1
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Tang K, Wang S, Gao W, Song Y, Yu B. Harnessing the cyclization strategy for new drug discovery. Acta Pharm Sin B 2022; 12:4309-4326. [PMID: 36562004 PMCID: PMC9764076 DOI: 10.1016/j.apsb.2022.09.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/07/2022] [Accepted: 09/23/2022] [Indexed: 12/25/2022] Open
Abstract
The design of new ligands with high affinity and specificity against the targets of interest has been a central focus in drug discovery. As one of the most commonly used methods in drug discovery, the cyclization represents a feasible strategy to identify new lead compounds by increasing structural novelty, scaffold diversity and complexity. Such strategy could also be potentially used for the follow-on drug discovery without patent infringement. In recent years, the cyclization strategy has witnessed great success in the discovery of new lead compounds against different targets for treating various diseases. Herein, we first briefly summarize the use of the cyclization strategy in the discovery of new small-molecule lead compounds, including the proteolysis targeting chimeras (PROTAC) molecules. Particularly, we focus on four main strategies including fused ring cyclization, chain cyclization, spirocyclization and macrocyclization and highlight the use of the cyclization strategy in lead generation. Finally, the challenges including the synthetic intractability, relatively poor pharmacokinetics (PK) profiles and the absence of the structural information for rational structure-based cyclization are also briefly discussed. We hope this review, not exhaustive, could provide a timely overview on the cyclization strategy for the discovery of new lead compounds.
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2
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Gilon C, Klazas M, Lahiani A, Schumacher-Klinger A, Merzbach S, Naoum JN, Ovadia H, Rubin L, Cornell-Kennon S, Schaefer EM, Katzhendler J, Marcinkiewicz C, Hoffman A, Lazarovici P. Synthesis and Pharmacological Characterization of Visabron, a Backbone Cyclic Peptide Dual Antagonist of α4β1 (VLA-4)/α9β1 Integrin for Therapy of Multiple Sclerosis. JACS AU 2021; 1:2361-2376. [PMID: 34977904 PMCID: PMC8717366 DOI: 10.1021/jacsau.1c00496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Indexed: 06/14/2023]
Abstract
Integrins α4β1/ α9β1 are important in the pathogenesis and progression of inflammatory and autoimmune diseases by their roles in leukocyte activation and trafficking. Natalizumab, a monoclonal antibody selectively targeting α4β1 integrin and blocking leukocyte trafficking to the central nervous system, is an immunotherapy for multiple sclerosis (MS). However, due to its adverse effects associated with chronic treatment, alternative strategies using small peptide mimetic inhibitors are being sought. In the present study, we synthesized and characterized visabron c (4-4), a backbone cyclic octapeptide based on the sequence TMLD, a non-RGD unique α4β1 integrin recognition sequence motif derived from visabres, a proteinous disintegrin from the viper venom. Visabron c (4-4) was selected from a minilibrary with conformational diversity based on its potency and selectivity in functional adhesion cellular assays. Visabron c (4-4)'s serum stability, pharmacokinetics, and therapeutic effects following ip injection were assessed in an experimental autoimmune encephalomyelitis (EAE) animal model. Furthermore, visabron c (4-4)'s lack of toxic effects in mice was verified by blood analysis, tissue pathology, immunogenicity, and "off-target" effects, indicating its significant tolerability and lack of immunogenicity. Visabron c (4-4) can be delivered systemically. The in vitro and in vivo data justify visabron c (4-4) as a safe alternative peptidomimetic lead compound/drug to monoclonal anti-α4 integrin antibodies, steroids, and other immunosuppressant drugs. Moreover, visabron c (4-4) design may pave the way for developing new therapies for a variety of other inflammatory and/or autoimmune diseases.
