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Chen CY, Elmore S, Lalami I, Neal H, Vadlamudi RK, Raj GV, Ahn JM. Oligo-benzamide-based peptide mimicking tools for modulating biology. Methods Enzymol 2024; 698:221-245. [PMID: 38886033 DOI: 10.1016/bs.mie.2024.04.022] [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] [Indexed: 06/20/2024]
Abstract
The oligo-benzamide scaffold is a rigid organic framework that can hold 2-3 functional groups as O-alkyl substituents on its benzamide units, mirroring their natural arrangement in an α-helix. Oligo-benzamides demonstrated outstanding α-helix mimicry and can be readily synthesized by following high yielding and iterative reaction steps in both solution-phase and solid-phase. A number of oligo-benzamides have been designed to emulate α-helical peptide segments in biologically active proteins and showed strong protein binding, in turn effectively disrupting protein-protein interactions in vitro and in vivo. In this chapter, the design of oligo-benzamides for mimicking α-helices, efficient synthetic routes for producing them, and their biomedical studies showing remarkable potency in inhibiting protein functions are discussed.
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Affiliation(s)
- Chia-Yuan Chen
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX, United States
| | - Scott Elmore
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX, United States
| | - Ismail Lalami
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX, United States
| | - Henry Neal
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX, United States
| | - Ratna K Vadlamudi
- Department of Obstetrics and Gynecology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Ganesh V Raj
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Jung-Mo Ahn
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX, United States.
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2
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Niu C, Du DM. Recent Advances in Organocatalyzed Asymmetric sulfa-Michael Addition Triggered Cascade Reactions. CHEM REC 2023:e202200258. [PMID: 36594608 DOI: 10.1002/tcr.202200258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 12/14/2022] [Indexed: 01/04/2023]
Abstract
The sulfa-Michael addition reaction is a crucial subset of the Michael addition reaction, and aroused the interest of numerous synthetic biologists and chemists. In particular, sulfa-Michael addition triggered cascade reaction has developed quickly in recent years because it offers an efficient method to construct C-S bonds and other bonds in one approach, which is widely applicable for building chiral pharmaceuticals, their intermediates, and natural compounds. This review emphasizes the recent advancements in sulfa-Michael addition-triggered cascade reactions for the stereoselective synthesis of sulfur-containing compounds, including sulfa-Michael/aldol, sulfa-Michael/Henry, sulfa-Michael/Michael, sulfa-Michael/Mannich and some sulfa-Michael triggered multi-step processes. Moreover, some reaction mechanisms and derivatization experiments are introduced appropriately.
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Affiliation(s)
- Cheng Niu
- Key Laboratory of Medical Molecule Science & Pharmaceutics Engineering (Ministry of Industry and Information Technology), School of Chemistry and Chemical Engineering, Beijing Institute of Technology, No. 5 Zhongguancun South Street, Beijing, 100081, People's Republic of China
| | - Da-Ming Du
- Key Laboratory of Medical Molecule Science & Pharmaceutics Engineering (Ministry of Industry and Information Technology), School of Chemistry and Chemical Engineering, Beijing Institute of Technology, No. 5 Zhongguancun South Street, Beijing, 100081, People's Republic of China
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3
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Tandem annulation and 1,2-alkyl migration reactions of α-bromo-β-oxoamides and amines: Access to polysubstituted pyrrolin-4-ones. Tetrahedron 2022. [DOI: 10.1016/j.tet.2022.132718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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4
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Ciber L, Ričko S, Gregorc J, Pozgan F, Svete J, Brodnik H, Štefane B, Grošelj U. Mechanistic Insights into Annulation of Arylidene‐Δ2‐pyrrolin‐4‐ones by Cinchona Squaramide‐Based Organocatalysts. Adv Synth Catal 2022. [DOI: 10.1002/adsc.202101369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Luka Ciber
- University of Ljubljana, Faculty of Chemistry and Chemical Technology SLOVENIA
| | - Sebastijan Ričko
- Univerza v Ljubljani Fakulteta za Kemijo in Kemijsko tehnologijo SLOVENIA
| | - Jure Gregorc
- University of Ljubljana Faculty of Chemistry and Chemical Technology SLOVENIA
| | | | | | | | | | - Uroš Grošelj
- University of Ljubljana Faculty of Chemistry and Chemical Technology SLOVENIA
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5
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Abstract
Arylidene-Δ2-pyrrolin-4-ones undergo organocatalyzed double spirocyclization with 3-isothiocianato oxindoles in a domino 1,4/1,2-addition sequence. The products contain three contiguous stereocenters (ee up to 98%, dr up to 99:1, 12 examples). The absolute configuration of the major diastereomer was determined by single crystal X-ray analysis. Along with heterocyclic Michael acceptors based on oxazolone, isoxazolone, thiazolidinone, pyrazolone, and pyrimidinedione, the reported results display the applicability of unsaturated Δ2-pyrrolin-4-ones (pyrrolones) for the organocatalyzed construction of 3D-rich pyrrolone-containing heterocycles.
