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Al-Karmalawy AA, Mousa MHA, Sharaky M, Mourad MAE, El-Dessouki AM, Hamouda AO, Alnajjar R, Ayed AA, Shaldam MA, Tawfik HO. Lead Optimization of BIBR1591 To Improve Its Telomerase Inhibitory Activity: Design and Synthesis of Novel Four Chemical Series with In Silico, In Vitro, and In Vivo Preclinical Assessments. J Med Chem 2024; 67:492-512. [PMID: 38117230 DOI: 10.1021/acs.jmedchem.3c01708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Herein, modifications to the previously reported BIBR1591 were conducted to obtain bioisosteric candidates with improved activities. The % inhibition of the newly afforded candidates against the telomerase target was investigated. Notably, 6f achieved superior telomerase inhibition (63.14%) compared to BIBR1532 and BIBR1591 (69.64 and 51.58%, respectively). In addition, 8a and 8b showed comparable promising telomerase inhibition with 58.65 and 55.57%, respectively, which were recorded to be frontier to that of BIBR1591. 6f, 8a, and 8b were tested against five cancer cell lines related to the lung and liver subtypes. Moreover, 6f was examined on both cell cycle progression and apoptosis induction in HuH7 cancer cells. Furthermore, the in vivo antitumor activity of 6f was further assessed in female mice with solid Ehrlich carcinoma. In addition, molecular docking and molecular dynamics simulations were carried out. Collectively, 6f, 8a, and 8b could be considered potential new telomerase inhibitors to be subjected to further investigation and/or optimization.
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Affiliation(s)
- Ahmed A Al-Karmalawy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Horus University-Egypt, New Damietta 34518, Egypt
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ahram Canadian University, 6h of October City, Giza 12566, Egypt
| | - Mai H A Mousa
- Pharmaceutical Chemistry Department, Faculty of Pharmacy and Drug Technology, Egyptian Chinese University, Cairo 11786, Egypt
| | - Marwa Sharaky
- Cancer Biology Department, Pharmacology Unit, National Cancer Institute (NCI), Cairo University, Cairo 12613, Egypt
| | - Mai A E Mourad
- Medicinal Chemistry Department, Faculty of Pharmacy, Port-Said University, Port-Said 42511, Egypt
| | - Ahmed M El-Dessouki
- Pharmacology and Toxicology Department, Faculty of Pharmacy, Ahram Canadian University, 6th of October City, Giza 12566, Egypt
| | - Amir O Hamouda
- Department of Biochemistry, Faculty of Pharmacy, Horus University-Egypt, New Damietta 34518, Egypt
| | - Radwan Alnajjar
- Department of Chemistry, Faculty of Science, University of Benghazi, Benghazi 1308, Libya
- PharmD, Faculty of Pharmacy, Libyan International Medical University, Benghazi 1308, Libya
| | - Abdelmoneim A Ayed
- Department of Chemistry, Faculty of Science, Tanta University, Tanta 31527, Egypt
| | - Moataz A Shaldam
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
| | - Haytham O Tawfik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta 31527, Egypt
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Roney M, Dubey A, Hassan Nasir M, Tufail A, Tajuddin SN, Mohd Aluwi MFF, Huq AM. Computer-aided anti-cancer drug discovery of EGFR protein based on virtual screening of drug bank, ADMET, docking, DFT and molecular dynamic simulation studies. J Biomol Struct Dyn 2023:1-16. [PMID: 37676262 DOI: 10.1080/07391102.2023.2252092] [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: 01/20/2023] [Accepted: 08/21/2023] [Indexed: 09/08/2023]
Abstract
Numerous malignancies, including breast cancer, non-small cell lung cancer, and chronic myeloid leukemia, are brought on by aberrant tyrosine kinase signaling. Since the current chemotherapeutic medicines are toxic, there is a great need and demand from cancer patients to find novel chemicals that are toxic-free or have low toxicity and that can kill tumor cells and stop their growth. This work describes the in-silico examination of substances from the drug bank as EGFR inhibitors. Firstly, drug-bank was screened using the pharmacophore technique to select the ligands and Erlotinib (DB00530) was used as matrix compound. The selected ligands were screened using ADMET and the hit compounds were subjected to docking. The lead compound from the docking was subjected to DFT and MD simulation study. Using the pharmacophore technique, 23 compounds were found through virtual drug bank screening. One hit molecule from the