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Desantis J, Bazzacco A, Eleuteri M, Tuci S, Bianconi E, Macchiarulo A, Mercorelli B, Loregian A, Goracci L. Design, synthesis, and biological evaluation of first-in-class indomethacin-based PROTACs degrading SARS-CoV-2 main protease and with broad-spectrum antiviral activity. Eur J Med Chem 2024; 268:116202. [PMID: 38394929 DOI: 10.1016/j.ejmech.2024.116202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/25/2024]
Abstract
To date, Proteolysis Targeting Chimera (PROTAC) technology has been successfully applied to mediate proteasomal-induced degradation of several pharmaceutical targets mainly related to oncology, immune disorders, and neurodegenerative diseases. On the other hand, its exploitation in the field of antiviral drug discovery is still in its infancy. Recently, we described two indomethacin (INM)-based PROTACs displaying broad-spectrum antiviral activity against coronaviruses. Here, we report the design, synthesis, and characterization of a novel series of INM-based PROTACs that recruit either Von-Hippel Lindau (VHL) or cereblon (CRBN) E3 ligases. The panel of INM-based PROTACs was also enlarged by varying the linker moiety. The antiviral activity resulted very susceptible to this modification, particularly for PROTACs hijacking VHL as E3 ligase, with one piperazine-based compound (PROTAC 6) showing potent anti-SARS-CoV-2 activity in infected human lung cells. Interestingly, degradation assays in both uninfected and virus-infected cells with the most promising PROTACs emerged so far (PROTACs 5 and 6) demonstrated that INM-PROTACs do not degrade human PGES-2 protein, as initially hypothesized, but induce the concentration-dependent degradation of SARS-CoV-2 main protease (Mpro) both in Mpro-transfected and in SARS-CoV-2-infected cells. Importantly, thanks to the target degradation, INM-PROTACs exhibited a considerable enhancement in antiviral activity with respect to indomethacin, with EC50 values in the low-micromolar/nanomolar range. Finally, kinetic solubility as well as metabolic and chemical stability were measured for PROTACs 5 and 6. Altogether, the identification of INM-based PROTACs as the first class of SARS-CoV-2 Mpro degraders demonstrating activity also in SARS-CoV-2-infected cells represents a significant advance in the development of effective, broad-spectrum anti-coronavirus strategies.
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Affiliation(s)
- Jenny Desantis
- Department of Chemistry, Biology, and Biotechnology, University of Perugia, Italy
| | | | - Michela Eleuteri
- Department of Chemistry, Biology, and Biotechnology, University of Perugia, Italy
| | - Sara Tuci
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Elisa Bianconi
- Department of Pharmaceutical Science, University of Perugia, Italy
| | | | | | - Arianna Loregian
- Department of Molecular Medicine, University of Padua, Padua, Italy.
| | - Laura Goracci
- Department of Chemistry, Biology, and Biotechnology, University of Perugia, Italy.
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2
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Ceccarelli G, Goracci L, Carotti A, Paccoia F, Passeri D, Cipolloni M, Di Bona S, Cruciani G, Pellicciari R, Gioiello A. Discovery and Structure-Activity Relationships of Novel ssDAF-12 Receptor Modulators. J Med Chem 2024; 67:4150-4169. [PMID: 38417155 DOI: 10.1021/acs.jmedchem.3c02421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2024]
Abstract
The nuclear receptor ssDAF-12 has been recognized as the key molecular player regulating the life cycle of the nematode parasite Strongyloides stercoralis. ssDAF-12 ligands permit the receptor to function as an on/off switch modulating infection, making it vulnerable to therapeutic intervention. In this study, we report the design and synthesis of a set of novel dafachronic acid derivatives, which were used to outline the first structure-activity relationship targeting the ssDAF-12 receptor and to unveil hidden properties shared by the molecular shape of steroidal ligands that are relevant to the receptor binding and modulation. Moreover, biological results led to the discovery of sulfonamide 3 as a submicromolar ssDAF-12 agonist endowed with a high receptor selectivity, no toxicity, and improved properties, as well as to the identification of unprecedented ssDAF-12 antagonists that can be exploited in the search for novel chemical tools and alternative therapeutic approaches for treating parasitism such as Strongyloidiasis.
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Affiliation(s)
- Giada Ceccarelli
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Laura Goracci
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via dell' Elce di Sotto 8, 06123 Perugia, Italy
| | - Andrea Carotti
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Federico Paccoia
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | | | | | - Stefano Di Bona
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via dell' Elce di Sotto 8, 06123 Perugia, Italy
| | - Gabriele Cruciani
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via dell' Elce di Sotto 8, 06123 Perugia, Italy
| | | | - Antimo Gioiello
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
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3
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Solidoro R, Miciaccia M, Bonaccorso C, Fortuna CG, Armenise D, Centonze A, Ferorelli S, Vitale P, Rodrigues P, Guimarães R, de Oliveira A, da Paz M, Rangel L, Sathler PC, Altomare A, Perrone MG, Scilimati A. A further pocket or conformational plasticity by mapping COX-1 catalytic site through modified-mofezolac structure-inhibitory activity relationships and their antiplatelet behavior. Eur J Med Chem 2024; 266:116135. [PMID: 38219659 DOI: 10.1016/j.ejmech.2024.116135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/04/2024] [Accepted: 01/08/2024] [Indexed: 01/16/2024]
Abstract
Cyclooxygenase enzymes have distinct roles in cardiovascular, neurological, and neurodegenerative disease. They are differently expressed in different type of cancers. Specific and selective COXs inhibitors are needed to be used alone or in combo-therapies. Fully understand the differences at the catalytic site of the two cyclooxygenase (COX) isoforms is still opened to investigation. Thus, two series of novel compounds were designed and synthesized in fair to good yields using the highly selective COX-1 inhibitor mofezolac as the lead compound to explore a COX-1 zone formed by the polar residues Q192, S353, H90 and Y355, as well as hydrophobic amino acids I523, F518 and L352. According to the structure of the COX-1:mofezolac complex, hydrophobic amino acids appear to have free volume eventually accessible to the more sterically hindering groups than the methoxy linked to the phenyl groups of mofezolac, in particular the methoxyphenyl at C4-mofezolac isoxazole. Mofezolac bears two methoxyphenyl groups linked to C3 and C4 of the isoxazole core ring. Thus, in the novel compounds, one or both methoxy groups were replaced by the higher homologous ethoxy, normal and isopropyl, normal and tertiary butyl, and phenyl and benzyl. Furthermore, a major difference between the two sets of compounds is the presence of either a methyl or acetic moiety at the C5 of the isoxazole. Among the C5-methyl series, 12 (direct precursor of mofezolac) (COX-1 IC50 = 0.076 μM and COX-2 IC50 = 0.35 μM) and 15a (ethoxy replacing the two methoxy groups in 12; COX-1 IC50 = 0.23 μM and COX-2 IC50 > 50 μM) were still active and with a Selectivity Index (SI = COX-2 IC50/COX-1 IC50) = 5 and 217, respectively. The other symmetrically substituted alkoxyphenyl moietis were inactive at 50 μM final concentration. Among the asymmetrically substituted, only the 16a (methoxyphenyl on C3-isoxazole and ethoxyphenyl on C4-isoxazole) and 16b (methoxyphenyl on C3-isoxazole and n-propoxyphenyl on C4-isoxazole) were active with SI = 1087 and 38, respectively. Among the set of compounds with the acetic moiety, structurally more similar to mofezolac (SI = 6329), SI ranged between 1.4 and 943. It is noteworthy that 17b (n-propoxyphenyl on both C3- and C4-isoxazole) were found to be a COX-2 slightly selective inhibitor with SI = 0.072 (COX-1 IC50 > 50 μM and COX-2 IC50 = 3.6 μM). Platelet aggregation induced by arachidonic acid (AA) can be in vitro suppressed by the synthesized compounds, without affecting of the secondary hemostasia, confirming the biological effect provided by the selective inhibition of COX-1. A positive profile of hemocompatibility in relation to erythrocyte and platelet toxicity was observed. Additionally, these compounds exhibited a positive profile of hemocompatibility and reduced cytotoxicity. Quantitative structure activity relationship (QSAR) models and molecular modelling (Ligand and Structure based virtual screening procedures) provide key information on the physicochemical and pharmacokinetic properties of the COX-1 inhibitors as well as new insights into the mechanisms of inhibition that will be used to guide the development of more effective and selective compounds. X-ray analysis was used to confirm the chemical structure of 14 (MSA17).
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Affiliation(s)
- Roberta Solidoro
- Research Laboratory for Woman and Child Health, Department of Pharmacy - Pharmaceutical Sciences, University of Bari "Aldo Moro", Via E. Orabona 4, 70125, Bari, Italy
| | - Morena Miciaccia
- Research Laboratory for Woman and Child Health, Department of Pharmacy - Pharmaceutical Sciences, University of Bari "Aldo Moro", Via E. Orabona 4, 70125, Bari, Italy
| | - Carmela Bonaccorso
- Laboratory of Molecular Modelling and Heterocyclic Compounds ModHet, Department of Chemical Sciences, University of Catania, Viale Andrea Doria 6, 95125, Catania, Italy
| | - Cosimo Gianluca Fortuna
- Laboratory of Molecular Modelling and Heterocyclic Compounds ModHet, Department of Chemical Sciences, University of Catania, Viale Andrea Doria 6, 95125, Catania, Italy
| | - Domenico Armenise
- Research Laboratory for Woman and Child Health, Department of Pharmacy - Pharmaceutical Sciences, University of Bari "Aldo Moro", Via E. Orabona 4, 70125, Bari, Italy
| | - Antonella Centonze
- Research Laboratory for Woman and Child Health, Department of Pharmacy - Pharmaceutical Sciences, University of Bari "Aldo Moro", Via E. Orabona 4, 70125, Bari, Italy
| | - Savina Ferorelli
- Research Laboratory for Woman and Child Health, Department of Pharmacy - Pharmaceutical Sciences, University of Bari "Aldo Moro", Via E. Orabona 4, 70125, Bari, Italy
| | - Paola Vitale
- Research Laboratory for Woman and Child Health, Department of Pharmacy - Pharmaceutical Sciences, University of Bari "Aldo Moro", Via E. Orabona 4, 70125, Bari, Italy
| | - Pryscila Rodrigues
- Laboratory of Experimental Hemostasis, Carlos Chagas Filho Avenue, 373, 21941599, Rio de Janeiro, Brazil
| | - Renilda Guimarães
- Laboratory of Experimental Hemostasis, Carlos Chagas Filho Avenue, 373, 21941599, Rio de Janeiro, Brazil
| | - Alana de Oliveira
- Laboratory of Experimental Hemostasis, Carlos Chagas Filho Avenue, 373, 21941599, Rio de Janeiro, Brazil
| | - Mariana da Paz
- Laboratory of Tumoral Biochemistry, Faculty of Pharmacy, Federal University of Rio de Janeiro, Carlos Chagas Filho Avenue, 373, 21941599, Rio de Janeiro, Brazil
| | - Luciana Rangel
- Laboratory of Tumoral Biochemistry, Faculty of Pharmacy, Federal University of Rio de Janeiro, Carlos Chagas Filho Avenue, 373, 21941599, Rio de Janeiro, Brazil
| | - Plínio Cunha Sathler
- Laboratory of Experimental Hemostasis, Carlos Chagas Filho Avenue, 373, 21941599, Rio de Janeiro, Brazil
| | - Angela Altomare
- Institute of Crystallography-CNR, Via Amendola 122/o, 70126, Bari, Italy
| | - Maria Grazia Perrone
- Research Laboratory for Woman and Child Health, Department of Pharmacy - Pharmaceutical Sciences, University of Bari "Aldo Moro", Via E. Orabona 4, 70125, Bari, Italy.
| | - Antonio Scilimati
- Research Laboratory for Woman and Child Health, Department of Pharmacy - Pharmaceutical Sciences, University of Bari "Aldo Moro", Via E. Orabona 4, 70125, Bari, Italy.
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4
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Miciaccia M, Rizzo F, Centonze A, Cavallaro G, Contino M, Armenise D, Baldelli OM, Solidoro R, Ferorelli S, Scarcia P, Agrimi G, Zingales V, Cimetta E, Ronsisvalle S, Sipala FM, Polosa PL, Fortuna CG, Perrone MG, Scilimati A. Harmaline to Human Mitochondrial Caseinolytic Serine Protease Activation for Pediatric Diffuse Intrinsic Pontine Glioma Treatment. Pharmaceuticals (Basel) 2024; 17:135. [PMID: 38276008 PMCID: PMC10821046 DOI: 10.3390/ph17010135] [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: 12/15/2023] [Revised: 01/09/2024] [Accepted: 01/15/2024] [Indexed: 01/27/2024] Open
Abstract
Diffuse intrinsic pontine glioma (DIPG), affecting children aged 4-7 years, is a rare, aggressive tumor that originates in the pons and then spreads to nearby tissue. DIPG is the leading cause of death for pediatric brain tumors due to its infiltrative nature and inoperability. Radiotherapy has only a palliative effect on stabilizing symptoms. In silico and preclinical studies identified ONC201 as a cytotoxic agent against some human cancer cell lines, including DIPG ones. A single-crystal X-ray analysis of the complex of the human mitochondrial caseinolytic serine protease type C (hClpP) and ONC201 (PDB ID: 6DL7) allowed hClpP to be identified as its main target. The hyperactivation of hClpP causes damage to mitochondrial oxidative phosphorylation and cell death. In some DIPG patients receiving ONC201, an acquired resistance was observed. In this context, a wide program was initiated to discover original scaffolds for new hClpP activators to treat ONC201-non-responding patients. Harmaline, a small molecule belonging to the chemical class of β-carboline, was identified through Fingerprints for Ligands and Proteins (FLAP), a structure-based virtual screening approach. Molecular dynamics simulations and a deep in vitro investigation showed interesting information on the interaction and activation of hClpP by harmaline.
