1
|
Gazzillo E, Colarusso E, Giordano A, Chini MG, Potenza M, Hofstetter RK, Iorizzi M, Werz O, Lauro G, Bifulco G. Repositioning of Small Molecules through the Inverse Virtual Screening in silico Tool: Case of Benzothiazole-Based Inhibitors of Soluble Epoxide Hydrolase (sEH). Chempluschem 2024:e202400234. [PMID: 38753468 DOI: 10.1002/cplu.202400234] [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: 03/28/2024] [Revised: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024]
Abstract
Computational techniques accelerate drug discovery by identifying bioactive compounds for specific targets, optimizing molecules with moderate activity, or facilitating the repositioning of inactive items onto new targets. Among them, the Inverse Virtual Screening (IVS) approach is aimed at the evaluation of one or a small set of molecules against a panel of targets for addressing target identification. In this work, a focused library of benzothiazole-based compounds was re-investigated by IVS. Four items, originally synthesized and tested on bromodomain-containing protein 9 (BRD9) but yielding poor binding, were critically re-analyzed, disclosing only a partial fit with 3D structure-based pharmacophore models, which, in the meanwhile, were developed for this target. Afterwards, these compounds were re-evaluated through IVS on a panel of proteins involved in inflammation and cancer, identifying soluble epoxide hydrolase (sEH) as a putative interacting target. Three items were subsequently confirmed as able to interfere with sEH activity, leading to inhibition percentages spanning from 70 % up to 30 % when tested at 10 μM. Finally, one benzothiazole-based compound emerged as the most promising inhibitor featuring an IC50 in the low micromolar range (IC50=6.62±0.13 μM). Our data confirm IVS as a predictive tool for accelerating the target identification and repositioning processes.
Collapse
Affiliation(s)
- Erica Gazzillo
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
- PhD Program in Drug Discovery and Development, Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
| | - Ester Colarusso
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
| | - Assunta Giordano
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
- Institute of Biomolecular Chemistry (ICB), Consiglio Nazionale delle Ricerche (CNR), Via Campi Flegrei 34, Pozzuoli, I-80078, Italy
| | - Maria Giovanna Chini
- Department of Biosciences and Territory, University of Molise, C.da Fonte Lappone, Pesche, 86090, Italy
| | - Marianna Potenza
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
| | - Robert Klaus Hofstetter
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich Schiller University, Philosophenweg 14, Jena, 07743, Germany
| | - Maria Iorizzi
- Department of Biosciences and Territory, University of Molise, C.da Fonte Lappone, Pesche, 86090, Italy
| | - Oliver Werz
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich Schiller University, Philosophenweg 14, Jena, 07743, Germany
| | - Gianluigi Lauro
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
| | - Giuseppe Bifulco
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano, 84084, Italy
| |
Collapse
|
2
|
De Vita S, Chini MG, Bifulco G, Lauro G. Target identification by structure-based computational approaches: Recent advances and perspectives. Bioorg Med Chem Lett 2023; 83:129171. [PMID: 36739998 DOI: 10.1016/j.bmcl.2023.129171] [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: 08/05/2022] [Revised: 12/15/2022] [Accepted: 02/01/2023] [Indexed: 02/05/2023]
Abstract
The use of computational techniques in the early stages of drug discovery has recently experienced a boost, especially in the target identification step. Finding the biological partner(s) for new or existing synthetic and/or natural compounds by "wet" approaches may be challenging; therefore, preliminary in silico screening is even more recommended. After a brief overview of some of the most known target identification techniques, recent advances in structure-based computational approaches for target identification are reported in this digest, focusing on Inverse Virtual Screening and its recent applications. Moreover, future perspectives concerning the use of such methodologies, coupled or not with other approaches, are analyzed.
Collapse
Affiliation(s)
- Simona De Vita
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano (SA), Italy
| | - Maria Giovanna Chini
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche (IS), Italy
| | - Giuseppe Bifulco
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano (SA), Italy.
| | - Gianluigi Lauro
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano (SA), Italy.
