1
|
Vasile F, Lavore F, Gazzola S, Vettraino C, Parisini E, Piarulli U, Belvisi L, Civera M. A combined fragment-based virtual screening and STD-NMR approach for the identification of E-cadherin ligands. Front Chem 2022; 10:946087. [PMID: 36059878 PMCID: PMC9437437 DOI: 10.3389/fchem.2022.946087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 07/22/2022] [Indexed: 12/02/2022] Open
Abstract
Cadherins promote cell-cell adhesion by forming homophilic interactions via their N-terminal extracellular domains. Hence, they have broad-ranging physiological effects on tissue organization and homeostasis. When dysregulated, cadherins contribute to different aspects of cancer progression and metastasis; therefore, targeting the cadherin adhesive interface with small-molecule antagonists is expected to have potential therapeutic and diagnostic value. Here, we used molecular docking simulations to evaluate the propensity of three different libraries of commercially available drug-like fragments (nearly 18,000 compounds) to accommodate into the Trp2 binding pocket of E-cadherin, a crucial site for the orchestration of the protein’s dimerization mechanism. Top-ranked fragments featuring five different aromatic chemotypes were expanded by means of a similarity search on the PubChem database (Tanimoto index >90%). Of this set, seven fragments containing an aromatic scaffold linked to an aliphatic chain bearing at least one amine group were finally selected for further analysis. Ligand-based NMR data (Saturation Transfer Difference, STD) and molecular dynamics simulations suggest that these fragments can bind E-cadherin mostly through their aromatic moiety, while their aliphatic portions may also diversely engage with the mobile regions of the binding site. A tetrahydro-β-carboline scaffold functionalized with an ethylamine emerged as the most promising fragment.
Collapse
Affiliation(s)
- Francesca Vasile
- Department of Chemistry, Università Degli Studi di Milano, Milan, Italy
| | - Francesca Lavore
- Department of Chemistry, Università Degli Studi di Milano, Milan, Italy
| | - Silvia Gazzola
- Department of Science and High Technology, Università Degli Studi Dell’Insubria, Como, Italy
| | - Chiara Vettraino
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia @Polimi, Milan, Italy
| | - Emilio Parisini
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia @Polimi, Milan, Italy
- Latvian Institute of Organic Synthesis, Riga, Latvia
- Department of Chemistry “Giacomo Ciamician”, Università Degli Studi di Bologna, Bologna, Italy
| | - Umberto Piarulli
- Department of Science and High Technology, Università Degli Studi Dell’Insubria, Como, Italy
| | - Laura Belvisi
- Department of Chemistry, Università Degli Studi di Milano, Milan, Italy
| | - Monica Civera
- Department of Chemistry, Università Degli Studi di Milano, Milan, Italy
- *Correspondence: Monica Civera,
| |
Collapse
|
2
|
Crean RM, Biler M, van der Kamp MW, Hengge AC, Kamerlin SCL. Loop Dynamics and Enzyme Catalysis in Protein Tyrosine Phosphatases. J Am Chem Soc 2021; 143:3830-3845. [PMID: 33661624 PMCID: PMC8031367 DOI: 10.1021/jacs.0c11806] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Indexed: 12/16/2022]
Abstract
Protein tyrosine phosphatases (PTPs) play an important role in cellular signaling and have been implicated in human cancers, diabetes, and obesity. Despite shared catalytic mechanisms and transition states for the chemical steps of catalysis, catalytic rates within the PTP family vary over several orders of magnitude. These rate differences have been implied to arise from differing conformational dynamics of the closure of a protein loop, the WPD-loop, which carries a catalytically critical residue. The present work reports computational studies of the human protein tyrosine phosphatase 1B (PTP1B) and YopH from Yersinia pestis, for which NMR has demonstrated a link between their respective rates of WPD-loop motion and catalysis rates, which differ by an order of magnitude. We have performed detailed structural analysis, both conventional and enhanced sampling simulations of their loop dynamics, as well as empirical valence bond simulations of the chemical step of catalysis. These analyses revealed the key residues and structural features responsible for these differences, as well as the residues and pathways that facilitate allosteric communication in these enzymes. Curiously, our wild-type YopH simulations also identify a catalytically incompetent hyper-open conformation of its WPD-loop, sampled as a rare event, previously only experimentally observed in YopH-based chimeras. The effect of differences within the WPD-loop and its neighboring loops on the modulation of loop dynamics, as revealed in this work, may provide a facile means for the family of PTP enzymes to respond to environmental changes and regulate their catalytic activities.
