1
|
Barbaraci C, di Giacomo V, Maruca A, Patamia V, Rocca R, Dichiara M, Di Rienzo A, Cacciatore I, Cataldi A, Balaha M, Rapino M, Zagni C, Zampieri D, Pasquinucci L, Parenti C, Amata E, Rescifina A, Alcaro S, Marrazzo A. Discovery of first novel sigma/HDACi dual-ligands with a potent in vitro antiproliferative activity. Bioorg Chem 2023; 140:106794. [PMID: 37659146 DOI: 10.1016/j.bioorg.2023.106794] [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: 04/19/2023] [Revised: 08/09/2023] [Accepted: 08/15/2023] [Indexed: 09/04/2023]
Abstract
Designing and discovering compounds for dual-target inhibitors is challenging to synthesize new, safer, and more efficient drugs than single-target drugs, especially to treat multifactorial diseases such as cancer. The simultaneous regulation of multiple targets might represent an alternative synthetic approach to optimize patient compliance and tolerance, minimizing the risk of target-based drug resistance due to the modulation of a few targets. To this end, we conceived for the first time the design and synthesis of dual-ligands σR/HDACi to evaluate possible employment as innovative candidates to address this complex disease. Among all synthesized compounds screened for several tumoral cell lines, compound 6 (Kiσ1R = 38 ± 3.7; Kiσ2R = 2917 ± 769 and HDACs IC50 = 0.59 µM) is the most promising candidate as an antiproliferative agent with an IC50 of 0.9 µM on the HCT116 cell line and no significant toxicity to normal cells. Studies of molecular docking, which confirmed the affinity over σ1R and a pan-HDACs inhibitory behavior, support a possible balanced affinity and activity between both targets.
Collapse
Affiliation(s)
- Carla Barbaraci
- Department of Drug and Health Sciences, Medicinal Chemistry Section, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Viviana di Giacomo
- Department of Pharmacy, University "G. d'Annunzio", Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
| | - Annalisa Maruca
- Net4science academic spinoff srl, Università degli Studi "Magna Græcia" di Catanzaro, Campus "Salvatore Venuta", Viale Europa, 88100, Catanzaro, Italy
| | - Vincenzo Patamia
- Department of Drug and Health Sciences, Medicinal Chemistry Section, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Roberta Rocca
- Net4science academic spinoff srl, Università degli Studi "Magna Græcia" di Catanzaro, Campus "Salvatore Venuta", Viale Europa, 88100, Catanzaro, Italy
| | - Maria Dichiara
- Department of Drug and Health Sciences, Medicinal Chemistry Section, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Annalisa Di Rienzo
- Department of Pharmacy, University "G. d'Annunzio", Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
| | - Ivana Cacciatore
- Department of Pharmacy, University "G. d'Annunzio", Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
| | - Amelia Cataldi
- Department of Pharmacy, University "G. d'Annunzio", Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
| | - Marwa Balaha
- Department of Pharmacy, University "G. d'Annunzio", Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafr El Sheikh 33516, Egypt
| | - Monica Rapino
- Genetic Molecular Institute of CNR, Unit of Chieti, "G. d' Annunzio" University, Via dei Vestini 31, 66100 Chieti-Pescara, Italy
| | - Chiara Zagni
- Department of Drug and Health Sciences, Medicinal Chemistry Section, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Daniele Zampieri
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Lorella Pasquinucci
- Department of Drug and Health Sciences, Medicinal Chemistry Section, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Carmela Parenti
- Department of Drug and Health Sciences, Medicinal Chemistry Section, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Emanuele Amata
- Department of Drug and Health Sciences, Medicinal Chemistry Section, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Antonio Rescifina
- Department of Drug and Health Sciences, Medicinal Chemistry Section, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Stefano Alcaro
- Net4science academic spinoff srl, Università degli Studi "Magna Græcia" di Catanzaro, Campus "Salvatore Venuta", Viale Europa, 88100, Catanzaro, Italy; Dipartimento di Scienze della Salute, Università degli Studi "Magna Græcia" di Catanzaro, Campus "Salvatore Venuta", Viale Europa, 88100, Catanzaro, Italy.
| | - Agostino Marrazzo
- Department of Drug and Health Sciences, Medicinal Chemistry Section, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy.
