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Broni E, Striegel A, Ashley C, Sakyi PO, Peracha S, Velazquez M, Bebla K, Sodhi M, Kwofie SK, Ademokunwa A, Khan S, Miller WA. Molecular Docking and Dynamics Simulation Studies Predict Potential Anti-ADAR2 Inhibitors: Implications for the Treatment of Cancer, Neurological, Immunological and Infectious Diseases. Int J Mol Sci 2023; 24:6795. [PMID: 37047766 PMCID: PMC10095294 DOI: 10.3390/ijms24076795] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/01/2023] [Accepted: 04/04/2023] [Indexed: 04/08/2023] Open
Abstract
Altered RNA editing has been linked to several neurodevelopmental disorders, including autism spectrum disorder (ASD) and intellectual disability, in addition to depression, schizophrenia, some cancers, viral infections and autoimmune disorders. The human ADAR2 is a potential therapeutic target for managing these various disorders due to its crucial role in adenosine to inosine editing. This study applied consensus scoring to rank potential ADAR2 inhibitors after performing molecular docking with AutoDock Vina and Glide (Maestro), using a library of 35,161 compounds obtained from traditional Chinese medicine. A total of 47 compounds were predicted to be good binders of the human ADAR2 and had insignificant toxicity concerns. Molecular dynamics (MD) simulations, including the molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) procedure, also emphasized the binding of the shortlisted compounds. The potential compounds had plausible binding free energies ranging from -81.304 to -1068.26 kJ/mol from the MM/PBSA calculations. ZINC000085511995, a naphthoquinone had more negative binding free energy (-1068.26 kJ/mol) than inositol hexakisphosphate (IHP) [-873.873 kJ/mol], an agonist and a strong binder of ADAR2. The potential displacement of IHP by ZINC000085511995 in the IHP binding site of ADAR2 could be explored for possible deactivation of ADAR2. Bayesian-based biological activity prediction corroborates the neuropharmacological, antineoplastic and antiviral activity of the potential lead compounds. All the potential lead compounds, except ZINC000014612330 and ZINC000013462928, were predicted to be inhibitors of various deaminases. The potential lead compounds also had probability of activity (Pa) > 0.442 and probability of inactivity (Pi) < 0.116 values for treating acute neurologic disorders, except for ZINC000085996580 and ZINC000013462928. Pursuing these compounds for their anti-ADAR2 activities holds a promising future, especially against neurological disorders, some cancers and viral infections caused by RNA viruses. Molecular interaction, hydrogen bond and per-residue decomposition analyses predicted Arg400, Arg401, Lys519, Trp687, Glu689, and Lys690 as hot-spot residues in the ADAR2 IHP binding site. Most of the top compounds were observed to have naphthoquinone, indole, furanocoumarin or benzofuran moieties. Serotonin and tryptophan, which are beneficial in digestive regulation, improving sleep cycle and mood, are indole derivatives. These chemical series may have the potential to treat neurological disorders, prion diseases, some cancers, specific viral infections, metabolic disorders and eating disorders through the disruption of ADAR2 pathways. A total of nine potential lead compounds were shortlisted as plausible modulators of ADAR2.
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Affiliation(s)
- Emmanuel Broni
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Andrew Striegel
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Chemical and Biochemistry, College of Science, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Carolyn Ashley
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Patrick O. Sakyi
- Department of Chemistry, School of Physical and Mathematical Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra P.O. Box LG 56, Ghana
- Department of Chemical Sciences, School of Sciences, University of Energy and Natural Resources, Sunyani P.O. Box 214, Ghana
| | - Saqib Peracha
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Miriam Velazquez
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Molecular Pharmacology & Neuroscience, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Kristeen Bebla
- Department of Molecular Pharmacology & Neuroscience, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Monsheel Sodhi
- Department of Molecular Pharmacology & Neuroscience, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Samuel K. Kwofie
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, Legon, Accra P.O. Box LG 77, Ghana
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra P.O. Box LG 54, Ghana
| | - Adesanya Ademokunwa
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Cognitive and Behavioral Neuroscience, Loyola University Chicago, Chicago, IL 60660, USA
| | - Sufia Khan
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Biology, Loyola University Chicago, Chicago, IL 60660, USA
| | - Whelton A. Miller
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Molecular Pharmacology & Neuroscience, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
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Papadakis G, Gerasi M, Snoeck R, Marakos P, Andrei G, Lougiakis N, Pouli N. Synthesis of New Imidazopyridine Nucleoside Derivatives Designed as Maribavir Analogues. Molecules 2020; 25:molecules25194531. [PMID: 33022923 PMCID: PMC7582934 DOI: 10.3390/molecules25194531] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 09/28/2020] [Accepted: 09/29/2020] [Indexed: 01/26/2023] Open
Abstract
The strong inhibition of Human Cytomegalovirus (HCMV) replication by benzimidazole nucleosides, like Triciribine and Maribavir, has prompted us to expand the structure-activity relationships of the benzimidazole series, using as a central core the imidazo[4,5-b]pyridine scaffold. We have thus synthesized a number of novel amino substituted imidazopyridine nucleoside derivatives, which can be considered as 4-(or 7)-aza-d-isosters of Maribavir and have evaluated their potential antiviral activity. The target compounds were synthesized upon glycosylation of suitably substituted 2-aminoimidazopyridines, which were prepared in six steps starting from 2-amino-6-chloropyridine. Even if the new compounds possessed only a slight structural modification when compared to the original drug, they were not endowed with interesting antiviral activity. Even so, three derivatives showed promising cytotoxic potential.
