1
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Hildebrandt ER, Hussain SA, Sieburg MA, Ravishankar R, Asad N, Gore S, Ito T, Hougland JL, Dore TM, Schmidt WK. Targeted genetic and small molecule disruption of N-Ras CaaX cleavage alters its localization and oncogenic potential. Bioorg Chem 2024; 147:107316. [PMID: 38583246 PMCID: PMC11098683 DOI: 10.1016/j.bioorg.2024.107316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/16/2024] [Accepted: 03/26/2024] [Indexed: 04/09/2024]
Abstract
Ras GTPases and other CaaX proteins undergo multiple post-translational modifications at their carboxyl-terminus. These events initiate with prenylation of a cysteine and are followed by endoproteolytic removal of the 'aaX' tripeptide and carboxylmethylation. Some CaaX proteins are only subject to prenylation, however, due to the presence of an uncleavable sequence. In this study, uncleavable sequences were used to stage Ras isoforms in a farnesylated and uncleaved state to address the impact of CaaX proteolysis on protein localization and function. This targeted strategy is more specific than those that chemically inhibit the Rce1 CaaX protease or delete the RCE1 gene because global abrogation of CaaX proteolysis impacts the entire CaaX protein proteome and effects cannot be attributed to any specific CaaX protein of the many concurrently affected. With this targeted strategy, clear mislocalization and reduced activity of farnesylated and uncleaved Ras isoforms was observed. In addition, new peptidomimetics based on cleavable Ras CaaX sequences and the uncleavable CAHQ sequence were synthesized and tested as Rce1 inhibitors using in vitro and cell-based assays. Consistently, these non-hydrolyzable peptidomimetic Rce1 inhibitors recapitulate Ras mislocalization effects when modeled on cleavable but not uncleavable CaaX sequences. These findings indicate that a prenylated and uncleavable CaaX sequence, which can be easily applied to a wide range of mammalian CaaX proteins, can be used to probe the specific impact of CaaX proteolysis on CaaX protein properties under conditions of an otherwise normally processed CaaX protein proteome.
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Affiliation(s)
- Emily R Hildebrandt
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, USA
| | - Shaneela A Hussain
- New York University Abu Dhabi, Saadiyat Island, PO Box 129188, Abu Dhabi, UAE
| | | | - Rajani Ravishankar
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, USA
| | - Nadeem Asad
- New York University Abu Dhabi, Saadiyat Island, PO Box 129188, Abu Dhabi, UAE
| | - Sangram Gore
- New York University Abu Dhabi, Saadiyat Island, PO Box 129188, Abu Dhabi, UAE
| | - Takahiro Ito
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, USA
| | - James L Hougland
- Department of Chemistry, Syracuse University, Syracuse, NY, USA; Department of Biology, Syracuse University, Syracuse, NY, USA; BioInspired Syracuse, Syracuse University, Syracuse, NY, USA
| | - Timothy M Dore
- New York University Abu Dhabi, Saadiyat Island, PO Box 129188, Abu Dhabi, UAE; Department of Chemistry, University of Georgia, Athens, GA, USA
| | - Walter K Schmidt
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, USA.
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2
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Yang Y, Ahmad E, Premkumar V, Liu A, Ashikur Rahman SM, Nikolovska‐Coleska Z. Structural studies of intrinsically disordered MLL-fusion protein AF9 in complex with peptidomimetic inhibitors. Protein Sci 2024; 33:e5019. [PMID: 38747396 PMCID: PMC11094776 DOI: 10.1002/pro.5019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 04/23/2024] [Accepted: 04/28/2024] [Indexed: 05/19/2024]
Abstract
AF9 (MLLT3) and its paralog ENL(MLLT1) are members of the YEATS family of proteins with important role in transcriptional and epigenetic regulatory complexes. These proteins are two common MLL fusion partners in MLL-rearranged leukemias. The oncofusion proteins MLL-AF9/ENL recruit multiple binding partners, including the histone methyltransferase DOT1L, leading to aberrant transcriptional activation and enhancing the expression of a characteristic set of genes that drive leukemogenesis. The interaction between AF9 and DOT1L is mediated by an intrinsically disordered C-terminal ANC1 homology domain (AHD) in AF9, which undergoes folding upon binding of DOT1L and other partner proteins. We have recently reported peptidomimetics that disrupt the recruitment of DOT1L by AF9 and ENL, providing a proof-of-concept for targeting AHD and assessing its druggability. Intrinsically disordered proteins, such as AF9 AHD, are difficult to study and characterize experimentally on a structural level. In this study, we present a successful protein engineering strategy to facilitate structural investigation of the intrinsically disordered AF9 AHD domain in complex with peptidomimetic inhibitors by using maltose binding protein (MBP) as a crystallization chaperone connected with linkers of varying flexibility and length. The strategic incorporation of disulfide bonds provided diffraction-quality crystals of the two disulfide-bridged MBP-AF9 AHD fusion proteins in complex with the peptidomimetics. These successfully determined first series of 2.1-2.6 Å crystal complex structures provide high-resolution insights into the interactions between AHD and its inhibitors, shedding light on the role of AHD in recruiting various binding partner proteins. We show that the overall complex structures closely resemble the reported NMR structure of AF9 AHD/DOT1L with notable difference in the conformation of the β-hairpin region, stabilized through conserved hydrogen bonds network. These first series of AF9 AHD/peptidomimetics complex structures are providing insights of the protein-inhibitor interactions and will facilitate further development of novel inhibitors targeting the AF9/ENL AHD domain.
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Affiliation(s)
- Yuting Yang
- Department of PathologyUniversity of Michigan Medical SchoolAnn ArborMichiganUSA
| | - Ejaz Ahmad
- Department of PathologyUniversity of Michigan Medical SchoolAnn ArborMichiganUSA
| | - Vidhya Premkumar
- Department of PathologyUniversity of Michigan Medical SchoolAnn ArborMichiganUSA
| | - Alicen Liu
- Department of PathologyUniversity of Michigan Medical SchoolAnn ArborMichiganUSA
| | - S. M. Ashikur Rahman
- Department of PathologyUniversity of Michigan Medical SchoolAnn ArborMichiganUSA
| | - Zaneta Nikolovska‐Coleska
- Department of PathologyUniversity of Michigan Medical SchoolAnn ArborMichiganUSA
- Rogel Cancer CenterUniversity of Michigan Medical SchoolAnn ArborMichiganUSA
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3
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Zhang Y, Liu Y, Wu X, Lu X, Wang M, Ye D, Iqbal C, Sun W, Zhang X, Zhang L, Yang X. A Novel Peptidomimetic Insecticide: Dippu-AstR-Based Rational Design and Biological Activity of Allatostatin Analogs. J Agric Food Chem 2024; 72:11341-11350. [PMID: 38713071 DOI: 10.1021/acs.jafc.3c09231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Insect neuropeptides play an essential role in regulating growth, development, reproduction, nerve conduction, metabolism, and behavior in insects; therefore, G protein-coupled receptors of neuropeptides are considered important targets for designing green insecticides. Cockroach-type allatostatins (ASTs) (FGLamides allatostatins) are important insect neuropeptides in Diploptera punctata that inhibit juvenile hormone (JH) synthesis in the corpora allata and affect growth, development, and reproduction of insects. Therefore, the pursuit of novel insecticides targeting the allatostatin receptor (AstR) holds significant importance. Previously, we identified an AST analogue, H17, as a promising candidate for pest control. Herein, we first modeled the 3D structure of AstR in D. punctata (Dippu-AstR) and predicted the binding mode of H17 with Dippu-AstR to study the critical interactions and residues favorable to its bioactivity. Based on this binding mode, we designed and synthesized a series of H17 derivatives and assessed their insecticidal activity against D. punctata. Among them, compound Q6 showed higher insecticidal activity than H17 against D. punctata by inhibiting JH biosynthesis, indicating that Q6 is a potential candidate for a novel insect growth regulator (IGR)-based insecticide. Moreover, Q6 exhibited insecticidal activity against Plutella xylostella, indicating that these AST analogs may have a wider insecticidal spectrum. The underlying mechanisms and molecular conformations mediating the interactions of Q6 with Dippu-AstR were explored to understand its effects on the bioactivity. The present work clarifies how a target-based strategy facilitates the discovery of new peptide mimics with better bioactivity, enabling improved IGR-based insecticide potency in sustainable agriculture.
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Affiliation(s)
- Yimeng Zhang
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Yan Liu
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Xiaoqing Wu
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Xingxing Lu
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Meizi Wang
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Dexing Ye
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Chandni Iqbal
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Wenyu Sun
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Xinyuan Zhang
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Li Zhang
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
- Key Laboratory of National Forestry and Grassland Administration on Pest Chemical Control, China Agricultural University, Beijing 100193, China
| | - Xinling Yang
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
- Key Laboratory of National Forestry and Grassland Administration on Pest Chemical Control, China Agricultural University, Beijing 100193, China
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4
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Guerinot C, Malige M, Charbonnel N, Malosse K, Jouffret L, Taillefumier C, Roy O, Forestier C, Faure S. Design of Triazolium-Grafted Peptidomimetic Macrocycles with Facial Amphipathicity to Target Pathogenic Bacteria. Org Lett 2024; 26:4088-4092. [PMID: 38709636 DOI: 10.1021/acs.orglett.4c01149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Access to 1,2,3-triazolium-grafted peptoid macrocycles was developed by macrocyclization and multivalent postmodification of linear peptoid oligomers carrying an alternance of benzylic and propargyl groups as side chains. X-ray analysis and NMR studies revealed a conformational preference for constrained hairpin-shaped structures leading to the facial amphipathic character of these macrocycles. A preliminary evaluation showed the antimicrobial activities of these new cationic amphipathic architectures.
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Affiliation(s)
- Cassandra Guerinot
- Université Clermont Auvergne, Clermont Auvergne INP, CNRS, ICCF, F-63000 Clermont-Ferrand, France
| | - Mélodie Malige
- Université Clermont Auvergne, CNRS, LMGE, F-63000 Clermont-Ferrand, France
| | - Nicolas Charbonnel
- Université Clermont Auvergne, CNRS, LMGE, F-63000 Clermont-Ferrand, France
| | - Killian Malosse
- Université Clermont Auvergne, Clermont Auvergne INP, CNRS, ICCF, F-63000 Clermont-Ferrand, France
| | - Laurent Jouffret
- Université Clermont Auvergne, Clermont Auvergne INP, CNRS, ICCF, F-63000 Clermont-Ferrand, France
| | - Claude Taillefumier
- Université Clermont Auvergne, Clermont Auvergne INP, CNRS, ICCF, F-63000 Clermont-Ferrand, France
| | - Olivier Roy
- Université Clermont Auvergne, Clermont Auvergne INP, CNRS, ICCF, F-63000 Clermont-Ferrand, France
| | | | - Sophie Faure
- Université Clermont Auvergne, Clermont Auvergne INP, CNRS, ICCF, F-63000 Clermont-Ferrand, France
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5
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Cekała K, Trepczyk K, Witkowska J, Jankowska E, Wieczerzak E. Rpt5-Derived Analogs Stimulate Human Proteasome Activity in Cells and Degrade Proteins Forming Toxic Aggregates in Age-Related Diseases. Int J Mol Sci 2024; 25:4663. [PMID: 38731881 PMCID: PMC11082943 DOI: 10.3390/ijms25094663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/15/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024] Open
Abstract
Aging and age-related diseases are associated with a decline in the capacity of protein turnover. Intrinsically disordered proteins, as well as proteins misfolded and oxidatively damaged, prone to aggregation, are preferentially digested by the ubiquitin-independent proteasome system (UIPS), a major component of which is the 20S proteasome. Therefore, boosting 20S activity constitutes a promising strategy to counteract a decrease in total proteasome activity during aging. One way to enhance the proteolytic removal of unwanted proteins appears to be the use of peptide-based activators of the 20S. In this study, we synthesized a series of peptides and peptidomimetics based on the C-terminus of the Rpt5 subunit of the 19S regulatory particle. Some of them efficiently stimulated human 20S proteasome activity. The attachment of the cell-penetrating peptide TAT allowed them to penetrate the cell membrane and stimulate proteasome activity in HEK293T cells, which was demonstrated using a cell-permeable substrate of the proteasome, TAS3. Furthermore, the best activator enhanced the degradation of aggregation-prone α-synuclein and Tau-441. The obtained compounds may therefore have the potential to compensate for the unbalanced proteostasis found in aging and age-related diseases.
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Affiliation(s)
| | | | | | - Elżbieta Jankowska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (K.C.)
| | - Ewa Wieczerzak
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (K.C.)
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6
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Müller P, Zimmer C, Frey A, Holzmann G, Weldert AC, Schirmeister T. Ligand-Based Design of Selective Peptidomimetic uPA and TMPRSS2 Inhibitors with Arg Bioisosteres. Int J Mol Sci 2024; 25:1375. [PMID: 38338655 PMCID: PMC10855164 DOI: 10.3390/ijms25031375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 01/20/2024] [Accepted: 01/21/2024] [Indexed: 02/12/2024] Open
Abstract
Trypsin-like serine proteases are involved in many important physiological processes like blood coagulation and remodeling of the extracellular matrix. On the other hand, they are also associated with pathological conditions. The urokinase-pwlasminogen activator (uPA), which is involved in tissue remodeling, can increase the metastatic behavior of various cancer types when overexpressed and dysregulated. Another member of this protease class that received attention during the SARS-CoV 2 pandemic is TMPRSS2. It is a transmembrane serine protease, which enables cell entry of the coronavirus by processing its spike protein. A variety of different inhibitors have been published against both proteases. However, the selectivity over other trypsin-like serine proteases remains a major challenge. In the current study, we replaced the arginine moiety at the P1 site of peptidomimetic inhibitors with different bioisosteres. Enzyme inhibition studies revealed that the phenylguanidine moiety in the P1 site led to strong affinity for TMPRSS2, whereas the cyclohexylguanidine derivate potently inhibited uPA. Both inhibitors exhibited high selectivity over other structurally similar and physiologically important proteases.
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Affiliation(s)
| | | | | | | | | | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany; (P.M.); (C.Z.); (A.F.); (G.H.); (A.C.W.)
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7
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Giorgio A, Del Gatto A, Pennacchio S, Saviano M, Zaccaro L. Peptoids: Smart and Emerging Candidates for the Diagnosis of Cancer, Neurological and Autoimmune Disorders. Int J Mol Sci 2023; 24:16333. [PMID: 38003529 PMCID: PMC10671428 DOI: 10.3390/ijms242216333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/10/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023] Open
Abstract
Early detection of fatal and disabling diseases such as cancer, neurological and autoimmune dysfunctions is still desirable yet challenging to improve quality of life and longevity. Peptoids (N-substituted glycine oligomers) are a relatively new class of peptidomimetics, being highly versatile and capable of mimicking the architectures and the activities of the peptides but with a marked resistance to proteases and a propensity to cross the cellular membranes over the peptides themselves. For these properties, they have gained an ever greater interest in applications in bioengineering and biomedical fields. In particular, the present manuscript is to our knowledge the only review focused on peptoids for diagnostic applications and covers the last decade's literature regarding peptoids as tools for early diagnosis of pathologies with a great impact on human health and social behavior. The review indeed provides insights into the peptoid employment in targeted cancer imaging and blood-based screening of neurological and autoimmune diseases, and it aims to attract the scientific community's attention to continuing and sustaining the investigation of these peptidomimetics in the diagnosis field considering their promising peculiarities.
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Affiliation(s)
- Anna Giorgio
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy;
| | - Annarita Del Gatto
- Institute of Biostructure and Bioimaging (IBB), CNR, 80131 Naples, Italy;
- Interuniversity Research Centre on Bioactive Peptides (CIRPeB) “Carlo Pedone”, University of Naples “Federico II”, 80131 Naples, Italy
| | - Simone Pennacchio
- Institute of Condensed Matter Chemistry and Technologies for Energy (ICMATE), CNR, 35127 Padova, Italy;
| | | | - Laura Zaccaro
- Institute of Biostructure and Bioimaging (IBB), CNR, 80131 Naples, Italy;
- Interuniversity Research Centre on Bioactive Peptides (CIRPeB) “Carlo Pedone”, University of Naples “Federico II”, 80131 Naples, Italy
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8
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Liu W, Hopkins AM, Yan P, Du S, Luyt LG, Li Y, Hou J. Can machine learning 'transform' peptides/peptidomimetics into small molecules? A case study with ghrelin receptor ligands. Mol Divers 2023; 27:2239-2255. [PMID: 36331785 DOI: 10.1007/s11030-022-10555-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022]
Abstract
There has been considerable interest in transforming peptides into small molecules as peptide-based molecules often present poorer bioavailability and lower metabolic stability. Our studies looked into building machine learning (ML) models to investigate if ML is able to identify the 'bioactive' features of peptides and use the features to accurately discriminate between binding and non-binding small molecules. The ghrelin receptor (GR), a receptor that is implicated in various diseases, was used as an example to demonstrate whether ML models derived from a peptide library can be used to predict small molecule binders. ML models based on three different algorithms, namely random forest, support vector machine, and extreme gradient boosting, were built based on a carefully curated dataset of peptide/peptidomimetic and small molecule GR ligands. The results indicated that ML models trained with a dataset exclusively composed of peptides/peptidomimetics provide limited predictive power for small molecules, but that ML models trained with a diverse dataset composed of an array of both peptides/peptidomimetics and small molecules displayed exceptional results in terms of accuracy and false rates. The diversified models can accurately differentiate the binding small molecules from non-binding small molecules using an external validation set with new small molecules that we synthesized previously. Structural features that are the most critical contributors to binding activity were extracted and are remarkably consistent with the crystallography and mutagenesis studies.
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Affiliation(s)
- Wenjie Liu
- Department of Chemistry, Lakehead University and Thunder Bay Regional Health Research Institute, 980 Oliver Road, Thunder Bay, ON, P7B 6V4, Canada
| | - Austin M Hopkins
- Department of Chemistry, Lakehead University and Thunder Bay Regional Health Research Institute, 980 Oliver Road, Thunder Bay, ON, P7B 6V4, Canada
| | - Peizhi Yan
- Department of Electrical and Computer Engineering, The University of British Columbia, Vancouver, BC, Canada
| | - Shan Du
- Department of Computer Science, Mathematics, Physics and Statistics, The University of British Columbia, Okanagan, Kelowna, BC, Canada
| | - Leonard G Luyt
- Department of Chemistry, University of Western Ontario, London, ON, Canada
- London Regional Cancer Program, Lawson Health Research Institute, London, ON, Canada
| | - Yifeng Li
- Department of Computer Science, Brock University, Saint Catharines, ON, Canada
| | - Jinqiang Hou
- Department of Chemistry, Lakehead University and Thunder Bay Regional Health Research Institute, 980 Oliver Road, Thunder Bay, ON, P7B 6V4, Canada.