| |
Collapse
|
2
|
Shahab M, Zulfat M, Zheng G. Structure-based virtual screening, molecular simulation and free energy calculations of traditional Chinese medicine, ZINC database revealed potent inhibitors of estrogen-receptor α (ERα). J Biomol Struct Dyn 2023:1-14. [PMID: 37904521 DOI: 10.1080/07391102.2023.2275174] [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: 07/15/2023] [Accepted: 09/07/2023] [Indexed: 11/01/2023]
Abstract
Breast Cancer, a heterogeneous disease at the molecular level, is the most common cause of woman mortality worldwide. We used molecular screening and simulation approaches to target nuclear receptor protein-estrogen receptor alpha (Erα) protein to design and develop of specific and compelling drugs from traditional Chinese medicine (TCM), and ZINC database against pathophysiology of breast cancer. Using virtual screening, only six hits TCM22717, TCM23524, TCM31953, while ZINC05632920, ZINC05773243, and ZINC12780336 demonstrated better pharmacological potential than the 4-hydroxytamoxifen (OHT) taken as control. Binding mode of each of the top hit revealed that these compounds could block the main active site residues and block the function of Erα protein. Moreover, molecular simulation revealed that the identified compounds exhibit stable dynamics and may induce stronger therapeutic effects in experimental setup. All the complexes reported tighter structural packing and less flexible behaviour. We found that the average hydrogen bonds in the identified complexes remained higher than the control drug. Finally, the total binding free energy demonstrated the best hits among the all. The BF energy results revealed -30.4525 ± 3.3565 for the 4-hydroxytamoxifen (OHT)/Erα complex, for the TCM22717/Erα -57.0597 ± 3.4852 kcal/mol, for the TCM23524/Erα complex the BF energy was -56.9084 ± 3.3737 kcal/mol, for the TCM31953/Erα the BF energy was -32.4191 ± 3.8864 kcal/mol while for the ZINC05632920/Erα complex -46.3182 ± 2.7380, ZINC05773243/Erα complex -38.3690 ± 2.8240, and ZINC12780336/Erα complex the BF energy was calculated to be -35.8048 ± 4.1571 kcal/mol.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Muhammad Shahab
- State Key Laboratories of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, China
| | - Maryam Zulfat
- Department of Biochemistry, Abdul Wali Khan University, Mardan, Pakistan
| | - Guojun Zheng
- State Key Laboratories of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, China
| |
Collapse
|
3
|
Shahab M, Akter S, Sarkar MMH, Banu TA, Goswami B, Chowdhury SF, Naser SR, Habib MA, Shaikh AA, Saki M, Zheng G, Khan MS. Computational design of medicinal compounds to inhibit RBD-hACE2 interaction in the Omicron variant: unveiling a vulnerable target site. INFORMATICS IN MEDICINE UNLOCKED 2023; 40:101281. [PMID: 37265644 PMCID: PMC10210851 DOI: 10.1016/j.imu.2023.101281] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/22/2023] [Accepted: 05/22/2023] [Indexed: 06/03/2023] Open
Abstract
The COVID-19 pandemic, caused by SARS-CoV-2, has globally affected both human health and economy. Several variants with a high potential for reinfection and the ability to evade immunity were detected shortly after the initial reported case of COVID-19. A total of 30 mutations in the spike protein (S) have been reported in the SARS-CoV-2 (BA.2) variant in India and South Africa, while half of these mutations are in the receptor-binding domain and have spread rapidly throughout the world. Drug repurposing offers potential advantages over the discovery of novel drugs, and one is that it can be delivered quickly without lengthy assessments and time-consuming clinical trials. In this study, computational drug design, such as pharmacophore-based virtual screening and MD simulation has been concentrated, in order to find a novel small molecular inhibitor that prevents hACE2 from binding to the receptor binding domain (RBD). three medicinal compound databases: North-East African, North African, and East African were screened and carried out a multi-step screening approach that identified three compounds, which are thymoquinol 2-O-beta-glucopyranoside (C1), lanneaflavonol (C2), and naringenin-4'-methoxy-7-O-Alpha-L-rhamnoside (C3), with excellent anti-viral properties against the RBD of the omicron variant. Furthermore, PAIN assay interference, computation bioactivity prediction, binding free energy, and dissociation constant were used to validate the top hits, which indicated good antiviral activity. The three compounds that were found may be useful against COVID-19, though more research is required. These findings could aid the development of novel therapeutic drugs against the emerging Omicron variant of SARS-CoV-2.
