1
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Nemetova U, Si̇yah P, Boran T, Bi̇lgi̇ Ç, Özyürek M, Şahi̇nler Ayla S. Synthesis and In Silico Evaluation of Piperazine-Substituted 2,3-Dichloro-5,8-dihydroxy-1,4-naphthoquinone Derivatives as Potential PARP-1 Inhibitors. ACS OMEGA 2024; 9:39733-39742. [PMID: 39346823 PMCID: PMC11425603 DOI: 10.1021/acsomega.4c04915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 08/28/2024] [Accepted: 08/30/2024] [Indexed: 10/01/2024]
Abstract
PARP-1 (poly(ADP-ribose)-polymerase 1) inhibitors are vital in synthetic lethality, primarily due to their specificity for PARP-1 over PARP-2 (PARP-1 > PARP-2). This specificity is crucial as it allows precise inhibition of PARP-1 in tumor cells with Breast Cancer 1 protein (BRCA1) or BRCA2 deficiencies. The development of highly specific PARP-1 inhibitors not only meets the therapeutic needs of tumor treatment but also has the potential to minimize the adverse effects associated with nonselective PARP-2 inhibition. In this study, a series of novel 2,3-dichloro-5,8-dihydroxy-1,4-naphthoquinone (DDNO) derivatives were synthesized, characterized, and evaluated regarding their PARP-1 inhibitory and cytotoxic activity. Compound 3 exhibited the highest cytotoxic potential against all cell lines, except for MDA-MB-231 cells. The inhibitory potential of these molecules against PARP-1 was evaluated through in silico molecular docking and molecular dynamics studies. Notably, compounds 5, 9, and 13 exhibited significant inhibitory activity in silico results, interacting with critical amino acids known to be important for PARP-1 inhibition during simulations. These compounds exhibited target-specific and strong binding profiles, with docking scores of -7.17, -7.41, and -7.37 kcal/mol, respectively, and MM/GBSA scores of -52.51, -43.77, and -62.87 kcal/mol, respectively. These novel compounds (DDNO derivatives) hold promise as potential PARP-1 inhibitors for the development of targeted therapeutics against cancer.
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Affiliation(s)
- Ulviyye Nemetova
- Engineering
Faculty, Department of Chemistry, Organic Chemistry, Istanbul University-Cerrahpaşa, 34320 Istanbul, Turkey
| | - Pınar Si̇yah
- Department
of Biochemistry, Faculty of Pharmacy, Bahcesehir
University, 34353 Istanbul, Turkey
| | - Tuğçe Boran
- Faculty
of Pharmacy, Department of Pharmaceutical Toxicology, Istanbul University-Cerrahpaşa, 34500 Istanbul, Turkey
| | - Çiğdem Bi̇lgi̇
- Faculty
of Pharmacy, Department of Pharmacognosy, Istanbul University-Cerrahpaşa, 34500 Istanbul, Turkey
| | - Mustafa Özyürek
- Engineering
Faculty, Department of Chemistry, Analytical Chemistry, Istanbul University-Cerrahpaşa, 34320 Istanbul, Turkey
| | - Sibel Şahi̇nler Ayla
- Engineering
Faculty, Department of Chemistry, Organic Chemistry, Istanbul University-Cerrahpaşa, 34320 Istanbul, Turkey
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2
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Baghel R, Maan K, Dhariwal S, Kumari M, Sharma A, Manda K, Trivedi R, Rana P. Mild Blast Exposure Dysregulates Metabolic Pathways and Correlation Networking as Evident from LC-MS-Based Plasma Profiling. Mol Neurobiol 2024:10.1007/s12035-024-04429-5. [PMID: 39235645 DOI: 10.1007/s12035-024-04429-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 08/08/2024] [Indexed: 09/06/2024]
Abstract
Blast-induced trauma is emerging as a serious threat due to its wide pathophysiology where not only the brain but also a spectrum of organs is being affected. In the present study, we aim to identify the plasma-based metabolic dysregulations along with the associated temporal changes at 5-6 h, day 1 and day 7 post-injury in a preclinical animal model for blast exposure, through liquid chromatography-mass spectrometry (LC-MS). Using significantly advanced metabolomic and statistical bioinformatic platforms, we were able to elucidate better and unravel the complex networks of blast-induced neurotrauma (BINT) and its interlinked systemic effects. Significant changes were evident at 5-6 h with maximal changes at day 1. Temporal analysis also depicted progressive changes which continued till day 7. Significant associations of metabolic markers belonging to the class of amino acids, energy-related molecules, lipids, vitamin, hormone, phenolic acid, keto and histidine derivatives, nucleic acid molecules, uremic toxins, and uronic acids were observed. Also, the present study is the first of its kind where comprehensive, detailed pathway dysregulations of amino acid metabolism and biosynthesis, perturbed nucleotides, lipid peroxidation, and nucleic acid damage followed by correlation networking and multiomics networking were explored on preclinical animal models exposed to mild blast trauma. In addition, markers for systemic changes (renal dysfunction) were also observed. Global pathway predictions of unannotated peaks also presented important insights into BINT pathophysiology. Conclusively, the present study depicts important findings that might help underpin the biological mechanisms of blast-induced brain or systemic trauma.