| |
Collapse
|
3
|
Di Micco S, Rahimova R, Sala M, Scala MC, Vivenzio G, Musella S, Andrei G, Remans K, Mammri L, Snoeck R, Bifulco G, Di Matteo F, Vestuto V, Campiglia P, Márquez JA, Fasano A. Rational design of the zonulin inhibitor AT1001 derivatives as potential anti SARS-CoV-2. Eur J Med Chem 2022; 244:114857. [PMID: 36332548 PMCID: PMC9579148 DOI: 10.1016/j.ejmech.2022.114857] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/26/2022] [Accepted: 10/14/2022] [Indexed: 11/28/2022]
Abstract
Although vaccines are greatly mitigating the worldwide pandemic diffusion of SARS-Cov-2, therapeutics should provide many distinct advantages as complementary approach to control the viral spreading. Here, we report the development of new tripeptide derivatives of AT1001 against SARS-CoV-2 Mpro. By molecular modeling, a small compound library was rationally designed and filtered for enzymatic inhibition through FRET assay, leading to the identification of compound 4. X-ray crystallography studies provide insights into its binding mode and confirm the formation of a covalent bond with Mpro C145. In vitro antiviral tests indicate the improvement of biological activity of 4 respect to AT1001. In silico and X-ray crystallography analysis led to 58, showing a promising activity against three SARS-CoV-2 variants and a valuable safety in Vero cells and human embryonic lung fibroblasts. The drug tolerance was also confirmed by in vivo studies, along with pharmacokinetics evaluation. In summary, 58 could pave the way to develop a clinical candidate for intranasal administration.
Collapse
Affiliation(s)
- Simone Di Micco
- European Biomedical Research Institute of Salerno (EBRIS), Via Salvatore de Renzi 50, 84125, Salerno, Italy,Corresponding author
| | - Rahila Rahimova
- European Molecular Biology Laboratory, EMBL, 71 Avenue des Martyrs, CS 90181, Grenoble Cedex 9, 38042, France
| | - Marina Sala
- Dipartimento di Farmacia, Università Degli Studi di Salerno, Via Giovanni Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Maria C. Scala
- Dipartimento di Farmacia, Università Degli Studi di Salerno, Via Giovanni Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Giovanni Vivenzio
- Dipartimento di Farmacia, Università Degli Studi di Salerno, Via Giovanni Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Simona Musella
- European Biomedical Research Institute of Salerno (EBRIS), Via Salvatore de Renzi 50, 84125, Salerno, Italy,Dipartimento di Farmacia, Università Degli Studi di Salerno, Via Giovanni Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Graciela Andrei
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000, Leuven, Belgium
| | - Kim Remans
- European Molecular Biology Laboratory, EMBL, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Léa Mammri
- European Molecular Biology Laboratory, EMBL, 71 Avenue des Martyrs, CS 90181, Grenoble Cedex 9, 38042, France
| | - Robert Snoeck
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000, Leuven, Belgium
| | - Giuseppe Bifulco
- Dipartimento di Farmacia, Università Degli Studi di Salerno, Via Giovanni Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Francesca Di Matteo
- Dipartimento di Farmacia, Università Degli Studi di Salerno, Via Giovanni Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Vincenzo Vestuto
- Dipartimento di Farmacia, Università Degli Studi di Salerno, Via Giovanni Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Pietro Campiglia
- European Biomedical Research Institute of Salerno (EBRIS), Via Salvatore de Renzi 50, 84125, Salerno, Italy,Dipartimento di Farmacia, Università Degli Studi di Salerno, Via Giovanni Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - José A. Márquez
- European Molecular Biology Laboratory, EMBL, 71 Avenue des Martyrs, CS 90181, Grenoble Cedex 9, 38042, France,ALPX S.A.S. 71, Avenue des Martyrs, France
| | - Alessio Fasano
- European Biomedical Research Institute of Salerno (EBRIS), Via Salvatore de Renzi 50, 84125, Salerno, Italy,Mucosal Immunology and Biology Research Center, Massachusetts General Hospital–Harvard Medical School, Boston, MA, 02114, USA
| |
Collapse
|
4
|
Di Micco S, Terracciano S, Pierri M, Cantone V, Liening S, König S, Garscha U, Hofstetter RK, Koeberle A, Werz O, Bruno I, Bifulco G. Identification of 2,4-Dinitro-Biphenyl-Based Compounds as MAPEG Inhibitors. ChemMedChem 2022; 17:e202200327. [PMID: 36111583 PMCID: PMC9827972 DOI: 10.1002/cmdc.202200327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/15/2022] [Indexed: 01/14/2023]
Abstract
We identified 2,4-dinitro-biphenyl-based compounds as new inhibitors of leukotriene C4 synthase (LTC4 S) and 5-lipoxygenase-activating protein (FLAP), both members of the "Membrane Associated Proteins in Eicosanoid and Glutathione metabolism" (MAPEG) family involved in the biosynthesis of pro-inflammatory eicosanoids. By molecular docking we evaluated the putative binding against the targets of interest, and by applying cell-free and cell-based assays we assessed the inhibition of LTC4 S and FLAP by the small molecules at low micromolar concentrations. The present results integrate the previously observed inhibitory profile of the tested compounds against another MAPEG member, i. e., microsomal prostaglandin E2 synthase (mPGES)-1, suggesting that the 2,4-dinitro-biphenyl scaffold is a suitable molecular platform for a multitargeting approach to modulate pro-inflammatory mediators in inflammation and cancer treatment.
