1
|
van der Ven AM, Gyamfi H, Suttisansanee U, Ahmad MS, Su Z, Taylor RM, Poole A, Chiorean S, Daub E, Urquhart T, Honek JF. Molecular Engineering of E. coli Bacterioferritin: A Versatile Nanodimensional Protein Cage. Molecules 2023; 28:4663. [PMID: 37375226 DOI: 10.3390/molecules28124663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/23/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Currently, intense interest is focused on the discovery and application of new multisubunit cage proteins and spherical virus capsids to the fields of bionanotechnology, drug delivery, and diagnostic imaging as their internal cavities can serve as hosts for fluorophores or bioactive molecular cargo. Bacterioferritin is unusual in the ferritin protein superfamily of iron-storage cage proteins in that it contains twelve heme cofactors and is homomeric. The goal of the present study is to expand the capabilities of ferritins by developing new approaches to molecular cargo encapsulation employing bacterioferritin. Two strategies were explored to control the encapsulation of a diverse range of molecular guests compared to random entrapment, a predominant strategy employed in this area. The first was the inclusion of histidine-tag peptide fusion sequences within the internal cavity of bacterioferritin. This approach allowed for the successful and controlled encapsulation of a fluorescent dye, a protein (fluorescently labeled streptavidin), or a 5 nm gold nanoparticle. The second strategy, termed the heme-dependent cassette strategy, involved the substitution of the native heme with heme analogs attached to (i) fluorescent dyes or (ii) nickel-nitrilotriacetate (NTA) groups (which allowed for controllable encapsulation of a histidine-tagged green fluorescent protein). An in silico docking approach identified several small molecules able to replace the heme and capable of controlling the quaternary structure of the protein. A transglutaminase-based chemoenzymatic approach to surface modification of this cage protein was also accomplished, allowing for future nanoparticle targeting. This research presents novel strategies to control a diverse set of molecular encapsulations and adds a further level of sophistication to internal protein cavity engineering.
Collapse
Affiliation(s)
- Anton M van der Ven
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Hawa Gyamfi
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | | | - Muhammad S Ahmad
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Zhengding Su
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Robert M Taylor
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Amanda Poole
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Sorina Chiorean
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Elisabeth Daub
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Taylor Urquhart
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - John F Honek
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| |
Collapse
|
2
|
Liu S, Ding W, Huang W, Zhang Z, Guo Y, Zhang Q, Wu L, Li Y, Qin R, Li J, Shi T, Zhang X, Lei J, Hu W. Discovery of Novel Benzo[4,5]imidazo[1,2- a]pyrazin-1-amine-3-amide-one Derivatives as Anticancer Human A 2A Adenosine Receptor Antagonists. J Med Chem 2022; 65:8933-8947. [PMID: 35714367 DOI: 10.1021/acs.jmedchem.2c00101] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The blockade of A2A adenosine receptor (A2AAR) activates immunostimulatory response through regulating signaling in tumor microenvironment. Thus, A2AAR has been proposed as a promising target for cancer immunotherapy. In this work, we designed a new series of benzo[4,5]imidazo[1,2-a]pyrazin-1-amine derivatives bearing an amide substitution at 3-position to obtain potent antitumor antagonist in vivo. The structure-activity relationship studies were performed by molecular modeling and radioactive assay. The in vitro anticancer activities were evaluated by 3',5'-cyclic adenosine monophosphate (cAMP) functional and T cell activation assay. The most potent compound 12o·2HCl showed much higher affinity toward A2AAR (Ki = 0.08 nM) and exhibited more significant in vitro immunostimulatory anticancer activity than clinical antagonist AZD4635. More importantly, 12o·2HCl significantly inhibited the growth of triple-negative breast cancer by reversing immunosuppressive tumor microenvironment in the xenograft mouse model without severe toxicity at the testing dose. These results make 12o·2HCl a promising immunotherapy anticancer drug candidate.
Collapse
Affiliation(s)
- Shuhao Liu
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Wen Ding
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Weifeng Huang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Zhijing Zhang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Yinfeng Guo
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Qiyi Zhang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China.,National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Linna Wu
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Yukai Li
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Rui Qin
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Jiahao Li
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Taoda Shi
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Xiaolei Zhang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China.,National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Jinping Lei
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| | - Wenhao Hu
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
| |
Collapse
|
3
|
Iwaloye O, Elekofehinti OO, Kikiowo B, Fadipe TM, Akinjiyan MO, Ariyo EO, Aiyeku OO, Adewumi NA. Discovery of Traditional Chinese Medicine Derived Compounds as Wild Type and Mutant Plasmodium falciparum Dihydrofolate Reductase Inhibitors: Induced Fit Docking and ADME Studies. Curr Drug Discov Technol 2021; 18:554-569. [PMID: 32729419 DOI: 10.2174/1570163817999200729122753] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/28/2020] [Accepted: 06/04/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND In a bid to come up with effective compounds as inhibitors for antimalarial treatment, we built a library of 2,000 traditional Chinese medicine(TCM)-derived compounds retrieved from TCM Database@Taiwan. METHODS The active sites of both the wild type and mutant Plasmodium falciparum dihydrofolatereductase (pfDHFR) were explored using computational tools. pfDHFR, one of the prime drug targets in the prevention of malaria infection induced by the female anopheles mosquito has continued to offer resistance to drugs (antifolates) due to mutation in some of the key amino acid residues crucial for its inhibition. RESULTS We utilized virtual throughput screening and glide XP docking to screen the compounds, and 8 compounds were found to have promising docking scores with both the wild type and mutant pfDHFR. They were further subjected to Induce Fit Docking (IFD) to affirm their inhibitory potency. The ADME properties and biological activity spectrum of the compounds were also considered. The inhibition profile of the compounds revealed that a number of compounds formed intermolecular interactions with ASP54, ILE14, LEU164, SER108/ASN108, ARG122 and ASP58. Most of the compounds can be considered as drug candidates due to their antiprotozoal activities and accordance with the Lipinski's Rule of Five (ROF). CONCLUSION The outcome of the present study should further be investigated to attest the efficacy of these compounds as better drug candidates than the antifolates.