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Grants
- (DHR)-YSF/DHR/12014/54/2020 Department of Health Research, India
- UGC Grant University Grants Commission
- UGC Grant University Grants Commission
- CSIR-Grant Council of Scientific and Industrial Research, India
- INM3 24 Defence R&D Organization (DRDO), Ministry of Defence, India
- INM3 24 Defence R&D Organization (DRDO), Ministry of Defence, India
- INM3 24 Defence R&D Organization (DRDO), Ministry of Defence, India
- INM3 24 Defence R&D Organization (DRDO), Ministry of Defence, India
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Affiliation(s)
- Ruchi Baghel
- Radiological, Nuclear and Imaging Sciences (RNAIS), Institute of Nuclear Medicine and Allied Science (INMAS), DRDO, New Delhi, 110054, India
- Department of Health Research (DHR), IRCS Building, 2 FloorRed Cross Road, New Delhi, 110001, India
- Metabolomics Research Facility, Institute of Nuclear Medicine and Allied Sciences (INMAS), DRDO, S. K Mazumdar Road, Timarpur, New Delhi, 110054, India
| | - Kiran Maan
- Radiological, Nuclear and Imaging Sciences (RNAIS), Institute of Nuclear Medicine and Allied Science (INMAS), DRDO, New Delhi, 110054, India
- Metabolomics Research Facility, Institute of Nuclear Medicine and Allied Sciences (INMAS), DRDO, S. K Mazumdar Road, Timarpur, New Delhi, 110054, India
| | - Seema Dhariwal
- Radiological, Nuclear and Imaging Sciences (RNAIS), Institute of Nuclear Medicine and Allied Science (INMAS), DRDO, New Delhi, 110054, India
- Metabolomics Research Facility, Institute of Nuclear Medicine and Allied Sciences (INMAS), DRDO, S. K Mazumdar Road, Timarpur, New Delhi, 110054, India
| | - Megha Kumari
- Radiological, Nuclear and Imaging Sciences (RNAIS), Institute of Nuclear Medicine and Allied Science (INMAS), DRDO, New Delhi, 110054, India
| | - Apoorva Sharma
- Radiological, Nuclear and Imaging Sciences (RNAIS), Institute of Nuclear Medicine and Allied Science (INMAS), DRDO, New Delhi, 110054, India
- Metabolomics Research Facility, Institute of Nuclear Medicine and Allied Sciences (INMAS), DRDO, S. K Mazumdar Road, Timarpur, New Delhi, 110054, India
| | - Kailash Manda
- Department of Neurobehavioral Sciences, Institute of Nuclear Medicine and Allied Science (INMAS), DRDO, New Delhi, 110054, India
| | - Richa Trivedi
- Radiological, Nuclear and Imaging Sciences (RNAIS), Institute of Nuclear Medicine and Allied Science (INMAS), DRDO, New Delhi, 110054, India
| | - Poonam Rana
- Radiological, Nuclear and Imaging Sciences (RNAIS), Institute of Nuclear Medicine and Allied Science (INMAS), DRDO, New Delhi, 110054, India.
- Metabolomics Research Facility, Institute of Nuclear Medicine and Allied Sciences (INMAS), DRDO, S. K Mazumdar Road, Timarpur, New Delhi, 110054, India.
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Kirsanov KI, Fetisov TI, Antoshina EE, Gor’kova TG, Trukhanova LS, Shram SI, Nagaev IY, Zolotarev YA, Qoura LA, Pokrovsky VS, Yakubovskaya MG, Švedas VK, Nilov DK. 7-Methylguanine Inhibits Colon Cancer Growth in Vivo. Acta Naturae 2024; 16:50-52. [PMID: 39188268 PMCID: PMC11345089 DOI: 10.32607/actanaturae.27422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 06/26/2024] [Indexed: 08/28/2024] Open
Abstract
7-Methylguanine (7-MG) is a natural inhibitor of poly(ADP-ribose) polymerase 1 and tRNA-guanine transglycosylase, the enzymatic activity of which is central for the proliferation of cancer cells. Recently, a number of preclinical tests have demonstrated the safety of 7-MG and a regimen of intragastric administration was established in mice. In the present work, the pharmacological activity of 7-MG was studied in BALB/c and BALB/c nude mice with transplanted tumors. It was found that 7-MG effectively penetrates tumor tissue and suppresses colon adenocarcinoma growth in the Akatol model, as well as in a xenograft model with human HCT116 cells.
