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Screening of a Library for Factor VIIa Inhibitors. LETT DRUG DES DISCOV 2022. [DOI: 10.2174/1570180818666211207125903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
As an alternative to the anticoagulant’s strategy using direct or indirect anti-Xa
drugs, considering other targets upstream in the coagulation cascade such as anti-Factor VIIa could represent
an effective and safer strategy in coagulation and pathological angiogenesis.
Objective:
The objective of the study was to assess a high technology methodology composed of virtual
screening, anticoagulant, and anti-angiogenesis assays to identify potent small-molecule FVIIa inhibitors.
Methods:
Chemical databanks were screened to select molecules bearing functional groups that could fit
into the active site of FVIIa, which were then tested. Ligands assigned with the lowest scores were retained
and then biologically assessed.
Results:
From the 500 molecules considered, 8 chemical structures revealed to be effective compounds in
vitro and to inhibit angiogenesis in the chick chorioallantoic membrane (CAM) model.
Conclusion:
New potent small-molecule FVIIa inhibitors have been identified; further biochemical and
chemical developments would be investigated directly from the selected scaffolds.
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A score years’ update in the synthesis and biological evaluation of medicinally important 2-pyridones. Eur J Med Chem 2022; 232:114199. [DOI: 10.1016/j.ejmech.2022.114199] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/06/2022] [Accepted: 02/10/2022] [Indexed: 12/18/2022]
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Optimization of peptide-based inhibitors targeting the HtrA serine protease in Chlamydia: Design, synthesis and biological evaluation of pyridone-based and N-Capping group-modified analogues. Eur J Med Chem 2021; 224:113692. [PMID: 34265463 DOI: 10.1016/j.ejmech.2021.113692] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/04/2021] [Accepted: 07/05/2021] [Indexed: 11/23/2022]
Abstract
The obligate intracellular bacterium Chlamydia trachomatis (C. trachomatis) is responsible for the most common bacterial sexually transmitted infection and is the leading cause of preventable blindness, representing a major global health burden. While C. trachomatis infection is currently treatable with broad-spectrum antibiotics, there would be many benefits of a chlamydia-specific therapy. Previously, we have identified a small-molecule lead compound JO146 [Boc-Val-Pro-ValP(OPh)2] targeting the bacterial serine protease HtrA, which is essential in bacterial replication, virulence and survival, particularly under stress conditions. JO146 is highly efficacious in attenuating infectivity of both human (C. trachomatis) as well as koala (C. pecorum) species in vitro and in vivo, without host cell toxicity. Herein, we present our continuing efforts on optimizing JO146 by modifying the N-capping group as well as replacing the parent peptide structure with the 2-pyridone scaffold at P3/P2. The drug optimization process was guided by molecular modelling, enzyme and cell-based assays. Compound 18b from the pyridone series showed improved inhibitory activity against CtHtrA by 5-fold and selectivity over human neutrophil elastase (HNE) by 109-fold compared to JO146, indicating that 2-pyridone is a suitable bioisostere of the P3/P2 amide/proline for developing CtHtrA inhibitors. Most pyridone-based inhibitors showed superior anti-chlamydial potency to JO146 especially at lower doses (25 and 50 μM) in C. trachomatis and C. pecorum cell culture assays. Modifications of the N-capping group of the peptidyl inhibitors did not have much influence on the anti-chlamydial activities, providing opportunities for more versatile alterations and future optimization. In summary, we present 2-pyridone based analogues as a new generation of non-peptidic CtHtrA inhibitors, which hold better promise as anti-chlamydial drug candidates.
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Design and synthesis of novel methoxypyridine-derived gamma-secretase modulators. Bioorg Med Chem 2020; 28:115734. [PMID: 33007551 DOI: 10.1016/j.bmc.2020.115734] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 08/18/2020] [Accepted: 08/21/2020] [Indexed: 11/19/2022]
Abstract
The evolution of gamma-secretase modulators (GSMs) through the introduction of novel heterocycles with the goal of aligning activity for reducing the levels of Aβ42 and properties consistent with a drug-like molecule are described. The insertion of a methoxypyridine motif within the tetracyclic scaffold provided compounds with improved activity for arresting Aβ42 production as well as improved properties, including solubility. In vivo pharmacokinetic analysis demonstrated that several compounds within the novel series were capable of crossing the BBB and accessing the therapeutic target. Treatment with methoxypyridine-derived compound 64 reduced Aβ42 levels in the plasma of J20 mice, in addition to reducing Aβ42 levels in the plasma and brain of Tg2576 mice.