Collapse
Affiliation(s)
- Opeyemi Iwaloye
- Department of Biochemistry, Bioinformatics and Molecular Biology Unit, Federal University of Technology Akure, Ondo State, Nigeria
| | - Olusola Olalekan Elekofehinti
- Department of Biochemistry, Bioinformatics and Molecular Biology Unit, Federal University of Technology Akure, Ondo State, Nigeria
| | - Babatomiwa Kikiowo
- Department of Biochemistry, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Toyin Mary Fadipe
- Department of Bioscience, International Institute of Agriculture, Ibadan, Oyo State, Nigeria
| | - Moses Orimoloye Akinjiyan
- Department of Biochemistry, Bioinformatics and Molecular Biology Unit, Federal University of Technology Akure, Ondo State, Nigeria
| | - Esther Opeyemi Ariyo
- Department of Biochemistry, Bioinformatics and Molecular Biology Unit, Federal University of Technology Akure, Ondo State, Nigeria
| | - Olabisi Olapade Aiyeku
- Department of Biochemistry, Bioinformatics and Molecular Biology Unit, Federal University of Technology Akure, Ondo State, Nigeria
| | - Nicholas Adeyemi Adewumi
- Department of Biochemistry, Bioinformatics and Molecular Biology Unit, Federal University of Technology Akure, Ondo State, Nigeria
| |
Collapse
|
4
|
Chen XZ, Huang Q, Yu XY, Dai C, Shen Y, Lin ZH. Insights into the structural requirements of PKCζ inhibitors as potential anti-arthritis agents based on 3D-QSAR, homology modeling and docking approach. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
5
|
Reddy GL, Sarma R, Liu S, Huang W, Lei J, Fu J, Hu W. Design, synthesis and biological evaluation of novel scaffold benzo[4,5]imidazo [1,2-a]pyrazin-1-amine: Towards adenosine A 2A receptor (A 2A AR) antagonist. Eur J Med Chem 2020; 210:113040. [PMID: 33316692 DOI: 10.1016/j.ejmech.2020.113040] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 11/11/2020] [Accepted: 11/14/2020] [Indexed: 12/23/2022]
Abstract
Antagonists of adenosine receptor are under exploration as potential drug candidates for treatment of neurological disorders, depression, certain cancers and potentially used as a cancer immunotherapy. Herein, we describe design and synthesis of novel scaffold benzo[4,5]imidazo [1,2-a]pyrazin-1-amine (6) derivatives. All the compounds were evaluated for A2A AR antagonist activity and displayed encouraging results (IC50 9-300 nM) of A2A AR antagonist binding affinity in biochemical assay. Compound 27 exhibits good activity in A2A AR antagonist cAMP functional assay (IC50 31 nM) and further this compound shows T-cell activation at the IL-2 production assay (EC50 165 nM). Molecular docking studies were carried out to rationalize the observed binding affinity of compound 27.
Collapse
Affiliation(s)
- G Lakshma Reddy
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Rupam Sarma
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, China; Department of Chemistry, Nalbari College, Assam, 781335, India
| | - Shuhao Liu
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Weifeng Huang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Jinping Lei
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, China.
| | - Jiasheng Fu
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, China.
| | - Wenhao Hu
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, 510006, China.
| |
Collapse
|
6
|
Binding Mode Exploration of B1 Receptor Antagonists' by the Use of Molecular Dynamics and Docking Simulation-How Different Target Engagement Can Determine Different Biological Effects. Int J Mol Sci 2020; 21:ijms21207677. [PMID: 33081372 PMCID: PMC7590058 DOI: 10.3390/ijms21207677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/10/2020] [Accepted: 10/12/2020] [Indexed: 01/24/2023] Open
Abstract
The kinin B1 receptor plays a critical role in the chronic phase of pain and inflammation. The development of B1 antagonists peaked in recent years but almost all promising molecules failed in clinical trials. Little is known about these molecules' mechanisms of action and additional information will be necessary to exploit the potential of the B1 receptor. With the aim of contributing to the available knowledge of the pharmacology of B1 receptors, we designed and characterized a novel class of allosteric non-peptidic inhibitors with peculiar binding characteristics. Here, we report the binding mode analysis and pharmacological characterization of a new allosteric B1 antagonist, DFL20656. We analyzed the binding of DFL20656 by single point mutagenesis and radioligand binding assays and we further characterized its pharmacology in terms of IC50, B1 receptor internalization and in vivo activity in comparison with different known B1 antagonists. We highlighted how different binding modes of DFL20656 and a Merck compound (compound 14) within the same molecular pocket can affect the biological and pharmacological properties of B1 inhibitors. DFL20656, by its peculiar binding mode, involving tight interactions with N114, efficiently induced B1 receptor internalization and evoked a long-lasting effect in an in vivo model of neuropathic pain. The pharmacological characterization of different B1 antagonists highlighted the effects of their binding modes on activity, receptor occupancy and internalization. Our results suggest that part of the failure of most B1 inhibitors could be ascribed to a lack of knowledge about target function and engagement.
Collapse
|
7
|
Pibiri I, Melfi R, Tutone M, Di Leonardo A, Pace A, Lentini L. Targeting Nonsense: Optimization of 1,2,4-Oxadiazole TRIDs to Rescue CFTR Expression and Functionality in Cystic Fibrosis Cell Model Systems. Int J Mol Sci 2020; 21:ijms21176420. [PMID: 32899265 PMCID: PMC7504161 DOI: 10.3390/ijms21176420] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/26/2020] [Accepted: 09/01/2020] [Indexed: 02/07/2023] Open
Abstract
Cystic fibrosis (CF) patients develop a severe form of the disease when the cystic fibrosis transmembrane conductance regulator (CFTR) gene is affected by nonsense mutations. Nonsense mutations are responsible for the presence of a premature termination codon (PTC) in the mRNA, creating a lack of functional protein. In this context, translational readthrough-inducing drugs (TRIDs) represent a promising approach to correct the basic defect caused by PTCs. By using computational optimization and biological screening, we identified three new small molecules showing high readthrough activity. The activity of these compounds has been verified by evaluating CFTR expression and functionality after treatment with the selected molecules in cells expressing nonsense–CFTR–mRNA. Additionally, the channel functionality was measured by the halide sensitive yellow fluorescent protein (YFP) quenching assay. All three of the new TRIDs displayed high readthrough activity and low toxicity and can be considered for further evaluation as a therapeutic approach toward the second major cause of CF.