Collapse
Affiliation(s)
- Rory M. Crean
- Science
for Life Laboratory, Department of Chemistry − BMC, Uppsala University, Box 576, S-751 23 Uppsala, Sweden
| | - Michal Biler
- Science
for Life Laboratory, Department of Chemistry − BMC, Uppsala University, Box 576, S-751 23 Uppsala, Sweden
| | - Marc W. van der Kamp
- School
of Biochemistry, University of Bristol, Biomedical Sciences Building, University
Walk, Bristol BS8 1TD, United Kingdom
| | - Alvan C. Hengge
- Department
of Chemistry and Biochemistry, Utah State
University, Logan, Utah 84322-0300, United States
| | - Shina C. L. Kamerlin
- Science
for Life Laboratory, Department of Chemistry − BMC, Uppsala University, Box 576, S-751 23 Uppsala, Sweden
| |
Collapse
|
3
|
Civera M, Vasile F, Potenza D, Colombo C, Parente S, Vettraino C, Prosdocimi T, Parisini E, Belvisi L. Exploring E-cadherin-peptidomimetics interaction using NMR and computational studies. PLoS Comput Biol 2019; 15:e1007041. [PMID: 31158220 PMCID: PMC6564044 DOI: 10.1371/journal.pcbi.1007041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 06/13/2019] [Accepted: 04/22/2019] [Indexed: 02/02/2023] Open
Abstract
Cadherins are homophilic cell-cell adhesion molecules whose aberrant expression has often been shown to correlate with different stages of tumor progression. In this work, we investigate the interaction of two peptidomimetic ligands with the extracellular portion of human E-cadherin using a combination of NMR and computational techniques. Both ligands have been previously developed as mimics of the tetrapeptide sequence Asp1-Trp2-Val3-Ile4 of the cadherin adhesion arm, and have been shown to inhibit E-cadherin-mediated adhesion in epithelial ovarian cancer cells with millimolar potency. To sample a set of possible interactions of these ligands with the E-cadherin extracellular portion, STD-NMR experiments in the presence of two slightly different constructs, the wild type E-cadherin-EC1-EC2 fragment and the truncated E-cadherin-(Val3)-EC1-EC2 fragment, were carried out at three temperatures. Depending on the protein construct, a different binding epitope of the ligand and also a different temperature effect on STD signals were observed, both suggesting an involvement of the Asp1-Trp2 protein sequence among all the possible binding events. To interpret the experimental results at the atomic level and to probe the role of the cadherin adhesion arm in the dynamic interaction with the peptidomimetic ligand, a computational protocol based on docking calculations and molecular dynamics simulations was applied. In agreement with NMR data, the simulations at different temperatures unveil high variability/dynamism in ligand-cadherin binding, thus explaining the differences in ligand binding epitopes. In particular, the modulation of the signals seems to be dependent on the protein flexibility, especially at the level of the adhesive arm, which appears to participate in the interaction with the ligand. Overall, these results will help the design of novel cadherin inhibitors that might prevent the swap dimer formation by targeting both the Trp2 binding pocket and the adhesive arm residues. Classical cadherins are the main adhesive proteins at the intercellular junctions and play an essential role in tissue morphogenesis and homeostasis. A large number of studies have shown that cadherin aberrant expression and/or dysregulation often correlate with pathological processes, such as tumor development and progression. Notwithstanding the emerging role played by cadherins in a number of solid tumors, the rational design of small inhibitors targeting these proteins is still in its infancy, likely due to the challenges posed by the development of small drug-like molecules that modulate protein-protein interactions and to the structural complexity of the various cadherin dimerization interfaces that constantly form and disappear as the protein moves along its highly dynamic and reversible homo-dimerization trajectory. In this work, we study the interaction of two small molecules with the extracellular portion of human E-cadherin using a combination of spectroscopic and computational techniques. The availability of molecules interfering in the cadherin homophilic interactions could provide a useful tool for the investigation of cadherin function in tumors, and potentially pave the way to the development of novel alternative diagnostic and therapeutic interventions in cadherin-expressing solid tumors.