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Affiliation(s)
- K. I. Kirsanov
- Blokhin National Medical Research Center of Oncology, Institute of Carcinogenesis, Moscow, 115478 Russian Federation
- RUDN University, Medical Institute, Moscow, 117198 Russian Federation
| | - T. I. Fetisov
- Blokhin National Medical Research Center of Oncology, Institute of Carcinogenesis, Moscow, 115478 Russian Federation
| | - E. E. Antoshina
- Blokhin National Medical Research Center of Oncology, Institute of Carcinogenesis, Moscow, 115478 Russian Federation
| | - T. G. Gor’kova
- Blokhin National Medical Research Center of Oncology, Institute of Carcinogenesis, Moscow, 115478 Russian Federation
| | - L. S. Trukhanova
- Blokhin National Medical Research Center of Oncology, Institute of Carcinogenesis, Moscow, 115478 Russian Federation
| | - S. I. Shram
- National Research Centre “Kurchatov Institute”, Moscow, 123182 Russian Federation
| | - I. Yu. Nagaev
- National Research Centre “Kurchatov Institute”, Moscow, 123182 Russian Federation
| | - Yu. A. Zolotarev
- National Research Centre “Kurchatov Institute”, Moscow, 123182 Russian Federation
| | - L. Abo Qoura
- Blokhin National Medical Research Center of Oncology, Institute of Carcinogenesis, Moscow, 115478 Russian Federation
- RUDN University, Medical Institute, Moscow, 117198 Russian Federation
| | - V. S. Pokrovsky
- Blokhin National Medical Research Center of Oncology, Institute of Carcinogenesis, Moscow, 115478 Russian Federation
- RUDN University, Medical Institute, Moscow, 117198 Russian Federation
| | - M. G. Yakubovskaya
- Blokhin National Medical Research Center of Oncology, Institute of Carcinogenesis, Moscow, 115478 Russian Federation
| | - V. K. Švedas
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Moscow, 119991 Russian Federation
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119234 Russian Federation
| | - D. K. Nilov
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Moscow, 119991 Russian Federation
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Li WH, Wang F, Song GY, Yu QH, Du RP, Xu P. PARP-1: a critical regulator in radioprotection and radiotherapy-mechanisms, challenges, and therapeutic opportunities. Front Pharmacol 2023; 14:1198948. [PMID: 37351512 PMCID: PMC10283042 DOI: 10.3389/fphar.2023.1198948] [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: 04/02/2023] [Accepted: 05/22/2023] [Indexed: 06/24/2023] Open
Abstract
Background: Since its discovery, poly (ADP-ribose) polymerase 1 (PARP-1) has been extensively studied due to its regulatory role in numerous biologically crucial pathways. PARP inhibitors have opened new therapeutic avenues for cancer patients and have gained approval as standalone treatments for certain types of cancer. With continued advancements in the research of PARP inhibitors, we can fully realize their potential as therapeutic targets for various diseases. Purpose: To assess the current understanding of PARP-1 mechanisms in radioprotection and radiotherapy based on the literature. Methods: We searched the PubMed database and summarized information on PARP inhibitors, the interaction of PARP-1 with DNA, and the relationships between PARP-1 and p53/ROS, NF-κB/DNA-PK, and caspase3/AIF, respectively. Results: The enzyme PARP-1 plays a crucial role in repairing DNA damage and modifying proteins. Cells exposed to radiation can experience DNA damage, such as single-, intra-, or inter-strand damage. This damage, associated with replication fork stagnation, triggers DNA repair mechanisms, including those involving PARP-1. The activity of PARP-1 increases 500-fold on DNA binding. Studies on PARP-1-knockdown mice have shown that the protein regulates the response to radiation. A lack of PARP-1 also increases the organism's sensitivity to radiation injury. PARP-1 has been found positively or negatively regulate the expression of specific genes through its modulation of key transcription factors and other molecules, including NF-κB, p53, Caspase 3, reactive oxygen species (ROS), and apoptosis-inducing factor (AIF). Conclusion: This review provides a comprehensive analysis of the physiological and pathological roles of PARP-1 and examines the impact of PARP-1 inhibitors under conditions of ionizing radiation exposure. The review also emphasizes the challenges and opportunities for developing PARP-1 inhibitors to improve the clinical outcomes of ionizing radiation damage.