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Affiliation(s)
- Georgios Papadakis
- Division of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771 Athens, Greece; (G.P.); (M.G.); (P.M.); (N.P.)
| | - Maria Gerasi
- Division of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771 Athens, Greece; (G.P.); (M.G.); (P.M.); (N.P.)
| | - Robert Snoeck
- Laboratory of Virology & Chemotherapy, Rega Institute, KU Leuven, 3000 Leuven, Belgium; (R.S.); (G.A.)
| | - Panagiotis Marakos
- Division of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771 Athens, Greece; (G.P.); (M.G.); (P.M.); (N.P.)
| | - Graciela Andrei
- Laboratory of Virology & Chemotherapy, Rega Institute, KU Leuven, 3000 Leuven, Belgium; (R.S.); (G.A.)
| | - Nikolaos Lougiakis
- Division of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771 Athens, Greece; (G.P.); (M.G.); (P.M.); (N.P.)
- Correspondence:
| | - Nicole Pouli
- Division of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771 Athens, Greece; (G.P.); (M.G.); (P.M.); (N.P.)
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Lougiakis N, Frakolaki E, Karmou P, Pouli N, Marakos P, Madan V, Bartenschlager R, Vassilaki N. Novel nucleoside analogues targeting HCV replication through an NS5A-dependent inhibition mechanism. Chem Biol Drug Des 2017; 90:352-367. [PMID: 28245093 DOI: 10.1111/cbdd.12966] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 01/20/2017] [Accepted: 02/10/2017] [Indexed: 12/25/2022]
Abstract
A series of new tricyclic nucleosides were synthesized and evaluated as hepatitis C virus (HCV) replication inhibitors. Initial screening in a HCV replicon system, derived from a genotype 1b isolate, identified 9-benzylamino-3-(β-D-ribofuranosyl)-3H-imidazo[4',5':5,6]pyrido[2,3-b]pyrazine (15d) as the most potent analogue. Comparative assessment of 15d activity against HCV full-length viruses or subgenomic replicons derived from genotypes 1 to 4 revealed a specificity of the compound for genotypes 1 and 3. Surprisingly, resistance mutations selected against 15d were mapped to domains II and III of the non-structural protein 5A (NS5A), but not to the RNA-dependent RNA polymerase residing in NS5B. These results argue that compound 15d might represent a lead for the development of a novel class of NS5A inhibitors.
