1
|
Miles SA, Nillama JA, Hunter L. Tinker, Tailor, Soldier, Spy: The Diverse Roles That Fluorine Can Play within Amino Acid Side Chains. Molecules 2023; 28:6192. [PMID: 37687021 PMCID: PMC10489206 DOI: 10.3390/molecules28176192] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/17/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023] Open
Abstract
Side chain-fluorinated amino acids are useful tools in medicinal chemistry and protein science. In this review, we outline some general strategies for incorporating fluorine atom(s) into amino acid side chains and for elaborating such building blocks into more complex fluorinated peptides and proteins. We then describe the diverse benefits that fluorine can offer when located within amino acid side chains, including enabling 19F NMR and 18F PET imaging applications, enhancing pharmacokinetic properties, controlling molecular conformation, and optimizing target-binding.
Collapse
Affiliation(s)
| | | | - Luke Hunter
- School of Chemistry, The University of New South Wales (UNSW), Sydney 2052, Australia
| |
Collapse
|
2
|
Yuan F, Zhao Y, Guo Q, Yin F, Lai J, Nian B, Zhang M, Tang E. Synthesis of 1-[1-(Amino)cyclopropyl]ketones by Tandem Reaction Involving Vinyl Selenium Salt. CHINESE J ORG CHEM 2022. [DOI: 10.6023/cjoc202111015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
3
|
Ghiasi T, Ahmadi S, Ahmadi E, Talei Bavil Olyai MR, Khodadadi Z. The index of ideality of correlation: QSAR studies of hepatitis C virus NS3/4A protease inhibitors using SMILES descriptors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2021; 32:495-520. [PMID: 34074200 DOI: 10.1080/1062936x.2021.1925344] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 04/29/2021] [Indexed: 06/12/2023]
Abstract
Robust and reliable QSAR models were developed to predict half-maximal inhibitory concentration (IC50) values of hepatitis C virus NS3/4A protease inhibitors from the Monte Carlo technique. 524 HCV NS3/4A protease inhibitors were extracted from the scientific literature to create a reasonably large set. The models were developed using CORAL software by using two target functions namely target function 1 (TF1) without applying the index of ideality of correlation (IIC) and target function 2 (TF2) that uses IIC. The constructed models based on TF2 were statistically more significant and robust than the models based on TF1. The determination coefficients (r2) of training and test sets were 0.86 and 0.88 for the best split based on TF2. The promoters of the increase/decrease of activity were also extracted and interpreted in detail. The model interpretation results explain the role of different structural attributes in predicting the pIC50 values of hepatitis C virus NS3/4A protease inhibitors. Based on the mechanistic model interpretation results, eight new compounds were designed and their pIC50 values were predicted based on the average prediction of ten models.
Collapse
Affiliation(s)
- T Ghiasi
- Department of Chemistry, Faculty of Science, Islamic Azad University, South Tehran Branch, Tehran, Iran
| | - S Ahmadi
- Department of Chemistry, Faculty of Pharmaceutical Chemistry, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - E Ahmadi
- Department of Chemistry, Kermanshah Branch, Islamic Azad University, Kermanshah, Iran
| | - M R Talei Bavil Olyai
- Department of Chemistry, Faculty of Science, Islamic Azad University, South Tehran Branch, Tehran, Iran
| | - Z Khodadadi
- Department of Chemistry, Faculty of Science, Islamic Azad University, South Tehran Branch, Tehran, Iran
| |
Collapse
|
4
|
Monga A, Bagchi S, Sharma A. DABCO-Catalysed Amidation under Assistance of Aerial Oxidation: Access to α-ketoamides. ChemistrySelect 2018. [DOI: 10.1002/slct.201801981] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Aparna Monga
- Department of Chemistry; Indian Institute of Technology Roorkee; Indian Institute of Technology Roorkee; Roorkee- 247667
| | - Sourav Bagchi
- Department of Chemistry; Indian Institute of Technology Roorkee; Indian Institute of Technology Roorkee; Roorkee- 247667
| | - Anuj Sharma
- Department of Chemistry; Indian Institute of Technology Roorkee; Indian Institute of Technology Roorkee; Roorkee- 247667
| |
Collapse
|
5
|
QSAR studies of the bioactivity of hepatitis C virus (HCV) NS3/4A protease inhibitors by multiple linear regression (MLR) and support vector machine (SVM). Bioorg Med Chem Lett 2017; 27:2931-2938. [PMID: 28501513 DOI: 10.1016/j.bmcl.2017.05.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 04/14/2017] [Accepted: 05/01/2017] [Indexed: 12/23/2022]
Abstract
In this study, quantitative structure-activity relationship (QSAR) models using various descriptor sets and training/test set selection methods were explored to predict the bioactivity of hepatitis C virus (HCV) NS3/4A protease inhibitors by using a multiple linear regression (MLR) and a support vector machine (SVM) method. 512 HCV NS3/4A protease inhibitors and their IC50 values which were determined by the same FRET assay were collected from the reported literature to build a dataset. All the inhibitors were represented with selected nine global and 12 2D property-weighted autocorrelation descriptors calculated from the program CORINA Symphony. The dataset was divided into a training set and a test set by a random and a Kohonen's self-organizing map (SOM) method. The correlation coefficients (r2) of training sets and test sets were 0.75 and 0.72 for the best MLR model, 0.87 and 0.85 for the best SVM model, respectively. In addition, a series of sub-dataset models were also developed. The performances of all the best sub-dataset models were better than those of the whole dataset models. We believe that the combination of the best sub- and whole dataset SVM models can be used as reliable lead designing tools for new NS3/4A protease inhibitors scaffolds in a drug discovery pipeline.