Collapse
Affiliation(s)
- Ivana Pibiri
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy; (R.M.); (M.T.); (A.D.L.); (A.P.)
- Correspondence: (I.P.); (L.L.); Tel.: +39-091-238-97545 (I.P.); +39-091-238-97341 (L.L.)
| | - Raffaella Melfi
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy; (R.M.); (M.T.); (A.D.L.); (A.P.)
| | - Marco Tutone
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy; (R.M.); (M.T.); (A.D.L.); (A.P.)
| | - Aldo Di Leonardo
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy; (R.M.); (M.T.); (A.D.L.); (A.P.)
- Centro di OncoBiologia Sperimentale (COBS), via San Lorenzo Colli, 90145 Palermo, Italy
| | - Andrea Pace
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy; (R.M.); (M.T.); (A.D.L.); (A.P.)
| | - Laura Lentini
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy; (R.M.); (M.T.); (A.D.L.); (A.P.)
- Correspondence: (I.P.); (L.L.); Tel.: +39-091-238-97545 (I.P.); +39-091-238-97341 (L.L.)
| |
Collapse
|
8
|
Mailavaram RP, Al-Attraqchi OH, Kar S, Ghosh S. Current Status in the Design and Development of Agonists and Antagonists of Adenosine A3 Receptor as Potential Therapeutic Agents. Curr Pharm Des 2019; 25:2772-2787. [DOI: 10.2174/1381612825666190716114056] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 07/03/2019] [Indexed: 12/31/2022]
Abstract
Adenosine receptors (ARs) belongs to the family of G-protein coupled receptors (GPCR) that are responsible
for the modulation of a wide variety of physiological functions. The ARs are also implicated in many
diseases such as cancer, arthritis, cardiovascular and renal diseases. The adenosine A3 receptor (A3AR) has
emerged as a potential drug target for the progress of new and effective therapeutic agents for the treatment of
various pathological conditions. This receptor’s involvement in many diseases and its validity as a target has been
established by many studies. Both agonists and antagonists of A3AR have been extensively investigated in the last
decade with the goal of developing novel drugs for treating diseases related to immune disorders, inflammation,
cancer, and others. In this review, we shall focus on the medicinal chemistry of A3AR ligands, exploring the
diverse chemical classes that have been projected as future leading drug candidates. Also, the recent advances in
the therapeuetic applications of A3AR ligands are highlighted.
Collapse
Affiliation(s)
- Raghu P. Mailavaram
- Department of Pharmaceutical Chemistry, Shri Vishnu College of Pharmacy, Vishnupur (Affiliated to Andhra University), Bhimavaram, W.G. Dist., AP, India
| | - Omar H.A. Al-Attraqchi
- Faculty of Pharmacy, Philadelphia University-Jordan, P.O BOX (1), Philadelphia University- 19392, Amman, Jordan
| | - Supratik Kar
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, Jackson, MS 39217, United States
| | - Shinjita Ghosh
- School of Public Health, Jackson State University, Jackson, MS 39217, United States
| |
Collapse
|
9
|
Stamatis D, Lagarias P, Barkan K, Vrontaki E, Ladds G, Kolocouris A. Structural Characterization of Agonist Binding to an A 3 Adenosine Receptor through Biomolecular Simulations and Mutagenesis Experiments. J Med Chem 2019; 62:8831-8846. [PMID: 31502843 DOI: 10.1021/acs.jmedchem.9b01164] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The adenosine A3 receptor (A3R) binds adenosine and is a drug target against cancer cell proliferation. Currently, there is no experimental structure of A3R. Here, we have generated a molecular model of A3R in complex with two agonists, the nonselective 1-(6-amino-9H-purin-9-yl)-1-deoxy-N-ethyl-β-d-ribofuranuronamide (NECA) and the selective 1-deoxy-1-[6-[[(3-iodophenyl)methyl]amino]-9H-purin-9-yl]-N-methyl-β-d-ribofuranuronamide (IB-MECA). Molecular dynamics simulations of the wild-type A3R in complex with both agonists, combined with in vitro mutagenic studies revealed important residues for binding. Further, molecular mechanics-generalized Born surface area calculations were able to distinguish mutations that reduce or negate agonistic activity from those that maintained or increased the activity. Our studies reveal that selectivity of IB-MECA toward A3R requires not only direct interactions with residues within the orthosteric binding area but also with remote residues. Although V1695.30 is considered to be a selectivity filter for A3R binders, when it was mutated to glutamic acid or alanine, the activity of IB-MECA increased by making new van der Waals contacts with TM5. This result may have implications in the design of new A3R agonists.
Collapse
Affiliation(s)
- Dimitrios Stamatis
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences , National and Kapodistrian University of Athens , Panepistimiopolis-Zografou , 15771 Athens , Greece
| | - Panagiotis Lagarias
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences , National and Kapodistrian University of Athens , Panepistimiopolis-Zografou , 15771 Athens , Greece
| | - Kerry Barkan
- Department of Pharmacology , University of Cambridge , Tennis Court Road , CB2 1PD Cambridge U.K
| | - Eleni Vrontaki
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences , National and Kapodistrian University of Athens , Panepistimiopolis-Zografou , 15771 Athens , Greece
| | - Graham Ladds
- Department of Pharmacology , University of Cambridge , Tennis Court Road , CB2 1PD Cambridge U.K
| | - Antonios Kolocouris
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences , National and Kapodistrian University of Athens , Panepistimiopolis-Zografou , 15771 Athens , Greece
| |
Collapse
|
10
|
Samanta PN, Kar S, Leszczynski J. Recent Advances of In-Silico Modeling of Potent Antagonists for the Adenosine Receptors. Curr Pharm Des 2019; 25:750-773. [DOI: 10.2174/1381612825666190304123545] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 02/26/2019] [Indexed: 11/22/2022]
Abstract
The rapid advancement of computer architectures and development of mathematical algorithms offer a
unique opportunity to leverage the simulation of macromolecular systems at physiologically relevant timescales.