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Khan T, Lawrence AJ, Azad I, Raza S, Joshi S, Khan AR. Computational Drug Designing and Prediction Of Important Parameters Using in silico Methods- A Review. Curr Comput Aided Drug Des 2020; 15:384-397. [PMID: 30914032 DOI: 10.2174/1573399815666190326120006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/28/2019] [Accepted: 02/25/2019] [Indexed: 01/02/2023]
Abstract
BACKGROUND Computational or in silico studies are undertaken to assess the drug like properties of lead compounds. These studies help in fast prediction of relevant properties. OBJECTIVE Through this review, an effort is made to encapsulate some of the important parameters which should be met by a compound for it to be considered as a potential drug candidate along with an overview of automated softwares which can be used for making various predictions. METHODS Drug uptake, its absorption, evacuation and associated hazardous effects are important factors for consideration in drug designing and should be known in early stages of drug development. Several important physicochemical properties like molecular weight, polar surface area (PSA), molecular flexibility etc. have to be taken into consideration in drug designing. Toxicological assessment is another important aspect of drug discovery which predicts the safety and adverse effects of a drug. RESULTS Additionally, bioactivity scores of probable drug leads against various human receptors can also be predicted to evaluate the probability of them to act as a potential drug candidate. The in vivo biological targets of a molecule can also be efficiently predicted by molecular docking studies. CONCLUSION Some important software like iGEMDOCK, AutoDock, OSIRIS property explorer, Molinspiration, MetaPrint2D, admetSAR and their working methodology and principle of working have been summarized in this review.
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Affiliation(s)
- Tahmeena Khan
- Department of Chemistry, Integral University, Lucknow, 226026, U.P., India
| | - Alfred J Lawrence
- Department of Chemistry, Isabella Thoburn College, Lucknow, 226007, U.P., India
| | - Iqbal Azad
- Department of Chemistry, Integral University, Lucknow, 226026, U.P., India
| | - Saman Raza
- Department of Chemistry, Isabella Thoburn College, Lucknow, 226007, U.P., India
| | - Seema Joshi
- Department of Chemistry, Isabella Thoburn College, Lucknow, 226007, U.P., India
| | - Abdul Rahman Khan
- Department of Chemistry, Integral University, Lucknow, 226026, U.P., India
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7
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Grošelj U, Ciber L, Gnidovec J, Testen Ž, Požgan F, Štefane B, Tavčar G, Svete J, Ričko S. Synthesis of Spiro‐Δ
2
‐Pyrrolin‐4‐One Pseudo Enantiomers
via
an Organocatalyzed Sulfa‐Michael/Aldol Domino Sequence. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201900747] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Uroš Grošelj
- Faculty of Chemistry and ChemicalTechnology, University of Ljubljana Večna pot 113 SI-1000 Ljubljana, Slovenia
| | - Luka Ciber
- Faculty of Chemistry and ChemicalTechnology, University of Ljubljana Večna pot 113 SI-1000 Ljubljana, Slovenia
| | - Jan Gnidovec
- Faculty of Chemistry and ChemicalTechnology, University of Ljubljana Večna pot 113 SI-1000 Ljubljana, Slovenia
| | - Žan Testen
- Faculty of Chemistry and ChemicalTechnology, University of Ljubljana Večna pot 113 SI-1000 Ljubljana, Slovenia
| | - Franc Požgan
- Faculty of Chemistry and ChemicalTechnology, University of Ljubljana Večna pot 113 SI-1000 Ljubljana, Slovenia
| | - Bogdan Štefane
- Faculty of Chemistry and ChemicalTechnology, University of Ljubljana Večna pot 113 SI-1000 Ljubljana, Slovenia
| | - Gašper Tavčar
- Inorganic Chemistry and Technology – K1J. Stefan Institute Jamova 39 1000 Ljubljana Slovenia
| | - Jurij Svete
- Faculty of Chemistry and ChemicalTechnology, University of Ljubljana Večna pot 113 SI-1000 Ljubljana, Slovenia
| | - Sebastijan Ričko
- Faculty of Chemistry and ChemicalTechnology, University of Ljubljana Večna pot 113 SI-1000 Ljubljana, Slovenia
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Ričko S, Meden A, Ciber L, Štefane B, Požgan F, Svete J, Grošelj U. Construction of Vicinal Tetrasubstituted Stereogenic Centersviaa Mannich-Type Organocatalyzed Addition of Δ2-Pyrrolin-4-ones to Isatin Imines. Adv Synth Catal 2018. [DOI: 10.1002/adsc.201701384] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Sebastijan Ričko
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Večna pot 113 SI-1000 Ljubljana Slovenia
| | - Anže Meden
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Večna pot 113 SI-1000 Ljubljana Slovenia
| | - Luka Ciber
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Večna pot 113 SI-1000 Ljubljana Slovenia
| | - Bogdan Štefane
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Večna pot 113 SI-1000 Ljubljana Slovenia
| | - Franc Požgan
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Večna pot 113 SI-1000 Ljubljana Slovenia
| | - Jurij Svete
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Večna pot 113 SI-1000 Ljubljana Slovenia
| | - Uroš Grošelj
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Večna pot 113 SI-1000 Ljubljana Slovenia
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Hybrid 2D/3D-quantitative structure-activity relationship and modeling studies perspectives of pepstatin A analogs as cathepsin D inhibitors. Future Med Chem 2017; 10:5-26. [PMID: 29235371 DOI: 10.4155/fmc-2017-0077] [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: 01/08/2023] Open
Abstract
AIM Cathepsin D, one of the attractive targets in the treatment of breast cancer, has been implicated in HIV neuropathogenesis with potential proteolytic effects on chemokines. Methodology/result: Diverse modeling tools were used to reveal the key structural features affecting the inhibitory activities of 78 pepstatin A analogs. Analyses were performed to investigate the stability, rationality and fluctuation of the analogs. Results showed a clear correlation between the experimental and predicted activities of the analogs as well as the variation in their activities relative to structural modifications. CONCLUSION The insight gained from this study offers theoretical references for understanding the mechanism of action of cathepsin D and will aid in the design of more potent and clinically-relevant drugs. Graphical abstract [Formula: see text].