Collapse
|
6
|
De Risi C, Pollini GP, Zanirato V. Recent Developments in General Methodologies for the Synthesis of α-Ketoamides. Chem Rev 2016; 116:3241-305. [DOI: 10.1021/acs.chemrev.5b00443] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Carmela De Risi
- Dipartimento
di Scienze Chimiche e Farmaceutiche, Università degli Studi di Ferrara, Via Fossato di Mortara 17, 44121 Ferrara, Italy
| | - Gian Piero Pollini
- Istituto Universitario
di Studi Superiori “IUSS−Ferrara 1391”, Via delle Scienze 41/b, 44121 Ferrara, Italy
| | - Vinicio Zanirato
- Dipartimento
di Scienze Chimiche e Farmaceutiche, Università degli Studi di Ferrara, Via Fossato di Mortara 17, 44121 Ferrara, Italy
| |
Collapse
|
7
|
TBAI-catalyzed synthesis of α-ketoamides via sp3 C–H radical/radical cross-coupling and domino aerobic oxidation. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2015.06.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
|
8
|
Ji F, Peng H, Zhang X, Lu W, Liu S, Jiang H, Liu B, Yin B. Base-Mediated Decomposition of Amide-Substituted Furfuryl Tosylhydrazones: Synthesis and Cytotoxic Activities of Enynyl-Ketoamides. J Org Chem 2015; 80:2092-102. [DOI: 10.1021/jo502328j] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Fanghua Ji
- School
of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510006, P.R. China
| | - Hui Peng
- School
of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510006, P.R. China
| | - Xiaoting Zhang
- School
of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510006, P.R. China
| | - Wenhua Lu
- State
Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou 510060, P.R. China
| | - Shubin Liu
- Research
Computing Center, University of North Carolina, Chapel Hill, North Carolina 27599-3420, United States
| | - Huanfeng Jiang
- School
of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510006, P.R. China
| | - Bo Liu
- Guangdong Provincial Academy of Chinese Medical Sciences, Guangzhou 510006, P.R. China
| | - Biaolin Yin
- School
of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510006, P.R. China
| |
Collapse
|
9
|
Martı́nez-González JÁ, González M, Masgrau L, Martı́nez R. Theoretical Study of the Free Energy Surface and Kinetics of the Hepatitis C Virus NS3/NS4A Serine Protease Reaction with the NS5A/5B Substrate. Does the Generally Accepted Tetrahedral Intermediate Really Exist? ACS Catal 2014. [DOI: 10.1021/cs5011162] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Miguel González
- Departament
de Quı́mica Fı́sica i IQTC, Universitat de Barcelona, C/Martı́ i Franquès, 1, 08028 Barcelona, Spain
| | - Laura Masgrau
- Institut
de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Rodrigo Martı́nez
- Departamento
de Quı́mica, Universidad de La Rioja, C/Madre de
Dios, 51, 26006 Logroño, Spain
| |
Collapse
|
10
|
Wadood A, Riaz M, Uddin R, ul-Haq Z. In silico identification and evaluation of leads for the simultaneous inhibition of protease and helicase activities of HCV NS3/4A protease using complex based pharmacophore mapping and virtual screening. PLoS One 2014; 9:e89109. [PMID: 24551230 PMCID: PMC3923879 DOI: 10.1371/journal.pone.0089109] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 01/17/2014] [Indexed: 01/09/2023] Open
Abstract
Hepatitis C virus (HCV) infection is an alarming and growing threat to public health. The present treatment gives limited efficacy and is poorly tolerated, recommending the urgent medical demand for novel therapeutics. NS3/4A protease is a significant emerging target for the treatment of HCV infection. This work reports the complex-based pharmacophore modeling to find out the important pharmacophoric features essential for the inhibition of both protease and helicase activity of NS3/4A protein of HCV. A seven featured pharmacophore model of HCV NS3/4A protease was developed from the crystal structure of NS3/4A protease in complex with a macrocyclic inhibitor interacting with both protease and helicase sites residues via MOE pharmacophore constructing tool. It consists of four hydrogen bond acceptors (Acc), one hydrophobic (Hyd), one for lone pair or active hydrogen (Atom L) and a heavy atom feature (Atom Q). The generated