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Saibu OA, Hammed SO, Oladipo OO, Odunitan TT, Ajayi TM, Adejuyigbe AJ, Apanisile BT, Oyeneyin OE, Oluwafemi AT, Ayoola T, Olaoba OT, Alausa AO, Omoboyowa DA. Protein-protein interaction and interference of carcinogenesis by supramolecular modifications. Bioorg Med Chem 2023; 81:117211. [PMID: 36809721 DOI: 10.1016/j.bmc.2023.117211] [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: 10/25/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/18/2023]
Abstract
Protein-protein interactions (PPIs) are essential in normal biological processes, but they can become disrupted or imbalanced in cancer. Various technological advancements have led to an increase in the number of PPI inhibitors, which target hubs in cancer cell's protein networks. However, it remains difficult to develop PPI inhibitors with desired potency and specificity. Supramolecular chemistry has only lately become recognized as a promising method to modify protein activities. In this review, we highlight recent advances in the use of supramolecular modification approaches in cancer therapy. We make special note of efforts to apply supramolecular modifications, such as molecular tweezers, to targeting the nuclear export signal (NES), which can be used to attenuate signaling processes in carcinogenesis. Finally, we discuss the strengths and weaknesses of using supramolecular approaches to targeting PPIs.
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Affiliation(s)
- Oluwatosin A Saibu
- Department of Environmental Toxicology, Universitat Duisburg-Essen, NorthRhine-Westphalia, Germany
| | - Sodiq O Hammed
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria; Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Oladapo O Oladipo
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria.
| | - Tope T Odunitan
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria; Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Temitope M Ajayi
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Aderonke J Adejuyigbe
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Boluwatife T Apanisile
- Department of Nutrition and Dietetics, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Oluwatoba E Oyeneyin
- Theoretical and Computational Chemistry Unit, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria
| | - Adenrele T Oluwafemi
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Tolulope Ayoola
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Olamide T Olaoba
- Department of Molecular Pathogenesis and Therapeutics, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Abdullahi O Alausa
- Department of Molecular Biology and Biotechnology, ITMO University, St Petersburg, Russia
| | - Damilola A Omoboyowa
- Department of Biochemistry, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria
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2
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Tedesco F, Calugi L, Lenci E, Trabocchi A. Peptidomimetic Small-Molecule Inhibitors of 3CLPro Activity and Spike-ACE2 Interaction: Toward Dual-Action Molecules against Coronavirus Infections. J Org Chem 2022; 87:12041-12051. [PMID: 36039955 PMCID: PMC9454270 DOI: 10.1021/acs.joc.2c01047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The development of molecules able to target protein-protein interactions (PPIs) is of interest for the development of novel therapeutic agents. Since a high percentage of PPIs are mediated by α-helical structure at the interacting surface, peptidomimetics that reproduce the essential conformational components of helices are useful templates for the development of PPIs inhibitors. In this work, the synthesis of a constrained dipeptide isostere and insertion in the short peptide epitope EDLFYQ of the angiotensin-converting enzyme 2 (ACE2) α1 helix domain resulted in the identification of a molecule capable of inhibiting the SARS-CoV-2 ACE2/spike interaction in the micromolar range. Moreover, inhibition of SARS-CoV-2 3CLPro main protease activity was assessed as an additional inhibitory property of the synthesized peptidomimetics, taking advantage of the C-terminal Q amino acid present in both the ACE2 epitope and the Mpro recognizing motif (APSTVxLQ), thus paving the way to the development of multitarget therapeutics toward coronavirus infections.
