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Xu G, Zhang S, Zheng L, Hu Z, Cheng L, Chen L, Li J, Shi Z. In silico identification of A1 agonists and A2a inhibitors in pain based on molecular docking strategies and dynamics simulations. Purinergic Signal 2023; 19:87-97. [PMID: 34677752 PMCID: PMC9984648 DOI: 10.1007/s11302-021-09808-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/05/2021] [Indexed: 12/19/2022] Open
Abstract
Most recently, the adenosine is considered as one of the most promising targets for treating pain, with few side effects. It exists in the central nervous system, and plays a key role in nociceptive afferent pathway. It is reported that the A1 receptor (A1R) could inhibit Ca2+ channels to reduce the pain like analgesic mechanism of morphine. And, A2a receptor (A2aR) was reported to enhance the accumulation of AMP (cAMP) and released peptides from sensory neurons, resulting in constitutive activation of pain. Much evidence showed that A1R and A2aR could be served as the interesting targets for the treatment of pain. Herein, virtual screening was utilized to identify the small molecule compounds towards A1R and A2aR, and top six molecules were considered as candidates via amber scores. The molecular dynamic (MD) simulations and molecular mechanics/generalized born surface area (MM/GBSA) were employed to further analyze the affinity and binding stability of the six molecules towards A1R and A2aR. Moreover, energy decomposition analysis showed significant residues in A1R and A2aR, including His1383, Phe1276, and Glu1277. It provided basics for discovery of novel agonists and antagonists. Finally, the agonists of A1R (ZINC19943625, ZINC13555217, and ZINC04698406) and inhibitors of A2aR (ZINC19370372, ZINC20176051, and ZINC57263068) were successfully recognized. Taken together, our discovered small molecules may serve as the promising candidate agents for future pain research.
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Affiliation(s)
- Guangya Xu
- Clinical Genetics Laboratory, Clinical Medical College & Affiliated Hospital & College of Basic Medicine & College of Food and Biological Engineering, Chengdu University, Chengdu, 610081, China
| | - Shutao Zhang
- Clinical Genetics Laboratory, Clinical Medical College & Affiliated Hospital & College of Basic Medicine & College of Food and Biological Engineering, Chengdu University, Chengdu, 610081, China
| | - Lulu Zheng
- Clinical Genetics Laboratory, Clinical Medical College & Affiliated Hospital & College of Basic Medicine & College of Food and Biological Engineering, Chengdu University, Chengdu, 610081, China
| | - Zhongjiao Hu
- Clinical Genetics Laboratory, Clinical Medical College & Affiliated Hospital & College of Basic Medicine & College of Food and Biological Engineering, Chengdu University, Chengdu, 610081, China.,School of Pharmacy, Zunyi Medical University, Zunyi, 563000, China
| | - Lijia Cheng
- Clinical Genetics Laboratory, Clinical Medical College & Affiliated Hospital & College of Basic Medicine & College of Food and Biological Engineering, Chengdu University, Chengdu, 610081, China
| | - Lvlin Chen
- Clinical Genetics Laboratory, Clinical Medical College & Affiliated Hospital & College of Basic Medicine & College of Food and Biological Engineering, Chengdu University, Chengdu, 610081, China
| | - Jun Li
- Clinical Genetics Laboratory, Clinical Medical College & Affiliated Hospital & College of Basic Medicine & College of Food and Biological Engineering, Chengdu University, Chengdu, 610081, China. .,Sichuan Wuyan Biotech Co. Ltd Company, Chengdu, 610041, China.
| | - Zheng Shi
- Clinical Genetics Laboratory, Clinical Medical College & Affiliated Hospital & College of Basic Medicine & College of Food and Biological Engineering, Chengdu University, Chengdu, 610081, China. .,School of Pharmacy, Zunyi Medical University, Zunyi, 563000, China.