pharmacophore model was validated by a test database of seventy known inhibitors containing 55 active and 15 inactive/least active compounds. The validated pharmacophore model was used to virtually screen the ChemBridge database. As a result of screening 1009 hits were retrieved and were subjected to filtering by Lipinski’s rule of five on the basis of which 786 hits were selected for further assessment using molecular docking studies. Finally, 15 hits of different scaffolds having interactions with important active site residues were predicted as lead candidates. These candidates having unique scaffolds have a strong likelihood to act as further starting points in the development of novel and potent NS3/4A protease inhibitors.
Collapse
Affiliation(s)
- Abdul Wadood
- Computational Medicinal Chemistry Laboratory, Department of Biochemistry Abdul Wali Khan University Mardan, Mardan, Khyber Pakhthunkhwa, Pakistan
- * E-mail:
| | - Muhammad Riaz
- Computational Medicinal Chemistry Laboratory, Department of Biochemistry Abdul Wali Khan University Mardan, Mardan, Khyber Pakhthunkhwa, Pakistan
| | - Reaz Uddin
- Dr. Panjwani Center for Molecular Medicine and Drug Research, University of Karachi, Karach, Sindh, Pakistan
| | - Zaheer ul-Haq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, University of Karachi, Karach, Sindh, Pakistan
| |
Collapse
|
11
|
Du B, Jin B, Sun P. The syntheses of α-ketoamides vianBu4NI-catalyzed multiple sp3C–H bond oxidation of ethylarenes and sequential coupling with dialkylformamides. Org Biomol Chem 2014; 12:4586-9. [DOI: 10.1039/c4ob00520a] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The nBu4NI-catalyzed sequential C–O and C–N bond formation via multiple sp3C–H bond activation of ethylarenes, using N,N-dialkylformamide as the amino source, provided α-ketoamides with moderate yields.
Collapse
Affiliation(s)
- Bingnan Du
- Jiangsu Key Laboratory of Biofunctional Materials
- College of Chemistry and Materials Science
- Nanjing Normal University
- Nanjing 210097, China
| | - Bo Jin
- Jiangsu Key Laboratory of Biofunctional Materials
- College of Chemistry and Materials Science
- Nanjing Normal University
- Nanjing 210097, China
| | - Peipei Sun
- Jiangsu Key Laboratory of Biofunctional Materials
- College of Chemistry and Materials Science
- Nanjing Normal University
- Nanjing 210097, China
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials
| |
Collapse
|
12
|
Reddy SR, Stella S, Chadha A. Simplified Procedure for TEMPO-Catalyzed Oxidation: Selective Oxidation of Alcohols, α-Hydroxy Esters, and Amides Using TEMPO and Calcium Hypochlorite. SYNTHETIC COMMUN 2012. [DOI: 10.1080/00397911.2011.584650] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Sabbasani Rajasekhara Reddy
- a Department of Biotechnology , Laboratory of Bioorganic Chemistry, Indian Institute of Technology Madras , Chennai , India
| | - Selvaraj Stella
- a Department of Biotechnology , Laboratory of Bioorganic Chemistry, Indian Institute of Technology Madras , Chennai , India
| | - Anju Chadha
- a Department of Biotechnology , Laboratory of Bioorganic Chemistry, Indian Institute of Technology Madras , Chennai , India
- b National Center for Catalysis Research, Indian Institute of Technology Madras , Chennai , India
| |
Collapse
|
13
|
Rodríguez A, Oliva C, González M. A comparative QM/MM study of the reaction mechanism of the Hepatitis C virus NS3/NS4A protease with the three main natural substrates NS5A/5B, NS4B/5A and NS4A/4B. Phys Chem Chem Phys 2010; 12:8001-15. [PMID: 20520921 DOI: 10.1039/c002116d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The reaction mechanism of the NS3/NS4A protease with the NS4B/5A and NS4A/4B natural substrates has been investigated using the QM/MM (quantum mechanics/molecular mechanics) approach, and some calculations have been performed on the reaction with the NS5A/5B natural substrate. This study widely extends a previous contribution of our group on the reaction mechanism with the NS5A/5B substrate, the main goal here being to understand the differences found between the reaction mechanism of each natural substrate and the role played by the enzymatic residues