Herein, we discuss the impact of diverse structure-based and ligand-based molecular modeling techniques in
designing potent and selective antagonists against each adenosine receptor (AR) subtype that constitutes multitude
of drug targets. The efficiency and robustness of high-throughput empirical scoring function-based approaches
for hit discovery and lead optimization in the AR family are assessed with the help of illustrative examples
that have led to nanomolar to sub-micromolar inhibition activities. Recent progress in computer-aided drug
discovery through homology modeling, quantitative structure-activity relation, pharmacophore models, and molecular
docking coupled with more accurate free energy calculation methods are reported and critically analyzed
within the framework of structure-based virtual screening of AR antagonists. Later, the potency and applicability
of integrated molecular dynamics (MD) methods are addressed in the context of diligent inspection of intricated
AR-antagonist binding processes. MD simulations are exposed to be competent for studying the role of the membrane
as well as the receptor flexibility toward the precise evaluation of the biological activities of antagonistbound
AR complexes such as ligand binding modes, inhibition affinity, and associated thermodynamic and kinetic
parameters.
Collapse
Affiliation(s)
- Pabitra Narayan Samanta
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, Jackson, MS 39217, United States
| | - Supratik Kar
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, Jackson, MS 39217, United States
| | - Jerzy Leszczynski
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, Jackson, MS 39217, United States
| |
Collapse
|
11
|
Pibiri I, Lentini L, Melfi R, Tutone M, Baldassano S, Ricco Galluzzo P, Di Leonardo A, Pace A. Rescuing the CFTR protein function: Introducing 1,3,4-oxadiazoles as translational readthrough inducing drugs. Eur J Med Chem 2018; 159:126-142. [PMID: 30278331 DOI: 10.1016/j.ejmech.2018.09.057] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 09/21/2018] [Accepted: 09/24/2018] [Indexed: 12/20/2022]
Abstract
Nonsense mutations in the CFTR gene prematurely terminate translation of the CFTR mRNA leading to the production of a truncated protein that lacks normal function causing a more severe form of the cystic fibrosis (CF) disease. About 10% of patients affected by CF show a nonsense mutation. A potential treatment of this alteration is to promote translational readthrough of premature termination codons (PTCs) by Translational Readthrough Inducing Drugs (TRIDs) such as PTC124. In this context we aimed to compare the activity of PTC124 with analogues differing in the heteroatoms position in the central heterocyclic core. By a validated protocol consisting of computational screening, synthesis and biological tests we identified a new small molecule (NV2445) with 1,3,4-oxadiazole core showing a high readthrough activity. Moreover, we evaluated the CFTR functionality after NV2445 treatment in CF model systems and in cells expressing a nonsense-CFTR-mRNA. Finally, we studied the supramolecular interactions between TRIDs and CFTR-mRNA to assess the biological target/mechanism and compared the predicted ADME properties of NV2445 and PTC124.
Collapse
Affiliation(s)
- Ivana Pibiri
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128, Palermo, Italy.
| | - Laura Lentini
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128, Palermo, Italy.
| | - Raffaella Melfi
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128, Palermo, Italy
| | - Marco Tutone
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128, Palermo, Italy
| | - Sara Baldassano
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128, Palermo, Italy
| | - Paola Ricco Galluzzo
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128, Palermo, Italy
| | - Aldo Di Leonardo
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128, Palermo, Italy; Centro di OncoBiologia Sperimentale (COBS), via San Lorenzo Colli, 90145, Palermo, Italy
| | - Andrea Pace
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128, Palermo, Italy
| |
Collapse
|
12
|
Vincenzi M, Bednarska K, Leśnikowski ZJ. Comparative Study of Carborane- and Phenyl-Modified Adenosine Derivatives as Ligands for the A2A and A3 Adenosine Receptors Based on a Rigid in Silico Docking and Radioligand Replacement Assay. Molecules 2018; 23:E1846. [PMID: 30044380 PMCID: PMC6222516 DOI: 10.3390/molecules23081846] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 07/16/2018] [Accepted: 07/18/2018] [Indexed: 12/16/2022] Open
Abstract
Adenosine receptors are involved in many physiological processes and pathological conditions and are therefore attractive therapeutic targets. To identify new types of effective ligands for these receptors, a library of adenosine derivatives bearing a boron cluster or phenyl group in the same position was designed. The ligands were screened in silico to determine their calculated affinities for the A2A and A3 adenosine receptors. An virtual screening protocol based on the PatchDock web server was developed. In the first screening phase, the effects of the functional group (organic or inorganic modulator) on the adenosine ligand affinity for the receptors were determined. Then, the lead compounds were identified for each receptor in the second virtual screening phase. Two pairs of the most promising ligands, compounds 3 and 4, and two ligands with lower affinity scores (compounds 11 and 12, one with a boron cluster and one with a phenyl group) were synthesized and tested in a radioligand replacement assay for affinity to the A2A and A3 receptors. A reasonable correlation of in silico and biological assay results was observed. In addition, the effects of a phenyl group and boron cluster, which is new adenosine modifiers, on the adenosine ligand binding were compared.
Collapse
Affiliation(s)
- Marian Vincenzi
- Laboratory of Molecular Virology and Biological Chemistry, Institute of Medical Biology of the Polish Academy of Sciences, 106 Lodowa St., 93-232 Lodz, Poland.
| | - Katarzyna Bednarska
- Laboratory of Experimental Immunology, Institute of Medical Biology, Polish Academy of Sciences, 106 Lodowa St., 93-232 Lodz, Poland.
| | - Zbigniew J Leśnikowski
- Laboratory of Molecular Virology and Biological Chemistry, Institute of Medical Biology of the Polish Academy of Sciences, 106 Lodowa St., 93-232 Lodz, Poland.
| |
Collapse
|
13
|
Geldenhuys WJ, Hanif A, Yun J, Nayeem MA. Exploring Adenosine Receptor Ligands: Potential Role in the Treatment of Cardiovascular Diseases. Molecules 2017; 22:molecules22060917. [PMID: 28587166 PMCID: PMC5568125 DOI: 10.3390/molecules22060917] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/08/2017] [Accepted: 05/25/2017] [Indexed: 02/07/2023] Open
Abstract
Cardiovascular diseases remain the number one diseases affecting patients’ morbidity and mortality. The adenosine receptors are G-protein coupled receptors which have been of interest for drugs target for the treatment of multiple diseases ranging from cardiovascular to neurological. Adenosine receptors have been connected to several biological pathways affecting the physiology and pathology of the cardiovascular system. In this review, we will cover the different adenosine receptor ligands that have been identified to interact with adenosine receptors and affect the vascular system. These ligands will be evaluated from clinical as well as medicinal chemistry perspectives with more emphasis on how structural changes in structure translate into ligand potency and efficacy. Adenosine receptors represent a novel therapeutic target for development of treatment options treating a wide variety of diseases, including vascular disease and obesity.
