1
|
Rational design of a helical peptide inhibitor targeting c-Myb–KIX interaction. Sci Rep 2022; 12:816. [PMID: 35058484 PMCID: PMC8776815 DOI: 10.1038/s41598-021-04497-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 12/22/2021] [Indexed: 01/05/2023] Open
Abstract
The transcription factor c-Myb promotes the proliferation of hematopoietic cells by interacting with the KIX domain of CREB-binding protein; however, its aberrant expression causes leukemia. Therefore, inhibitors of the c-Myb–KIX interaction are potentially useful as antitumor drugs. Since the intrinsically disordered transactivation domain (TAD) of c-Myb binds KIX via a conformational selection mechanism where helix formation precedes binding, stabilizing the helical structure of c-Myb TAD is expected to increase the KIX-binding affinity. Here, to develop an inhibitor of the c-Myb–KIX interaction, we designed mutants of the c-Myb TAD peptide fragment where the helical structure is stabilized, based on theoretical predictions using AGADIR. Three of the four initially designed peptides each had a different Lys-to-Arg substitution on the helix surface opposite the KIX-binding interface. Furthermore, the triple mutant with three Lys-to-Arg substitutions, named RRR, showed a high helical propensity and achieved three-fold higher affinity to KIX than the wild-type TAD with a dissociation constant of 80 nM. Moreover, the RRR inhibitor efficiently competed out the c-Myb–KIX interaction. These results suggest that stabilizing the helical structure based on theoretical predictions, especially by conservative Lys-to-Arg substitutions, is a simple and useful strategy for designing helical peptide inhibitors of protein–protein interactions.
Collapse
|
2
|
Sørensen KK, Mishra NK, Paprocki MP, Mehrotra A, Jensen KJ. High-Performance Reversed-Phase Flash Chromatography Purification of Peptides and Chemically Modified Insulins. Chembiochem 2021; 22:1818-1822. [PMID: 33443297 DOI: 10.1002/cbic.202000826] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/12/2021] [Indexed: 12/21/2022]
Abstract
Preparative reversed-phase HPLC is the established method for the purification of peptides, but has significant limitations. We systematically investigated the use of high-performance reversed-phase flash chromatography (HPFC) to rapidly purify laboratory-scale quantities of crude, synthetic peptides and chemically modified insulins. We demonstrated these methods for a diverse set of peptides, including short, medium, and long peptides. Depending on the purity profile of the peptide, HPFC can be used either as the sole purification method, or as a pre-purification method prior to final HPLC purification. Furthermore, HPFC is suitable for the purification of peptides that are not fully in solution. We provide guidelines for the HPFC of synthetic peptides and small proteins, including the choice of columns, eluents, and gradients. We believe that HPFC is a valuable alternative to HPLC purification of peptides and small proteins.
Collapse
Affiliation(s)
- Kasper K Sørensen
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Narendra K Mishra
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Maciej P Paprocki
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | | | - Knud J Jensen
- Department of Chemistry, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| |
Collapse
|
3
|
Algar S, Martín-Martínez M, González-Muñiz R. Evolution in non-peptide α-helix mimetics on the road to effective protein-protein interaction modulators. Eur J Med Chem 2020; 211:113015. [PMID: 33423841 DOI: 10.1016/j.ejmech.2020.113015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/04/2020] [Accepted: 11/09/2020] [Indexed: 02/04/2023]
Abstract
Modulation of interactome networks, essentially protein-protein interactions (PPIs), might represent valuable therapeutic approaches to different pathological conditions. Since a high percentage of PPIs are mediated by α-helical structures at the interacting surface, the development of compounds able to reproduce the amino acid side-chain organization of α-helices (e.g. stabilized α-helix peptides and β-derivatives, proteomimetics, and α-helix small-molecule mimetics) focuses the attention of different research groups. This appraisal describes the recent progress in the non-peptide α-helix mimetics field, which has evolved from single-face to multi-face reproducing compounds and from oligomeric to monomeric scaffolds able to bear different substituents in similar spatial dispositions as the side-chains in canonical helices. Grouped by chemical structures, the review contemplates terphenyl-like molecules, oligobenzamides and heterocyclic analogues, benzamide-amino acid conjugates and non-oligomeric small-molecules mimetics, among others, and their effectiveness to stabilize/disrupt therapeutically relevant PPIs. The X-ray structures of a couple of oligomeric peptidomimetics and of some small-molecules complexed with the MDM2 protein, as well as the state of the art on their development in clinical trials, are also remarked. The discovery of a continuously increasing number of new disease-relevant PPIs could offer future opportunities for these and other forthcoming α-helix mimetics.