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Affiliation(s)
- Morena Miciaccia
- Research Laboratory for Woman and Child Health, Department of Pharmacy-Pharmaceutical Sciences, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy; (M.M.); (A.C.); (D.A.); (O.M.B.); (R.S.); (S.F.)
| | - Francesca Rizzo
- Department of Biosciences, Biotechnologies, and Environment, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy; (F.R.); (P.S.); (G.A.); (P.L.P.)
| | - Antonella Centonze
- Research Laboratory for Woman and Child Health, Department of Pharmacy-Pharmaceutical Sciences, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy; (M.M.); (A.C.); (D.A.); (O.M.B.); (R.S.); (S.F.)
| | - Gianfranco Cavallaro
- Laboratory of Molecular Modelling and Heterocyclic Compounds ModHet, Department of Chemical Sciences, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy;
| | - Marialessandra Contino
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy;
| | - Domenico Armenise
- Research Laboratory for Woman and Child Health, Department of Pharmacy-Pharmaceutical Sciences, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy; (M.M.); (A.C.); (D.A.); (O.M.B.); (R.S.); (S.F.)
| | - Olga Maria Baldelli
- Research Laboratory for Woman and Child Health, Department of Pharmacy-Pharmaceutical Sciences, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy; (M.M.); (A.C.); (D.A.); (O.M.B.); (R.S.); (S.F.)
| | - Roberta Solidoro
- Research Laboratory for Woman and Child Health, Department of Pharmacy-Pharmaceutical Sciences, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy; (M.M.); (A.C.); (D.A.); (O.M.B.); (R.S.); (S.F.)
| | - Savina Ferorelli
- Research Laboratory for Woman and Child Health, Department of Pharmacy-Pharmaceutical Sciences, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy; (M.M.); (A.C.); (D.A.); (O.M.B.); (R.S.); (S.F.)
| | - Pasquale Scarcia
- Department of Biosciences, Biotechnologies, and Environment, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy; (F.R.); (P.S.); (G.A.); (P.L.P.)
| | - Gennaro Agrimi
- Department of Biosciences, Biotechnologies, and Environment, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy; (F.R.); (P.S.); (G.A.); (P.L.P.)
| | - Veronica Zingales
- Department of Industrial Engineering (DII), University of Padua, Via Marzolo 9, 35131 Padova, Italy; (V.Z.); (E.C.)
| | - Elisa Cimetta
- Department of Industrial Engineering (DII), University of Padua, Via Marzolo 9, 35131 Padova, Italy; (V.Z.); (E.C.)
| | - Simone Ronsisvalle
- Department of Drug and Health Sciences, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy; (S.R.); (F.M.S.)
| | - Federica Maria Sipala
- Department of Drug and Health Sciences, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy; (S.R.); (F.M.S.)
| | - Paola Loguercio Polosa
- Department of Biosciences, Biotechnologies, and Environment, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy; (F.R.); (P.S.); (G.A.); (P.L.P.)
| | - Cosimo Gianluca Fortuna
- Laboratory of Molecular Modelling and Heterocyclic Compounds ModHet, Department of Chemical Sciences, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy;
| | - Maria Grazia Perrone
- Research Laboratory for Woman and Child Health, Department of Pharmacy-Pharmaceutical Sciences, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy; (M.M.); (A.C.); (D.A.); (O.M.B.); (R.S.); (S.F.)
| | - Antonio Scilimati
- Research Laboratory for Woman and Child Health, Department of Pharmacy-Pharmaceutical Sciences, University of Bari “Aldo Moro”, Via E. Orabona 4, 70125 Bari, Italy; (M.M.); (A.C.); (D.A.); (O.M.B.); (R.S.); (S.F.)
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5
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Tucci FJ, Jodts RJ, Hoffman BM, Rosenzweig AC. Product analog binding identifies the copper active site of particulate methane monooxygenase. Nat Catal 2023; 6:1194-1204. [PMID: 38187819 PMCID: PMC10766429 DOI: 10.1038/s41929-023-01051-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 09/22/2023] [Indexed: 01/09/2024]
Abstract
Nature's primary methane-oxidizing enzyme, the membrane-bound particulate methane monooxygenase (pMMO), catalyzes the oxidation of methane to methanol. pMMO activity requires copper, and decades of structural and spectroscopic studies have sought to identify the active site among three candidates: the CuB, CuC, and CuD sites. Challenges associated with the isolation of active pMMO have hindered progress toward locating its catalytic center. However, reconstituting pMMO into native lipid nanodiscs stabilizes its structure and recovers its activity. Here, these active samples were incubated with 2,2,2,-trifluoroethanol (TFE), a product analog that serves as a readily visualized active-site probe. Interactions of TFE with the CuD site were observed by both pulsed ENDOR spectroscopy and cryoEM, implicating CuD and the surrounding hydrophobic pocket as the likely site of methane oxidation. Use of these orthogonal techniques on parallel samples is a powerful approach that can circumvent difficulties in interpreting metalloenzyme cryoEM maps.
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Affiliation(s)
- Frank J Tucci
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL, USA
- These authors contributed equally
| | - Richard J Jodts
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL, USA
- These authors contributed equally
| | - Brian M Hoffman
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL, USA
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL, USA
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6
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Sipala F, Cavallaro G, Forte G, Satriano C, Giuffrida A, Fraix A, Spadaro A, Petralia S, Bonaccorso C, Fortuna CG, Ronsisvalle S. Different In Silico Approaches Using Heterocyclic Derivatives against the Binding between Different Lineages of SARS-CoV-2 and ACE2. Molecules 2023; 28:molecules28093908. [PMID: 37175318 PMCID: PMC10180195 DOI: 10.3390/molecules28093908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/24/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
Over the last few years, the study of the SARS-CoV-2 spike protein and its mutations has become essential in understanding how it interacts with human host receptors. Since the crystallized structure of the spike protein bound to the angiotensin-converting enzyme 2 (ACE2) receptor was released (PDB code 6M0J), in silico studies have been performed to understand the interactions between these two proteins. Specifically, in this study, heterocyclic compounds with different chemical characteristics were examined to highlight the possibility of interaction with the spike protein and the disruption of the interaction between ACE2 and the spike protein. Our results showed that these compounds interacted with the spike protein and interposed in the interaction zone with ACE2. Although further studies are needed, this work points to these heterocyclic push-pull compounds as possible agents capable of interacting with the spike protein, with the potential for the inhibition of spike protein-ACE2 binding.
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Affiliation(s)
- Federica Sipala
- Department of Drug and Health Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Gianfranco Cavallaro
- Department of Chemical Science, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Giuseppe Forte
- Department of Drug and Health Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Cristina Satriano
- Department of Chemical Science, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Alessandro Giuffrida
- Department of Chemical Science, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Aurore Fraix
- Department of Drug and Health Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Angelo Spadaro
- Department of Drug and Health Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Salvatore Petralia
- Department of Drug and Health Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Carmela Bonaccorso
- Department of Chemical Science, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Cosimo Gianluca Fortuna
- Department of Chemical Science, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Simone Ronsisvalle
- Department of Drug and Health Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
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7
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Luque-Navarro PM, Carrasco-Jiménez MP, Goracci L, Paredes JM, Espinar-Barranco L, Valverde-Pozo J, Torretta A, Parisini E, Mariotto E, Marchioro C, Laso A, Marco C, Viola G, Lanari D, López Cara LC. New bioisosteric sulphur-containing choline kinase inhibitors with a tracked mode of action. Eur J Med Chem 2023; 246:115003. [PMID: 36493617 DOI: 10.1016/j.ejmech.2022.115003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
Since the identification of human choline kinase as a protein target against cancer progression, many compounds have been designed to inhibit its function and reduce the biosynthesis of phosphatidylcholine. Herein, we propose a series of bioisosteric inhibitors that are based on the introduction of sulphur and feature improved activity and lipophilic/hydrophilic balance. The evaluation of the inhibitory and of the antiproliferative properties of the PL (dithioethane) and FP (disulphide) libraries led to the identification of PL 48, PL 55 and PL 69 as the most active compounds of the series. Docking analysis using FLAP suggests that for hits to leads, binding mostly involves an interaction with the Mg2+ cofactor, or its destabilization. The most active compounds of the two series are capable of inducing apoptosis following the mitochondrial pathway and to significantly reduce the expression of anti-apoptotic proteins such as the Mcl-1. The fluorescence properties of the compounds of the PL library allowed the tracking of their mode of action, while PAINS (Pan Assays Interference Structures) filtration databases suggest the lack of any unspecific biological response.
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Affiliation(s)
- Pilar M Luque-Navarro
- Department of Pharmaceutical and Organic Chemistry, Faculty of Pharmacy, University of Granada, Campus of Cartuja s/n, Granada, 18071, Spain; Department of Pharmaceutical Sciences, University of Perugia, Perugia, 06123 Italy
| | - M Paz Carrasco-Jiménez
- Department of Biochemistry and Molecular Biology I, University of Granada, Campus of Fuentenueva s/n, Granada, 18071, Spain.
| | - Laura Goracci
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, 06123, Italy
| | - Jose M Paredes
- Department of Physical-Chemistry, Faculty of Pharmacy, University of Granada, Campus of Cartuja s/n, Granada, 18071, Spain
| | - Laura Espinar-Barranco
- Department of Physical-Chemistry, Faculty of Pharmacy, University of Granada, Campus of Cartuja s/n, Granada, 18071, Spain
| | - Javier Valverde-Pozo
- Department of Physical-Chemistry, Faculty of Pharmacy, University of Granada, Campus of Cartuja s/n, Granada, 18071, Spain
| | - Archimede Torretta
- Center for Nano Science and Technology @PoliMi, Istituto Italiano di Tecnologia, Via Pascoli 70/3, Milano, 20133, Italy
| | - Emilio Parisini
- Center for Nano Science and Technology @PoliMi, Istituto Italiano di Tecnologia, Via Pascoli 70/3, Milano, 20133, Italy; Department of Biotechnology, Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV, 1006, Latvia; Department of Chemistry "G. Ciamician", University of Bologna, Via Selmi 2, Bologna, 40126, Italy
| | - Elena Mariotto
- Department of Woman's and Child's Health, Laboratory of Oncohematology, University of Padova, Padova, 35128, Italy
| | - Chiara Marchioro
- Department of Woman's and Child's Health, Laboratory of Oncohematology, University of Padova, Padova, 35128, Italy
| | - Alejandro Laso
- Department of Biochemistry and Molecular Biology I, University of Granada, Campus of Fuentenueva s/n, Granada, 18071, Spain
| | - Carmen Marco
- Department of Biochemistry and Molecular Biology I, University of Granada, Campus of Fuentenueva s/n, Granada, 18071, Spain
| | - Giampietro Viola
- Department of Woman's and Child's Health, Laboratory of Oncohematology, University of Padova, Padova, 35128, Italy; Istituto di Ricerca Pediatrica (IRP) Fondazione Città della Speranza, Corso Stati Uniti 4, Padova, 35128, Italy.
| | - Daniela Lanari
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, 06123 Italy.
| | - Luisa Carlota López Cara
- Department of Pharmaceutical and Organic Chemistry, Faculty of Pharmacy, University of Granada, Campus of Cartuja s/n, Granada, 18071, Spain.
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8
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Lopes J, Machado A, Batista A, Iglesias B, Araujo P, Barbosa Neto N. Fluorinated phenyl meso-substituents regulating excited state absorption-driven protonation of free-base porphyrins. J Photochem Photobiol A Chem 2023. [DOI: 10.1016/j.jphotochem.2023.114568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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9
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Hönig SMN, Lemmen C, Rarey M. Small molecule superposition: A comprehensive overview on pose scoring of the latest methods. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Sophia M. N. Hönig
- ZBH ‐ Center for Bioinformatics Universität Hamburg Hamburg Germany
- BioSolveIT Sankt Augustin Germany
| | | | - Matthias Rarey
- ZBH ‐ Center for Bioinformatics Universität Hamburg Hamburg Germany
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10
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Discovery of novel SARS-CoV-2 inhibitors targeting the main protease M pro by virtual screenings and hit optimization. Antiviral Res 2022; 204:105350. [PMID: 35688349 PMCID: PMC9172283 DOI: 10.1016/j.antiviral.2022.105350] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 11/21/2022]
Abstract
Two years after its emergence, SARS-CoV-2 still represents a serious and global threat to human health. Antiviral drug development usually takes a long time and, to increase the chances of success, chemical variability of hit compounds represents a valuable source for the discovery of new antivirals. In this work, we applied a platform of variably oriented virtual screening campaigns to seek for novel chemical scaffolds for SARS-CoV-2 main protease (Mpro) inhibitors. The study on the resulting 30 best hits led to the identification of a series of structurally unrelated Mpro inhibitors. Some of them exhibited antiviral activity in the low micromolar range against SARS-CoV-2 and other human coronaviruses (HCoVs) in different cell lines. Time-of-addition experiments demonstrated an antiviral effect during the viral replication cycle at a time frame consistent with the inhibition of SARS-CoV-2 Mpro activity. As a proof-of-concept, to validate the pharmaceutical potential of the selected hits against SARS-CoV-2, we rationally optimized one of the hit compounds and obtained two potent SARS-CoV-2 inhibitors with increased activity against Mpro both in vitro and in a cellular context, as well as against SARS-CoV-2 replication in infected cells. This study significantly contributes to the expansion of the chemical variability of SARS-CoV-2 Mpro inhibitors and provides new scaffolds to be exploited for pan-coronavirus antiviral drug development.
