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Muñoz-Vega MC, López-Hernández S, Sierra-Chavarro A, Scotti MT, Scotti L, Coy-Barrera E, Herrera-Acevedo C. Machine-Learning- and Structure-Based Virtual Screening for Selecting Cinnamic Acid Derivatives as Leishmania major DHFR-TS Inhibitors. Molecules 2023; 29:179. [PMID: 38202763 PMCID: PMC10779987 DOI: 10.3390/molecules29010179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 12/02/2023] [Accepted: 12/06/2023] [Indexed: 01/12/2024] Open
Abstract
The critical enzyme dihydrofolate reductase-thymidylate synthase in Leishmania major (LmDHFR-TS) serves a dual-purpose role and is essential for DNA synthesis, a cornerstone of the parasite's reproductive processes. Consequently, the development of inhibitors against LmDHFR-TS is crucial for the creation of novel anti-Leishmania chemotherapies. In this study, we employed an in-house database containing 314 secondary metabolites derived from cinnamic acid that occurred in the Asteraceae family. We conducted a combined ligand/structure-based virtual screening to identify potential inhibitors against LmDHFR-TS. Through consensus analysis of both approaches, we identified three compounds, i.e., lithospermic acid (237), diarctigenin (306), and isolappaol A (308), that exhibited a high probability of being inhibitors according to both approaches and were consequently classified as promising hits. Subsequently, we expanded the binding mode examination of these compounds within the active site of the test enzyme through molecular dynamics simulations, revealing a high degree of structural stability and minimal fluctuations in its tertiary structure. The in silico predictions were then validated through in vitro assays to examine the inhibitory capacity of the top-ranked naturally occurring compounds against LmDHFR-TS recombinant protein. The test compounds effectively inhibited the enzyme with IC50 values ranging from 6.1 to 10.1 μM. In contrast, other common cinnamic acid derivatives (i.e., flavonoid glycosides) from the Asteraceae family, such as hesperidin, isovitexin 4'-O-glucoside, and rutin, exhibited low activity against this target. The selective index (SI) for all tested compounds was determined using HsDHFR with moderate inhibitory effect. Among these hits, lignans 306 and 308 demonstrated the highest selectivity, displaying superior SI values compared to methotrexate, the reference inhibitor of DHFR-TS. Therefore, continued research into the anti-leishmanial potential of these C6C3-hybrid butyrolactone lignans may offer a brighter outlook for combating this neglected tropical disease.
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Affiliation(s)
- Maria Camila Muñoz-Vega
- Department of Chemical Engineering, Universidad ECCI, Bogotá, Distrito Capital 111311, Colombia; (M.C.M.-V.); (S.L.-H.); (A.S.-C.)
- Laboratorio de Investigación en Biocatálisis y Biotransformaciones (LIBB), Grupo de Investigación en Ingeniería de los Procesos Agroalimentarios y Biotecnológicos (GIPAB), Departamento de Química Universidad del Valle, Cali 760042, Colombia
| | - Sofía López-Hernández
- Department of Chemical Engineering, Universidad ECCI, Bogotá, Distrito Capital 111311, Colombia; (M.C.M.-V.); (S.L.-H.); (A.S.-C.)
| | - Adrián Sierra-Chavarro
- Department of Chemical Engineering, Universidad ECCI, Bogotá, Distrito Capital 111311, Colombia; (M.C.M.-V.); (S.L.-H.); (A.S.-C.)
| | - Marcus Tullius Scotti
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil; (M.T.S.); (L.S.)
| | - Luciana Scotti
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil; (M.T.S.); (L.S.)
| | - Ericsson Coy-Barrera
- Bioorganic Chemistry Laboratory, Facultad de Ciencias Básicas y Aplicadas, Universidad Militar Nueva Granada, Cajicá 250247, Colombia;
| | - Chonny Herrera-Acevedo
- Department of Chemical Engineering, Universidad ECCI, Bogotá, Distrito Capital 111311, Colombia; (M.C.M.-V.); (S.L.-H.); (A.S.-C.)
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil; (M.T.S.); (L.S.)