Collapse
Affiliation(s)
- Muhammad Shahab
- State Key Laboratories of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Shahina Akter
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | | | - Tanjina Akhtar Banu
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Barna Goswami
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | | | - Showti Raheel Naser
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Md Ahashan Habib
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Aftab Ali Shaikh
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | - Morteza Saki
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Guojun Zheng
- State Key Laboratories of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Md Salim Khan
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| |
Collapse
|
4
|
Bivacqua R, Romeo I, Barreca M, Barraja P, Alcaro S, Montalbano A. HSV-1 Glycoprotein D and Its Surface Receptors: Evaluation of Protein-Protein Interaction and Targeting by Triazole-Based Compounds through In Silico Approaches. Int J Mol Sci 2023; 24:ijms24087092. [PMID: 37108255 PMCID: PMC10138673 DOI: 10.3390/ijms24087092] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/27/2023] [Accepted: 04/09/2023] [Indexed: 04/29/2023] Open
Abstract
Protein-protein interactions (PPI) represent attractive targets for drug design. Thus, aiming at a deeper insight into the HSV-1 envelope glycoprotein D (gD), protein-protein docking and dynamic simulations of gD-HVEM and gD-Nectin-1 complexes were performed. The most stable complexes and the pivotal key residues useful for gD to anchor human receptors were identified and used as starting points for a structure-based virtual screening on a library of both synthetic and designed 1,2,3-triazole-based compounds. Their binding properties versus gD interface with HVEM and Nectin-1 along with their structure-activity relationships (SARs) were evaluated. Four [1,2,3]triazolo[4,5-b]pyridines were identified as potential HSV-1 gD inhibitors, for their good theoretical affinity towards all conformations of HSV-1 gD. Overall, this study suggests promising basis for the design of new antiviral agents targeting gD as a valuable strategy to prevent viral attachment and penetration into the host cell.
Collapse
Affiliation(s)
- Roberta Bivacqua
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Isabella Romeo
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, 88100 Catanzaro, Italy
- Net4Science Academic Spin-Off, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, 88100 Catanzaro, Italy
| | - Marilia Barreca
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Paola Barraja
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, 88100 Catanzaro, Italy
- Net4Science Academic Spin-Off, Università degli Studi "Magna Græcia" di Catanzaro, Campus "S. Venuta", Viale Europa, 88100 Catanzaro, Italy
| | - Alessandra Montalbano
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
| |
Collapse
|
5
|
Grillone K, Riillo C, Rocca R, Ascrizzi S, Spanò V, Scionti F, Polerà N, Maruca A, Barreca M, Juli G, Arbitrio M, Di Martino MT, Caracciolo D, Tagliaferri P, Alcaro S, Montalbano A, Barraja P, Tassone P. The New Microtubule-Targeting Agent SIX2G Induces Immunogenic Cell Death in Multiple Myeloma. Int J Mol Sci 2022; 23:ijms231810222. [PMID: 36142133 PMCID: PMC9499408 DOI: 10.3390/ijms231810222] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/30/2022] [Accepted: 09/01/2022] [Indexed: 12/31/2022] Open
Abstract
Microtubule-targeting agents (MTAs) are effective drugs for cancer treatment. A novel diaryl [1,2]oxazole class of compounds binding the colchicine site was synthesized as cis-restricted-combretastatin-A-4-analogue and then chemically modified to have improved solubility and a wider therapeutic index as compared to vinca alkaloids and taxanes. On these bases, a new class of tricyclic compounds, containing the [1,2]oxazole ring and an isoindole moiety, has been synthetized, among which SIX2G emerged as improved MTA. Several findings highlighted the ability of some chemotherapeutics to induce immunogenic cell death (ICD), which is defined by the cell surface translocation of Calreticulin (CALR) via dissociation of the PP1/GADD34 complex. In this regard, we computationally predicted the ability of SIX2G to induce CALR exposure by interacting with the PP1 RVxF domain. We then assessed both the potential cytotoxic and immunogenic activity of SIX2G on in vitro models of multiple myeloma (MM), which is an incurable hematological malignancy characterized by an immunosuppressive milieu. We found that the treatment with SIX2G inhibited cell viability by inducing G2/M phase cell cycle arrest and apoptosis. Moreover, we observed the increase of hallmarks of ICD such as CALR exposure, ATP release and phospho-eIF2α protein level. Through co-culture experiments with immune cells, we demonstrated the increase of (i) CD86 maturation marker on dendritic cells, (ii) CD69 activation marker on cytotoxic T cells, and (iii) phagocytosis of tumor cells following treatment with SIX2G, confirming the onset of an immunogenic cascade. In conclusion, our findings provide a framework for further development of SIX2G as a new potential anti-MM agent.
