I16G mutant cannot tetramerize, likely due to impaired insertion of its N terminus into its "activation pocket," indicating allosteric linkage at multiple sites on each protomer. We engineered cysteines into each of the two distinct interfaces (Y75C for small or I99C for large) to assess the activity of each tetramer and disulfide-locked dimer. Using size-exclusion chromatography and enzymatic assays, we demonstrate that the two large tetramer interfaces regulate enzymatic activity, elucidating the importance of this protein-protein interaction for allosteric regulation. Notably, the I99C large interface dimer is active, even in the absence of heparin. We show that a monomeric β-tryptase mutant (I99C*/Y75A/Y37bA, where C* is cysteinylated Cys-99) cannot form a dimer or tetramer, yet it is active but only in the presence of heparin. Thus heparin both stabilizes the tetramer and allosterically conditions the active site. We hypothesize that each β-tryptase protomer in the tetramer has two distinct roles, acting both as a protease and as a cofactor for its neighboring protomer, to allosterically regulate enzymatic activity, providing a rationale for direct correlation of tetramer stability with proteolytic activity.
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Affiliation(s)
- Henry R Maun
- From the Departments of Early Discovery Biochemistry
| | | | | | | | - William F Forrest
- Bioinformatics and Computational Biology, Genentech, Inc., South San Francisco, California 94080 and
| | - Lawrence B Schwartz
- the Division of Rheumatology, Allergy and Immunology, Department of Internal Medicine, Virginia Commonwealth University, Richmond, Virginia 23298
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7
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Abstract
BACKGROUND Inhibitors of chymase appear to be interesting compounds to develop drugs for the treatment of cardiovascular diseases. We used a computational approach to screen molecules from ZINC Biogenic Compounds database and to investigate their interactions with the enzyme, in order to predict their binding energy with respect to known ligands and to evaluate their selectivity. RESULTS Some screened compounds have a predicted binding energy comparable or even better with respect to that of known chymase inhibitors, and they interact with chymase key amino acids responsible for substrate selectivity. Moreover, these compounds appear to be more selective for chymase than to other serine proteases. CONCLUSION These compounds are promising for the development of a new class of drugs for cardiovascular diseases. [Formula: see text] Pharmacophore model obtained for human chymase (PDB ID: 1T31).
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8
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Dubey A, Marabotti A, Ramteke PW, Facchiano A. Interaction of human chymase with ginkgolides, terpene trilactones of Ginkgo biloba investigated by molecular docking simulations. Biochem Biophys Res Commun 2016; 473:449-54. [DOI: 10.1016/j.bbrc.2016.03.028] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 03/08/2016] [Indexed: 11/26/2022]
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9
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Dev D, Chandra J, Palakurthy NB, Thalluri K, Kalita T, Mandal B. Benzoxazole and Benzothiazole Synthesis from Carboxylic Acids in Solution and on Resin by Using Ethyl 2-Cyano-2-(2-nitrobenzenesulfonyloxyimino)acetate and para
-Toluenesulfonic Acid. ASIAN J ORG CHEM 2016. [DOI: 10.1002/ajoc.201500527] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Dharm Dev
- Department of Chemistry; Indian Institute of Technology Guwahati; North Guwahati- 781039 India
| | - Jyoti Chandra
- Department of Chemistry; Indian Institute of Technology Guwahati; North Guwahati- 781039 India
| | - Nani Babu Palakurthy
- Department of Chemistry; Indian Institute of Technology Guwahati; North Guwahati- 781039 India
| | - Kishore Thalluri
- Department of Chemistry; Indian Institute of Technology Guwahati; North Guwahati- 781039 India
| | - Tapasi Kalita
- Department of Chemistry; Indian Institute of Technology Guwahati; North Guwahati- 781039 India
| | - Bhubaneswar Mandal
- Department of Chemistry; Indian Institute of Technology Guwahati; North Guwahati- 781039 India
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10
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Jiang QQ, Sicking W, Ehlers M, Schmuck C. Discovery of potent inhibitors of human β-tryptase from pre-equilibrated dynamic combinatorial libraries. Chem Sci 2014; 6:1792-1800. [PMID: 29163876 PMCID: PMC5644118 DOI: 10.1039/c4sc02943g] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 12/05/2014] [Indexed: 01/07/2023] Open
Abstract
Pre-equilibrated combinatorial libraries based on multivalent peptide acyl hydrazones were used to find potent inhibitors of β-tryptase. The best inhibitors bind to the protein surface, and inhibit β-tryptase with nanomolar affinity (Kica. 10 nM) and high selectivity in a reversible and non-competitive way.
