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R D, S W, D P D, R S. Cracking a cancer code DNA methylation in epigenetic modification: an in-silico approach on efficacy assessment of Sri Lanka-oriented nutraceuticals. J Biomol Struct Dyn 2024:1-21. [PMID: 38425013 DOI: 10.1080/07391102.2024.2321235] [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: 08/02/2023] [Accepted: 02/14/2024] [Indexed: 03/02/2024]
Abstract
DNA methyltransferase (DNMTs) are essential epigenetic modifiers that play a critical role in gene regulation. These enzymes add a methyl group to cytosine's 5'-carbon, specifically within CpG dinucleotides, using S-adenosyl-L-methionine. Abnormal overexpression of DNMTs can alter the gene expression patterns and contribute to cancer development in the human body. Therefore, the inhibition of DNMT is a promising therapeutic approach to cancer treatment. This study was aimed to identify potential nutraceutical inhibitors from the Sri Lanka Flora database using computational methods, which provided an atomic-level description of the drug binding site and examined the interactions between nutraceuticals and amino acids of the DNMT enzyme. A series of nutraceuticals from Sri Lanka-oriented plants were selected and evaluated to assess their inhibitory effects on DNMT using absorption, distribution, metabolism, excretion and toxicity analysis, virtual screening, molecular docking, molecular dynamics simulation and trajectory analysis. Azacitidine, a DNMT inhibitor approved by the US Food and Drug Administration, was selected as a reference inhibitor. The complexes with more negative binding energies were selected and further assessed for their potency. Seven molecules were identified from 200 nutraceuticals, demonstrating significantly negative binding energies against the DNMT enzyme. Various trajectory analyses were conducted to investigate the stability of the DNMT enzyme. The results indicated that petchicine (NP#0003), ouregidione (NP#0011) and azacitidine increased the stability of the DNMT enzyme. Consequently, these two nutraceuticals showed inhibitory efficacies similar to azacitidine, making them potential candidates for therapeutic interventions targeting DNMT enzyme-related cancers. Additional bioassay testing is recommended to confirm the efficacies of these nutraceuticals and explore their applicability in clinical treatments.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dushanan R
- Department of Chemistry, Faculty of Natural Sciences, The Open University of Sri Lanka, Nawala, Sri Lanka
| | - Weerasinghe S
- Department of Chemistry, Faculty of Science, University of Colombo, Colombo, Sri Lanka
| | - Dissanayake D P
- Department of Chemistry, Faculty of Science, University of Colombo, Colombo, Sri Lanka
| | - Senthilnithy R
- Department of Chemistry, Faculty of Natural Sciences, The Open University of Sri Lanka, Nawala, Sri Lanka
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Paligaspe PR, Weerasinghe S, Dissanayake DP, Senthilnithy R, Abeysinghe T, Jayasinghe CD. Computational investigation of impact of Pb(II) and Ni(II) ions on hUNG enzyme: insights from molecular dynamics simulations. J Biomol Struct Dyn 2024:1-10. [PMID: 38279925 DOI: 10.1080/07391102.2024.2307442] [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: 07/08/2023] [Accepted: 01/08/2024] [Indexed: 01/29/2024]
Abstract
Human uracil DNA glycosylase (hUNG), a crucial player in the initiation of the base excision repair pathway, is susceptible to alterations in function and conformation induced by the accumulation of toxic metals. Despite the recognized impact of toxic metals on DNA repair enzymes, there exists a notable deficiency in theoretical investigations addressing this phenomenon. This study investigates the impact of toxic heavy metal ions, Pb(II) and Ni(II), on the stability of hUNG through molecular dynamics (MD) simulations. The initial analysis involved the identification of key cavities in the hUNG enzyme. Notably, the active site cavity emerged as a promising site for ligand binding. Subsequently, AutoDockTools software was employed to dock Pb(II) and Ni(II) onto the identified cavities, followed by extensive MD simulations. The MD analysis, encompassing parameters such as root mean square deviation, radius of gyration, solvent accessible surface area, hydrogen bond variations, Ramachandran plot, principal component analysis, and root mean square fluctuations, collectively revealed distinct alterations in the behavior of the enzyme upon complexation with Pb(II) and Ni(II). Interestingly, the enzyme exhibited enhanced structural stability, reduced flexibility, and modified hydrogen bonding patterns in the presence of these toxic metal ions. The observed limitation in structural flexibility implies a more rigid and stable conformation when the enzyme complex with Pb(II) and Ni(II) compared to its free form. This structural alteration may lead to a potential reduction in enzymatic activity, suggesting that toxic metal ions influence the functional dynamics of hUNG. These computational findings offer valuable insights into the molecular interactions between metal ions and enzymes.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Priyani R Paligaspe
- Department of Chemistry, Faculty of Natural Sciences, The Open University of Sri Lanka, Nawala, Nugegoda, Sri Lanka
| | - Samantha Weerasinghe