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10
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Photolysis and cycloaddition reactivity of diferrocenyl substituted cyclopentadienone. Chem Res Chin Univ 2016. [DOI: 10.1007/s40242-016-6158-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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11
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Miaskiewicz S, Weibel JM, Pale P, Blanc A. Gold(I)-Catalyzed Cyclization/Nucleophilic Substitution of 1-(N-Sulfonylazetidin-2-yl) Ynones into N-Sulfonylpyrrolin-4-ones. Org Lett 2016; 18:844-7. [DOI: 10.1021/acs.orglett.6b00135] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Solène Miaskiewicz
- Laboratoire de Synthèse,
Réactivité Organiques et Catalyse, Institut de Chimie, UMR 7177-CNRS, Université de Strasbourg, 4 rue Blaise Pascal, 67070 Strasbourg, France
| | - Jean-Marc Weibel
- Laboratoire de Synthèse,
Réactivité Organiques et Catalyse, Institut de Chimie, UMR 7177-CNRS, Université de Strasbourg, 4 rue Blaise Pascal, 67070 Strasbourg, France
| | - Patrick Pale
- Laboratoire de Synthèse,
Réactivité Organiques et Catalyse, Institut de Chimie, UMR 7177-CNRS, Université de Strasbourg, 4 rue Blaise Pascal, 67070 Strasbourg, France
| | - Aurélien Blanc
- Laboratoire de Synthèse,
Réactivité Organiques et Catalyse, Institut de Chimie, UMR 7177-CNRS, Université de Strasbourg, 4 rue Blaise Pascal, 67070 Strasbourg, France
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12
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McConnell RM, Inapudi K, Kadasala N, Yarlagadda K, Velusamy P, McConnell MS, Green A, Trana C, Sayyar K, McConnell JS. New cathepsin D inhibitor library utilizing hydroxyethyl isosteres with cyclic tertiary amines. Med Chem 2013; 8:1146-54. [PMID: 22830497 DOI: 10.2174/1573406411208061146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Revised: 05/10/2012] [Accepted: 05/21/2012] [Indexed: 12/23/2022]
Abstract
The design and synthesis of hydroxyethylamine isosteres as inhibitors of cathepsin D based on SAR data have been accomplished. A library of 96 of these hydroxyethylamine isosteres are described and many have proven to be very potent inhibitors of human cathepsin D activity as measured using a fluorometric assay technique, via peptide substrate Ac-Glu-Glu(Edans)-Lys-Pro-Ile-Cys-Phe-Phe-Arg-Leu-Gly-Lys(Methyl Red)-Glu-NH(2). Compounds showing strongest inhibition of cathepsin D activity were those that contain a hydroxyethyl-N'-2- or N'-(4-chlorophenyl)piperazine moiety (IC(50) values range from 0.55 to 8.5 nM), with N'-(2-pyrimidyl)piperizine (IC(50) values range from 0.5 to 21.6 nM), with N-N'- L-piperazinocolinamide (IC(50) values range from 0.001 - 0.25 nM), or N-N'-L-piperazinocolin-N-methylamide (IC(50) values range from 0.015 - 7.3 nM).
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Affiliation(s)
- Rose M McConnell
- Department of Chemistry, Western Illinois University, Macomb, IL 61455, USA.
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13
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Hydrogen-bonded synthetic mimics of protein secondary structure as disruptors of protein-protein interactions. Curr Top Microbiol Immunol 2011; 348:1-23. [PMID: 20827522 DOI: 10.1007/82_2010_91] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Small molecules which can mimic the key structural facets of protein secondary structure, in particular the α-helix, β-strand, and β-sheet, have been shown to be potent disruptors of protein-protein interactions. Researchers have recently taken the organizational imitation of protein secondary structure to a new level by using intramolecular hydrogen bonds as stabilizing forces in these small molecule mimetics. The inclusion of these interactions invokes a conformational bias of the system, allowing for greater control of the appearance, and thus often function, of these molecules by design.