Pre-equilibrated dynamic combinatorial libraries based on acyl hydrazone interchange of peptide-derived hydrazides and di- and tri-aldehydes have been used to discover potent inhibitors with nanomolar affinities for β-tryptase. To identify potent inhibitors the activity of the full library containing 95 members was compared with those of sub-libraries in which individual building blocks were missing. The most active library members contain a rigid central aromatic scaffold with three cationic peptide arms. The arms of the best inhibitors also contained a tailor-made GCP oxoanion binding motif attached to a lysine side chain. The most potent tri-armed hydrazones with peptide arms GKWR or GKWK(GCP) were shown to inhibit β-tryptase (Kica. 10–20 nM) reversibly, non-competitively and selectively (compared to related serine proteases, e.g. trypsin and chymotrypsin), most likely by binding to the protein surface, also in agreement with molecular modelling calculations. These new inhibitors are one order of magnitude more efficient than related tetravalent inhibitors obtained from previous work on a split-mix-combinatorial library and were identified with significantly less effort, demonstrating the usefulness of this approach for the identification of enzyme inhibitors in general.
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Affiliation(s)
- Qian-Qian Jiang
- Institut für Organische Chemie , Universität Duisburg-Essen , Universitätsstraße 7 , 45141 Essen , Germany .
| | - Wilhelm Sicking
- Institut für Organische Chemie , Universität Duisburg-Essen , Universitätsstraße 7 , 45141 Essen , Germany .
| | - Martin Ehlers
- Institut für Organische Chemie , Universität Duisburg-Essen , Universitätsstraße 7 , 45141 Essen , Germany .
| | - Carsten Schmuck
- Institut für Organische Chemie , Universität Duisburg-Essen , Universitätsstraße 7 , 45141 Essen , Germany .
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11
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Mikulskis P, Genheden S, Rydberg P, Sandberg L, Olsen L, Ryde U. Binding affinities in the SAMPL3 trypsin and host-guest blind tests estimated with the MM/PBSA and LIE methods. J Comput Aided Mol Des 2011; 26:527-41. [PMID: 22198518 DOI: 10.1007/s10822-011-9524-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Accepted: 12/08/2011] [Indexed: 11/28/2022]
Abstract
We have estimated affinities for the binding of 34 ligands to trypsin and nine guest molecules to three different hosts in the SAMPL3 blind challenge, using the MM/PBSA, MM/GBSA, LIE, continuum LIE, and Glide score methods. For the trypsin challenge, none of the methods were able to accurately predict the experimental results. For the MM/GB(PB)SA and LIE methods, the rankings were essentially random and the mean absolute deviations were much worse than a null hypothesis giving the same affinity to all ligand. Glide scoring gave a Kendall's τ index better than random, but the ranking is still only mediocre, τ = 0.2. However, the range of affinities is small and most of the pairs of ligands have an experimental affinity difference that is not statistically significant. Removing those pairs improves the ranking metric to 0.4-1.0 for all methods except CLIE. Half of the trypsin ligands were non-binders according to the binding assay. The LIE methods could not separate the inactive ligands from the active ones better than a random guess, whereas MM/GBSA and MM/PBSA were slightly better than random (area under the receiver-operating-characteristic curve, AUC = 0.65-0.68), and Glide scoring was even better (AUC = 0.79). For the first host, MM/GBSA and MM/PBSA reproduce the experimental ranking fairly good, with τ = 0.6 and 0.5, respectively, whereas the Glide scoring was considerably worse, with a τ = 0.4, highlighting that the success of the methods is system-dependent.