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Shaldam MA, Almahli H, Angeli A, Badi RM, Khaleel EF, Zain-Alabdeen AI, Elsayed ZM, Elkaeed EB, Salem R, Supuran CT, Eldehna WM, Tawfik HO. Discovery of sulfonamide-tethered isatin derivatives as novel anticancer agents and VEGFR-2 inhibitors. J Enzyme Inhib Med Chem 2023; 38:2203389. [PMID: 37122176 PMCID: PMC10134960 DOI: 10.1080/14756366.2023.2203389] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
In this work, new isatin-based sulphonamides (6a-i, 11a-c, 12a-c) were designed and synthesised as potential dual VEGFR-2 and carbonic anhydrase inhibitors with anticancer activities. Firstly, all target isatins were examined for in vitro antitumor action on NCI-USA panel (58 tumour cell lines). Then, the most potent derivatives were examined for the potential CA inhibitory action towards the physiologically relevant hCA isoforms I, II, and tumour-linked hCA IX isoform, in addition, the VEGFR-2 inhibitory activity was evaluated. The target sulphonamides failed to inhibit the CA isoforms that could be attributable to the steric effect of the neighbouring methoxy group, whereas they displayed potent VEGFR-2 inhibitory effect. Following that, isatins 11b and 12b were tested for their influence on the cell cycle disturbance, and towards the apoptotic potential. Finally, detailed molecular modelling analyses, including docking and molecular dynamics, were carried out to assess the binding mode and stability of target isatins.
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Affiliation(s)
- Moataz A Shaldam
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Hadia Almahli
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Andrea Angeli
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Sesto Fiorentino, Italy
| | - Rehab Mustafa Badi
- Department of Medical Physiology, College of Medicine, King Khalid University, Abha, Saudi Arabia
| | - Eman F Khaleel
- Department of Medical Physiology, College of Medicine, King Khalid University, Abha, Saudi Arabia
| | | | - Zainab M Elsayed
- Scientific Research and Innovation Support Unit, Faculty of Pharmacy, Kafrelsheikh Uinversity, Kafrelsheikh, Egypt
| | - Eslam B Elkaeed
- Department of Pharmaceutical Sciences, College of Pharmacy, AlMaarefa University, Riyadh, Saudi Arabia
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
| | - Rofaida Salem
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Claudiu T Supuran
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Sesto Fiorentino, Italy
| | - Wagdy M Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
- School of Biotechnology, Badr University in Cairo, Badr City, Egypt
| | - Haytham O Tawfik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta, Egypt
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ElNaggar MH, Elgazar AA, Gamal G, Hamed SM, Elsayed ZM, El-Ashrey MK, Abood A, El Hassab MA, Soliman AM, El-Domany RA, Badria FA, Supuran CT, Eldehna WM. Identification of sulphonamide-tethered N-((triazol-4-yl)methyl)isatin derivatives as inhibitors of SARS-CoV-2 main protease. J Enzyme Inhib Med Chem 2023; 38:2234665. [PMID: 37434404 PMCID: PMC10405867 DOI: 10.1080/14756366.2023.2234665] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/09/2023] [Accepted: 07/03/2023] [Indexed: 07/13/2023] Open
Abstract
SARS-CoV-2 pandemic in the end of 2019 led to profound consequences on global health and economy. Till producing successful vaccination strategies, the healthcare sectors suffered from the lack of effective therapeutic agents that could control the spread of infection. Thus, academia and the pharmaceutical sector prioritise SARS-CoV-2 antiviral drug discovery. Here, we exploited previous reports highlighting the anti-SARS-CoV-2 activities of isatin-based molecules to develop novel triazolo-isatins for inhibiting main protease (Mpro) of the virus, a crucial enzyme for its replication in the host cells. Particularly, sulphonamide 6b showed promising inhibitory activity with an IC50= 0.249 µM. Additionally, 6b inhibited viral cell proliferation with an IC50 of 4.33 µg/ml, and was non-toxic to VERO-E6 cells (CC50 = 564.74 µg/ml) displaying a selectivity index of 130.4. In silico analysis of 6b disclosed its ability to interact with key residues in the enzyme active site, supporting the obtained in vitro findings.