Collapse
Affiliation(s)
- Monica Civera
- Dipartimento di Chimica, Università degli Studi di Milano, Milan, Italy
- Istituto di Scienze e Tecnologie Molecolari (ISTM), Consiglio Nazionale delle Ricerche, Milan, Italy
- * E-mail: (MC); (FV)
| | - Francesca Vasile
- Dipartimento di Chimica, Università degli Studi di Milano, Milan, Italy
- Istituto di Scienze e Tecnologie Molecolari (ISTM), Consiglio Nazionale delle Ricerche, Milan, Italy
- * E-mail: (MC); (FV)
| | - Donatella Potenza
- Dipartimento di Chimica, Università degli Studi di Milano, Milan, Italy
| | - Cinzia Colombo
- Dipartimento di Chimica, Università degli Studi di Milano, Milan, Italy
| | - Sara Parente
- Dipartimento di Scienza e Alta Tecnologia, Università degli Studi dell'Insubria, Como, Italy
| | - Chiara Vettraino
- Center for Nano Science and Technology @PoliMi, Istituto Italiano di Tecnologia, Milan, Italy
| | - Tommaso Prosdocimi
- Center for Nano Science and Technology @PoliMi, Istituto Italiano di Tecnologia, Milan, Italy
| | - Emilio Parisini
- Center for Nano Science and Technology @PoliMi, Istituto Italiano di Tecnologia, Milan, Italy
| | - Laura Belvisi
- Dipartimento di Chimica, Università degli Studi di Milano, Milan, Italy
- Istituto di Scienze e Tecnologie Molecolari (ISTM), Consiglio Nazionale delle Ricerche, Milan, Italy
| |
Collapse
|
4
|
Liu Y, Li W, Mu Y. Optimization of replica exchange temperature ladder under the well-tempered ensemble. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.09.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
5
|
Gandini E, Dapiaggi F, Oliva F, Pieraccini S, Sironi M. Well-Tempered MetaDynamics based method to evaluate universal peptidomimetics. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.07.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
6
|
Valsson O, Tiwary P, Parrinello M. Enhancing Important Fluctuations: Rare Events and Metadynamics from a Conceptual Viewpoint. Annu Rev Phys Chem 2016; 67:159-84. [DOI: 10.1146/annurev-physchem-040215-112229] [Citation(s) in RCA: 355] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Omar Valsson
- Department of Chemistry and Applied Biosciences, ETH Zurich, c/o Università della Swizzera Italiana Campus, 6900 Lugano, Switzerland;
- Facoltà di Informatica, Instituto di Scienze Computationali, Università della Svizzera Italiana, 6900 Lugano, Switzerland
| | - Pratyush Tiwary
- Department of Chemistry, Columbia University, New York, NY 10027
| | - Michele Parrinello
- Department of Chemistry and Applied Biosciences, ETH Zurich, c/o Università della Swizzera Italiana Campus, 6900 Lugano, Switzerland;
- Facoltà di Informatica, Instituto di Scienze Computationali, Università della Svizzera Italiana, 6900 Lugano, Switzerland
| |
Collapse
|