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11
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van der Westhuizen CJ, Stander A, Riley DL, Panayides JL. Discovery of Novel Acetylcholinesterase Inhibitors by Virtual Screening, In Vitro Screening, and Molecular Dynamics Simulations. J Chem Inf Model 2022; 62:1550-1572. [PMID: 35139637 DOI: 10.1021/acs.jcim.1c01443] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Alzheimer's disease is the most common neurodegenerative disease and currently poses a significant socioeconomic problem. This study describes the uses of computer-aided drug discovery techniques to identify novel inhibitors of acetylcholinesterase, a target for Alzheimer's disease. High-throughput virtual screening was employed to predict potential inhibitors of acetylcholinesterase. Validation of enrichment was performed with the DUD-E data set, showing that an ensemble of binding pocket conformations is critical when a diverse set of ligands are being screened. A total of 720 compounds were submitted for in vitro screening, which led to 25 hits being identified with IC50 values of less than 50 μM. The majority of these hits belonged to two scaffolds: 1-ethyl-3-methoxy-3-methylpyrrolidine and 1H-pyrrolo[3,2-c]pyridin-6-amine both of which are noted to be promising compounds for further optimization. As various possible binding poses were suggested from molecular docking, molecular dynamics simulations were employed to validate the poses. In the case of the most active compounds identified, a critical, stable water bridge formed deep within the binding pocket was identified potentially explaining in part the lack of activity for subsets of compounds that are not able to form this water bridge.
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Affiliation(s)
- C Johan van der Westhuizen
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of Pretoria, Lynnwood Road, Pretoria 0028, South Africa.,Pharmaceutical Technologies, CSIR Future Production: Chemicals, Meiring Naudé Road, Pretoria 0184, South Africa
| | - André Stander
- Department of Physiology, Faculty of Health Science, University of Pretoria, Lynnwood Road, Pretoria 0031, South Africa
| | - Darren L Riley
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of Pretoria, Lynnwood Road, Pretoria 0028, South Africa
| | - Jenny-Lee Panayides
- Pharmaceutical Technologies, CSIR Future Production: Chemicals, Meiring Naudé Road, Pretoria 0184, South Africa
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12
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Zephyr J, Nageswara Rao D, Vo SV, Henes M, Kosovrasti K, Matthew AN, Hedger AK, Timm J, Chan ET, Ali A, Kurt Yilmaz N, Schiffer CA. Deciphering the Molecular Mechanism of HCV Protease Inhibitor Fluorination as a General Approach to Avoid Drug Resistance. J Mol Biol 2022; 434:167503. [PMID: 35183560 PMCID: PMC9189784 DOI: 10.1016/j.jmb.2022.167503] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 02/07/2023]
Abstract
Third generation Hepatitis C virus (HCV) NS3/4A protease inhibitors (PIs), glecaprevir and voxilaprevir, are highly effective across genotypes and against many resistant variants. Unlike earlier PIs, these compounds have fluorine substitutions on the P2-P4 macrocycle and P1 moieties. Fluorination has long been used in medicinal chemistry as a strategy to improve physicochemical properties and potency. However, the molecular basis by which fluorination improves potency and resistance profile of HCV NS3/4A PIs is not well understood. To systematically analyze the contribution of fluorine substitutions to inhibitor potency and resistance profile, we used a multi-disciplinary approach involving inhibitor design and synthesis, enzyme inhibition assays, co-crystallography, and structural analysis. A panel of inhibitors in matched pairs were designed with and without P4 cap fluorination, tested against WT protease and the D168A resistant variant, and a total of 22 high-resolution co-crystal structures were determined. While fluorination did not significantly improve potency against the WT protease, PIs with fluorinated P4 caps retained much better potency against the D168A protease variant. Detailed analysis of the co-crystal structures revealed that PIs with fluorinated P4 caps can sample alternate binding conformations that enable adapting to structural changes induced by the D168A substitution. Our results elucidate molecular mechanisms of fluorine-specific inhibitor interactions that can be leveraged in avoiding drug resistance.
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13
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Desantis J, Mercorelli B, Celegato M, Croci F, Bazzacco A, Baroni M, Siragusa L, Cruciani G, Loregian A, Goracci L. Indomethacin-based PROTACs as pan-coronavirus antiviral agents. Eur J Med Chem 2021; 226:113814. [PMID: 34534839 PMCID: PMC8416298 DOI: 10.1016/j.ejmech.2021.113814] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/26/2021] [Accepted: 08/28/2021] [Indexed: 11/29/2022]
Abstract
Indomethacin (INM), a well-known non-steroidal anti-inflammatory drug, has recently gained attention for its antiviral activity demonstrated in drug repurposing studies against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Although the mechanism of action of INM is not yet fully understood, recent studies have indicated that it acts at an early stage of the coronaviruses (CoVs) replication cycle. In addition, a proteomic study reported that the anti-SARS-CoV-2 activity of INM could be also ascribed to its ability to inhibit human prostaglandin E synthase type 2 (PGES-2), a host protein which interacts with the SARS-CoV-2 NSP7 protein. Although INM does not potently inhibit SARS-CoV-2 replication in infected Vero E6 cells, here we have explored for the first time the application of the Proteolysis Targeting Chimeras (PROTACs) technology in order to develop more potent INM-derived PROTACs with anti-CoV activity. In this study, we report the design, synthesis, and biological evaluation of a series of INM-based PROTACs endowed with antiviral activity against a panel of human CoVs, including different SARS-CoV-2 strains. Two PROTACs showed a strong improvement in antiviral potency compared to INM. Molecular modelling studies support human PGES-2 as a potential target of INM-based antiviral PROTACs, thus paving the way toward the development of host-directed anti-CoVs strategies. To the best of our knowledge, these PROTACs represent the first-in-class INM-based PROTACs with antiviral activity and also the first example of the application of PROTACs to develop pan-coronavirus agents.
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Affiliation(s)
- Jenny Desantis
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | | | - Marta Celegato
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Federico Croci
- Department of Chemistry, Biology, and Biotechnology, University of Perugia, Italy
| | | | - Massimo Baroni
- Molecular Discovery Ltd., Centennial Park, Borehamwood, Hertfordshire, United Kingdom
| | | | - Gabriele Cruciani
- Department of Chemistry, Biology, and Biotechnology, University of Perugia, Italy
| | - Arianna Loregian
- Department of Molecular Medicine, University of Padua, Padua, Italy.
| | - Laura Goracci
- Department of Chemistry, Biology, and Biotechnology, University of Perugia, Italy.
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14
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Conjugation of Aminoadamantane and γ-Carboline Pharmacophores Gives Rise to Unexpected Properties of Multifunctional Ligands. Molecules 2021; 26:molecules26185527. [PMID: 34576998 PMCID: PMC8471380 DOI: 10.3390/molecules26185527] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/01/2021] [Accepted: 09/09/2021] [Indexed: 11/21/2022] Open
Abstract
A new series of conjugates of aminoadamantane and γ-carboline, which are basic scaffolds of the known neuroactive agents, memantine and dimebon (Latrepirdine) was synthesized and characterized. Conjugates act simultaneously on several biological structures and processes involved in the pathogenesis of Alzheimer’s disease and some other neurodegenerative disorders. In particular, these compounds inhibit enzymes of the cholinesterase family, exhibiting higher inhibitory activity against butyrylcholinesterase (BChE), but having almost no effect on the activity of carboxylesterase (anti-target). The compounds serve as NMDA-subtype glutamate receptor ligands, show mitoprotective properties by preventing opening of the mitochondrial permeability transition (MPT) pore, and act as microtubule stabilizers, stimulating the polymerization of tubulin and microtubule-associated proteins. Structure–activity relationships were studied, with particular attention to the effect of the spacer on biological activity. The synthesized conjugates showed new properties compared to their prototypes (memantine and dimebon), including the ability to bind to the ifenprodil-binding site of the NMDA receptor and to occupy the peripheral anionic site of acetylcholinesterase (AChE), which indicates that these compounds can act as blockers of AChE-induced β-amyloid aggregation. These new attributes of the conjugates represent improvements to the pharmacological profiles of the separate components by conferring the potential to act as neuroprotectants and cognition enhancers with a multifunctional mode of action.
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15
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Heteroaryl-Ethylenes as New Lead Compounds in the Fight against High Priority Bacterial Strains. Antibiotics (Basel) 2021; 10:antibiotics10091034. [PMID: 34572616 PMCID: PMC8466554 DOI: 10.3390/antibiotics10091034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 11/20/2022] Open
Abstract
The widespread use of antibiotics has led to a gradual increase in drug-resistant bacterial infections, which severely weakens the clinical efficacy of antibacterial therapies. In recent decades, stilbenes aroused great interest because of their high bioavailability, as well as their manifold biological activity. Our research efforts are focused on synthetic heteroaromatic stilbene derivatives as they represent a potentially new type of antibiotic with a wide antibacterial spectrum. Herein, a preliminary molecular modeling study and a versatile synthetic scheme allowed us to define eight heteroaromatic stilbene derivatives with potential antimicrobial activity. In order to evaluate our compound’s activity spectrum and antibacterial ability, minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) tests have been performed on Gram-positive and Gram-negative ATCC strains. Compounds PB4, PB5, PB7, and PB8 showed the best values in terms of MIC and were also evaluated for MBC, which was found to be greater than MIC, confirming a bacteriostatic activity. For all compounds, we evaluated toxicity on colon-rectal adenocarcinoma cells tumor cells (CaCo2), once it was established that the whole selected set was more active than 5-Fluorouracil in reducing CaCo-2 cells viability. To the best of our knowledge, the biological assays have shown for these derivatives an excellent bacteriostatic activity, compared to similar molecular structures previously reported, thus paving the way for a new class of antibiotic compounds.
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16
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Mancino V, Ceccarelli G, Carotti A, Goracci L, Sardella R, Passeri D, Pellicciari R, Gioiello A. Synthesis and biological activity of cyclopropyl Δ7-dafachronic acids as DAF-12 receptor ligands. Org Biomol Chem 2021; 19:5403-5412. [PMID: 34056641 DOI: 10.1039/d1ob00912e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The four cyclopropyl stereoisomers of Δ7-dafachronic acids were prepared from the bile acid hyodeoxycholic acid and employed as chemical tools to exploit the importance of the orientation and spatial disposition of the carboxyl tail and the C25-methyl group for the binding at the DAF-12 receptor. The synthesis route was based on (a) Walden inversion and stereoselective PtO2-hydrogenation to convert the L-shaped 5β-cholanoid scaffold into the planar 5α-sterol intermediate; (b) two-carbon homologation of the side chain by Wittig and cyclopropanation reaction; and (c) formation of the 3-keto group and Δ7 double bond. The synthesized isomers were isolated and tested for their activity as DAF-12 ligands by AlphaScreen assays. Results showed a significant loss of potency and efficacy for all the four stereoisomers when compared to the parent endogenous ligand. Computational analysis has evidenced the configurational and conformational arrangement of both the carboxylic and the C25-methyl group of dafachronic acids as key structural determinants for DAF-12 binding and activation.
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Affiliation(s)
- Valentina Mancino
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123, Perugia, Italy. and TES Pharma S.r.l., Corso Vannucci 47, 06121, Perugia, Italy
| | - Giada Ceccarelli
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123, Perugia, Italy.
| | - Andrea Carotti
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123, Perugia, Italy.
| | - Laura Goracci
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via dell'Elce di Sotto 8, 06123, Perugia, Italy
| | - Roccaldo Sardella
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123, Perugia, Italy.
| | | | | | - Antimo Gioiello
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123, Perugia, Italy.
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17
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Kassab SE, Mowafy S. Structural Basis of Selective Human Indoleamine-2,3-dioxygenase 1 (hIDO1) Inhibition. ChemMedChem 2021; 16:3149-3164. [PMID: 34174026 DOI: 10.1002/cmdc.202100253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/23/2021] [Indexed: 11/08/2022]
Abstract
hIDO1 is a heme-dioxygenase overexpressed in the tumor microenvironment and is implicated in the survival of cancer cells. Metabolism of tryptophan to N-formyl-kynurenine by hIDO1 leads to immune suppression to result in cancer cell immune escape. In this article, we discuss the discovery of selective hIDO1 inhibitors for therapeutic intervention that have been promoted to clinical trials and for which crystallographic structural information is available for the respective inhibitor-enzyme complex. The structural insights are based on the complex crystal structures and the relative biological data profiles. The structural basis of selective hIDO1 inhibition, as discussed herein, opens new avenues to the discovery of novel inhibitors with improved activity profiles, selectivity, and distinct structure frameworks.