Collapse
Affiliation(s)
- Simone Di Micco
- European Biomedical Research Institute of Salerno (EBRIS)Via Salvatore De Renzi 5084125SalernoItaly
| | - Stefania Terracciano
- Department of PharmacyUniversity of SalernoVia Giovanni Paolo II 13284084FiscianoSAItaly
| | - Martina Pierri
- Department of PharmacyUniversity of SalernoVia Giovanni Paolo II 13284084FiscianoSAItaly
| | - Vincenza Cantone
- Department of PharmacyUniversity of SalernoVia Giovanni Paolo II 13284084FiscianoSAItaly,Department of Pharmaceutical/Medicinal ChemistryInstitute of PharmacyFriedrich-Schiller-University JenaPhilosophenweg 147743JenaGermany
| | - Stefanie Liening
- Department of Pharmaceutical/Medicinal ChemistryInstitute of PharmacyFriedrich-Schiller-University JenaPhilosophenweg 147743JenaGermany
| | - Stefanie König
- Department of Pharmaceutical/Medicinal ChemistryInstitute of PharmacyFriedrich-Schiller-University JenaPhilosophenweg 147743JenaGermany
| | - Ulrike Garscha
- Department of Pharmaceutical/Medicinal ChemistryInstitute of PharmacyFriedrich-Schiller-University JenaPhilosophenweg 147743JenaGermany
| | - Robert Klaus Hofstetter
- Department of Pharmaceutical/Medicinal ChemistryInstitute of PharmacyFriedrich-Schiller-University JenaPhilosophenweg 147743JenaGermany
| | - Andreas Koeberle
- Michael Popp Research InstituteUniversity of InnsbruckMitterweg 246020InnsbruckAustria
| | - Oliver Werz
- Department of Pharmaceutical/Medicinal ChemistryInstitute of PharmacyFriedrich-Schiller-University JenaPhilosophenweg 147743JenaGermany
| | - Ines Bruno
- Department of PharmacyUniversity of SalernoVia Giovanni Paolo II 13284084FiscianoSAItaly
| | - Giuseppe Bifulco
- Department of PharmacyUniversity of SalernoVia Giovanni Paolo II 13284084FiscianoSAItaly
| |
Collapse
|
5
|
Drug Discovery of Plausible Lead Natural Compounds That Target the Insulin Signaling Pathway: Bioinformatics Approaches. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:2832889. [PMID: 35356248 PMCID: PMC8958086 DOI: 10.1155/2022/2832889] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/16/2022] [Accepted: 02/09/2022] [Indexed: 12/11/2022]
Abstract
The growing smooth talk in the field of natural compounds is due to the ancient and current interest in herbal medicine and their potentially positive effects on health. Dozens of antidiabetic natural compounds were reported and tested in vivo, in silico, and in vitro. The role of these natural compounds, their actions on the insulin signaling pathway, and the stimulation of the glucose transporter-4 (GLUT4) insulin-responsive translocation to the plasma membrane (PM) are all crucial in the treatment of diabetes and insulin resistance. In this review, we collected and summarized a group of available in vivo and in vitro studies which targeted isolated phytochemicals with possible antidiabetic activity. Moreover, the in silico docking of natural compounds with some of the insulin signaling cascade key proteins is also summarized based on the current literature. In this review, hundreds of recent studies on pure natural compounds that alleviate type II diabetes mellitus (type II DM) were revised. We focused on natural compounds that could potentially regulate blood glucose and stimulate GLUT4 translocation through the phosphoinositide 3-kinase (PI3K)/protein kinase B (Akt) pathway. On attempt to point out potential new natural antidiabetic compounds, this review also focuses on natural ingredients that were shown to interact with proteins in the insulin signaling pathway in silico, regardless of their in vitro/in vivo antidiabetic activity. We invite interested researchers to test these compounds as potential novel type II DM drugs and explore their therapeutic mechanisms.