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Affiliation(s)
- Filomena Tedesco
- Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 13, Sesto Fiorentino, 50019 Florence, Italy
| | - Lorenzo Calugi
- Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 13, Sesto Fiorentino, 50019 Florence, Italy
| | - Elena Lenci
- Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 13, Sesto Fiorentino, 50019 Florence, Italy
| | - Andrea Trabocchi
- Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 13, Sesto Fiorentino, 50019 Florence, Italy
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3
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Trobe M, Vareka M, Schreiner T, Dobrounig P, Doler C, Holzinger EB, Steinegger A, Breinbauer R. Modular Synthesis of Teraryl‐based alpha ‐Helix Mimetics, Part 3: Iodophenyltriflate Core Fragments Featuring Side Chains of Proteinogenic Amino Acids. European J Org Chem 2022; 2022:e202101278. [PMID: 35910459 PMCID: PMC9306992 DOI: 10.1002/ejoc.202101278] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 02/08/2022] [Indexed: 11/18/2022]
Abstract
Teraryl‐based α‐helix mimetics have proven to be useful compounds for the inhibition of protein‐protein interactions (PPI). We have developed a modular and flexible approach for the synthesis of teraryl‐based α‐helix mimetics using a benzene core unit featuring two leaving groups of differentiated reactivity in the Pd‐catalyzed cross‐coupling used for teraryl assembly. In previous publications we have introduced the methodology of 4‐iodophenyltriflates decorated with the side chains of some of the proteinogenic amino acids. We herein report the core fragments corresponding to the previously missing amino acids Arg, Asn, Asp, Met, Trp and Tyr. Therefore, our set now encompasses all relevant amino acid analogues with the exception of His. In order to be compatible with the triflate moiety, some of the nucleophilic side chains had to be provided in a protected form to serve as stable building blocks. Additionally, cross‐coupling procedures for the assembly of teraryls were investigated.
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Affiliation(s)
- Melanie Trobe
- Graz University of Technology: Technische Universitat Graz Institute of Organic Chemistry AUSTRIA
| | - Martin Vareka
- Graz University of Technology: Technische Universitat Graz Institute of Organic Chemistry AUSTRIA
| | - Till Schreiner
- Graz University of Technology: Technische Universitat Graz Institute of Organic Chemistry AUSTRIA
| | - Patrick Dobrounig
- Graz University of Technology: Technische Universitat Graz Institute of Organic Chemistry AUSTRIA
| | - Carina Doler
- Graz University of Technology: Technische Universitat Graz Institute of Organic Chemistry AUSTRIA
| | - Ella B. Holzinger
- Graz University of Technology: Technische Universitat Graz Institute of Organic Chemistry AUSTRIA
| | - Andreas Steinegger
- Graz University of Technology: Technische Universitat Graz Institute of Organic Chemistry AUSTRIA
| | - Rolf Breinbauer
- Technische Universitat Graz Institute of Organic Chemistry Stremayrgasse 9 A-8010 Graz AUSTRIA
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4
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Marshall GR, Ballante F. Limiting Assumptions in the Design of Peptidomimetics. Drug Dev Res 2017; 78:245-267. [DOI: 10.1002/ddr.21406] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Garland R. Marshall
- Department of Biochemistry and Molecular Biophysics; Washington University School of Medicine; St. Louis Missouri 63110
| | - Flavio Ballante
- Department of Biochemistry and Molecular Biophysics; Washington University School of Medicine; St. Louis Missouri 63110
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Drennen B, MacKerell AD, Fletcher S. Expedient access to pre-organized α-helix mimetics based on an isocinchomeronic acid core. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2015.10.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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6
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Trobe M, Breinbauer R. Improved and scalable synthesis of building blocks for the modular synthesis of teraryl-based alpha-helix mimetics. MONATSHEFTE FUR CHEMIE 2015. [DOI: 10.1007/s00706-015-1599-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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7
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Liu C, Ponder JW, Marshall GR. Helix stability of oligoglycine, oligoalanine, and oligo-β-alanine dodecamers reflected by hydrogen-bond persistence. Proteins 2014; 82:3043-61. [PMID: 25116421 PMCID: PMC4206583 DOI: 10.1002/prot.24665] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 08/03/2014] [Indexed: 02/03/2023]
Abstract
Helices are important structural/recognition elements in proteins and peptides. Stability and conformational differences between helices composed of α- and β-amino acids as scaffolds for mimicry of helix recognition has become a theme in medicinal chemistry. Furthermore, helices formed by β-amino acids are experimentally more stable than those formed by α-amino acids. This is paradoxical because the larger sizes of the hydrogen-bonding rings required by the extra methylene groups should lead to entropic destabilization. In this study, molecular dynamics simulations using the second-generation force field, AMOEBA (Ponder, J.W., et al., Current status of the AMOEBA polarizable force field. J Phys Chem B, 2010. 114(8): p. 2549-64.) explored the stability and hydrogen-bonding patterns of capped oligo-β-alanine, oligoalanine, and oligoglycine dodecamers in water. The MD simulations showed that oligo-β-alanine has strong acceptor+2 hydrogen bonds, but surprisingly did not contain a large content of 3(12) -helical structures, possibly due to the sparse distribution of the 3(12) -helical structure and other structures with acceptor+2 hydrogen bonds. On the other hand, despite its backbone flexibility, the β-alanine dodecamer had more stable and persistent <3.0 Å hydrogen bonds. Its structure was dominated more by multicentered hydrogen bonds than either oligoglycine or oligoalanine helices. The 3(1) (PII) helical structure, prevalent in oligoglycine and oligoalanine, does not appear to be stable in oligo-β-alanine indicating its competition with other structures (stacking structure as indicated by MD analyses). These differences are among the factors that shape helical structural preferences and the relative stabilities of these three oligopeptides.