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Immobilized Carbodiimide Assisted Flow Combinatorial Protocol to Facilitate Amide Coupling and Lactamization. ACS COMBINATORIAL SCIENCE 2020; 22:255-267. [PMID: 32283009 DOI: 10.1021/acscombsci.0c00001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Through a screen of over one hundred and 30 permutations of reaction temperatures, solvents, carbodiimide resins, and carbodiimide molar equivalences, in the presence, absence, or combination of diisopropylamine and benzotriazole additives, a convenient and first reported carbodiimide polymer-assisted flow approach to effect amide coupling and lactamization was developed. The protocol entails injecting a single solution (1:9 dimethylformamide: dichloromethane) containing a carboxylic acid and an amine or linear peptide sequence into a continuous stream of dichloromethane. The protocol remained viable in the absence of base, did not require carboxylate preactivation which, and in concert with minimal workup requirements, enabled the isolation of products in high yields. Compared to the utilization of untethered carbodiimide reagents, the flow procedure was also observed to provide a degree of racemization safety.
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Structural and Thermodynamic Basis of the Enhanced Interaction between Kinesin Spindle Protein Eg5 and STLC-type Inhibitors. ACS OMEGA 2018; 3:12284-12294. [PMID: 31459302 PMCID: PMC6644766 DOI: 10.1021/acsomega.8b00778] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 08/22/2018] [Indexed: 06/10/2023]
Abstract
For a better understanding of protein-inhibitor interactions, we report structural, thermodynamic, and biological analyses of the interactions between S-trityl-l-cysteine (STLC) derivatives and the motor domain of kinesin spindle protein Eg5. Binding of STLC-type inhibitors to Eg5 was enthalpically driven and entropically unfavorable. The introduction of a para-methoxy substituent in one phenyl ring of STLC enhances its inhibitory activity resulting from a larger enthalpy gain possibly due to the increased shape complementarity. The substituent fits to a recess in the binding pocket. To avoid steric hindrance, the substituted STLC is nudged toward the side opposite to the recess, which enhances the interaction of Eg5 with the remaining part of the inhibitor. Further introduction of an ethylene linkage between two phenyl rings enhances Eg5 inhibitory activity by reducing the loss of entropy in forming the complex. This study provides valuable examples of enhancing protein-inhibitor interactions without forming additional hydrogen bonds.
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Fluorine and Fluorinated Motifs in the Design and Application of Bioisosteres for Drug Design. J Med Chem 2018; 61:5822-5880. [PMID: 29400967 DOI: 10.1021/acs.jmedchem.7b01788] [Citation(s) in RCA: 1276] [Impact Index Per Article: 212.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The electronic properties and relatively small size of fluorine endow it with considerable versatility as a bioisostere and it has found application as a substitute for lone pairs of electrons, the hydrogen atom, and the methyl group while also acting as a functional mimetic of the carbonyl, carbinol, and nitrile moieties. In this context, fluorine substitution can influence the potency, conformation, metabolism, membrane permeability, and P-gp recognition of a molecule and temper inhibition of the hERG channel by basic amines. However, as a consequence of the unique properties of fluorine, it features prominently in the design of higher order structural metaphors that are more esoteric in their conception and which reflect a more sophisticated molecular construction that broadens biological mimesis. In this Perspective, applications of fluorine in the construction of bioisosteric elements designed to enhance the in vitro and in vivo properties of a molecule are summarized.
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The selectivity and bioavailability improvement of novel oral anticoagulants: An overview. Eur J Med Chem 2018; 146:299-317. [PMID: 29407959 DOI: 10.1016/j.ejmech.2018.01.067] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 01/18/2018] [Accepted: 01/19/2018] [Indexed: 01/23/2023]
Abstract
Anticoagulants have exhibited a critical role in the prevention and/or treatment of thrombotic diseases. Up to now, kinds of novel oral anticoagulants, inhibiting plasma serine proteases in the coagulation cascade, have been developed to overcome the clinical limitations of classical anticoagulants (like warfarin and heparins). Some of them, such as Apixaban, Rivaroxaban, Edoxaban, and Dabigatran, have been approved by FDA in recent years. This review summarizes the discovery and optimization of representative novel oral anticoagulants with the aim to improve selectivity and bioavailability of compounds. The impact of different targets in the cascade on bleeding risk also is discussed. We hope some more effective, selective, and safer anticoagulants can be developed in the future on the basis of these design experiences.