Collapse
Affiliation(s)
- Katia Grillone
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy
| | - Caterina Riillo
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy
| | - Roberta Rocca
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy
- Net4Science s.r.l., Academic Spinoff, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy
| | - Serena Ascrizzi
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy
| | - Virginia Spanò
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128 Palermo, Italy
| | - Francesca Scionti
- Institute of Research and Biomedical Innovation (IRIB), Italian National Council (CNR), 98122 Messina, Italy
| | - Nicoletta Polerà
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy
| | - Annalisa Maruca
- Net4Science s.r.l., Academic Spinoff, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy
| | - Marilia Barreca
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128 Palermo, Italy
| | - Giada Juli
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy
| | - Mariamena Arbitrio
- Institute of Research and Biomedical Innovation (IRIB), Italian National Council (CNR), 98122 Messina, Italy
| | - Maria Teresa Di Martino
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy
| | - Daniele Caracciolo
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy
| | - Pierosandro Tagliaferri
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy
| | - Stefano Alcaro
- Net4Science s.r.l., Academic Spinoff, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy
- Institute of Research and Biomedical Innovation (IRIB), Italian National Council (CNR), 88100 Catanzaro, Italy
| | - Alessandra Montalbano
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128 Palermo, Italy
- Correspondence: (A.M.); (P.T.); Tel.: +39-0912-389682 (A.M.); +39-0961-364-7029 (P.T.)
| | - Paola Barraja
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128 Palermo, Italy
| | - Pierfrancesco Tassone
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy
- Correspondence: (A.M.); (P.T.); Tel.: +39-0912-389682 (A.M.); +39-0961-364-7029 (P.T.)
| |
Collapse
|
6
|
Prejanò M, Romeo I, La Serra MA, Russo N, Marino T. Computational Study Reveals the Role of Water Molecules in the Inhibition Mechanism of LAT1 by 1,2,3-Dithiazoles. J Chem Inf Model 2021; 61:5883-5892. [PMID: 34788052 PMCID: PMC8715508 DOI: 10.1021/acs.jcim.1c01012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The L-type amino
acid transporter LAT1, involved in many biological
processes including the overexpression of some tumors, is considered
a potential pharmacological target. The 1,2,3-Dithiazole scaffold
was predicted to inhibit LAT1 by the formation of an intermolecular
disulfide bond with the thiolate group of cysteine(s). As a result
of the identification of these irreversible covalent inhibitors, we
decided to deeply investigate the recognition stage and the covalent
interaction, characterizing the chemical structures of the selected
ligands. With the aim to provide new insights into the access of the
ligands to the binding pocket and to reveal the residues involved
in the inhibition, we performed docking, molecular dynamics simulations,
and density functional theory-based investigation of three 1,2,3-dithiazoles
against LAT1. Our computational analysis further highlighted the crucial
role played by water molecules in the inhibition mechanism. The results
here presented are consistent with experimental observations and provide
insights that can be helpful for the rational design of new-to-come
LAT1’s inhibitors.
Collapse
Affiliation(s)
- Mario Prejanò
- Department of Chemistry and Chemical Technologies, University of Calabria, 87036 Arcavacata di Rende, Cosenza, Italy
| | - Isabella Romeo
- Department of Chemistry and Chemical Technologies, University of Calabria, 87036 Arcavacata di Rende, Cosenza, Italy
| | - Maria Antonietta La Serra
- Department of Chemistry and Chemical Technologies, University of Calabria, 87036 Arcavacata di Rende, Cosenza, Italy
| | - Nino Russo
- Department of Chemistry and Chemical Technologies, University of Calabria, 87036 Arcavacata di Rende, Cosenza, Italy
| | - Tiziana Marino
- Department of Chemistry and Chemical Technologies, University of Calabria, 87036 Arcavacata di Rende, Cosenza, Italy
| |
Collapse
|
7
|
Asiedu SO, Kwofie SK, Broni E, Wilson MD. Computational Identification of Potential Anti-Inflammatory Natural Compounds Targeting the p38 Mitogen-Activated Protein Kinase (MAPK): Implications for COVID-19-Induced Cytokine Storm. Biomolecules 2021; 11:653. [PMID: 33946644 PMCID: PMC8146027 DOI: 10.3390/biom11050653] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/24/2021] [Accepted: 04/26/2021] [Indexed: 02/06/2023] Open
Abstract
Severely ill coronavirus disease 2019 (COVID-19) patients show elevated concentrations of pro-inflammatory cytokines, a situation commonly known as a cytokine storm. The p38 MAPK receptor is considered a plausible therapeutic target because of its involvement in the platelet activation processes leading to inflammation. This study aimed to identify potential natural product-derived inhibitory molecules against the p38α MAPK receptor to mitigate the eliciting of pro-inflammatory cytokines using computational techniques. The 3D X-ray structure of the receptor with PDB ID 3ZS5 was energy minimized using GROMACS and used for molecular docking via AutoDock Vina. The molecular docking was validated with an acceptable area under the curve (AUC) of 0.704, which was computed from the receiver operating characteristic (ROC) curve. A compendium of 38,271 natural products originating from Africa and China together with eleven known p38 MAPK inhibitors were screened against the receptor. Four potential lead compounds ZINC1691180, ZINC5519433, ZINC4520996 and ZINC5733756 were identified. The compounds formed strong intermolecular bonds with critical residues Val38, Ala51, Lys53, Thr106, Leu108, Met109 and Phe169. Additionally, they exhibited appreciably low binding energies which were corroborated via molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) calculations. The compounds were also predicted to have plausible pharmacological profiles with insignificant toxicity. The molecules were also predicted to be anti-inflammatory, kinase inhibitors, antiviral, platelet aggregation inhibitors, and immunosuppressive, with probable activity (Pa) greater than probable inactivity (Pi). ZINC5733756 is structurally similar to estradiol with a Tanimoto coefficient value of 0.73, which exhibits anti-inflammatory activity by targeting the activation of Nrf2. Similarly, ZINC1691180 has been reported to elicit anti-inflammatory activity in vitro. The compounds may serve as scaffolds for the design of potential biotherapeutic molecules against the cytokine storm associated with COVID-19.