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Affiliation(s)
- Chaim Gilon
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Michal Klazas
- Pharmacy, Pharmacology, and Medicinal Chemistry, Institute
for Drug Research, School of Pharmacy, Faculty
of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Adi Lahiani
- Pharmacy, Pharmacology, and Medicinal Chemistry, Institute
for Drug Research, School of Pharmacy, Faculty
of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Adi Schumacher-Klinger
- Pharmacy, Pharmacology, and Medicinal Chemistry, Institute
for Drug Research, School of Pharmacy, Faculty
of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Shira Merzbach
- Pharmacy, Pharmacology, and Medicinal Chemistry, Institute
for Drug Research, School of Pharmacy, Faculty
of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Johnny N. Naoum
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Haim Ovadia
- Neurology and Allergy and Clinical Immunology Unit, Hadassah-Hebrew
University Medical Center, Jerusalem 9112001, Israel
| | - Limor Rubin
- Neurology and Allergy and Clinical Immunology Unit, Hadassah-Hebrew
University Medical Center, Jerusalem 9112001, Israel
| | - Susan Cornell-Kennon
- AssayQuant
Technologies, Inc., 260
Cedar Hill Street, Marlboro, Massachusetts 01752, United States
| | - Erik M. Schaefer
- AssayQuant
Technologies, Inc., 260
Cedar Hill Street, Marlboro, Massachusetts 01752, United States
| | - Jehoshua Katzhendler
- Pharmacy, Pharmacology, and Medicinal Chemistry, Institute
for Drug Research, School of Pharmacy, Faculty
of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Cezary Marcinkiewicz
- Department
of Bioengineering, College of Engineering, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Amnon Hoffman
- Pharmacy, Pharmacology, and Medicinal Chemistry, Institute
for Drug Research, School of Pharmacy, Faculty
of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Philip Lazarovici
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
- Pharmacy, Pharmacology, and Medicinal Chemistry, Institute
for Drug Research, School of Pharmacy, Faculty
of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
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3
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Talhami A, Swed A, Hess S, Ovadia O, Greenberg S, Schumacher-Klinger A, Rosenthal D, Shalev DE, Hurevich M, Lazarovici P, Hoffman A, Gilon C. Cyclizing Painkillers: Development of Backbone-Cyclic TAPS Analogs. Front Chem 2020; 8:532577. [PMID: 33282822 PMCID: PMC7689096 DOI: 10.3389/fchem.2020.532577] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 10/07/2020] [Indexed: 12/02/2022] Open
Abstract
Painkillers are commonly used medications. Native peptide painkillers suffer from various pharmacological disadvantages, while small molecule painkillers like morphine are highly addictive. We present a general approach aimed to use backbone-cyclization to develop a peptidomimetic painkiller. Backbone-cyclization was applied to transform the linear peptide Tyr-Arg-Phe-Sar (TAPS) into an active backbone-cyclic peptide with improved drug properties. We designed and synthesized a focused backbone-cyclic TAPS library with conformational diversity, in which the members of the library have the generic name TAPS c(n-m) where n and m represent the lengths of the alkyl chains on the nitrogens of Gly and Arg, respectively. We used a combined screening approach to evaluate the pharmacological properties and the potency of the TAPS c(n-m) library. We focused on an in vivo active compound, TAPS c(2-6), which is metabolically stable and has the potential to become a peripheral painkiller being a full μ opioid receptor functional agonist. To prepare a large quantity of TAPS c(2-6), we optimized the conditions of the on-resin reductive alkylation step to increase the efficiency of its SPPS. NMR was used to determine the solution conformation of the peptide lead TAPS c(2-6).
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Affiliation(s)
- Alaa Talhami
- Department of Organic Chemistry, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Avi Swed
- School of Pharmacy, Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shmuel Hess
- Meytav Technologies Incubator, Kiryat Shmona, Israel
| | - Oded Ovadia
- School of Pharmacy, Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sarit Greenberg
- School of Pharmacy, Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Adi Schumacher-Klinger
- School of Pharmacy, Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - David Rosenthal
- Department of Organic Chemistry, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Deborah E Shalev
- Department of Pharmaceutical Engineering, Azrieli College of Engineering Jerusalem, Jerusalem, Israel.,Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Mattan Hurevich
- Department of Organic Chemistry, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Philip Lazarovici
- School of Pharmacy, Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Amnon Hoffman
- School of Pharmacy, Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Chaim Gilon
- Department of Organic Chemistry, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
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4
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Maurya NS, Kushwaha S, Mani A. Recent Advances and Computational Approaches in Peptide Drug Discovery. Curr Pharm Des 2020; 25:3358-3366. [PMID: 31544714 DOI: 10.2174/1381612825666190911161106] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 09/05/2019] [Indexed: 12/19/2022]
Abstract
BACKGROUND Drug design and development is a vast field that requires huge investment along with a long duration for providing approval to suitable drug candidates. With the advancement in the field of genomics, the information about druggable targets is being updated at a fast rate which is helpful in finding a cure for various diseases. METHODS There are certain biochemicals as well as physiological advantages of using peptide-based therapeutics. Additionally, the limitations of peptide-based drugs can be overcome by modulating the properties of peptide molecules through various biomolecular engineering techniques. Recent advances in computational approaches have been helpful in studying the effect of peptide drugs on the biomolecular targets. Receptor - ligand-based molecular docking studies have made it easy to screen compatible inhibitors against a target.Furthermore, there are simulation tools available to evaluate stability of complexes at the molecular level. Machine learning methods have added a new edge by enabling accurate prediction of therapeutic peptides. RESULTS Peptide-based drugs are expected to take over many popular drugs in the near future due to their biosafety, lower off-target binding chances and multifunctional properties. CONCLUSION This article summarises the latest developments in the field of peptide-based therapeutics related to their usage, tools, and databases.