- Department of Chemistry, Faculty of Science, University of Colombo, Colombo, Sri Lanka
| | | | - Rajendram Senthilnithy
- Department of Chemistry, Faculty of Natural Sciences, The Open University of Sri Lanka, Nawala, Nugegoda, Sri Lanka
| | - Thelma Abeysinghe
- Department of Chemistry, Faculty of Natural Sciences, The Open University of Sri Lanka, Nawala, Nugegoda, Sri Lanka
| | - Chanika D Jayasinghe
- Department of Zoology, Faculty of Natural Sciences, The Open University of Sri Lanka, Nawala, Nugegoda, Sri Lanka
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Ho T, Coleman C, Shah P, Yazbeck V. Advances in Hodgkin's lymphoma pharmacotherapy: a focus on histone deacetylase inhibitors. Expert Opin Pharmacother 2023; 24:1427-1438. [PMID: 37249399 DOI: 10.1080/14656566.2023.2219392] [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: 03/16/2023] [Accepted: 05/25/2023] [Indexed: 05/31/2023]
Abstract
INTRODUCTION Classical Hodgkin lymphomas (cHL) usually have excellent cure rates. Yet, for patients with refractory or relapsed cHL, prognosis deteriorates as the disease becomes resistant to subsequent lines of therapies: autologous stem cell transplantation, brentuximab vedotin, and checkpoint inhibitors. Immune escape and drug resistance are hallmarks of Hodgkin Reed Sternberg cell survival, prompting the need for additional therapeutic strategies. Histone modification-based combination is an effective clinical strategy. AREAS COVERED In this review, we discuss the different histone deacetylase (HDAC) inhibitor molecules that have been developed and studied in cancer therapy with a focus on cHL. We review their preclinical and clinical activities both as single agents and in combination studies. Literature search was conducted in PubMed, Google Scholar, and ClinicalTrials.gov databases, using search terms 'Hodgkin lymphoma,' 'histone deacetylase inhibitor', and variations on such (e.g. 'HDAC' and individual drug names) in combination using operators 'AND,' 'OR,' and 'NOT' according to Boolean logic. EXPERT OPINION HDAC inhibitors alone will not be sufficient for the treatment of R/RcHL, but given their disease control capacity, synergistic interaction with currently approved drugs, and ability to overcome drug resistance, particularly PD-1 inhibitors, we believe that HDACinhibitors will eventually become incorporated into the treatment armamentarium of cHL.
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Affiliation(s)
- Thuy Ho
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Cara Coleman
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Palak Shah
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Victor Yazbeck
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
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Basha NJ. Therapeutic Efficacy of Benzimidazole and Its Analogs: An Update. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2118334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- N. Jeelan Basha
- Department of Chemistry, Indian Academy Degree College-Autonomous Bengaluru, India
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Dushanan R, Weerasinghe S, Dissanayake DP, Senthilinithy R. Implication of Ab Initio, QM/MM, and molecular dynamics calculations on the prediction of the therapeutic potential of some selected HDAC inhibitors. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2097672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Ramachandren Dushanan
- Department of Chemistry, Faculty of Natural Sciences, The Open University of Sri Lanka, Nugegoda, Sri Lanka
| | - Samantha Weerasinghe
- Department of Chemistry, Faculty of Science, University of Colombo, Colombo, Sri Lanka
| | | | - Rajendram Senthilinithy
- Department of Chemistry, Faculty of Natural Sciences, The Open University of Sri Lanka, Nugegoda, Sri Lanka
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Chen X, Song X, Li L, Chen Y, Jia R, Zou Y, Wan H, Zhao L, Tang H, Lv C, Zhao X, Yin Z. Resveratrol Inhibits Pseudorabies Virus Replication by Targeting IE180 Protein. Front Microbiol 2022; 13:891978. [PMID: 35722304 PMCID: PMC9203040 DOI: 10.3389/fmicb.2022.891978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/12/2022] [Indexed: 11/13/2022] Open
Abstract
Resveratrol is a natural polyphenolic product in red wine and peanuts and has many pharmacological activities in humans. Our previous studies showed that resveratrol has good antiviral activity against the pseudorabies virus (PRV). However, little is known about the antiviral mechanism of resveratrol against PRV. In this study, we found that resveratrol inhibited the nuclear localization of IE180 protein, which is an important step for activating early/late genes transcription. Interestingly, the results show that resveratrol inhibited the activity of IE180 protein by dual-luciferase assay. Furthermore, molecular docking analysis shows that resveratrol could bind to the Thr601, Ser603, and Pro606 of IE180 protein. Point mutation assay confirmed that resveratrol lost its inhibition activity against the mutant IE180 protein. The results demonstrate that resveratrol exerts its antiviral activity against PRV by targeting the Thr601/Ser603/Pro606 sites of IE180 protein and inhibiting the transcriptional activation activity of IE180 protein. This study provides a novel insight into the antiviral mechanism of resveratrol against herpes viruses.