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Antithrombotic properties of JJ1, a potent and novel thrombin inhibitor. Sci Rep 2017; 7:14862. [PMID: 29093471 PMCID: PMC5665883 DOI: 10.1038/s41598-017-13868-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 10/03/2017] [Indexed: 11/09/2022] Open
Abstract
The development of new anticoagulants is an important goal for the improvement of thrombosis treatment. Recent studies have suggested the importance of thrombin inhibitors in the modulation of thromboembolic disorders. The aim of this study was to discover a new small-molecule thrombin inhibitor. In this study, the compound JJ1, which has a novel scaffold, was selected by structure-based docking simulation to determine its potential inhibitory activity against thrombin. JJ1 was shown to inhibit the catalytic activity of human α-thrombin with a K i of 0.019 μM by direct binding to the active site and with at least 10,000-fold selectivity relative to that reported for the inhibition of other biologically important serine proteases. JJ1 prolonged clotting times (activated partial thromboplastin time and prothrombin time) and inhibited the activity and production of thrombin. Furthermore, it inhibited thrombin-catalyzed fibrin polymerization and platelet aggregation. Similar to its in vitro antithrombotic activities, JJ1 showed enhanced antithrombotic effects in an in vivo pulmonary embolism and arterial thrombosis model. It also exhibited anticoagulant effects in mice. Collectively, these results demonstrated that JJ1 was a potent, direct, and selective thrombin inhibitor that may be useful in the management of various thrombotic disorders.
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Green synthesis of 2-pyrazinones in deep eutectic solvents: From α-chloro oximes to peptidomimetic scaffolds. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.09.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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11
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Synthesis and in vitro anticoagulant activity of 3-(1H-imidazo[4,5-c]pyridin-2-yl)-1,5-diarylpyridin-2(1H)-one derivatives. RESEARCH ON CHEMICAL INTERMEDIATES 2015. [DOI: 10.1007/s11164-015-1927-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Abstract
On the basis of a crystal structure of a phenylpyrrolidine lead and subsequent molecular modeling results, we designed and synthesized a novel series of macrocyclic FVIIa inhibitors. The optimal 16-membered macrocycle was 60-fold more potent than an acyclic analog. Further potency optimization by incorporation of P1' alkyl sulfone and P2 methyl groups provided a macrocycle with TF/FVIIa Ki = 1.6 nM, excellent selectivity against a panel of seven serine proteases, and FVII-deficient prothrombin time EC2x = 1.2 μM. Discovery of this potent, selective macrocyclic scaffold opens new possibilities for the development of orally bioavailable FVIIa inhibitors.
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Immobilized coupling reagents: synthesis of amides/peptides. ACS COMBINATORIAL SCIENCE 2014; 16:579-601. [PMID: 25330282 DOI: 10.1021/co500126y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The primary idea of using immobilized reagents in organic synthetic chemistry is to simplify the downstream process, product workup and isolation, and therefore avoiding time-consuming and expensive chromatographic separations, which are intrinsic to every synthetic process. Numerous polymer-bounded reagents are commercially available and applicable to almost all kinds of synthetic chemistry conversions. Herein, we have covered all known supported-coupling reagents and bases which have had a great impact in amide/peptide bond formation. These coupling reagents have been used for the activation of a carboxyl moiety; thus generating an active acylating species that is ready to couple with an amine nucleophile liberating the amide/peptide and polymeric support which can be regenerated for reuse. This also addresses a large variety of anchored coupling reagents, additives, and bases that have only been employed in amide/peptide syntheses during the last six decades.
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Abstract
INTRODUCTION Heparin and warfarin have historically been the only antithrombotics available. Recently, however, newer anticoagulants have been developed. Factor VIIa (fVIIa) inhibitors represent one of the new and potentially exciting classes of anticoagulants currently under development. Indeed, several methodologies have been used to develop fVIIa inhibitors. AREAS COVERED The authors highlight some of the methologies applied for the discovery of fVIIa inhibitors including phage display, isolation of endogenous peptides from hematophagous animals and the use of the 1,5-benzothiazepine molecular scaffolds and screens of large chemical libraries previously used to identify other serine protease inhibitors. Although these screens were intended to identify thrombin and factor Xa inhibitors, the compounds often had concomitant fVIIa activity. The authors also discuss the utilization of medical chemistry techniques for the discovery of these compounds. EXPERT OPINION FVIIa inhibitors represent a viable option for the development of new anticoagulants. There are theoretical advantages that fVIIa inhibitors may possess over existing anticoagulants and highly specific inhibitors that possess oral bioavailability and low bleeding risk may succeed.