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Affiliation(s)
- Neha S Maurya
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, India
| | - Sandeep Kushwaha
- Department of Plant Breeding, Sveriges lantbruksuniversitet, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ashutosh Mani
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, India
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5
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Molecular Docking Studies of a Cyclic Octapeptide-Cyclosaplin from Sandalwood. Biomolecules 2019; 9:biom9110740. [PMID: 31731771 PMCID: PMC6920920 DOI: 10.3390/biom9110740] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 11/12/2019] [Indexed: 12/11/2022] Open
Abstract
Natural products from plants, such as chemopreventive agents, attract huge attention because of their low toxicity and high specificity. The rational drug design in combination with structure-based modeling and rapid screening methods offer significant potential for identifying and developing lead anticancer molecules. Thus, the molecular docking method plays an important role in screening a large set of molecules based on their free binding energies and proposes structural hypotheses of how the molecules can inhibit the target. Several peptide-based therapeutics have been developed to combat several health disorders, including cancers, metabolic disorders, heart-related diseases, and infectious diseases. Despite the discovery of hundreds of such therapeutic peptides however, only few peptide-based drugs have made it to the market. Moreover, the in silico activities of cyclic peptides towards molecular targets, such as protein kinases, proteases, and apoptosis related proteins have not been extensively investigated. In this study, we explored the in silico kinase and protease inhibitor potentials of cyclosaplin, and studied the interactions of cyclosaplin with other apoptosis-related proteins. Previously, the structure of cyclosaplin was elucidated by molecular modeling associated with dynamics that were used in the current study as well. Docking studies showed strong affinity of cyclosaplin towards cancer-related proteins. The binding affinity closer to 10 kcal/mol indicated efficient binding. Cyclosaplin showed strong binding affinities towards protein kinases such as EGFR, VEGFR2, PKB, and p38, indicating its potential role in protein kinase inhibition. Moreover, it displayed strong binding affinity to apoptosis-related proteins and revealed the possible role of cyclosaplin in apoptotic cell death. The protein–ligand interactions using LigPlot displayed some similar interactions between cyclosaplin and peptide-based ligands, especially in case of protein kinases and a few apoptosis related proteins. Thus, the in silico analyses gave the insights of cyclosaplin being a potential apoptosis inducer and protein kinase inhibitor.
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6
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Jenardhanan P, Panneerselvam M, Mathur PP. Targeting Kinase Interaction Networks: A New Paradigm in PPI Based Design of Kinase Inhibitors. Curr Top Med Chem 2019; 19:467-485. [PMID: 31184298 DOI: 10.2174/1568026619666190304155711] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 01/20/2019] [Accepted: 02/06/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND Kinases are key modulators in regulating diverse range of cellular activities and are an essential part of the protein-protein interactome. Understanding the interaction of kinases with different substrates and other proteins is vital to decode the cell signaling machinery as well as causative mechanism for disease onset and progression. OBJECTIVE The objective of this review is to present all studies on the structure and function of few important kinases and highlight the protein-protein interaction (PPI) mechanism of kinases and the kinase specific interactome databases and how such studies could be utilized to develop anticancer drugs. METHODS The article is a review of the detailed description of the various domains in kinases that are involved in protein-protein interactions and specific inhibitors developed targeting these PPI domains. RESULTS The review has surfaced in depth the interacting domains in key kinases and their features and the roles of PPI in the human kinome and the various signaling cascades that are involved in certain types of cancer. CONCLUSION The insight availed into the mechanism of existing peptide inhibitors and peptidomimetics against kinases will pave way for the design and generation of domain specific peptide inhibitors with better productivity and efficiency and the various software and servers available can be of great use for the identification and analysis of protein-protein interactions.