in the catalytic cycle. This knowledge will ultimately help in developing new NS3/NS4A protease inhibitors. The two first steps of the mechanism have been considered: Acylation and breaking of the peptide bond, with emphasis on the former one (rate limiting process). Energy and free energy profiles for both steps have been calculated at the AM1/MM level and corrected by means of MP2 ab initio calculations, being evident the importance of correlation energy. Acylation is the rate limiting step in all cases and occurs through a tetracoordinated intermediate, as previously suggested for other serine proteases. Specificities in the NS4B/5A mechanism can be attributed to the presence of a Proline residue in the substrate P2 position. The analysis of structures and energies confirm the importance of the oxyanion hole in the electrostatic stabilization of the tetracoordinated intermediate. Finally, the role of other residues, e.g., Arg-155 and Asp-79, has been explained, and the viability of Arg-155 mutants and its resistance to some protease inhibitors has been understood thanks to virtual mutation studies.
Collapse
Affiliation(s)
- Alejandro Rodríguez
- Departament de Química Física i IQTC, Universitat de Barcelona, C/Martí i Franquès 1, 08028 Barcelona, Spain
| | | | | |
Collapse
|
14
|
3-Oxo-2-(triphenyl-λ5-phosphanylidene)-4-(phenylsulfinyl)butanenitrile:An Efficient Reagent for α-Keto (Cyanomethylene)triphenylphosphoranesfrom Alkyl Bromides. B KOREAN CHEM SOC 2009. [DOI: 10.5012/bkcs.2009.30.11.2521] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
15
|
Roche SP, Faure S, El Blidi L, Aitken DJ. Total Synthesis of Cyclotheonamide C by Use of an α-Keto Cyanophosphorane Methodology for Peptide Assembly. European J Org Chem 2008. [DOI: 10.1002/ejoc.200800591] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
16
|
Hu Z, Han W. An efficient chiral synthesis of fluoro-containing amino acids: N-benzyloxycarbonyl-2-amino-4,4-difluorobutyric acid methyl ester and its analogs. Tetrahedron Lett 2008. [DOI: 10.1016/j.tetlet.2007.11.163] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
17
|
Cesium carbonate promoted aerobic oxidation of arylacetamides: an efficient access to N-substituted α-keto amides. Tetrahedron Lett 2007. [DOI: 10.1016/j.tetlet.2007.10.099] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
18
|
Diethyl [3-Cyano-2-Oxo-3-(Triphenylphosphoranylidene)propyl]phosphonate: A Useful Horner-Wadsworth-Emmons Reagent for α-Keto (Cyanomethylene)triphenylphosphoranes from Carbonyl Compounds. B KOREAN CHEM SOC 2007. [DOI: 10.5012/bkcs.2007.28.10.1641] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
19
|
Oliva C, Rodríguez A, González M, Yang W. A quantum mechanics/molecular mechanics study of the reaction mechanism of the hepatitis C virus NS3 protease with the NS5A/5B substrate. Proteins 2007; 66:444-55. [PMID: 17094110 DOI: 10.1002/prot.21190] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Combined quantum mechanics and molecular mechanics (QM/MM) calculations were carried out to characterize the reaction mechanism of the NS3 protease with its preferred substrate (NS5A/5B). The main purpose of this study was to locate the barrier states and intermediates along the distinguished coordinate path (DCP) involved in this process. These structures, and in particular the one corresponding to the first barrier state and intermediate (B1 and I1), could be a starting point for the synthesis of inhibitors of this protease, which could be used to treat hepatitis C. The two first steps of the reaction mechanism were studied, i.e., the acylation step and the breaking of the peptide bond. The first step takes place through a tetracoordinated intermediate, as suggested from previous works on other Serine proteases. The importance of the different amino acid residues was also considered (perturbation study where the MM charges of each residue were set to zero independently). The residues of the oxyanion hole were confirmed as the most important for the electrostatic stabilization of the tetracoordinate intermediate. Moreover, the role of other residues, e.g., Arg-155 and Asp-79, was also explained.