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Affiliation(s)
- Xiangxiu Chen
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xu Song
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Lixia Li
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yaqin Chen
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Renyong Jia
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yuanfeng Zou
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Hongping Wan
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ling Zhao
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Huaqiao Tang
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Cheng Lv
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xinghong Zhao
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Zhongqiong Yin
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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Al-Warhi T, Aldhahrani A, Althobaiti F, Fayad E, Abu Ali OA, Albogami S, Abu Almaaty AH, Khedr AIM, Bukhari SNA, Zaki I. Design, Synthesis and Cytotoxic Activity Evaluation of Newly Synthesized Amides-Based TMP Moiety as Potential Anticancer Agents over HepG2 Cells. Molecules 2022; 27:molecules27123960. [PMID: 35745081 PMCID: PMC9227250 DOI: 10.3390/molecules27123960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 05/21/2022] [Accepted: 06/07/2022] [Indexed: 11/17/2022] Open
Abstract
A novel series of amides based TMP moiety was designed, synthesized and evaluated for their antiproliferative as well as enzyme inhibition activity. Compounds 6a and 6b showed remarkable cytotoxic activity against HepG2 cells with IC50 values 0.65 and 0.92 μM, respectively compared with SAHA and CA-4 as reference compounds. In addition, compound 6a demonstrated good HDAC-tubulin dual inhibition activity as it showed better HDAC activity as well as anti-tubulin activity. Moreover, compound 6a exhibited G2/M phase arrest and pre-G1 apoptosis as demonstrated by cell cycle analysis and Annexin V assays. Further apoptosis studies demonstrated that compound 6a boosted the level of caspase 3/7. Caspase 3/7 activation and apoptosis induction were evidenced by decrease in mitochondrial permeability suggesting that activation of caspase 3/7 may occur via mitochondrial apoptotic pathway.
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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;
| | - Adil Aldhahrani
- Clinical Laboratory Sciences Department, Turabah University Faculty, Taif University, Taif 21995, Saudi Arabia;
| | - Fayez Althobaiti
- Department of Biotechnology, Faculty of Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia; (F.A.); (E.F.); (S.A.)
| | - Eman Fayad
- Department of Biotechnology, Faculty of Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia; (F.A.); (E.F.); (S.A.)
| | - Ola A. Abu Ali
- Department of Chemistry, College of Science, Taif University, P.O. Box 11099 Taif 21944, Saudi Arabia;
| | - Sarah Albogami
- Department of Biotechnology, Faculty of Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia; (F.A.); (E.F.); (S.A.)
| | - Ali H. Abu Almaaty
- Zoology Department, Faculty of Science, Port Said University, Port Said 42526, Egypt;
| | - Amgad I. M. Khedr
- Department of Pharmacognosy, Faculty of Pharmacy, Port Said University, Port Said 42526, Egypt;
| | - Syed Nasir Abbas Bukhari
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka 72388, Saudi Arabia;
| | - Islam Zaki
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Port Said University, Port Said 42526, Egypt
- Correspondence: ; Tel.: +20-1153436140
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Paligaspe P, Weerasinghe S, Dissanayake D, Senthilnithy R. Identify the effect of As(III) on the structural stability of monomeric PKM2 and its carcinogenicity: A molecular dynamics and QM/MM based approach. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130257] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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