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Affiliation(s)
- Chengyu Liu
- Department of Chemistry, Washington University, St. Louis, Missouri, 63130
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8
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Structure-based inhibition of protein-protein interactions. Eur J Med Chem 2014; 94:480-8. [PMID: 25253637 DOI: 10.1016/j.ejmech.2014.09.047] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 09/03/2014] [Accepted: 09/12/2014] [Indexed: 12/24/2022]
Abstract
Protein-protein interactions (PPIs) are emerging as attractive targets for drug design because of their central role in directing normal and aberrant cellular functions. These interactions were once considered "undruggable" because their large and dynamic interfaces make small molecule inhibitor design challenging. However, landmark advances in computational analysis, fragment screening and molecular design have enabled development of a host of promising strategies to address the fundamental molecular recognition challenge. An attractive approach for targeting PPIs involves mimicry of protein domains that are critical for complex formation. This approach recognizes that protein subdomains or protein secondary structures are often present at interfaces and serve as organized scaffolds for the presentation of side chain groups that engage the partner protein(s). Design of protein domain mimetics is in principle rather straightforward but is enabled by a host of computational strategies that provide predictions of important residues that should be mimicked. Herein we describe a workflow proceeding from interaction network analysis, to modeling a complex structure, to identifying a high-affinity sub-structure, to developing interaction inhibitors. We apply the design procedure to peptidomimetic inhibitors of Ras-mediated signaling.
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Krzeszewski M, Thorsted B, Brewer J, Gryko DT. Tetraaryl-, pentaaryl-, and hexaaryl-1,4-dihydropyrrolo[3,2-b]pyrroles: synthesis and optical properties. J Org Chem 2014; 79:3119-28. [PMID: 24655027 DOI: 10.1021/jo5002643] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Efficient conditions for the synthesis of tetra-, penta-, and hexasubstituted derivatives of 1,4-dihydropyrrolo[3,2-b]pyrrole were developed. The tetraaryl derivatives were obtained in a novel one-pot reaction among aromatic aldehydes, aromatic amines, and butane-2,3-dione. After a thorough examination of various reaction parameters (solvent, acid, temperature) p-toluenesulfonic acid was identified as the crucial catalyst. As a result, 1,4-dihydropyrrolo[3,2-b]pyrroles were obtained in the highest yields reported to date. The scope and limitation studies showed that this new method was particularly efficient for sterically hindered aldehydes (yields 45-49%). Pentaaryl- and hexaaryl-1,4-dihydropyrrolo[3,2-b]pyrroles were prepared from tetraaryl-1,4-dihydropyrrolo[3,2-b]pyrroles via direct arylation by employing both electron-poor and electron-rich aromatic and heteroaromatic haloarenes. Strategic placement of electron-withdrawing substituents at the 2-, 3-, 5-, and 6-positions produced an acceptor-donor-acceptor type fluorophore. The resulting multiply substituted heteropentalenes displayed intriguing optical properties. The relationship between the structure and photophysical properties for all compounds were directly compared and thoroughly elucidated. All synthesized products displayed strong blue fluorescence and exhibited moderate to large Stokes shifts (3000-7300 cm(-1)) as well as high quantum yields of fluorescence up to 88%. Two-photon absorption cross-section values measured in the near-IR region were surprisingly high (hundreds of GM), given the limited conjugation in these propeller-shaped dyes.