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16
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Nonbenzamidine acylsulfonamide tissue factor–factor VIIa inhibitors. Bioorg Med Chem Lett 2013; 23:5244-8. [DOI: 10.1016/j.bmcl.2013.06.027] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 06/05/2013] [Accepted: 06/11/2013] [Indexed: 10/26/2022]
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17
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Achiral pyrazinone-based inhibitors of the hepatitis C virus NS3 protease and drug-resistant variants with elongated substituents directed toward the S2 pocket. J Med Chem 2013; 57:1790-801. [PMID: 23517538 DOI: 10.1021/jm301887f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Herein we describe the design, synthesis, inhibitory potency, and pharmacokinetic properties of a novel class of achiral peptidomimetic HCV NS3 protease inhibitors. The compounds are based on a dipeptidomimetic pyrazinone glycine P3P2 building block in combination with an aromatic acyl sulfonamide in the P1P1' position. Structure-activity relationship data and molecular modeling support occupancy of the S2 pocket from elongated R(6) substituents on the 2(1H)-pyrazinone core and several inhibitors with improved inhibitory potency down to Ki = 0.11 μM were identified. A major goal with the design was to produce inhibitors structurally dissimilar to the di- and tripeptide-based HCV protease inhibitors in advanced stages of development for which cross-resistance might be an issue. Therefore, the retained and improved inhibitory potency against the drug-resistant variants A156T, D168V, and R155K further strengthen the potential of this class of inhibitors. A number of the inhibitors were tested in in vitro preclinical profiling assays to evaluate their apparent pharmacokinetic properties. The various R(6) substituents were found to have a major influence on solubility, metabolic stability, and cell permeability.
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Design and synthesis of bicyclic pyrazinone and pyrimidinone amides as potent TF–FVIIa inhibitors. Bioorg Med Chem Lett 2013; 23:1604-7. [DOI: 10.1016/j.bmcl.2013.01.094] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 01/14/2013] [Accepted: 01/22/2013] [Indexed: 11/20/2022]
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Discovery of achiral inhibitors of the hepatitis C virus NS3 protease based on 2(1H)-pyrazinones. Bioorg Med Chem 2010; 18:6512-25. [DOI: 10.1016/j.bmc.2010.06.101] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Revised: 06/21/2010] [Accepted: 06/29/2010] [Indexed: 10/19/2022]
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Analysis of structural water and CH···π interactions in HIV-1 protease and PTP1B complexes using a hydrogen bond prediction tool, HBPredicT. J Mol Model 2010; 17:401-13. [PMID: 20490879 DOI: 10.1007/s00894-010-0736-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Accepted: 04/27/2010] [Indexed: 11/29/2022]
Abstract
A hydrogen bond prediction tool HBPredicT is developed for detecting structural water molecules and CH···π interactions in PDB files of protein-ligand complexes. The program adds the missing hydrogen atoms to the protein, ligands, and oxygen atoms of water molecules and subsequently all the hydrogen bonds in the complex are located using specific geometrical criteria. Hydrogen bonds are classified into various types based on (i) donor and acceptor atoms, and interactions such as (ii) protein-protein, (iii) protein-ligand, (iv) protein-water, (v) ligand-water, (vi) water-water, and (vii) protein-water-ligand. Using the information in category (vii), the water molecules which form hydrogen bonds with the ligand and the protein simultaneously-the structural water-is identified and retrieved along with the associated ligand and protein residues. For CH···π interactions, the relevant portions of the corresponding structures are also extracted in the output. The application potential of this program is tested using 19 HIV-1 protease and 11 PTP1B inhibitor complexes. All the systems showed presence of structural water molecules and in several cases, the CH···π interaction between ligand and protein are detected. A rare occurrence of CH···π interactions emanating from both faces of a phenyl ring of the inhibitor is identified in HIV-1 protease 1D4L.