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Affiliation(s)
- Shaymaa Emam Kassab
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Damanhour University, Damanhour, El-Buhaira, 22516, Egypt
| | - Samar Mowafy
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Misr International University, Cairo, 11431, Egypt.,Department of Chemistry, University of Washington, Seattle, Washington, 98195, United States of America
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18
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Vulpetti A, Dalvit C. Hydrogen Bond Acceptor Propensity of Different Fluorine Atom Types: An Analysis of Experimentally and Computationally Derived Parameters. Chemistry 2021; 27:8764-8773. [PMID: 33949737 DOI: 10.1002/chem.202100301] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Indexed: 12/29/2022]
Abstract
The propensity of organic fluorine acting as a weak hydrogen bond acceptor (HBA) in intermolecular and intramolecular interactions has been the subject of many experimental and theoretical studies often reaching different conclusions. Over the last few years, new and stronger evidences have emerged for the direct involvement of fluorine in weak hydrogen bond (HB) formation. However, not all the fluorine atom types can act as weak HBA. In this work, the differential HBA propensity of various types of fluorine atoms was analyzed with a particular emphasis for the different types of alkyl fluorides. This was carried out by evaluating ab initio computed parameters, experimental 19 F NMR chemical shifts and small molecule crystallographic structures (extracted from the CSD database). According to this analysis, shielded (with reference to the 19 F NMR chemical shift) alkyl mono-fluorinated motifs display the highest HBA propensity in agreement with solution studies. Although much weaker than other well-characterized HB complexes, the fragile HBs formed by these fluorinated motifs have important implications for the chemical-physical and structural properties of the molecules, chemical reactions, and protein-ligand recognition.
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Affiliation(s)
- Anna Vulpetti
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, 4002, Basel, Switzerland
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19
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Anbar HS, El-Gamal MI, Tarazi H, Lee BS, Jeon HR, Kwon D, Oh CH. Imidazothiazole-based potent inhibitors of V600E-B-RAF kinase with promising anti-melanoma activity: biological and computational studies. J Enzyme Inhib Med Chem 2021; 35:1712-1726. [PMID: 32962435 PMCID: PMC7534351 DOI: 10.1080/14756366.2020.1819260] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
A series of imidazothiazole derivatives possessing potential activity against melanoma cells were investigated for molecular mechanism of action. The target compounds were tested against V600E-B-RAF and RAF1 kinases. Compound 1zb is the most potent against both kinases with IC50 values 0.978 and 8.2 nM, respectively. It showed relative selectivity against V600E mutant B-RAF kinase. Compound 1zb was also tested against four melanoma cell lines and exerted superior potency (IC50 0.18-0.59 µM) compared to the reference standard drug, sorafenib (IC50 1.95-5.45 µM). Compound 1zb demonstrated also prominent selectivity towards melanoma cells than normal skin cells. It was further tested in whole-cell kinase assay and showed in-cell V600E-B-RAF kinase inhibition with IC50 of 0.19 µM. Compound 1zb induces apoptosis not necrosis in the most sensitive melanoma cell line, UACC-62. Furthermore, molecular dynamic and 3D-QSAR studies were done to investigate the binding mode and understand the pharmacophoric features of this series of compounds.
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Affiliation(s)
- Hanan S Anbar
- Department of Clinical Pharmacy and Pharmacotherapeutics, Dubai Pharmacy College for Girls, Dubai, United Arab Emirates
| | - Mohammed I El-Gamal
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates.,Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates.,Department of Medicinal Chemistry, Faculty of Pharmacy, University of Mansoura, Mansoura, Egypt
| | - Hamadeh Tarazi
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates.,Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Bong S Lee
- CTC SCIENCE, Hwaseong, Gyeonggi-do, Republic of Korea
| | - Hong R Jeon
- CTCBIO Inc., Hwaseong, Gyeonggi-do, Republic of Korea
| | - Dow Kwon
- CTC SCIENCE, Hwaseong, Gyeonggi-do, Republic of Korea
| | - Chang-Hyun Oh
- CTC SCIENCE, Hwaseong, Gyeonggi-do, Republic of Korea.,CTCBIO Inc., Hwaseong, Gyeonggi-do, Republic of Korea.,Center for Biomaterials, Korea Institute of Science & Technology (KIST), Seoul, Republic of Korea, Seoul.,Department of Biomolecular Science, University of Science & Technology (UST), Daejeon, Republic of Korea
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20
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Residue-based pharmacophore approaches to study protein-protein interactions. Curr Opin Struct Biol 2021; 67:205-211. [PMID: 33486430 DOI: 10.1016/j.sbi.2020.12.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/04/2020] [Accepted: 12/28/2020] [Indexed: 01/22/2023]
Abstract
This review focuses on pharmacophore approaches in researching protein interfaces that bind protein ligands. Pharmacophore descriptions of binding interfaces that employ molecular dynamics simulation can account for effects of solvation and conformational flexibility. In addition, these calculations provide an approximation to entropic considerations and as such, a better approximation of the free energy of binding. Residue-based pharmacophore approaches can facilitate a variety of drug discovery tasks such as the identification of receptor-ligand partners, identifying their binding poses, designing protein interfaces for selectivity, or defining a reduced mutational combinatorial exploration for subsequent experimental engineering techniques by orders of magnitudes.
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21
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Lammi C, Aiello G, Dellafiora L, Bollati C, Boschin G, Ranaldi G, Ferruzza S, Sambuy Y, Galaverna G, Arnoldi A. Assessment of the Multifunctional Behavior of Lupin Peptide P7 and Its Metabolite Using an Integrated Strategy. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:13179-13188. [PMID: 32223157 PMCID: PMC7997369 DOI: 10.1021/acs.jafc.0c00130] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
LTFPGSAED (P7) is a multifunctional hypocholesterolemic and hypoglycemic lupin peptide. While assessing its angiotensin-converting enzyme (ACE) inhibitory activity, it was more effective in intestinal Caco-2 cells (IC50 of 13.7 μM) than in renal HK-2 cells (IC50 of 79.6 μM). This discrepancy was explained by the metabolic transformation mediated by intestinal peptidases, which produced two main detected peptides, TFPGSAED and LTFPG. Indeed LTFPG, dynamically generated by intestinal dipeptidyl peptidase IV as well as its parent peptide P7 were linearly absorbed by mature Caco-2 cells. An in silico study demonstrated that the metabolite was a better ligand of the ACE enzyme than P7. These results are in agreement with an in vivo study, previously performed by Aluko et al., which has shown that LTFPG is an effective hypotensive peptide. Our work highlights the dynamic nature of bioactive food peptides that may be modulated by the metabolic activity of intestinal cells.
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Affiliation(s)
- Carmen Lammi
- Department of Pharmaceutical
Sciences, University of Milan, 20133 Milan, Italy
- Telephone: +39-0250319912. Fax: +39-0250319372. E-mail:
| | - Gilda Aiello
- Department of Pharmaceutical
Sciences, University of Milan, 20133 Milan, Italy
| | - Luca Dellafiora
- Department of Food and Drug, University of Parma, 43124 Parma, Italy
| | - Carlotta Bollati
- Department of Pharmaceutical
Sciences, University of Milan, 20133 Milan, Italy
| | - Giovanna Boschin
- Department of Pharmaceutical
Sciences, University of Milan, 20133 Milan, Italy
| | - Giulia Ranaldi
- Food and Nutrition Research Centre, Council
for Agricultural Research and Economics (CREA), 00178 Rome, Italy
| | - Simonetta Ferruzza
- Food and Nutrition Research Centre, Council
for Agricultural Research and Economics (CREA), 00178 Rome, Italy
| | - Yula Sambuy
- Food and Nutrition Research Centre, Council
for Agricultural Research and Economics (CREA), 00178 Rome, Italy
| | - Gianni Galaverna
- Department of Food and Drug, University of Parma, 43124 Parma, Italy
| | - Anna Arnoldi
- Department of Pharmaceutical
Sciences, University of Milan, 20133 Milan, Italy
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22
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Perrone MG, Miciaccia M, Vitale P, Ferorelli S, Araújo CDCB, de Almeida GS, Souza Domingos TF, da Silva LCRP, de Pádula M, Cabral LM, Sathler PC, Bonaccorso C, Fortuna CG, Scilimati A. An attempt to chemically state the cross-talk between monomers of COX homodimers by double/hybrid inhibitors mofezolac-spacer-mofezolac and mofezolac-spacer-arachidonic acid. Eur J Med Chem 2020; 209:112919. [PMID: 33129592 DOI: 10.1016/j.ejmech.2020.112919] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/18/2020] [Accepted: 10/05/2020] [Indexed: 12/14/2022]
Abstract
Cardiovascular diseases (CVDs) account for over 17 million death globally each year, including arterial thrombosis. Platelets are key components in the pathogenesis of this disease and modulating their activity is an effective strategy to treat such thrombotic events. Cyclooxygenase-1 (COX-1) isoenzyme is involved in platelet activation and is the main target of non-steroidal anti-inflammatory drugs (NSAIDs) and new selective inhibitor research. Inhibitors of general formula mofezolac-spacer-mofezolac (mof-spacer-mof) and mofezolac-spacer-arachidonic acid (mof-spacer-AA) were projected to investigate the possible cross-talk between the two monomers (Eallo and Ecat) forming the COX-1 homodimer. Mofezolac was chosen as either one or two moieties of these molecules being the known most potent and selective COX-1 inhibitor and administrated to humans as Disopain™, then arachidonic acid (AA) was used to develop molecules bearing, in the same compound, in addition to the inhibitor moiety (mofezolac) also the natural COX substrate. Depending on the nature of the spacer, COX-1 and COX-2 activity was differently inhibited by mof-spacer-mof set with a preferential COX-1 inhibition. The highest COX-1 selectivity was exhibited by the compound in which the spacer was the benzidine [N,N'-(biphenyl-4,4'-di-yl)bis (2-[3,4-bis(4-methoxyphenyl)isoxazol-5-yl]acetamide) (15): COX-1 IC50 = 0.08 μM, COX-2 IC50 > 50 μM, Selectivity Index (SI) > 625]. In the case of mof-spacer-AA set, the COX inhibitory potency and also the isoform preference changed. (5Z, 8Z, 11Z, 14Z)-N-(4-{2-[3,4-Bis(4-methoxyphenyl)isoxazol-5-yl]acetamido}butyl)icosa-5,8,11,14-tetraenamide (19) and (5Z, 8Z, 11Z, 14Z)-N-(4'-{2-[3,4-bis(4-methoxyphenyl)isoxazol-5-yl]acetamido}-[1,1'-biphenyl]-4-yl)icosa-5,8,11,14-tetraenamide (21), in which the spacer is the 1,2-diaminobutane or benzidine, respectively, selectively inhibited the COX-2, whereas when the spacer is the 1,4-phenylendiamine [(5Z, 8Z, 11Z, 14Z)-N-(4-{2-[3,4-bis(4-methoxyphenyl)isoxazol-5-yl]acetamido}phenyl)icosa-5,8,11,14-tetraenamide) (20) the COX preference is COX-1 (COX-1 IC50 = 0.05 μM, COX-2 IC50 > 50 μM, with a COX-1 selectivity > 1000). Molecular modelling by using FLAP algorithm shows fundamental interactions of the novel compounds at the entry channel of COX and inside its catalytic cavity. The effect of these mof-spacer-mof and mof-spacer-AA in inhibiting in vitro free arachidonic acid-induced platelet aggregation was also determined. A positive profile of hemocompatibility in relation to their influence on the blood coagulation cascade and erythrocyte toxicity was observed. Cytotoxicity and genotoxicity safety were also found for these two novel sets of compounds.
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Affiliation(s)
- Maria Grazia Perrone
- Department of Pharmacy - Pharmaceutical Sciences, University of Bari "Aldo Moro", Via E. Orabona 4, 70125, Bari, Italy
| | - Morena Miciaccia
- Department of Pharmacy - Pharmaceutical Sciences, University of Bari "Aldo Moro", Via E. Orabona 4, 70125, Bari, Italy
| | - Paola Vitale
- Department of Pharmacy - Pharmaceutical Sciences, University of Bari "Aldo Moro", Via E. Orabona 4, 70125, Bari, Italy
| | - Savina Ferorelli
- Department of Pharmacy - Pharmaceutical Sciences, University of Bari "Aldo Moro", Via E. Orabona 4, 70125, Bari, Italy
| | - Cristina da Costa Bernardes Araújo
- Faculty of Pharmacy, Federal University of Rio de Janeiro, Center of Health Sciences, Carlos Chagas Filho Avenue, 373, 21941599, Rio de Janeiro, Brazil
| | - Gabriella Silva de Almeida
- Faculty of Pharmacy, Federal University of Rio de Janeiro, Center of Health Sciences, Carlos Chagas Filho Avenue, 373, 21941599, Rio de Janeiro, Brazil
| | - Thaisa Francielle Souza Domingos
- Faculty of Pharmacy, Federal University of Rio de Janeiro, Center of Health Sciences, Carlos Chagas Filho Avenue, 373, 21941599, Rio de Janeiro, Brazil
| | | | - Marcelo de Pádula
- Faculty of Pharmacy, Federal University of Rio de Janeiro, Center of Health Sciences, Carlos Chagas Filho Avenue, 373, 21941599, Rio de Janeiro, Brazil
| | - Lucio Mendes Cabral
- Faculty of Pharmacy, Federal University of Rio de Janeiro, Center of Health Sciences, Carlos Chagas Filho Avenue, 373, 21941599, Rio de Janeiro, Brazil
| | - Plínio Cunha Sathler
- Faculty of Pharmacy, Federal University of Rio de Janeiro, Center of Health Sciences, Carlos Chagas Filho Avenue, 373, 21941599, Rio de Janeiro, Brazil
| | - Carmela Bonaccorso
- Department of Chemical Science, University of Catania, Viale Andrea Doria 6, 95125, Catania, Italy
| | - Cosimo G Fortuna
- Department of Chemical Science, University of Catania, Viale Andrea Doria 6, 95125, Catania, Italy
| | - Antonio Scilimati
- Department of Pharmacy - Pharmaceutical Sciences, University of Bari "Aldo Moro", Via E. Orabona 4, 70125, Bari, Italy.