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Affiliation(s)
| | - Manivel Panneerselvam
- Department of Biotechnology, BJM School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - Premendu P Mathur
- Department of Biochemistry & Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, India
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7
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Ricardo MG, Marrrero JF, Valdés O, Rivera DG, Wessjohann LA. A Peptide Backbone Stapling Strategy Enabled by the Multicomponent Incorporation of Amide N-Substituents. Chemistry 2018; 25:769-774. [PMID: 30412333 DOI: 10.1002/chem.201805318] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Indexed: 12/12/2022]
Abstract
The multicomponent backbone N-modification of peptides on solid-phase is presented as a powerful and general method to enable peptide stapling at the backbone instead of the side chains. This work shows that a variety of functionalized N-substituents suitable for backbone stapling can be readily introduced by means of on-resin Ugi multicomponent reactions conducted during solid-phase peptide synthesis. Diverse macrocyclization chemistries were implemented with such backbone N-substituents, including the ring-closing metathesis, lactamization, and thiol alkylation. The backbone N-modification method was also applied to the synthesis of α-helical peptides by linking N-substituents to the peptide N-terminus, thus featuring hydrogen-bond surrogate structures. Overall, the strategy proves useful for peptide backbone macrocyclization approaches that show promise in peptide drug discovery.
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Affiliation(s)
- Manuel G Ricardo
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle/Saale, Germany.,Center for Natural Products Research, Faculty of Chemistry, University of Havana, Zapata y G, 10400, La Habana, Cuba
| | - Javiel F Marrrero
- Center for Natural Products Research, Faculty of Chemistry, University of Havana, Zapata y G, 10400, La Habana, Cuba
| | - Oscar Valdés
- Vicerrectoría de Investigación y Postgrado, Universidad Católica del Maule, Talca, 3460000, Chile
| | - Daniel G Rivera
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle/Saale, Germany.,Center for Natural Products Research, Faculty of Chemistry, University of Havana, Zapata y G, 10400, La Habana, Cuba
| | - Ludger A Wessjohann
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle/Saale, Germany
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8
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Rubin SJS, Tal-Gan Y, Gilon C, Qvit N. Conversion of Protein Active Regions into Peptidomimetic Therapeutic Leads Using Backbone Cyclization and Cycloscan - How to Do it Yourself! Curr Top Med Chem 2018; 18:556-565. [PMID: 29773063 DOI: 10.2174/1568026618666180518094322] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 04/24/2018] [Accepted: 04/26/2018] [Indexed: 12/21/2022]
Abstract
Protein-protein Interactions (PPIs) are particularly important for controlling both physiologic and pathologic biological processes but are difficult to target due to their large and/or shallow interaction surfaces unsuitable for small molecules. Linear peptides found in nature interact with some PPIs, and protein active regions can be used to design synthetic peptide compounds for inhibition of PPIs. However, linear peptides are limited therapeutically by poor metabolic and conformational stability, which can compromise their bioactivity and half-life. Cyclic peptidomimetics (modified peptides) can be used to overcome these challenges because they are more resistant to metabolic degradation and can be engineered to adopt desired conformations. Backbone cyclization is a strategy that we developed to improve drug-like properties of linear peptide leads without jeopardizing the integrity of functionally relevant side-chains. Here, we provide the first description of an entire approach for developing backbone cyclized peptide compounds, based upon two straightforward 'ABC' and 'DEF' processes. We present practical examples throughout our discussion of revealing active regions important for PPIs and identifying critical pharmacophores, as well as developing backbone cyclized peptide libraries and screening them using cycloscan. Finally, we review the impact of these advances and provide a summary of current ongoing work in the field.
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Affiliation(s)
- Samuel J S Rubin
- Stanford Immunology Program, School of Medicine, Stanford University, 269 Campus drive, Stanford CA 94305-5174, United States
| | - Yftah Tal-Gan
- Department of Chemistry, University of Nevada, Reno, 1664 North Virginia Street, NV 89557, United States
| | - Chaim Gilon
- The Institute of Chemistry, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
| | - Nir Qvit
- The Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Henrietta Szold St. 8, POB 1589, Safed, Israel
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9
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Development of a Novel Backbone Cyclic Peptide Inhibitor of the Innate Immune TLR/IL1R Signaling Protein MyD88. Sci Rep 2018; 8:9476. [PMID: 29930295 PMCID: PMC6013495 DOI: 10.1038/s41598-018-27773-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 06/04/2018] [Indexed: 12/28/2022] Open
Abstract
MyD88 is a cytoplasmic adaptor protein that plays a central role in signaling downstream of the TLRs and the IL1R superfamily. We previously demonstrated that MyD88 plays a critical role in EAE, the murine model of multiple sclerosis, and showed that the MyD88 BB-loop decoy peptide RDVLPGT ameliorates EAE. We now designed and screened a library of backbone cyclized peptides based on the linear BB loop peptide, to identify a metabolically stable inhibitor of MyD88 that retains the binding properties of the linear peptide. We identified a novel cyclic peptide protein mimetic that inhibits inflammatory responses to TLR ligands, and NFκB activation in response to IL-1 activation. The inhibitor, c(MyD 4-4), is metabolically stable in comparison to the linear peptide, blocks MyD88 in a specific manner, and inhibits MyD88 function by preventing MyD88 dimerization. Finally, treatment of mice with c(MyD 4-4) reduced the severity of clinical disease in the murine EAE model of multiple sclerosis. Thus, modulation of MyD88-dependent signaling using c(MyD 4-4) is a potential therapeutic strategy to lower innate immune inflammation in autoimmune CNS disease.