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9
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Sahrawat P, Kowalczyk P, Koszelewski D, Szymczak M, Kramkowski K, Wypych A, Ostaszewski R. Influence of Open Chain and Cyclic Structure of Peptidomimetics on Antibacterial Activity in E. coli Strains. Molecules 2022; 27:molecules27113633. [PMID: 35684570 PMCID: PMC9182016 DOI: 10.3390/molecules27113633] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 05/25/2022] [Accepted: 05/31/2022] [Indexed: 12/25/2022] Open
Abstract
An efficient method for the synthesis of functionalized peptidomimetics via multicomponent Ugi reaction has been developed. The application of trifluoroethanol (TFE) as a reaction medium provided desired products with good yields. Further, using the developed cyclisation reaction, the obtained peptidomimetics were transformed into the cyclic analogues (diketopiperazines, DKPs). The goal of the performed studies was to revised and compare whether the structure of the obtained structurally flexible acyclic peptidomimetics and their rigid cycling analogue DKPs affect antimicrobial activity. We studied the potential of synthesized peptidomimetics, both cyclic and acyclic, as antimicrobial drugs on model E. coli bacteria strains (k12, R2–R4). The biological assays reveal that DKPs hold more potential as antimicrobial drugs compared to open chain Ugi peptidomimetics. We believe that it can be due to the rigid cyclic structure of DKPs which promotes the membrane penetration in the cell of studied pathogens. The obtained data clearly indicate the high antibiotic potential of synthesized diketopiperazine derivatives over tested antibiotics.
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Affiliation(s)
- Parul Sahrawat
- Institute of Organic Chemistry PAS, Kasprzaka 44/52, 01-224 Warsaw, Poland; (P.S.); (D.K.)
| | - Paweł Kowalczyk
- Department of Animal Nutrition, The Kielanowski Institute of Animal Physiology and Nutrition, Polish Academy of Sciences, Instytucka 3, 05-110 Jabłonna, Poland
- Correspondence: (P.K.); (R.O.)
| | - Dominik Koszelewski
- Institute of Organic Chemistry PAS, Kasprzaka 44/52, 01-224 Warsaw, Poland; (P.S.); (D.K.)
| | - Mateusz Szymczak
- Department of Molecular Virology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland;
| | - Karol Kramkowski
- Department of Physical Chemistry, Medical University of Bialystok, Kilińskiego 1 Str., 15-089 Białystok, Poland;
| | - Aleksandra Wypych
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Torun, ul. Wileńska 4, 87-100 Toruń, Poland;
| | - Ryszard Ostaszewski
- Institute of Organic Chemistry PAS, Kasprzaka 44/52, 01-224 Warsaw, Poland; (P.S.); (D.K.)
- Correspondence: (P.K.); (R.O.)
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10
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Aathi MS, Kumar C, Prabhudesai KS, Shanmugarajan D, Idicula-Thomas S. Mapping of FSHR agonists and antagonists binding sites to identify potential peptidomimetic modulators. Biochim Biophys Acta Biomembr 2022; 1864:183842. [PMID: 34954201 DOI: 10.1016/j.bbamem.2021.183842] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/06/2021] [Accepted: 12/13/2021] [Indexed: 12/14/2022]
Abstract
Owing to the critical role of follicle stimulating hormone receptor (FSHR) signaling in human reproduction, FSHR has been widely explored for development of fertility regulators. Using high-throughput screening approaches, several low molecular weight (LMW) compounds that can modulate FSHR activity have been identified. However, the information about the binding sites of these molecules on FSHR is not known. In the present study, we extracted the structural and functional information of 161 experimentally validated LMW FSHR modulators available in PubMed records. The potential FSHR binding sites for these modulators were identified through molecular docking experiments. The binding sites were further mapped to the agonist or antagonist activity reported for these molecules in literature. MD simulations were performed to evaluate the effect of ligand binding on conformational changes in the receptor, specifically the transmembrane domain. A peptidomimetic library was screened using these binding sites. Six peptidomimetics that interacted with the residues of transmembrane domain and extracellular loops were evaluated for binding activity using in vitro cAMP assay. Two of the six peptidomimetics exhibited positive allosteric modulatory activity and four peptidomimetics exhibited negative allosteric modulatory activity. All six peptidomimetics interacted with Asp521 of hFSHR(TMD). Several of the experimentally known LMW FSHR modulators also participated in H-bond interactions with Asp521, suggesting its important role in FSHR modulatory activity.
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Affiliation(s)
- Muthu Sankar Aathi
- Biomedical Informatics Centre, ICMR-National Institute for Research in Reproductive and Child Health, Mumbai 400012, India
| | - Chandan Kumar
- Biomedical Informatics Centre, ICMR-National Institute for Research in Reproductive and Child Health, Mumbai 400012, India
| | - Kaushiki S Prabhudesai
- Biomedical Informatics Centre, ICMR-National Institute for Research in Reproductive and Child Health, Mumbai 400012, India
| | | | - Susan Idicula-Thomas
- Biomedical Informatics Centre, ICMR-National Institute for Research in Reproductive and Child Health, Mumbai 400012, India.
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11
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Dai W, Jochmans D, Xie H, Yang H, Li J, Su H, Chang D, Wang J, Peng J, Zhu L, Nian Y, Hilgenfeld R, Jiang H, Chen K, Zhang L, Xu Y, Neyts J, Liu H. Design, Synthesis, and Biological Evaluation of Peptidomimetic Aldehydes as Broad-Spectrum Inhibitors against Enterovirus and SARS-CoV-2. J Med Chem 2022; 65:2794-2808. [PMID: 33872498 PMCID: PMC8084273 DOI: 10.1021/acs.jmedchem.0c02258] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Indexed: 12/30/2022]
Abstract
A novel series of peptidomimetic aldehydes was designed and synthesized to target 3C protease (3Cpro) of enterovirus 71 (EV71). Most of the compounds exhibited high antiviral activity, and among them, compound 18p demonstrated potent enzyme inhibitory activity and broad-spectrum antiviral activity on a panel of enteroviruses and rhinoviruses. The crystal structure of EV71 3Cpro in complex with 18p determined at a resolution of 1.2 Å revealed that 18p covalently linked to the catalytic Cys147 with an aldehyde group. In addition, these compounds also exhibited good inhibitory activity against the 3CLpro and the replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), especially compound 18p (IC50 = 0.034 μM, EC50 = 0.29 μM). According to our previous work, these compounds have no reasons for concern regarding acute toxicity. Compared with AG7088, compound 18p also exhibited good pharmacokinetic properties and more potent anticoronavirus activity, making it an excellent lead for further development.
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Affiliation(s)
- Wenhao Dai
- State Key Laboratory of Drug Research, CAS Key
Laboratory of Receptor Research, Shanghai Institute of Materia Medica,
Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203,
China
- University of Chinese Academy of
Sciences, Beijing 100049, China
| | - Dirk Jochmans
- KU Leuven, Department of Microbiology and Immunology,
Rega Institute for Medical Research, Laboratory of Virology and
Chemotherapy, Leuven B-3000, Belgium
| | - Hang Xie
- State Key Laboratory of Drug Research, CAS Key
Laboratory of Receptor Research, Shanghai Institute of Materia Medica,
Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203,
China
| | - Hang Yang
- State Key Laboratory of Virology, Wuhan
Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of
Sciences, Wuhan, Hubei 430071, China
| | - Jian Li
- State Key Laboratory of Drug Research, CAS Key
Laboratory of Receptor Research, Shanghai Institute of Materia Medica,
Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203,
China
- College of Pharmacy, Nanjing University
of Chinese Medicine, 138 Xianlin Avenue, Qixia District, Nanjing, 210023,
China
| | - Haixia Su
- State Key Laboratory of Drug Research, CAS Key
Laboratory of Receptor Research, Shanghai Institute of Materia Medica,
Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203,
China
- University of Chinese Academy of
Sciences, Beijing 100049, China
| | - Di Chang
- Shanghai Key Laboratory of New Drug Design, School of
Pharmacy, East China University of Science and Technology, 130
Meilong Road, Shanghai 200237, China
| | - Jiang Wang
- State Key Laboratory of Drug Research, CAS Key
Laboratory of Receptor Research, Shanghai Institute of Materia Medica,
Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203,
China
- University of Chinese Academy of
Sciences, Beijing 100049, China
- School of Pharmaceutical Science and Technology,
Hangzhou Institute for Advanced Study, University of Chinese Academy of
Sciences, Hangzhou 310024, China
| | - Jingjing Peng
- State Key Laboratory of Drug Research, CAS Key
Laboratory of Receptor Research, Shanghai Institute of Materia Medica,
Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203,
China
- University of Chinese Academy of
Sciences, Beijing 100049, China
| | - Lili Zhu
- Shanghai Key Laboratory of New Drug Design, School of
Pharmacy, East China University of Science and Technology, 130
Meilong Road, Shanghai 200237, China
| | - Yong Nian
- State Key Laboratory of Drug Research, CAS Key
Laboratory of Receptor Research, Shanghai Institute of Materia Medica,
Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203,
China
- College of Pharmacy, Nanjing University
of Chinese Medicine, 138 Xianlin Avenue, Qixia District, Nanjing, 210023,
China
| | - Rolf Hilgenfeld
- Institute of Molecular Medicine,
University of Lübeck, 23562 Lübeck,
Germany
- German Center for Infection Research (DZIF),
University of Lübeck, 23562 Lübeck,
Germany
| | - Hualiang Jiang
- State Key Laboratory of Drug Research, CAS Key
Laboratory of Receptor Research, Shanghai Institute of Materia Medica,
Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203,
China
- University of Chinese Academy of
Sciences, Beijing 100049, China
- School of Pharmaceutical Science and Technology,
Hangzhou Institute for Advanced Study, University of Chinese Academy of
Sciences, Hangzhou 310024, China
| | - Kaixian Chen
- State Key Laboratory of Drug Research, CAS Key
Laboratory of Receptor Research, Shanghai Institute of Materia Medica,
Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203,
China
- University of Chinese Academy of
Sciences, Beijing 100049, China
| | - Leike Zhang
- State Key Laboratory of Virology, Wuhan
Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of
Sciences, Wuhan, Hubei 430071, China
| | - Yechun Xu
- State Key Laboratory of Drug Research, CAS Key
Laboratory of Receptor Research, Shanghai Institute of Materia Medica,
Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203,
China
- University of Chinese Academy of
Sciences, Beijing 100049, China
- School of Pharmaceutical Science and Technology,
Hangzhou Institute for Advanced Study, University of Chinese Academy of
Sciences, Hangzhou 310024, China
| | - Johan Neyts
- KU Leuven, Department of Microbiology and Immunology,
Rega Institute for Medical Research, Laboratory of Virology and
Chemotherapy, Leuven B-3000, Belgium
| | - Hong Liu
- State Key Laboratory of Drug Research, CAS Key
Laboratory of Receptor Research, Shanghai Institute of Materia Medica,
Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203,
China
- College of Pharmacy, Nanjing University
of Chinese Medicine, 138 Xianlin Avenue, Qixia District, Nanjing, 210023,
China
- University of Chinese Academy of
Sciences, Beijing 100049, China
- School of Pharmaceutical Science and Technology,
Hangzhou Institute for Advanced Study, University of Chinese Academy of
Sciences, Hangzhou 310024, China
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12
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Bai B, Belovodskiy A, Hena M, Kandadai AS, Joyce MA, Saffran HA, Shields JA, Khan MB, Arutyunova E, Lu J, Bajwa SK, Hockman D, Fischer C, Lamer T, Vuong W, van Belkum MJ, Gu Z, Lin F, Du Y, Xu J, Rahim M, Young HS, Vederas JC, Tyrrell DL, Lemieux MJ, Nieman JA. Peptidomimetic α-Acyloxymethylketone Warheads with Six-Membered Lactam P1 Glutamine Mimic: SARS-CoV-2 3CL Protease Inhibition, Coronavirus Antiviral Activity, and in Vitro Biological Stability. J Med Chem 2022; 65:2905-2925. [PMID: 34242027 PMCID: PMC8291138 DOI: 10.1021/acs.jmedchem.1c00616] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Indexed: 12/11/2022]
Abstract
Recurring coronavirus outbreaks, such as the current COVID-19 pandemic, establish a necessity to develop direct-acting antivirals that can be readily administered and are active against a broad spectrum of coronaviruses. Described in this Article are novel α-acyloxymethylketone warhead peptidomimetic compounds with a six-membered lactam glutamine mimic in P1. Compounds with potent SARS-CoV-2 3CL protease and in vitro viral replication inhibition were identified with low cytotoxicity and good plasma and glutathione stability. Compounds 15e, 15h, and 15l displayed selectivity for SARS-CoV-2 3CL protease over CatB and CatS and superior in vitro SARS-CoV-2 antiviral replication inhibition compared with the reported peptidomimetic inhibitors with other warheads. The cocrystallization of 15l with SARS-CoV-2 3CL protease confirmed the formation of a covalent adduct. α-Acyloxymethylketone compounds also exhibited antiviral activity against an alphacoronavirus and non-SARS betacoronavirus strains with similar potency and a better selectivity index than remdesivir. These findings demonstrate the potential of the substituted heteroaromatic and aliphatic α-acyloxymethylketone warheads as coronavirus inhibitors, and the described results provide a basis for further optimization.
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Affiliation(s)
- Bing Bai
- Li Ka Shing Applied Virology Institute,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Medical Microbiology and Immunology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
| | - Alexandr Belovodskiy
- Li Ka Shing Applied Virology Institute,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Medical Microbiology and Immunology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
| | - Mostofa Hena
- Li Ka Shing Applied Virology Institute,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Medical Microbiology and Immunology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
| | - Appan Srinivas Kandadai
- Li Ka Shing Applied Virology Institute,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Medical Microbiology and Immunology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
| | - Michael A. Joyce
- Li Ka Shing Institute of Virology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Medical Microbiology and Immunology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
| | - Holly A. Saffran
- Li Ka Shing Institute of Virology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Medical Microbiology and Immunology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
| | - Justin A. Shields
- Li Ka Shing Institute of Virology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Medical Microbiology and Immunology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
| | - Muhammad Bashir Khan
- Department of Biochemistry, University of
Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Elena Arutyunova
- Li Ka Shing Institute of Virology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Biochemistry, University of
Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Jimmy Lu
- Li Ka Shing Institute of Virology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Biochemistry, University of
Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Sardeev K. Bajwa
- Department of Biochemistry, University of
Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Darren Hockman
- Li Ka Shing Applied Virology Institute,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Medical Microbiology and Immunology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
| | - Conrad Fischer
- Department of Chemistry, University of
Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Tess Lamer
- Department of Chemistry, University of
Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Wayne Vuong
- Department of Chemistry, University of
Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Marco J. van Belkum
- Department of Chemistry, University of
Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Zhengxian Gu
- WuXi AppTec (Shanghai) Co., Ltd.,
G Warehouse #101, No. 10 Building, #227 Meisheng Road, WaiGaoQiao Free Trade Zone,
Shanghai 200131, China
| | - Fusen Lin
- WuXi AppTec (Shanghai) Co., Ltd.,
G Warehouse #101, No. 10 Building, #227 Meisheng Road, WaiGaoQiao Free Trade Zone,
Shanghai 200131, China
| | - Yanhua Du
- WuXi AppTec (Shanghai) Co., Ltd.,
G Warehouse #101, No. 10 Building, #227 Meisheng Road, WaiGaoQiao Free Trade Zone,
Shanghai 200131, China
| | - Jia Xu
- WuXi AppTec (Shanghai) Co., Ltd.,
G Warehouse #101, No. 10 Building, #227 Meisheng Road, WaiGaoQiao Free Trade Zone,
Shanghai 200131, China
| | - Mohammad Rahim
- Rane Pharmaceuticals, Inc.
4290 91a Street NW, Edmonton, Alberta T6E 5V2, Canada
| | - Howard S. Young
- Department of Biochemistry, University of
Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - John C. Vederas
- Department of Chemistry, University of
Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - D. Lorne Tyrrell
- Li Ka Shing Applied Virology Institute,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Li Ka Shing Institute of Virology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Medical Microbiology and Immunology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
| | - M. Joanne Lemieux
- Li Ka Shing Institute of Virology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Biochemistry, University of
Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - James A. Nieman
- Li Ka Shing Applied Virology Institute,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
- Department of Medical Microbiology and Immunology,
University of Alberta, Edmonton, Alberta T6G 2E1,
Canada
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13
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Han SH, Goins CM, Arya T, Shin WJ, Maw J, Hooper A, Sonawane DP, Porter MR, Bannister BE, Crouch RD, Lindsey AA, Lakatos G, Martinez SR, Alvarado J, Akers WS, Wang NS, Jung JU, Macdonald JD, Stauffer SR. Structure-Based Optimization of ML300-Derived, Noncovalent Inhibitors Targeting the Severe Acute Respiratory Syndrome Coronavirus 3CL Protease (SARS-CoV-2 3CL pro). J Med Chem 2022; 65:2880-2904. [PMID: 34347470 PMCID: PMC8353992 DOI: 10.1021/acs.jmedchem.1c00598] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Indexed: 12/18/2022]
Abstract
Starting from the MLPCN probe compound ML300, a structure-based optimization campaign was initiated against the recent severe acute respiratory syndrome coronavirus (SARS-CoV-2) main protease (3CLpro). X-ray structures of SARS-CoV-1 and SARS-CoV-2 3CLpro enzymes in complex with multiple ML300-based inhibitors, including the original probe ML300, were obtained and proved instrumental in guiding chemistry toward probe compound 41 (CCF0058981). The disclosed inhibitors utilize a noncovalent mode of action and complex in a noncanonical binding mode not observed by peptidic 3CLpro inhibitors. In vitro DMPK profiling highlights key areas where further optimization in the series is required to obtain useful in vivo probes. Antiviral activity was established using a SARS-CoV-2-infected Vero E6 cell viability assay and a plaque formation assay. Compound 41 demonstrates nanomolar activity in these respective assays, comparable in potency to remdesivir. These findings have implications for antiviral development to combat current and future SARS-like zoonotic coronavirus outbreaks.