Collapse
Affiliation(s)
- Seth O. Asiedu
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra P.O. Box LG 581, Ghana; (S.O.A); (M.D.W)
| | - Samuel K. Kwofie
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra P.O. Box LG 77, Ghana;
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra P.O. Box LG 54, Ghana
| | - Emmanuel Broni
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra P.O. Box LG 77, Ghana;
| | - Michael D. Wilson
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra P.O. Box LG 581, Ghana; (S.O.A); (M.D.W)
- Department of Medicine, Loyola University Medical Center, Maywood, IL 60153, USA
| |
Collapse
|
8
|
In Silico Food-Drug Interaction: A Case Study of Eluxadoline and Fatty Meal. Int J Mol Sci 2020; 21:ijms21239127. [PMID: 33266221 PMCID: PMC7731208 DOI: 10.3390/ijms21239127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/24/2020] [Accepted: 11/29/2020] [Indexed: 11/17/2022] Open
Abstract
Food-drug interaction is an infrequently considered aspect in clinical practice. Usually, drugs are taken together with meals and what follows may adversely affect pharmacokinetic and pharmacodynamic properties, and hence, the therapeutic effects. In this study, a computational protocol was proposed to explain the different assimilations of two µ-receptors agonists, eluxadoline and loperamide, with a peculiar pharmacokinetic profile. Compared to loperamide, eluxadoline is absorbed less after the intake of a fatty meal, and the LogP values do not explain this event. Firstly, keeping in mind the different pH in the intestinal tract, the protonation states of both compounds were calculated. Then, all structures were subjected to a conformational search by using MonteCarlo and Molecular Dynamics methods, with solvation terms mimicking the water and weak polar solvent (octanol). Both computational results showed that eluxadoline has less conformational freedom in octanol, unlike loperamide, which exhibits constant behavior in both solvents. Therefore, we hypothesize that fatty meal causes the "closure" of the eluxadoline molecule to prevent the exposure of the polar groups and their interaction with water, necessary for the drug absorption. Based on our results, this work could be a reasonable "case study", useful for future investigation of the drug pharmacokinetic profile.
Collapse
|
9
|
Maruca A, Rocca R, Catalano R, Mesiti F, Costa G, Lanzillotta D, Salatino A, Ortuso F, Trapasso F, Alcaro S, Artese A. Natural Products Extracted from Fungal Species as New Potential Anti-Cancer Drugs: A Structure-Based Drug Repurposing Approach Targeting HDAC7. Molecules 2020; 25:E5524. [PMID: 33255661 PMCID: PMC7728054 DOI: 10.3390/molecules25235524] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 11/16/2020] [Accepted: 11/23/2020] [Indexed: 02/06/2023] Open
Abstract
Mushrooms can be considered a valuable source of natural bioactive compounds with potential polypharmacological effects due to their proven antimicrobial, antiviral, antitumor, and antioxidant activities. In order to identify new potential anticancer compounds, an in-house chemical database of molecules extracted from both edible and non-edible fungal species was employed in a virtual screening against the isoform 7 of the Histone deacetylase (HDAC). This target is known to be implicated in different cancer processes, and in particular in both breast and ovarian tumors. In this work, we proposed the ibotenic acid as lead compound for the development of novel HDAC7 inhibitors, due to its antiproliferative activity in human breast cancer cells (MCF-7). These promising results represent the starting point for the discovery and the optimization of new HDAC7 inhibitors and highlight the interesting opportunity to apply the "drug repositioning" paradigm also to natural compounds deriving from mushrooms.