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Federico S, Margiotta E, Moro S, Kachler S, Klotz KN, Spalluto G. Potent and selective A 3 adenosine receptor antagonists bearing aminoesters as heterobifunctional moieties. RSC Med Chem 2020; 12:254-262. [PMID: 34046614 DOI: 10.1039/d0md00380h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 11/23/2020] [Indexed: 11/21/2022] Open
Abstract
A3 adenosine receptors were found to have a role in different pathological states, such as glaucoma, renal fibrosis, neuropathic pain and cancer. Consequently, it is important to utilize any molecular tool which could help to study these conditions. In the present study we continue our search for potent A3 adenosine receptor ligands which could be successively conjugated to other molecules with the aim of obtaining more potent (e.g. allosteric ligand conjugation) or detectable ligands (e.g. fluorescent molecule or biotin conjugation). Specifically, different aminoester moieties were introduced at the 5 position of the pyrazolo[4,3-e]-1,2,4-triazolo[1,5-c]pyrimidine core. The ester functionalization represents the candidate for the subsequent conjugation. All the reported compounds are potent hA3 adenosine receptor antagonists and some of them exhibited high selectivity against the other adenosine receptors. The main structural terms of ligand recognition and selectivity were disclosed by molecular modelling studies. Molecular docking results led to the characterization of an alternative binding mode for antagonists at the orthosteric binding site of the hA3 adenosine receptor, evaluated and assessed by classical molecular dynamics simulations.
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Affiliation(s)
- Stephanie Federico
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste Via Licio Giorgieri 1 34127 Trieste Italy
| | - Enrico Margiotta
- Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco, Università di Padova via Marzolo 5 35131 Padova Italy.,Department of Physics, University of Cagliari Cittadella Universitaria S.P. Monserrato-Sestu Km 0.700 09042 Monserrato (CA), Cagliari Italy
| | - Stefano Moro
- Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco, Università di Padova via Marzolo 5 35131 Padova Italy
| | - Sonja Kachler
- Institut für Pharmakologie und Toxikologie, Universität Würzburg Versbacher Strasse 9 97078 Würzburg Germany
| | - Karl-Norbert Klotz
- Institut für Pharmakologie und Toxikologie, Universität Würzburg Versbacher Strasse 9 97078 Würzburg Germany
| | - Giampiero Spalluto
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste Via Licio Giorgieri 1 34127 Trieste Italy
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Pineux F, Federico S, Klotz KN, Kachler S, Michiels C, Sturlese M, Prato M, Spalluto G, Moro S, Bonifazi D. Targeting G Protein-Coupled Receptors with Magnetic Carbon Nanotubes: The Case of the A 3 Adenosine Receptor. ChemMedChem 2020; 15:1909-1920. [PMID: 32706529 DOI: 10.1002/cmdc.202000466] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Indexed: 12/14/2022]
Abstract
The A3 adenosine receptor (AR) is a G protein-coupled receptor (GPCR) overexpressed in the membrane of specific cancer cells. Thus, the development of nanosystems targeting this receptor could be a strategy to both treat and diagnose cancer. Iron-filled carbon nanotubes (CNTs) are an optimal platform for theranostic purposes, and the use of a magnetic field can be exploited for cancer magnetic cell sorting and thermal therapy. In this work, we have conjugated an A3 AR ligand on the surface of iron-filled CNTs with the aim of targeting cells overexpressing A3 ARs. In particular, two conjugates bearing PEG linkers of different length were designed. A docking analysis of A3 AR showed that neither CNT nor linker interferes with ligand binding to the receptor; this was confirmed by in vitro preliminary radioligand competition assays on A3 AR. Encouraged by this result, magnetic cell sorting was applied to a mixture of cells overexpressing or not the A3 AR in which our compound displayed indiscriminate binding to all cells. Despite this, it is the first time that a GPCR ligand has been anchored to a magnetic nanosystem, thus it opens the door to new applications for cancer treatment.