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Qin X, Vila-Sanjurjo C, Singh R, Philipp B, Goycoolea FM. Screening of Bacterial Quorum Sensing Inhibitors in a Vibrio fischeri LuxR-Based Synthetic Fluorescent E. coli Biosensor. Pharmaceuticals (Basel) 2020; 13:E263. [PMID: 32971993 PMCID: PMC7559085 DOI: 10.3390/ph13090263] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/15/2020] [Accepted: 09/18/2020] [Indexed: 02/07/2023] Open
Abstract
A library of 23 pure compounds of varying structural and chemical characteristics was screened for their quorum sensing (QS) inhibition activity using a synthetic fluorescent Escherichia coli biosensor that incorporates a modified version of lux regulon of Vibrio fischeri. Four such compounds exhibited QS inhibition activity without compromising bacterial growth, namely, phenazine carboxylic acid (PCA), 2-heptyl-3-hydroxy-4-quinolone (PQS), 1H-2-methyl-4-quinolone (MOQ) and genipin. When applied at 50 µM, these compounds reduced the QS response of the biosensor to 33.7% ± 2.6%, 43.1% ± 2.7%, 62.2% ± 6.3% and 43.3% ± 1.2%, respectively. A series of compounds only showed activity when tested at higher concentrations. This was the case of caffeine, which, when applied at 1 mM, reduced the QS to 47% ± 4.2%. In turn, capsaicin, caffeic acid phenethyl ester (CAPE), furanone and polygodial exhibited antibacterial activity when applied at 1mM, and reduced the bacterial growth by 12.8% ± 10.1%, 24.4% ± 7.0%, 91.4% ± 7.4% and 97.5% ± 3.8%, respectively. Similarly, we confirmed that trans-cinnamaldehyde and vanillin, when tested at 1 mM, reduced the QS response to 68.3% ± 4.9% and 27.1% ± 7.4%, respectively, though at the expense of concomitantly reducing cell growth by 18.6% ± 2.5% and 16% ± 2.2%, respectively. Two QS natural compounds of Pseudomonas aeruginosa, namely PQS and PCA, and the related, synthetic compounds MOQ, 1H-3-hydroxyl-4-quinolone (HOQ) and 1H-2-methyl-3-hydroxyl-4-quinolone (MHOQ) were used in molecular docking studies with the binding domain of the QS receptor TraR as a target. We offer here a general interpretation of structure-function relationships in this class of compounds that underpins their potential application as alternatives to antibiotics in controlling bacterial virulence.
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Affiliation(s)
- Xiaofei Qin
- Department of Bioengineering, Zhuhai Campus of Zunyi Medical University, Zhuhai 519041, China;
- Laboratory of Nanobiotechnology, Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, D-48143 Münster, Germany;
| | - Celina Vila-Sanjurjo
- Laboratory of Nanobiotechnology, Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, D-48143 Münster, Germany;
- Department of Pharmacology, Pharmacy and Pharmaceutical Technology, University of Santiago de Compostela. Campus Vida, s/n, 15782 Santiago de Compostela, Spain
| | - Ratna Singh
- Laboratory of Molecular Phytopathology and Renewable Resources, Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, D-48143 Münster, Germany;
| | - Bodo Philipp
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Corrensstraße 3, D-48149 Münster, Germany;
| | - Francisco M. Goycoolea
- Laboratory of Nanobiotechnology, Institute of Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, D-48143 Münster, Germany;
- School of Food Science and Nutrition, University of Leeds, Leeds LS2 9JT, UK
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24
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Interaction of zearalenone-14-sulfate with cyclodextrins and the removal of the modified mycotoxin from aqueous solution by beta-cyclodextrin bead polymer. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113236] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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25
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Alternaria toxins as casein kinase 2 inhibitors and possible consequences for estrogenicity: a hybrid in silico/in vitro study. Arch Toxicol 2020; 94:2225-2237. [PMID: 32328700 PMCID: PMC7303061 DOI: 10.1007/s00204-020-02746-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 04/08/2020] [Indexed: 01/05/2023]
Abstract
Emerging mycotoxins produced by Alternaria spp. were previously reported to exert cytotoxic, genotoxic, but also estrogenic effects in human cells. The involved mechanisms are very complex and not fully elucidated yet. Thus, we followed an in silico target fishing approach to extend knowledge on the possible biological targets underlying the activity of alternariol, taken as the signature compound of Alternaria toxins. Combining ligand-based screening and structure-based modeling, the ubiquitous casein kinase 2 (CK2) was identified as a potential target for the compound. This result was validated in a cell-free in vitro CK2 activity assay, where alternariol inhibited CK2 with an IC50 of 707 nM. As CK2 was recently discussed to influence estrogen receptor (ER) transcription and DNA-binding affinity, we assessed a potential impact on the mRNA levels of ERα or ERβ by qRT-PCR and on nuclear localization of the receptors by confocal microscopy, using estrogen-sensitive Ishikawa cells as a model. While AOH did not affect the transcription of ERα or ERβ, an increase in nuclear localization of ERα after incubation with 10 µM AOH was observed. However, this effect might be due to ER binding affinity and therefore estrogenicity of AOH. Furthermore, in silico docking simulation revealed not only AOH, but also a number of other Alternaria toxins as potential inhibitors of CK2, including alternariol monomethyl ether and the perylene quinone derivative altertoxin II (ATX-II). These findings were representatively confirmed in vitro for the perylene quinone derivative altertoxin II, which was found to inhibit the kinase with an IC50 of 5.1 µM. Taken together, we propose CK2 inhibition as an additional mechanism to consider in future studies for alternariol and several other Alternaria toxins.
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26
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A Structural Study on the Listeria Monocytogenes Internalin A-Human E-cadherin Interaction: A Molecular Tool to Investigate the Effects of Missense Mutations. Toxins (Basel) 2020; 12:toxins12010060. [PMID: 31968631 PMCID: PMC7020427 DOI: 10.3390/toxins12010060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/14/2020] [Accepted: 01/16/2020] [Indexed: 02/07/2023] Open
Abstract
Listeria monocytogenes is a widespread foodborne pathogen of high concern and internalin A is an important virulence factor that mediates cell invasion upon the interaction with the host protein E-cadherin. Nonsense mutations of internalin A are known to reduce virulence. Although missense mutations are largely overlooked, they need to be investigated in respect to their effects in cell invasion processes. This work presented a computational workflow to early characterize internalin A missense mutations. The method reliably estimated the effects of a set of engineered missense mutations in terms of their effects on internalin A–E-cadherin interaction. Then, the effects of mutations of an internalin A variant from a L. monocytogenes isolate were calculated. Mutations showed impairing effects on complex stability providing a mechanistic explanation of the low cells invasion capacity previously observed. Overall, our results provided a rational approach to explain the effects of internalin A missense mutations. Moreover, our findings highlighted that the strength of interaction may not directly relate to the cell invasion capacity reflecting the non-exclusive role of internalin A in determining the virulence of L. monocytogenes. The workflow could be extended to other virulence factors providing a promising platform to support a better molecular understanding of L. monocytogenes epidemiology.
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Gabriele F, Goracci L, Germani R, Spreti N. Refining the model to design α-chymotrypsin superactivators: the role of the binding mode of quaternary ammonium salts. NEW J CHEM 2020. [DOI: 10.1039/d0nj04676k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Modelling, synthesis and kinetic studies were combined to investigate the interactions responsible for the superactivation of α-chymotrypsin by ammonium-based additives.
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Affiliation(s)
- Francesco Gabriele
- Department of Physical and Chemical Sciences
- University of L'Aquila
- I-67100 Coppito
- Italy
| | - Laura Goracci
- Department of Chemistry
- Biology and Biotechnology
- University of Perugia
- Perugia
- Italy
| | - Raimondo Germani
- Department of Chemistry
- Biology and Biotechnology
- University of Perugia
- Perugia
- Italy
| | - Nicoletta Spreti
- Department of Physical and Chemical Sciences
- University of L'Aquila
- I-67100 Coppito
- Italy
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28
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Dellafiora L, Oswald IP, Dorne JL, Galaverna G, Battilani P, Dall'Asta C. An in silico structural approach to characterize human and rainbow trout estrogenicity of mycotoxins: Proof of concept study using zearalenone and alternariol. Food Chem 2019; 312:126088. [PMID: 31911350 DOI: 10.1016/j.foodchem.2019.126088] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 11/28/2019] [Accepted: 12/18/2019] [Indexed: 02/06/2023]
Abstract
The mycotoxins zearalenone and alternariol may contaminate food and feed raising toxicological concerns due to their estrogenicity. Inter-species differences in their toxicokinetics and toxicodynamics may occur depending on evolution of taxa-specific traits. As a proof of principle, this manuscript investigates the comparative toxicodynamics of zearalenone, its metabolites (alpha-zearalenol and beta-zearalenol), and alternariol with regards to estrogenicity in humans and rainbow trout. An in silico structural approach based on docking simulations, pharmacophore modeling and molecular dynamics was applied and computational results were analyzed in comparison with available experimental data. The differences of estrogenicity among species of zearalenone and its metabolites have been structurally explained. Also, the low estrogenicity of alternariol in trout has been characterized here for the first time. This approach can provide a powerful tool for the characterization of interspecies differences in mycotoxin toxicity for a range of protein targets and relevant compounds for the food- and feed-safety area.
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Affiliation(s)
- Luca Dellafiora
- Department of Food and Drug, University of Parma, Area Parco delle Scienze 27/A, 43124 Parma, Italy.
| | - Isabelle P Oswald
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, 31027 Toulouse, France.
| | | | - Gianni Galaverna
- Department of Food and Drug, University of Parma, Area Parco delle Scienze 27/A, 43124 Parma, Italy.
| | - Paola Battilani
- Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy.
| | - Chiara Dall'Asta
- Department of Food and Drug, University of Parma, Area Parco delle Scienze 27/A, 43124 Parma, Italy.
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29
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Bruno A, Costantino G, Sartori L, Radi M. The In Silico Drug Discovery Toolbox: Applications in Lead Discovery and Optimization. Curr Med Chem 2019; 26:3838-3873. [PMID: 29110597 DOI: 10.2174/0929867324666171107101035] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 09/27/2017] [Accepted: 09/28/2017] [Indexed: 01/04/2023]
Abstract
BACKGROUND Discovery and development of a new drug is a long lasting and expensive journey that takes around 20 years from starting idea to approval and marketing of new medication. Despite R&D expenditures have been constantly increasing in the last few years, the number of new drugs introduced into market has been steadily declining. This is mainly due to preclinical and clinical safety issues, which still represent about 40% of drug discontinuation. To cope with this issue, a number of in silico techniques are currently being used for an early stage evaluation/prediction of potential safety issues, allowing to increase the drug-discovery success rate and reduce costs associated with the development of a new drug. METHODS In the present review, we will analyse the early steps of the drug-discovery pipeline, describing the sequence of steps from disease selection to lead optimization and focusing on the most common in silico tools used to assess attrition risks and build a mitigation plan. RESULTS A comprehensive list of widely used in silico tools, databases, and public initiatives that can be effectively implemented and used in the drug discovery pipeline has been provided. A few examples of how these tools can be problem-solving and how they may increase the success rate of a drug discovery and development program have been also provided. Finally, selected examples where the application of in silico tools had effectively contributed to the development of marketed drugs or clinical candidates will be given. CONCLUSION The in silico toolbox finds great application in every step of early drug discovery: (i) target identification and validation; (ii) hit identification; (iii) hit-to-lead; and (iv) lead optimization. Each of these steps has been described in details, providing a useful overview on the role played by in silico tools in the decision-making process to speed-up the discovery of new drugs.
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Affiliation(s)
- Agostino Bruno
- Experimental Therapeutics Unit, IFOM - The FIRC Institute for Molecular Oncology Foundation, Via Adamello 16 - 20139 Milano, Italy
| | - Gabriele Costantino
- Dipartimento di Scienze degli Alimenti e del Farmaco, Universita degli Studi di Parma, Viale delle Scienze, 27/A, 43124 Parma, Italy
| | - Luca Sartori
- Experimental Therapeutics Unit, IFOM - The FIRC Institute for Molecular Oncology Foundation, Via Adamello 16 - 20139 Milano, Italy
| | - Marco Radi
- Dipartimento di Scienze degli Alimenti e del Farmaco, Universita degli Studi di Parma, Viale delle Scienze, 27/A, 43124 Parma, Italy
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30
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Faisal Z, Fliszár-Nyúl E, Dellafiora L, Galaverna G, Dall'Asta C, Lemli B, Kunsági-Máté S, Szente L, Poór M. Cyclodextrins Can Entrap Zearalenone-14-Glucoside: Interaction of the Masked Mycotoxin with Cyclodextrins and Cyclodextrin Bead Polymer. Biomolecules 2019; 9:E354. [PMID: 31405003 PMCID: PMC6724229 DOI: 10.3390/biom9080354] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/07/2019] [Accepted: 08/07/2019] [Indexed: 01/07/2023] Open
Abstract
Zearalenone (ZEN) is a Fusarium-derived xenoestrogenic mycotoxin. In plants, zearalenone-14-O-β-d-glucoside (Z14G) is the major conjugated metabolite of ZEN, and is a masked mycotoxin. Masked mycotoxins are plant-modified derivatives, which are not routinely screened in food and feed samples. Cyclodextrins (CDs) are cyclic oligosaccharides built up from D-glucopyranose units. CDs can form stable host-guest type complexes with lipophilic molecules (e.g., with some mycotoxins). In this study, the interaction of Z14G with native and chemically modified β- and γ-CDs was examined employing fluorescence spectroscopy and molecular modeling. Furthermore, the removal of Z14G from aqueous solution by insoluble β-CD bead polymer (BBP) was also tested. Our results demonstrate that Z14G forms the most stable complexes with γ-CDs under acidic and neutral conditions (K ≈ 103 L/mol). Among the CDs tested, randomly methylated γ-CD induced the highest increase in the fluorescence of Z14G (7.1-fold) and formed the most stable complexes with the mycotoxin (K = 2 × 103 L/mol). Furthermore, BBP considerably reduced the Z14G content of aqueous solution. Based on these observations, CD technology seems a promising tool to improve the fluorescence analytical detection of Z14G and to discover new mycotoxin binders which can also remove masked mycotoxins (e.g., Z14G).
