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Guzmán Ramírez JE, Mancilla Percino T. Synthesis of N-aminophalimides derived from α-amino acids: Theoretical study to find them as HDAC8 inhibitors by docking simulations and in vitro assays. Chem Biol Drug Des 2023; 102:1367-1386. [PMID: 37641461 DOI: 10.1111/cbdd.14323] [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: 06/17/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/31/2023]
Abstract
Phthalimides are valuable for synthesis and biological properties. New acetamides 3(a-c) and 4(a-c) were synthesized and characterized as precursors for novel N-aminophalimides 5(a-c) and 6(a-c). Structures of 4a, 5(a-b), and 6(a-b) were confirmed by single crystal X-ray. Docking studies identified compounds with favorable Gibbs free energy values for binding to histone deacetylase 8 (HDAC8), an enzyme targeted for anticancer drug development. These compounds bound to both the orthosteric and allosteric pockets of HDAC8, similar to Trichostatin A (TSA), an HDAC8 inhibitor. 6(a-c) contain hydroxyacetamide moiety as a zinc-binding group, a phthalimide moiety as a capping group, and aminoacetamide moiety as a linker group, which are important for ligand-receptor binding. ΔG values indicated that compounds 5b, 6b, and 6c had higher affinity for HDAC8 in the allosteric pocket compared to TSA. In vitro evaluation of inhibitory activities on HDAC8 revealed that compounds 3(a-c) and 5(a-c) showed similar inhibitory effects (IC50 ) ranging from 0.445 to 0.751 μM. Compounds 6(a-c) showed better affinity, with 6a (IC50 = 28 nM) and 6b (IC50 = 0.18 μM) showing potent inhibitory effects slightly lower than TSA (IC50 = 26 nM). These findings suggest that the studied compounds hold promise as potential candidates for further biological investigations.
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Affiliation(s)
- José Eduardo Guzmán Ramírez
- Departamento de Química, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Teresa Mancilla Percino
- Departamento de Química, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
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2
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Matore BW, Banjare P, Sarthi AS, Roy PP, Singh J. Phthalimides Represent a Promising Scaffold for Multi‐Targeted Anticancer Agents. ChemistrySelect 2023. [DOI: 10.1002/slct.202204851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Affiliation(s)
- Balaji Wamanrao Matore
- Department of Pharmacy Guru Ghasidas Vishwavidyalaya (A Central University) Bilaspur Chhattisgarh 495009 India
| | - Purusottam Banjare
- Department of Pharmacy Guru Ghasidas Vishwavidyalaya (A Central University) Bilaspur Chhattisgarh 495009 India
| | - Ajay Singh Sarthi
- Rungta College of Pharmaceutical Sciences and Research Raipur Chhattisgarh 492009 India
| | - Partha Pratim Roy
- Department of Pharmacy Guru Ghasidas Vishwavidyalaya (A Central University) Bilaspur Chhattisgarh 495009 India
| | - Jagadish Singh
- Department of Pharmacy Guru Ghasidas Vishwavidyalaya (A Central University) Bilaspur Chhattisgarh 495009 India
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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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Slastikhina PV, Chirkova ZV, Kabanova MV, Abramov IG, Filimonov SI, Begunov RS, Suponitsky KY. Synthesis of substituted isoindole-1,3-diones with an amide fragment using the Schmidt rearrangement. Russ Chem Bull 2020. [DOI: 10.1007/s11172-020-3027-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Kumar V, Brodyagin N, Rozners E. Triplex-Forming Peptide Nucleic Acids with Extended Backbones. Chembiochem 2020; 21:3410-3416. [PMID: 32697857 PMCID: PMC7783598 DOI: 10.1002/cbic.202000432] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 07/20/2020] [Indexed: 01/15/2023]
Abstract
Peptide nucleic acid (PNA) forms a triple helix with double-stranded RNA (dsRNA) stabilized by a hydrogen-bonding zipper formed by PNA's backbone amides (N-H) interacting with RNA phosphate oxygens. This hydrogen-bonding pattern is enabled by the matching ∼5.7 Å spacing (typical for A-form dsRNA) between PNA's backbone amides and RNA phosphate oxygens. We hypothesized that extending the PNA's backbone by one -CH2 - group might bring the distance between PNA amide groups closer to 7 Å, which is favourable for hydrogen bonding to the B-form dsDNA phosphate oxygens. Extension of the PNA backbone was expected to selectively stabilize PNA-DNA triplexes compared to PNA-RNA. To test this hypothesis, we synthesized triplex-forming PNAs that had the pseudopeptide backbones extended by an additional -CH2 - group in three different positions. Isothermal titration calorimetry measurements of the binding affinity of these extended PNA analogues for the matched dsDNA and dsRNA showed that, contrary to our structural reasoning, extending the PNA backbone at any position had a strong negative effect on triplex stability. Our results suggest that PNAs might have an inherent preference for A-form-like conformations when binding double-stranded nucleic acids. It appears that the original six-atom-long PNA backbone is an almost perfect fit for binding to A-form nucleic acids.