Collapse
|
6
|
Esposito C, Johansson C, Di Micco S. Editorial: Novel Strategies in Drug Development Against Multifactorial Diseases. Front Chem 2022; 10:838063. [PMID: 35141200 PMCID: PMC8819009 DOI: 10.3389/fchem.2022.838063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/04/2022] [Indexed: 11/28/2022] Open
Affiliation(s)
- Cinzia Esposito
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Catrine Johansson
- Oxford NIHR BRU, Botnar Research Centre, Oxford Centre for Translational Myeloma Research, Oxford University, Oxford, United Kingdom
| | - Simone Di Micco
- European Biomedical Research Institute of Salerno (EBRIS), Salerno, Italy
- *Correspondence: Simone Di Micco,
| |
Collapse
|
7
|
Zouboulis VA, Zouboulis KC, Zouboulis CC. Hidradenitis Suppurativa and Comorbid Disorder Biomarkers, Druggable Genes, New Drugs and Drug Repurposing-A Molecular Meta-Analysis. Pharmaceutics 2021; 14:pharmaceutics14010044. [PMID: 35056940 PMCID: PMC8779519 DOI: 10.3390/pharmaceutics14010044] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/20/2021] [Accepted: 12/23/2021] [Indexed: 12/28/2022] Open
Abstract
Chronic inflammation and dysregulated epithelial differentiation, especially of hair follicle keratinocytes, have been suggested as the major pathogenetic pathways of hidradenitis suppurativa/acne inversa (HS). On the other hand, obesity and metabolic syndrome have additionally been considered as an important risk factor. With adalimumab, a drug has already been approved and numerous other compounds are in advanced-stage clinical studies. A systematic review was conducted to detect and corroborate HS pathogenetic mechanisms at the molecular level and identify HS molecular markers. The obtained data were used to confirm studied and off-label administered drugs and to identify additional compounds for drug repurposing. A robust, strongly associated group of HS biomarkers was detected. The triad of HS pathogenesis, namely upregulated inflammation, altered epithelial differentiation and dysregulated metabolism/hormone signaling was confirmed, the molecular association of HS with certain comorbid disorders, such as inflammatory bowel disease, arthritis, type I diabetes mellitus and lipids/atherosclerosis/adipogenesis was verified and common biomarkers were identified. The molecular suitability of compounds in clinical studies was confirmed and 31 potential HS repurposing drugs, among them 10 drugs already launched for other disorders, were detected. This systematic review provides evidence for the importance of molecular studies to advance the knowledge regarding pathogenesis, future treatment and biomarker-supported clinical course follow-up in HS.
Collapse
Affiliation(s)
- Viktor A. Zouboulis
- Faculty of Medicine, Universitaetsklinikum Hamburg-Eppendorf (UKE), 20251 Hamburg, Germany;
| | - Konstantin C. Zouboulis
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH) Zurich, 8092 Zurich, Switzerland;
| | - Christos C. Zouboulis
- Departments of Dermatology, Venereology, Allergology and Immunology, Dessau Medical Center, Brandenburg Medical School Theodor Fontane and Faculty of Health Sciences Brandenburg, 06847 Dessau, Germany
- Correspondence: ; Tel.: +49-340-5014000
| |
Collapse
|
8
|
Di Micco S, Musella S, Sala M, Scala MC, Andrei G, Snoeck R, Bifulco G, Campiglia P, Fasano A. Peptide Derivatives of the Zonulin Inhibitor Larazotide (AT1001) as Potential Anti SARS-CoV-2: Molecular Modelling, Synthesis and Bioactivity Evaluation. Int J Mol Sci 2021; 22:ijms22179427. [PMID: 34502335 PMCID: PMC8431481 DOI: 10.3390/ijms22179427] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 12/25/2022] Open
Abstract
A novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been identified as the pathogen responsible for the outbreak of a severe, rapidly developing pneumonia (Coronavirus disease 2019, COVID-19). The virus enzyme, called 3CLpro or main protease (Mpro), is essential for viral replication, making it a most promising target for antiviral drug development. Recently, we adopted the drug repurposing as appropriate strategy to give fast response to global COVID-19 epidemic, by demonstrating that the zonulin octapeptide inhibitor AT1001 (Larazotide acetate) binds Mpro catalytic domain. Thus, in the present study we tried to investigate the antiviral activity of AT1001, along with five derivatives, by cell-based assays. Our results provide with the identification of AT1001 peptide molecular framework for lead optimization step to develop new generations of antiviral agents of SARS-CoV-2 with an improved biological activity, expanding the chance for success in clinical trials.
Collapse
Affiliation(s)
- Simone Di Micco
- European Biomedical Research Institute of Salerno (EBRIS), Via Salvatore de Renzi 50, 84125 Salerno, Italy; (S.M.); (A.F.)
- Correspondence:
| | - Simona Musella
- European Biomedical Research Institute of Salerno (EBRIS), Via Salvatore de Renzi 50, 84125 Salerno, Italy; (S.M.); (A.F.)
| | - Marina Sala
- Dipartimento di Farmacia, Università degli Studi di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy; (M.S.); (M.C.S.); (G.B.); (P.C.)
| | - Maria C. Scala
- Dipartimento di Farmacia, Università degli Studi di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy; (M.S.); (M.C.S.); (G.B.); (P.C.)
| | - Graciela Andrei
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (G.A.); (R.S.)
| | - Robert Snoeck
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (G.A.); (R.S.)
| | - Giuseppe Bifulco
- Dipartimento di Farmacia, Università degli Studi di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy; (M.S.); (M.C.S.); (G.B.); (P.C.)
| | - Pietro Campiglia
- Dipartimento di Farmacia, Università degli Studi di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy; (M.S.); (M.C.S.); (G.B.); (P.C.)
| | - Alessio Fasano
- European Biomedical Research Institute of Salerno (EBRIS), Via Salvatore de Renzi 50, 84125 Salerno, Italy; (S.M.); (A.F.)