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Affiliation(s)
- Paulius Mikulskis
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, 221 00 Lund, Sweden
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12
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Gohda K, Teno N, Wanaka K, Tsuda Y. Predicting subsite interactions of plasmin with substrates and inhibitors through computational docking analysis. J Enzyme Inhib Med Chem 2011; 27:571-7. [DOI: 10.3109/14756366.2011.603129] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Keigo Gohda
- Computer-Aided Molecular Modeling Research Center, Kansai (CAMM-Kansai),
Kobe, Japan
| | - Naoki Teno
- Faculty of Pharmaceutical Science, Hiroshima International University,
Kure, Japan
| | - Keiko Wanaka
- Kobe Research Projects on Thrombosis and Haemostasis,
Kobe, Japan
| | - Yuko Tsuda
- Faculty of Pharmaceutical Sciences, Kobe Gakuin University,
Kobe, Japan
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13
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Gondal HY, Mashooda H, Ali M. New Antibacterial Peptide Analogs of 5-Aminobenzimidazoles. JOURNAL OF THE KOREAN CHEMICAL SOCIETY-DAEHAN HWAHAK HOE JEE 2011. [DOI: 10.5012/jkcs.2011.55.4.650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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14
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Genheden S, Mikulskis P, Hu L, Kongsted J, Söderhjelm P, Ryde U. Accurate Predictions of Nonpolar Solvation Free Energies Require Explicit Consideration of Binding-Site Hydration. J Am Chem Soc 2011; 133:13081-92. [DOI: 10.1021/ja202972m] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Samuel Genheden
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Paulius Mikulskis
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - LiHong Hu
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
- School of Computer Science and Information Technology, Northeast Normal University, Changchun, 130024, People's Republic of China
| | - Jacob Kongsted
- Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Pär Söderhjelm
- Department of Chemistry and Applied Biosciences—Computational Science, ETH Zürich, Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
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15
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Faust MR, Höfner G, Pabel J, Wanner KT. Azetidine derivatives as novel γ-aminobutyric acid uptake inhibitors: Synthesis, biological evaluation, and structure–activity relationship. Eur J Med Chem 2010; 45:2453-66. [DOI: 10.1016/j.ejmech.2010.02.029] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Revised: 02/08/2010] [Accepted: 02/10/2010] [Indexed: 11/29/2022]
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16
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Tetsuhashi M, Ishikawa M, Hashimoto M, Hashimoto Y, Aoyama H. Development of tryptase inhibitors derived from thalidomide. Bioorg Med Chem 2010; 18:5323-38. [PMID: 20561792 DOI: 10.1016/j.bmc.2010.05.037] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Revised: 05/13/2010] [Accepted: 05/14/2010] [Indexed: 11/26/2022]
Abstract
A novel series of tryptase inhibitors with a N-phenylphthalimide skeleton structurally derived from thalidomide (1) has been developed. Structure-activity relationship studies led to a potent and selective tryptase inhibitor, 2-(4-cyanophenyl)isoindole-1,3-dione-5-yl 3-(2-aminopyridin-5-yl)propanoate (7), with the IC50 value of 78 nM.
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Affiliation(s)
- Masashi Tetsuhashi
- Institute of Molecular & Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
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17
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Berg M, Van der Veken P, Joossens J, Muthusamy V, Breugelmans M, Moss CX, Rudolf J, Cos P, Coombs GH, Maes L, Haemers A, Mottram JC, Augustyns K. Design and evaluation of Trypanosoma brucei metacaspase inhibitors. Bioorg Med Chem Lett 2010; 20:2001-6. [PMID: 20167486 DOI: 10.1016/j.bmcl.2010.01.099] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Revised: 01/14/2010] [Accepted: 01/16/2010] [Indexed: 02/01/2023]
Abstract
Metacaspase (MCA) is an important enzyme in Trypanosoma brucei, absent from humans and differing significantly from the orthologous human caspases. Therefore MCA constitutes a new attractive drug target for antiparasitic chemotherapeutics, which needs further characterization to support the discovery of innovative drug candidates. A first series of inhibitors has been prepared on the basis of known substrate specificity and the predicted catalytic mechanism of the enzyme. In this Letter we present the first inhibitors of TbMCA2 with low micromolar enzymatic and antiparasitic activity in vitro combined with low cytotoxicity.