Collapse
Affiliation(s)
- Annalisa Maruca
- Dipartimento di Scienze della Salute, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy; (A.M.); (R.C.); (F.M.); (G.C.); (F.O.); (A.A.)
- Net4Science Academic Spin-Off, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy;
| | - Roberta Rocca
- Net4Science Academic Spin-Off, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy;
- Dipartimento di Medicina Sperimentale e Clinica, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy; (D.L.); (A.S.); (F.T.)
| | - Raffaella Catalano
- Dipartimento di Scienze della Salute, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy; (A.M.); (R.C.); (F.M.); (G.C.); (F.O.); (A.A.)
- Net4Science Academic Spin-Off, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy;
| | - Francesco Mesiti
- Dipartimento di Scienze della Salute, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy; (A.M.); (R.C.); (F.M.); (G.C.); (F.O.); (A.A.)
- Net4Science Academic Spin-Off, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy;
| | - Giosuè Costa
- Dipartimento di Scienze della Salute, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy; (A.M.); (R.C.); (F.M.); (G.C.); (F.O.); (A.A.)
- Net4Science Academic Spin-Off, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy;
| | - Delia Lanzillotta
- Dipartimento di Medicina Sperimentale e Clinica, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy; (D.L.); (A.S.); (F.T.)
| | - Alessandro Salatino
- Dipartimento di Medicina Sperimentale e Clinica, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy; (D.L.); (A.S.); (F.T.)
| | - Francesco Ortuso
- Dipartimento di Scienze della Salute, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy; (A.M.); (R.C.); (F.M.); (G.C.); (F.O.); (A.A.)
- Net4Science Academic Spin-Off, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy;
| | - Francesco Trapasso
- Dipartimento di Medicina Sperimentale e Clinica, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy; (D.L.); (A.S.); (F.T.)
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy; (A.M.); (R.C.); (F.M.); (G.C.); (F.O.); (A.A.)
- Net4Science Academic Spin-Off, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy;
| | - Anna Artese
- Dipartimento di Scienze della Salute, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy; (A.M.); (R.C.); (F.M.); (G.C.); (F.O.); (A.A.)
- Net4Science Academic Spin-Off, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy;
| |
Collapse
|
10
|
Coricello A, Mesiti F, Lupia A, Maruca A, Alcaro S. Inside Perspective of the Synthetic and Computational Toolbox of JAK Inhibitors: Recent Updates. Molecules 2020; 25:E3321. [PMID: 32707925 PMCID: PMC7435994 DOI: 10.3390/molecules25153321] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/18/2020] [Accepted: 07/20/2020] [Indexed: 01/10/2023] Open
Abstract
The mechanisms of inflammation and cancer are intertwined by complex networks of signaling pathways. Dysregulations in the Janus kinase/signal transducer and activator of transcription (JAK/STAT) pathway underlie several pathogenic conditions related to chronic inflammatory states, autoimmune diseases and cancer. Historically, the potential application of JAK inhibition has been thoroughly explored, thus triggering an escalation of favorable results in this field. So far, five JAK inhibitors have been approved by the Food and Drug Administration (FDA) for the treatment of different diseases. Considering the complexity of JAK-depending processes and their involvement in multiple disorders, JAK inhibitors are the perfect candidates for drug repurposing and for the assessment of multitarget strategies. Herein we reviewed the recent progress concerning JAK inhibition, including the innovations provided by the release of JAKs crystal structures and the improvement of synthetic strategies aimed to simplify of the industrial scale-up.