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Affiliation(s)
- Mai H. ElNaggar
- Department of Pharmacognosy, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Abdullah A. Elgazar
- Department of Pharmacognosy, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Ghada Gamal
- Department of Pharmacognosy, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Shimaa M. Hamed
- Scientific Research and Innovation Support Unit, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Zainab M. Elsayed
- Scientific Research and Innovation Support Unit, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Mohamed K. El-Ashrey
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Amira Abood
- Chemistry of Natural and microbial products, National Research center, Egypt
- Department of Bioscience, University of Kent, Canterbury, UK
| | - Mahmoud A. El Hassab
- Department of Medicinal Chemistry, Faculty of Pharmacy, King Salman International University (KSIU), Egypt
| | - Ahmed M. Soliman
- Department of Microbiology and Immunology, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Ramadan A. El-Domany
- Department of Microbiology and Immunology, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Farid A. Badria
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Claudiu T. Supuran
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Firenze, Italy
| | - Wagdy M. Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
- School of Biotechnology, Badr University in Cairo, Badr City, Egypt
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Sabt A, Abdelraof M, Hamissa MF, Noamaan MA. Antibacterial Activity of Quinoline-Based Derivatives against Methicillin-Resistant Staphylococcus aureus and Pseudomonas aeruginosa: Design, Synthesis, DFT and Molecular Dynamic Simulations. Chem Biodivers 2023; 20:e202300804. [PMID: 37933986 DOI: 10.1002/cbdv.202300804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/05/2023] [Indexed: 11/08/2023]
Abstract
Bacterial virulence becomes a significant challenge for clinical treatments, particularly those characterized as Multi-Drug-Resistant (MDR) strains. Therefore, the preparation of new compounds with active moieties could be a successful approach for eradication of MDR strains. For this purpose, newly synthesized quinoline compounds were prepared and tested for their antimicrobial activity against Methicillin-Resistant Staphylococcus Aureus (MRSA) and Pseudomonas Aeruginosa (PA). Among the synthesized derivatives, compounds 1-(quinolin-2-ylamino)pyrrolidine-2,5-dione (8) and 2-(2-((5-methylfuran-2-yl)methylene)hydrazinyl)quinoline (12) were shown to possess the highest antimicrobial activity with the minimum inhibitory concentration with the values of 5±2.2 and10±1.5 μg/mL towards Pseudomonas aeruginosa without any activity towards MRSA. Interestingly, compounds 2-(2-((1H-indol-3-yl)methylene)hydrazinyl)quinoline (13) and 2-(4-bromophenyl)-3-(quinolin-2-ylamino)thiazolidin-4-one (16c) showed significant inhibition activity against Staphylococcus aureus MRSA and Pseudomonas aeruginosa. Compound 13 (with indole moiety) particularly displayed excellent bactericidal activity with low MIC values 20±3.3 and 10±1.5 μg/mL against Staphylococcus aureus MRSA and Pseudomonas aeruginosa, respectively. Effects molecular modelling was used to determine the mode of action for the antimicrobial effect. The stability of complexes formed by docking and target-ligand pairing was evaluated using molecular dynamics simulations. The compounds were also tested for binding affinity to the target protein using MM-PBSA. Density-functional theory (DFT) calculations were also used to investigate the electrochemical properties of various compounds.
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Affiliation(s)
- Ahmed Sabt
- Chemistry of Natural Compounds Department, Pharmaceutical and Drug Industries Research Institute, National Research Center, Dokki, Cairo, 12622, Egypt
| | - Mohamed Abdelraof
- Microbial Chemistry Department, Biotechnology Research Institute, National Research Center (NRC), 33 El Behouth St., Giza P.O., 12622, Egypt
| | - Mohamed Farouk Hamissa
- Department of Biomolecular Spectroscopy, Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Prague, Czech Republic
| | - Mahmoud A Noamaan
- Mathematics Department, Faculty of Science, Cairo University, Giza, 12613, Egypt
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Al-Warhi T, Almahli H, Maklad RM, Elsayed ZM, El Hassab MA, Alotaibi OJ, Aljaeed N, Ayyad RR, Ghabour HA, Eldehna WM, El-Ashrey MK. 1-Benzyl-5-bromo-3-hydrazonoindolin-2-ones as Novel Anticancer Agents: Synthesis, Biological Evaluation and Molecular Modeling Insights. Molecules 2023; 28:molecules28073203. [PMID: 37049966 PMCID: PMC10096524 DOI: 10.3390/molecules28073203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/24/2023] [Accepted: 03/26/2023] [Indexed: 04/07/2023] Open
Abstract
Human health is experiencing several obstacles in the modern medical era, particularly cancer. As a result, the cancer therapeutic arsenal should be continually expanded with innovative small molecules that preferentially target tumour cells. In this study, we describe the development of two small molecule series (7a–d and 12a–e) based on the 1-benzyl-5-bromoindolin-2-one scaffold that connected through a hydrazone linker to a 4-arylthiazole (7a–d) or 4-methyl-5-(aryldiazenyl)thiazole (12a–e) moiety. The anticancer activity of all the reported indolin-2-one derivatives was assessed against breast (MCF-7) and lung (A-549) cancer cell lines. The 4-arylthiazole-bearing derivatives 7c and 7d revealed the best anticancer activity toward MCF-7 cells (IC50 = 7.17 ± 0.94 and 2.93 ± 0.47, respectively). Furthermore, the VEGFR-2 inhibitory activity for 7c and 7d was evaluated. Both molecules disclosed good inhibitory activity, and their IC50 values were equal to 0.728 µM and 0.503 µM, respectively. Additionally, the impacts of 7d on the cell cycle phases as well as on the levels of different apoptotic markers (caspase-3, caspase-9, Bax, and Bcl-2) were assessed. Molecular docking and dynamic simulations are carried out to explore the binding mode of 7d within the VEGFR-2 active site.