Collapse
Affiliation(s)
- Carolina Oliva
- Departament de Química Física i Centre de Recerca en Química Teòrica, Universitat de Barcelona i Parc Científic de Barcelona, C/ Martí i Franquès 1, 08028 Barcelona, Spain.
| | | | | | | |
Collapse
|
20
|
White PW, Llinas-Brunet M, Bös M. Blunting the Swiss army knife of hepatitis C virus: inhibitors of NS3/4A protease. PROGRESS IN MEDICINAL CHEMISTRY 2006; 44:65-107. [PMID: 16697895 DOI: 10.1016/s0079-6468(05)44402-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
|
21
|
Bogen S, Saksena AK, Arasappan A, Gu H, Njoroge FG, Girijavallabhan V, Pichardo J, Butkiewicz N, Prongay A, Madison V. Hepatitis C virus NS3-4A serine protease inhibitors: Use of a P2–P1 cyclopropyl alanine combination for improved potency. Bioorg Med Chem Lett 2005; 15:4515-9. [PMID: 16112862 DOI: 10.1016/j.bmcl.2005.07.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2005] [Revised: 07/06/2005] [Accepted: 07/06/2005] [Indexed: 12/21/2022]
Abstract
Modification of the P(2) and P(1) side chains of earlier P(3)-capped alpha-ketoamide inhibitor of HCV NS3 serine protease 1 resulted in the discovery of compound 24 with about 10-fold improvement in potency.
Collapse
Affiliation(s)
- S Bogen
- Chemical Research, Schering Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Bennett F, Liu YT, Saksena AK, Arasappan A, Butkiewicz N, Dasmahapatra B, Pichardo JS, Njoroge FG, Patel NM, Huang Y, Yang X. Novel inhibitors of the hepatitis C virus NS3 proteinase. Bioorg Med Chem Lett 2005; 15:4275-8. [PMID: 16087334 DOI: 10.1016/j.bmcl.2005.06.079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2005] [Accepted: 06/21/2005] [Indexed: 11/25/2022]
Abstract
The hepatitis C virus proteinase inhibitor 4-methyl-1-(phenylmethyl)-2,6-pyridinedione 1 undergoes a novel autoxidation process, on silica gel, leading to the dimer 2 as the major product, a relatively more potent inhibitor of the enzyme.
Collapse
Affiliation(s)
- Frank Bennett
- Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Arasappan A, Njoroge FG, Chan TY, Bennett F, Bogen SL, Chen K, Gu H, Hong L, Jao E, Liu YT, Lovey RG, Parekh T, Pike RE, Pinto P, Santhanam B, Venkatraman S, Vaccaro H, Wang H, Yang X, Zhu Z, Mckittrick B, Saksena AK, Girijavallabhan V, Pichardo J, Butkiewicz N, Ingram R, Malcolm B, Prongay A, Yao N, Marten B, Madison V, Kemp S, Levy O, Lim-Wilby M, Tamura S, Ganguly AK. Hepatitis C virus NS3-4A serine protease inhibitors: SAR of moiety with improved potency. Bioorg Med Chem Lett 2005; 15:4180-4. [PMID: 16087332 DOI: 10.1016/j.bmcl.2005.06.091] [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: 03/19/2005] [Revised: 06/28/2005] [Accepted: 06/29/2005] [Indexed: 11/22/2022]
Abstract
We have discovered that introduction of appropriate amino acid derivatives at P'2 position improved the binding potency of P3-capped alpha-ketoamide inhibitors of HCV NS3 serine protease. X-ray crystal structure of one of the inhibitors (43) bound to the protease revealed the importance of the P'2 moiety.