Collapse
Affiliation(s)
- Werner J Geldenhuys
- Department of Pharmaceutical Sciences, West Virginia University, School of Pharmacy, Morgantown, WV 26506, USA.
| | - Ahmad Hanif
- Department of Pharmaceutical Sciences, West Virginia University, School of Pharmacy, Morgantown, WV 26506, USA.
| | - June Yun
- Department of Integrative Medical Sciences, Northeast Ohio Medical University College of Medicine, Rootstown, OH 44272, USA.
| | - Mohammed A Nayeem
- Department of Pharmaceutical Sciences, West Virginia University, School of Pharmacy, Morgantown, WV 26506, USA.
| |
Collapse
|
14
|
Indelicato S, Bongiorno D, Calabrese V, Perricone U, Almerico AM, Ceraulo L, Piazzese D, Tutone M. Micelles, Rods, Liposomes, and Other Supramolecular Surfactant Aggregates: Computational Approaches. Interdiscip Sci 2017; 9:392-405. [PMID: 28478537 DOI: 10.1007/s12539-017-0234-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 03/31/2017] [Accepted: 04/24/2017] [Indexed: 12/31/2022]
Abstract
Surfactants are an interesting class of compounds characterized by the segregation of polar and apolar domains in the same molecule. This peculiarity makes possible a whole series of microscopic and macroscopic effects. Among their features, their ability to segregate particles (fluids or entire domains) and to reduce the surface/interfacial tension is the utmost important. The interest in the chemistry of surfactants never weakened; instead, waves of increasing interest have occurred every time a new field of application of these molecules has been discovered. All these special characteristics depend largely on the ability of surfactants to self-assemble and constitute supramolecular structures where their chemical properties are amplified. The possibility to obtain structural and energy information and, above all, the possibility of forecast the self-organizing mechanisms of surfactants have had a significant boost via computational chemistry. The molecular dynamics models, initially coarse-grained and subsequently (with the increasing computer power) using more accurate models, allowed, over the years, to better understand different aspects of the processes of dispersion, self-assembly, segregation of surfactant. Moreover, several other aspects have been investigated as the effect of the counterions of many ionic surfactants in defining the final supramolecular structures, the mobility of side chains, and the capacity of some surfactant to envelope entire proteins. This review constitutes a perspective/prospective view of these results. On the other hand, some comparison of in silico results with experimental information recently acquired through innovative analytical techniques such as ion mobility mass spectrometry which have been introduced.
Collapse
Affiliation(s)
- Serena Indelicato
- Dipartimento di Scienze della Terra e del Mare (DISTEM), Università degli Studi di Palermo, Palermo, Italy
| | - David Bongiorno
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche, Università degli Studi di Palermo (STEBICEF), Palermo, Italy
| | - Valentina Calabrese
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche, Università degli Studi di Palermo (STEBICEF), Palermo, Italy
| | - Ugo Perricone
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche, Università degli Studi di Palermo (STEBICEF), Palermo, Italy
| | - Anna Maria Almerico
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche, Università degli Studi di Palermo (STEBICEF), Palermo, Italy
| | - Leopoldo Ceraulo
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche, Università degli Studi di Palermo (STEBICEF), Palermo, Italy
| | - Daniela Piazzese
- Dipartimento di Scienze della Terra e del Mare (DISTEM), Università degli Studi di Palermo, Palermo, Italy
| | - Marco Tutone
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche, Università degli Studi di Palermo (STEBICEF), Palermo, Italy.
| |
Collapse
|
15
|
Perricone U, Wieder M, Seidel T, Langer T, Padova A, Almerico AM, Tutone M. A Molecular Dynamics-Shared Pharmacophore Approach to Boost Early-Enrichment Virtual Screening: A Case Study on Peroxisome Proliferator-Activated Receptor α. ChemMedChem 2017; 12:1399-1407. [PMID: 28135036 DOI: 10.1002/cmdc.201600526] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 01/26/2017] [Indexed: 12/21/2022]
Abstract
Molecular dynamics (MD) simulations can be used, prior to virtual screening, to add flexibility to proteins and study them in a dynamic way. Furthermore, the use of multiple crystal structures of the same protein containing different co-crystallized ligands can help elucidate the role of the ligand on a protein's active conformation, and then explore the most common interactions between small molecules and the receptor. In this work, we evaluated the contribution of the combined use of MD on crystal structures containing the same protein but different ligands to examine the crucial ligand-protein interactions within the complexes. The study was carried out on peroxisome proliferator-activated receptor α (PPARα). Findings derived from the dynamic analysis of interactions were then used as features for pharmacophore generation and constraints for generating the docking grid for use in virtual screening. We found that information derived from short multiple MD simulations using different molecules within the binding pocket of the target can improve the early enrichment of active ligands in the virtual screening process for this receptor. In the end we adopted a consensus scoring based on docking score and pharmacophore alignment to rank our dataset. Our results showed an improvement in virtual screening performance in early recognition when screening was performed with the Molecular dYnamics SHAred PharmacophorE (MYSHAPE) approach.