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Affiliation(s)
- Sang Hoon Han
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Christopher M. Goins
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Tarun Arya
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Woo-Jin Shin
- Cleveland Clinic Florida Research & Innovation Center, Port St. Lucie, FL, 34987, USA
| | - Joshua Maw
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Alice Hooper
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Dhiraj P. Sonawane
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Matthew R. Porter
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Breyanne E. Bannister
- Department of Pharmaceutical Science, Lipscomb University College of Pharmacy, Nashville, TN, 37204, USA
| | - Rachel D. Crouch
- Department of Pharmaceutical Science, Lipscomb University College of Pharmacy, Nashville, TN, 37204, USA
| | - A. Abigail Lindsey
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Gabriella Lakatos
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Steven R. Martinez
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Joseph Alvarado
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Wendell S. Akers
- Department of Pharmaceutical Science, Lipscomb University College of Pharmacy, Nashville, TN, 37204, USA
| | - Nancy S. Wang
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Jae U. Jung
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
- Center for Global and Emerging Pathogens Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Jonathan D. Macdonald
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Shaun R. Stauffer
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
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14
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Konno S, Kobayashi K, Senda M, Funai Y, Seki Y, Tamai I, Schäkel L, Sakata K, Pillaiyar T, Taguchi A, Taniguchi A, Gütschow M, Müller CE, Takeuchi K, Hirohama M, Kawaguchi A, Kojima M, Senda T, Shirasaka Y, Kamitani W, Hayashi Y. 3CL Protease Inhibitors with an Electrophilic Arylketone Moiety as Anti-SARS-CoV-2 Agents. J Med Chem 2022; 65:2926-2939. [PMID: 34313428 PMCID: PMC8340582 DOI: 10.1021/acs.jmedchem.1c00665] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Indexed: 02/08/2023]
Abstract
The novel coronavirus, SARS-CoV-2, has been identified as the causative agent for the current coronavirus disease (COVID-19) pandemic. 3CL protease (3CLpro) plays a pivotal role in the processing of viral polyproteins. We report peptidomimetic compounds with a unique benzothiazolyl ketone as a warhead group, which display potent activity against SARS-CoV-2 3CLpro. The most potent inhibitor YH-53 can strongly block the SARS-CoV-2 replication. X-ray structural analysis revealed that YH-53 establishes multiple hydrogen bond interactions with backbone amino acids and a covalent bond with the active site of 3CLpro. Further results from computational and experimental studies, including an in vitro absorption, distribution, metabolism, and excretion profile, in vivo pharmacokinetics, and metabolic analysis of YH-53 suggest that it has a high potential as a lead candidate to compete with COVID-19.
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Affiliation(s)
- Sho Konno
- School of Pharmacy, Department of Medicinal Chemistry,
Tokyo University of Pharmacy and Life Sciences, Hachioji,
Tokyo, 192-0392, Japan
| | - Kiyotaka Kobayashi
- School of Pharmacy, Department of Medicinal Chemistry,
Tokyo University of Pharmacy and Life Sciences, Hachioji,
Tokyo, 192-0392, Japan
| | - Miki Senda
- Structural Biology Research Center, Institute of
Materials Structure Science, High Energy Accelerator Research Organization
(KEK), Tsukuba 305-0801, Japan
| | - Yuta Funai
- Faculty of Pharmacy, Institute of Medical,
Pharmaceutical and Health Sciences, Kanazawa University,
Kanazawa 920-1192, Japan
| | - Yuta Seki
- Faculty of Pharmacy, Institute of Medical,
Pharmaceutical and Health Sciences, Kanazawa University,
Kanazawa 920-1192, Japan
| | - Ikumi Tamai
- Faculty of Pharmacy, Institute of Medical,
Pharmaceutical and Health Sciences, Kanazawa University,
Kanazawa 920-1192, Japan
| | - Laura Schäkel
- Pharmaceutical Institute, Pharmaceutical &
Medicinal Chemistry, University of Bonn, Bonn 53121,
Germany
| | - Kyousuke Sakata
- School of Life Sciences, Tokyo University
of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392,
Japan
| | - Thanigaimalai Pillaiyar
- Pharmaceutical Institute, Pharmaceutical/Medicinal Chemistry,
University of Tübingen, Tübingen 72076,
Germany
| | - Akihiro Taguchi
- School of Pharmacy, Department of Medicinal Chemistry,
Tokyo University of Pharmacy and Life Sciences, Hachioji,
Tokyo, 192-0392, Japan
| | - Atsuhiko Taniguchi
- School of Pharmacy, Department of Medicinal Chemistry,
Tokyo University of Pharmacy and Life Sciences, Hachioji,
Tokyo, 192-0392, Japan
| | - Michael Gütschow
- Pharmaceutical Institute, Pharmaceutical &
Medicinal Chemistry, University of Bonn, Bonn 53121,
Germany
| | - Christa E. Müller
- Pharmaceutical Institute, Pharmaceutical &
Medicinal Chemistry, University of Bonn, Bonn 53121,
Germany
| | - Koh Takeuchi
- Cellular and Molecular Biotechnology Research
Institute, National Institute of Advanced Industrial Science and
Technology, Koto, Tokyo 135-0064, Japan
| | - Mikako Hirohama
- Faculty of Medicine, Transborder Medical Research
Center, University of Tsukuba, Tsukuba 305-8575,
Japan
| | - Atsushi Kawaguchi
- Faculty of Medicine, Transborder Medical Research
Center, University of Tsukuba, Tsukuba 305-8575,
Japan
| | - Masaki Kojima
- School of Life Sciences, Tokyo University
of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392,
Japan
| | - Toshiya Senda
- Structural Biology Research Center, Institute of
Materials Structure Science, High Energy Accelerator Research Organization
(KEK), Tsukuba 305-0801, Japan
| | - Yoshiyuki Shirasaka
- Faculty of Pharmacy, Institute of Medical,
Pharmaceutical and Health Sciences, Kanazawa University,
Kanazawa 920-1192, Japan
| | - Wataru Kamitani
- Department of Infectious Diseases and Host Defense,
Gunma University Graduate School of Medicine, Maebashi
371-8511, Japan
| | - Yoshio Hayashi
- School of Pharmacy, Department of Medicinal Chemistry,
Tokyo University of Pharmacy and Life Sciences, Hachioji,
Tokyo, 192-0392, Japan
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15
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Wang Y, Xu B, Ma S, Wang H, Shang L, Zhu C, Ye S. Discovery of SARS-CoV-2 3CL Pro Peptidomimetic Inhibitors through the Catalytic Dyad Histidine-Specific Protein-Ligand Interactions. Int J Mol Sci 2022; 23:ijms23042392. [PMID: 35216507 PMCID: PMC8878928 DOI: 10.3390/ijms23042392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/16/2022] [Accepted: 02/19/2022] [Indexed: 12/22/2022] Open
Abstract
As the etiological agent for the coronavirus disease 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) challenges the ongoing efforts of vaccine development and drug design. Due to the accumulating cases of breakthrough infections, there are urgent needs for broad-spectrum antiviral medicines. Here, we designed and examined five new tetrapeptidomimetic anti-SARS-CoV-2 inhibitors targeting the 3C-Like protease (3CLPro), which is highly conserved among coronaviruses and essential for viral replications. We significantly improved the efficacy of a ketoamide lead compound based on high-resolution co-crystal structures, all-atom simulations, and binding energy calculations. The inhibitors successfully engaged the catalytic dyad histidine residue (H41) of 3CLPro as designed, and they exhibited nanomolar inhibitory capacity as well as mitigated the viral loads of SARS-CoV-2 in cellular assays. As a widely applicable design principle, our results revealed that the potencies of 3CLPro-specific drug candidates were determined by the interplay between 3CLPro H41 residue and the peptidomimetic inhibitors.
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Affiliation(s)
- Yaxin Wang
- Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin 300072, China; (Y.W.); (B.X.); (S.M.)
| | - Binghong Xu
- Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin 300072, China; (Y.W.); (B.X.); (S.M.)
| | - Sen Ma
- Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin 300072, China; (Y.W.); (B.X.); (S.M.)
| | - Hao Wang
- KLMDASR of Tianjin and Drug Discovery Center for Infectious Disease, State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin 300353, China; (H.W.); (L.S.)
| | - Luqing Shang
- KLMDASR of Tianjin and Drug Discovery Center for Infectious Disease, State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin 300353, China; (H.W.); (L.S.)
| | - Cheng Zhu
- Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin 300072, China; (Y.W.); (B.X.); (S.M.)
- Correspondence: (C.Z.); (S.Y.)
| | - Sheng Ye
- Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin 300072, China; (Y.W.); (B.X.); (S.M.)
- Correspondence: (C.Z.); (S.Y.)
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16
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Witkowska E, Godlewska M, Osiejuk J, Gątarz S, Wileńska B, Kosińska K, Starnowska-Sokół J, Piotrowska A, Lipiński PFJ, Matalińska J, Dyniewicz J, Halik PK, Gniazdowska E, Przewlocka B, Misicka A. Bifunctional Opioid/Melanocortin Peptidomimetics for Use in Neuropathic Pain: Variation in the Type and Length of the Linker Connecting the Two Pharmacophores. Int J Mol Sci 2022; 23:674. [PMID: 35054860 PMCID: PMC8775902 DOI: 10.3390/ijms23020674] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 01/25/2023] Open
Abstract
Based on the mechanism of neuropathic pain induction, a new type of bifunctional hybrid peptidomimetics was obtained for potential use in this type of pain. Hybrids consist of two types of pharmacophores that are connected by different types of linkers. The first pharmacophore is an opioid agonist, and the second pharmacophore is an antagonist of the pronociceptive system, i.e., an antagonist of the melanocortin-4 receptor. The results of tests in acute and neuropathic pain models of the obtained compounds have shown that the type of linker used to connect pharmacophores had an effect on antinociceptive activity. Peptidomimetics containing longer flexible linkers were very effective at low doses in the neuropathic pain model. To elucidate the effect of linker lengths, two hybrids showing very high activity and two hybrids with lower activity were further tested for affinity for opioid (mu, delta) and melanocortin-4 receptors. Their complexes with the target receptors were also studied by molecular modelling. Our results do not show a simple relationship between linker length and affinity for particular receptor types but suggest that activity in neuropathic pain is related to a proper balance of receptor affinity rather than maximum binding to any or all of the target receptors.
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Affiliation(s)
- Ewa Witkowska
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland; (M.G.); (J.O.); (S.G.); (B.W.); (K.K.)
| | - Magda Godlewska
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland; (M.G.); (J.O.); (S.G.); (B.W.); (K.K.)
| | - Jowita Osiejuk
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland; (M.G.); (J.O.); (S.G.); (B.W.); (K.K.)
| | - Sandra Gątarz
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland; (M.G.); (J.O.); (S.G.); (B.W.); (K.K.)
| | - Beata Wileńska
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland; (M.G.); (J.O.); (S.G.); (B.W.); (K.K.)
- Biological and Chemical Research Centre, University of Warsaw, 101 Zwirki i Wigury St., 02-097 Warsaw, Poland
| | - Katarzyna Kosińska
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland; (M.G.); (J.O.); (S.G.); (B.W.); (K.K.)
| | - Joanna Starnowska-Sokół
- Department of Pain Pharmacology, Maj Institute of Pharmacology, Polish Academy of Sciences, 12 Smetna Str., 31-343 Krakow, Poland; (J.S.-S.); (A.P.); (B.P.)
| | - Anna Piotrowska
- Department of Pain Pharmacology, Maj Institute of Pharmacology, Polish Academy of Sciences, 12 Smetna Str., 31-343 Krakow, Poland; (J.S.-S.); (A.P.); (B.P.)
| | - Piotr F. J. Lipiński
- Department of Neuropeptides, Mossakowski Medical Research Institute Polish Academy of Sciences, Pawińskiego 5, 02-106 Warsaw, Poland; (P.F.J.L.); (J.M.); (J.D.)
| | - Joanna Matalińska
- Department of Neuropeptides, Mossakowski Medical Research Institute Polish Academy of Sciences, Pawińskiego 5, 02-106 Warsaw, Poland; (P.F.J.L.); (J.M.); (J.D.)
| | - Jolanta Dyniewicz
- Department of Neuropeptides, Mossakowski Medical Research Institute Polish Academy of Sciences, Pawińskiego 5, 02-106 Warsaw, Poland; (P.F.J.L.); (J.M.); (J.D.)
| | - Paweł K. Halik
- Centre of Radiochemistry and Nuclear Chemistry, Institute of Nuclear Chemistry and Technology, Dorodna 16, 03-195 Warsaw, Poland; (P.K.H.); (E.G.)
| | - Ewa Gniazdowska
- Centre of Radiochemistry and Nuclear Chemistry, Institute of Nuclear Chemistry and Technology, Dorodna 16, 03-195 Warsaw, Poland; (P.K.H.); (E.G.)
| | - Barbara Przewlocka
- Department of Pain Pharmacology, Maj Institute of Pharmacology, Polish Academy of Sciences, 12 Smetna Str., 31-343 Krakow, Poland; (J.S.-S.); (A.P.); (B.P.)
| | - Aleksandra Misicka
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland; (M.G.); (J.O.); (S.G.); (B.W.); (K.K.)
- Biological and Chemical Research Centre, University of Warsaw, 101 Zwirki i Wigury St., 02-097 Warsaw, Poland
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Ye X, Gaucher JF, Vidal M, Broussy S. A Structural Overview of Vascular Endothelial Growth Factors Pharmacological Ligands: From Macromolecules to Designed Peptidomimetics. Molecules 2021; 26:6759. [PMID: 34833851 PMCID: PMC8625919 DOI: 10.3390/molecules26226759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 12/27/2022] Open
Abstract
The vascular endothelial growth factor (VEGF) family of cytokines plays a key role in vasculogenesis, angiogenesis, and lymphangiogenesis. VEGF-A is the main member of this family, alongside placental growth factor (PlGF), VEGF-B/C/D in mammals, and VEGF-E/F in other organisms. To study the activities of these growth factors under physiological and pathological conditions, resulting in therapeutic applications in cancer and age-related macular degeneration, blocking ligands have been developed. These have mostly been large biomolecules like antibodies. Ligands with high affinities, at least in the nanomolar range, and accurate structural data from X-ray crystallography and NMR spectroscopy have been described. They constitute the main focus of this overview, which evidences similarities and differences in their binding modes. For VEGF-A ligands, and to a limited extent also for PlGF, a transition is now observed towards developing smaller ligands like nanobodies and peptides. These include unnatural amino acids and chemical modifications for designed and improved properties, such as serum stability and greater affinity. However, this review also highlights the scarcity of such small molecular entities and the striking lack of small organic molecule ligands. It also shows the gap between the rather large array of ligands targeting VEGF-A and the general absence of ligands binding other VEGF members, besides some antibodies. Future developments in these directions are expected in the upcoming years, and the study of these growth factors and their promising therapeutic applications will be welcomed.
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Affiliation(s)
- Xiaoqing Ye
- Faculté de Pharmacie de Paris, Université de Paris, CiTCoM, 8038 CNRS, U 1268 INSERM, 75006 Paris, France; (X.Y.); (M.V.)
| | - Jean-François Gaucher
- Laboratoire de Cristallographie et RMN Biologiques, Faculté de Pharmacie de Paris, Université de Paris, CiTCoM, 8038 CNRS, 75006 Paris, France;
| | - Michel Vidal
- Faculté de Pharmacie de Paris, Université de Paris, CiTCoM, 8038 CNRS, U 1268 INSERM, 75006 Paris, France; (X.Y.); (M.V.)
- Service Biologie du Médicament, Toxicologie, AP-HP, Hôpital Cochin, 75014 Paris, France
| | - Sylvain Broussy
- Faculté de Pharmacie de Paris, Université de Paris, CiTCoM, 8038 CNRS, U 1268 INSERM, 75006 Paris, France; (X.Y.); (M.V.)
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Surmiak E, Magiera-Mularz K, Musielak B, Muszak D, Kocik-Krol J, Kitel R, Plewka J, Holak TA, Skalniak L. PD-L1 Inhibitors: Different Classes, Activities, and Mechanisms of Action. Int J Mol Sci 2021; 22:ijms222111797. [PMID: 34769226 PMCID: PMC8583776 DOI: 10.3390/ijms222111797] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 10/24/2021] [Accepted: 10/26/2021] [Indexed: 01/02/2023] Open
Abstract
Targeting the programmed cell death protein 1/programmed cell death 1 ligand 1 (PD-1/PD-L1) interaction has become an established strategy for cancer immunotherapy. Although hundreds of small-molecule, peptide, and peptidomimetic inhibitors have been proposed in recent years, only a limited number of drug candidates show good PD-1/PD-L1 blocking activity in cell-based assays. In this article, we compare representative molecules from different classes in terms of their PD-1/PD-L1 dissociation capacity measured by HTRF and in vitro bioactivity determined by the immune checkpoint blockade (ICB) co-culture assay. We point to recent discoveries that underscore important differences in the mechanisms of action of these molecules and also indicate one principal feature that needs to be considered, which is the eventual human PD-L1 specificity.
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Sartori A, Bugatti K, Portioli E, Baiula M, Casamassima I, Bruno A, Bianchini F, Curti C, Zanardi F, Battistini L. New 4-Aminoproline-Based Small Molecule Cyclopeptidomimetics as Potential Modulators of α 4β 1 Integrin. Molecules 2021; 26:molecules26196066. [PMID: 34641610 PMCID: PMC8512764 DOI: 10.3390/molecules26196066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/01/2021] [Accepted: 10/04/2021] [Indexed: 02/01/2023] Open
Abstract
Integrin α4β1 belongs to the leukocyte integrin family and represents a therapeutic target of relevant interest given its primary role in mediating inflammation, autoimmune pathologies and cancer-related diseases. The focus of the present work is the design, synthesis and characterization of new peptidomimetic compounds that are potentially able to recognize α4β1 integrin and interfere with its function. To this aim, a collection of seven new cyclic peptidomimetics possessing both a 4-aminoproline (Amp) core scaffold grafted onto key α4β1-recognizing sequences and the (2-methylphenyl)ureido-phenylacetyl (MPUPA) appendage, was designed, with the support of molecular modeling studies. The new compounds were synthesized through SPPS procedures followed by in-solution cyclization maneuvers. The biological evaluation of the new cyclic ligands in cell adhesion assays on Jurkat cells revealed promising submicromolar agonist activity in one compound, namely, the c[Amp(MPUPA)Val-Asp-Leu] cyclopeptide. Further investigations will be necessary to complete the characterization of this class of compounds.