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Affiliation(s)
- Zelma Faisal
- Department of Pharmacology, Faculty of Pharmacy, University of Pécs, Szigeti út 12, H-7624 Pécs, Hungary
- János Szentágothai Research Center, University of Pécs, Ifjúság útja 20, H-7624 Pécs, Hungary
| | - Eszter Fliszár-Nyúl
- Department of Pharmacology, Faculty of Pharmacy, University of Pécs, Szigeti út 12, H-7624 Pécs, Hungary
- János Szentágothai Research Center, University of Pécs, Ifjúság útja 20, H-7624 Pécs, Hungary
| | - Luca Dellafiora
- Department of Food and Drug, University of Parma, Via G.P. 7 Usberti 17/A, 43124 Parma, Italy
| | - Gianni Galaverna
- Department of Food and Drug, University of Parma, Via G.P. 7 Usberti 17/A, 43124 Parma, Italy
| | - Chiara Dall'Asta
- Department of Food and Drug, University of Parma, Via G.P. 7 Usberti 17/A, 43124 Parma, Italy
| | - Beáta Lemli
- János Szentágothai Research Center, University of Pécs, Ifjúság útja 20, H-7624 Pécs, Hungary
- Institute of Organic and Medicinal Chemistry, Medical School, University of Pécs, Szigeti út 12, H-7624 Pécs, Hungary
| | - Sándor Kunsági-Máté
- János Szentágothai Research Center, University of Pécs, Ifjúság útja 20, H-7624 Pécs, Hungary
- Institute of Organic and Medicinal Chemistry, Medical School, University of Pécs, Szigeti út 12, H-7624 Pécs, Hungary
| | - Lajos Szente
- CycloLab Cyclodextrin Research & Development Laboratory, Ltd., Illatos út 7, H-1097 Budapest, Hungary
| | - Miklós Poór
- Department of Pharmacology, Faculty of Pharmacy, University of Pécs, Szigeti út 12, H-7624 Pécs, Hungary.
- János Szentágothai Research Center, University of Pécs, Ifjúság útja 20, H-7624 Pécs, Hungary.
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31
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Ebejer JP, Finn PW, Wong WK, Deane CM, Morris GM. Ligity: A Non-Superpositional, Knowledge-Based Approach to Virtual Screening. J Chem Inf Model 2019; 59:2600-2616. [PMID: 31117509 PMCID: PMC7007185 DOI: 10.1021/acs.jcim.8b00779] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We present Ligity, a hybrid ligand-structure-based, non-superpositional method for virtual screening of large databases of small molecules. Ligity uses the relative spatial distribution of pharmacophoric interaction points (PIPs) derived from the conformations of small molecules. These are compared with the PIPs derived from key interaction features found in protein-ligand complexes and are used to prioritize likely binders. We investigated the effect of generating PIPs using the single lowest energy conformer versus an ensemble of conformers for each screened ligand, using different bin sizes for the distance between two features, utilizing triangular sets of pharmacophoric features (3-PIPs) versus chiral tetrahedral sets (4-PIPs), fusing data for targets with multiple protein-ligand complex structures, and applying different similarity measures. Ligity was benchmarked using the Directory of Useful Decoys-Enhanced (DUD-E). Optimal results were obtained using the tetrahedral PIPs derived from an ensemble of bound ligand conformers and a bin size of 1.5 Å, which are used as the default settings for Ligity. The high-throughput screening mode of Ligity, using only the lowest-energy conformer of each ligand, was used for benchmarking against the whole of the DUD-E, and a more resource-intensive, "information-rich" mode of Ligity, using a conformational ensemble of each ligand, were used for a representative subset of 10 targets. Against the full DUD-E database, mean area under the receiver operating characteristic curve (AUC) values ranged from 0.44 to 0.99, while for the representative subset they ranged from 0.61 to 0.86. Data fusion further improved Ligity's performance, with mean AUC values ranging from 0.64 to 0.95. Ligity is very efficient compared to a protein-ligand docking method such as AutoDock Vina: if the time taken for the precalculation of Ligity descriptors is included in the comparason, then Ligity is about 20 times faster than docking. A direct comparison of the virtual screening steps shows Ligity to be over 5000 times faster. Ligity highly ranks the lowest-energy conformers of DUD-E actives, in a statistically significant manner, behavior that is not observed for DUD-E decoys. Thus, our results suggest that active compounds tend to bind in relatively low-energy conformations compared to decoys. This may be because actives-and thus their lowest-energy conformations-have been optimized for conformational complementarity with their cognate binding sites.
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Affiliation(s)
- Jean-Paul Ebejer
- Centre for Molecular Medicine and Biobanking , University of Malta , Msida , MSD 2080 , Malta
| | - Paul W Finn
- Oxford Drug Design Limited, Oxford Centre for Innovation , New Road , Oxford OX1 1BY , U.K.,The School of Computing , University of Buckingham , Hunter Street , Buckingham , MK18 1EG , U.K
| | - Wing Ki Wong
- Oxford Protein Informatics Group, Department of Statistics , University of Oxford , 24-29 St. Giles' , Oxford , OX1 3LB , U.K
| | - Charlotte M Deane
- Oxford Protein Informatics Group, Department of Statistics , University of Oxford , 24-29 St. Giles' , Oxford , OX1 3LB , U.K
| | - Garrett M Morris
- Oxford Protein Informatics Group, Department of Statistics , University of Oxford , 24-29 St. Giles' , Oxford , OX1 3LB , U.K
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32
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Bošnjaković-Pavlović N, Xu X, Krstić D, Gillet JM, Wei Y, Wu P, Čolović M, Spasojević-de Biré A. Experimental and theoretical insights of functionalized hexavanadates on Na +/K +-ATPase activity; molecular interaction field, ab initio calculations and in vitro assays. J Inorg Biochem 2019; 198:110720. [PMID: 31150927 DOI: 10.1016/j.jinorgbio.2019.110720] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 04/27/2019] [Accepted: 05/13/2019] [Indexed: 02/02/2023]
Abstract
The influence of three functionalized hexavanadates (V6): Na2 [V6O13{(OCH2)3CCH3}2], [H2]2 [V6O13{(OCH2)3CCH2OCOCH2CH3}2] and [(C4H9)4N]2 [V6O13{(OCH2)3CCH2OOC(CH3)2-COOH}2 on Na+/K+-ATPase activity, was investigated in vitro. Including compounds already tested by Xu et al. (Journal of Inorganic Biochemistry 161 (2016) 27-36), all functionalized hexavanadates inhibit the activity of Na+/K+-ATPase in a dose-dependent manner but with different inhibitory potencies. Na2 [V6O13{(OCH2)3CCH3}2] was found to have the best inhibition properties - showing 50% inhibition IC50 = 5.50 × 10-5 M, while [(C4H9)4N]2 [V6O13{(OCH2)3CCH2OOC(CH3)2-COOH}2] showed the lowest inhibitory power, IC50 = 1.31 × 10-4 M. In order to understand the bioactivity of functionalized hexavanadates series, we have also used a combined theoretical approach: determination of electrostatic potential from ab initio theoretical calculations and computation of the molecular interaction field (MIF) surface.
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Affiliation(s)
- Nada Bošnjaković-Pavlović
- Université Paris-Saclay, CentraleSupélec, Campus de Paris-Saclay, 8-10 rue Joliot-Curie, 91190 Gif-sur-Yvette, France; CNRS, UMR 8580, Laboratory "Structures Propriétés et Modélisation des Solides" (SPMS), Campus de Gif, 8-10 rue Joliot-Curie, 91190 Gif-sur-Yvette, France
| | - Xiao Xu
- Université Paris-Saclay, CentraleSupélec, Campus de Paris-Saclay, 8-10 rue Joliot-Curie, 91190 Gif-sur-Yvette, France; CNRS, UMR 8580, Laboratory "Structures Propriétés et Modélisation des Solides" (SPMS), Campus de Gif, 8-10 rue Joliot-Curie, 91190 Gif-sur-Yvette, France
| | - Danijela Krstić
- Institute of Medical Chemistry, Faculty of Medicine, University of Belgrade, Serbia
| | - Jean-Michel Gillet
- Université Paris-Saclay, CentraleSupélec, Campus de Paris-Saclay, 8-10 rue Joliot-Curie, 91190 Gif-sur-Yvette, France; CNRS, UMR 8580, Laboratory "Structures Propriétés et Modélisation des Solides" (SPMS), Campus de Gif, 8-10 rue Joliot-Curie, 91190 Gif-sur-Yvette, France
| | - Yongge Wei
- Department of Chemistry, Tsinghua University, 100084 Beijing, PR China
| | - Pingfan Wu
- Institute of POM-based Materials, The Synergistic Innovation Center of Catalysis Materials of Hubei Province, Hubei University of Technology, 430086 Wuhan, Hubei Province, PR China
| | - Mirjana Čolović
- Department of Physical Chemistry, Vinča Institute of Nuclear Sciences, University of Belgrade, Serbia
| | - Anne Spasojević-de Biré
- Université Paris-Saclay, CentraleSupélec, Campus de Paris-Saclay, 8-10 rue Joliot-Curie, 91190 Gif-sur-Yvette, France; CNRS, UMR 8580, Laboratory "Structures Propriétés et Modélisation des Solides" (SPMS), Campus de Gif, 8-10 rue Joliot-Curie, 91190 Gif-sur-Yvette, France.
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33
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Shinada NK, de Brevern AG, Schmidtke P. Halogens in Protein-Ligand Binding Mechanism: A Structural Perspective. J Med Chem 2019; 62:9341-9356. [PMID: 31117513 DOI: 10.1021/acs.jmedchem.8b01453] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Halogen atoms have been at the center of many rational medicinal chemistry applications in drug design. While fluorine and chlorine atoms are often added to enhance physicochemical properties, bromine and iodine elements are generally inserted to improve selectivity. Favorable halogen interactions such as halogen bond have been thoroughly studied through quantum mechanics and statistical analyses. Although most of the studies focus on halogen interaction through its σ-hole, hydrogen bonding also has a significant impact. Here, we present an analysis describing the interacting environment of halogen atoms in protein-ligand context. With consideration of structural redundancy in the PDB, tendencies toward specific molecular interactions consideration have been refined and implications for rational drug design with halogens further discussed. Finally, we highlight the moderate occurrence of halogen bonding and present the other roles of halogen in protein-ligand complexes, completing the medicinal chemistry guide to rational halogen interactions.
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Affiliation(s)
- Nicolas K Shinada
- Discngine S.A.S. , 79 Avenue Ledru Rollin , 75012 Paris , France.,Biologie Intégrée du Globule Rouge UMR S1134, Inserm, Université Paris Diderot, Sorbonne Paris Cité, Université de la Réunion, Université des Antilles , 75739 Paris , France.,Laboratoire d'Excellence GR-Ex , 75739 Paris , France.,Institut National de la Transfusion Sanguine (INTS) , 75739 Paris , France
| | - Alexandre G de Brevern
- Biologie Intégrée du Globule Rouge UMR S1134, Inserm, Université Paris Diderot, Sorbonne Paris Cité, Université de la Réunion, Université des Antilles , 75739 Paris , France.,Laboratoire d'Excellence GR-Ex , 75739 Paris , France.,Institut National de la Transfusion Sanguine (INTS) , 75739 Paris , France
| | - Peter Schmidtke
- Discngine S.A.S. , 79 Avenue Ledru Rollin , 75012 Paris , France
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34
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Dellafiora L, Galaverna G, Cruciani G, Dall'Asta C. A computational study toward the "personalized" activity of alternariol - Does it matter for safe food at individual level? Food Chem Toxicol 2019; 130:199-206. [PMID: 31128219 DOI: 10.1016/j.fct.2019.05.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 05/18/2019] [Accepted: 05/21/2019] [Indexed: 02/08/2023]
Abstract
Mycotoxins in food may threat public health at a global scale. However, for most of them, the current body of knowledge does not support a proper risk assessment and more data are needed to clarify their toxicity. In particular, the assessment of "personalized" action may succeed in understanding and counteracting the effects of many toxicants. Therefore, the assessment of "personalized" toxicology of mycotoxins might deserve attention to foster the understanding of their mechanisms of toxicity and to eventually improve the assessment of risk. This work dealt with the early warning analysis of possible differences in eliciting androgenic stimuli by alternariol, a widespread mycotoxin produce by Alternaria species, when mutations on the androgen receptor occur. It was applied a computational study based on docking simulations, pharmacophore modeling and molecular dynamics to assess the capability of alternariol to interact with the androgen receptor bearing the M749I substitution - which confers insensitivity to androgens stimulation. The results collected pointed to possible "protective" effects against alternariol suggesting: i) the likely existence of inter-individual responses to alternariol stimulation; ii) the meaningfulness of collecting data on "personalized" response to mycotoxins toward a more precise paradigm addressing the risk assessment at the individual level.