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital–Harvard Medical School, Boston, MA 02114, USA
| |
Collapse
|
9
|
Chini MG, Lauro G, Bifulco G. Addressing the Target Identification and Accelerating the Repositioning of Anti‐Inflammatory/Anti‐Cancer Organic Compounds by Computational Approaches. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100245] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Maria Giovanna Chini
- Department of Biosciences and Territory University of Molise C.da Fonte Lappone 86090 Pesche (IS) Italy
| | - Gianluigi Lauro
- Department of Pharmacy University of Salerno Via Giovanni Paolo II 132 84084 Fisciano (SA) Italy
| | - Giuseppe Bifulco
- Department of Pharmacy University of Salerno Via Giovanni Paolo II 132 84084 Fisciano (SA) Italy
| |
Collapse
|
10
|
Di Micco S, Terracciano S, Ruggiero D, Potenza M, Vaccaro MC, Fischer K, Werz O, Bruno I, Bifulco G. Identification of 2-(thiophen-2-yl)acetic Acid-Based Lead Compound for mPGES-1 Inhibition. Front Chem 2021; 9:676631. [PMID: 34046398 PMCID: PMC8144515 DOI: 10.3389/fchem.2021.676631] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 04/07/2021] [Indexed: 11/13/2022] Open
Abstract
We report the implementation of our in silico/synthesis pipeline by targeting the glutathione-dependent enzyme mPGES-1, a valuable macromolecular target in both cancer therapy and inflammation therapy. Specifically, by using a virtual fragment screening approach of aromatic bromides, straightforwardly modifiable by the Suzuki-Miyaura reaction, we identified 3-phenylpropanoic acid and 2-(thiophen-2-yl)acetic acid to be suitable chemical platforms to develop tighter mPGES-1 inhibitors. Among these, compounds 1c and 2c showed selective inhibitory activity against mPGES-1 in the low micromolar range in accordance with molecular modeling calculations. Moreover, 1c and 2c exhibited interesting IC50 values on A549 cell lines compared to CAY10526, selected as reference compound. The most promising compound 2c induced the cycle arrest in the G0/G1 phase at 24 h of exposure, whereas at 48 and 72 h, it caused an increase of subG0/G1 fraction, suggesting an apoptosis/necrosis effect.
Collapse
Affiliation(s)
- Simone Di Micco
- European Biomedical Research Institute of Salerno (EBRIS), Salerno, Italy
| | | | - Dafne Ruggiero
- Dipartimento di Farmacia, University degli Studi di Salerno, Fisciano, Italy
| | - Marianna Potenza
- Dipartimento di Farmacia, University degli Studi di Salerno, Fisciano, Italy
| | - Maria C Vaccaro
- Dipartimento di Farmacia, University degli Studi di Salerno, Fisciano, Italy
| | - Katrin Fischer
- Institute of Pharmacy, Friedrich-Schiller-University Jena, Jena, Germany
| | - Oliver Werz
- Institute of Pharmacy, Friedrich-Schiller-University Jena, Jena, Germany
| | - Ines Bruno
- Dipartimento di Farmacia, University degli Studi di Salerno, Fisciano, Italy
| | - Giuseppe Bifulco
- Dipartimento di Farmacia, University degli Studi di Salerno, Fisciano, Italy
| |
Collapse
|
11
|
Srinivas R, Verma N, Kraka E, Larson EC. Deep Learning-Based Ligand Design Using Shared Latent Implicit Fingerprints from Collaborative Filtering. J Chem Inf Model 2021; 61:2159-2174. [PMID: 33899481 DOI: 10.1021/acs.jcim.0c01355] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In their previous work, Srinivas et al. [ J. Cheminf. 2018, 10, 56] have shown that implicit fingerprints capture ligands and proteins in a shared latent space, typically for the purposes of virtual screening with collaborative filtering models applied on known bioactivity data. In this work, we extend these implicit fingerprints/descriptors using deep learning techniques to translate latent descriptors into discrete representations of molecules (SMILES), without explicitly optimizing for chemical properties. This allows the design of new compounds based upon the latent representation of nearby proteins, thereby encoding druglike properties including binding affinities to known proteins. The implicit descriptor method does not require any fingerprint similarity search, which makes the method free of any bias arising from the empirical nature of the fingerprint models [Srinivas, R.; J. Cheminf. 2018, 10, 56]. We evaluate the properties of the potentially novel drugs generated by our approach using physical properties of druglike molecules and chemical complexity. Additionally, we analyze the reliability of the biological activity of the new compounds generated using this method by employing models of protein-ligand interaction, which assists in assessing the potential binding affinity of the designed compounds. We find that the generated compounds exhibit properties of chemically feasible compounds and are predicted to be excellent binders to known proteins. Furthermore, we also analyze the diversity of compounds created using the Tanimoto distance and conclude that there is a wide diversity in the generated compounds.