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Synthesis of a versatile 2 (1H)-pyrazinone core for the preparation of Tissue Factor-Factor VIIa inhibitors. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.02.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Design, synthesis, and biological activity of isophthalic acid derivatives targeted to the C1 domain of protein kinase C. J Med Chem 2009; 52:3969-81. [PMID: 19438240 DOI: 10.1021/jm900229p] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein kinase C (PKC) is a widely studied molecular target for the treatment of cancer and other diseases. We have approached the issue of modifying PKC function by targeting the C1 domain in the regulatory region of the enzyme. Using the X-ray crystal structure of the PKC delta C1b domain, we have discovered conveniently synthesizable derivatives of dialkyl 5-(hydroxymethyl)isophthalate that can act as potential C1 domain ligands. Structure-activity studies confirmed that the important functional groups predicted by modeling were indispensable for binding to the C1 domain and that the modifications of these groups diminished binding. The most promising compounds were able to displace radiolabeled phorbol ester ([(3)H]PDBu) from PKC alpha and delta at K(i) values in the range of 200-900 nM. Furthermore, the active isophthalate derivatives could modify PKC activation in living cells either by inducing PKC-dependent ERK phosphorylation or by inhibiting phorbol-induced ERK phosphorylation. In conclusion, we report here, for the first time, that derivatives of isophthalic acid represent an attractive novel group of C1 domain ligands that can be used as research tools or further modified for potential drug development.
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Design, synthesis, and biological evaluation of 1,5-benzothiazepine-4-one derivatives targeting factor VIIa/tissue factor. Bioorg Med Chem Lett 2009; 19:1386-91. [DOI: 10.1016/j.bmcl.2009.01.039] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2008] [Revised: 01/13/2009] [Accepted: 01/14/2009] [Indexed: 11/18/2022]
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25
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A straightforward microwave method for rapid synthesis of N-1, C-6 functionalized 3,5-dichloro-2(1H)-pyrazinones. Org Biomol Chem 2009; 7:2809-15. [DOI: 10.1039/b905501k] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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Fusarielin A as an anti-angiogenic and anti-proliferative agent: basic biological characterization. Chem Pharm Bull (Tokyo) 2008; 56:298-304. [PMID: 18310939 DOI: 10.1248/cpb.56.298] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Fusarielin A shows anti-angiogenic activity in the human umbilical vein endothelial cell (HUVEC) tube formation assay. Structural development studies indicated the importance of the hydroxyl groups in this molecule. A 3H-labeled derivative and a fluorescent affinity-labeling agent were prepared and used to examine the cellular distribution and biological behavior of fusarielin A.
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Novel syntheses of 3-anilino-pyrazin-2(1H)-ones and 3-anilino-quinoxalin-2-(1H)-ones via microwave-mediated Smiles rearrangement. Tetrahedron Lett 2008. [DOI: 10.1016/j.tetlet.2008.01.056] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Design, synthesis, and biological evaluation of pyrazinones containing novel P1 needles as inhibitors of TF/VIIa. Bioorg Med Chem Lett 2007; 17:4568-74. [PMID: 17566736 DOI: 10.1016/j.bmcl.2007.05.090] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2007] [Revised: 05/29/2007] [Accepted: 05/30/2007] [Indexed: 11/23/2022]
Abstract
Herein is described the design, synthesis, and enzymatic activity of a series of substituted pyrazinones as inhibitors of the TF/VIIa complex. These inhibitors were designed to explore replacement and variation of the P1 amidine described previously [J. Med. Chem.2003, 46, 4050]. The P1 needle replacements were selected based upon their reduced basicity compared to the parent phenyl amidine (pKa approximately 12). A contributing factor towards the oral bioavailability of a compound is the ionization state of the compound in the intestinal tract. The desired outcome of the study was to identify an orally bioavailable TF-VIIa inhibitor.
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Palladium-catalyzed copper(i)-mediated cross-coupling of arylboronic acids and 2(1H)-pyrazinones facilitated by microwave irradiation with simultaneous cooling. Org Biomol Chem 2007; 5:2962-5. [PMID: 17728862 DOI: 10.1039/b704389a] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The application of a palladium-catalyzed Cu(I)-mediated Liebeskind-Srogl protocol for the decoration of the 2(1H)-pyrazinone scaffold resulted in significantly improved yields and rates when performed under microwave irradiation with simultaneous cooling.