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Affiliation(s)
- Andrea Sartori
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy; (A.S.); (K.B.); (E.P.); (A.B.); (C.C.); (F.Z.)
| | - Kelly Bugatti
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy; (A.S.); (K.B.); (E.P.); (A.B.); (C.C.); (F.Z.)
| | - Elisabetta Portioli
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy; (A.S.); (K.B.); (E.P.); (A.B.); (C.C.); (F.Z.)
| | - Monica Baiula
- Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 48, 40126 Bologna, Italy; (M.B.); (I.C.)
| | - Irene Casamassima
- Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 48, 40126 Bologna, Italy; (M.B.); (I.C.)
| | - Agostino Bruno
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy; (A.S.); (K.B.); (E.P.); (A.B.); (C.C.); (F.Z.)
| | - Francesca Bianchini
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Viale G.B. Morgagni 50, 50134 Firenze, Italy;
| | - Claudio Curti
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy; (A.S.); (K.B.); (E.P.); (A.B.); (C.C.); (F.Z.)
| | - Franca Zanardi
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy; (A.S.); (K.B.); (E.P.); (A.B.); (C.C.); (F.Z.)
| | - Lucia Battistini
- Department of Food and Drug, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy; (A.S.); (K.B.); (E.P.); (A.B.); (C.C.); (F.Z.)
- Correspondence: ; Tel.: +39-0521-906040
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Abstract
The selective tagging of amino acids within a peptide framework while using atom-economical C-H counterparts poses an unmet challenge within peptide chemistry. Herein, we report a novel Pd-catalyzed late-stage C-H acylation of a collection of Tyr-containing peptides with alcohols. This water-compatible labeling technique is distinguished by its reliable scalability and features the use of ethanol as a renewable feedstock for the assembly of a variety of peptidomimetics.
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Affiliation(s)
- Iñaki Urruzuno
- Department
of Organic Chemistry I, University of the
Basque Country (UPV/EHU), Joxe Mari Korta
R&D Center, Avenida Tolosa 72, 20018 Donostia-San Sebastián, Spain
| | - Paula Andrade-Sampedro
- Department
of Organic Chemistry I, University of the
Basque Country (UPV/EHU), Joxe Mari Korta
R&D Center, Avenida Tolosa 72, 20018 Donostia-San Sebastián, Spain
- Donostia
International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, 20018 Donostia-San Sebastián, Spain
| | - Arkaitz Correa
- Department
of Organic Chemistry I, University of the
Basque Country (UPV/EHU), Joxe Mari Korta
R&D Center, Avenida Tolosa 72, 20018 Donostia-San Sebastián, Spain
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Gadais C, Piekielna-Ciesielska J, De Neve J, Martin C, Janecka A, Ballet S. Harnessing the Anti-Nociceptive Potential of NK2 and NK3 Ligands in the Design of New Multifunctional μ/δ-Opioid Agonist-Neurokinin Antagonist Peptidomimetics. Molecules 2021; 26:molecules26175406. [PMID: 34500841 PMCID: PMC8434392 DOI: 10.3390/molecules26175406] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 08/26/2021] [Accepted: 09/03/2021] [Indexed: 11/16/2022] Open
Abstract
Opioid agonists are well-established analgesics, widely prescribed for acute but also chronic pain. However, their efficiency comes with the price of drastically impacting side effects that are inherently linked to their prolonged use. To answer these liabilities, designed multiple ligands (DMLs) offer a promising strategy by co-targeting opioid and non-opioid signaling pathways involved in nociception. Despite being intimately linked to the Substance P (SP)/neurokinin 1 (NK1) system, which is broadly examined for pain treatment, the neurokinin receptors NK2 and NK3 have so far been neglected in such DMLs. Herein, a series of newly designed opioid agonist-NK2 or -NK3 antagonists is reported. A selection of reported peptidic, pseudo-peptidic, and non-peptide neurokinin NK2 and NK3 ligands were covalently linked to the peptidic μ-opioid selective pharmacophore Dmt-DALDA (H-Dmt-d-Arg-Phe-Lys-NH2) and the dual μ/δ opioid agonist H-Dmt-d-Arg-Aba-βAla-NH2 (KGOP01). Opioid binding assays unequivocally demonstrated that only hybrids SBL-OPNK-5, SBL-OPNK-7 and SBL-OPNK-9, bearing the KGOP01 scaffold, conserved nanomolar range μ-opioid receptor (MOR) affinity, and slightly reduced affinity for the δ-opioid receptor (DOR). Moreover, NK binding experiments proved that compounds SBL-OPNK-5, SBL-OPNK-7, and SBL-OPNK-9 exhibited (sub)nanomolar binding affinity for NK2 and NK3, opening promising opportunities for the design of next-generation opioid hybrids.
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Affiliation(s)
- Charlène Gadais
- Research Group of Organic Chemistry, Departments of Bioengineering Sciences and Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; (J.D.N.); (C.M.)
- Institut des Sciences Chimiques de Rennes, Equipe CORINT, UMR 6226, Université de Rennes 1, 2 Avenue du Pr. Léon Bernard, CEDEX, 35043 Rennes, France
- Correspondence: (C.G.); (S.B.); Tel.: +32-2-6293-292 (S.B.)
| | - Justyna Piekielna-Ciesielska
- Department of Biomolecular Chemistry, Faculty of Medicine, Medical University of Lodz, 92-215 Lodz, Poland; (J.P.-C.); (A.J.)
| | - Jolien De Neve
- Research Group of Organic Chemistry, Departments of Bioengineering Sciences and Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; (J.D.N.); (C.M.)
| | - Charlotte Martin
- Research Group of Organic Chemistry, Departments of Bioengineering Sciences and Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; (J.D.N.); (C.M.)
| | - Anna Janecka
- Department of Biomolecular Chemistry, Faculty of Medicine, Medical University of Lodz, 92-215 Lodz, Poland; (J.P.-C.); (A.J.)
| | - Steven Ballet
- Research Group of Organic Chemistry, Departments of Bioengineering Sciences and Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; (J.D.N.); (C.M.)
- Correspondence: (C.G.); (S.B.); Tel.: +32-2-6293-292 (S.B.)
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Stemler T, Hoffmann C, Hierlmeier IM, Maus S, Krause E, Ezziddin S, Jung G, Bartholomä MD. A Structure-Activity Relationship Study of Bimodal BODIPY-Labeled PSMA-Targeting Bioconjugates. ChemMedChem 2021; 16:2535-2545. [PMID: 33905162 PMCID: PMC8453963 DOI: 10.1002/cmdc.202100210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Indexed: 12/15/2022]
Abstract
The aim of this study was to identify a high-affinity BODIPY peptidomimetic that targets the prostate-specific membrane antigen (PSMA) as a potential bimodal imaging probe for prostate cancer. For the structure-activity study, several BODIPY (difluoroboron dipyrromethene) derivatives with varying spacers between the BODIPY dye and the PSMA Glu-CO-Lys binding motif were prepared. Corresponding affinities were determined by competitive binding assays in PSMA-positive LNCaP cells. One compound was identified with comparable affinity (IC50 =21.5±0.1 nM) to Glu-CO-Lys-Ahx-HBED-CC (PSMA-11) (IC50 =18.4±0.2 nM). Radiolabeling was achieved by Lewis-acid-mediated 19 F/18 F exchange in moderate molar activities (∼0.7 MBq nmol-1 ) and high radiochemical purities (>99 %) with mean radiochemical yields of 20-30 %. Cell internalization of the 18 F-labeled high-affinity conjugate was demonstrated in LNCaP cells showing gradual increasing PSMA-mediated internalization over time. By fluorescence microscopy, localization of the high-affinity BODIPY-PSMA conjugate was found in the cell membrane at early time points and also in subcellular compartments at later time points. In summary, a high-affinity BODIPY-PSMA conjugate has been identified as a suitable candidate for the development of PSMA-specific dual-imaging agents.
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Affiliation(s)
- Tobias Stemler
- Department of Nuclear MedicineSaarland University – Medical CenterKirrbergerstrasse66421HomburgGermany
| | - Caroline Hoffmann
- Department of Biophysical ChemistrySaarland UniversityCampus B2 266123SaarbrückenGermany
| | - Ina M. Hierlmeier
- Department of Nuclear MedicineSaarland University – Medical CenterKirrbergerstrasse66421HomburgGermany
| | - Stephan Maus
- Department of Nuclear MedicineSaarland University – Medical CenterKirrbergerstrasse66421HomburgGermany
| | - Elmar Krause
- Department of Cellular NeurophysiologyCenter for Integrative Physiology and Molecular Medicine (CIPMM)Saarland UniversityKirrbergerstrasse66421HomburgGermany
| | - Samer Ezziddin
- Department of Nuclear MedicineSaarland University – Medical CenterKirrbergerstrasse66421HomburgGermany
| | - Gregor Jung
- Department of Biophysical ChemistrySaarland UniversityCampus B2 266123SaarbrückenGermany
| | - Mark D. Bartholomä
- Department of Nuclear MedicineSaarland University – Medical CenterKirrbergerstrasse66421HomburgGermany
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Das S, Amin SA, Jha T. Insight into the structural requirement of aryl sulphonamide based gelatinases (MMP-2 and MMP-9) inhibitors - Part I: 2D-QSAR, 3D-QSAR topomer CoMFA and Naïve Bayes studies - First report of 3D-QSAR Topomer CoMFA analysis for MMP-9 inhibitors and jointly inhibitors of gelatinases together. SAR QSAR Environ Res 2021; 32:655-687. [PMID: 34355614 DOI: 10.1080/1062936x.2021.1955414] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/11/2021] [Indexed: 06/13/2023]
Abstract
Gelatinases [gelatinase A - matrix metalloproteinase-2 (MMP-2), gelatinase B - matrix metalloproteinase-9 (MMP-9)] play key roles in many disease conditions including cancer. Despite some research work on gelatinases inhibitors both jointly and individually had been reported, challenges still exist in achieving potency as well as selectivity. Here in part I of a series of work, we have reported the structural requirement of some arylsulfonamides. In particular, regression-based 2D-QSARs, topomer CoMFA (comparative molecular field analysis) and Bayesian classification models were constructed to refine structural features for attaining better gelatinase inhibitory activity. The 2D-QSAR models exhibited good statistical significance. The descriptors nsssN, SHBint6, SHBint7, PubchemFP629 were directly correlated with the MMP-2 binding affinities whereas nsssN, SHBint10 and AATS2i were directly proportional to MMP-9 binding affinities. The topomer CoMFA results indicated that the steric and electrostatic fields play key roles in gelatinase inhibition. The established Naïve Bayes prediction models were evaluated by fivefold cross validation and an external test set. Furthermore, important molecular descriptors related to MMP-2 and MMP-9 binding affinities and some active/inactive fragments were identified. Thus, these observations may be helpful for further work of aryl sulphonamide based gelatinase inhibitors in future.
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Affiliation(s)
- S Das
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - S A Amin
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - T Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
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Herlan CN, Sonnefeld A, Gloge T, Brückel J, Schlee LC, Muhle-Goll C, Nieger M, Bräse S. Macrocyclic Tetramers-Structural Investigation of Peptide-Peptoid Hybrids. Molecules 2021; 26:molecules26154548. [PMID: 34361700 PMCID: PMC8348019 DOI: 10.3390/molecules26154548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 07/23/2021] [Accepted: 07/24/2021] [Indexed: 11/16/2022] Open
Abstract
Outstanding affinity and specificity are the main characteristics of peptides, rendering them interesting compounds for basic and medicinal research. However, their biological applicability is limited due to fast proteolytic degradation. The use of mimetic peptoids overcomes this disadvantage, though they lack stereochemical information at the α-carbon. Hybrids composed of amino acids and peptoid monomers combine the unique properties of both parent classes. Rigidification of the backbone increases the affinity towards various targets. However, only little is known about the spatial structure of such constrained hybrids. The determination of the three-dimensional structure is a key step for the identification of new targets as well as the rational design of bioactive compounds. Herein, we report the synthesis and the structural elucidation of novel tetrameric macrocycles. Measurements were taken in solid and solution states with the help of X-ray scattering and NMR spectroscopy. The investigations made will help to find diverse applications for this new, promising compound class.
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Affiliation(s)
- Claudine Nicole Herlan
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany; (C.N.H.); (J.B.); (L.C.S.)
| | - Anna Sonnefeld
- Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany; (A.S.); (T.G.); (C.M.-G.)
| | - Thomas Gloge
- Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany; (A.S.); (T.G.); (C.M.-G.)
| | - Julian Brückel
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany; (C.N.H.); (J.B.); (L.C.S.)
| | - Luisa Chiara Schlee
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany; (C.N.H.); (J.B.); (L.C.S.)
| | - Claudia Muhle-Goll
- Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany; (A.S.); (T.G.); (C.M.-G.)
| | - Martin Nieger
- Department of Chemistry, University of Helsinki, P.O. Box 55 (A.I. Virtasen aukio 1), FIN-00014 Helsinki, Finland;
| | - Stefan Bräse
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany; (C.N.H.); (J.B.); (L.C.S.)
- Institute of Biological and Chemical Systems—Functional Molecular Systems, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Correspondence:
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Yu TT, Kuppusamy R, Yasir M, Hassan MM, Sara M, Ho J, Willcox MDP, Black DS, Kumar N. Polyphenylglyoxamide-Based Amphiphilic Small Molecular Peptidomimetics as Antibacterial Agents with Anti-Biofilm Activity. Int J Mol Sci 2021; 22:7344. [PMID: 34298964 PMCID: PMC8303886 DOI: 10.3390/ijms22147344] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/01/2021] [Accepted: 07/04/2021] [Indexed: 01/02/2023] Open
Abstract
The rapid emergence of drug-resistant bacteria is a major global health concern. Antimicrobial peptides (AMPs) and peptidomimetics have arisen as a new class of antibacterial agents in recent years in an attempt to overcome antibiotic resistance. A library of phenylglyoxamide-based small molecular peptidomimetics was synthesised by incorporating an N-alkylsulfonyl hydrophobic group with varying alkyl chain lengths and a hydrophilic cationic group into a glyoxamide core appended to phenyl ring systems. The quaternary ammonium iodide salts 16d and 17c showed excellent minimum inhibitory concentration (MIC) of 4 and 8 μM (2.9 and 5.6 μg/mL) against Staphylococcus aureus, respectively, while the guanidinium hydrochloride salt 34a showed an MIC of 16 μM (8.5 μg/mL) against Escherichia coli. Additionally, the quaternary ammonium iodide salt 17c inhibited 70% S. aureus biofilm formation at 16 μM. It also disrupted 44% of pre-established S. aureus biofilms at 32 μM and 28% of pre-established E. coli biofilms 64 μM, respectively. A cytoplasmic membrane permeability study indicated that the synthesised peptidomimetics acted via disruption and depolarisation of membranes. Moreover, the quaternary ammonium iodide salts 16d and 17c were non-toxic against human cells at their therapeutic dosages against S. aureus.
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Affiliation(s)
- Tsz Tin Yu
- School of Chemistry, The University of New South Wales, Sydney, NSW 2052, Australia; (T.T.Y.); (R.K.); (M.M.H.); (J.H.)
| | - Rajesh Kuppusamy
- School of Chemistry, The University of New South Wales, Sydney, NSW 2052, Australia; (T.T.Y.); (R.K.); (M.M.H.); (J.H.)
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW 2052, Australia; (M.Y.); (M.S.); (M.D.P.W.)
| | - Muhammad Yasir
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW 2052, Australia; (M.Y.); (M.S.); (M.D.P.W.)
| | - Md. Musfizur Hassan
- School of Chemistry, The University of New South Wales, Sydney, NSW 2052, Australia; (T.T.Y.); (R.K.); (M.M.H.); (J.H.)
| | - Manjulatha Sara
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW 2052, Australia; (M.Y.); (M.S.); (M.D.P.W.)
| | - Junming Ho
- School of Chemistry, The University of New South Wales, Sydney, NSW 2052, Australia; (T.T.Y.); (R.K.); (M.M.H.); (J.H.)
| | - Mark D. P. Willcox
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW 2052, Australia; (M.Y.); (M.S.); (M.D.P.W.)
| | - David StC. Black
- School of Chemistry, The University of New South Wales, Sydney, NSW 2052, Australia; (T.T.Y.); (R.K.); (M.M.H.); (J.H.)
| | - Naresh Kumar
- School of Chemistry, The University of New South Wales, Sydney, NSW 2052, Australia; (T.T.Y.); (R.K.); (M.M.H.); (J.H.)
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Frederiksen N, Louka S, Mudaliar C, Domraceva I, Kreicberga A, Pugovics O, Żabicka D, Tomczak M, Wygoda W, Björkling F, Franzyk H. Peptide/β-Peptoid Hybrids with Ultrashort PEG-Like Moieties: Effects on Hydrophobicity, Antibacterial Activity and Hemolytic Properties. Int J Mol Sci 2021; 22:ijms22137041. [PMID: 34208826 PMCID: PMC8268887 DOI: 10.3390/ijms22137041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 12/01/2022] Open
Abstract
PEGylation of antimicrobial peptides as a shielding tool that increases stability toward proteolytic degradation typically leads to concomitant loss of activity, whereas incorporation of ultrashort PEG-like amino acids (sPEGs) remains essentially unexplored. Here, modification of a peptide/β-peptoid hybrid with sPEGs was examined with respect to influence on hydrophobicity, antibacterial activity and effect on viability of mammalian cells for a set of 18 oligomers. Intriguingly, the degree of sPEG modification did not significantly affect hydrophobicity as measured by retention in reverse-phase HPLC. Antibacterial activity against both wild-type and drug-resistant strains of Escherichia coli and Acinetobacter baumannii (both Gram-negative pathogens) was retained or slightly improved (MICs in the range 2–16 µg/mL equal to 0.7–5.2 µM). All compounds in the series exhibited less than 10% hemolysis at 400 µg/mL. While the number of sPEG moieties appeared not to be clearly correlated with hemolytic activity, a trend toward slightly increased hemolytic activity was observed for analogues displaying the longest sPEGs. In contrast, within a subseries the viability of HepG2 liver cells was least affected by analogues displaying the longer sPEGs (with IC50 values of ~1280 µg/mL) as compared to most other analogues and the parent peptidomimetic (IC50 values in the range 330–800 µg/mL).