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10
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Hanold LE, Fulton MD, Kennedy EJ. Targeting kinase signaling pathways with constrained peptide scaffolds. Pharmacol Ther 2017; 173:159-170. [PMID: 28185915 DOI: 10.1016/j.pharmthera.2017.02.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Kinases are amongst the largest families in the human proteome and serve as critical mediators of a myriad of cell signaling pathways. Since altered kinase activity is implicated in a variety of pathological diseases, kinases have become a prominent class of proteins for targeted inhibition. Although numerous small molecule and antibody-based inhibitors have already received clinical approval, several challenges may still exist with these strategies including resistance, target selection, inhibitor potency and in vivo activity profiles. Constrained peptide inhibitors have emerged as an alternative strategy for kinase inhibition. Distinct from small molecule inhibitors, peptides can provide a large binding surface area that allows them to bind shallow protein surfaces rather than defined pockets within the target protein structure. By including chemical constraints within the peptide sequence, additional benefits can be bestowed onto the peptide scaffold such as improved target affinity and target selectivity, cell permeability and proteolytic resistance. In this review, we highlight examples of diverse chemistries that are being employed to constrain kinase-targeting peptide scaffolds and highlight their application to modulate kinase signaling as well as their potential clinical implications.
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Affiliation(s)
- Laura E Hanold
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, United States
| | - Melody D Fulton
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, United States
| | - Eileen J Kennedy
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, United States.
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11
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Rational, computer-enabled peptide drug design: principles, methods, applications and future directions. Future Med Chem 2015; 7:2173-93. [PMID: 26510691 DOI: 10.4155/fmc.15.142] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Peptides provide promising templates for developing drugs to occupy a middle space between small molecules and antibodies and for targeting 'undruggable' intracellular protein-protein interactions. Importantly, rational or in cerebro design, especially when coupled with validated in silico tools, can be used to efficiently explore chemical space and identify islands of 'drug-like' peptides to satisfy diverse drug discovery program objectives. Here, we consider the underlying principles of and recent advances in rational, computer-enabled peptide drug design. In particular, we consider the impact of basic physicochemical properties, potency and ADME/Tox opportunities and challenges, and recently developed computational tools for enabling rational peptide drug design. Key principles and practices are spotlighted by recent case studies. We close with a hypothetical future case study.
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12
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Fernández-Llamazares AI, Spengler J, Albericio F. Review backboneN-modified peptides: How to meet the challenge of secondary amine acylation. Biopolymers 2015; 104:435-52. [DOI: 10.1002/bip.22696] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 05/21/2015] [Accepted: 05/26/2015] [Indexed: 12/29/2022]
Affiliation(s)
- Ana I. Fernández-Llamazares
- Institute for Research in Biomedicine; Deparment of Chemistry and Molecular Pharmacology, Barcelona Science Park; Baldiri Reixac 10 Barcelona 08028 Spain
- CIBER-BBN; Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park; Baldiri Reixac 10 Barcelona 08028 Spain
| | - Jan Spengler
- Institute for Research in Biomedicine; Deparment of Chemistry and Molecular Pharmacology, Barcelona Science Park; Baldiri Reixac 10 Barcelona 08028 Spain
- CIBER-BBN; Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park; Baldiri Reixac 10 Barcelona 08028 Spain
| | - Fernando Albericio
- Institute for Research in Biomedicine; Deparment of Chemistry and Molecular Pharmacology, Barcelona Science Park; Baldiri Reixac 10 Barcelona 08028 Spain
- CIBER-BBN; Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park; Baldiri Reixac 10 Barcelona 08028 Spain
- Department of Organic Chemistry; University of Barcelona; Martí i Franquès 1-11 Barcelona 08028 Spain
- School of Chemistry and Physics; University of KwaZulu-Natal; 4001 Durban South Africa
- School of Life Sciences, Department of Chemistry, Yachay Tech, Yachay City of Knowledge; Urcuquι 100119 Ecuador. Department of Chemistry; College of Science, King Saud University; P.O. Box 2455 Riyadh 11451 Saudi Arabia
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13
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Fang Z, Simard JR, Plenker D, Nguyen HD, Phan T, Wolle P, Baumeister S, Rauh D. Discovery of inter-domain stabilizers-a novel assay system for allosteric akt inhibitors. ACS Chem Biol 2015; 10:279-88. [PMID: 24959717 DOI: 10.1021/cb500355c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In addition to the catalytically active kinase domain, most kinases feature regulatory domains that govern their activity. Modulating and interfering with these interdomain interactions presents a major opportunity for understanding biological systems and developing novel therapeutics. Therefore, small molecule inhibitors that target these interactions through an allosteric mode of action have high intrinsic selectivity, as these interactions are often unique to a single kinase or kinase family. Here we report the development of iFLiK (interface-Fluorescent Labels in Kinases), a fluorescence-based assay that can monitor such interdomain interactions. Using iFLiK, we have demonstrated selective detection of allosteric Akt inhibitors that induce an inactive closed conformation unique to Akt. This methodology easily distinguished small molecule allosteric inhibitors from classic ATP-competitive inhibitors. Screening an in-house compound library with iFLiK, we were able to identify novel compounds with a scaffold that has not been previously described for allosteric Akt inhibitors.