Collapse
Affiliation(s)
- Sergio Algar
- Instituto de Química Médica, IQM-CSIC, Juan de La Cierva 3, 28006, Madrid, Spain
| | | | | |
Collapse
|
4
|
Zanella S, Bocchinfuso G, De Zotti M, Arosio D, Marino F, Raniolo S, Pignataro L, Sacco G, Palleschi A, Siano AS, Piarulli U, Belvisi L, Formaggio F, Gennari C, Stella L. Rational Design of Antiangiogenic Helical Oligopeptides Targeting the Vascular Endothelial Growth Factor Receptors. Front Chem 2019; 7:170. [PMID: 30984741 PMCID: PMC6449863 DOI: 10.3389/fchem.2019.00170] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 03/05/2019] [Indexed: 01/25/2023] Open
Abstract
Tumor angiogenesis, essential for cancer development, is regulated mainly by vascular endothelial growth factors (VEGFs) and their receptors (VEGFRs), which are overexpressed in cancer cells. Therefore, the VEGF/VEGFR interaction represents a promising pharmaceutical target to fight cancer progression. The VEGF surface interacting with VEGFRs comprises a short α-helix. In this work, helical oligopeptides mimicking the VEGF-C helix were rationally designed based on structural analyses and computational studies. The helical conformation was stabilized by optimizing intramolecular interactions and by introducing helix-inducing Cα,α-disubstituted amino acids. The conformational features of the synthetic peptides were characterized by circular dichroism and nuclear magnetic resonance, and their receptor binding properties and antiangiogenic activity were determined. The best hits exhibited antiangiogenic activity in vitro at nanomolar concentrations and were resistant to proteolytic degradation.
Collapse
Affiliation(s)
- Simone Zanella
- Department of Chemistry, University of Milan, Milan, Italy
| | - Gianfranco Bocchinfuso
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome, Italy
| | - Marta De Zotti
- Padova Unit, Department of Chemistry, Institute of Biomolecular Chemistry, CNR, University of Padova, Padova, Italy
| | - Daniela Arosio
- National Research Council, Institute of Molecular Science and Technologies, Milan, Italy
| | - Franca Marino
- Center for Research in Medical Pharmacology, University of Insubria, Varese, Italy
| | - Stefano Raniolo
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome, Italy
| | - Luca Pignataro
- Department of Chemistry, University of Milan, Milan, Italy
| | - Giovanni Sacco
- Department of Chemistry, University of Milan, Milan, Italy
| | - Antonio Palleschi
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome, Italy
| | - Alvaro S Siano
- Departamento de Química Organica, Facultad de Bioquímica y Ciencias Biologicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Umberto Piarulli
- Center for Research in Medical Pharmacology, University of Insubria, Varese, Italy
| | - Laura Belvisi
- Department of Chemistry, University of Milan, Milan, Italy.,National Research Council, Institute of Molecular Science and Technologies, Milan, Italy
| | - Fernando Formaggio
- Padova Unit, Department of Chemistry, Institute of Biomolecular Chemistry, CNR, University of Padova, Padova, Italy
| | - Cesare Gennari
- Department of Chemistry, University of Milan, Milan, Italy.,National Research Council, Institute of Molecular Science and Technologies, Milan, Italy
| | - Lorenzo Stella
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome, Italy
| |
Collapse
|
5
|
Pérez de Vega MJ, Ferrer-Montiel A, González-Muñiz R. Recent progress in non-opioid analgesic peptides. Arch Biochem Biophys 2018; 660:36-52. [DOI: 10.1016/j.abb.2018.10.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/15/2018] [Accepted: 10/16/2018] [Indexed: 02/08/2023]
|
6
|
De Rosa L, Di Stasi R, D'Andrea LD. Pro-angiogenic peptides in biomedicine. Arch Biochem Biophys 2018; 660:72-86. [DOI: 10.1016/j.abb.2018.10.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 10/11/2018] [Accepted: 10/13/2018] [Indexed: 12/12/2022]
|
7
|
Disrupting VEGF-VEGFR1 Interaction: De Novo Designed Linear Helical Peptides to Mimic the VEGF 13-25 Fragment. Molecules 2017; 22:molecules22111846. [PMID: 29143774 PMCID: PMC6150346 DOI: 10.3390/molecules22111846] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 10/20/2017] [Accepted: 10/26/2017] [Indexed: 12/20/2022] Open
Abstract
The interaction between vascular endothelial growth factor (VEGF) and its receptors (VEGFR) has important implications in angiogenesis and cancer, which moved us to search for peptide derivatives able to block this protein–protein interaction. In a previous work we had described a collection of linear 13-mer peptides specially designed to adopt helical conformations (Ac-SSEEX5ARNX9AAX12N-NH2), as well as the evaluation of seven library components for the inhibition of the interaction of VEGF with its Receptor 1 (VEGFR1). This study led to the discovery of some new, quite potent inhibitors of this protein–protein system. The results we found prompted us to extend the study to other peptides of the library. We describe here the evaluation of a new selection of peptides from the initial library that allow us to identify new VEGF-VEGFR1 inhibitors. Among them, the peptide sequence containing F, W, and I residues at the 5, 9, and 12 positions, show a very significant nanomolar IC50 value, competing with VEGF for its receptor 1, VEGFR1 (Flt-1), which could represent a new tool within the therapeutic arsenal for cancer detection and therapy.