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Affiliation(s)
- Nicki Frederiksen
- Center for Peptide-Based Antibiotics, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark; (N.F.); (S.L.); (C.M.); (F.B.)
| | - Stavroula Louka
- Center for Peptide-Based Antibiotics, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark; (N.F.); (S.L.); (C.M.); (F.B.)
| | - Chirag Mudaliar
- Center for Peptide-Based Antibiotics, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark; (N.F.); (S.L.); (C.M.); (F.B.)
| | - Ilona Domraceva
- Latvian Institute of Organic Synthesis, Aizkraukles 21, 1006 Riga, Latvia; (I.D.); (A.K.); (O.P.)
| | - Agrita Kreicberga
- Latvian Institute of Organic Synthesis, Aizkraukles 21, 1006 Riga, Latvia; (I.D.); (A.K.); (O.P.)
| | - Osvalds Pugovics
- Latvian Institute of Organic Synthesis, Aizkraukles 21, 1006 Riga, Latvia; (I.D.); (A.K.); (O.P.)
| | - Dorota Żabicka
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, ul. Chełmska 30/34, 00-725 Warsaw, Poland; (D.Ż.); (M.T.); (W.W.)
| | - Magdalena Tomczak
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, ul. Chełmska 30/34, 00-725 Warsaw, Poland; (D.Ż.); (M.T.); (W.W.)
| | - Weronika Wygoda
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, ul. Chełmska 30/34, 00-725 Warsaw, Poland; (D.Ż.); (M.T.); (W.W.)
| | - Fredrik Björkling
- Center for Peptide-Based Antibiotics, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark; (N.F.); (S.L.); (C.M.); (F.B.)
| | - Henrik Franzyk
- Center for Peptide-Based Antibiotics, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark; (N.F.); (S.L.); (C.M.); (F.B.)
- Correspondence:
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Wang L, Shen Q, Liao H, Fu H, Wang Q, Yu J, Zhang W, Chen C, Dong Y, Yang X, Guo Q, Zhang J, Zhang J, Zhang W, Lin H, Duan Y. Multi-Arm PEG/Peptidomimetic Conjugate Inhibitors of DR6/APP Interaction Block Hematogenous Tumor Cell Extravasation. Adv Sci (Weinh) 2021; 8:e2003558. [PMID: 34105277 PMCID: PMC8188212 DOI: 10.1002/advs.202003558] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 01/16/2021] [Indexed: 05/05/2023]
Abstract
The binding of amyloid precursor protein (APP) expressed on tumor cells to death receptor 6 (DR6) could initiate the necroptosis pathway, which leads to necroptotic cell death of vascular endothelial cells (ECs) and results in tumor cells (TCs) extravasation and metastasis. This study reports the first inhibitor of DR6/APP interaction as a novel class of anti-hematogenous metastatic agent. By rationally utilizing three combined strategies including selection based on phage display library, d-retro-inverso modification, and multiple conjugation of screened peptidomimetic with 4-arm PEG, the polymer-peptidomimetic conjugate PEG-tAHP-DRI (tetra-(D-retro-inverso isomer of AHP-12) substitued 4-arm PEG5k ) is obtained as the most promising agent with the strongest binding potency (KD = 51.12 × 10-9 m) and excellent pharmacokinetic properties. Importantly, PEG-tAHP-DRI provides efficient protection against TC-induced ECs necroptosis both in vitro and in vivo. Moreover, this ligand exhibits prominent anti-hematogenous metastatic activity in serval different metastatic mouse models (B16F10, 4T1, CT26, and spontaneous lung metastasis of 4T1 orthotopic tumor model) and displays no apparent detrimental effects in preliminary safety evaluation. Collectively, this study demonstrates the feasibility of exploiting DR6/APP interaction to regulate hematogenous tumor cells transendothelial migration and provides PEG-tAHP-DRI as a novel and promising inhibitor of DR6/APP interaction for developments of anti-hematogenous metastatic therapies.
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Affiliation(s)
- Liting Wang
- State Key Laboratory of Oncogenes and Related GenesShanghai Cancer InstituteSchool of Biomedical EngineeringRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200032China
| | - Qing Shen
- State Key Laboratory of Oncogenes and Related GenesShanghai Cancer InstituteSchool of Biomedical EngineeringRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200032China
| | - Hongze Liao
- Research Center for Marine DrugsState Key Laboratory of Oncogenes and Related GenesDepartment of PharmacyRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Hao Fu
- State Key Laboratory of Oncogenes and Related GenesShanghai Cancer InstituteSchool of Biomedical EngineeringRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200032China
| | - Qi Wang
- Shanghai Key Laboratory of Functional Materials ChemistrySchool of Chemistry and Molecular EngineeringEast China University of Science and TechnologyShanghai200237China
| | - Jian Yu
- State Key Laboratory of Oncogenes and Related GenesShanghai Cancer InstituteSchool of Biomedical EngineeringRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200032China
| | - Wei Zhang
- State Key Laboratory of Oncogenes and Related GenesShanghai Cancer InstituteSchool of Biomedical EngineeringRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200032China
| | - Chuanrong Chen
- State Key Laboratory of Oncogenes and Related GenesShanghai Cancer InstituteSchool of Biomedical EngineeringRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200032China
| | - Yang Dong
- State Key Laboratory of Oncogenes and Related GenesShanghai Cancer InstituteSchool of Biomedical EngineeringRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200032China
| | - Xupeng Yang
- State Key Laboratory of Oncogenes and Related GenesShanghai Cancer InstituteSchool of Biomedical EngineeringRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200032China
| | - Qianqian Guo
- State Key Laboratory of Oncogenes and Related GenesShanghai Cancer InstituteSchool of Biomedical EngineeringRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200032China
| | - Jiali Zhang
- State Key Laboratory of Oncogenes and Related GenesShanghai Cancer InstituteSchool of Biomedical EngineeringRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200032China
| | - Jian Zhang
- Department of PathophysiologyKey Laboratory of Cell Differentiation and Apoptosis of Ministry of EducationShanghai Jiao Tong University School of MedicineShanghai200025China
| | - Wei Zhang
- Research Center for Marine DrugsState Key Laboratory of Oncogenes and Related GenesDepartment of PharmacyRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Houwen Lin
- State Key Laboratory of Oncogenes and Related GenesShanghai Cancer InstituteSchool of Biomedical EngineeringRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200032China
- Research Center for Marine DrugsState Key Laboratory of Oncogenes and Related GenesDepartment of PharmacyRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Yourong Duan
- State Key Laboratory of Oncogenes and Related GenesShanghai Cancer InstituteSchool of Biomedical EngineeringRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200032China
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Abstract
Natural peptides are an important class of chemical mediators, essential for most vital processes. What limits the potential of the use of peptides as drugs is their low bioavailability and enzymatic degradation in vivo. To overcome this limitation, the development of new molecules mimicking peptides is of great importance for the development of new biologically active molecules. Therefore, replacing the amide bond in a peptide with a heterocyclic bioisostere, such as the 1,2,3-triazole ring, can be considered an effective solution for the synthesis of biologically relevant peptidomimetics. These 1,2,3-triazoles may have an interesting biological activity, because they behave as rigid link units, which can mimic the electronic properties of amide bonds and show bioisosteric effects. Additionally, triazole can be used as a linker moiety to link peptides to other functional groups.
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Affiliation(s)
- Naima Agouram
- Laboratory of Applied Organic Chemistry, Faculty of Science and Technology, Sidi Mohammed Ben Abdellah University, Immouzer Road, Fez 30050, Morocco; (E.M.E.H.); (A.B.)
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Illa O, Ospina J, Sánchez-Aparicio JE, Pulido X, Abengozar MÁ, Gaztelumendi N, Carbajo D, Nogués C, Rivas L, Maréchal JD, Royo M, Ortuño RM. Hybrid Cyclobutane/Proline-Containing Peptidomimetics: The Conformational Constraint Influences Their Cell-Penetration Ability. Int J Mol Sci 2021; 22:ijms22105092. [PMID: 34065025 PMCID: PMC8151717 DOI: 10.3390/ijms22105092] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 01/22/2023] Open
Abstract
A new family of hybrid β,γ-peptidomimetics consisting of a repetitive unit formed by a chiral cyclobutane-containing trans-β-amino acid plus a Nα-functionalized trans-γ-amino-l-proline joined in alternation were synthesized and evaluated as cell penetrating peptides (CPP). They lack toxicity on the human tumoral cell line HeLa, with an almost negligible cell uptake. The dodecapeptide showed a substantial microbicidal activity on Leishmania parasites at 50 µM but with a modest intracellular accumulation. Their previously published γ,γ-homologues, with a cyclobutane γ-amino acid, showed a well-defined secondary structure with an average inter-guanidinium distance of 8–10 Å, a higher leishmanicidal activity as well as a significant intracellular accumulation. The presence of a very rigid cyclobutane β-amino acid in the peptide backbone precludes the acquisition of a defined conformation suitable for their cell uptake ability. Our results unveiled the preorganized charge-display as a relevant parameter, additional to the separation among the charged groups as previously described. The data herein reinforce the relevance of these descriptors in the design of CPPs with improved properties.
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Affiliation(s)
- Ona Illa
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (J.O.); (J.-E.S.-A.); (J.-D.M.)
- Correspondence: (O.I.); (M.R.); (R.M.O.)
| | - Jimena Ospina
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (J.O.); (J.-E.S.-A.); (J.-D.M.)
| | - José-Emilio Sánchez-Aparicio
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (J.O.); (J.-E.S.-A.); (J.-D.M.)
| | - Ximena Pulido
- Institut de Recerca Biomèdica, c/Baldiri Reixac 10, 08028 Barcelona, Spain;
- Centro de Investigación Biomédica en Red Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), c/ Jordi Girona 18–26, 08034 Barcelona, Spain
- Departamento de Química, Universidad del Tolima, Santa Helena Parte Alta, Ibagué 730006299, Tolima, Colombia
| | - María Ángeles Abengozar
- Centro de Investigaciones Biológicas Margarita Salas, c/ Ramiro de Maeztu 9, CSIC, 28040 Madrid, Spain; (M.Á.A.); (L.R.)
| | - Nerea Gaztelumendi
- Departament de Biologia Cellular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (N.G.); (C.N.)
| | - Daniel Carbajo
- Institut de Química Avançada de Catalunya (IQAC-CSIC), c/ Jordi Girona, 18-26, 08034 Barcelona, Spain;
| | - Carme Nogués
- Departament de Biologia Cellular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (N.G.); (C.N.)
| | - Luis Rivas
- Centro de Investigaciones Biológicas Margarita Salas, c/ Ramiro de Maeztu 9, CSIC, 28040 Madrid, Spain; (M.Á.A.); (L.R.)
| | - Jean-Didier Maréchal
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (J.O.); (J.-E.S.-A.); (J.-D.M.)
| | - Miriam Royo
- Centro de Investigación Biomédica en Red Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), c/ Jordi Girona 18–26, 08034 Barcelona, Spain
- Institut de Química Avançada de Catalunya (IQAC-CSIC), c/ Jordi Girona, 18-26, 08034 Barcelona, Spain;
- Correspondence: (O.I.); (M.R.); (R.M.O.)
| | - Rosa M. Ortuño
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (J.O.); (J.-E.S.-A.); (J.-D.M.)
- Correspondence: (O.I.); (M.R.); (R.M.O.)
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Wohlford GF, Buckley LF, Kadariya D, Park T, Chiabrando JG, Carbone S, Mihalick V, Halquist MS, Pearcy A, Austin D, Gelber C, Abbate A, Van Tassell B. A phase 1 clinical trial of SP16, a first-in-class anti-inflammatory LRP1 agonist, in healthy volunteers. PLoS One 2021; 16:e0247357. [PMID: 33956804 PMCID: PMC8101931 DOI: 10.1371/journal.pone.0247357] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 02/02/2021] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Endogenous serine protease inhibitors are associated with anti-inflammatory and pro-survival signaling mediated via Low-density lipoprotein receptor-related protein 1 (LRP1) signaling. SP16 is a short polypeptide that mimics the LRP1 binding portion of alpha-1 antitrypsin. METHODS A pilot phase I, first-in-man, randomized, double blind, placebo-controlled safety study was conducted to evaluate a subcutaneous injection at three dose levels of SP16 (0.0125, 0.05, and 0.2 mg/kg [up to 12 mg]) or matching placebo in 3:1 ratio in healthy individuals. Safety monitoring included vital signs, laboratory examinations (including hematology, coagulation, platelet function, chemistry, myocardial toxicity) and electrocardiography (to measure effect on PR, QRS, and QTc). RESULTS Treatment with SP16 was not associated with treatment related serious adverse events. SP16 was associated with mild-moderate pain at the time of injection that was significantly higher than placebo on a 0-10 pain scale (6.0+/-1.4 [0.2 mg/kg] versus 1.5+/-2.1 [placebo], P = 0.0088). No differences in vital signs, laboratory examinations and electrocardiography were found in those treated with SP16 versus placebo. CONCLUSION A one-time treatment with SP16 for doses up to 0.2 mg/kg or 12 mg was safe in healthy volunteers.
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Affiliation(s)
- George F. Wohlford
- Virginia Commonwealth University School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Pauley Heart Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Leo F. Buckley
- Virginia Commonwealth University School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Dinesh Kadariya
- Pauley Heart Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Taeshik Park
- Pauley Heart Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Juan Guido Chiabrando
- Pauley Heart Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Salvatore Carbone
- Pauley Heart Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Virginia Mihalick
- Virginia Commonwealth University School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Matthew S. Halquist
- Virginia Commonwealth University School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Adam Pearcy
- Virginia Commonwealth University School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Dana Austin
- Serpin Pharma LLC, Manassas, Virginia, United States of America
| | - Cohava Gelber
- Serpin Pharma LLC, Manassas, Virginia, United States of America
| | - Antonio Abbate
- Pauley Heart Center, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Benjamin Van Tassell
- Virginia Commonwealth University School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, United States of America
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Citarella A, Scala A, Piperno A, Micale N. SARS-CoV-2 M pro: A Potential Target for Peptidomimetics and Small-Molecule Inhibitors. Biomolecules 2021; 11:607. [PMID: 33921886 PMCID: PMC8073203 DOI: 10.3390/biom11040607] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 04/13/2021] [Accepted: 04/16/2021] [Indexed: 12/17/2022] Open
Abstract
The uncontrolled spread of the COVID-19 pandemic caused by the new coronavirus SARS-CoV-2 during 2020-2021 is one of the most devastating events in the history, with remarkable impacts on the health, economic systems, and habits of the entire world population. While some effective vaccines are nowadays approved and extensively administered, the long-term efficacy and safety of this line of intervention is constantly under debate as coronaviruses rapidly mutate and several SARS-CoV-2 variants have been already identified worldwide. Then, the WHO's main recommendations to prevent severe clinical complications by COVID-19 are still essentially based on social distancing and limitation of human interactions, therefore the identification of new target-based drugs became a priority. Several strategies have been proposed to counteract such viral infection, including the repurposing of FDA already approved for the treatment of HIV, HCV, and EBOLA, inter alia. Among the evaluated compounds, inhibitors of the main protease of the coronavirus (Mpro) are becoming more and more promising candidates. Mpro holds a pivotal role during the onset of the infection and its function is intimately related with the beginning of viral replication. The interruption of its catalytic activity could represent a relevant strategy for the development of anti-coronavirus drugs. SARS-CoV-2 Mpro is a peculiar cysteine protease of the coronavirus family, responsible for the replication and infectivity of the parasite. This review offers a detailed analysis of the repurposed drugs and the newly synthesized molecules developed to date for the treatment of COVID-19 which share the common feature of targeting SARS-CoV-2 Mpro, as well as a brief overview of the main enzymatic and cell-based assays to efficaciously screen such compounds.
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Affiliation(s)
| | | | | | - Nicola Micale
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, 98166 Messina, Italy; (A.C.); (A.S.); (A.P.)
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Singh SS, Mattheolabakis G, Gu X, Withers S, Dahal A, Jois S. A grafted peptidomimetic for EGFR heterodimerization inhibition: Implications in NSCLC models. Eur J Med Chem 2021; 216:113312. [PMID: 33667849 PMCID: PMC8044046 DOI: 10.1016/j.ejmech.2021.113312] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/16/2021] [Accepted: 02/18/2021] [Indexed: 02/06/2023]
Abstract
Among the lung cancers, approximately 85% are histologically classified as non-small-cell lung cancer (NSCLC), a leading cause of cancer deaths worldwide. Epidermal growth factor receptors (EGFRs) are known to play a crucial role in lung cancer. HER2 overexpression is detected by immunohistochemistry in 2.4%-38% of NSCLC samples. EGFRs have been targeted with three generations of tyrosine kinase inhibitors (TKIs), and drug resistance has become a major issue; HER2 dimerization with EGFR also plays a major role in the development of resistance to TKI therapy. We have designed grafted peptides to bind to the HER2 extracellular domain (ECD) and inhibit protein-protein interactions of EGFR:HER2 and HER2:HER3. A sunflower trypsin inhibitor (SFTI-1) template was used to graft a peptidomimetic compound. Among several grafted peptides, SFTI-G5 exhibited antiproliferative activity in HER2-positive NSCLC cell lines such as Calu-3 cells with an IC50 value of 0.073 μM. SFTI-G5 was shown to bind to ECD of HER2 and inhibit EGFR:HER2 and HER2:HER3 dimerization and inhibit the phosphorylation of HER2 and downstream signaling proteins. As a proof-of-concept, the in vivo activity of SFTI-G5 was evaluated in two NSCLC mouse models. SFTI-G5 was able to inhibit tumor growth in both models. Furthermore, SFTI-G5 was shown to inhibit EGFR dimerization in tissue samples obtained from in vivo models. These grafted peptides can be used as novel dual inhibitors of EGFR dimerization in NSCLC.
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Affiliation(s)
- Sitanshu S Singh
- School of Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana at Monroe, Monroe, LA, 71201, USA
| | - George Mattheolabakis
- School of Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana at Monroe, Monroe, LA, 71201, USA
| | - Xin Gu
- Department of Pathology, Louisiana State University Health Sciences Center, 1501 Kings Hwy, Shreveport, LA, 71103, USA
| | - Sita Withers
- Department of Veterinary Clinical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Achyut Dahal
- School of Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana at Monroe, Monroe, LA, 71201, USA
| | - Seetharama Jois
- School of Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana at Monroe, Monroe, LA, 71201, USA.