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Affiliation(s)
- Zhizhou Fang
- Technische Universität Dortmund, Fakultät
für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
- Chemical
Genomics
Centre of the Max Planck Society, Otto-Hahn-Strasse
15, 44227 Dortmund, Germany
| | - Jeffrey R. Simard
- Chemical
Genomics
Centre of the Max Planck Society, Otto-Hahn-Strasse
15, 44227 Dortmund, Germany
| | - Dennis Plenker
- University of Cologne, Medical Faculty, Department
of Translational Genomics, Weyertal 115b, 50931 Cologne, Germany
| | - Hoang D. Nguyen
- Chemical
Genomics
Centre of the Max Planck Society, Otto-Hahn-Strasse
15, 44227 Dortmund, Germany
| | - Trang Phan
- Chemical
Genomics
Centre of the Max Planck Society, Otto-Hahn-Strasse
15, 44227 Dortmund, Germany
| | - Patrik Wolle
- Technische Universität Dortmund, Fakultät
für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Stefan Baumeister
- Technische Universität Dortmund, Fakultät
für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Daniel Rauh
- Technische Universität Dortmund, Fakultät
für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
- Chemical
Genomics
Centre of the Max Planck Society, Otto-Hahn-Strasse
15, 44227 Dortmund, Germany
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14
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Kim YB, Kang CW, Ranatunga S, Yang H, Sebti SM, Del Valle JR. Imidazo[1,2-a]pyridine-based peptidomimetics as inhibitors of Akt. Bioorg Med Chem Lett 2014; 24:4650-4653. [PMID: 25205195 DOI: 10.1016/j.bmcl.2014.08.040] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 08/16/2014] [Accepted: 08/19/2014] [Indexed: 12/26/2022]
Abstract
We report the design, synthesis, and biological evaluation of imidazopyridine-based peptidomimetics based on the substrate consensus sequence of Akt, an AGC family serine/threonine kinase hyperactivated in over 50% of human tumors. Our ligand-based approach led to the identification of novel substrate mimetic inhibitors of Akt1 featuring an unnatural extended dipeptide surrogate. Compound 11 inhibits Akt isoforms in the sub-micromolar range and exhibits improved proteolytic stability relative to a parent pentapeptide.
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Affiliation(s)
- Young B Kim
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Chang Won Kang
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Sujeewa Ranatunga
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Hua Yang
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Said M Sebti
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Juan R Del Valle
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
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15
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Davoudi Z, Akbarzadeh A, Rahmatiyamchi M, Movassaghpour AA, Alipour M, Nejati-Koshki K, Sadeghi Z, Dariushnejad H, Zarghami N. Molecular Target Therapy of AKT and NF-kB Signaling Pathways and Multidrug Resistance by Specific Cell Penetrating Inhibitor Peptides in HL-60 Cells. Asian Pac J Cancer Prev 2014; 15:4353-8. [DOI: 10.7314/apjcp.2014.15.10.4353] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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16
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Chandra K, Roy TK, Shalev DE, Loyter A, Gilon C, Gerber RB, Friedler A. A tandem in situ peptide cyclization through trifluoroacetic acid cleavage. Angew Chem Int Ed Engl 2014; 53:9450-5. [PMID: 24827640 DOI: 10.1002/anie.201402789] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Indexed: 12/31/2022]
Abstract
We present a new approach for peptide cyclization during solid phase synthesis under highly acidic conditions. Our approach involves simultaneous in situ deprotection, cyclization and trifluoroacetic acid (TFA) cleavage of the peptide, which is achieved by forming an amide bond between a lysine side chain and a succinic acid linker at the peptide N-terminus. The reaction proceeds via a highly active succinimide intermediate, which was isolated and characterized. The structure of a model cyclic peptide was solved by NMR spectroscopy. Theoretical calculations support the proposed mechanism of cyclization. Our new methodology is applicable for the formation of macrocycles in solid-phase synthesis of peptides and organic molecules.