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Affiliation(s)
- Wen-Hao Li
- School of Food and Biomedicine, Zaozhuang University, Zaozhuang, Shandong, China
| | - Fei Wang
- School of Food and Biomedicine, Zaozhuang University, Zaozhuang, Shandong, China
| | - Gui-Yuan Song
- School of Public Health, Weifang Medical University, Weifang, Shandong, China
| | - Qing-Hua Yu
- School of Public Health, Weifang Medical University, Weifang, Shandong, China
| | - Rui-Peng Du
- School of Food and Biomedicine, Zaozhuang University, Zaozhuang, Shandong, China
| | - Ping Xu
- School of Food and Biomedicine, Zaozhuang University, Zaozhuang, Shandong, China
- School of Public Health, Weifang Medical University, Weifang, Shandong, China
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5
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Shram SI, Shcherbakova TA, Abramova TV, Baradieva EC, Efremova AS, Smirnovskaya MS, Silnikov VN, Švedas VK, Nilov DK. Natural Guanine Derivatives Exert PARP-Inhibitory and Cytoprotective Effects in a Model of Cardiomyocyte Damage under Oxidative Stress. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:783-791. [PMID: 37748874 DOI: 10.1134/s0006297923060068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/27/2023] [Accepted: 03/27/2023] [Indexed: 09/27/2023]
Abstract
Inhibitors of human poly(ADP-ribose) polymerase (PARP) are considered as promising agents for treatment of cardiovascular, neurological, and other diseases accompanied by inflammation and oxidative stress. Previously, the ability of natural compounds 7-methylguanine (7mGua) and 8-hydroxy-7-methylguanine (8h7mGua) to suppress activity of the recombinant PARP protein was demonstrated. In the present work, we have investigated the possibility of PARP-inhibitory and cytoprotective action of 7mGua and 8h7mGua against the rat cardiomyoblast cultures (undifferentiated and differentiated H9c2). It was found that 7mGua and 8h7mGua rapidly penetrate into the cells and effectively suppress the H2O2-stimulated PARP activation (IC50 = 270 and 55 μM, respectively). The pronounced cytoprotective effects of 7mGua and 8h7mGua were shown in a cellular model of oxidative stress, and effectiveness of 8h7mGua exceeded the classic PARP inhibitor 3-aminobenzamide. The obtained data indicate promise for the development of PARP inhibitors based on guanine derivatives and their testing using the models of ischemia-reperfusion tissue damage.
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Affiliation(s)
- Stanislav I Shram
- Institute of Molecular Genetics, National Research Centre "Kurchatov Institute", Moscow, 123182, Russia.
| | - Tatyana A Shcherbakova
- Lomonosov Moscow State University, Belozersky Institute of Physico-Chemical Biology, Moscow, 119991, Russia
| | - Tatyana V Abramova
- Institute of Chemical Biology and Fundamental Medicine, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia
| | - Erzhena C Baradieva
- Institute of Molecular Genetics, National Research Centre "Kurchatov Institute", Moscow, 123182, Russia
| | - Anna S Efremova
- Research Centre for Medical Genetics, Moscow, 115522, Russia
| | | | - Vladimir N Silnikov
- Institute of Chemical Biology and Fundamental Medicine, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia
| | - Vytas K Švedas
- Lomonosov Moscow State University, Belozersky Institute of Physico-Chemical Biology, Moscow, 119991, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Dmitry K Nilov
- Lomonosov Moscow State University, Belozersky Institute of Physico-Chemical Biology, Moscow, 119991, Russia.
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6
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Volcho KP, Lavrik OI. Inhibition of DNA Repair Enzymes as a Valuable Pharmaceutical Approach. Int J Mol Sci 2023; 24:ijms24097954. [PMID: 37175662 PMCID: PMC10177907 DOI: 10.3390/ijms24097954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
The DNA repair system plays a crucial role in maintaining the integrity of the genome [...].
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Affiliation(s)
- Konstantin P Volcho
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
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7
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Khanam T, Liang S, Xu S, Musstjab Akber Shah Eqani SA, Shafqat MN, Rasheed H, Bibi N, Shen H, Zhang J. Arsenic exposure induces urinary metabolome disruption in Pakistani male population. CHEMOSPHERE 2023; 312:137228. [PMID: 36372340 DOI: 10.1016/j.chemosphere.2022.137228] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
Millions of people are at risk of consuming arsenic (As) contaminated drinking water in Pakistan. The current study aimed to investigate urinary arsenic species [iAsIII, iAsV, dimethylarsinic acid (DMA), methylarsonic acid (MMA)] and their potential toxicity biomarkers (based on urinary metabolome) in order to characterize the health effects in general adult male participants (n = 588) exposed to various levels of arsenic in different floodplain areas of Pakistan. The total urinary arsenic concentration (mean; 161 μg/L) of studied participants was lower and/or comparable than those values reported from other highly contaminated regions, but exceeded the Agency for Toxic Substances and Disease Registry (ATSDR) limits. For all the participants, the most excreted species was DMA accounting for 65% of the total arsenic, followed by MMA (20%) and iAs (16%). The percentage of MMA detected in this study was higher than those of previously reported data from other countries. These results suggested that studied population might have high risk of developing arsenic exposure related adverse health outcomes. Furthermore, random forest machine learning algorithm, partial correlation and binary logistic regression analysis were performed to screen the arsenic species-related urinary metabolites. A total of thirty-eight metabolites were extracted from 2776 metabolic features and identified as the potential arsenic toxicity biomarkers. The metabolites were mainly classified into xanthines, purines, and amino acids, which provided the clues linking the arsenic exposure with oxidative stress, one-carbon metabolism, purine metabolism, caffeine metabolism and hormone metabolism. These results would be helpful to develop early health warning system in context of arsenic exposure among the general populations of Pakistan.