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Jervis PJ, Amorim C, Pereira T, Martins JA, Ferreira PMT. Dehydropeptide Supramolecular Hydrogels and Nanostructures as Potential Peptidomimetic Biomedical Materials. Int J Mol Sci 2021; 22:2528. [PMID: 33802425 PMCID: PMC7959283 DOI: 10.3390/ijms22052528] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 02/24/2021] [Accepted: 02/25/2021] [Indexed: 12/20/2022] Open
Abstract
Supramolecular peptide hydrogels are gaining increased attention, owing to their potential in a variety of biomedical applications. Their physical properties are similar to those of the extracellular matrix (ECM), which is key to their applications in the cell culture of specialized cells, tissue engineering, skin regeneration, and wound healing. The structure of these hydrogels usually consists of a di- or tripeptide capped on the N-terminus with a hydrophobic aromatic group, such as Fmoc or naphthalene. Although these peptide conjugates can offer advantages over other types of gelators such as cross-linked polymers, they usually possess the limitation of being particularly sensitive to proteolysis by endogenous proteases. One of the strategies reported that can overcome this barrier is to use a peptidomimetic strategy, in which natural amino acids are switched for non-proteinogenic analogues, such as D-amino acids, β-amino acids, or dehydroamino acids. Such peptides usually possess much greater resistance to enzymatic hydrolysis. Peptides containing dehydroamino acids, i.e., dehydropeptides, are particularly interesting, as the presence of the double bond also introduces a conformational restraint to the peptide backbone, resulting in (often predictable) changes to the secondary structure of the peptide. This review focuses on peptide hydrogels and related nanostructures, where α,β-didehydro-α-amino acids have been successfully incorporated into the structure of peptide hydrogelators, and the resulting properties are discussed in terms of their potential biomedical applications. Where appropriate, their properties are compared with those of the corresponding peptide hydrogelator composed of canonical amino acids. In a wider context, we consider the presence of dehydroamino acids in natural compounds and medicinally important compounds as well as their limitations, and we consider some of the synthetic strategies for obtaining dehydropeptides. Finally, we consider the future direction for this research area.
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Affiliation(s)
- Peter J. Jervis
- Centre of Chemistry, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (C.A.); (T.P.); (J.A.M.); (P.M.T.F.)
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Viveros-Ceballos JL, Matías-Valdez LA, Sayago FJ, Cativiela C, Ordóñez M. New approaches towards the synthesis of 1,2,3,4-tetrahydro isoquinoline-3-phosphonic acid (Tic P). Amino Acids 2021; 53:451-459. [PMID: 33646426 DOI: 10.1007/s00726-021-02962-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 02/17/2021] [Indexed: 11/25/2022]
Abstract
Two new strategies for the efficient synthesis of racemic 1,2,3,4-tetrahydroisoquinoline-3-phosphonic acid (TicP) (±)-2 have been developed. The first strategy involves the electron-transfer reduction of the easily obtained α,β-dehydro phosphonophenylalanine followed by a Pictet-Spengler cyclization. The second strategy involves a radical decarboxylation-phosphorylation reaction on 1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid (Tic). In both strategies, the highly electrophilic N-acyliminium ion is formed as a key intermediate, and the target compound is obtained in good yield using mild reaction conditions and readily available starting materials, complementing existing methodologies and contributing to the easy accessibility of (±)-2 for further research.
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Affiliation(s)
- José Luis Viveros-Ceballos
- Centro de Investigaciones Químicas-IICBA, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, 62209, Cuernavaca, Morelos, Mexico.
| | - Lizeth A Matías-Valdez
- Centro de Investigaciones Químicas-IICBA, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, 62209, Cuernavaca, Morelos, Mexico
| | - Francisco J Sayago
- Departamento de Química Orgánica, ISQCH, Universidad de Zaragoza, CSIC, 50009, Zaragoza, Spain
| | - Carlos Cativiela
- Departamento de Química Orgánica, ISQCH, Universidad de Zaragoza, CSIC, 50009, Zaragoza, Spain
| | - Mario Ordóñez
- Centro de Investigaciones Químicas-IICBA, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, 62209, Cuernavaca, Morelos, Mexico.
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Kashapov R, Zakharova L. The Self-Assembly and Design of Polyfunctional Nanosystems. Int J Mol Sci 2021; 22:ijms22042223. [PMID: 33672369 PMCID: PMC7926804 DOI: 10.3390/ijms22042223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 02/19/2021] [Indexed: 11/16/2022] Open
Abstract
The current task of the molecular sciences is to create unique nanostructured materials with a given structure and with specific physicochemical properties on the basis of the existing wide range of molecules of natural and synthetic origin. A promising and inexpensive way to obtain nanostructured materials is the spontaneous self-assembly of molecular building blocks during random collisions in real dispersive systems in solution and at interfaces. This editorial aims to summarize the major points from the 11 scientific papers that contributed to the special issue “The Self-Assembly and Design of Polyfunctional Nanosystems”, assessing the modern self-assembly potential and strategies for maintaining sustainable development of the nanoindustry.
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Affiliation(s)
- Ruslan Kashapov
- A.E. Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, 8 Arbuzov Street, Kazan 420088, Russia
- A.E. Arbuzov Institute of Organic and Physical Chemistry, Kazan National Research Technological University, 68 Karl Marx Street, Kazan 420015, Russia
- Correspondence: (R.K.); (L.Z.); Tel.: +7-(843)-273-22-93 (R.K.); Fax: +7-(843)-273-22-53 (R.K.)
| | - Lucia Zakharova
- A.E. Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, 8 Arbuzov Street, Kazan 420088, Russia
- A.E. Arbuzov Institute of Organic and Physical Chemistry, Kazan National Research Technological University, 68 Karl Marx Street, Kazan 420015, Russia
- Correspondence: (R.K.); (L.Z.); Tel.: +7-(843)-273-22-93 (R.K.); Fax: +7-(843)-273-22-53 (R.K.)
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Gudasheva TA, Tallerova AV, Mezhlumyan AG, Antipova TA, Logvinov IO, Firsova YN, Povarnina PY, Seredenin SB. Low-Molecular Weight BDNF Mimetic, Dimeric Dipeptide GSB-106, Reverses Depressive Symptoms in Mouse Chronic Social Defeat Stress. Biomolecules 2021; 11:biom11020252. [PMID: 33578683 PMCID: PMC7916338 DOI: 10.3390/biom11020252] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 12/12/2022] Open
Abstract
A mimetic of the BDNF loop 4, bis (N-monosuccinyl-L-seryl-L-lysine) hexamethylenediamide, named GSB-106, was designed and synthesized in our scientific group. The compound activated TrkB, MAPK/ERK, PI3K/AKT, and PLCγ in in vitro experiments. In vivo experiments with rodents revealed its antidepressant-like activity in the forced swim and the tail suspension tests at the dose range of 0.1–5.0 mg/kg (i.p., p.o.). However, GSB-106 was not studied in depression models modulating major depression in humans. In the present study, the GSB-106 antidepressant-like activity was revealed in mice at the depression model induced by 28-day social defeat stress with 21-days oral administration (0.1 mg/kg) after stress. At the same time, GSB-106 restored reduced locomotor activity and completely eliminated the anhedonia manifestations. The compound also restored reduced levels of synaptophysin and CREB in the hippocampus. In addition, the Trk receptor antagonist K252A, and the PLC inhibitor U73122, were found to completely block the antidepressant-like activity of GSB-106 in the forced swimming test in mice. Thus, the present results demonstrate the dipeptide BDNF mimetic GSB-106 reversed depressive-like behavior and restored hippocampal neuroplasticity in a rodent depression model. These effects of GSB-106 are probably regulated by TrkB signaling.
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Affiliation(s)
- Tatiana A. Gudasheva
- Department of Medicinal Chemistry, V.V. Zakusov Research Institute of Pharmacology, Baltijskaya 8, 125315 Moscow, Russia; (A.V.T.); (A.G.M.); (Y.N.F.); (P.Y.P.)
- Correspondence:
| | - Anna V. Tallerova
- Department of Medicinal Chemistry, V.V. Zakusov Research Institute of Pharmacology, Baltijskaya 8, 125315 Moscow, Russia; (A.V.T.); (A.G.M.); (Y.N.F.); (P.Y.P.)
| | - Armen G. Mezhlumyan
- Department of Medicinal Chemistry, V.V. Zakusov Research Institute of Pharmacology, Baltijskaya 8, 125315 Moscow, Russia; (A.V.T.); (A.G.M.); (Y.N.F.); (P.Y.P.)
| | - Tatyana A. Antipova
- Department of Pharmacogenetics, V.V. Zakusov Research Institute of Pharmacology, Baltijskaya 8, 125315 Moscow, Russia; (T.A.A.); (I.O.L.); (S.B.S.)
| | - Ilya O. Logvinov
- Department of Pharmacogenetics, V.V. Zakusov Research Institute of Pharmacology, Baltijskaya 8, 125315 Moscow, Russia; (T.A.A.); (I.O.L.); (S.B.S.)
| | - Yulia N. Firsova
- Department of Medicinal Chemistry, V.V. Zakusov Research Institute of Pharmacology, Baltijskaya 8, 125315 Moscow, Russia; (A.V.T.); (A.G.M.); (Y.N.F.); (P.Y.P.)
| | - Polina Y. Povarnina
- Department of Medicinal Chemistry, V.V. Zakusov Research Institute of Pharmacology, Baltijskaya 8, 125315 Moscow, Russia; (A.V.T.); (A.G.M.); (Y.N.F.); (P.Y.P.)
| | - Sergey B. Seredenin
- Department of Pharmacogenetics, V.V. Zakusov Research Institute of Pharmacology, Baltijskaya 8, 125315 Moscow, Russia; (T.A.A.); (I.O.L.); (S.B.S.)
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Barriga A, Morán-Lalangui M, Castillo-Sánchez JC, Mingarro I, Pérez-Gil J, García-Álvarez B. Role of pulmonary surfactant protein Sp-C dimerization on membrane fragmentation: An emergent mechanism involved in lung defense and homeostasis. Biochim Biophys Acta Biomembr 2021; 1863:183572. [PMID: 33548215 DOI: 10.1016/j.bbamem.2021.183572] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 01/18/2021] [Accepted: 01/29/2021] [Indexed: 01/22/2023]
Abstract
Surfactant protein C (SP-C) is a protein present in the pulmonary surfactant system that is involved in the biophysical properties of this lipoprotein complex, but it also has a role in lung defense and homeostasis. In this article, we propose that the link between both functions could rely on the ability of SP-C to induce fragmentation of phospholipid membranes and generate small vesicles that serve as support to present different ligands to cells in the lungs. Our results using bimolecular fluorescence complementation and tunable resistive pulse sensing setups suggest that SP-C oligomerization could be the triggering event that causes membrane budding and nanovesiculation. As shown by fluorescence microscopy and flow cytometry, these vesicles are differentially assimilated by alveolar macrophages and alveolar type II cells, indicating distinct roles of these alveoli-resident cells in the processing of the SP-C- induced vesicles and their cargo. These results depict a more accurate picture of the mechanisms of this protein, which could be relevant for the comprehension of pulmonary pathologies and the development of new therapeutic approaches.
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Affiliation(s)
- Alejandro Barriga
- Department of Biochemistry and Molecular Biology, Faculty of Biology and Faculty of Chemistry, Complutense University, Madrid, Spain; Research Institute "Hospital 12 de Octubre (imas12)", Madrid, Spain
| | - Michelle Morán-Lalangui
- Department of Biochemistry and Molecular Biology, Faculty of Biology and Faculty of Chemistry, Complutense University, Madrid, Spain; Research Institute "Hospital 12 de Octubre (imas12)", Madrid, Spain
| | - José Carlos Castillo-Sánchez
- Department of Biochemistry and Molecular Biology, Faculty of Biology and Faculty of Chemistry, Complutense University, Madrid, Spain; Research Institute "Hospital 12 de Octubre (imas12)", Madrid, Spain
| | - Ismael Mingarro
- Department of Biochemistry and Molecular Biology, Institute for Biotechnology and Biomedicine (BIOTECMED), University of Valencia, Valencia, Spain
| | - Jesús Pérez-Gil
- Department of Biochemistry and Molecular Biology, Faculty of Biology and Faculty of Chemistry, Complutense University, Madrid, Spain; Research Institute "Hospital 12 de Octubre (imas12)", Madrid, Spain
| | - Begoña García-Álvarez
- Department of Biochemistry and Molecular Biology, Faculty of Biology and Faculty of Chemistry, Complutense University, Madrid, Spain; Research Institute "Hospital 12 de Octubre (imas12)", Madrid, Spain.
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Panzeri S, Arosio D, Gazzola S, Belvisi L, Civera M, Potenza D, Vasile F, Kemker I, Ertl T, Sewald N, Reiser O, Piarulli U. Cyclic RGD and isoDGR Integrin Ligands Containing cis-2-amino-1-cyclopentanecarboxylic ( cis-β-ACPC) Scaffolds. Molecules 2020; 25:molecules25245966. [PMID: 33339382 PMCID: PMC7766232 DOI: 10.3390/molecules25245966] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 12/08/2020] [Accepted: 12/14/2020] [Indexed: 02/06/2023] Open
Abstract
Integrin ligands containing the tripeptide sequences Arg-Gly-Asp (RGD) and iso-Asp-Gly- Arg (isoDGR) were actively investigated as inhibitors of tumor angiogenesis and directing unit in tumor-targeting drug conjugates. Reported herein is the synthesis, of two RGD and one isoDGR cyclic peptidomimetics containing (1S,2R) and (1R,2S) cis-2-amino-1-cyclopentanecarboxylic acid (cis-β-ACPC), using a mixed solid phase/solution phase synthetic protocol. The three ligands were examined in vitro in competitive binding assays to the purified αvβ3 and α5β1 receptors using biotinylated vitronectin (αvβ3) and fibronectin (α5β1) as natural displaced ligands. The IC50 values of the ligands ranged from nanomolar (the two RGD ligands) to micromolar (the isoDGR ligand) with a pronounced selectivity for αvβ3 over α5β1. In vitro cell adhesion assays were also performed using the human skin melanoma cell line WM115 (rich in integrin αvβ3). The two RGD ligands showed IC50 values in the same micromolar range as the reference compound (cyclo[RGDfV]), while for the isoDGR derivative an IC50 value could not be measured for the cell adhesion assay. A conformational analysis of the free RGD and isoDGR ligands by NMR (VT-NMR and NOESY experiments) and computational studies (MC/EM and MD), followed by docking simulations performed in the αVβ3 integrin active site, provided a rationale for the behavior of these ligands toward the receptor.
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Affiliation(s)
- Silvia Panzeri
- Dipartimento di Scienza e Alta Tecnologia, Università degli Studi dell’Insubria, Via Valleggio 11, 22100 Como, Italy; (S.P.); (S.G.)
- Institute of Organic Chemistry, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany; (T.E.); (O.R.)
| | - Daniela Arosio
- Consiglio Nazionale delle Ricerche (CNR), Istituto di Scienze e Tecnologie Chimiche (SCITEC), Giulio Natta, Via C. Golgi 19, 20133 Milan, Italy;
| | - Silvia Gazzola
- Dipartimento di Scienza e Alta Tecnologia, Università degli Studi dell’Insubria, Via Valleggio 11, 22100 Como, Italy; (S.P.); (S.G.)
| | - Laura Belvisi
- Dipartimento di Chimica, Università degli Studi di Milano, Via C. Golgi 19, 20133 Milan, Italy; (L.B.); (M.C.); (D.P.); (F.V.)
| | - Monica Civera
- Dipartimento di Chimica, Università degli Studi di Milano, Via C. Golgi 19, 20133 Milan, Italy; (L.B.); (M.C.); (D.P.); (F.V.)
| | - Donatella Potenza
- Dipartimento di Chimica, Università degli Studi di Milano, Via C. Golgi 19, 20133 Milan, Italy; (L.B.); (M.C.); (D.P.); (F.V.)
| | - Francesca Vasile
- Dipartimento di Chimica, Università degli Studi di Milano, Via C. Golgi 19, 20133 Milan, Italy; (L.B.); (M.C.); (D.P.); (F.V.)
| | - Isabell Kemker
- Department of Chemistry, Organic and Bioorganic Chemistry, University of Bielefeld, Universitätsstraße 25, 33615 Bielefeld, Germany; (I.K.); (N.S.)
| | - Thomas Ertl
- Institute of Organic Chemistry, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany; (T.E.); (O.R.)
| | - Norbert Sewald
- Department of Chemistry, Organic and Bioorganic Chemistry, University of Bielefeld, Universitätsstraße 25, 33615 Bielefeld, Germany; (I.K.); (N.S.)
| | - Oliver Reiser
- Institute of Organic Chemistry, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany; (T.E.); (O.R.)
| | - Umberto Piarulli
- Dipartimento di Scienza e Alta Tecnologia, Università degli Studi dell’Insubria, Via Valleggio 11, 22100 Como, Italy; (S.P.); (S.G.)
- Correspondence:
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Sani S, Messe M, Fuchs Q, Pierrevelcin M, Laquerriere P, Entz-Werle N, Reita D, Etienne-Selloum N, Bruban V, Choulier L, Martin S, Dontenwill M. Biological Relevance of RGD-Integrin Subtype-Specific Ligands in Cancer. Chembiochem 2020; 22:1151-1160. [PMID: 33140906 DOI: 10.1002/cbic.202000626] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/02/2020] [Indexed: 12/13/2022]
Abstract
Integrins are heterodimeric transmembrane proteins able to connect cells with the micro-environment. They represent a family of receptors involved in almost all the hallmarks of cancer. Integrins recognizing the Arg-Gly-Asp (RGD) peptide in their natural extracellular matrix ligands have been particularly investigated as tumoral therapeutic targets. In the last 30 years, intense research has been dedicated to designing specific RGD-like ligands able to discriminate selectively the different RGD-recognizing integrins. Chemists' efforts have led to the proposition of modified peptide or peptidomimetic libraries to be used for tumor targeting and/or tumor imaging. Here we review, from the biological point of view, the rationale underlying the need to clearly delineate each RGD-integrin subtype by selective tools. We describe the complex roles of RGD-integrins (mainly the most studied αvβ3 and α5β1 integrins) in tumors, the steps towards selective ligands and the current usefulness of such ligands. Although the impact of integrins in cancer is well acknowledged, the biological characteristics of each integrin subtype in a specific tumor are far from being completely resolved. Selective ligands might help us to reconsider integrins as therapeutic targets in specific clinical settings.