Collapse
Affiliation(s)
- A Arasappan
- Schering Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Han W, Jiang X, Hu Z, Wasserman ZR, Decicco CP. Investigation of glycine α-ketoamide HCV NS3 protease inhibitors: Effect of carboxylic acid isosteres. Bioorg Med Chem Lett 2005; 15:3487-90. [PMID: 15982872 DOI: 10.1016/j.bmcl.2005.06.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2005] [Revised: 05/27/2005] [Accepted: 06/02/2005] [Indexed: 10/25/2022]
Abstract
The design and synthesis of tetrapeptide-based alpha-ketoamides containing prime side acid isosteres HCV NS3 protease inhibitors are described. Tetrazole, sulfonic acid, and N-sulfonylcarboxamids were demonstrated to be efficient carboxylic acid replacements. Further optimization yielded a series of potent HCV NS3 protease inhibitors with IC(50) of 0.020-0.060 microM.
Collapse
Affiliation(s)
- Wei Han
- Discovery Chemistry, Pharmaceutical Research Institute, Bristol-Myers Squibb Company, P.O. Box 5400, Princeton, NJ 08543, USA.
| | | | | | | | | |
Collapse
|
25
|
Malancona S, Colarusso S, Ontoria JM, Marchetti A, Poma M, Stansfield I, Laufer R, Di Marco A, Taliani M, Verdirame M, Gonzalez-Paz O, Matassa VG, Narjes F. SAR and pharmacokinetic studies on phenethylamide inhibitors of the hepatitis C virus NS3/NS4A serine protease. Bioorg Med Chem Lett 2005; 14:4575-9. [PMID: 15357995 DOI: 10.1016/j.bmcl.2004.05.093] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2004] [Revised: 05/21/2004] [Accepted: 05/27/2004] [Indexed: 12/22/2022]
Abstract
SAR on the phenethylamide 1 (Ki 1.2 microM) in the P2- and the P'-position led to potent inhibitors, one of which showed good exposure and low clearance when administered intramuscularly to rat.
Collapse
Affiliation(s)
- Savina Malancona
- Department of Chemistry, Istituto di Ricerche di Biologia Molecolare, Merck Research Laboratories, Via Pontina Km 30.600, 00040 Pomezia, Rome, Italy
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Arasappan A, Njoroge FG, Parekh TN, Yang X, Pichardo J, Butkiewicz N, Prongay A, Yao N, Girijavallabhan V. Novel 2-oxoimidazolidine-4-carboxylic acid derivatives as Hepatitis C virus NS3-4A serine protease inhibitors: synthesis, activity, and X-ray crystal structure of an enzyme inhibitor complex. Bioorg Med Chem Lett 2004; 14:5751-5. [PMID: 15501035 DOI: 10.1016/j.bmcl.2004.09.058] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2004] [Revised: 09/15/2004] [Accepted: 09/17/2004] [Indexed: 11/28/2022]
Abstract
Synthesis and HCV NS3 serine protease inhibitory activity of some novel 2-oxoimidazolidine-4-carboxylic acid derivatives are reported. Inhibitors derived from this new P2 core exhibited activity in the low microM range. X-ray structure of an inhibitor, 15c bound to the protease is presented.
Collapse
Affiliation(s)
- Ashok Arasappan
- Schering Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Perni RB, Pitlik J, Britt SD, Court JJ, Courtney LF, Deininger DD, Farmer LJ, Gates CA, Harbeson SL, Levin RB, Lin C, Lin K, Moon YC, Luong YP, O'Malley ET, Rao BG, Thomson JA, Tung RD, Van Drie JH, Wei Y. Inhibitors of hepatitis C virus NS3.4A protease 2. Warhead SAR and optimization. Bioorg Med Chem Lett 2004; 14:1441-6. [PMID: 15006379 DOI: 10.1016/j.bmcl.2004.01.022] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2003] [Revised: 01/12/2004] [Accepted: 01/14/2004] [Indexed: 11/19/2022]
Abstract
The alpha-ketoamide warhead (e.g., 15) was found to be a practical replacement for aliphatic aldehydes in a series of HCV NS3.4A protease inhibitors. Structure-activity relationships and prime side optimization are discussed.