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Affiliation(s)
- Tasawar Khanam
- Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | - Shijia Liang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, 361102, Xiamen, China
| | - Song Xu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, 361102, Xiamen, China
| | | | | | - Hifza Rasheed
- National Laboratory for the Water Quality, Pakistan Council Research Water Resources, Islamabad, Pakistan
| | - Nazia Bibi
- Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | - Heqing Shen
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, 361102, Xiamen, China
| | - Jie Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, 361102, Xiamen, China.
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8
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Okunlola FO, Olotu FA, Soliman MES. Unveiling the mechanistic roles of chlorine substituted phthalazinone-based compounds containing chlorophenyl moiety towards the differential inhibition of poly (ADP-ribose) polymerase-1 in the treatment of lung cancer. J Biomol Struct Dyn 2022; 40:10878-10886. [PMID: 34463214 DOI: 10.1080/07391102.2021.1951354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
PARP-1 has become an attractive target in cancer treatment owing to its significant role in breast and ovarian cancers. The design of highly selective and effective poly (ADP ribose) polymerase-1 inhibitors has significant therapeutic advantages and has remained the core of several PARP-1-based drug discovery research. The pharmacophoric relevance of a chlorine substituent in a recent study led to the design of compounds 11c (meta-chlorophenyl) and 11d (para-chlorophenyl). In this study, we resolved the mechanistic effects of the changes in chlorine positional orientation, which underlie the inhibitory potencies and selectivity exhibited disparately by 11c and 11d. Compared to 11d, among other multiple higher-affinity complementary interactions with key site residues, the meta-Cl positioning in 11c facilitated its optimal motion and orientation towards conserved residues Arg878 and Asp766 with consistent pi-cation and pi-anion interactions, respectively, thereby favoring the stability of the ligand towards PARP-1. These could account for the higher inhibitory potency exhibited by 11c relative to 11d against PARP-1. The thermodynamics calculation revealed that 11c had a relatively higher total binding energy (ΔGbind) than 11d. We also observed that 11d displayed high deviations, compared to 11c, indicative of its unstable binding orientation. Furthermore, we reported in this study that the high involvement of electrostatic and van der Waal effects potentiated the binding affinity and strength of 11c (ΔEvdW = -50.58 and ΔEele = -27.20) relative to 11d (ΔEvdW = -49.46 and ΔEele = -19.96) at PARP-1 binding pocket. We believe the findings in this current study would provide valuable insights into the design of selective PARP-1 inhibitors containing chlorine substituent for cancer treatment, including lung cancer.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Felix O Okunlola
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Fisayo A Olotu
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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Rushing BR, Fogle HM, Sharma J, You M, McCormac JP, Molina S, Sumner S, Krupenko NI, Krupenko SA. Exploratory Metabolomics Underscores the Folate Enzyme ALDH1L1 as a Regulator of Glycine and Methylation Reactions. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238394. [PMID: 36500483 PMCID: PMC9740053 DOI: 10.3390/molecules27238394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/22/2022] [Accepted: 11/28/2022] [Indexed: 12/02/2022]
Abstract
Folate (vitamin B9) is involved in one-carbon transfer reactions and plays a significant role in nucleic acid synthesis and control of cellular proliferation, among other key cellular processes. It is now recognized that the role of folates in different stages of carcinogenesis is complex, and more research is needed to understand how folate reactions become dysregulated in cancers and the metabolic consequences that occur as a result. ALDH1L1 (cytosolic 10-formyltetrahydrofolate dehydrogenase), an enzyme of folate metabolism expressed in many tissues, is ubiquitously downregulated in cancers and is not expressed in cancer cell lines. The RT4 cell line (derived from papillary bladder cancer) which expresses high levels of ALDH1L1 represents an exception, providing an opportunity to explore the metabolic consequences of the loss of this enzyme. We have downregulated this protein in RT4 cells (shRNA driven knockdown or CRISPR driven knockout) and compared metabolomes of ALDH1L1-expressing and -deficient cells to determine if metabolic changes linked to the loss of this enzyme might provide proliferative and/or survival advantages for cancer cells. In this study, cell extracts were analyzed using Ultra High Performance Liquid Chromatography High Resolution Mass Spectrometry (UHPLC-HR-MS). A total of 13,339 signals were identified or annotated using an in-house library and public databases. Supervised and unsupervised multivariate analysis revealed metabolic differences between RT4 cells and ALDH1L1-deficient clones. Glycine (8-fold decrease) and metabolites derived from S-adenosylmethionine utilizing pathways were significantly decreased in the ALDH1L1-deficient clones, compared with RT4 cells. Other changes linked to ALDH1L1 downregulation include decreased levels of amino acids, Krebs cycle intermediates, and ribose-5-phosphate, and increased nicotinic acid. While the ALDH1L1-catalyzed reaction is directly linked to glycine biosynthesis and methyl group flux, its overall effect on cellular metabolism extends beyond immediate metabolic pathways controlled by this enzyme.