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Affiliation(s)
- Maciej Krzeszewski
- Institute of Organic Chemistry, Polish Academy of Sciences , Kasprzaka 44/52, 00-224 Warsaw, Poland
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Lim Z, Duggan PJ, Meyer AG, Tuck KL. An iterative in silico and modular synthetic approach to aqueous soluble tercyclic α-helix mimetics. Org Biomol Chem 2014; 12:4432-44. [DOI: 10.1039/c4ob00647j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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11
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Recapitulating the α-helix: nonpeptidic, low-molecular-weight ligands for the modulation of helix-mediated protein–protein interactions. Future Med Chem 2013; 5:2157-74. [DOI: 10.4155/fmc.13.176] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Protein–protein interactions play critical roles in a wide variety of biological processes, and their dysregulations contribute to the pathogenesis of several diseases, including cancer. Chemical entities that can abrogate aberrant protein–protein interactions may provide novel therapeutic agents. A large number of protein–protein interactions are mediated by protein secondary structure, the most commonly encountered form of which is the α-helix. Accordingly, over the last decade, there has been a flood of nonpeptidic small molecules that recapitulate the projection and chemical nature of key side chains of the canonical α-helix as a strategy to disrupt helix-mediated protein–protein interactions. In this review, we discuss recent advances (post 2006) in the design of synthetic α-helix mimetics, which include single-faced and two-faced/amphipathic structures, for the modulation of protein–protein interactions.
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12
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Hack V, Reuter C, Opitz R, Schmieder P, Beyermann M, Neudörfl JM, Kühne R, Schmalz HG. Efficient α-Helix Induction in a Linear Peptide Chain byN-Capping with a Bridged-tricyclic Diproline Analogue. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201302014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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13
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Hack V, Reuter C, Opitz R, Schmieder P, Beyermann M, Neudörfl JM, Kühne R, Schmalz HG. Efficient α-Helix Induction in a Linear Peptide Chain byN-Capping with a Bridged-tricyclic Diproline Analogue. Angew Chem Int Ed Engl 2013; 52:9539-43. [DOI: 10.1002/anie.201302014] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2013] [Revised: 04/11/2013] [Indexed: 11/11/2022]
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Isvoran A, Craciun D, Martiny V, Sperandio O, Miteva MA. Computational analysis of protein-protein interfaces involving an alpha helix: insights for terphenyl-like molecules binding. BMC Pharmacol Toxicol 2013; 14:31. [PMID: 23768251 PMCID: PMC3689098 DOI: 10.1186/2050-6511-14-31] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 06/11/2013] [Indexed: 12/23/2022] Open
Abstract
Background Protein-Protein Interactions (PPIs) are key for many cellular processes. The characterization of PPI interfaces and the prediction of putative ligand binding sites and hot spot residues are essential to design efficient small-molecule modulators of PPI. Terphenyl and its derivatives are small organic molecules known to mimic one face of protein-binding alpha-helical peptides. In this work we focus on several PPIs mediated by alpha-helical peptides. Method We performed computational sequence- and structure-based analyses in order to evaluate several key physicochemical and surface properties of proteins known to interact with alpha-helical peptides and/or terphenyl and its derivatives. Results Sequence-based analysis revealed low sequence identity between some of the analyzed proteins binding alpha-helical peptides. Structure-based analysis was performed to calculate the volume, the fractal dimension roughness and the hydrophobicity of the binding regions. Besides the overall hydrophobic character of the binding pockets, some specificities were detected. We showed that the hydrophobicity is not uniformly distributed in different alpha-helix binding pockets that can help to identify key hydrophobic hot spots. Conclusions The presence of hydrophobic cavities at the protein surface with a more complex shape than the entire protein surface seems to be an important property related to the ability of proteins to bind alpha-helical peptides and low molecular weight mimetics. Characterization of similarities and specificities of PPI binding sites can be helpful for further development of small molecules targeting alpha-helix binding proteins.