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14
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Loughlin WA, Tyndall JDA, Glenn MP, Hill TA, Fairlie DP. Update 1 of: Beta-Strand Mimetics. Chem Rev 2011; 110:PR32-69. [DOI: 10.1021/cr900395y] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Wendy A. Loughlin
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - Joel D. A. Tyndall
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - Matthew P. Glenn
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - Timothy A. Hill
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - David P. Fairlie
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
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Smith AB, Charnley AK, Hirschmann R. Pyrrolinone-based peptidomimetics. "Let the enzyme or receptor be the judge". Acc Chem Res 2011; 44:180-93. [PMID: 21175156 PMCID: PMC3078624 DOI: 10.1021/ar1001186] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Peptides and proteins, evolved by nature to perform vital biological functions, would constitute ideal candidates for therapeutic intervention were it not for their generally poor pharmacokinetic profiles. Nonpeptide peptidomimetics have thus been pursued because they might overcome these limitations while maintaining both the potency and selectivity of the parent peptide or protein. Since the late 1980s, we have sought to design, synthesize, and evaluate a novel, proteolytically stable nonpeptide peptidomimetic scaffold consisting of a repeating structural unit amenable to iterative construction; a primary concern is maintaining both the appropriate peptide-like side-chains and requisite hydrogen bonding. In this Account, we detail how efforts in the Smith-Hirschmann laboratories culminated in the identification of the 3,5-linked polypyrrolinone scaffold. We developed effective synthetic protocols, both in solution and on solid supports, for iterative construction of diverse polypyrrolinones that present functionalized peptide-like side-chains. As a result of the rigid nature of the pyrrolinone scaffold, control over the backbone conformation could be exerted by modulation of the stereogenicity of the constituent monomers and the network of intramolecular hydrogen bonding. The extended conformation of the homochiral 3,5-linked polypyrrolinone scaffold proved to be an excellent mimic for β-strands and β-sheets. Application to enzyme inhibitor design and synthesis led not only to modest inhibitors of the aspartic acid protease renin and the matrix metalloprotease class of enzymes, but importantly to bioavailable HIV-1 protease inhibitors with subnanomolar binding constants. The design and synthesis of a competent peptide-pyrrolinone hybrid ligand for the class II major histocompatibility complex (MHC) antigen protein HLA-DR1 further demonstrated the utility of the 3,5-polypyrrolinone motif as a mimic for the extended polyproline type II peptide backbone. Equally important, we sought to define, by synthesis, the additional conformational space accessible to the polypyrrolinone structural motif, with the ultimate goal of accessing pyrrolinone-based turn and helix mimetics. Toward this end, a mono-N-methylated bispyrrolinone was found to adopt an extended helical array in the solid state. Subsequent synthesis of d,l-alternating (heterochiral) tetrapyrrolinones both validated the expected turn conformations in solution and led to a functionally active mimetic of a peptidal β-turn (similar to somatostatin). Finally, the design, synthesis, and structural evaluation of both acyclic and cyclic heterochiral (that is, d,l-alternating) hexapyrrolinones yielded nanotube-like assemblies in the solid state. Taken together, these results illustrate the remarkable potential of the 3,5-linked polypyrrolinone scaffold as β-strand, β-sheet, β-turn, and potentially helical peptidomimetics.
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Affiliation(s)
- Amos B Smith
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
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16
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Targeting Protein–Protein Interactions and Fragment-Based Drug Discovery. Top Curr Chem (Cham) 2011; 317:145-79. [DOI: 10.1007/128_2011_265] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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17
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Freidinger RM, Veber DF. Obituary. J Pept Sci 2009. [DOI: 10.1002/psc.1186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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18
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Wilson AJ. Inhibition of protein-protein interactions using designed molecules. Chem Soc Rev 2009; 38:3289-300. [PMID: 20449049 DOI: 10.1039/b807197g] [Citation(s) in RCA: 198] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Although many cellular processes depend upon enzymatic reactions, protein-protein interactions (PPIs) mediate a large number of important regulatory pathways and thus play a central role in disease development. In order to understand and selectively inhibit cellular signalling pathways, there is a pressing need for small molecules that target PPIs, particularly in the context of pharmaceutical development. This tutorial review will introduce the relevance of PPIs to chemical biology and highlight the key challenges in designing inhibitors. Some of the successes using conventional approaches to the identification of small-molecule PPI inhibitors will be highlighted, and also the reasons why these approaches have not always proven successful. Several general approaches tailored to particular protein topologies are emerging for the design of scaffolds that inhibit PPIs-these will form the major content of this review. Finally a summary of the challenges to be faced in developing inhibitors of PPIs into drug leads and how these challenges may differ from those encountered with enzyme-like targets will be given.
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Affiliation(s)
- Andrew J Wilson
- School of Chemistry, University of Leeds, Woodhouse Lane, LS2 9JT, Leeds, UK.
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19
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Balan G, Bauman J, Bhattacharya S, Castrodad M, Healy DR, Herr M, Humphries P, Jennings S, Kalgutkar AS, Kapinos B, Khot V, Lazarra K, Li M, Li Y, Neagu C, Oliver R, Piotrowski DW, Price D, Qi H, Simmons HA, Southers J, Wei L, Zhang Y, Paralkar VM. The discovery of novel calcium sensing receptor negative allosteric modulators. Bioorg Med Chem Lett 2009; 19:3328-32. [PMID: 19442519 DOI: 10.1016/j.bmcl.2009.04.044] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2009] [Revised: 04/06/2009] [Accepted: 04/08/2009] [Indexed: 11/26/2022]
Abstract
The design and profile of a series of zwitterionic calcium sensing receptor negative allosteric modulators is described. Evaluation of key analogues using a rat model demonstrate a robust response, significantly improved potency over ronacaleret and have the potential as an oral, anabolic treatment for osteoporosis.
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Affiliation(s)
- Gayatri Balan
- Pfizer Global Research and Development, Groton/New London Laboratories, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA
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20
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Zhang R, Nickl CK, Mamai A, Flemer S, Natarajan A, Dostmann WR, Madalengoitia JS. Poly-L-proline type II peptide mimics as probes of the active site occupancy requirements of cGMP-dependent protein kinase. ACTA ACUST UNITED AC 2007; 66:151-9. [PMID: 16138853 DOI: 10.1111/j.1399-3011.2005.00280.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Based on the X-ray crystal structure of cAMP-dependent protein kinase (PKA) with the endogenous inhibitor PKI and the X-ray crystal structure of cyclin-dependent kinase 2 (CDK2) with a substrate peptide, a proposal is put forth that some protein kinases bind peptide substrates in their active sites in the poly-L-proline type II (PPII) conformation. In this work, PPII peptide mimics are evaluated as pseudosubstrate inhibitors of cGMP-dependent protein kinase (PKG) to explore if PKG also binds peptide substrates in the PPII conformation. Inhibition data of our PPII mimetics provide evidence that the P-1, P-2, and P-3 residues of substrate peptides bind in the PPII conformation (phi approximately -75 degrees, psi approximately 145 degrees). In addition, the inhibition data also suggest that the P-1, P-2, and P-3 residues in substrate peptides bind with a gauche(-) chi1 angle.