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Affiliation(s)
- Vipin Kumar
- Department of Chemistry, Binghamton University Binghamton, New York, 13902, USA
| | - Nikita Brodyagin
- Department of Chemistry, Binghamton University Binghamton, New York, 13902, USA
| | - Eriks Rozners
- Department of Chemistry, Binghamton University Binghamton, New York, 13902, USA
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6
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Wang R, Ding J, Zhang Y. Naphthalimide/benzimide-based excited-state intramolecular proton transfer active luminogens: aggregation-induced enhanced emission and potential for chemical modification. NEW J CHEM 2019. [DOI: 10.1039/c9nj01685f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two ESIPT- and AIEE-active molecules, HPIBT, which is superior to HNIBT, and HPIBT-yl can be further modified through high-efficiency click chemistry.
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Affiliation(s)
- Rong Wang
- College of Chemistry & Pharmacy
- Northwest A&F University
- Yangling
- P. R. China
| | - Ju Ding
- College of Chemistry & Pharmacy
- Northwest A&F University
- Yangling
- P. R. China
| | - Yanrong Zhang
- College of Chemistry & Pharmacy
- Northwest A&F University
- Yangling
- P. R. China
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7
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Ji F, Li J, Li X, Guo W, Wu W, Jiang H. Carbonylation Access to Phthalimides Using Self-Sufficient Directing Group and Nucleophile. J Org Chem 2017; 83:104-112. [DOI: 10.1021/acs.joc.7b02433] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Fanghua Ji
- Key
Laboratory of Functional Molecular Engineering of Guangdong Province,
School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, P. R. China
| | - Jianxiao Li
- Key
Laboratory of Functional Molecular Engineering of Guangdong Province,
School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, P. R. China
| | - Xianwei Li
- Key
Laboratory of Functional Molecular Engineering of Guangdong Province,
School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, P. R. China
| | - Wei Guo
- Key
Laboratory of Functional Molecular Engineering of Guangdong Province,
School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, P. R. China
| | - Wanqing Wu
- Key
Laboratory of Functional Molecular Engineering of Guangdong Province,
School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, P. R. China
| | - Huanfeng Jiang
- Key
Laboratory of Functional Molecular Engineering of Guangdong Province,
School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, P. R. China
- State
Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, P. R. China
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Yokomatsu T. Development of Biologically Active Compounds on the Basis of Phosphonic and Phosphinic Acid Functionalities. YAKUGAKU ZASSHI 2017; 137:1051-1086. [PMID: 28867694 DOI: 10.1248/yakushi.17-00110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Phosphonic and phosphinic acids, especially α-heteroatom-substituted ones, possess unique structural and physical features which enable them to act as hydrotically stable analogs to biological phosphates in biological processes. They also act as mimetics in the transition state of the protease-induced hydrolysis of dipeptides. The first half of this review focuses on selected new synthetic methods developed by our research group for the stereoselective synthesis of α-heteroatom-substituted phosphonic and phosphinic acid derivatives, including modified nucleotide analogs and phosphinyl dipeptide isosteres. In the latter half, this review summarizes the utility of difluoromethylenephosphonic acids and phosphonic acid esters in the development of enzyme inhibitors against protein tyrosine phosphatases, sphingomyelinases, purine nucleoside phosphorylases and thrombin. The enzyme inhibitors developed were used as probes to elucidate signal transductions and the mechanisms of enzyme actions. The findings of the studies are briefly described.
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9
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Hemdan MM, El-Sayed AAE. Use of Phthalimidoacetyl Isothiocyanate as a Scaffold in the Synthesis of Target Heterocyclic Systems, and Their Antimicrobial Assessment. Chem Pharm Bull (Tokyo) 2017; 64:483-9. [PMID: 27150480 DOI: 10.1248/cpb.c16-00099] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Phthalimidoacetyl isothiocyanate underwent addition-cyclization reactions with some nitrogen and carbon nucleophilic reagents. Simultaneous or subsequent cyclization of the obtained adducts gave target heterocyclic systems such as 1,2,4-triazoles, 1,3-diazines, 1,3-oxazines and thiourea attached to a phthalimido moiety. The antimicrobial activity of the synthesized compounds was tested.