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Affiliation(s)
- Adriana Isvoran
- Department of Biology and Chemistry, West University of Timisoara, 16 Pestalozzi, Timisoara 300115, Romania
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15
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Peters M, Trobe M, Tan H, Kleineweischede R, Breinbauer R. A modular synthesis of teraryl-based α-helix mimetics, part 1: Synthesis of core fragments with two electronically differentiated leaving groups. Chemistry 2013; 19:2442-9. [PMID: 23292813 DOI: 10.1002/chem.201203005] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 11/12/2012] [Indexed: 01/12/2023]
Abstract
Teraryl-based α-helix mimetics have proven to be useful compounds for the inhibition of protein-protein interactions (PPI). We have developed a modular and flexible approach for the synthesis of teraryl-based α-helix mimetics. Central to our strategy is the use of a benzene core unit featuring two leaving groups of differentiated reactivity in the Pd-catalyzed cross-coupling used for terphenyl assembly. With the halogen/diazonium route and the halogen/triflate route, two strategies have successfully been established. The synthesis of core building blocks with aliphatic (Ala, Val, Leu, Ile), aromatic (Phe), polar (Cys, Lys), hydrophilic (Ser, Gln), and acidic (Glu) amino acid side chains are reported.
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Affiliation(s)
- Martin Peters
- Institute of Organic Chemistry, Graz University of Technology, Stremayrgasse 9, 8010 Graz, Austria
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16
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Wrobel M, Aubé J, König B. Parallel solid-phase synthesis of diaryltriazoles. Beilstein J Org Chem 2012; 8:1027-36. [PMID: 23019430 PMCID: PMC3458720 DOI: 10.3762/bjoc.8.115] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 06/13/2012] [Indexed: 11/30/2022] Open
Abstract
A series of substituted diaryltriazoles was prepared by a solid-phase-synthesis protocol using a modified Wang resin. The copper(I)- or ruthenium(II)-catalyzed 1,3-cycloaddition on the polymer bead allowed a rapid synthesis of the target compounds in a parallel fashion with in many cases good to excellent yields. Substituted diaryltriazoles resemble a molecular structure similar to established terphenyl-alpha-helix peptide mimics and have therefore the potential to act as selective inhibitors for protein-protein interactions.
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Affiliation(s)
- Matthias Wrobel
- Fakultät für Chemie und Pharmazie, Universität Regensburg, D-93040 Regensburg, Germany, Fax: +49 9419431717
| | - Jeffrey Aubé
- Department of Medicinal Chemistry and the Chemical Methodology and Library Development Center, University of Kansas, Delbert M. Shankel Structural Biology Center, 2121 Simons Drive, West Campus, Lawrence, KS 66047, USA
| | - Burkhard König
- Fakultät für Chemie und Pharmazie, Universität Regensburg, D-93040 Regensburg, Germany, Fax: +49 9419431717
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Fricke T, Mart RJ, Watkins CL, Wiltshire M, Errington RJ, Smith PJ, Jones AT, Allemann RK. Chemical Synthesis of Cell-Permeable Apoptotic Peptides from in Vivo Produced Proteins. Bioconjug Chem 2011; 22:1763-7. [DOI: 10.1021/bc200338u] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Thomas Fricke
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Robert J. Mart
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Catherine L. Watkins
- School of Medicine,
- Welsh School of Pharmacy, Cardiff University, King Edward VII Avenue, Cardiff, CF10 3XF, United Kingdom
| | | | | | | | - Arwyn T. Jones
- Welsh School of Pharmacy, Cardiff University, King Edward VII Avenue, Cardiff, CF10 3XF, United Kingdom
| | - Rudolf K. Allemann
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, United Kingdom
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18
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Mort M, Evani US, Krishnan VG, Kamati KK, Baenziger PH, Bagchi A, Peters BJ, Sathyesh R, Li B, Sun Y, Xue B, Shah NH, Kann MG, Cooper DN, Radivojac P, Mooney SD. In silico functional profiling of human disease-associated and polymorphic amino acid substitutions. Hum Mutat 2010; 31:335-46. [PMID: 20052762 DOI: 10.1002/humu.21192] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