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Affiliation(s)
- Blake R. Rushing
- Nutrition Research Institute, UNC Chapel Hill, Kannapolis, NC 28081, USA
- Department of Nutrition, UNC Chapel Hill, Chapel Hill, NC 27599, USA
| | - Halle M. Fogle
- Nutrition Research Institute, UNC Chapel Hill, Kannapolis, NC 28081, USA
- Department of Nutrition, UNC Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jaspreet Sharma
- Nutrition Research Institute, UNC Chapel Hill, Kannapolis, NC 28081, USA
| | - Mikyoung You
- Nutrition Research Institute, UNC Chapel Hill, Kannapolis, NC 28081, USA
| | | | - Sabrina Molina
- Nutrition Research Institute, UNC Chapel Hill, Kannapolis, NC 28081, USA
| | - Susan Sumner
- Nutrition Research Institute, UNC Chapel Hill, Kannapolis, NC 28081, USA
- Department of Nutrition, UNC Chapel Hill, Chapel Hill, NC 27599, USA
- Correspondence: (S.S.); (S.A.K.)
| | - Natalia I. Krupenko
- Nutrition Research Institute, UNC Chapel Hill, Kannapolis, NC 28081, USA
- Department of Nutrition, UNC Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sergey A. Krupenko
- Nutrition Research Institute, UNC Chapel Hill, Kannapolis, NC 28081, USA
- Department of Nutrition, UNC Chapel Hill, Chapel Hill, NC 27599, USA
- Correspondence: (S.S.); (S.A.K.)
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10
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Kurgina TA, Shram SI, Kutuzov MM, Abramova TV, Shcherbakova TA, Maltseva EA, Poroikov VV, Lavrik OI, Švedas VK, Nilov DK. Inhibitory Effects of 7-Methylguanine and Its Metabolite 8-Hydroxy-7-Methylguanine on Human Poly(ADP-Ribose) Polymerase 1. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:823-831. [PMID: 36171646 DOI: 10.1134/s0006297922080132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/23/2022] [Accepted: 05/23/2022] [Indexed: 06/16/2023]
Abstract
Previously, we have found that a nucleic acid metabolite, 7-methylguanine (7mGua), produced in the body can have an inhibitory effect on the poly(ADP-ribose) polymerase 1 (PARP1) enzyme, an important pharmacological target in anticancer therapy. In this work, using an original method of analysis of PARP1 activity based on monitoring fluorescence anisotropy, we studied inhibitory properties of 7mGua and its metabolite, 8-hydroxy-7-methylguanine (8h7mGua). Both compounds inhibited PARP1 enzymatic activity in a dose-dependent manner, however, 8h7mGua was shown to be a stronger inhibitor. The IC50 values for 8h7mGua at different concentrations of the NAD+ substrate were found to be 4 times lower, on average, than those for 7mGua. The more efficient binding of 8h7mGua in the PARP1 active site is explained by the presence of an additional hydrogen bond with the Glu988 catalytic residue. Experimental and computational studies did not reveal the effect of 7mGua and 8h7mGua on the activity of other DNA repair enzymes, indicating selectivity of their inhibitory action.
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Affiliation(s)
- Tatyana A Kurgina
- Institute of Chemical Biology and Fundamental Medicine, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia
| | - Stanislav I Shram
- Institute of Molecular Genetics of National Research Center "Kurchatov Institute", Moscow, 123182, Russia
| | - Mikhail M Kutuzov
- Institute of Chemical Biology and Fundamental Medicine, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia
| | - Tatyana V Abramova
- Institute of Chemical Biology and Fundamental Medicine, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia
| | - Tatyana A Shcherbakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Ekaterina A Maltseva
- Institute of Chemical Biology and Fundamental Medicine, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia
| | | | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Vytas K Švedas
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia
- Research Computing Center, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Dmitry K Nilov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
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11
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Kirsanov K, Fetisov T, Antoshina E, Trukhanova L, Gor'kova T, Vlasova O, Khitrovo I, Lesovaya E, Kulbachevskaya N, Shcherbakova T, Belitsky G, Yakubovskaya M, Švedas V, Nilov D. Toxicological Properties of 7-Methylguanine, and Preliminary Data on its Anticancer Activity. Front Pharmacol 2022; 13:842316. [PMID: 35873588 PMCID: PMC9299380 DOI: 10.3389/fphar.2022.842316] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 06/13/2022] [Indexed: 11/13/2022] Open
Abstract
7-Methylguanine (7-MG) competitively inhibits the DNA repair enzyme poly(ADP-ribose) polymerase (PARP) and RNA-modifying enzyme tRNA-guanine transglycosylase (TGT) and represents a potential anticancer drug candidate. Furthermore, as a natural compound, it could escape the serious side effects characteristic for approved synthetic PARP inhibitors. Here we present a comprehensive study of toxicological and carcinogenic properties of 7-MG. It was demonstrated that 7-MG does not induce mutations or structural chromosomal abnormalities, and has no blastomogenic activity. A treatment regimen with 7-MG has been established in mice (50 mg/kg per os, 3 times per week), exerting no adverse effects or changes in morphology. Preliminary data on the 7-MG anticancer activity obtained on transplantable tumor models support our conclusions that 7-MG can become a promising new component of chemotherapy.