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Affiliation(s)
- Luca Dellafiora
- Department of Food and Drug, University of Parma, Area Parco delle Scienze 27/A, 43124, Parma, Italy.
| | - Gianni Galaverna
- Department of Food and Drug, University of Parma, Area Parco delle Scienze 27/A, 43124, Parma, Italy
| | - Gabriele Cruciani
- Department of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di Sotto, 8, 06123, Perugia, Italy
| | - Chiara Dall'Asta
- Department of Food and Drug, University of Parma, Area Parco delle Scienze 27/A, 43124, Parma, Italy
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35
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Fliszár-Nyúl E, Lemli B, Kunsági-Máté S, Dellafiora L, Dall'Asta C, Cruciani G, Pethő G, Poór M. Interaction of Mycotoxin Alternariol with Serum Albumin. Int J Mol Sci 2019; 20:ijms20092352. [PMID: 31083629 PMCID: PMC6539399 DOI: 10.3390/ijms20092352] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 05/08/2019] [Accepted: 05/08/2019] [Indexed: 01/29/2023] Open
Abstract
Alternariol (AOH) is a mycotoxin produced by Alternaria species. In vitro studies suggest the genotoxic, mutagenic, and endocrine disruptor effects of AOH, and an increased incidence of esophageal cancer has been reported related to higher AOH exposure. Human serum albumin (HSA) is the most abundant plasma protein in the circulation, it is able to affect toxicokinetic properties of numerous xenobiotics. HSA forms stable complexes with several mycotoxins, however, the interaction of AOH with albumin has not been examined. In this study, the complex formation of AOH with HSA was tested, employing fluorescence spectroscopy, ultrafiltration, and molecular modeling. Each spectroscopic measurement shows the formation of stable AOH-HSA complexes (K = 4 × 105 L/mol). Investigations with site markers (in spectroscopic and ultrafiltration models) as well as modeling studies suggest that AOH occupies Sudlow’s site I as a high-affinity binding site in HSA. The binding affinity of AOH towards bovine, porcine, and rat albumins was also tested, suggesting that AOH binds to rat albumin with considerably higher affinity than other albumins tested. Our results demonstrate the strong interaction of AOH with serum albumins, suggesting the potential in vivo importance of these interactions.
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Affiliation(s)
- Eszter Fliszár-Nyúl
- Department of Pharmacology, Faculty of Pharmacy, University of Pécs, Szigeti út 12, H-7642 Pécs; Hungary.
- János Szentágothai Research Centre, University of Pécs, Ifjúság útja 20, H-7642 Pécs; Hungary.
| | - Beáta Lemli
- János Szentágothai Research Centre, University of Pécs, Ifjúság útja 20, H-7642 Pécs; Hungary.
- Institute of Organic and Medicinal Chemistry, Medical School, University of Pécs, Szigeti út 12, H-7624 Pécs, Hungary.
| | - Sándor Kunsági-Máté
- János Szentágothai Research Centre, University of Pécs, Ifjúság útja 20, H-7642 Pécs; Hungary.
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Pécs, Rókus utca 2, H-7642 Pécs, Hungary.
| | - Luca Dellafiora
- Department of Food and Drug, University of Parma, Via G.P. 7 Usberti 17/A, 43124 Parma, Italy.
| | - Chiara Dall'Asta
- Department of Food and Drug, University of Parma, Via G.P. 7 Usberti 17/A, 43124 Parma, Italy.
| | - Gabriele Cruciani
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy.
| | - Gábor Pethő
- Department of Pharmacology, Faculty of Pharmacy, University of Pécs, Szigeti út 12, H-7642 Pécs; Hungary.
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, H-7624 Pécs, Hungary.
| | - Miklós Poór
- Department of Pharmacology, Faculty of Pharmacy, University of Pécs, Szigeti út 12, H-7642 Pécs; Hungary.
- János Szentágothai Research Centre, University of Pécs, Ifjúság útja 20, H-7642 Pécs; Hungary.
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36
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von Rudorff GF, Watermann T, Guo XY, Sebastiani D. Conformational Space of a Polyphilic Molecule with a Fluorophilic Side Chain Integrated in a DPPC Bilayer. J Comput Chem 2019; 38:576-583. [PMID: 28211109 DOI: 10.1002/jcc.24711] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 11/17/2016] [Accepted: 11/18/2016] [Indexed: 12/21/2022]
Abstract
We investigate the conformational space of a polyphilic molecule with hydrophilic, lipophilic and fluorophilic parts inserted as a transmembrane agent into a dipalmitoylphosphatidylcholine bilayer by means of all-atom molecular dynamics simulations. Special focus is put on the competing structural driving forces arising from the hydrophilic, lipophilic and fluorophilic side chains and the aromatic backbone of the polyphile. We observe a significant difference between the lipophilic and the fluorophilic side chains regarding their intramembrane distribution. While the lipophilic groups remain membrane-centered, the fluorophilic parts tend to orient toward the phosphate headgroups. This trend is important for understanding the influence of polyphile agents on the properties of phospholipid membranes. From a fundamental point of view, our computed distribution functions of the side chains are related to the interplay of sterical, enthalpic and entropic driving forces. Our findings illustrate the potential of rationally designed membrane additives which can be exploited to tune the properties of phospholipid membranes. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Guido F von Rudorff
- Department of Physics and Astronomy, University College London, Gower Street, London, United Kingdom.,Institute of Chemistry, Martin-Luther-Universität Halle-Wittenberg, von-Danckelmann-Platz 4, Halle, 06120, Germany
| | - Tobias Watermann
- Institute of Chemistry, Martin-Luther-Universität Halle-Wittenberg, von-Danckelmann-Platz 4, Halle, 06120, Germany
| | - Xiang-Yang Guo
- Institute of Chemistry, Martin-Luther-Universität Halle-Wittenberg, von-Danckelmann-Platz 4, Halle, 06120, Germany
| | - Daniel Sebastiani
- Institute of Chemistry, Martin-Luther-Universität Halle-Wittenberg, von-Danckelmann-Platz 4, Halle, 06120, Germany
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37
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Beshnova D, Carolan C, Grigorenko V, Rubtsova M, Gbekor E, Lewis J, Lamzin V, Egorov A. Scaffold hopping computational approach for searching novel β-lactamase inhibitors. ACTA ACUST UNITED AC 2019; 65:468-476. [DOI: 10.18097/pbmc20196506468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We present a novel computational ligand-based virtual screening approach with scaffold hopping capabilities for the identification of novel inhibitors of β-lactamases which confer bacterial resistance to β-lactam antibiotics. The structures of known β-lactamase inhibitors were used as query ligands, and a virtual in silico screening a database of 8 million drug-like compounds was performed in order to select the ligands with similar shape and charge distribution. A set of numerical descriptors was used such as chirality, eigen spectrum of matrices of interatomic distances and connectivity together with higher order moment invariants that showed their efficiency in the field of pattern recognition but have not yet been employed in drug discovery. The developed scaffold-hopping approach was applied for the discovery of analogues of four allosteric inhibitors of serine β-lactamases. After a virtual in silico screening, the effect of two selected ligands on the activity of TEM type β-lactamase was studied experimentally. New non-β-lactam inhibitors were found that showed more effective inhibition of β-lactamases compared to query ligands.
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Affiliation(s)
- D.A. Beshnova
- European Molecular Biology Laboratory, c/o DESY, Hamburg, Germany; UT Southwestern Medical Center, Dallas, TX, United States
| | - C. Carolan
- European Molecular Biology Laboratory, c/o DESY, Hamburg, Germany; International Civil Aviation Organization (ICAO), Montreal, Quebec, Canada
| | - V.G. Grigorenko
- Chemistry Department, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - M.Yu. Rubtsova
- Chemistry Department, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - E. Gbekor
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - J. Lewis
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - V.S. Lamzin
- European Molecular Biology Laboratory, c/o DESY, Hamburg, Germany
| | - A.M. Egorov
- Chemistry Department, M.V. Lomonosov Moscow State University, Moscow, Russia
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38
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Dellafiora L, Galaverna G, Cruciani G, Dall'Asta C, Bruni R. On the Mechanism of Action of Anti-Inflammatory Activity of Hypericin: An In Silico Study Pointing to the Relevance of Janus Kinases Inhibition. Molecules 2018; 23:E3058. [PMID: 30467287 PMCID: PMC6321526 DOI: 10.3390/molecules23123058] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 11/19/2018] [Accepted: 11/20/2018] [Indexed: 01/27/2023] Open
Abstract
St. John's Wort (Hypericum perforatum L.) flowers are commonly used in ethnomedical preparations with promising outcomes to treat inflammation both per os and by topical application. However, the underlying molecular mechanisms need to be described toward a rational, evidence-based, and reproducible use. For this purpose, the aptitude of the prominent Hypericum metabolite hypericin was assessed, along with that of its main congeners, to behave as an inhibitor of janus kinase 1, a relevant enzyme in inflammatory response. It was used a molecular modeling approach relying on docking simulations, pharmacophoric modeling, and molecular dynamics to estimate the capability of molecules to interact and persist within the enzyme pocket. Our results highlighted the capability of hypericin, and some of its analogues and metabolites, to behave as ATP-competitive inhibitor providing: (i) a likely mechanistic elucidation of anti-inflammatory activity of H. perforatum extracts containing hypericin and related compounds; and (ii) a rational-based prioritization of H. perforatum components to further characterize their actual effectiveness as anti-inflammatory agents.
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Affiliation(s)
- Luca Dellafiora
- Department of Food and Drug, University of Parma, Area Parco delle Scienze 27/A, 43124 Parma, Italy.
| | - Gianni Galaverna
- Department of Food and Drug, University of Parma, Area Parco delle Scienze 27/A, 43124 Parma, Italy.
| | - Gabriele Cruciani
- Department of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di Sotto, 8, 06123 Perugia, Italy.
| | - Chiara Dall'Asta
- Department of Food and Drug, University of Parma, Area Parco delle Scienze 27/A, 43124 Parma, Italy.
| | - Renato Bruni
- Department of Food and Drug, University of Parma, Area Parco delle Scienze 27/A, 43124 Parma, Italy.
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39
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Paciotti R, Storchi L, Marrone A. An insight of early PrP-E200K aggregation by combined molecular dynamics/fragment molecular orbital approaches. Proteins 2018; 87:51-61. [PMID: 30367504 DOI: 10.1002/prot.25621] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 10/01/2018] [Accepted: 10/16/2018] [Indexed: 01/30/2023]
Abstract
Unveiling the events leading to the formation of prion particles is a nowadays challenge in the field of neurochemistry. Pathogenic mutants of prion protein (PrP) are characterized by both an intrinsic tendency to aggregation and scrapie conversion propensity. However, the question about a possible correlation between these two events lasts still unanswered. Here, a multilayered computational workflow was employed to investigate structure, stability, and molecular interaction properties of a dimer of PrPC -E200K, a well-known mutant of the PrP that represents a reduced model of early aggregates of this protein. Based on the combination of molecular dynamics and quantum mechanical approaches, this study provided for an in depth insight of PrPC -E200K dimer in terms of residue-residue interactions. Assembly hypotheses for the early aggregation of PrPC -E200K are paved and compared with PrPSc models reported in the literature to find a structural link between early and late (scrapie) aggregates of this protein.