ADMET prediction was the subject of docking study. According to the findings, DB03365 molecule fits to the EGFR active site by several hydrogen bonding interactions with amino acids. Furthermore, DFT analysis revealed high reactivity for DB03365 compound in the binding pocket of the target protein, based on ELUMO, EHOMO and band energy gap. Furthermore, MD simulations for 100 ns revealed that the ligand interactions with the residues of EGFR protein were part of the essential residues for structural stability and functionality. However, DB03365 was a promising lead molecule that outperformed the reference compound in terms of performance and in-vitro and in-vivo experiments needs to validate the study.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Miah Roney
- Faculty of Industrial Sciences and Technology, Universiti Malafysia Pahang Al-Sultan Abdullah, Lebuhraya Tun Razak, Pahang, Darul Makmur, Malaysia
- Centre for Bio-Aromatic Research, Universiti Malaysia Pahang Al-Sultan Abdullah, Lebuhraya Tun Razak, Pahang, Darul Makmur, Malaysia
| | - Amit Dubey
- Department of Pharmacology, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, Tamil Nadu, India
- Computational Chemistry and Drug Discovery Division, Quanta Calculus, Greater Noida, Uttar Pradesh, India
| | - Muhammad Hassan Nasir
- Faculty of Medicine, University Sultan Zainal Abidin (UniSZA), Terengganu, Darul Iman, Malaysia
| | - Aisha Tufail
- Department of Pharmacology, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, Tamil Nadu, India
| | - Saiful Nizam Tajuddin
- Centre for Bio-Aromatic Research, Universiti Malaysia Pahang Al-Sultan Abdullah, Lebuhraya Tun Razak, Pahang, Darul Makmur, Malaysia
| | - Mohd Fadhlizil Fasihi Mohd Aluwi
- Faculty of Industrial Sciences and Technology, Universiti Malafysia Pahang Al-Sultan Abdullah, Lebuhraya Tun Razak, Pahang, Darul Makmur, Malaysia
- Centre for Bio-Aromatic Research, Universiti Malaysia Pahang Al-Sultan Abdullah, Lebuhraya Tun Razak, Pahang, Darul Makmur, Malaysia
| | - Akm Moyeenul Huq
- Centre for Bio-Aromatic Research, Universiti Malaysia Pahang Al-Sultan Abdullah, Lebuhraya Tun Razak, Pahang, Darul Makmur, Malaysia
- Department of Pharmacy, School of Medicine, University of Asia Pacific 74/A, Dhaka, Bangladesh
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Culletta G, Tutone M, Ettari R, Perricone U, Di Chio C, Almerico AM, Zappalà M. Virtual Screening Strategy and In Vitro Tests to Identify New Inhibitors of the Immunoproteasome. Int J Mol Sci 2023; 24:10504. [PMID: 37445688 DOI: 10.3390/ijms241310504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/16/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Immunoproteasome inhibition is a promising strategy for the treatment of hematological malignancies, autoimmune diseases, and inflammatory diseases. The design of non-covalent inhibitors of the immunoproteasome β1i/β5i catalytic subunits could be a novel approach to avoid the drawbacks of the known covalent inhibitors, such as toxicity due to off-target binding. In this work, we report the biological evaluation of thirty-four compounds selected from a commercially available collection. These hit compounds are the outcomes of a virtual screening strategy including a dynamic pharmacophore modeling approach onto the β1i subunit and a pharmacophore/docking approach onto the β5i subunit. The computational studies were first followed by in vitro enzymatic assays at 100 μM. Only compounds capable of inhibiting the enzymatic activity by more than 50% were characterized in detail using Tian continuous assays, determining the dissociation constant (Ki) of the non-covalent complex where Ki is also the measure of the binding affinity. Seven out of thirty-four hits showed to inhibit β1i and/or β5i subunit. Compound 3 is the most active on the β1i subunit with Ki = 11.84 ± 1.63 µM, and compound 17 showed Ki = 12.50 ± 0.77 µM on the β5i subunit. Compound 2 showed inhibitory activity on both subunits (Ki = 12.53 ± 0.18 and Ki = 31.95 ± 0.81 on the β1i subunit and β5i subunit, respectively). The induced fit docking analysis revealed interactions with Thr1 and Phe31 of β1i subunit and that represent new key residues as reported in our previous work. Onto β5i subunit, it interacts with the key residues Thr1, Thr21, and Tyr169. This last hit compound identified represents an interesting starting point for further optimization of β1i/β5i dual inhibitors of the immunoproteasome.