Collapse
Affiliation(s)
- Ugo Perricone
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università di Palermo, Via Archirafi 32, 90123, Palermo, Italy.,Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Althanstraße 14, 1090, Vienna, Austria.,Fondazione Ri.MED, Via Bandiera 11, 90133, Palermo, Italy
| | - Marcus Wieder
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Althanstraße 14, 1090, Vienna, Austria.,Department of Computational Biological Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 42, 1090, Vienna, Austria
| | - Thomas Seidel
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Althanstraße 14, 1090, Vienna, Austria
| | - Thierry Langer
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Althanstraße 14, 1090, Vienna, Austria
| | | | - Anna Maria Almerico
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università di Palermo, Via Archirafi 32, 90123, Palermo, Italy
| | - Marco Tutone
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università di Palermo, Via Archirafi 32, 90123, Palermo, Italy
| |
Collapse
|
16
|
Tutone M, Perricone U, Almerico AM. Conf-VLKA: A structure-based revisitation of the Virtual Lock-and-key Approach. J Mol Graph Model 2016; 71:50-57. [PMID: 27842227 DOI: 10.1016/j.jmgm.2016.11.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 11/03/2016] [Accepted: 11/07/2016] [Indexed: 02/02/2023]
Abstract
In a previous work, we developed the in house Virtual Lock-and-Key Approach (VLKA) in order to evaluate target assignment starting from molecular descriptors calculated on known inhibitors used as an information source. This protocol was able to predict the correct biological target for the whole dataset with a good degree of reliability (80%), and proved experimentally, which was useful for the target fishing of unknown compounds. In this paper, we tried to remodel the previous in house developed VLKA in a more sophisticated one in order to evaluate the influence of 3D conformation of ligands on the accuracy of the prediction. We applied the same previous algorithm of scoring and ranking but, this time, combining it with a structure-based approach as docking. For this reason, we retrieved from the RCSB Protein Data Bank (PDB), the available 3D structures of the biological targets included into the previous work, and we used them to calculate poses of the 7352 dataset compounds in the VLKA biological targets. First, docking protocol has been used to retrieve docking scores, then, from the docked poses of each molecule, 3D-descriptors were calculated (Conf-VLKA), While the use of the simple docking scores proved to be inadequate to improve compounds classification, the Conf-VLKA showed some interesting variations compared to the original VLKA, especially for targets whose ligands present a high number of rotamers. This work represent a first preliminary study to be completed using other techniques such as induced fit docking or molecular dynamics structure clustering to take into account the protein side chains adaptation to ligands structures.
Collapse
Affiliation(s)
- Marco Tutone
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università di Palermo, Via Archirafi 28, Palermo, Italy.
| | - Ugo Perricone
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università di Palermo, Via Archirafi 28, Palermo, Italy
| | - Anna Maria Almerico
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università di Palermo, Via Archirafi 28, Palermo, Italy
| |
Collapse
|
17
|
Tutone M, Chinnici A, Almerico AM, Perricone U, Sutera FM, De Caro V. Design, synthesis and preliminary evaluation of dopamine-amino acid conjugates as potential D1 dopaminergic modulators. Eur J Med Chem 2016; 124:435-444. [PMID: 27597419 DOI: 10.1016/j.ejmech.2016.08.051] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/09/2016] [Accepted: 08/22/2016] [Indexed: 12/31/2022]
Abstract
The dopamine-amino acid conjugate DA-Phen was firstly designed to obtain a useful prodrug for the therapy of Parkinson's disease, but experimental evidence shows that it effectively interacts with D1 dopamine receptors (D1DRs), leading to an enhancement in cognitive flexibility and to the development of adaptive strategies in aversive mazes, together with a decrease in despair-like behavior. In this paper, homology modelling, molecular dynamics, and site mapping of D1 receptor were carried out with the aim of further performing docking studies on other dopamine conjugates compared with D1 agonists, in the attempt to identify new compounds with potential dopaminergic activity. Two new conjugates (DA-Trp 2C, and DA-Leu 3C) have been identified as the most promising candidates, and consequently synthesized. Preliminary evaluation in terms of distribution coefficient (DpH7.4), stability in rat brain homogenate, and in human plasma confirmed that DA-Trp (2C), and DA-Leu (3C) could be considered as very valuable candidates for further in vivo studies as new dopaminergic drugs.
Collapse
Affiliation(s)
- Marco Tutone
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università di Palermo, Via Archirafi 32, 90123, Palermo, Italy.
| | - Aurora Chinnici
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università di Palermo, Via Archirafi 32, 90123, Palermo, Italy; Humanitas Clinical and Research Center, Via Manzoni 113, 20089, Rozzano, MI, Italy
| | - Anna Maria Almerico
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università di Palermo, Via Archirafi 32, 90123, Palermo, Italy
| | - Ugo Perricone
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università di Palermo, Via Archirafi 32, 90123, Palermo, Italy
| | - Flavia Maria Sutera
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università di Palermo, Via Archirafi 32, 90123, Palermo, Italy; SiSaf Ltd, Innovation Centre, Northern Ireland Science Park, Queen's Island, Belfast, BT3 9DT, UK
| | - Viviana De Caro
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università di Palermo, Via Archirafi 32, 90123, Palermo, Italy
| |
Collapse
|
18
|
Pibiri I, Lentini L, Tutone M, Melfi R, Pace A, Di Leonardo A. Exploring the readthrough of nonsense mutations by non-acidic Ataluren analogues selected by ligand-based virtual screening. Eur J Med Chem 2016; 122:429-435. [PMID: 27404557 DOI: 10.1016/j.ejmech.2016.06.048] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 06/09/2016] [Accepted: 06/27/2016] [Indexed: 10/21/2022]
Abstract
Ataluren, also known as PTC124, is a 5-(fluorophenyl)-1,2,4-oxadiazolyl-benzoic acid suggested to suppress nonsense mutations by readthrough of premature stop codons in the mRNA. Potential interaction of PTC124 with mRNA has been recently studied by molecular dynamics simulations highlighting the importance of H-bonding and stacking π-π interactions. A series of non-acidic analogues of PTC124 were selected from a large database via a ligand-based virtual screening approach. Eight of them were synthesized and tested for their readthrough activity using the Fluc reporter harboring the UGA premature stop codon. The most active compound was further tested for suppression of the UGA nonsense mutation in the bronchial epithelial IB3.1 cell line carrying the W1282X mutation in the CFTR gene.