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Affiliation(s)
- Roberto Paciotti
- Department of Pharmacy, Università "G d'Annunzio" di Chieti-Pescara, Chieti, Italy
| | - Loriano Storchi
- Department of Pharmacy, Università "G d'Annunzio" di Chieti-Pescara, Chieti, Italy.,Molecular Discovery Limited, Middlesex, London, United Kingdom.,ISTM - CNR, Perugia, Italy
| | - Alessandro Marrone
- Department of Pharmacy, Università "G d'Annunzio" di Chieti-Pescara, Chieti, Italy
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40
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41
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Dellafiora L, Galaverna G, Dall’Asta C. Mechanisms of Fumonisin B1 Toxicity: A Computational Perspective beyond the Ceramide Synthases Inhibition. Chem Res Toxicol 2018; 31:1203-1212. [DOI: 10.1021/acs.chemrestox.8b00188] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Luca Dellafiora
- Department of Food and Drug, University of Parma, 43124 Parma, Italy
| | - Gianni Galaverna
- Department of Food and Drug, University of Parma, 43124 Parma, Italy
| | - Chiara Dall’Asta
- Department of Food and Drug, University of Parma, 43124 Parma, Italy
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42
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O'Reilly D, Stein RS, Patrascu MB, Jana SK, Kurian J, Moitessier N, Damha MJ. Exploring Atypical Fluorine-Hydrogen Bonds and Their Effects on Nucleoside Conformations. Chemistry 2018; 24:16432-16439. [PMID: 30125398 DOI: 10.1002/chem.201803940] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Indexed: 12/16/2022]
Affiliation(s)
- Daniel O'Reilly
- Department of Chemistry; McGill University; Otto Maass Chemistry Bldg.; 801 Sherbrooke St. West Montreal QC, H3C0B8 Canada
| | - Robin S. Stein
- Department of Chemistry; McGill University; Otto Maass Chemistry Bldg.; 801 Sherbrooke St. West Montreal QC, H3C0B8 Canada
| | - Mihai Burai Patrascu
- Department of Chemistry; McGill University; Otto Maass Chemistry Bldg.; 801 Sherbrooke St. West Montreal QC, H3C0B8 Canada
| | - Sunit Kumar Jana
- Department of Chemistry; McGill University; Otto Maass Chemistry Bldg.; 801 Sherbrooke St. West Montreal QC, H3C0B8 Canada
| | - Jerry Kurian
- Department of Chemistry; McGill University; Otto Maass Chemistry Bldg.; 801 Sherbrooke St. West Montreal QC, H3C0B8 Canada
| | - Nicolas Moitessier
- Department of Chemistry; McGill University; Otto Maass Chemistry Bldg.; 801 Sherbrooke St. West Montreal QC, H3C0B8 Canada
| | - Masad J. Damha
- Department of Chemistry; McGill University; Otto Maass Chemistry Bldg.; 801 Sherbrooke St. West Montreal QC, H3C0B8 Canada
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43
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Del Favero G, Woelflingseder L, Braun D, Puntscher H, Kütt ML, Dellafiora L, Warth B, Pahlke G, Dall’Asta C, Adam G, Marko D. Response of intestinal HT-29 cells to the trichothecene mycotoxin deoxynivalenol and its sulfated conjugates. Toxicol Lett 2018; 295:424-437. [DOI: 10.1016/j.toxlet.2018.07.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 07/03/2018] [Accepted: 07/05/2018] [Indexed: 11/30/2022]
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44
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Hebeisen P, Weiss U, Alker A, Kuhn B, Müller K, Wang F, Surya Prakash GK. Molecular Structure and Crystal Packing of Monofluoromethoxyarenes. European J Org Chem 2018. [DOI: 10.1002/ejoc.201701758] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Paul Hebeisen
- Pharmaceutical Research & Early Development; Roche Innovation Center Basel; F. Hoffmann-La Roche AG; Grenzacherstrasse 124 4070 Basel Switzerland
| | - Urs Weiss
- Pharmaceutical Research & Early Development; Roche Innovation Center Basel; F. Hoffmann-La Roche AG; Grenzacherstrasse 124 4070 Basel Switzerland
| | - André Alker
- Pharmaceutical Research & Early Development; Roche Innovation Center Basel; F. Hoffmann-La Roche AG; Grenzacherstrasse 124 4070 Basel Switzerland
| | - Bernd Kuhn
- Pharmaceutical Research & Early Development; Roche Innovation Center Basel; F. Hoffmann-La Roche AG; Grenzacherstrasse 124 4070 Basel Switzerland
| | - Klaus Müller
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Fang Wang
- Loker Hydrocarbon Research Institute; Department of Chemistry; University of Southern California; 1661 Los Angeles CA 90089- USA
| | - G. K. Surya Prakash
- Loker Hydrocarbon Research Institute; Department of Chemistry; University of Southern California; 1661 Los Angeles CA 90089- USA
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45
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Skalic M, Varela-Rial A, Jiménez J, Martínez-Rosell G, De Fabritiis G. LigVoxel: inpainting binding pockets using 3D-convolutional neural networks. Bioinformatics 2018; 35:243-250. [DOI: 10.1093/bioinformatics/bty583] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 07/04/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Miha Skalic
- Computational Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB)
| | - Alejandro Varela-Rial
- Acellera, Barcelona Biomedical Research Park (PRBB), Doctor Aiguader 88, Barcelona, Spain
| | - José Jiménez
- Computational Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB)
| | - Gerard Martínez-Rosell
- Computational Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB)
| | - Gianni De Fabritiis
- Computational Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB)
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluis Companys 23, Barcelona, Spain
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46
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Dellafiora L, Aichinger G, Geib E, Sánchez-Barrionuevo L, Brock M, Cánovas D, Dall'Asta C, Marko D. Hybrid in silico/in vitro target fishing to assign function to "orphan" compounds of food origin - The case of the fungal metabolite atromentin. Food Chem 2018; 270:61-69. [PMID: 30174092 DOI: 10.1016/j.foodchem.2018.07.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 05/21/2018] [Accepted: 07/02/2018] [Indexed: 01/18/2023]
Abstract
Many small molecules of food origin may effect human health but lack an adequate description of their biological activity. To fill this knowledge gap, a first-line workflow is needed to assign putative functions, rank the endpoints for testing and guide wet-lab experiments. In this framework, the identification of potential biological targets can be used to probe the activity of orphan compounds using a so-called "target fishing" approach. Here, we present a proof of concept study using an in silico/in vitro target fishing approach on the fungal secondary metabolite atromentin. The procedure relies on a computational screening for activity identification coupled with experimental trials for dose-response characterization. Computational results identified estrogen receptors and 17-β-hydroxysteroid dehydrogenase as potential targets. Experiments confirmed a weak estrogenic activity, supporting the reliability of the procedure. Despite limited estrogenicity of atromentin, the proposed inhibition of 17-β-hydroxysteroid dehydrogenase should be considered as a source for endocrine disruptive effects.
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Affiliation(s)
- Luca Dellafiora
- Department of Food and Drug, University of Parma, Via G.P. Usberti 27/A, 43124 Parma, Italy.
| | - Georg Aichinger
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090 Vienna, Austria.
| | - Elena Geib
- Fungal Genetics and Biology Groups, School of Life Sciences, University of Nottingham, University Park, NG7 2RD Nottingham, UK.
| | | | - Matthias Brock
- Fungal Genetics and Biology Groups, School of Life Sciences, University of Nottingham, University Park, NG7 2RD Nottingham, UK.
| | - David Cánovas
- Department of Genetics, Faculty of Biology, University of Sevilla, 41012, Spain.
| | - Chiara Dall'Asta
- Department of Food and Drug, University of Parma, Via G.P. Usberti 27/A, 43124 Parma, Italy.
| | - Doris Marko
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090 Vienna, Austria.
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Nongonierma AB, Dellafiora L, Paolella S, Galaverna G, Cozzini P, FitzGerald RJ. In Silico Approaches Applied to the Study of Peptide Analogs of Ile-Pro-Ile in Relation to Their Dipeptidyl Peptidase IV Inhibitory Properties. Front Endocrinol (Lausanne) 2018; 9:329. [PMID: 29963014 PMCID: PMC6010526 DOI: 10.3389/fendo.2018.00329] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 05/31/2018] [Indexed: 12/17/2022] Open
Abstract
Inhibition of dipeptidyl peptidase IV (DPP-IV) may be exploited to maintain the incretin effect during the postprandial phase. As a result, glycemic regulation and energy homeostasis may be improved. Food protein-derived peptides have been identified as natural agents capable of inhibiting DPP-IV. Ile-Pro-Ile is the most potent DPP-IV inhibitory peptide identified to date. A minimum analog peptide set approach was used to study peptide analogs of Ile-Pro-Ile. The DPP-IV half maximal inhibitory concentration (IC50) values of the 25 peptides evaluated ranged from 3.9 ± 1.0 µM (Ile-Pro-Ile) to 247.0 ± 32.7 µM (Phe-Pro-Phe). The presence of Pro at position 2 of tripeptides was required to achieve high DPP-IV inhibition. Most peptides behaved as competitive inhibitors of DPP-IV with the exception of peptides with a N-terminal Trp, which were mixed-type inhibitors. While possessing the structure of preferred DPP-IV substrates, most peptides studied were particularly stable during 30 min incubation with DPP-IV. Molecular docking revealed that Ile-Pro-Ile and its peptide analogs interacted in a very similar manner with the active site of DPP-IV. In addition, no correlation was found between the Hydropathic INTeraction score and the DPP-IV IC50 values of the peptides studied. This outcome suggests that free energy may not be directly responsible for enzyme inhibition by the peptides. Finally, novel DPP-IV inhibitory peptides were identified using the strategy employed herein. These results may be relevant for the development of food protein-derived peptides with serum glucose lowering and food intake regulatory properties in humans.
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Affiliation(s)
- Alice B. Nongonierma
- Department of Biological Sciences and Food for Health Ireland (FHI), University of Limerick, Limerick, Ireland
| | | | - Sara Paolella
- Department of Biological Sciences and Food for Health Ireland (FHI), University of Limerick, Limerick, Ireland
| | | | - Pietro Cozzini
- Food and Drug Department, University of Parma, Parma, Italy
| | - Richard J. FitzGerald
- Department of Biological Sciences and Food for Health Ireland (FHI), University of Limerick, Limerick, Ireland
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Righetti L, Dellafiora L, Cavanna D, Rolli E, Galaverna G, Bruni R, Suman M, Dall’Asta C. Identification of acetylated derivatives of zearalenone as novel plant metabolites by high-resolution mass spectrometry. Anal Bioanal Chem 2018; 410:5583-5592. [DOI: 10.1007/s00216-018-1066-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 03/08/2018] [Accepted: 04/05/2018] [Indexed: 11/27/2022]
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49
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Sacre L, O'Flaherty DK, Archambault P, Copp W, Peslherbe GH, Muchall HM, Wilds CJ. O 4 -Alkylated-2-Deoxyuridine Repair by O 6 -Alkylguanine DNA Alkyltransferase is Augmented by a C5-Fluorine Modification. Chembiochem 2018; 19:575-582. [PMID: 29243336 DOI: 10.1002/cbic.201700660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Indexed: 11/10/2022]
Abstract
Oligonucleotides containing various adducts, including ethyl, benzyl, 4-hydroxybutyl and 7-hydroxyheptyl groups, at the O4 atom of 5-fluoro-O4 -alkyl-2'-deoxyuridine were prepared by solid-phase synthesis. UV thermal denaturation studies demonstrated that these modifications destabilised the duplex by approximately 10 °C, relative to the control containing 5-fluoro-2'-deoxyuridine. Circular dichroism spectroscopy revealed that these modified duplexes all adopted a B-form DNA structure. O6 -Alkylguanine DNA alkyltransferase (AGT) from humans (hAGT) was most efficient at repair of the 5-fluoro-O4 -benzyl-2'-deoxyuridine adduct, whereas the thymidine analogue was refractory to repair. The Escherichia coli AGT variant (OGT) was also efficient at removing O4 -ethyl and benzyl adducts of 5-fluoro-2-deoxyuridine. Computational assessment of N1-methyl analogues of the O4 -alkylated nucleobases revealed that the C5-fluorine modification had an influence on reducing the electron density of the O4 -Cα bond, relative to thymine (C5-methyl) and uracil (C5-hydrogen). These results reveal the positive influence of the C5-fluorine atom on the repair of larger O4 -alkyl adducts to expand knowledge of the range of substrates able to be repaired by AGT.
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Affiliation(s)
- Lauralicia Sacre
- Department of Chemistry and Biochemistry and, Centre for Research in Molecular Modeling (CERMM), Concordia University, 7141 Sherbrooke St. West, Montréal, Québec, H4B 1R6, Canada
| | - Derek K O'Flaherty
- Department of Chemistry and Biochemistry and, Centre for Research in Molecular Modeling (CERMM), Concordia University, 7141 Sherbrooke St. West, Montréal, Québec, H4B 1R6, Canada.,Present address: Howard Hughes Medical Institute, Department of Molecular Biology and, Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA
| | - Philippe Archambault
- Department of Chemistry and Biochemistry and, Centre for Research in Molecular Modeling (CERMM), Concordia University, 7141 Sherbrooke St. West, Montréal, Québec, H4B 1R6, Canada
| | - William Copp
- Department of Chemistry and Biochemistry and, Centre for Research in Molecular Modeling (CERMM), Concordia University, 7141 Sherbrooke St. West, Montréal, Québec, H4B 1R6, Canada
| | - Gilles H Peslherbe
- Department of Chemistry and Biochemistry and, Centre for Research in Molecular Modeling (CERMM), Concordia University, 7141 Sherbrooke St. West, Montréal, Québec, H4B 1R6, Canada
| | - Heidi M Muchall
- Department of Chemistry and Biochemistry and, Centre for Research in Molecular Modeling (CERMM), Concordia University, 7141 Sherbrooke St. West, Montréal, Québec, H4B 1R6, Canada
| | - Christopher J Wilds
- Department of Chemistry and Biochemistry and, Centre for Research in Molecular Modeling (CERMM), Concordia University, 7141 Sherbrooke St. West, Montréal, Québec, H4B 1R6, Canada
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Computational and biological profile of boronic acids for the detection of bacterial serine- and metallo-β-lactamases. Sci Rep 2017; 7:17716. [PMID: 29255163 PMCID: PMC5735191 DOI: 10.1038/s41598-017-17399-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 11/16/2017] [Indexed: 12/21/2022] Open
Abstract
β-Lactamases (BLs) able to hydrolyze β-lactam antibiotics and more importantly the last resort carbapenems, represent a major mechanism of resistance in Gram-negative bacteria showing multi-drug or extensively drug resistant phenotypes. The early detection of BLs responsible of resistant infections is challenging: approaches aiming at the identification of new BLs inhibitors (BLI) can thus serve as the basis for the development of highly needed diagnostic tools. Starting from benzo-[b]-thiophene-2-boronic acid (BZB), a nanomolar inhibitor of AmpC β-lactamase (K i = 27 nM), we have identified and characterized a set of BZB analogues able to inhibit clinically-relevant β-lactamases, including AmpC, Extended-Spectrum BLs (ESBL), KPC- and OXA-type carbapenemases and metallo-β-lactamases (MBL). A multiligand set of boronic acid (BA) β-lactamase inhibitors was obtained using covalent molecular modeling, synthetic chemistry, enzyme kinetics and antibacterial susceptibility testing. Data confirmed the possibility to discriminate between clinically-relevant β-lactamases on the basis of their inhibition profile. Interestingly, this work also allowed the identification of potent KPC-2 and NDM-1 inhibitors able to potentiate the activity of cefotaxime (CTX) and ceftazidime (CAZ) against resistant clinical isolates (MIC reduction, 32-fold). Our results open the way to the potential use of our set of compounds as a diagnostic tool for the sensitive detection of clinically-relevant β-lactamases.
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