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Affiliation(s)
- Giulia Culletta
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università di Messina, Viale Annunziata, 98168 Messina, Italy
| | - Marco Tutone
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Roberta Ettari
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università di Messina, Viale Annunziata, 98168 Messina, Italy
| | - Ugo Perricone
- Drug Discovery Unit, Fondazione Ri.MED, 90133 Palermo, Italy
| | - Carla Di Chio
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università di Messina, Viale Annunziata, 98168 Messina, Italy
| | - Anna Maria Almerico
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Maria Zappalà
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche ed Ambientali, Università di Messina, Viale Annunziata, 98168 Messina, Italy
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Carollo PS, Tutone M, Culletta G, Fiduccia I, Corrao F, Pibiri I, Di Leonardo A, Zizzo MG, Melfi R, Pace A, Almerico AM, Lentini L. Investigating the Inhibition of FTSJ1, a Tryptophan tRNA-Specific 2'-O-Methyltransferase by NV TRIDs, as a Mechanism of Readthrough in Nonsense Mutated CFTR. Int J Mol Sci 2023; 24:9609. [PMID: 37298560 PMCID: PMC10253411 DOI: 10.3390/ijms24119609] [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: 04/18/2023] [Revised: 05/19/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023] Open
Abstract
Cystic Fibrosis (CF) is an autosomal recessive genetic disease caused by mutations in the CFTR gene, coding for the CFTR chloride channel. About 10% of the CFTR gene mutations are "stop" mutations that generate a premature termination codon (PTC), thus synthesizing a truncated CFTR protein. A way to bypass PTC relies on ribosome readthrough, which is the ribosome's capacity to skip a PTC, thus generating a full-length protein. "TRIDs" are molecules exerting ribosome readthrough; for some, the mechanism of action is still under debate. We investigate a possible mechanism of action (MOA) by which our recently synthesized TRIDs, namely NV848, NV914, and NV930, could exert their readthrough activity by in silico analysis and in vitro studies. Our results suggest a likely inhibition of FTSJ1, a tryptophan tRNA-specific 2'-O-methyltransferase.
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Affiliation(s)
| | - Marco Tutone
- Department of Biological, Chemical, and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy; (P.S.C.); (G.C.); (I.F.); (F.C.); (I.P.); (A.D.L.); (M.G.Z.); (R.M.); (A.P.); (A.M.A.)
| | | | | | | | | | | | | | | | | | | | - Laura Lentini
- Department of Biological, Chemical, and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy; (P.S.C.); (G.C.); (I.F.); (F.C.); (I.P.); (A.D.L.); (M.G.Z.); (R.M.); (A.P.); (A.M.A.)
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Telomerase: A prominent oncological target for development of chemotherapeutic agents. Eur J Med Chem 2023; 249:115121. [PMID: 36669398 DOI: 10.1016/j.ejmech.2023.115121] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/26/2022] [Accepted: 01/11/2023] [Indexed: 01/15/2023]
Abstract
Telomerase is a ribonucleoprotein (RNP) responsible for the maintenance of chromosomal integrity by stabilizing telomere length. Telomerase is a widely expressed hallmark responsible for replicative immortality in 80-90% of malignant tumors. Cancer cells produce telomerase which prevents telomere shortening by adding telomeres sequences beyond Hayflick's limit; which enables them to divide uncontrollably. The activity of telomerase is relatively low in somatic cells and absent in normal cells, but the re-activation of this RNP in normal cells suppresses p53 activity which leads to the avoidance of senescence causing malignancy. Here, we have focused explicitly on various anti-telomerase therapies and telomerase-inhibiting molecules for the treatment of cancer. We have covered molecules that are reported in developmental, preclinical, and clinical trial stages as potent telomerase inhibitors. Apart from chemotherapy, we have also included details of immunotherapy, gene therapy, G-quadruplex stabilizers, and HSP-90 inhibitors. The purpose of this work is to discuss the challenges behind the development of novel telomerase inhibitors and to identify various perspectives for designing anti-telomerase compounds.