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Affiliation(s)
- R Zhang
- Department of Chemistry, University of Vermont, Burlington, VT 05405, USA
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Brown AD, Bunnage ME, Glossop PA, James K, Jones R, Lane CAL, Lewthwaite RA, Mantell S, Perros-Huguet C, Price DA, Trevethick M, Webster R. The discovery of long acting β2-adrenoreceptor agonists. Bioorg Med Chem Lett 2007; 17:4012-5. [PMID: 17498952 DOI: 10.1016/j.bmcl.2007.04.081] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2007] [Revised: 04/19/2007] [Accepted: 04/25/2007] [Indexed: 11/19/2022]
Abstract
The design and profile of a series of saligenin containing long acting beta(2)-adrenoreceptor agonists is described. Evaluation of these analogues using a guinea-pig tissue model demonstrates that analogues within this series have significantly longer durations of action than salmeterol and have the potential for a once daily profile in human.
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Affiliation(s)
- Alan D Brown
- Pfizer Global Research and Development, Sandwich Laboratories, Ramsgate Road, Sandwich, Kent CT13 9NJ, UK
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22
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Yin H, Hamilton AD. Strategies for targeting protein-protein interactions with synthetic agents. Angew Chem Int Ed Engl 2006; 44:4130-63. [PMID: 15954154 DOI: 10.1002/anie.200461786] [Citation(s) in RCA: 375] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The development of small-molecule modulators of protein-protein interactions is a formidable goal, albeit one that possesses significant potential for the discovery of novel therapeutics. Despite the daunting challenges, a variety of examples exists for the inhibition of two large protein partners with low-molecular-weight ligands. This review discusses the strategies for targeting protein-protein interactions and the state of the art in the rational design of molecules that mimic the structures and functions of their natural targets.
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Affiliation(s)
- Hang Yin
- Yale University, New Haven, CT, USA
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23
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Smith AB, Charnley AK, Harada H, Beiger JJ, Cantin LD, Kenesky CS, Hirschmann R, Munshi S, Olsen DB, Stahlhut MW, Schleif WA, Kuo LC. Design, synthesis, and biological evaluation of monopyrrolinone-based HIV-1 protease inhibitors possessing augmented P2' side chains. Bioorg Med Chem Lett 2005; 16:859-63. [PMID: 16298527 DOI: 10.1016/j.bmcl.2005.11.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2005] [Accepted: 11/03/2005] [Indexed: 11/28/2022]
Abstract
A series of monopyrrolinone-based HIV-1 protease inhibitors possessing rationally designed P2' side chains have been synthesized and evaluated for activity against wild-type HIV-1 protease. The most potent inhibitor displays subnanomolar potency in vitro for the wild-type HIV-1 protease. Additionally, the monopyrrolinone inhibitors retain potency in cellular assays against clinically significant mutant forms of the virus. X-ray structures of these inhibitors bound in the wild-type enzyme reveal important insights into the observed biological activity.
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Affiliation(s)
- Amos B Smith
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.
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24
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Yin H, Hamilton AD. Strategien zur Modulation von Protein-Protein-Wechselwirkungen mit synthetischen Substanzen. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200461786] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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25
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Affiliation(s)
- Wendy A Loughlin
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia.
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26
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27
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Tu RS, Tirrell M. Bottom-up design of biomimetic assemblies. Adv Drug Deliv Rev 2004; 56:1537-63. [PMID: 15350288 DOI: 10.1016/j.addr.2003.10.047] [Citation(s) in RCA: 168] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2003] [Accepted: 05/15/2004] [Indexed: 11/16/2022]
Abstract
Nature has evolved the ability to assemble a variety of molecules into functional architectures that can specifically bind cellular ligands. Mimicking this strategy requires the design of a set of multifaceted molecules, where elements that direct assembly were conjugated to biologically specific components. The development of functional molecular building-blocks that assemble to form compartments for therapeutics addresses the desire to have controllable morphologies that interact with biological interfaces at nanometer length scales. The practical application of such 'bottom-up' assemblies requires the ability to predict the type of aggregated structure and to synthesize molecules in a highly controlled fashion. This bottom-up approach results in a molecular platform that mimics biological systems with potential for encapsulating and delivering drug molecules.
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Affiliation(s)
- Raymond S Tu
- Department of Chemical Engineering, College of Engineering, Office of the Dean of Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106-5130, USA
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28
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29
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Shenai BR, Lee BJ, Alvarez-Hernandez A, Chong PY, Emal CD, Neitz RJ, Roush WR, Rosenthal PJ. Structure-activity relationships for inhibition of cysteine protease activity and development of Plasmodium falciparum by peptidyl vinyl sulfones. Antimicrob Agents Chemother 2003; 47:154-60. [PMID: 12499184 PMCID: PMC149004 DOI: 10.1128/aac.47.1.154-160.2003] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Plasmodium falciparum cysteine proteases falcipain-2 and falcipain-3 appear to be required for hemoglobin hydrolysis by intraerythrocytic malaria parasites. Previous studies showed that peptidyl vinyl sulfone inhibitors of falcipain-2 blocked the development of P. falciparum in culture and exerted antimalarial effects in vivo. We now report the structure-activity relationships for inhibition of falcipain-2, falcipain-3, and parasite development by 39 new vinyl sulfone, vinyl sulfonate ester, and vinyl sulfonamide cysteine protease inhibitors. Levels of inhibition of falcipain-2 and falcipain-3 were generally similar, and many potent compounds were identified. Optimal antimalarial compounds, which inhibited P. falciparum development at low nanomolar concentrations, were phenyl vinyl sulfones, vinyl sulfonate esters, and vinyl sulfonamides with P(2) leucine moieties. Our results identify independent structural correlates of falcipain inhibition and antiparasitic activity and suggest that peptidyl vinyl sulfones have promise as antimalarial agents.