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10
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Mohamed NA, Abd El-Ghany NA, Fahmy MM. Thermogravimetric analysis in the evaluation of the inhibition of degradation of rigid poly(vinyl chloride) using biologically active phthalimido aromatic hydrazide derivatives. Polym Degrad Stab 2016. [DOI: 10.1016/j.polymdegradstab.2016.02.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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11
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Aoyama H, Ijuin R, Kato JY, Urushiyama S, Tetsuhashi M, Hashimoto Y, Yokomatsu T. Discovery of non-competitive thrombin inhibitor derived from competitive tryptase inhibitor skeleton: Shift in molecular recognition resulted from skeletal conversion of carboxylate into phosphonate. Bioorg Med Chem Lett 2015; 25:3676-80. [DOI: 10.1016/j.bmcl.2015.06.039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 06/09/2015] [Accepted: 06/11/2015] [Indexed: 11/16/2022]
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12
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Study on the synthesis of novel 5-substituted 2-[2-(pyridyl)ethenyl]-1,3,4-oxadiazoles and their acid-base interactions. MONATSHEFTE FUR CHEMIE 2015; 146:303-311. [PMID: 26166897 PMCID: PMC4495023 DOI: 10.1007/s00706-014-1355-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 11/10/2014] [Indexed: 01/05/2023]
Abstract
Abstract A series of novel 5-substituted 2-[2-(pyridyl)ethenyl]-1,3,4-oxadiazoles were efficiently synthesized by cyclocondensation of the appropriate 3-(pyridyl)acrylohydrazides with triethyl orthoesters in the presence of glacial acetic acid. The products were identified by means of spectroscopic methods and their pKA ionization constants were determined. The influence of substituents on the basicity of the pyridine system has been discussed. Graphical Abstract ![]() ![]()
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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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Jiang QQ, Bartsch L, Sicking W, Wich PR, Heider D, Hoffmann D, Schmuck C. A new approach to inhibit human β-tryptase by protein surface binding of four-armed peptide ligands with two different sets of arms. Org Biomol Chem 2013; 11:1631-9. [DOI: 10.1039/c3ob27302d] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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15
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Krivec M, Gazvoda M, Kranjc K, Polanc S, Kočevar M. A Way to Avoid Using Precious Metals: The Application of High-Surface Activated Carbon for the Synthesis of Isoindoles via the Diels–Alder Reaction of 2H-Pyran-2-ones. J Org Chem 2012; 77:2857-64. [DOI: 10.1021/jo3000783] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Marko Krivec
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5,
SI-1000 Ljubljana, Slovenia
| | - Martin Gazvoda
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5,
SI-1000 Ljubljana, Slovenia
| | - Krištof Kranjc
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5,
SI-1000 Ljubljana, Slovenia
| | - Slovenko Polanc
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5,
SI-1000 Ljubljana, Slovenia
| | - Marijan Kočevar
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5,
SI-1000 Ljubljana, Slovenia
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Liang G, Choi-Sledeski YM, Chen X, Gong Y, MacMillan EW, Tsay J, Sides K, Cairns J, Kulitzscher B, Aldous DJ, Morize I, Pauls HW. Dimerization of β-tryptase inhibitors, does it work for both basic and neutral P1 groups? Bioorg Med Chem Lett 2012; 22:3370-6. [PMID: 22483389 DOI: 10.1016/j.bmcl.2012.01.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2011] [Revised: 01/04/2012] [Accepted: 01/09/2012] [Indexed: 11/16/2022]
Abstract
The tetrameric folding of β-tryptase and the pair-wise distribution of its substrate binding sites offer a unique opportunity for development of inhibitors that span two adjacent binding sites. A series of dimeric inhibitors with two basic P1 moieties was discovered using this design strategy and exhibited tight-binder characteristics. Using the same strategy, an attempt was made to design and synthesize dimeric inhibitors with two neutral-P1 groups in hope to exploit the dimeric binding mode to achieve a starting point for further optimization. The unsuccessful attempt, however, demonstrated the important role played by Ala190 in neutral-P1 binding and casted further doubt on the possibility of developing neutral-P1 inhibitors for β-tryptase.
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Affiliation(s)
- Guyan Liang
- Molecular Innovative Therapeutics, Sanofi Pharmaceuticals, United States.
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