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Efforts toward oral bioavailability in factor VIIa inhibitors. Bioorg Med Chem Lett 2006; 16:3829-32. [PMID: 16650987 DOI: 10.1016/j.bmcl.2006.04.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2005] [Revised: 04/11/2006] [Accepted: 04/11/2006] [Indexed: 10/24/2022]
Abstract
Efforts toward developing orally bioavailable factor VIIa inhibitors starting from parenteral lead compound 1 are described. SAR resulted in improved physicochemical properties, leading to enhanced oral absorption in rat.
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Abstract
The success or failure of a small-molecule drug discovery project ultimately lies in the choice of the scaffolds to be screened -- chosen from among the many millions of available compounds. Therefore, the methods used to design compound screening libraries are key for the development of new drugs that target a wide range of diseases. Currently, there is a trend towards the construction of receptor-structure-based focused libraries. Recent advances in high-throughput computational docking, NMR and crystallography have facilitated the development of these libraries. A structure-based target-specific library can save time and money by reducing the number of compounds to be experimentally tested, also improving the drug discovery success rate by identifying more-potent and specific binders.
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Dose-dependent antithrombotic activity of an orally active tissue factor/factor VIIa inhibitor without concomitant enhancement of bleeding propensity. Bioorg Med Chem 2006; 14:5357-69. [PMID: 16621574 DOI: 10.1016/j.bmc.2006.03.042] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2005] [Revised: 03/15/2006] [Accepted: 03/22/2006] [Indexed: 11/29/2022]
Abstract
The discovery of a highly potent and selective tissue factor/factor VIIa inhibitor is described. Upon oral administration of its double prodrug in the guinea pig, a dose-dependent antithrombotic effect is observed in an established model of arterial thrombosis without prolonging bleeding time. The pharmacodynamic properties of this selective inhibitor are compared to the behaviour of a mixed factor VIIa/factor Xa inhibitor.
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Discovery of novel heterocyclic factor VIIa inhibitors. Bioorg Med Chem Lett 2006; 16:2270-3. [PMID: 16460932 DOI: 10.1016/j.bmcl.2006.01.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2005] [Revised: 01/04/2006] [Accepted: 01/06/2006] [Indexed: 11/30/2022]
Abstract
Structure-activity relationships and binding mode of novel heterocyclic factor VIIa inhibitors will be described. In these inhibitors, a highly basic 5-amidinoindole moiety has been successfully replaced with a less basic 5-aminopyrrolo[3,2-b]pyridine scaffold.
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The Chemistry of 2-(1H)-Pyrazinones in Solution and on Solid Support. TOPICS IN HETEROCYCLIC CHEMISTRY 2006. [DOI: 10.1007/7081_007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Structure-based drug design meets the ribosome. Biochem Pharmacol 2006; 71:1016-25. [PMID: 16443192 DOI: 10.1016/j.bcp.2005.12.026] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2005] [Revised: 12/08/2005] [Accepted: 12/13/2005] [Indexed: 11/19/2022]
Abstract
The high-resolution structures of the bacterial ribosomal subunits and those of their complexes with antibiotics have advanced significantly our understanding of small-molecule interactions with RNA. The wealth of RNA structural data generated by these structures has allowed computational chemists to employ a drug discovery paradigm focused on RNA-based targets. The structures also show how target-based resistance affects antibiotics acting at the level of the ribosome. Not only are the sites pinpointed where different classes of antibiotics inhibit protein synthesis, but their orientations, relative dispositions, and unique mechanisms of action are also revealed at the atomic level. Both the 30S and the 50S ribosomal subunits have been shown to be "targets of targets", offering several adjacent, functionally relevant binding pockets for antibiotics. It is the detailed knowledge of these validated locations, or ribofunctional loci, plus the mapping of the resistance hot-spots that allow the rational design of next-generation antibacterials. When the structural information is combined with a data-driven computational toolkit able to describe and predict molecular properties appropriate for bacterial cell penetration and drug-likeness, a structure-based drug design approach for novel antibacterials shows great promise.