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Affiliation(s)
- Bhaskar R Shenai
- Department of Medicine, San Francisco General Hospital, University of California, San Francisco, California 94143, USA.
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30
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Saha B, Nandy JP, Shukla S, Siddiqui I, Iqbal J. Stereoselective synthesis of beta-substituted phenylalanine-beta-phenylisoserine-derived tripeptides using N-cinnamoyl-L-proline as template: synthesis of structural analogues of HIV protease inhibitors. J Org Chem 2002; 67:7858-60. [PMID: 12398514 DOI: 10.1021/jo0109826] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
N-Cinnamoyl-L-proline can be used as a template on which beta-substituted phenylalanine and beta-phenylisoserine residues can be synthesized leading to tripeptide derivatives as structural analogues of HIV protease inhibitors.
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Affiliation(s)
- Biswajit Saha
- Department of Chemistry, Indian Institute of Technology, Kanpur 208 016, India
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31
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Gao J, Sudoh M, Aubé J, Borchardt RT. Transport characteristics of peptides and peptidomimetics: I. N-methylated peptides as substrates for the oligopeptide transporter and P-glycoprotein in the intestinal mucosa. THE JOURNAL OF PEPTIDE RESEARCH : OFFICIAL JOURNAL OF THE AMERICAN PEPTIDE SOCIETY 2001; 57:316-29. [PMID: 11328489 DOI: 10.1046/j.1397-002x.2001.00000.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Peptides and peptidomimetics often exhibit poor oral bioavailability due to their metabolic instability and low permeation across the intestinal mucosa. N-Methylation has been used successfully in peptide-based drug design in an attempt to improve the metabolic stability of a peptide-based lead compound. However, the effect of N-methylation on the absorption of peptides through the intestinal mucosa is not well understood, particularly when transporters, i.e. the oligopeptide transporter (OPT) and P-glycoprotein (P-gp), modulate the passive diffusion of these types of molecules. To examine this, terminally free and terminally modified (N-acetylated and C-amidated) analogs of H-Ala-Phe-Ala-OH with N-methyl groups on either the Ala-Phe or Phe-Ala peptide bond were synthesized. Transport studies using Caco-2 cell monolayers, an in vitro model of the intestinal mucosa, showed that N-methylation of the Ala-Phe peptide bond of H-Ala-Phe-Ala-OH stabilized the molecule to protease degradation, and the resulting analog exhibited significant substrate activity for OPT. However, N-methylation of the Phe-Ala peptide bond of H-Ala-Phe-Ala-OH did not stabilize the molecule to protease degradation, and the substrate activity of the resulting molecule for OPT could not be determined. Interestingly, N-methylation of the Phe-Ala peptide bond of the terminally modified tripeptide Ac-Ala-Phe-Ala-NH2 decreased the substrate activity of the molecule for the efflux transporter P-gp. In contrast, N-methylation of the Ala-Phe peptide bond of the terminally modified tripeptide Ac-Ala-Phe-Ala-NH2 increased the substrate activity of the molecule for P-gp.
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Affiliation(s)
- J Gao
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence 66047, USA
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32
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Smith AB, Nittoli T, Sprengeler PA, Duan JJ, Liu RQ, Hirschmann RF. Design, synthesis, and evaluation of a pyrrolinone-based matrix metalloprotease inhibitor. Org Lett 2000; 2:3809-12. [PMID: 11101425 DOI: 10.1021/ol000254p] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text] A pyrrolinone-based hydroxamate matrix metalloprotease inhibitor, (-)-1, has been designed and synthesized. Enzymatic assay revealed that (-)-1 inhibited three of the ten matrix metalloprotease enzymes examined and as such represents a new, potentially important lead structure.
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Affiliation(s)
- A B Smith
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
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33
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Shin I, Lee M, Lee J, Jung M, Lee W, Yoon J. Synthesis of optically active phthaloyl D-aminooxy acids from L-amino acids or L-hydroxy acids as building blocks for the preparation of aminooxy peptides. J Org Chem 2000; 65:7667-75. [PMID: 11076633 DOI: 10.1021/jo0006573] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- I Shin
- Department of Chemistry and Department of Biochemistry, Yonsei University, Seoul 120-749, Korea.