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Affiliation(s)
- Florent Pineux
- Department of Chemistry and Namur Research College (NARC), University of Namur, Rue de Bruxelles 61, 5000, Namur, Belgium
| | - Stephanie Federico
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, Via L.Giorgeri 1, 34127, Trieste, Italy
| | - Karl-Norbert Klotz
- Institut für Pharmakologie und Toxikologie, Universität Würzburg, Versbacher Straße 9, 97078, Würzburg, Germany
| | - Sonja Kachler
- Institut für Pharmakologie und Toxikologie, Universität Würzburg, Versbacher Straße 9, 97078, Würzburg, Germany
| | - Carine Michiels
- Namur Research Institute for Life Science (NARILIS), Unité de Recherche en Biologie Cellulaire (URBC), University of Namur, 5000, Namur, Belgium
| | - Mattia Sturlese
- Dipartimento di Scienze del Farmaco Molecular Modeling Section (MMS), Università degli Studi di Padova, Via F. Marzolo 5, 35131, Padova, Italy
| | - Maurizio Prato
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, Via L.Giorgeri 1, 34127, Trieste, Italy.,Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 182, 20014, Donostia-San Sebastián, Spain.,Basque Foundation for Science, Ikerbasque, 48013, Bilbao, Spain
| | - Giampiero Spalluto
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, Via L.Giorgeri 1, 34127, Trieste, Italy
| | - Stefano Moro
- Dipartimento di Scienze del Farmaco Molecular Modeling Section (MMS), Università degli Studi di Padova, Via F. Marzolo 5, 35131, Padova, Italy
| | - Davide Bonifazi
- Institut für Organische Chemie, Universität Wien, Währinger Str. 38, 1090, Wien, Austria
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Federico S, Margiotta E, Moro S, Kozma E, Gao ZG, Jacobson KA, Spalluto G. Conjugable A 3 adenosine receptor antagonists for the development of functionalized ligands and their use in fluorescent probes. Eur J Med Chem 2019; 186:111886. [PMID: 31787357 DOI: 10.1016/j.ejmech.2019.111886] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/12/2019] [Accepted: 11/12/2019] [Indexed: 12/31/2022]
Abstract
Compounds able to simultaneously bind a biological target and be conjugated to a second specific moiety are attractive tools for the development of multi-purpose ligands useful as multi-target ligands, receptor probes or drug delivery systems, with both therapeutic and diagnostic applications. The human A3 adenosine receptor is a G protein-coupled receptor involved in many physio-pathological conditions, e.g. cancer and inflammation, thus representing a promising research target. In this work, two series of conjugable hA3AR antagonists, based on the pyrazolo[4,3-e]-1,2,4-triazolo[1,5-c]pyrimidine nucleus, were developed. The introduction of an aromatic ring at the 5 position of the scaffold, before (phenylacetamido moiety) or after (1,2,3-triazole obtained by click chemistry) the conjugation is aimed to increase affinity and selectivity towards the hA3AR receptor. As expected, conjugable compounds showed good affinity towards the hA3AR. In order to prove their potential in the development of hA3AR ligands for different purposes, compounds were also functionalized with fluorescent probes. Unfortunately, conjugation decreased affinity and selectivity for the target as compared to the hA2AAR. Computational studies identified specific non-conserved residues of the extracellular loops which constitute a structural barrier able to discriminate between ligands, giving insights into the rational development of new highly selective ligands.
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Affiliation(s)
- Stephanie Federico
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università Degli Studi di Trieste, Via Licio Giorgeri 1, 34127, Trieste, Italy.
| | - Enrico Margiotta
- Molecular Modeling Section (MMS), Dipartimento di Scienze Del Farmaco, Università di Padova, Via Marzolo 5, 35131, Padova, Italy
| | - Stefano Moro
- Molecular Modeling Section (MMS), Dipartimento di Scienze Del Farmaco, Università di Padova, Via Marzolo 5, 35131, Padova, Italy
| | - Eszter Kozma
- Laboratory of Bioorganic Chemistry, NIDDK, National Institute of Health, Bethesda, MD, USA
| | - Zhan-Guo Gao
- Laboratory of Bioorganic Chemistry, NIDDK, National Institute of Health, Bethesda, MD, USA
| | - Kenneth A Jacobson
- Laboratory of Bioorganic Chemistry, NIDDK, National Institute of Health, Bethesda, MD, USA
| | - Giampiero Spalluto
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università Degli Studi di Trieste, Via Licio Giorgeri 1, 34127, Trieste, Italy
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