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Affiliation(s)
- Maya Berg
- Laboratory of Medicinal Chemistry, University of Antwerp, Antwerp, Belgium
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18
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Gianti E, Sartori L. Identification and selection of "privileged fragments" suitable for primary screening. J Chem Inf Model 2009; 48:2129-39. [PMID: 18991373 DOI: 10.1021/ci800219h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The use of small molecule libraries for fragment-based primary screening (FBS) is a well-known approach to identify protein binders in the low affinity range. However, the search, analysis, and selection of suitable screening fragments can be a lengthy process, because of the large number of compounds that must be analyzed for different levels of ring/substituents identification and submitted to selection/exclusion criteria based on their physicochemical properties. The purpose of the present work is to propose a strategy to identify substructures from databases of known drugs, which can be used as templates for the generation of libraries of "privileged fragments" that are able to provide high-quality hits. The entire process has been developed integrating Pipeline Pilot (Accelrys Inc., San Diego, CA; http://www.accelrys.com ) native components and user-defined molecular files containing ISIS-like substructure query features (Symyx, San Ramon, CA; http://www.symyx.com ). The method is effortless, easy to put in place, and fast enough to be iteratively applied to different sources of druglike compounds.
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Affiliation(s)
- Eleonora Gianti
- Computational Sciences Group, Department of Chemistry (Congenia s.r.l.), Genextra S.p.A., Milan MI 20100, Italy
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Solid phase synthesis of peptides containing novel amino acids, substituted 3-benzimidazolealanines. Amino Acids 2008; 36:309-15. [PMID: 18392772 DOI: 10.1007/s00726-008-0070-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2007] [Accepted: 03/12/2008] [Indexed: 11/27/2022]
Abstract
A direct solid-phase synthesis of a series of substituted benzimidazole-containing peptides is described. The method involves on-resin formation of new amino acids containing benzimidazole derivatives in the side chain. The heterocycle conjugates were obtained by reaction between aldehydes and peptides containing beta-(3,4-diaminophenyl)alanine residue, immobilized on a polymeric solid support.
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Ueda M, Kubo T, Miyatake K, Nakamura T. Purification and characterization of fibrinolytic alkaline protease from Fusarium sp. BLB. Appl Microbiol Biotechnol 2007; 74:331-8. [PMID: 17221202 DOI: 10.1007/s00253-006-0621-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2006] [Revised: 08/03/2006] [Accepted: 08/08/2006] [Indexed: 01/22/2023]
Abstract
Fusarium sp. BLB, which produces a strongly fibrinolytic enzyme, was isolated from plant leaf (Hibiscus). Fibrinolytic alkaline protease was purified from a culture filtrate of Fusarium sp. BLB by precipitation with (NH4)2(SO4) and column chromatography with CM-Toyopearl 650 M and Superdex 75. The purified enzyme was homogeneous on sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). The molecular weight was 27,000 by SDS-PAGE. Maximum activity of protease was observed at pH 9.5 and 50 degrees C. Purified protease was active between pH 2.5 and 11.5 and was found to be stable up to 50 degrees C. The enzyme derived from Fusarium sp. BLB is useful for thrombolytic therapy because this enzyme showed pH resistance. The activity was inhibited by diisopropylfluorophosphate and phenylmethylsulfonyl fluoride. The N-terminal amino acid sequence of the enzyme showed a similarity to those of proteases from Fusarium sp., Streptomyces griseus, Bos taurus bovine, Katsuwo pelamis digestive tract, and Lumbricus rubellus.
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Affiliation(s)
- Mitsuhiro Ueda
- Laboratory of Biocycle Engineering, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan.
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Congreve M, Murray CW, Carr R, Rees DC. Chapter 28 Fragment-Based Lead Discovery. ANNUAL REPORTS IN MEDICINAL CHEMISTRY VOLUME 42 2007. [DOI: 10.1016/s0065-7743(07)42028-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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