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34
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Smith AB, Wang W, Sprengeler PA, Hirschmann R. Design, Synthesis, and Solution Structure of a Pyrrolinone-Based β-Turn Peptidomimetic. J Am Chem Soc 2000. [DOI: 10.1021/ja002964w] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Amos B. Smith
- Department of Chemistry University of Pennsylvania Philadelphia, Pennsylvania 19104
| | - Wenyong Wang
- Department of Chemistry University of Pennsylvania Philadelphia, Pennsylvania 19104
| | - Paul A. Sprengeler
- Department of Chemistry University of Pennsylvania Philadelphia, Pennsylvania 19104
| | - Ralph Hirschmann
- Department of Chemistry University of Pennsylvania Philadelphia, Pennsylvania 19104
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Smith AB, Liu H, Okumura H, Favor DA, Hirschmann R. Synthesis of polypyrrolinones on solid support. Org Lett 2000; 2:2041-4. [PMID: 10891225 DOI: 10.1021/ol005931u] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text] An efficient, three-step iterative synthesis of polypyrrolinones has been achieved on solid support, setting the stage for the construction of a wide variety of libraries based on the pyrrolinone scaffold. Central to the approach is an effective end-game sequence featuring pyrrolinone ring construction with traceless release from the solid support.
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Affiliation(s)
- A B Smith
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
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36
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Smith AB, Liu H, Hirschmann R. A second-generation synthesis of polypyrrolinone nonpeptidomimetics: prelude to the synthesis of polypyrrolinones on solid support. Org Lett 2000; 2:2037-40. [PMID: 10891224 DOI: 10.1021/ol0059293] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[reaction: see text] A second-generation asymmetric synthesis of polypyrrolinones (3) has been achieved exploiting scalemic alpha-aminolactones (1) as building blocks. Imine formation between an appropriate lactone (1) and aldehyde (2), followed in turn by pyrrolinone ring construction promoted by KHMDS in the presence of 18-crown-6 and modified Swern oxidation furnished pyrrolinone aldehyde 3. This iterative, efficient three-step protocol paves the way for the synthesis of polypyrrolinones on solid support.
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Affiliation(s)
- A B Smith
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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37
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Smith AB, Benowitz AB, Sprengeler PA, Barbosa J, Guzman MC, Hirschmann R, Schweiger EJ, Bolin DR, Nagy Z, Campbell RM, Cox DC, Olson GL. Design and Synthesis of a Competent Pyrrolinone−Peptide Hybrid Ligand for the Class II Major Histocompatibility Complex Protein HLA-DR1. J Am Chem Soc 1999. [DOI: 10.1021/ja991251e] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Amos B. Smith
- Contribution from the Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, and Department of Inflammation/Autoimmune Diseases, Hoffman-La Roche, Inc., Nutley, New Jersey 07110
| | - Andrew B. Benowitz
- Contribution from the Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, and Department of Inflammation/Autoimmune Diseases, Hoffman-La Roche, Inc., Nutley, New Jersey 07110
| | - Paul A. Sprengeler
- Contribution from the Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, and Department of Inflammation/Autoimmune Diseases, Hoffman-La Roche, Inc., Nutley, New Jersey 07110
| | - Joseph Barbosa
- Contribution from the Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, and Department of Inflammation/Autoimmune Diseases, Hoffman-La Roche, Inc., Nutley, New Jersey 07110
| | - Mark C. Guzman
- Contribution from the Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, and Department of Inflammation/Autoimmune Diseases, Hoffman-La Roche, Inc., Nutley, New Jersey 07110
| | - Ralph Hirschmann
- Contribution from the Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, and Department of Inflammation/Autoimmune Diseases, Hoffman-La Roche, Inc., Nutley, New Jersey 07110
| | - Edwin J. Schweiger
- Contribution from the Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, and Department of Inflammation/Autoimmune Diseases, Hoffman-La Roche, Inc., Nutley, New Jersey 07110
| | - David R. Bolin
- Contribution from the Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, and Department of Inflammation/Autoimmune Diseases, Hoffman-La Roche, Inc., Nutley, New Jersey 07110
| | - Zoltan Nagy
- Contribution from the Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, and Department of Inflammation/Autoimmune Diseases, Hoffman-La Roche, Inc., Nutley, New Jersey 07110
| | - Robert M. Campbell
- Contribution from the Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, and Department of Inflammation/Autoimmune Diseases, Hoffman-La Roche, Inc., Nutley, New Jersey 07110
| | - Donald C. Cox
- Contribution from the Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, and Department of Inflammation/Autoimmune Diseases, Hoffman-La Roche, Inc., Nutley, New Jersey 07110
| | - Gary L. Olson
- Contribution from the Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, and Department of Inflammation/Autoimmune Diseases, Hoffman-La Roche, Inc., Nutley, New Jersey 07110
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38
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Smith AB, Favor DA, Sprengeler PA, Guzman MC, Carroll PJ, Furst GT, Hirschmann R. Molecular modeling, synthesis, and structures of N-methylated 3,5-linked pyrrolin-4-ones toward the creation of a privileged nonpeptide scaffold. Bioorg Med Chem 1999; 7:9-22. [PMID: 10199652 DOI: 10.1016/s0968-0896(98)00234-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The molecular modeling, synthesis, and elucidations of the solid state and solution structures of N-methylated 3,5-linked bispyrrolin-4-ones are described. Prior investigations established that the 3,5-linked pyrrolin-4-one based scaffold can be incorporated into mimics of beta-sheet/beta-strands and into potent, orally bioavailable inhibitors of the HIV-1 protease. To extend the utility of this scaffold beyond that of the initially designed mimics of beta-sheet/beta-strands, we have now explored the structure of N-methylated pyrrolinones. Molecular modeling indicated that N-methylated bispyrrolinones could adopt three low-energy backbone conformations (ca. 165 degrees, 289 degrees, and 320 degrees). Upon their successful synthesis, structural elucidation both in the solid state and in solution revealed the existence of two of the three predicted backbone conformers (ca. 165 degrees and 289 degrees). Two structures were particularly noteworthy and completely unexpected. Mono-N-methyl bispyrrolinone (+)-1 self assembled in the solid state to form a novel helix, while the acetylene-linked dimer of (+)-1, designed to potentiate the observed helical array, instead associated via an intermolecular hydrogen bond in parallel columns. These serendipitous observations led us to speculate that the pyrrolinone moiety may in fact represent a privileged nonpeptide scaffold, able to mimic not only the extended beta-sheet/beta-strand conformation as initially targeted, but also diverse conformations including those analogous to beta-turns and helices. These seemingly unlimited conformations greatly expand the scope of this scaffold for the development of low-molecular weight ligands for biologically important macromolecules.