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Affiliation(s)
- Koushik Chandra
- Institute of Chemistry, Edmond J. Safra campus The Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904 (Israel) http://chem.ch.huji.ac.il/∼assaf
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17
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Chandra K, Roy TK, Shalev DE, Loyter A, Gilon C, Gerber RB, Friedler A. A Tandem In Situ Peptide Cyclization through Trifluoroacetic Acid Cleavage. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402789] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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18
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Proctor A, Wang Q, Lawrence DS, Allbritton NL. Development of a peptidase-resistant substrate for single-cell measurement of protein kinase B activation. Anal Chem 2012; 84:7195-202. [PMID: 22881604 PMCID: PMC3428732 DOI: 10.1021/ac301489d] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
An iterative design strategy using three criteria was utilized to develop a peptidase-resistant substrate peptide for protein kinase B. Libraries of peptides possessing non-native amino acids were screened for time to 50% phosphorylation, degradation half-life within a lysate, and appearance of a dominant fragment. The lead peptide possessed a half-life of 92 ± 7 and 16 ± 2 min in HeLa and LNCaP cytosolic lysates, respectively, representing a 4.6- and 2.7-fold lifetime improvement over that of the starting peptide. The redesigned peptide possessed a 4.5-fold improvement in phosphorylation efficiency compared to the starting peptide. The same peptide fragments were formed when the lead peptide was incubated in a lysate or loaded into single cells although the fragments formed in significantly different ratios suggesting that distinct peptidases metabolized the peptide in the two preparations. The rate of peptide degradation and phosphorylation was on average 0.1 ± 0.2 zmol pg(-1) s(-1) and 0.04 ± 0.08 zmol pg(-1) s(-1), respectively, for single LNCaP cells loaded with 4 ± 8 μM of peptide. Peptidase-resistant kinase substrates should find widespread utility in both lysate-based and single-cell assays of kinase activity.
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Affiliation(s)
- Angela Proctor
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Qunzhao Wang
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - David S. Lawrence
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
- Division of Chemical Biology and Medicinal Chemistry, School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Nancy L. Allbritton
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Biomedical Engineering, University of North Carolina, Chapel Hill, NC 27599, USA and North Carolina State University, Raleigh, NC 27695, USA
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19
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Proctor A, Wang Q, Lawrence DS, Allbritton NL. Metabolism of peptide reporters in cell lysates and single cells. Analyst 2012; 137:3028-38. [PMID: 22314840 PMCID: PMC3697743 DOI: 10.1039/c2an16162a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The stability of an Abl kinase substrate peptide in a cytosolic lysate and in single cells was characterized. In the cytosolic lysate, the starting peptide was metabolized at an average initial rate of 1.7 ± 0.3 zmol pg(-1) s(-1) with a t(1/2) of 1.3 min. Five different fragments formed over time; however, a dominant cleavage site was identified. Multiple rational design cycles were utilized to develop a lead peptide with a phenylalanine and alanine replaced by an (N-methyl)phenylalanine and isoleucine, respectively, to attain cytosolic peptidase resistance while maintaining Abl substrate efficacy. This lead peptide possessed a 15-fold greater lifetime in the cytosolic lysate while attaining a 7-fold improvement in k(cat) as an Abl kinase substrate compared to the starting peptide. However, when loaded into single cells, the starting peptide and lead peptide possessed nearly identical degradation rates and an altered pattern of fragmentation relative to that in cell lysates. Preferential accumulation of a fragment with cleavage at an Ala-Ala bond in single cells suggested that dissimilar peptidases act on the peptides in the lysate versus single cells. A design strategy for peptide stabilization, analogous to that demonstrated for the lysate, should be effective for stabilization in single cells.