Collapse
Affiliation(s)
- Ivana Pibiri
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy
| | - Laura Lentini
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy.
| | - Marco Tutone
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy
| | - Raffaella Melfi
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy
| | - Andrea Pace
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy; Istituto EuroMediterraneo di Scienza e Tecnologia (IEMEST), Via Emerico Amari 123, 90139 Palermo, Italy.
| | - Aldo Di Leonardo
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed. 16-17, 90128 Palermo, Italy; Centro di OncoBiologia Sperimentale (COBS), via San Lorenzo Colli, 90145 Palermo, Italy
| |
Collapse
|
19
|
Broadley KJ, Burnell E, Davies RH, Lee ATL, Snee S, Thomas EJ. The synthesis of a series of adenosine A3 receptor agonists. Org Biomol Chem 2016; 14:3765-81. [PMID: 27001924 DOI: 10.1039/c6ob00244g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A series of 1'-(6-aminopurin-9-yl)-1'-deoxy-N-methyl-β-d-ribofuranuronamides that were characterised by 2-dialkylamino-7-methyloxazolo[4,5-b]pyridin-5-ylmethyl substituents on N6 of interest for screening as selective adenosine A3 receptor agonists, have been synthesised. This work involved the synthesis of 2-dialkylamino-5-aminomethyl-7-methyloxazolo[4,5-b]pyridines and analogues that were coupled with the known 1'-(6-chloropurin-9-yl)-1'-deoxy-N-methyl-β-d-ribofuranuronamide. The oxazolo[4,5-b]pyridines were synthesized by regioselective functionalisation of 2,4-dimethylpyridine N-oxides. The regioselectivities of these reactions were found to depend upon the nature of the heterocycle with 2-dimethylamino-5,7-dimethyloxazolo[4,5-b]pyridine-N-oxide undergoing regioselective functionalisation at the 7-methyl group on reaction with trifluoroacetic anhydride in contrast to the reaction of 4,6-dimethyl-3-hydroxypyridine-N-oxide with acetic anhydride that resulted in functionalisation of the 6-methyl group. To optimise selectivity for the A3 receptor, 5-aminomethyl-7-bromo-2-dimethylamino-4-[(3-methylisoxazol-5-yl)methoxy]benzo[d]oxazole was synthesised and coupled with the 1'-(6-chloropurin-9-yl)-1'-deoxy-N-methyl-β-d-ribofuranuronamide. The products were active as selective adenosine A3 agonists.
Collapse
Affiliation(s)
- Kenneth J Broadley
- Cardiff School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Redwood Building, King Edward VII Avenue, Cardiff, CF10 3NB, UK
| | - Erica Burnell
- The School of Chemistry, The University of Manchester, Manchester, M13 9PL, UK.
| | | | - Alan T L Lee
- The School of Chemistry, The University of Manchester, Manchester, M13 9PL, UK.
| | - Stephen Snee
- The School of Chemistry, The University of Manchester, Manchester, M13 9PL, UK.
| | - Eric J Thomas
- The School of Chemistry, The University of Manchester, Manchester, M13 9PL, UK.
| |
Collapse
|
20
|
Allegra M, Carletti F, Gambino G, Tutone M, Attanzio A, Tesoriere L, Ferraro G, Sardo P, Almerico AM, Livrea MA. Indicaxanthin from Opuntia ficus-indica Crosses the Blood-Brain Barrier and Modulates Neuronal Bioelectric Activity in Rat Hippocampus at Dietary-Consistent Amounts. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:7353-7360. [PMID: 26227670 DOI: 10.1021/acs.jafc.5b02612] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Indicaxanthin is a bioactive and bioavailable betalain pigment from the Opuntia ficus-indica fruits. In this in vivo study, kinetic measurements showed that indicaxanthin is revealed in the rat brain within 1 h from oral administration of 2 μmol/kg, an amount compatible with a dietary consumption of cactus pear fruits in humans. A peak (20 ± 2.4 ng of indicaxanthin per whole brain) was measured after 2.5 h; thereafter the molecule disappeared with first order kinetics within 4 h. The potential of indicaxanthin to affect neural activities was in vivo investigated by a microiontophoretic approach. Indicaxanthin, administered in a range between 0.085 ng and 0.34 ng per neuron, dose-dependently modulated the rate of discharge of spontaneously active neurons of the hippocampus, with reduction of the discharge and related changes of latency and duration of the effect. Indicaxanthin (0.34 ng/neuron) showed inhibitory effects on glutamate-induced excitation, indicating activity at the level of glutamatergic synapses. A molecular target of indicaxanthin is suggested by in silico molecular modeling of indicaxanthin with N-methyl-D-aspartate receptor (NMDAR), the most represented of the glutamate receptor family in hippocampus. Therefore, at nutritionally compatible amounts indicaxanthin (i) crosses the rat BBB and accumulates in brain; (ii) can affect the bioelectric activity of hippocampal neurons locally treated with amounts comparable with those measured in the brain; and (iii) modulates glutamate-induced neuronal excitation. The potential of dietary indicaxanthin as a natural neuromodulatory agent deserves further mechanistic and neurophysiologic investigation.