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Affiliation(s)
- A B Smith
- Department of Chemistry, University of Pennsylvania, Philadelphia 19104, USA
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39
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Smith AB, Benowitz AB, Guzman MC, Sprengeler PA, Hirschmann R, Schweiger EJ, Bolin DR, Nagy Z, Campbell RM, Cox DC, Olson GL. Design, Synthesis, and Evaluation of a Pyrrolinone−Peptide Hybrid Ligand for the Class II MHC Protein HLA-DR1. J Am Chem Soc 1998. [DOI: 10.1021/ja982973t] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Medou M, Bouygues M, Rocheblave L, Chermann JC, Kraus JL. Synthesis and anti-HIV activities of symmetrical N1,N3-dibenzyl-2-hydroxy-propane derivatives. Bioorg Med Chem Lett 1998; 8:1861-6. [PMID: 9873448 DOI: 10.1016/s0960-894x(98)00323-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We report the synthesis and the anti-HIV activities of new C2-symmetrical and achiral N1,N3-dibenzyl-2-hydroxy-propane isosteres. Some of them showed significant inhibitory activity with respect to HIV-infected MT4 cells (compound 6a and 7a, IC50 = 0.1 microM). These new structurally simple compounds represent new synthons which can be suitable for combinatorial chemistry purposes.
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Affiliation(s)
- M Medou
- Laboratoire de Chimie Biomoléculaire, Faculté des Sciences de Luminy, Université de la Méditerranée, Marseille
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41
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Sudoh M, Pauletti GM, Yao W, Moser W, Yokoyama A, Pasternak A, Sprengeler PA, Smith AB, Hirschmann R, Borchardt RT. Transport characteristics of peptidomimetics. Effect of the pyrrolinone bioisostere on transport across Caco-2 cell monolayers. Pharm Res 1998; 15:719-25. [PMID: 9619780 DOI: 10.1023/a:1011966918959] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PURPOSE To compare the permeation characteristics of amide bond-containing HIV-1 protease inhibitors and their pyrrolinone-containing counterparts across Caco-2 cell monolayers, a model of the intestinal mucosa. METHODS Transepithelial transport and cellular uptake of three pairs of amide bond-containing and pyrrolinone-based peptidomimetics were assessed in the presence and absence of cyclosporin A using the Caco-2 cell culture model. The potential of the peptidomimetics to interact with biological membranes was estimated by IAM chromatography. RESULTS In the absence of cyclosporin A, apical (AP) to basolateral (BL) flux of all compounds studied was less than the flux determined in the opposite direction (i.e., BL-to-AP). The ratio of the apparent permeability coefficients (Papp) calculated for the BL-to-AP and AP-to-BL transport (P(BL-->AP)/P(AP-->BL)) varied between 1.7 and 36.2. When individual pairs were ompared, P(BL-->AP)/P(AP-BL) ratios of the pyrrolinone-containing compounds were 1.5 to 11.5 times greater than those determined for the amide bond-containing analogs. Addition of 25 microM cyclosporin A to the transport buffer reduced the P(BL-->AP)/P(AP-->BL) ratios for all protease inhibitors to a value close to unity. Under these conditions, the amide bond-containing peptidomimetics were at least 1.6 to 2.8 times more able to permeate Caco-2 cell monolayers than were the pyrrolinone-containing compounds. The intrinsic uptake characteristics into Caco-2 cells determined in the presence of 25 microM cyclosporin A were slightly greater for the amide bond-containing protease inhibitors than for the pyrrolinone-containing analogs. These uptake results are consistent with the transepithelial transport results determined across this in vitro model of the intestinal mucosa. CONCLUSIONS The amide bond-containing and pyrrolinone-based peptidomimetics are substrates for apically polarized efflux systems present in Caco-2 cell monolayers. The intrinsic permeabilities of the amide bond-containing protease inhibitors are slightly greater than the intrinsic permeabilities of the pyrrolinone-based analogs through Caco-2 cell monolayers.
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Affiliation(s)
- M Sudoh
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence 66047, USA
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42
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Bouygues M, Medou M, Quéléver G, Chermann JC, Camplo M, Kraus JL. Syntheses of new modified Phe-Pro peptides. Use of proline replacements in potential HIV inhibitors. Bioorg Med Chem Lett 1998; 8:277-80. [PMID: 9871669 DOI: 10.1016/s0960-894x(98)00006-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The syntheses consisting of replacement of proline amino acid by a 3-pyrrolidinone ring in Phe-Pro analogues are described. Preliminary anti-HIV studies demonstrated the potential activity of this new class of compounds.
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Affiliation(s)
- M Bouygues
- Laboratoire de Chimie Biomoléculaire, Faculté des Sciences de Luminy, Université de la Méditerranée, Marseille, France
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