Collapse
|
8
|
Pérez de Vega MJ, Gómez-Monterrey I, Ferrer-Montiel A, González-Muñiz R. Transient Receptor Potential Melastatin 8 Channel (TRPM8) Modulation: Cool Entryway for Treating Pain and Cancer. J Med Chem 2016; 59:10006-10029. [PMID: 27437828 DOI: 10.1021/acs.jmedchem.6b00305] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
TRPM8 ion channels, the primary cold sensors in humans, are activated by innocuous cooling (<28 °C) and cooling compounds (menthol, icilin) and are implicated in sensing unpleasant cold stimuli as well as in mammalian thermoregulation. Overexpression of these thermoregulators in prostate cancer and in other life-threatening tumors, along with their contribution to an increasing number of pathological conditions, opens a plethora of medicinal chemistry opportunities to develop receptor modulators. This Perspective seeks to describe current known modulators for this ion channel because both agonists and antagonists may be useful for the treatment of most TRPM8-mediated pathologies. We primarily focus on SAR data for the different families of compounds and the pharmacological properties of the most promising ligands. Furthermore, we also address the knowledge about the channel structure, although still in its infancy, and the role of the TRPM8 protein signalplex to channel function and dysfunction. We finally outline the potential future prospects of the challenging TRPM8 drug discovery field.
Collapse
Affiliation(s)
| | - Isabel Gómez-Monterrey
- Dipartimento di Farmacia, Università "Federico II" de Napoli , Via D. Montesano 49, 80131, Naples, Italy
| | - Antonio Ferrer-Montiel
- Instituto de Biología Molecular y Celular. Universitas Miguel Hernández . 03202 Alicante, Spain
| | | |
Collapse
|
9
|
Gao M, Cheng K, Yin H. Targeting protein-protein interfaces using macrocyclic peptides. Biopolymers 2016; 104:310-6. [PMID: 25664609 DOI: 10.1002/bip.22625] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 01/29/2015] [Accepted: 02/01/2015] [Indexed: 01/10/2023]
Abstract
Protein-protein interactions (PPIs) are critical in numerous biological processes including signaling transduction, function regulations, and disease development. To regulate PPIs has been thought to be challenging due to their highly dynamic and expansive interfacial areas. Nonetheless, successful examples have been reported of targeting PPIs using small molecules, peptides, and proteins. Peptides, especially macrocyclic peptides have proven to be a particularly useful tool to inhibit PPIs for their exquisite potency, stability and selectivity. Herein we review the recent developments of this area of research, focusing on the macrocyclic peptides isolated from natural products, identified from library screening, and rationally designed based on structures, as PPI regulators.
Collapse
Affiliation(s)
- Meng Gao
- Department of Chemistry, Center of Basic Molecular Science, Tsinghua University, Beijing, China , 100082
| | - Kui Cheng
- Department of Chemistry, Center of Basic Molecular Science, Tsinghua University, Beijing, China , 100082
| | - Hang Yin
- Department of Chemistry, Center of Basic Molecular Science, Tsinghua University, Beijing, China , 100082.,Department of Chemistry and Biochemistry, the BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80309-0596
| |
Collapse
|
10
|
Bopp B, Ciglia E, Ouald-Chaib A, Groth G, Gohlke H, Jose J. Design and biological testing of peptidic dimerization inhibitors of human Hsp90 that target the C-terminal domain. Biochim Biophys Acta Gen Subj 2016; 1860:1043-55. [DOI: 10.1016/j.bbagen.2016.01.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 12/18/2015] [Accepted: 01/06/2016] [Indexed: 11/16/2022]
|
11
|
Pérez-Faginas P, Teresa Aranda M, Torre-Martínez RDL, Quirce S, Fernández-Carvajal A, Ferrer-Montiel A, González-Muñiz R. New transient receptor potential TRPV1, TRPM8 and TRPA1 channel antagonists from a single linear β,γ-diamino ester scaffold. RSC Adv 2016. [DOI: 10.1039/c5ra25709c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Incorporation of minor changes in the structure of a single β,γ-diaminoester linear scaffold resulted in selective hits for TRPV1, TRPM8 and TRPA1 blockade, as well as some dual antagonists.