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Affiliation(s)
- Saidu Sani
- Laboratoire de Bioimagerie et Pathologies (LBP), UMR CNRS 7021, Institut Thématique Interdisciplinaire InnoVec, Université de Strasbourg, Faculté de Pharmacie, 74 route du, Rhin, CS 60024, 67401, Illkirch Cedex, France
- Cancer and Diabetic Research Group, Department of Biochemistry and Molecular Biology, Faculty of Science, Federal University Ndufu-Alike Ikwo, P.M.B, 1010, Abakaliki, Ebonyi State, Nigeria
| | - Mélissa Messe
- Laboratoire de Bioimagerie et Pathologies (LBP), UMR CNRS 7021, Institut Thématique Interdisciplinaire InnoVec, Université de Strasbourg, Faculté de Pharmacie, 74 route du, Rhin, CS 60024, 67401, Illkirch Cedex, France
- Institut Pluridisciplinaire Hubert Curien (IPHC), UMR CNRS 7178, Université de Strasbourg, 67000, Strasbourg, France
| | - Quentin Fuchs
- Laboratoire de Bioimagerie et Pathologies (LBP), UMR CNRS 7021, Institut Thématique Interdisciplinaire InnoVec, Université de Strasbourg, Faculté de Pharmacie, 74 route du, Rhin, CS 60024, 67401, Illkirch Cedex, France
| | - Marina Pierrevelcin
- Laboratoire de Bioimagerie et Pathologies (LBP), UMR CNRS 7021, Institut Thématique Interdisciplinaire InnoVec, Université de Strasbourg, Faculté de Pharmacie, 74 route du, Rhin, CS 60024, 67401, Illkirch Cedex, France
| | - Patrice Laquerriere
- Institut Pluridisciplinaire Hubert Curien (IPHC), UMR CNRS 7178, Université de Strasbourg, 67000, Strasbourg, France
| | - Natacha Entz-Werle
- Laboratoire de Bioimagerie et Pathologies (LBP), UMR CNRS 7021, Institut Thématique Interdisciplinaire InnoVec, Université de Strasbourg, Faculté de Pharmacie, 74 route du, Rhin, CS 60024, 67401, Illkirch Cedex, France
- Pediatric Onco-Hematology Department, Pediatrics, University Hospital of Strasbourg, 1 avenue Molière, 67098, Strasbourg, France
| | - Damien Reita
- Laboratoire de Bioimagerie et Pathologies (LBP), UMR CNRS 7021, Institut Thématique Interdisciplinaire InnoVec, Université de Strasbourg, Faculté de Pharmacie, 74 route du, Rhin, CS 60024, 67401, Illkirch Cedex, France
- Department of Oncobiology, Laboratory of Biochemistry and Molecular Biology, University Hospital of Strasbourg, France
| | - Nelly Etienne-Selloum
- Laboratoire de Bioimagerie et Pathologies (LBP), UMR CNRS 7021, Institut Thématique Interdisciplinaire InnoVec, Université de Strasbourg, Faculté de Pharmacie, 74 route du, Rhin, CS 60024, 67401, Illkirch Cedex, France
- Institut du Cancer Strasbourg Europe (ICANS), Service de Pharmacie, 17 rue Albert Calmette, 67200 Strasbourg, France
| | - Véronique Bruban
- Laboratoire de Bioimagerie et Pathologies (LBP), UMR CNRS 7021, Institut Thématique Interdisciplinaire InnoVec, Université de Strasbourg, Faculté de Pharmacie, 74 route du, Rhin, CS 60024, 67401, Illkirch Cedex, France
| | - Laurence Choulier
- Laboratoire de Bioimagerie et Pathologies (LBP), UMR CNRS 7021, Institut Thématique Interdisciplinaire InnoVec, Université de Strasbourg, Faculté de Pharmacie, 74 route du, Rhin, CS 60024, 67401, Illkirch Cedex, France
| | - Sophie Martin
- Laboratoire de Bioimagerie et Pathologies (LBP), UMR CNRS 7021, Institut Thématique Interdisciplinaire InnoVec, Université de Strasbourg, Faculté de Pharmacie, 74 route du, Rhin, CS 60024, 67401, Illkirch Cedex, France
| | - Monique Dontenwill
- Laboratoire de Bioimagerie et Pathologies (LBP), UMR CNRS 7021, Institut Thématique Interdisciplinaire InnoVec, Université de Strasbourg, Faculté de Pharmacie, 74 route du, Rhin, CS 60024, 67401, Illkirch Cedex, France
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Pandit A, Khare L, Jahagirdar D, Srivastav A, Jain R, Dandekar P. Probing synergistic interplay between bio-inspired peptidomimetic chitosan-copper complexes and doxorubicin. Int J Biol Macromol 2020; 161:1475-1483. [PMID: 32750482 DOI: 10.1016/j.ijbiomac.2020.07.241] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 07/13/2020] [Accepted: 07/22/2020] [Indexed: 01/23/2023]
Abstract
The current investigation reports a novel and facile method for modification of low molecular weight chitosan (Cs) with guanidine moieties, aimed at enhancing its cellular interaction and thus augmenting its cellular internalization. Guadinylated chitosan-copper (Cs-Gn-Cu) chelates, based on copper-nitrogen co-ordination, were established. Characterization of chelates was conducted using 1H NMR, 13C NMR, XPS, XRD, TGA-DTA, and GPC techniques. Anticancer activity of formed chelates was confirmed against A549 cells using MTT assay. Experimental outcomes, for the first time, have provided an empirical evidence for synergistic interaction between the chelated polymer (Cs-Gn-Cu) and the established anti-cancer agent, Doxorubicin (Dox), based on analysis by the Chou Talalay method and estimation of their combination indices. ROS induction was demonstrated as the mechanism of action of the chelated polymer, which supplemented rapid destruction of cancerous cells by Dox. These findings strongly advocate the need for harnessing unexplored potential of these innovative metal polymer chelates in cases of Dox resistant lung cancer, wherein the polymeric system itself would serve as an anti-cancer agent.
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Affiliation(s)
- A Pandit
- Department of Chemical Engineering, Institute of Chemical Technology, Matunga, Mumbai-19, India
| | - L Khare
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Matunga, Mumbai-19, India
| | - D Jahagirdar
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Matunga, Mumbai-19, India
| | - A Srivastav
- Department of Chemical Engineering, Institute of Chemical Technology, Matunga, Mumbai-19, India
| | - R Jain
- Department of Chemical Engineering, Institute of Chemical Technology, Matunga, Mumbai-19, India.
| | - P Dandekar
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Matunga, Mumbai-19, India.
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Shen W, Zhang Y, Wan P, An L, Zhang P, Xiao C, Chen X. Antineoplastic Drug-Free Anticancer Strategy Enabled by Host-Defense-Peptides-Mimicking Synthetic Polypeptides. Adv Mater 2020; 32:e2001108. [PMID: 32700437 DOI: 10.1002/adma.202001108] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 05/22/2020] [Indexed: 06/11/2023]
Abstract
An antineoplastic drug-free anticancer strategy enabled by host defense peptides (HDPs)-mimicking synthetic polypeptides is reported. The polypeptide exhibits a broad spectrum of anticancer activity in 12 cancer cell lines, including drug-resistant and highly metastatic tumor cells. Detailed mechanistic studies reveal that the cationic anticancer polypeptide (ACPP) can directly induce rapid necrosis of cancer cells within minutes through a membrane-lytic mechanism. Moreover, a pH-sensitive zwitterionic derivative of ACPP (DA-ACPP) is prepared for in vivo application. DA-ACPP shows negligible hemolysis under neutral physiological conditions, and can be converted back to ACPP in slightly acidic tumor environments, resulting in selective killing of cancer cells. Consequently, DA-ACPP shows an effective inhibition of tumor growth in both 4T1 orthotopic breast tumor models and B16-F10 melanoma pulmonary metastatic models. Overall, these findings demonstrate that synthetic HDPs-mimicking polypeptides represent safe and effective antineoplastic agents, which sheds new light on the development of drug-free synthetic polymers for cancer therapy.
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Affiliation(s)
- Wei Shen
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yu Zhang
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
| | - Pengqi Wan
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
- Department of Chemistry, Northeast Normal University, Changchun, Jilin, 130022, P. R. China
| | - Lin An
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
- Department of Dermatology, China-Japan Union Hospital, Jilin University, Changchun, Jilin, 130033, P. R. China
| | - Peng Zhang
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
- Jilin Biomedical Polymers Engineering Laboratory, Changchun, 130022, P. R. China
| | - Chunsheng Xiao
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
- Jilin Biomedical Polymers Engineering Laboratory, Changchun, 130022, P. R. China
| | - Xuesi Chen
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
- Jilin Biomedical Polymers Engineering Laboratory, Changchun, 130022, P. R. China
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Bendre S, Zhang Z, Kuo HT, Rousseau J, Zhang C, Merkens H, Roxin Á, Bénard F, Lin KS. Evaluation of Met-Val-Lys as a Renal Brush Border Enzyme-Cleavable Linker to Reduce Kidney Uptake of 68Ga-Labeled DOTA-Conjugated Peptides and Peptidomimetics. Molecules 2020; 25:molecules25173854. [PMID: 32854201 PMCID: PMC7503470 DOI: 10.3390/molecules25173854] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/17/2020] [Accepted: 08/21/2020] [Indexed: 12/24/2022] Open
Abstract
High kidney uptake is a common feature of peptide-based radiopharmaceuticals, leading to reduced detection sensitivity for lesions adjacent to kidneys and lower maximum tolerated therapeutic dose. In this study, we evaluated if the Met-Val-Lys (MVK) linker could be used to lower kidney uptake of 68Ga-labeled DOTA-conjugated peptides and peptidomimetics. A model compound, [68Ga]Ga-DOTA-AmBz-MVK(Ac)-OH (AmBz: aminomethylbenzoyl), and its derivative, [68Ga]Ga-DOTA-AmBz-MVK(HTK01166)-OH, coupled with the PSMA (prostate-specific membrane antigen)-targeting motif of the previously reported HTK01166 were synthesized and evaluated to determine if they could be recognized and cleaved by the renal brush border enzymes. Additionally, positron emission tomography (PET) imaging, ex vivo biodistribution and in vivo stability studies were conducted in mice to evaluate their pharmacokinetics. [68Ga]Ga-DOTA-AmBz-MVK(Ac)-OH was effectively cleaved specifically by neutral endopeptidase (NEP) of renal brush border enzymes at the Met-Val amide bond, and the radio-metabolite [68Ga]Ga-DOTA-AmBz-Met-OH was rapidly excreted via the renal pathway with minimal kidney retention. [68Ga]Ga-DOTA-AmBz-MVK(HTK01166)-OH retained its PSMA-targeting capability and was also cleaved by NEP, although less effectively when compared to [68Ga]Ga-DOTA-AmBz-MVK(Ac)-OH. The kidney uptake of [68Ga]Ga-DOTA-AmBz-MVK(HTK01166)-OH was 30% less compared to that of [68Ga]Ga-HTK01166. Our data demonstrated that derivatives of [68Ga]Ga-DOTA-AmBz-MVK-OH can be cleaved specifically by NEP, and therefore, MVK can be a promising cleavable linker for use to reduce kidney uptake of radiolabeled DOTA-conjugated peptides and peptidomimetics.
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Affiliation(s)
- Shreya Bendre
- Department of Molecular Oncology, BC Cancer, Vancouver, BC V5Z 1L3, Canada; (S.B.); (Z.Z.); (H.-T.K.); (J.R.); (C.Z.); (H.M.); (Á.R.); (F.B.)
| | - Zhengxing Zhang
- Department of Molecular Oncology, BC Cancer, Vancouver, BC V5Z 1L3, Canada; (S.B.); (Z.Z.); (H.-T.K.); (J.R.); (C.Z.); (H.M.); (Á.R.); (F.B.)
| | - Hsiou-Ting Kuo
- Department of Molecular Oncology, BC Cancer, Vancouver, BC V5Z 1L3, Canada; (S.B.); (Z.Z.); (H.-T.K.); (J.R.); (C.Z.); (H.M.); (Á.R.); (F.B.)
| | - Julie Rousseau
- Department of Molecular Oncology, BC Cancer, Vancouver, BC V5Z 1L3, Canada; (S.B.); (Z.Z.); (H.-T.K.); (J.R.); (C.Z.); (H.M.); (Á.R.); (F.B.)
| | - Chengcheng Zhang
- Department of Molecular Oncology, BC Cancer, Vancouver, BC V5Z 1L3, Canada; (S.B.); (Z.Z.); (H.-T.K.); (J.R.); (C.Z.); (H.M.); (Á.R.); (F.B.)
| | - Helen Merkens
- Department of Molecular Oncology, BC Cancer, Vancouver, BC V5Z 1L3, Canada; (S.B.); (Z.Z.); (H.-T.K.); (J.R.); (C.Z.); (H.M.); (Á.R.); (F.B.)
| | - Áron Roxin
- Department of Molecular Oncology, BC Cancer, Vancouver, BC V5Z 1L3, Canada; (S.B.); (Z.Z.); (H.-T.K.); (J.R.); (C.Z.); (H.M.); (Á.R.); (F.B.)
| | - François Bénard
- Department of Molecular Oncology, BC Cancer, Vancouver, BC V5Z 1L3, Canada; (S.B.); (Z.Z.); (H.-T.K.); (J.R.); (C.Z.); (H.M.); (Á.R.); (F.B.)
- Department of Functional Imaging, BC Cancer, Vancouver, BC V5Z 4E6, Canada
- Department of Radiology, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Kuo-Shyan Lin
- Department of Molecular Oncology, BC Cancer, Vancouver, BC V5Z 1L3, Canada; (S.B.); (Z.Z.); (H.-T.K.); (J.R.); (C.Z.); (H.M.); (Á.R.); (F.B.)
- Department of Functional Imaging, BC Cancer, Vancouver, BC V5Z 4E6, Canada
- Department of Radiology, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
- Correspondence:
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43
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Kennedy AC, Belgi A, Husselbee BW, Spanswick D, Norton RS, Robinson AJ. α-Conotoxin Peptidomimetics: Probing the Minimal Binding Motif for Effective Analgesia. Toxins (Basel) 2020; 12:E505. [PMID: 32781580 PMCID: PMC7472027 DOI: 10.3390/toxins12080505] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/29/2020] [Accepted: 08/03/2020] [Indexed: 12/18/2022] Open
Abstract
Several analgesic α-conotoxins have been isolated from marine cone snails. Structural modification of native peptides has provided potent and selective analogues for two of its known biological targets-nicotinic acetylcholine and γ-aminobutyric acid (GABA) G protein-coupled (GABAB) receptors. Both of these molecular targets are implicated in pain pathways. Despite their small size, an incomplete understanding of the structure-activity relationship of α-conotoxins at each of these targets has hampered the development of therapeutic leads. This review scrutinises the N-terminal domain of the α-conotoxin family of peptides, a region defined by an invariant disulfide bridge, a turn-inducing proline residue and multiple polar sidechain residues, and focusses on structural features that provide analgesia through inhibition of high-voltage-activated Ca2+ channels. Elucidating the bioactive conformation of this region of these peptides may hold the key to discovering potent drugs for the unmet management of debilitating chronic pain associated with a wide range of medical conditions.
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Affiliation(s)
- Adam C. Kennedy
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia; (A.C.K.); (A.B.); (B.W.H.)
| | - Alessia Belgi
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia; (A.C.K.); (A.B.); (B.W.H.)
| | - Benjamin W. Husselbee
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia; (A.C.K.); (A.B.); (B.W.H.)
| | - David Spanswick
- Biomedicine Discovery Institute and the Department of Physiology, Monash University, Victoria 3800, Australia;
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
- NeuroSolutions Ltd., Coventry CV4 7AL, UK
| | - Raymond S. Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Science, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia;
- ARC Centre for Fragment-Based Design, Monash University, Parkville, Victoria 3052, Australia
| | - Andrea J. Robinson
- School of Chemistry, Monash University, Clayton, Victoria 3800, Australia; (A.C.K.); (A.B.); (B.W.H.)
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44
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Rečnik LM, Kandioller W, Mindt TL. 1,4-Disubstituted 1,2,3-Triazoles as Amide Bond Surrogates for the Stabilisation of Linear Peptides with Biological Activity. Molecules 2020; 25:E3576. [PMID: 32781656 PMCID: PMC7465391 DOI: 10.3390/molecules25163576] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 12/20/2022] Open
Abstract
Peptides represent an important class of biologically active molecules with high potential for the development of diagnostic and therapeutic agents due to their structural diversity, favourable pharmacokinetic properties, and synthetic availability. However, the widespread use of peptides and conjugates thereof in clinical applications can be hampered by their low stability in vivo due to rapid degradation by endogenous proteases. A promising approach to circumvent this potential limitation includes the substitution of metabolically labile amide bonds in the peptide backbone by stable isosteric amide bond mimetics. In this review, we focus on the incorporation of 1,4-disubstituted 1,2,3-triazoles as amide bond surrogates in linear peptides with the aim to increase their stability without impacting their biological function(s). We highlight the properties of this heterocycle as a trans-amide bond surrogate and summarise approaches for the synthesis of triazole-containing peptidomimetics via the Cu(I)-catalysed azide-alkyne cycloaddition (CuAAC). The impacts of the incorporation of triazoles in the backbone of diverse peptides on their biological properties such as, e.g., blood serum stability and affinity as well as selectivity towards their respective molecular target(s) are discussed.