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Affiliation(s)
- Nikolaos Lougiakis
- Division of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Efseveia Frakolaki
- Molecular Virology Laboratory, Hellenic Pasteur Institute, Athens, Greece
| | - Panagiota Karmou
- Division of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Nicole Pouli
- Division of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Panagiotis Marakos
- Division of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Vanesa Madan
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany.,German Center for Infection Research, Heidelberg University, Heidelberg, Germany.,Division of Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Niki Vassilaki
- Molecular Virology Laboratory, Hellenic Pasteur Institute, Athens, Greece
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Design and synthesis of novel 7-aminosubstituted pyrido[2,3-b]pyrazines exhibiting anti-breast cancer activity. Eur J Med Chem 2016; 126:954-968. [PMID: 28006668 DOI: 10.1016/j.ejmech.2016.12.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 12/08/2016] [Accepted: 12/09/2016] [Indexed: 12/13/2022]
Abstract
Breast cancer (BrCa) remains an unmet medical need despite the revolutionary development of antibody treatments and protein kinase inhibitors. In the current study, a series of novel substituted pyridopyrazine derivatives have been rationally designed and evaluated as multi-kinase inhibitors in the PI3K pathway. The target compounds were prepared from 6-amino-2-picoline, which upon nitration and selective reduction was converted to suitably substituted 6-methyl-7-aminopyrido[2,3-b]pyrazines. Suitable manipulation of the former amines provided the designed analogues, which were then assessed in vitro against several BrCa cell lines using the MTT cytotoxicity assay. The most potent compounds underwent evaluation in a broad spectrum of protein kinases, while their pharmacokinetic parameters were measured by LC-MS/MS. In vivo evaluation of a hit compound (14a) was performed in a HER2 amplified BrCa xenograft model (HCC1954) and efficacy was determined using Western blot based phosphokinase assays and immunohistochemistry. This derivative showed low micromolar cytotoxic potency in all BrCa cell lines, a mild inhibition of the PI3Kα wild type and H1047R mutated enzyme and excellent pharmacokinetic parameters following oral and intraperitoneal administration at the designed dose of 10 mg/kg, with absence of in vivo phenotypic toxicity. Interestingly, compound 14a inhibited the growth of xenografted tumors. Analysis of excised tumors from the treated animals showed a significantly reduced population of Ki-67 positive cells, as well as downregulated levels of phosphorylated AKT, ERK1/2 and SRC compared to vehicle treated animals. Finally, the specificity of 14a was assessed in a panel of 31 kinases where a mild, but direct, inhibition of the MET receptor tyrosine kinase was observed.
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Rodrigues MVN, Barbosa AF, da Silva JF, dos Santos DA, Vanzolini KL, de Moraes MC, Corrêa AG, Cass QB. 9-Benzoyl 9-deazaguanines as potent xanthine oxidase inhibitors. Bioorg Med Chem 2015; 24:226-31. [PMID: 26712096 DOI: 10.1016/j.bmc.2015.12.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/23/2015] [Accepted: 12/05/2015] [Indexed: 11/28/2022]
Abstract
A novel potent xanthine oxidase inhibitor, 3-nitrobenzoyl 9-deazaguanine (LSPN451), was selected from a series of 10 synthetic derivatives. The enzymatic assays were carried out using an on-flow bidimensional liquid chromatography (2D LC) system, which allowed the screening¸ the measurement of the kinetic inhibition constant and the characterization of the inhibition mode. This compound showed a non-competitive inhibition mechanism with more affinity for the enzyme-substrate complex than for the free enzyme, and inhibition constant of 55.1±9.80 nM, about thirty times more potent than allopurinol. Further details of synthesis and enzymatic studies are presented herein.
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Affiliation(s)
- Marili V N Rodrigues
- Centro Pluridisciplinar de Pesquisas Químicas, Biológicas e Agrícolas, Universidade Estadual de Campinas, 13148-218 Paulínia, SP, Brazil; Separare-Nucleo de Pesquisa em Cromatografia, Departamento de Química, Universidade Federal de São Carlos, 13565-905 São Carlos, SP, Brazil
| | - Alexandre F Barbosa
- Laboratório de Síntese de Produtos Naturais-LSPN, Departamento de Química, Universidade Federal de São Carlos, 13565-905 São Carlos, SP, Brazil
| | - Júlia F da Silva
- Laboratório de Síntese de Produtos Naturais-LSPN, Departamento de Química, Universidade Federal de São Carlos, 13565-905 São Carlos, SP, Brazil
| | - Deborah A dos Santos
- Laboratório de Síntese de Produtos Naturais-LSPN, Departamento de Química, Universidade Federal de São Carlos, 13565-905 São Carlos, SP, Brazil
| | - Kenia L Vanzolini
- Separare-Nucleo de Pesquisa em Cromatografia, Departamento de Química, Universidade Federal de São Carlos, 13565-905 São Carlos, SP, Brazil
| | - Marcela C de Moraes
- Separare-Nucleo de Pesquisa em Cromatografia, Departamento de Química, Universidade Federal de São Carlos, 13565-905 São Carlos, SP, Brazil; Departamento de Química Orgânica, Instituto de Química, Universidade Federal Fluminense, 24020-141 Niterói, RJ, Brazil
| | - Arlene G Corrêa
- Laboratório de Síntese de Produtos Naturais-LSPN, Departamento de Química, Universidade Federal de São Carlos, 13565-905 São Carlos, SP, Brazil.
| | - Quezia B Cass
- Separare-Nucleo de Pesquisa em Cromatografia, Departamento de Química, Universidade Federal de São Carlos, 13565-905 São Carlos, SP, Brazil.
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