An important challenge in translational bioinformatics is to understand how genetic variation gives rise to molecular changes at the protein level that can precipitate both monogenic and complex disease. To this end, we compiled datasets of human disease-associated amino acid substitutions (AAS) in the contexts of inherited monogenic disease, complex disease, functional polymorphisms with no known disease association, and somatic mutations in cancer, and compared them with respect to predicted functional sites in proteins. Using the sequence homology-based tool SIFT to estimate the proportion of deleterious AAS in each dataset, only complex disease AAS were found to be indistinguishable from neutral polymorphic AAS. Investigation of monogenic disease AAS predicted to be nondeleterious by SIFT were characterized by a significant enrichment for inherited AAS within solvent accessible residues, regions of intrinsic protein disorder, and an association with the loss or gain of various posttranslational modifications. Sites of structural and/or functional interest were therefore surmised to constitute useful additional features with which to identify the molecular disruptions caused by deleterious AAS. A range of bioinformatic tools, designed to predict structural and functional sites in protein sequences, were then employed to demonstrate that intrinsic biases exist in terms of the distribution of different types of human AAS with respect to specific structural, functional and pathological features. Our Web tool, designed to potentiate the functional profiling of novel AAS, has been made available at http://profile.mutdb.org/.
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Affiliation(s)
- Matthew Mort
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
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Abstract
Phenylpyridal- and phenyldipyridal-based scaffolds have been designed and synthesized as novel helical peptide mimetics. The synthesis required optimisation and selective alkylation in producing 2,6-functionalized 3-hydroxypyridine derivatives for a convergent scheme. The pyridine analogues were coupled by a series of Suzuki/Stille types cross-coupling reactions. A series of biaryl and ter-aryl substituted heterocycles were produced. The synthetic approach was concise and high yielding allowing large variability at the wanted side-chain attachment points. A number of compounds were synthesised to show the versatility of the strategy.
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Affiliation(s)
- Gregory T Bourne
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, Missouri 63110, USA.
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20
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Martelli G, Marcucci E, Orena M, Rinaldi S. Enantiopure derivatives of aza-Baylis-Hillman adducts by subsequent SN'-SN' reactions of acylcarbamates bearing a chiral auxiliary. Molecules 2009; 14:2824-35. [PMID: 19701126 PMCID: PMC6255381 DOI: 10.3390/molecules14082824] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Revised: 07/22/2009] [Accepted: 07/30/2009] [Indexed: 11/24/2022] Open
Abstract
Reactions of (4S,5R)-1-(3,4-Dimethyl-2-oxo-5-phenylimidazolidine)carbonyl-isocyanate (4) with appropriate Baylis-Hillman adducts 5 gave the corresponding acyl carbamates 6,7 as equimolar diastereomeric mixtures. These mixtures were treated with DABCO, to afford with moderate diastereoselection easily separable [2-(3",4"-dimethyl-2"-oxo-5"-phenylimidazolidine-1-carboxamido)(aryl)methyl]acrylates 8 and 9.
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Affiliation(s)
| | | | - Mario Orena
- Author to whom correspondence should be addressed; E-mail:
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Hu L, Maurer K, Moeller KD. Building addressable libraries: site-selective Suzuki reactions on microelectrode arrays. Org Lett 2009; 11:1273-6. [PMID: 19239260 PMCID: PMC3947858 DOI: 10.1021/ol900056u] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A site-selective Suzuki reaction has been developed for use on microelectrode arrays. The reaction conditions employed are similar to those used to achieve site-selective Heck reactions. The reaction can be run with either an aryliodide attached to the surface of the array and an arylboronic acid in solution or with an arylboronic acid attached to the surface of the array and an arylbromide in solution. Both allyl acetate and air are effective confining agents for the reaction. The reactions are compatible with arrays containing either 1024 microelectrodes cm(-2) or 12,544 microelectrodes cm(-2).