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Affiliation(s)
- Lisa-Maria Rečnik
- Ludwig Boltzmann Institute Applied Diagnostics, General Hospital Vienna, 1090 Vienna, Austria;
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria;
- Department of Biomedical Imaging and Image Guided Therapy, Division of Nuclear Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Wolfgang Kandioller
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria;
| | - Thomas L. Mindt
- Ludwig Boltzmann Institute Applied Diagnostics, General Hospital Vienna, 1090 Vienna, Austria;
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria;
- Department of Biomedical Imaging and Image Guided Therapy, Division of Nuclear Medicine, Medical University of Vienna, 1090 Vienna, Austria
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45
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Wtorek K, Piekielna-Ciesielska J, Janecki T, Janecka A. The search for opioid analgesics with limited tolerance liability. Peptides 2020; 130:170331. [PMID: 32497566 DOI: 10.1016/j.peptides.2020.170331] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/03/2020] [Accepted: 05/14/2020] [Indexed: 01/01/2023]
Abstract
Reducing the well-known side effects of opioids prescribed to treat chronic pain remains unresolved, despite extensive research in this field. Among several options to tackle this problem the synthesis of multifunctional compounds containing hybridized structures gained a lot of interest. Recently, extensively investigated are combinations of opioid agonist and antagonist pharmacophores embodied in a single molecule. To this end, agonism at the μ opioid receptor (MOR) with simultaneous antagonism at the δ opioid receptor (DOR) emerged as a promising avenue to obtaining novel analogs devoid of serious adverse effects associated with morphine-based analgesics. In this review we covered up-to-date research on the synthesis of peptide-based ligands with MOR agonist/DOR antagonist profile.
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Affiliation(s)
- Karol Wtorek
- Department of Biomolecular Chemistry, Medical University of Lodz, Lodz, Poland
| | | | - Tomasz Janecki
- Institute of Organic Chemistry, Lodz University of Technology, Lodz, Poland
| | - Anna Janecka
- Department of Biomolecular Chemistry, Medical University of Lodz, Lodz, Poland.
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46
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Meriño-Cabrera Y, Severiche Castro JG, Rios Diez JD, Rodrigues Macedo ML, de Oliveira Mendes TA, Goreti de Almeida Oliveira M. Rational design of mimetic peptides based on the interaction between Inga laurina inhibitor and trypsins for Spodoptera cosmioides pest control. Insect Biochem Mol Biol 2020; 122:103390. [PMID: 32360954 DOI: 10.1016/j.ibmb.2020.103390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 03/23/2020] [Accepted: 04/13/2020] [Indexed: 06/11/2023]
Abstract
The interaction of Inga laurina Kunitz inhibitor with insect trypsins is an example of protein-protein interaction with potential application for the pest control. However, the crop field application of proteins as inhibitors is limited due to high production cost, the large molecular size and low environmental stability. The use of mimetic peptides that have molecular features associated with the protein inhibitor can result in a product with lower cost and higher efficiency for the agricultural application. Here, we designed mimetic peptides deriving from globular domains of ILTI that are predicted to interact with trypsin enzymes of Lepidoptera pest. Two linear peptides were identified and synthetized from the interface of interaction between trypsin-ILTI complexes. These peptides were derived due to its high-energy contribution for the biding affinity between the enzyme-protein inhibitor. The peptides showed structural stability, propensity to adopt the bound conformation also without the context of the protein, inhibitory activity of digestive trypsins and toxic effects on the S. cosmioides, indicating that they can be used as potential inhibitor for pest control.
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Affiliation(s)
- Yaremis Meriño-Cabrera
- Departamento de Bioquímica e Biologia molecular, Universidade Federal de Viçosa, Minas Gerais, Brazil; Instituto de Biotecnologia aplicada à Agropecuaria, BIOAGRO-UFV, Viçosa, Minas Gerais, Brazil
| | | | - Juan Diego Rios Diez
- Instituto de Biotecnologia aplicada à Agropecuaria, BIOAGRO-UFV, Viçosa, Minas Gerais, Brazil
| | - Maria Ligia Rodrigues Macedo
- Laboratório de Purificação de Proteínas e suas Funções Biológicas, Unidade de Tecnologia de Alimentos e da Saúde Pública, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil
| | - Tiago Antônio de Oliveira Mendes
- Departamento de Bioquímica e Biologia molecular, Universidade Federal de Viçosa, Minas Gerais, Brazil; Instituto de Biotecnologia aplicada à Agropecuaria, BIOAGRO-UFV, Viçosa, Minas Gerais, Brazil.
| | - Maria Goreti de Almeida Oliveira
- Departamento de Bioquímica e Biologia molecular, Universidade Federal de Viçosa, Minas Gerais, Brazil; Instituto de Biotecnologia aplicada à Agropecuaria, BIOAGRO-UFV, Viçosa, Minas Gerais, Brazil
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47
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Leman JK, Weitzner BD, Lewis SM, Adolf-Bryfogle J, Alam N, Alford RF, Aprahamian M, Baker D, Barlow KA, Barth P, Basanta B, Bender BJ, Blacklock K, Bonet J, Boyken SE, Bradley P, Bystroff C, Conway P, Cooper S, Correia BE, Coventry B, Das R, De Jong RM, DiMaio F, Dsilva L, Dunbrack R, Ford AS, Frenz B, Fu DY, Geniesse C, Goldschmidt L, Gowthaman R, Gray JJ, Gront D, Guffy S, Horowitz S, Huang PS, Huber T, Jacobs TM, Jeliazkov JR, Johnson DK, Kappel K, Karanicolas J, Khakzad H, Khar KR, Khare SD, Khatib F, Khramushin A, King IC, Kleffner R, Koepnick B, Kortemme T, Kuenze G, Kuhlman B, Kuroda D, Labonte JW, Lai JK, Lapidoth G, Leaver-Fay A, Lindert S, Linsky T, London N, Lubin JH, Lyskov S, Maguire J, Malmström L, Marcos E, Marcu O, Marze NA, Meiler J, Moretti R, Mulligan VK, Nerli S, Norn C, Ó'Conchúir S, Ollikainen N, Ovchinnikov S, Pacella MS, Pan X, Park H, Pavlovicz RE, Pethe M, Pierce BG, Pilla KB, Raveh B, Renfrew PD, Burman SSR, Rubenstein A, Sauer MF, Scheck A, Schief W, Schueler-Furman O, Sedan Y, Sevy AM, Sgourakis NG, Shi L, Siegel JB, Silva DA, Smith S, Song Y, Stein A, Szegedy M, Teets FD, Thyme SB, Wang RYR, Watkins A, Zimmerman L, Bonneau R. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nat Methods 2020; 17:665-680. [PMID: 32483333 PMCID: PMC7603796 DOI: 10.1038/s41592-020-0848-2] [Citation(s) in RCA: 373] [Impact Index Per Article: 93.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 04/22/2020] [Indexed: 12/12/2022]
Abstract
The Rosetta software for macromolecular modeling, docking and design is extensively used in laboratories worldwide. During two decades of development by a community of laboratories at more than 60 institutions, Rosetta has been continuously refactored and extended. Its advantages are its performance and interoperability between broad modeling capabilities. Here we review tools developed in the last 5 years, including over 80 methods. We discuss improvements to the score function, user interfaces and usability. Rosetta is available at http://www.rosettacommons.org.
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Affiliation(s)
- Julia Koehler Leman
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA.
- Department of Biology, New York University, New York, New York, USA.
| | - Brian D Weitzner
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Lyell Immunopharma Inc., Seattle, WA, USA
| | - Steven M Lewis
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Biochemistry, Duke University, Durham, NC, USA
- Cyrus Biotechnology, Seattle, WA, USA
| | - Jared Adolf-Bryfogle
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Nawsad Alam
- Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Rebecca F Alford
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Melanie Aprahamian
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Kyle A Barlow
- Graduate Program in Bioinformatics, University of California San Francisco, San Francisco, CA, USA
| | - Patrick Barth
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Baylor College of Medicine, Department of Pharmacology, Houston, TX, USA
| | - Benjamin Basanta
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Biological Physics Structure and Design PhD Program, University of Washington, Seattle, WA, USA
| | - Brian J Bender
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA
| | - Kristin Blacklock
- Institute of Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Jaume Bonet
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Scott E Boyken
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Lyell Immunopharma Inc., Seattle, WA, USA
| | - Phil Bradley
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Chris Bystroff
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Patrick Conway
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Seth Cooper
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Bruno E Correia
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Brian Coventry
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Rhiju Das
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Lorna Dsilva
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Roland Dunbrack
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Alexander S Ford
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Brandon Frenz
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Cyrus Biotechnology, Seattle, WA, USA
| | - Darwin Y Fu
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - Caleb Geniesse
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Ragul Gowthaman
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Jeffrey J Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Dominik Gront
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Sharon Guffy
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Scott Horowitz
- Department of Chemistry & Biochemistry, University of Denver, Denver, CO, USA
- The Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA
| | - Po-Ssu Huang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Tim M Jacobs
- Program in Bioinformatics and Computational Biology, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - David K Johnson
- Center for Computational Biology, University of Kansas, Lawrence, KS, USA
| | - Kalli Kappel
- Biophysics Program, Stanford University, Stanford, CA, USA
| | - John Karanicolas
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Hamed Khakzad
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Institute for Computational Science, University of Zurich, Zurich, Switzerland
- S3IT, University of Zurich, Zurich, Switzerland
| | - Karen R Khar
- Cyrus Biotechnology, Seattle, WA, USA
- Center for Computational Biology, University of Kansas, Lawrence, KS, USA
| | - Sagar D Khare
- Institute of Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, The State University of New Jersey, Piscataway, NJ, USA
- Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Computational Biology and Molecular Biophysics Program, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Firas Khatib
- Department of Computer and Information Science, University of Massachusetts Dartmouth, Dartmouth, MA, USA
| | - Alisa Khramushin
- Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Indigo C King
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Cyrus Biotechnology, Seattle, WA, USA
| | - Robert Kleffner
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Brian Koepnick
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Georg Kuenze
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Daisuke Kuroda
- Medical Device Development and Regulation Research Center, School of Engineering, University of Tokyo, Tokyo, Japan
- Department of Bioengineering, School of Engineering, University of Tokyo, Tokyo, Japan
| | - Jason W Labonte
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA, USA
| | - Jason K Lai
- Baylor College of Medicine, Department of Pharmacology, Houston, TX, USA
| | - Gideon Lapidoth
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Andrew Leaver-Fay
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA
| | - Thomas Linsky
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Nir London
- Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Joseph H Lubin
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Sergey Lyskov
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jack Maguire
- Program in Bioinformatics and Computational Biology, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lars Malmström
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Institute for Computational Science, University of Zurich, Zurich, Switzerland
- S3IT, University of Zurich, Zurich, Switzerland
- Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden
| | - Enrique Marcos
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Research in Biomedicine Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Orly Marcu
- Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nicholas A Marze
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jens Meiler
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
- Departments of Chemistry, Pharmacology and Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
- Institute for Chemical Biology, Vanderbilt University, Nashville, TN, USA
| | - Rocco Moretti
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - Vikram Khipple Mulligan
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Santrupti Nerli
- Department of Computer Science, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Christoffer Norn
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Shane Ó'Conchúir
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Noah Ollikainen
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Sergey Ovchinnikov
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Michael S Pacella
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Xingjie Pan
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Hahnbeom Park
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Ryan E Pavlovicz
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Cyrus Biotechnology, Seattle, WA, USA
| | - Manasi Pethe
- Department of Chemistry and Chemical Biology, The State University of New Jersey, Piscataway, NJ, USA
- Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Brian G Pierce
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Kala Bharath Pilla
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Barak Raveh
- Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - P Douglas Renfrew
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Shourya S Roy Burman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Aliza Rubenstein
- Institute of Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Computational Biology and Molecular Biophysics Program, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Marion F Sauer
- Chemical and Physical Biology Program, Vanderbilt Vaccine Center, Vanderbilt University, Nashville, TN, USA
| | - Andreas Scheck
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - William Schief
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yuval Sedan
- Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Alexander M Sevy
- Chemical and Physical Biology Program, Vanderbilt Vaccine Center, Vanderbilt University, Nashville, TN, USA
| | - Nikolaos G Sgourakis
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Lei Shi
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Justin B Siegel
- Department of Chemistry, University of California, Davis, Davis, CA, USA
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, California, USA
- Genome Center, University of California, Davis, Davis, CA, USA
| | | | - Shannon Smith
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - Yifan Song
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Cyrus Biotechnology, Seattle, WA, USA
| | - Amelie Stein
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Maria Szegedy
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Frank D Teets
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Summer B Thyme
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Ray Yu-Ruei Wang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Andrew Watkins
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Lior Zimmerman
- Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Richard Bonneau
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA.
- Department of Biology, New York University, New York, New York, USA.
- Department of Computer Science, New York University, New York, NY, USA.
- Center for Data Science, New York University, New York, NY, USA.
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48
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Abstract
Protein-protein interactions (PPIs) play a critical role in fundamental biological processes. Competitive inhibition of these interfaces requires compounds that can access discontinuous binding epitopes along a large, shallow binding surface area. Conformationally defined protein surface mimics present a viable route to target these interactions. However, the development of minimal protein mimics that engage intracellular targets with high affinity remains a major challenge because mimicry of a portion of the binding interface is often associated with the loss of critical binding interactions. Covalent targeting provides an attractive approach to overcome the loss of noncovalent contacts but have the inherent risk of dominating noncovalent contacts and increasing the likelihood of nonselective binding. Here, we report the iterative design of a proteolytically stable α3β chimeric helix mimic that covalently targets oncogenic Ras G12C as a model system. We explored several electrophiles to optimize preferential alkylation with the desired C12 on Ras. The designed lead peptide modulates nucleotide exchange, inhibits activation of the Ras-mediated signaling cascade, and is selectively toxic toward mutant Ras G12C cancer cells. The relatively high frequency of acquired cysteines as missense mutations in cancer and other diseases suggests that covalent peptides may offer an untapped therapeutic approach for targeting aberrant protein interactions.
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Affiliation(s)
- Daniel Y. Yoo
- Department of Chemistry, New York University, New York, 10003, U.S.A
| | - Andrew D. Hauser
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, U.S.A
| | - Stephen T. Joy
- Department of Chemistry, New York University, New York, 10003, U.S.A
| | - Dafna Bar-Sagi
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, U.S.A
| | - Paramjit S. Arora
- Department of Chemistry, New York University, New York, 10003, U.S.A
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49
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Baxter M, Chapagai D, Craig S, Hurtado C, Varghese J, Nurmemmedov E, Wyatt MD, McInnes C. Peptidomimetic Polo-Box-Targeted Inhibitors that Engage PLK1 in Tumor Cells and Are Selective against the PLK3 Tumor Suppressor. ChemMedChem 2020; 15:1058-1066. [PMID: 32232973 PMCID: PMC7703809 DOI: 10.1002/cmdc.202000137] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Indexed: 12/26/2022]
Abstract
The polo-box domain (PBD) of PLK1 determines mitotic substrate recognition and subcellular localization. Compounds that target PLK1 selectively are required due to the tumor-suppressor roles of PLK3. A structure-activity analysis of the PBD phosphopeptide binding motif has identified potent peptides that delineate the determinants required for mimicry by nonpeptidic inhibitors and provide insights into the structural basis for the selectivity of inhibitors for the PLK1 PBD. Fragment-ligated inhibitory peptides (FLIPs) obtained through REPLACE have been optimized to enhance in vitro binding and a systematic analysis of selectivity for PLK1 vs PLK3 has been carried out for peptides and peptidomimetics. Furthermore, these more drug-like non-ATP-competitive inhibitors had on-target engagement in a cellular context, as evidenced by stabilization of PLK1 in a thermal-shift assay and by inhibition of the phosphorylation of TCTP, a target of PLK1. Investigation in cells expressing a mutant PLK1 showed that these cells are sensitive to PBD inhibitors but dramatically resistant to clinically investigated ATP-competitive compounds. These results further validate targeting the PBD binding site in the move towards PLK1 inhibitors that are active against tumors resistant to ATP inhibitors.
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Affiliation(s)
- Merissa Baxter
- Drug Discovery and Biomedical Sciences College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
- Present Address: NCI Shady Grove, Rockville, MD 20850-9702, USA
| | - Danda Chapagai
- Drug Discovery and Biomedical Sciences College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
| | - Sandra Craig
- Drug Discovery and Biomedical Sciences College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
- Present Address: Department of Chemistry, Wake Forest University, Winston-Salem, NC 27109, USA
| | - Cecilia Hurtado
- Drug Discovery and Biomedical Sciences College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
- Present Address: University of California San Francisco, San Francisco, CA 94115, USA
| | - Jessy Varghese
- Drug Discovery and Biomedical Sciences College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
| | - Elmar Nurmemmedov
- John Wayne Cancer Institute and Pacific Neuroscience Institute Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Michael D Wyatt
- Drug Discovery and Biomedical Sciences College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
| | - Campbell McInnes
- Drug Discovery and Biomedical Sciences College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
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50
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Soengas R, Lorca M, Pampín B, Sánchez-Pedregal VM, Estévez RJ, Estévez JC. New Morphiceptin Peptidomimetic Incorporating (1 S,2 R,3 S,4 S,5 R)-2-Amino-3,4,5-trihydroxycyclopen-tane-1-carboxylic acid: Synthesis and Structural Study. Molecules 2020; 25:molecules25112574. [PMID: 32492956 PMCID: PMC7321350 DOI: 10.3390/molecules25112574] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/28/2020] [Accepted: 05/28/2020] [Indexed: 12/03/2022] Open
Abstract
We present the synthesis and structural study of a new peptidomimetic of morphiceptin, which can formally be considered as the result of the replacement of the central proline residue of this natural analgesic drug with a subunit of (1S,2R,3S,4S,5R)-2-amino-3,4,5-trihydroxycyclopentane-1-carboxylic acid, previously obtained from L-idose. An optimized synthesis of this trihydroxylated cispentacin derivative is also reported. Molecular docking calculations on the target receptor support a favorable role of the hydroxy substituents of the non-natural β-amino acid incorporated into the peptidomimetic.
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Affiliation(s)
- Raquel Soengas
- Departmento de Química Orgánica e Inorgánica, Universidad de Oviedo, Julián Clavería 8, 33006 Oviedo, Spain;
| | - Marcos Lorca
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain;
| | - Begoña Pampín
- Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain; (B.P.); (V.M.S.-P.)
| | - Víctor M. Sánchez-Pedregal
- Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain; (B.P.); (V.M.S.-P.)
| | - Ramón J. Estévez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain;
- Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain; (B.P.); (V.M.S.-P.)
- Correspondence: (R.J.E.); (J.C.E.)
| | - Juan C. Estévez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain;
- Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain; (B.P.); (V.M.S.-P.)
- Correspondence: (R.J.E.); (J.C.E.)
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