Collapse
Affiliation(s)
- Raghuram Srinivas
- Department of Computer Science, Southern Methodist University, Dallas, Texas 75205, United States
| | - Niraj Verma
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75205, United States
| | - Elfi Kraka
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75205, United States
| | - Eric C Larson
- Department of Computer Science, Southern Methodist University, Dallas, Texas 75205, United States
| |
Collapse
|
12
|
Di Micco S, Musella S, Scala MC, Sala M, Campiglia P, Bifulco G, Fasano A. In silico Analysis Revealed Potential Anti-SARS-CoV-2 Main Protease Activity by the Zonulin Inhibitor Larazotide Acetate. Front Chem 2021; 8:628609. [PMID: 33520943 PMCID: PMC7843458 DOI: 10.3389/fchem.2020.628609] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 12/15/2020] [Indexed: 12/11/2022] Open
Abstract
The most severe outcome of COVID-19 infection is the development of interstitial pneumonia causing acute lung injury (ALI) and/or acute respiratory distress syndrome (ARDS), both responsible for the infected patients' mortality. ALI and ARDS are characterized by a leakage of plasma components into the lungs, compromising their ability to expand and optimally engage in gas exchange with blood, resulting in respiratory failure. We have previously reported that zonulin, a protein dictating epithelial and endothelial permeability in several districts, including the airways, is involved in ALI pathogenesis in mouse models, and that its peptide inhibitor Larazotide acetate (also called AT1001) ameliorated ALI and subsequent mortality by decreasing mucosal permeability to fluid and extravasation of neutrophils into the lungs. With the recent crystallographic resolution of the SARS-CoV-2 main protease (Mpro), an enzyme fundamental in the viral lifecycle, bound to peptidomimetic inhibitors N3 and 13b, we were able to perform molecular modeling investigation showing that AT1001 presents structural motifs similar to co-crystallized ligands. Specifically, molecular docking, MM-GBSA-based predictions and molecular dynamics showed that AT1001 docks extremely well in the Mpro catalytic domain through a global turn conformational arrangement without any unfavorable steric hindrance. Finally, we have observed that AT1001 can be superimposed onto the crystallized structures of N3 and 13b, establishing a higher number of interactions and accordingly a tighter binding. In vitro studies confirmed AT1001 anti-Mpro and preliminary investigation indicted an anti-viral activity. Combined, these studies suggest that AT1001, besides its well-demonstrated effect in ameliorating mucosal permeability in ALI/ARDS, may also exert a direct anti-SARS-CoV-2 effect by blocking the Mpro. AT1001 has been used extensively in a variety of animal models of ALI demonstrating robust safety and efficacy; it is currently in phase 3 trials in celiac subjects showing strong safety and efficacy profiles. We therefore propose its use as a specific anti-SARS-CoV-2 multitargeting treatment for the current pandemic.
Collapse
Affiliation(s)
- Simone Di Micco
- European Biomedical Research Institute of Salerno (EBRIS), Salerno, Italy
| | - Simona Musella
- European Biomedical Research Institute of Salerno (EBRIS), Salerno, Italy
| | - Maria C Scala
- Department of Pharmacy, University of Salerno, Salerno, Italy
| | - Marina Sala
- Department of Pharmacy, University of Salerno, Salerno, Italy
| | - Pietro Campiglia
- European Biomedical Research Institute of Salerno (EBRIS), Salerno, Italy.,Department of Pharmacy, University of Salerno, Salerno, Italy
| | | | - Alessio Fasano
- European Biomedical Research Institute of Salerno (EBRIS), Salerno, Italy.,Mucosal Immunology and Biology Research Center, Massachusetts General Hospital-Harvard Medical School, Boston, MA, United States
| |
Collapse
|
13
|
Di Micco S, Masullo M, Bandak AF, Berger JM, Riccio R, Piacente S, Bifulco G. Garcinol and Related Polyisoprenylated Benzophenones as Topoisomerase II Inhibitors: Biochemical and Molecular Modeling Studies. JOURNAL OF NATURAL PRODUCTS 2019; 82:2768-2779. [PMID: 31618025 DOI: 10.1021/acs.jnatprod.9b00382] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Garcinol, a polyisoprenylated benzophenone isolated from Garcinia genus, has been reported to inhibit eukaryotic topoisomerase I and topoisomerase II at concentrations comparable to that of etoposide (∼25-100 μM). With the aim to clarify the underlying molecular mechanisms by which garcinol inhibits human topoisomerase IIα and topoisomerase IIβ, biochemical assays along with molecular docking and molecular dynamics studies were carried out on garcinol and six congeners. The biochemical results revealed that garcinol derivatives appear to act as catalytic inhibitors of topoisomerase II and to inhibit ATP hydrolysis by topoisomerase II via some form of mixed inhibition. The computational investigation identified the structural elements responsible for binding to the biological target and also provided information for the eventual design of more selective and potent analogues. Collectively, our data suggest that garcinol-type agents may bind to the DNA binding surface and/or ATP domain of type II topoisomerases to antagonize function.