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Affiliation(s)
- Libo Hu
- Department of Chemistry, Washington UniVersity, St. Louis, Missouri 63130
| | - Karl Maurer
- CombiMatrix Corporation, 6500 Harbor Heights Parkway, Suite 301, Mukilteo, Washington 98275
| | - Kevin D. Moeller
- Department of Chemistry, Washington UniVersity, St. Louis, Missouri 63130
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Gardella TJ. Mimetic ligands for the PTHR1: Approaches, developments, and considerations. ACTA ACUST UNITED AC 2009. [DOI: 10.1138/20090364] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Abstract
During molecular recognition of proteins in biological systems, helices, reverse turns, and beta-sheets are dominant motifs. Often there are therapeutic reasons for blocking such recognition sites, and significant progress has been made by medicinal chemists in the design and synthesis of semirigid molecular scaffolds on which to display amino acid side chains. The basic premise is that preorganization of the competing ligand enhances the binding affinity and potential selectivity of the inhibitor. In this chapter, current progress in these efforts is reviewed.
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Che Y, Marshall GR. Privileged scaffolds targeting reverse-turn and helix recognition. Expert Opin Ther Targets 2008; 12:101-14. [PMID: 18076374 DOI: 10.1517/14728222.12.1.101] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND Protein-protein interactions dominate molecular recognition in biologic systems. One major challenge for drug discovery arises from the very large surfaces that are characteristic of many protein-protein interactions. OBJECTIVES To identify 'drug-like' small molecule leads capable of modulating protein-protein interactions based on common protein-recognition motifs, such as alpha-helices, beta-strands, reverse-turns and polyproline motifs for example. OVERVIEW Many proteins/peptides are unstructured under physiologic conditions and only fold into ordered structures on binding to their cellular targets. Therefore, preorganization of an inhibitor into its protein-bound conformation reduces the entropy of binding and enhances the relative affinity of the inhibitor. Accordingly, this review describes a general strategy to address the challenge based on the 'privileged structure hypothesis' [Che, PhD thesis, Washington University, 2003] that chemical templates capable of mimicking surfaces of protein-recognition motifs are potential privileged scaffolds as small-molecule inhibitors of protein-protein interactions. The authors highlight recent advances in the design of privileged scaffolds targeting reverse-turn and helical recognition. CONCLUSIONS Privileged scaffolds targeting common protein-recognition motifs are useful to help elucidate the receptor-bound conformation and to provide non-peptidic, bioavailable substructures suitable for optimization to modulate protein-protein interactions.
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Affiliation(s)
- Ye Che
- Washington University, Center for Computational Biology and Department of Biochemistry and Molecular Biophysics, St. Louis, MO 63110, USA
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Abstract
Pancreatic ribonuclease A (EC 3.1.27.5, RNase) is, perhaps, the best-studied enzyme of the 20th century. It was isolated by René Dubos, crystallized by Moses Kunitz, sequenced by Stanford Moore and William Stein, and synthesized in the laboratory of Bruce Merrifield, all at the Rockefeller Institute/University. It has proven to be an excellent model system for many different types of experiments, both as an enzyme and as a well-characterized protein for biophysical studies. Of major significance was the demonstration by Chris Anfinsen at NIH that the primary sequence of RNase encoded the three-dimensional structure of the enzyme. Many other prominent protein chemists/enzymologists have utilized RNase as a dominant theme in their research. In this review, the history of RNase and its offspring, RNase S (S-protein/S-peptide), will be considered, especially the work in the Merrifield group, as a preface to preliminary data and proposed experiments addressing topics of current interest. These include entropy-enthalpy compensation, entropy of ligand binding, the impact of protein modification on thermal stability, and the role of protein dynamics in enzyme action. In continuing to use RNase as a prototypical enzyme, we stand on the shoulders of the giants of protein chemistry to survey the future.
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Affiliation(s)
- Garland R Marshall
- Center for Computational Biology, Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.
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