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Phenotypic Discovery of Thiocarbohydrazone with Anticancer Properties and Catalytic Inhibition of Human DNA Topoisomerase IIα. Pharmaceuticals (Basel) 2023; 16:ph16030341. [PMID: 36986441 PMCID: PMC10054454 DOI: 10.3390/ph16030341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/06/2023] [Accepted: 02/21/2023] [Indexed: 02/25/2023] Open
Abstract
Phenotypic screening of α-substituted thiocarbohydrazones revealed promising activity of 1,5-bis(salicylidene)thiocarbohydrazide against leukemia and breast cancer cells. Supplementary cell-based studies indicated an impairment of DNA replication via the ROS-independent pathway. The structural similarity of α-substituted thiocarbohydrazone to previously published thiosemicarbazone catalytic inhibitors targeting the ATP-binding site of human DNA topoisomerase IIα prompted us to investigate the inhibition activity on this target. Thiocarbohydrazone acted as a catalytic inhibitor and did not intercalate the DNA molecule, which validated their engagement with this cancer target. A comprehensive computational assessment of molecular recognition for a selected thiosemicarbazone and thiocarbohydrazone provided useful information for further optimization of this discovered lead compound for chemotherapeutic anticancer drug discovery.
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Deciphering the Potential of Pre and Pro-Vitamin D of Mushrooms against Mpro and PLpro Proteases of COVID-19: An In Silico Approach. Molecules 2022; 27:molecules27175620. [PMID: 36080385 PMCID: PMC9458008 DOI: 10.3390/molecules27175620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 08/18/2022] [Indexed: 11/17/2022] Open
Abstract
Vitamin D’s role in combating the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the virus causing COVID-19, has been established in unveiling viable inhibitors of COVID-19. The current study investigated the role of pre and pro-vitamin D bioactives from edible mushrooms against Mpro and PLpro proteases of SARS-CoV-2 by computational experiments. The bioactives of mushrooms, specifically ergosterol (provitamin D2), 7-dehydrocholesterol (provitamin-D3), 22,23-dihydroergocalciferol (provitamin-D4), cholecalciferol (vitamin-D3), and ergocalciferol (vitamin D2) were screened against Mpro and PLpro. Molecular docking analyses of the generated bioactive protease complexes unravelled the differential docking energies, which ranged from −7.5 kcal/mol to −4.5 kcal/mol. Ergosterol exhibited the lowest binding energy (−7.5 kcal/mol) against Mpro and PLpro (−5.9 kcal/mol). The Molecular Mechanics Poisson–Boltzmann Surface Area (MMPBSA) and MD simulation analyses indicated that the generated complexes were stable, thus affirming the putative binding of the bioactives to viral proteases. Considering the pivotal role of vitamin D bioactives, their direct interactions against SARS-CoV-2 proteases highlight the promising role of bioactives present in mushrooms as potent nutraceuticals against COVID-19.
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Synthesis, In Vitro and In Silico Analysis of New Oleanolic Acid and Lupeol Derivatives against Leukemia Cell Lines: Involvement of the NF-κB Pathway. Int J Mol Sci 2022; 23:ijms23126594. [PMID: 35743037 PMCID: PMC9223357 DOI: 10.3390/ijms23126594] [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: 05/16/2022] [Revised: 06/08/2022] [Accepted: 06/11/2022] [Indexed: 12/02/2022] Open
Abstract
Oleanolic acid (OA) and Lupeol (LU) belong to the class of natural triterpenes and are endowed with a wide range of biological activities, including cytotoxicity toward several cancer cell lines. In this context, we investigated a set of compounds obtained from the two natural precursors for the cytotoxicity against leukemia HL60 cells and the multidrug-resistant (MDR) variant HL60R. Six new semi-synthetic triterpenes have been synthetized, fully characterized, and were investigated together with other triterpenes compounds for their pharmacological mechanism of action. The interaction of the more cytotoxic compounds with the nuclear factor kappa B (NF-κB) pathway has been also evaluated with the aid of docking. The lupane-like compounds were more active than the precursor, while the oleane-like compounds showed more complex behavior. Both OA and LU derivatives possess a similar interaction pattern with the p65 subunit of NF-κB, justifying the similar trend in their ability to inhibit the binding of p65 to DNA. Further, some of the derivatives tested were able to increase IκB-α levels preventing the translocation of NF-κB to the nucleus. In conclusion, this study offers a deeper insight on the pharmacological action of triterpenes toward leukemia cells, and it improves the background useful for the development of new anti-cancer drugs.
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