Collapse
Affiliation(s)
- Simone Di Micco
- European Biomedical Research Institute of Salerno (EBRIS) , Via Salvatore De Renzi 50 , 84125 Salerno , Italy
- Dipartimento di Farmacia , Università degli Studi di Salerno , Via Giovanni Paolo II 132 , 84084 Fisciano (SA) , Italy
| | - Milena Masullo
- Dipartimento di Farmacia , Università degli Studi di Salerno , Via Giovanni Paolo II 132 , 84084 Fisciano (SA) , Italy
| | - Afif F Bandak
- Department of Biophysics and Biophysical Chemistry , Johns Hopkins University School of Medicine , 725 N. Wolfe Street, WBSB 713 , Baltimore , Maryland 21205 , United States
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry , Johns Hopkins University School of Medicine , 725 N. Wolfe Street, WBSB 713 , Baltimore , Maryland 21205 , United States
| | - Raffaele Riccio
- Dipartimento di Farmacia , Università degli Studi di Salerno , Via Giovanni Paolo II 132 , 84084 Fisciano (SA) , Italy
| | - Sonia Piacente
- Dipartimento di Farmacia , Università degli Studi di Salerno , Via Giovanni Paolo II 132 , 84084 Fisciano (SA) , Italy
| | - Giuseppe Bifulco
- Dipartimento di Farmacia , Università degli Studi di Salerno , Via Giovanni Paolo II 132 , 84084 Fisciano (SA) , Italy
| |
Collapse
|
14
|
Giordano A, Forte G, Terracciano S, Russo A, Sala M, Scala MC, Johansson C, Oppermann U, Riccio R, Bruno I, Di Micco S. Identification of the 2-Benzoxazol-2-yl-phenol Scaffold as New Hit for JMJD3 Inhibition. ACS Med Chem Lett 2019; 10:601-605. [PMID: 30996803 DOI: 10.1021/acsmedchemlett.8b00589] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/25/2019] [Indexed: 12/11/2022] Open
Abstract
JMJD3 is a member of the KDM6 subfamily and catalyzes the demethylation of lysine 27 on histone H3 (H3K27). This protein was identified as a useful tool in understanding the role of epigenetics in inflammatory conditions and in cancer as well. Guided by a virtual fragment screening approach, we identified the benzoxazole scaffold as a new hit suitable for the development of tighter JMJD3 inhibitors. Compounds were synthesized by a microwave-assisted one-pot reaction under catalyst and solvent-free conditions. Among these, compound 8 presented the highest inhibitory activity (IC50 = 1.22 ± 0.22 μM) in accordance with molecular modeling calculations. Moreover, 8 induced the cycle arrest in S-phase on A375 melanoma cells.