Collapse
Affiliation(s)
- Robert B Perni
- Vertex Pharmaceuticals Inc., 130 Waverly Street, Cambridge, MA 02139, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Portal-Núñez S, González-Navarro CJ, García-Delgado M, Vizmanos JL, Lasarte JJ, Borrás-Cuesta F. Peptide inhibitors of hepatitis C virus NS3 protease. Antivir Chem Chemother 2004; 14:225-33. [PMID: 14694985 DOI: 10.1177/095632020301400501] [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] [Indexed: 11/16/2022] Open
Abstract
Hepatitis C virus (HCV) is a highly prevalent virus and one of the major agents of chronic hepatitis. Since HCV NS3 protease is essential for the processing of HCV polyprotein, this protease is a target of choice to control HCV replication. Peptide inhibitors of NS3 were developed by selective amino acid replacement of six leader sequences, corresponding to regions of HCV polyprotein that are cleaved by NS3. The large numbers of potential 14-mer and 16-mer peptide inhibitors thus obtained were tested against NS3 using the fluorescent probe RETS1 and peptide cofactor SVVIVGRIILSGRA from NS4A protein. This afforded several peptide inhibitors with an IC50 of around 2 microM. These peptides may be good leading compounds for the development of peptidomimetics to control HCV replication in the treatment of chronic hepatitis C.
Collapse
Affiliation(s)
- Sergio Portal-Núñez
- Department of Genetics, Faculty of Science, University of Navarra, Pamplona, Spain
| | | | | | | | | | | |
Collapse
|
29
|
Meanwell NA, Serrano-Wu MH, Snyder LB. Chapter 22. Non-HIV antiviral agents. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2004; 38:213-228. [PMID: 32287463 PMCID: PMC7126470 DOI: 10.1016/s0065-7743(03)38023-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
This chapter focuses on non-HIV antiviral agents. The development of antiviral agents to treat non-HIV infections is largely focused on therapies for the treatment of chronic hepatitis infections B and C. Nucleoside analog continue to be the mainstay of Hepatitis B Virus (HBV) therapeutics. The first small molecule inhibitor of Hepatitis C Virus (HCV), the NS3 protease inhibitor BILN-2061, entered phase 2 clinical trials, producing a striking reduction in viral load in treated individuals. The development of the HCV replicon system and its application to screening for antiviral agents provided tangible benefit with the disclosure of mechanistically and structurally diverse HCV inhibitors. Adefovir dipivoxil has been approved in the United States and the European Union for the treatment of HBV, providing a second small molecule antiviral to add to lamivudine (3TC) and the injectable protein IFNα as the only approved agents for treating HBV infection. The chapter also provides details of the inhibitors of hepatitis B and C virus, the inhibitors of simplex virus and human cytomegalovirus, the inhibitors of respiratory viruses and the inhibitors of West Nile virus and Papilloma virus.
Collapse
Affiliation(s)
- Nicholas A Meanwell
- Department of Chemistry, The Bristol-Myers Squibb Pharmaceutical Research Institute 5 Research Parkway, Wallingford, CT 06492, USA
| | - Michael H Serrano-Wu
- Department of Chemistry, The Bristol-Myers Squibb Pharmaceutical Research Institute 5 Research Parkway, Wallingford, CT 06492, USA
| | - Lawrence B Snyder
- Department of Chemistry, The Bristol-Myers Squibb Pharmaceutical Research Institute 5 Research Parkway, Wallingford, CT 06492, USA
| |
Collapse
|
30
|
Victor F, Lamar J, Snyder N, Yip Y, Guo D, Yumibe N, Johnson RB, Wang QM, Glass JI, Chen SH. P1 and P3 optimization of novel bicycloproline P2 bearing tetrapeptidyl α-ketoamide based HCV protease inhibitors. Bioorg Med Chem Lett 2004; 14:257-61. [PMID: 14684338 DOI: 10.1016/j.bmcl.2003.09.075] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
With the aim of discovering potent and selective HCV protease inhibitors, we synthesized and evaluated a series of 1a based tetrapeptidyl ketoamides with additional modification(s) at P1', P1, and P3 positions. As a result of this effort, we found that replacement of the P3 valine with tert-leucine resulted in the discovery of a series of inhibitors (e.g., 3a, 3c, and 4c) endowed with improved enzyme and/or cellular activity relative to 1a. When dosed to F-344 rats orally at 50mg/kg, 3a achieved 2.5x higher liver and plasma exposure in comparison to that detected with 1a.
Collapse
Affiliation(s)
- Frantz Victor
- Lilly Research Laboratory, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Chen JJ, Deshpande SV. Rapid synthesis of α-ketoamides using microwave irradiation–simultaneous cooling method. Tetrahedron Lett 2003. [DOI: 10.1016/j.tetlet.2003.09.180] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|