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Affiliation(s)
- Kirill Kirsanov
- Blokhin Cancer Research Center, Moscow, Russia.,Peoples' Friendship University of Russia, Moscow, Russia
| | | | | | | | | | | | | | - Ekaterina Lesovaya
- Blokhin Cancer Research Center, Moscow, Russia.,Pavlov Ryazan State Medical University, Ryazan, Russia
| | | | - Tatiana Shcherbakova
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | | | - Vytas Švedas
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Dmitry Nilov
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russia
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12
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Pushkarev SV, Vinnik VA, Shapovalova IV, Švedas VK, Nilov DK. Modeling the Structure of Human tRNA-Guanine Transglycosylase in Complex with 7-Methylguanine and Revealing the Factors that Determine the Enzyme Interaction with Inhibitors. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:443-449. [PMID: 35790378 DOI: 10.1134/s0006297922050054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/22/2022] [Accepted: 03/23/2022] [Indexed: 06/15/2023]
Abstract
tRNA-guanine transglycosylase, an enzyme catalyzing replacement of guanine with queuine in human tRNA and participating in the translation mechanism, is involved in the development of cancer. However, information on the small-molecule inhibitors that can suppress activity of this enzyme is very limited. Molecular dynamics simulations were used to determine the amino acid residues that provide efficient binding of inhibitors in the active site of tRNA-guanine transglycosylase. It was demonstrated using 7-methylguanine molecule as a probe that the ability of the inhibitor to adopt a charged state in the environment of hydrogen bond acceptors Asp105 and Asp159 plays a key role in complex formation. Formation of the hydrogen bonds and hydrophobic contacts with Gln202, Gly229, Phe109, and Met259 residues are also important. It has been predicted that introduction of the substituents would have a different effect on the ability to inhibit tRNA-guanine transglycosylase, as well as the DNA repair protein poly(ADP-ribose) polymerase 1, which can contribute to the development of more efficient and selective compounds.
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Affiliation(s)
- Sergey V Pushkarev
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Valeriia A Vinnik
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Irina V Shapovalova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Vytas K Švedas
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Dmitry K Nilov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
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13
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Maluchenko NV, Nilov DK, Pushkarev SV, Kotova EY, Gerasimova NS, Kirpichnikov MP, Langelier MF, Pascal JM, Akhtar MS, Feofanov AV, Studitsky VM. Mechanisms of Nucleosome Reorganization by PARP1. Int J Mol Sci 2021; 22:ijms222212127. [PMID: 34830005 PMCID: PMC8620739 DOI: 10.3390/ijms222212127] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/30/2021] [Accepted: 11/04/2021] [Indexed: 01/14/2023] Open
Abstract
Poly(ADP-ribose) polymerase 1 (PARP1) is an enzyme involved in DNA repair, chromatin organization and transcription. During transcription initiation, PARP1 interacts with gene promoters where it binds to nucleosomes, replaces linker histone H1 and participates in gene regulation. However, the mechanisms of PARP1-nucleosome interaction remain unknown. Here, using spFRET microscopy, molecular dynamics and biochemical approaches we identified several different PARP1-nucleosome complexes and two types of PARP1 binding to mononucleosomes: at DNA ends and end-independent. Two or three molecules of PARP1 can bind to a nucleosome depending on the presence of linker DNA and can induce reorganization of the entire nucleosome that is independent of catalytic activity of PARP1. Nucleosome reorganization depends upon binding of PARP1 to nucleosomal DNA, likely near the binding site of linker histone H1. The data suggest that PARP1 can induce the formation of an alternative nucleosome state that is likely involved in gene regulation and DNA repair.
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Affiliation(s)
- Natalya V. Maluchenko
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (N.V.M.); (N.S.G.); (M.P.K.)
| | - Dmitry K. Nilov
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Sergey V. Pushkarev
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | | | - Nadezhda S. Gerasimova
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (N.V.M.); (N.S.G.); (M.P.K.)
| | - Mikhail P. Kirpichnikov
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (N.V.M.); (N.S.G.); (M.P.K.)
| | - Marie-France Langelier
- Department of Biochemistry and Molecular Medicine, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montreal, QC H3T 1J4, Canada; (M.-F.L.); (J.M.P.)
| | - John M. Pascal
- Department of Biochemistry and Molecular Medicine, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montreal, QC H3T 1J4, Canada; (M.-F.L.); (J.M.P.)
| | - Md. Sohail Akhtar
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, Uttar Pradesh, India;
| | - Alexey V. Feofanov
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (N.V.M.); (N.S.G.); (M.P.K.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Correspondence: (A.V.F.); (V.M.S.)
| | - Vasily M. Studitsky
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (N.V.M.); (N.S.G.); (M.P.K.)