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Factor VIIa inhibitors: chemical optimization, preclinical pharmacokinetics, pharmacodynamics, and efficacy in an arterial baboon thrombosis model. Bioorg Med Chem Lett 2006; 16:2037-41. [PMID: 16412633 DOI: 10.1016/j.bmcl.2005.12.059] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2005] [Revised: 12/13/2005] [Accepted: 12/15/2005] [Indexed: 11/26/2022]
Abstract
Highly selective and potent factor VIIa-tissue factor (fVIIa.TF) complex inhibitors were generated through structure-based design. The pharmacokinetic properties of an optimized analog (9) were characterized in several preclinical species, demonstrating pharmacokinetic characteristics suitable for once-a-day dosing in humans. Analog 9 inhibited platelet and fibrin deposition in a dose-dependent manner after intravenous administration in a baboon thrombosis model, and a pharmacodynamic concentration-response model was developed to describe the platelet deposition data. Results for heparin and enoxaparin (Lovenox) in the baboon model are also presented.
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Recent applications of protein crystallography and structure-guided drug design. Curr Opin Chem Biol 2005; 9:371-80. [PMID: 16006182 DOI: 10.1016/j.cbpa.2005.06.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2005] [Accepted: 06/22/2005] [Indexed: 10/25/2022]
Abstract
Technological advances to increase the throughput of purified protein production and co-crystallization of target proteins with small molecules have helped to solidify the role that structure via crystallography has on drug discovery. Visualization of how drug-like molecules bind to the target protein is a key step in driving follow-up or preclinical chemistry to improve characteristics of the molecule. Using structural information to guide small-molecule design and generate new chemical ideas is now a mainstay in the drug discovery process.
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Selective and orally bioavailable phenylglycine tissue factor/factor VIIa inhibitors. Bioorg Med Chem Lett 2005; 15:5344-52. [PMID: 16213138 DOI: 10.1016/j.bmcl.2005.04.079] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2005] [Revised: 04/25/2005] [Accepted: 04/28/2005] [Indexed: 11/20/2022]
Abstract
We describe the structure-based design and synthesis of highly potent, orally bioavailable tissue factor/factor VIIa inhibitors which interfere with the coagulation cascade by selective inhibition of the extrinsic pathway.
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Expression, crystallization, and three-dimensional structure of the catalytic domain of human plasma kallikrein. J Biol Chem 2005; 280:41077-89. [PMID: 16199530 DOI: 10.1074/jbc.m506766200] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Plasma kallikrein is a serine protease that has many important functions, including modulation of blood pressure, complement activation, and mediation and maintenance of inflammatory responses. Although plasma kallikrein has been purified for 40 years, its structure has not been elucidated. In this report, we described two systems (Pichia pastoris and baculovirus/Sf9 cells) for expression of the protease domain of plasma kallikrein, along with the purification and high resolution crystal structures of the two recombinant forms. In the Pichia pastoris system, the protease domain was expressed as a heterogeneously glycosylated zymogen that was activated by limited trypsin digestion and treated with endoglycosidase H deglycosidase to reduce heterogeneity from the glycosylation. The resulting protein was chromatographically resolved into four components, one of which was crystallized. In the baculovirus/Sf9 system, homogeneous, crystallizable, and nonglycosylated protein was expressed after mutagenizing three asparagines (the glycosylation sites) to glutamates. When assayed against the peptide substrates, pefachrome-PK and oxidized insulin B chain, both forms of the protease domain were found to have catalytic activity similar to that of the full-length protein. Crystallization and x-ray crystal structure determination of both forms have yielded the first three-dimensional views of the catalytic domain of plasma kallikrein. The structures, determined at 1.85 A for the endoglycosidase H-deglycosylated protease domain produced from P. pastoris and at 1.40 A for the mutagenically deglycosylated form produced from Sf9 cells, show that the protease domain adopts a typical chymotrypsin-like serine protease conformation. The structural information provides insights into the biochemical and enzymatic properties of plasma kallikrein and paves the way for structure-based design of protease inhibitors that are selective either for or against plasma kallikrein.
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Novel pyrazinone and pyridinone thrombin inhibitors incorporating weakly basic heterobicyclic P1-arginine mimetics. Eur J Med Chem 2005; 40:782-91. [PMID: 15890436 DOI: 10.1016/j.ejmech.2005.03.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2004] [Revised: 03/07/2005] [Accepted: 03/07/2005] [Indexed: 11/30/2022]
Abstract
The design, synthesis and biological activity of new thrombin inhibitors with a pyridinone or pyrazinone core and different heterobicyclic P(1) arginine side-chain mimetics are described. The arginine side-chain mimetics used in this study are (+/-)-4,5,6,7-tetrahydro-2H-indazol-5-ylmethanamine and both enantiomers thereof, (+/-)-4,5,6,7-tetrahydro-1,3-benzothiazole-2,6-diamine and the corresponding R enantiomer. Compound 25, the most potent in the series of pyrazinone inhibitors, exhibited a K(i) of 41 nM in vitro and high selectivity against trypsin and factor Xa.