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Affiliation(s)
- Tarfah Al-Warhi
- Department of Chemistry, College of Science, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Hadia Almahli
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Raed M. Maklad
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
| | - Zainab M. Elsayed
- Scientific Research and Innovation Support Unit, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
| | - Mahmoud A. El Hassab
- Department of Medicinal Chemistry, Faculty of Pharmacy, King Salman International University (KSIU), South Sinai 46612, Egypt
| | - Ohoud J. Alotaibi
- Department of Chemistry, College of Science, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Nada Aljaeed
- Department of Chemistry, College of Science, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Rezk R. Ayyad
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Al-Azhar University, Cairo 11884, Egypt
| | - Hazem A. Ghabour
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Wagdy M. Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
- School of Biotechnology, Badr University in Cairo, Badr City 11829, Egypt
| | - Mohamed K. El-Ashrey
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Kasr Elini St., Cairo 11562, Egypt
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Herrera-Acevedo C, de Menezes RPB, de Sousa NF, Scotti L, Scotti MT, Coy-Barrera E. Kaurane-Type Diterpenoids as Potential Inhibitors of Dihydrofolate Reductase-Thymidylate Synthase in New World Leishmania Species. Antibiotics (Basel) 2023; 12:antibiotics12040663. [PMID: 37107025 PMCID: PMC10135059 DOI: 10.3390/antibiotics12040663] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/14/2023] [Accepted: 03/26/2023] [Indexed: 03/30/2023] Open
Abstract
The bifunctional enzyme Dihydrofolate reductase-thymidylate synthase (DHFR-TS) plays a crucial role in the survival of the Leishmania parasite, as folates are essential cofactors for purine and pyrimidine nucleotide biosynthesis. However, DHFR inhibitors are largely ineffective in controlling trypanosomatid infections, largely due to the presence of Pteridine reductase 1 (PTR1). Therefore, the search for structures with dual inhibitory activity against PTR1/DHFR-TS is crucial in the development of new anti-Leishmania chemotherapies. In this research, using the Leishmania major DHFR-TS recombinant protein, enzymatic inhibitory assays were performed on four kauranes and two derivatives that had been previously tested against LmPTR1. The structure 302 (6.3 µM) and its derivative 302a (4.5 µM) showed the lowest IC50 values among the evaluated molecules. To evaluate the mechanism of action of these structures, molecular docking calculations and molecular dynamics simulations were performed using a DHFR-TS hybrid model. Results showed that hydrogen bond interactions are critical for the inhibitory activity against LmDHFR-TS, as well as the presence of the p-hydroxyl group of the phenylpropanoid moiety of 302a. Finally, additional computational studies were performed on DHFR-TS structures from Leishmania species that cause cutaneous and mucocutaneous leishmaniasis in the New World (L. braziliensis, L. panamensis, and L. amazonensis) to explore the targeting potential of these kauranes in these species. It was demonstrated that structures 302 and 302a are multi-Leishmania species compounds with dual DHFR-TS/PTR1 inhibitory activity.
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Affiliation(s)
- Chonny Herrera-Acevedo
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil (M.T.S.)
- Department of Chemical Engineering, Universidad ECCI, Bogotá, Distrito Capital 111311, Colombia
| | - Renata Priscila Barros de Menezes
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil (M.T.S.)
| | - Natália Ferreira de Sousa
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil (M.T.S.)
| | - Luciana Scotti
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil (M.T.S.)
| | - Marcus Tullius Scotti
- Post-Graduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa 58051-900, PB, Brazil (M.T.S.)
| | - Ericsson Coy-Barrera
- Bioorganic Chemistry Laboratory, Facultad de Ciencias Básicas y Aplicadas, Universidad Militar Nueva Granada, Cajicá 250247, Colombia
- Correspondence:
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