Collapse
Affiliation(s)
- Assunta Giordano
- Institute of Biomolecular Chemistry (ICB), Consiglio Nazionale delle Ricerche (CNR), Via Campi Flegrei 34, I-80078 Pozzuoli, Napoli, Italy
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, I-84084 Fisciano, Salerno, Italy
| | - Giovanni Forte
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, I-84084 Fisciano, Salerno, Italy
| | - Stefania Terracciano
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, I-84084 Fisciano, Salerno, Italy
| | - Alessandra Russo
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, I-84084 Fisciano, Salerno, Italy
| | - Marina Sala
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, I-84084 Fisciano, Salerno, Italy
| | - Maria C. Scala
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, I-84084 Fisciano, Salerno, Italy
| | - Catrine Johansson
- Botnar Research Centre, Oxford NIHR BRU, Oxford University, Oxford Centre for Translational Myeloma Research, Oxford, OX3 7LD, U.K
| | - Udo Oppermann
- Botnar Research Centre, Oxford NIHR BRU, Oxford University, Oxford Centre for Translational Myeloma Research, Oxford, OX3 7LD, U.K
| | - Raffaele Riccio
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, I-84084 Fisciano, Salerno, Italy
| | - Ines Bruno
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, I-84084 Fisciano, Salerno, Italy
| | - Simone Di Micco
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, I-84084 Fisciano, Salerno, Italy
| |
Collapse
|
15
|
Identification of an indol-based multi-target kinase inhibitor through phenotype screening and target fishing using inverse virtual screening approach. Eur J Med Chem 2019; 167:61-75. [DOI: 10.1016/j.ejmech.2019.01.066] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 01/25/2019] [Accepted: 01/27/2019] [Indexed: 12/23/2022]
|
16
|
GNS HS, GR S, Murahari M, Krishnamurthy M. An update on Drug Repurposing: Re-written saga of the drug’s fate. Biomed Pharmacother 2019; 110:700-716. [DOI: 10.1016/j.biopha.2018.11.127] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 11/16/2018] [Accepted: 11/27/2018] [Indexed: 12/20/2022] Open
|
17
|
Khalfaoui A, Chini MG, Bouheroum M, Belaabed S, Lauro G, Terracciano S, Vaccaro MC, Bruno I, Benayache S, Mancini I, Bifulco G. Glucopyranosylbianthrones from the Algerian Asphodelus tenuifolius: Structural Insights and Biological Evaluation on Melanoma Cancer Cells. JOURNAL OF NATURAL PRODUCTS 2018; 81:1786-1794. [PMID: 30063349 DOI: 10.1021/acs.jnatprod.8b00234] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Two new glucopyranosylbianthrones (1 and 2) were isolated from the aerial part of the plant Asphodelus tenuifolius, collected in Southwest Algeria. The 2D structures of 1 and 2 were defined by NMR analysis, HRESIMS data, and comparison with literature data. The comparison of experimental and calculated electronic circular dichroism and NMR data led to characterization of the ( M) and ( P) atropisomeric forms of the glucopyranosylbianthrones, asphodelins (1) and (2), respectively. The in vitro activities of these two metabolites were evaluated in human melanoma A375 cells, and both the compounds inhibited cell proliferation in a concentration-dependent manner, with IC50 values of 20.6 ± 0.8 and 23.2 ± 1.1 μM, respectively. Considering their biological profile, an inverse virtual screening approach was employed to identify and suggest putative anticancer interacting targets.
Collapse
Affiliation(s)
- Ayoub Khalfaoui
- Department of Chemistry, Research Unit, Development of Natural Resources, Bioactive Molecules, Physicochemical and Biological Analysis , University Mentouri Constantine , Route Ain ElBey , 25000 , Constantine , Algeria
| | - Maria G Chini
- Department of Pharmacy , University of Salerno , Via Giovanni Paolo II 132 , 84084 Fisciano ( SA ), Italy
| | - Mohamed Bouheroum
- Department of Chemistry, Research Unit, Development of Natural Resources, Bioactive Molecules, Physicochemical and Biological Analysis , University Mentouri Constantine , Route Ain ElBey , 25000 , Constantine , Algeria
| | - Soumia Belaabed
- Department of Chemistry, Research Unit, Development of Natural Resources, Bioactive Molecules, Physicochemical and Biological Analysis , University Mentouri Constantine , Route Ain ElBey , 25000 , Constantine , Algeria
| | - Gianluigi Lauro
- Department of Pharmacy , University of Salerno , Via Giovanni Paolo II 132 , 84084 Fisciano ( SA ), Italy
| | - Stefania Terracciano
- Department of Pharmacy , University of Salerno , Via Giovanni Paolo II 132 , 84084 Fisciano ( SA ), Italy
| | - Maria C Vaccaro
- Department of Pharmacy , University of Salerno , Via Giovanni Paolo II 132 , 84084 Fisciano ( SA ), Italy
| | - Ines Bruno
- Department of Pharmacy , University of Salerno , Via Giovanni Paolo II 132 , 84084 Fisciano ( SA ), Italy
| | - Samir Benayache
- Department of Chemistry, Research Unit, Development of Natural Resources, Bioactive Molecules, Physicochemical and Biological Analysis , University Mentouri Constantine , Route Ain ElBey , 25000 , Constantine , Algeria
| | - Ines Mancini
- Department of Physics , University of Trento , Via Sommarive 14 , I-38123 Povo-Trento , Italy
| | - Giuseppe Bifulco
- Department of Pharmacy , University of Salerno , Via Giovanni Paolo II 132 , 84084 Fisciano ( SA ), Italy
| |
Collapse
|
18
|
Identification by Inverse Virtual Screening of magnolol-based scaffold as new tankyrase-2 inhibitors. Bioorg Med Chem 2018; 26:3953-3957. [DOI: 10.1016/j.bmc.2018.06.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 06/12/2018] [Accepted: 06/13/2018] [Indexed: 12/27/2022]
|