Collapse
Affiliation(s)
- Mario Allegra
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, University of Palermo , Via M. Cipolla 74, 90121 Palermo, Italy
| | - Fabio Carletti
- Dipartimento di Biomedicina Sperimentale e Neuroscienze Cliniche, Sezione di Fisiologia Umana "G. Pagano", University of Palermo , Corso Tukory 129, 90134 Palermo, Italy
| | - Giuditta Gambino
- Dipartimento di Biomedicina Sperimentale e Neuroscienze Cliniche, Sezione di Fisiologia Umana "G. Pagano", University of Palermo , Corso Tukory 129, 90134 Palermo, Italy
| | - Marco Tutone
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, University of Palermo , Via M. Cipolla 74, 90121 Palermo, Italy
| | - Alessandro Attanzio
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, University of Palermo , Via M. Cipolla 74, 90121 Palermo, Italy
| | - Luisa Tesoriere
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, University of Palermo , Via M. Cipolla 74, 90121 Palermo, Italy
| | - Giuseppe Ferraro
- Dipartimento di Biomedicina Sperimentale e Neuroscienze Cliniche, Sezione di Fisiologia Umana "G. Pagano", University of Palermo , Corso Tukory 129, 90134 Palermo, Italy
| | - Pierangelo Sardo
- Dipartimento di Biomedicina Sperimentale e Neuroscienze Cliniche, Sezione di Fisiologia Umana "G. Pagano", University of Palermo , Corso Tukory 129, 90134 Palermo, Italy
| | - Anna Maria Almerico
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, University of Palermo , Via M. Cipolla 74, 90121 Palermo, Italy
| | - Maria Antonia Livrea
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, University of Palermo , Via M. Cipolla 74, 90121 Palermo, Italy
| |
Collapse
|
21
|
De Caro V, Sutera FM, Gentile C, Tutone M, Livrea MA, Almerico AM, Cannizzaro C, Giannola LI. Studies on a new potential dopaminergic agent: in vitro BBB permeability, in vivo behavioural effects and molecular docking evaluation. J Drug Target 2015; 23:910-25. [PMID: 26000952 DOI: 10.3109/1061186x.2015.1035275] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
2-Amino-N-[2-(3,4-dihydroxy-phenyl)-ethyl]-3-phenyl-propionamide (DA-PHEN) has been previously synthesized to obtain a potential prodrug capable of release dopamine (DA) into CNS. However, DA-PHEN could act per se as a dopaminergic drug. In this study, the permeability transport (Pe), obtained by parallel artificial permeability assay (PAMPA), indicated a low passive transcellular transport (Pe = 0.32 ± 0.01 × 10(-6 )cm/s). Using the Caco-2 cell system, the Papp AP-BL in absorptive direction (3.36 ± 0.02 × 10(-5 )cm/s) was significantly higher than the Papp BL-AP in secretive direction (1.75 ± 0.07 × 10(-5 )cm/s), suggesting a polarized transport. The efflux ratio (Papp AP-BL/Papp BL-AP = 0.52 ± 0.02) indicated a low affinity of DA-PHEN to efflux carriers. The forced swim test highlighted a reduction of immobility time in both pre-test and test sessions (p < 0.0001), with an exacerbation in the number of headshakes and divings in the pretest (p < 0.0001). Morris water maze strengthened the hypothesis that DA-PHEN induces adaptive responses to environmental challenges which are involved on cognitive functions (DA-PHEN versus CTR: escape latency; p < 0.001; distance swum p < 0.001, time spent on target quadrant p < 0.001), without any change in locomotor activity for the administered dose. The molecular docking revealed the interaction of DA-PHEN with the identified D1 site mapping human brain receptor.
Collapse
Affiliation(s)
- Viviana De Caro
- a Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF) , Università degli Studi di Palermo , Palermo , Italy
| | - Flavia Maria Sutera
- b Dipartimento di Biomedicina Sperimentale e Neuroscienze Cliniche (BioNeC) , Università degli Studi di Palermo , Palermo , Italy , and
| | - Carla Gentile
- a Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF) , Università degli Studi di Palermo , Palermo , Italy
| | - Marco Tutone
- a Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF) , Università degli Studi di Palermo , Palermo , Italy
| | - Maria Antonia Livrea
- a Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF) , Università degli Studi di Palermo , Palermo , Italy
| | - Anna Maria Almerico
- a Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF) , Università degli Studi di Palermo , Palermo , Italy
| | - Carla Cannizzaro
- c Dipartimento di Scienze per la Promozione della Salute e Materno Infantile "G. D'Alessandro" , Università degli Studi di Palermo , Palermo , Italy
| | - Libero Italo Giannola
- a Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF) , Università degli Studi di Palermo , Palermo , Italy
| |
Collapse
|
22
|
Yu R, Wang J, Wang R, Lin Y, Hu Y, Wang Y, Shu M, Lin Z. Combined pharmacophore modeling, 3D-QSAR, homology modeling and docking studies on CYP11B1 inhibitors. Molecules 2015; 20:1014-30. [PMID: 25584832 PMCID: PMC6272247 DOI: 10.3390/molecules20011014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 11/29/2014] [Indexed: 11/16/2022] Open
Abstract
The mitochondrial cytochrome P450 enzymes inhibitor steroid 11β-hydroxylase (CYP11B1) can decrease the production of cortisol. Therefore, these inhibitors have an effect in the treatment of Cushing’s syndrome. A pharmacophore model generated by Genetic Algorithm with Linear Assignment for Hypermolecular Alignment of Datasets (GALAHAD) was used to align the compounds and perform comparative molecular field analysis (CoMFA) with Q2 = 0.658, R2 = 0.959. The pharmacophore model contained six hydrophobic regions and one acceptor atom, and electropositive and bulky substituents would be tolerated at the A and B sites, respectively. A three-dimensional quantitative structure-activity relationship (3D-QSAR) study based on the alignment with the atom root mean square (RMS) was applied using comparative molecular field analysis (CoMFA) with Q2 = 0.666, R2 = 0.978, and comparative molecular similarity indices analysis (CoMSIA) with Q2 = 0.721, R2 = 0.972. These results proved that all the models have good predictability of the bioactivities of inhibitors. Furthermore, the QSAR models indicated that a hydrogen bond acceptor substituent would be disfavored at the A and B groups, while hydrophobic groups would be favored at the B site. The three-dimensional (3D) model of the CYP11B1 was generated based on the crystal structure of the CYP11B2 (PDB code 4DVQ). In order to probe the ligand-binding modes, Surflex-dock was employed to dock CYP11B1 inhibitory compounds into the active site of the receptor. The docking result showed that the imidazolidine ring of CYP11B1 inhibitors form H bonds with the amino group of residue Arg155 and Arg519, which suggested that an electronegative substituent at these positions could enhance the activities of compounds. All the models generated by GALAHAD QSAR and Docking methods provide guidance about how to design novel and potential drugs for Cushing’s syndrome treatment.
Collapse
Affiliation(s)
- Rui Yu
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China.
| | - Juan Wang
- College of Bioengineering, Chongqing University, Chongqing 400044, China.
| | - Rui Wang
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China.
| | - Yong Lin
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, China.
| | - Yong Hu
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China.
| | - Yuanqiang Wang
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China.
| | - Mao Shu
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China.
| | - Zhihua Lin
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China.
| |
Collapse
|
23
|
Molecular dynamics, dynamic site mapping, and highthroughput virtual screening on leptin and the Ob receptor as anti-obesity target. J Mol Model 2014; 20:2247. [DOI: 10.1007/s00894-014-2247-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 04/09/2014] [Indexed: 10/25/2022]
|