Collapse
Affiliation(s)
- Adriana Coricello
- Dipartimento di Scienze della Salute, Università "Magna Græcia" di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Francesco Mesiti
- Dipartimento di Scienze della Salute, Università "Magna Græcia" di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
- Net4Science srl, Università 'Magna Græcia' di Catanzaro, Campus Universitario 'S. Venuta', Viale Europa, 88100 Catanzaro, Italy
| | - Antonio Lupia
- Net4Science srl, Università 'Magna Græcia' di Catanzaro, Campus Universitario 'S. Venuta', Viale Europa, 88100 Catanzaro, Italy
| | - Annalisa Maruca
- Dipartimento di Scienze della Salute, Università "Magna Græcia" di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
- Net4Science srl, Università 'Magna Græcia' di Catanzaro, Campus Universitario 'S. Venuta', Viale Europa, 88100 Catanzaro, Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università "Magna Græcia" di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
- Net4Science srl, Università 'Magna Græcia' di Catanzaro, Campus Universitario 'S. Venuta', Viale Europa, 88100 Catanzaro, Italy
| |
Collapse
|
11
|
Maruca A, Lanzillotta D, Rocca R, Lupia A, Costa G, Catalano R, Moraca F, Gaudio E, Ortuso F, Artese A, Trapasso F, Alcaro S. Multi-Targeting Bioactive Compounds Extracted from Essential Oils as Kinase Inhibitors. Molecules 2020; 25:E2174. [PMID: 32384767 PMCID: PMC7249159 DOI: 10.3390/molecules25092174] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 05/01/2020] [Accepted: 05/03/2020] [Indexed: 12/12/2022] Open
Abstract
Essential oils (EOs) are popular in aromatherapy, a branch of alternative medicine that claims their curative effects. Moreover, several studies reported EOs as potential anti-cancer agents by inducing apoptosis in different cancer cell models. In this study, we have considered EOs as a potential resource of new kinase inhibitors with a polypharmacological profile. On the other hand, computational methods offer the possibility to predict the theoretical activity profile of ligands, discovering dangerous off-targets and/or synergistic effects due to the potential multi-target action. With this aim, we performed a Structure-Based Virtual Screening (SBVS) against X-ray models of several protein kinases selected from the Protein Data Bank (PDB) by using a chemoinformatics database of EOs. By evaluating theoretical binding affinity, 13 molecules were detected among EOs as new potential kinase inhibitors with a multi-target profile. The two compounds with higher percentages in the EOs were studied more in depth by means Induced Fit Docking (IFD) protocol, in order to better predict their binding modes taking into account also structural changes in the receptor. Finally, given its good binding affinity towards five different kinases, cinnamyl cinnamate was biologically tested on different cell lines with the aim to verify the antiproliferative activity. Thus, this work represents a starting point for the optimization of the most promising EOs structure as kinase inhibitors with multi-target features.
Collapse
Affiliation(s)
- Annalisa Maruca
- Dipartimento di Scienze della Salute, Università “Magna Græcia” di Catanzaro, Campus Universitario “S. Venuta”, Viale Europa, Loc. Germaneto, 88100 Catanzaro, Italy; (A.M.); (G.C.); (R.C.); (F.O.); (A.A.)
- Net4Science srl, Università “Magna Græcia” di Catanzaro, Campus Universitario “S. Venuta”, Viale Europa, Loc. Germaneto, 88100 Catanzaro, Italy; (R.R.); (A.L.); (F.M.)
| | - Delia Lanzillotta
- Department of Experimental and Clinical Medicine, Università “Magna Græcia” di Catanzaro, Campus Universitario “S. Venuta”, Viale Europa, Loc. Germaneto, 88100 Catanzaro, Italy; (D.L.); (F.T.)
| | - Roberta Rocca
- Net4Science srl, Università “Magna Græcia” di Catanzaro, Campus Universitario “S. Venuta”, Viale Europa, Loc. Germaneto, 88100 Catanzaro, Italy; (R.R.); (A.L.); (F.M.)
- Department of Experimental and Clinical Medicine, Università “Magna Græcia” di Catanzaro, Campus Universitario “S. Venuta”, Viale Europa, Loc. Germaneto, 88100 Catanzaro, Italy; (D.L.); (F.T.)
| | - Antonio Lupia
- Net4Science srl, Università “Magna Græcia” di Catanzaro, Campus Universitario “S. Venuta”, Viale Europa, Loc. Germaneto, 88100 Catanzaro, Italy; (R.R.); (A.L.); (F.M.)
| | - Giosuè Costa
- Dipartimento di Scienze della Salute, Università “Magna Græcia” di Catanzaro, Campus Universitario “S. Venuta”, Viale Europa, Loc. Germaneto, 88100 Catanzaro, Italy; (A.M.); (G.C.); (R.C.); (F.O.); (A.A.)
- Net4Science srl, Università “Magna Græcia” di Catanzaro, Campus Universitario “S. Venuta”, Viale Europa, Loc. Germaneto, 88100 Catanzaro, Italy; (R.R.); (A.L.); (F.M.)
| | - Raffaella Catalano
- Dipartimento di Scienze della Salute, Università “Magna Græcia” di Catanzaro, Campus Universitario “S. Venuta”, Viale Europa, Loc. Germaneto, 88100 Catanzaro, Italy; (A.M.); (G.C.); (R.C.); (F.O.); (A.A.)