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Affiliation(s)
- Angela Proctor
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
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20
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Studying protein–peptide interactions using benzophenone units: A case study of protein kinase B/Akt and its inhibitor PTR6154. Anal Biochem 2012; 421:750-4. [DOI: 10.1016/j.ab.2011.11.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 11/17/2011] [Accepted: 11/23/2011] [Indexed: 11/20/2022]
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21
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Ben-Shimon A, Niv MY. Deciphering the Arginine-binding preferences at the substrate-binding groove of Ser/Thr kinases by computational surface mapping. PLoS Comput Biol 2011; 7:e1002288. [PMID: 22125489 PMCID: PMC3219626 DOI: 10.1371/journal.pcbi.1002288] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2011] [Accepted: 10/12/2011] [Indexed: 11/18/2022] Open
Abstract
Protein kinases are key signaling enzymes that catalyze the transfer of γ-phosphate from an ATP molecule to a phospho-accepting residue in the substrate. Unraveling the molecular features that govern the preference of kinases for particular residues flanking the phosphoacceptor is important for understanding kinase specificities toward their substrates and for designing substrate-like peptidic inhibitors. We applied ANCHORSmap, a new fragment-based computational approach for mapping amino acid side chains on protein surfaces, to predict and characterize the preference of kinases toward Arginine binding. We focus on positions P−2 and P−5, commonly occupied by Arginine (Arg) in substrates of basophilic Ser/Thr kinases. The method accurately identified all the P−2/P−5 Arg binding sites previously determined by X-ray crystallography and produced Arg preferences that corresponded to those experimentally found by peptide arrays. The predicted Arg-binding positions and their associated pockets were analyzed in terms of shape, physicochemical properties, amino acid composition, and in-silico mutagenesis, providing structural rationalization for previously unexplained trends in kinase preferences toward Arg moieties. This methodology sheds light on several kinases that were described in the literature as having non-trivial preferences for Arg, and provides some surprising departures from the prevailing views regarding residues that determine kinase specificity toward Arg. In particular, we found that the preference for a P−5 Arg is not necessarily governed by the 170/230 acidic pair, as was previously assumed, but by several different pairs of acidic residues, selected from positions 133, 169, and 230 (PKA numbering). The acidic residue at position 230 serves as a pivotal element in recognizing Arg from both the P−2 and P−5 positions. Protein kinases are key signaling enzymes and major drug targets that catalyze the transfer of phosphate group to a phospho-accepting residue in the substrate. Unraveling molecular features that govern the preference of kinases for particular residues flanking the phosphoacceptor (substrate consensus sequence, SCS) is important for understanding kinase-substrates specificities and for designing peptidic inhibitors. Current methods used to predict this set of essential residues usually rely on linking between experimentally determined SCSs to kinase sequences. As such, these methods are less sensitive when specificity is dictated by subtle or kinase-unique sequence/structural features. In this study, we took a different approach for studying kinases specificities, by applying a new fragment-based method for mapping amino acid side chains on protein surfaces. We predicted and characterized the preference of Ser/Thr kinases toward Arginine binding, using the unbound kinase structures. The method produced high quality predictions and was able to provide novel insights and interesting departures from the prevailing views regarding the specificity-determining elements governing specificity toward Arginine. This work paves the way for studying the kinase binding preferences for other amino acids, for predicting protein-peptide structures, for facilitating the design of novel inhibitors, and for re-engineering of kinase specificities.
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Affiliation(s)
- Avraham Ben-Shimon
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment and The Fritz Haber Center for Molecular Dynamics, The Hebrew University, Israel
| | - Masha Y. Niv
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment and The Fritz Haber Center for Molecular Dynamics, The Hebrew University, Israel
- * E-mail:
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22
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Ranatunga S, Del Valle JR. Synthesis of GSK3β mimetic inhibitors of Akt featuring a novel extended dipeptide surrogate. Bioorg Med Chem Lett 2011; 21:7166-9. [PMID: 22001093 DOI: 10.1016/j.bmcl.2011.09.079] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Revised: 09/16/2011] [Accepted: 09/19/2011] [Indexed: 12/27/2022]
Abstract
Akt is a cardinal nodal point in PI3K signaling pathway and confers resistance to apoptosis through inactivation of regulatory substrates such as GSK3β. Efforts to inhibit the kinase activity of Akt have largely focused on targeting the ATP-binding domain of Akt. Here, we present the design and synthesis of conformationally constrained GSK3β mimics featuring a novel extended dipeptide surrogate core. This effort resulted in the identification of a novel substrate mimetic Akt inhibitor (11) with low micromolar activity in vitro (Akt1 IC(50)=3.1 μM).
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Affiliation(s)
- Sujeewa Ranatunga
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
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