Collapse
Affiliation(s)
| | | | - Roberto de la Torre-Martínez
- Instituto de Biología Molecular y Celular
- Universidad Miguel Hernández
- Avenida de la Universidad s/n
- 03202 Elche
- Spain
| | - Susana Quirce
- Instituto de Biología Molecular y Celular
- Universidad Miguel Hernández
- Avenida de la Universidad s/n
- 03202 Elche
- Spain
| | - Asia Fernández-Carvajal
- Instituto de Biología Molecular y Celular
- Universidad Miguel Hernández
- Avenida de la Universidad s/n
- 03202 Elche
- Spain
| | - Antonio Ferrer-Montiel
- Instituto de Biología Molecular y Celular
- Universidad Miguel Hernández
- Avenida de la Universidad s/n
- 03202 Elche
- Spain
| | | |
Collapse
|
12
|
Nevola L, Giralt E. Modulating protein-protein interactions: the potential of peptides. Chem Commun (Camb) 2015; 51:3302-15. [PMID: 25578807 DOI: 10.1039/c4cc08565e] [Citation(s) in RCA: 187] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Protein-protein interactions (PPIs) have emerged as important and challenging targets in chemical biology and medicinal chemistry. The main difficulty encountered in the discovery of small molecule modulators derives from the large contact surfaces involved in PPIs when compared with those that participate in protein-small molecule interactions. Because of their intrinsic features, peptides can explore larger surfaces and therefore represent a useful alternative to modulate PPIs. The use of peptides as therapeutics has been held back by their instability in vivo and poor cell internalization. However, more than 200 peptide drugs and homologous compounds (proteins or antibodies) containing peptide bonds are (or have been) on the market, and many alternatives are now available to tackle these limitations. This review will focus on the latest progress in the field, spanning from "lead" identification methods to binding evaluation techniques, through an update of the most successful examples described in the literature.
Collapse
Affiliation(s)
- Laura Nevola
- Institute for Research in Biomedicine (IRB Barcelona), C/Baldiri Reixac 10, 08028 Barcelona, Spain.
| | | |
Collapse
|
13
|
Abstract
Low molecular weight compound competing for the binding of the p53 tumor suppressor to the MDM2 oncoprotein.
Collapse
Affiliation(s)
- Didier Rognan
- Laboratory for Therapeutical Innovation
- UMR7200 CNRS-Université de Strasbourg
- MEDALIS Drug Discovery Center
- 67400 Illkirch
- France
| |
Collapse
|
14
|
Ortar G, Schiano Moriello A, Morera E, Nalli M, Di Marzo V, De Petrocellis L. Effect of acyclic monoterpene alcohols and their derivatives on TRP channels. Bioorg Med Chem Lett 2014; 24:5507-11. [PMID: 25455494 DOI: 10.1016/j.bmcl.2014.10.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 09/30/2014] [Accepted: 10/01/2014] [Indexed: 10/24/2022]
Abstract
A series of thirty-six geraniol, nerol, citronellol, geranylamine, and nerylamine derivatives was synthesized and tested on TRPA1, TRPM8, and TRPV1 channels. Most of them acted as strong modulators of TRPA1 channels with EC50 and/or IC50 values <1 μM. None was able to significantly activate TRPM8 channels, while thirteen of them behaved as 'true' TRPM8 antagonists. Little or no effect was generally observed on TRPV1 channels. Some of the compounds examined, that is, compounds 1d,g,n, 2c,d,h,i,o, 3b,e exhibited an appreciable selectivity for TRPA1 subtype.
Collapse
Affiliation(s)
- Giorgio Ortar
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, piazzale Aldo Moro 5, 00185 Roma, Italy.
| | - Aniello Schiano Moriello
- Endocannabinoid Research Group, Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche, via dei Campi Flegrei 34, 80078 Pozzuoli (Napoli), Italy
| | - Enrico Morera
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Marianna Nalli
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Vincenzo Di Marzo
- Endocannabinoid Research Group, Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche, via dei Campi Flegrei 34, 80078 Pozzuoli (Napoli), Italy
| | - Luciano De Petrocellis
- Endocannabinoid Research Group, Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche, via dei Campi Flegrei 34, 80078 Pozzuoli (Napoli), Italy.
| |
Collapse
|