- Net4Science srl, Università “Magna Græcia” di Catanzaro, Campus Universitario “S. Venuta”, Viale Europa, Loc. Germaneto, 88100 Catanzaro, Italy; (R.R.); (A.L.); (F.M.)
| | - Federica Moraca
- Net4Science srl, Università “Magna Græcia” di Catanzaro, Campus Universitario “S. Venuta”, Viale Europa, Loc. Germaneto, 88100 Catanzaro, Italy; (R.R.); (A.L.); (F.M.)
- Department of Pharmacy, University “Federico II” of Naples, Via D. Montesano 49, 80131 Naples, Italy
| | - Eugenio Gaudio
- Lymphoma and Genomics Research Program, the Institute of Oncology Research, 6500 Bellinzona, Switzerland;
| | - Francesco Ortuso
- Dipartimento di Scienze della Salute, Università “Magna Græcia” di Catanzaro, Campus Universitario “S. Venuta”, Viale Europa, Loc. Germaneto, 88100 Catanzaro, Italy; (A.M.); (G.C.); (R.C.); (F.O.); (A.A.)
- Net4Science srl, Università “Magna Græcia” di Catanzaro, Campus Universitario “S. Venuta”, Viale Europa, Loc. Germaneto, 88100 Catanzaro, Italy; (R.R.); (A.L.); (F.M.)
| | - Anna Artese
- Dipartimento di Scienze della Salute, Università “Magna Græcia” di Catanzaro, Campus Universitario “S. Venuta”, Viale Europa, Loc. Germaneto, 88100 Catanzaro, Italy; (A.M.); (G.C.); (R.C.); (F.O.); (A.A.)
- Net4Science srl, Università “Magna Græcia” di Catanzaro, Campus Universitario “S. Venuta”, Viale Europa, Loc. Germaneto, 88100 Catanzaro, Italy; (R.R.); (A.L.); (F.M.)
| | - Francesco Trapasso
- Department of Experimental and Clinical Medicine, Università “Magna Græcia” di Catanzaro, Campus Universitario “S. Venuta”, Viale Europa, Loc. Germaneto, 88100 Catanzaro, Italy; (D.L.); (F.T.)
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università “Magna Græcia” di Catanzaro, Campus Universitario “S. Venuta”, Viale Europa, Loc. Germaneto, 88100 Catanzaro, Italy; (A.M.); (G.C.); (R.C.); (F.O.); (A.A.)
- Net4Science srl, Università “Magna Græcia” di Catanzaro, Campus Universitario “S. Venuta”, Viale Europa, Loc. Germaneto, 88100 Catanzaro, Italy; (R.R.); (A.L.); (F.M.)
| |
Collapse
|
12
|
Mediterranean Diet Nutrients to Turn the Tide against Insulin Resistance and Related Diseases. Nutrients 2020; 12:nu12041066. [PMID: 32290535 PMCID: PMC7230471 DOI: 10.3390/nu12041066] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/06/2020] [Accepted: 04/10/2020] [Indexed: 12/11/2022] Open
Abstract
Insulin resistance (IR), defined as an attenuated biological response to circulating insulin, is a fundamental defect in obesity and type 2 diabetes (T2D), and is also linked to a wide spectrum of pathological conditions, such as non-alcoholic fatty liver disease (NAFLD), cognitive impairment, endothelial dysfunction, chronic kidney disease (CKD), polycystic ovary syndrome (PCOS), and some endocrine tumors, including breast cancer. In obesity, the unbalanced production of pro- and anti-inflammatory adipocytokines can lead to the development of IR and its related metabolic complications, which are potentially reversible through weight-loss programs. The Mediterranean diet (MedDiet), characterized by high consumption of extra-virgin olive oil (EVOO), nuts, red wine, vegetables and other polyphenol-rich elements, has proved to be associated with greater improvement of IR in obese individuals, when compared to other nutritional interventions. Also, recent studies in either experimental animal models or in humans, have shown encouraging results for insulin-sensitizing nutritional supplements derived from MedDiet food sources in the modulation of pathognomonic traits of certain IR-related conditions, including polyunsaturated fatty acids from olive oil and seeds, anthocyanins from purple vegetables and fruits, resveratrol from grapes, and the EVOO-derived, oleacein. Although the pharmacological properties and clinical uses of these functional nutrients are still under investigation, the molecular mechanism(s) underlying the metabolic benefits appear to be compound-specific and, in some cases, point to a role in gene expression through an involvement of the nuclear high-mobility group A1 (HMGA1) protein.
Collapse
|