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Structure-based design and synthesis of pyrazinones containing novel P1 ‘side pocket’ moieties as inhibitors of TF/VIIa. Bioorg Med Chem Lett 2005; 15:3006-11. [PMID: 15913999 DOI: 10.1016/j.bmcl.2005.04.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2004] [Revised: 04/21/2005] [Accepted: 04/22/2005] [Indexed: 11/25/2022]
Abstract
We describe the structure-based design, synthesis, and enzymatic activity of a series of substituted pyrazinones as inhibitors of the TF/VIIa complex. These inhibitors contain substituents meta to the P(1) amidine designed to explore additional interactions with the VIIa residues in the so-called 'S(1) side pocket'. A crystal structure of the designed inhibitors demonstrates the ability of the P(1) side pocket moiety to engage Lys192 and main chain of Gly216 via hydrogen bond interactions, thus, providing additional possibility for chemical modification to improve selectivity and/or physical properties of inhibitors.
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Design of selective phenylglycine amide tissue factor/factor VIIa inhibitors. Bioorg Med Chem Lett 2005; 15:817-22. [PMID: 15664864 DOI: 10.1016/j.bmcl.2004.10.092] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2004] [Revised: 10/25/2004] [Accepted: 10/28/2004] [Indexed: 11/16/2022]
Abstract
Proof of concept experiments have shown that tissue factor/factor VIIa inhibitors have antithrombotic activity without enhancing bleeding propensity. Starting from lead compounds generated by a biased combinatorial approach, phenylglycine amide tissue factor/factor VIIa inhibitors with low nanomolar affinity and good selectivity against other serine proteases of the coagulation cascade were designed, using the guidance of X-ray structural analysis and molecular modelling.
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Structure-based design of P3 moieties in the peptide mimetic factor VIIa inhibitor. Biochem Biophys Res Commun 2005; 327:589-96. [DOI: 10.1016/j.bbrc.2004.12.042] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2004] [Indexed: 10/26/2022]
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A selective, slow binding inhibitor of factor VIIa binds to a nonstandard active site conformation and attenuates thrombus formation in vivo. J Biol Chem 2005; 280:9160-9. [PMID: 15632123 DOI: 10.1074/jbc.m409068200] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The serine protease factor VIIa (FVIIa) in complex with its cellular cofactor tissue factor (TF) initiates the blood coagulation reactions. TF.FVIIa is also implicated in thrombosis-related disorders and constitutes an appealing therapeutic target for treatment of cardiovascular diseases. To this end, we generated the FVIIa active site inhibitor G17905, which displayed great potency toward TF.FVIIa (Ki = 0.35 +/- 0.11 nM). G17905 did not appreciably inhibit 12 of the 14 examined trypsin-like serine proteases, consistent with its TF.FVIIa-specific activity in clotting assays. The crystal structure of the FVIIa.G17905 complex provides insight into the molecular basis of the high selectivity. It shows that, compared with other serine proteases, FVIIa is uniquely equipped to accommodate conformational disturbances in the Gln217-Gly219 region caused by the ortho-hydroxy group of the inhibitor's aminobenzamidine moiety located in the S1 recognition pocket. Moreover, the structure revealed a novel, nonstandard conformation of FVIIa active site in the region of the oxyanion hole, a "flipped" Lys192-Gly193 peptide bond. Macromolecular substrate activation assays demonstrated that G17905 is a noncompetitive, slow-binding inhibitor. Nevertheless, G17905 effectively inhibited thrombus formation in a baboon arterio-venous shunt model, reducing platelet and fibrin deposition by approximately 70% at 0.4 mg/kg + 0.1 mg/kg/min infusion. Therefore, the in vitro potency of G17905, characterized by slow binding kinetics, correlated with efficacious antithrombotic activity in vivo.
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Small Molecule Anticoagulant/Antithrombotic Agents. ANNUAL REPORTS IN MEDICINAL CHEMISTRY VOLUME 40 2005. [DOI: 10.1016/s0065-7743(05)40006-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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Chapter 6.2 Six-membered ring systems: Diazines and benzo derivatives. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/s0959-6380(05)80055-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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