- Fox Chase Cancer Center, Philadelphia, PA 19111-2497, USA;
- Correspondence: (A.V.F.); (V.M.S.)
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14
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Okunlola FO, Akawa OB, Soliman MES. Could the spanning of NAM-AD subsites by poly (ADP ribose) polymerase inhibitors potentiate their selective inhibitory activity in breast cancer treatment? Insight from biophysical computations. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1994562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Felix O. Okunlola
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Oluwole B. Akawa
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Mahmoud E. S. Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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15
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Maluchenko NV, Feofanov AV, Studitsky VM. PARP-1-Associated Pathological Processes: Inhibition by Natural Polyphenols. Int J Mol Sci 2021; 22:11441. [PMID: 34768872 PMCID: PMC8584120 DOI: 10.3390/ijms222111441] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/18/2021] [Accepted: 10/21/2021] [Indexed: 02/06/2023] Open
Abstract
Poly (ADP-ribose) polymerase-1 (PARP-1) is a nuclear enzyme involved in processes of cell cycle regulation, DNA repair, transcription, and replication. Hyperactivity of PARP-1 induced by changes in cell homeostasis promotes development of chronic pathological processes leading to cell death during various metabolic disorders, cardiovascular and neurodegenerative diseases. In contrast, tumor growth is accompanied by a moderate activation of PARP-1 that supports survival of tumor cells due to enhancement of DNA lesion repair and resistance to therapy by DNA damaging agents. That is why PARP inhibitors (PARPi) are promising agents for the therapy of tumor and metabolic diseases. A PARPi family is rapidly growing partly due to natural polyphenols discovered among plant secondary metabolites. This review describes mechanisms of PARP-1 participation in the development of various pathologies, analyzes multiple PARP-dependent pathways of cell degeneration and death, and discusses representative plant polyphenols, which can inhibit PARP-1 directly or suppress unwanted PARP-dependent cellular processes.
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Affiliation(s)
- Natalya V. Maluchenko
- Biology Faculty, Lomonosov Moscow State University, Lenin Hills 1/12, 119234 Moscow, Russia; (A.V.F.); (V.M.S.)
| | - Alexey V. Feofanov
- Biology Faculty, Lomonosov Moscow State University, Lenin Hills 1/12, 119234 Moscow, Russia; (A.V.F.); (V.M.S.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Mikluko-Maklaya Str., 16/10, 117997 Moscow, Russia
| | - Vasily M. Studitsky
- Biology Faculty, Lomonosov Moscow State University, Lenin Hills 1/12, 119234 Moscow, Russia; (A.V.F.); (V.M.S.)
- Fox Chase Cancer Center, Cottman Avenue 333, Philadelphia, PA 19111, USA
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16
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Maluchenko NV, Koshkina DO, Feofanov AV, Studitsky VM, Kirpichnikov MP. Poly(ADP-Ribosyl) Code Functions. Acta Naturae 2021; 13:58-69. [PMID: 34377556 PMCID: PMC8327145 DOI: 10.32607/actanaturae.11089] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 09/10/2020] [Indexed: 01/14/2023] Open
Abstract
Poly(ADP-ribosyl)ation plays a key role in cellular metabolism. Covalent poly(ADP-ribosyl)ation affects the activity of the proteins engaged in DNA repair, chromatin structure regulation, gene expression, RNA processing, ribosome biogenesis, and protein translation. Non-covalent PAR-dependent interactions are involved in the various types of cellular response to stress and viral infection, such as inflammation, hormonal signaling, and the immune response. The review discusses how structurally different poly(ADP-ribose) (PAR) molecules composed of identical monomers can differentially participate in various cellular processes acting as the so-called "PAR code." The article describes the ability of PAR polymers to form functional biomolecular clusters through a phase-separation in response to various signals. This phase-separation contributes to rapid spatial segregation of biochemical processes and effective recruitment of the necessary components. The cellular PAR level is tightly controlled by a network of regulatory proteins: PAR code writers, readers, and erasers. Impaired PAR metabolism is associated with the development of pathological processes causing oncological, cardiovascular, and neurodegenerative diseases. Pharmacological correction of the PAR level may represent a new approach to the treatment of various diseases.
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Affiliation(s)
- N. V. Maluchenko
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234 Russia
| | - D. O. Koshkina
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234 Russia
| | - A. V. Feofanov
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234 Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997 Russia
| | - V. M. Studitsky
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234 Russia
- Fox Chase Cancer Center, Philadelphia, PA, 19111-2497 USA
| | - M. P. Kirpichnikov
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234 Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997 Russia
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17
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Bioinformatic Analysis of the Nicotinamide Binding Site in Poly(ADP-Ribose) Polymerase Family Proteins. Cancers (Basel) 2021; 13:cancers13061201. [PMID: 33801950 PMCID: PMC8002165 DOI: 10.3390/cancers13061201] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/02/2021] [Accepted: 03/05/2021] [Indexed: 12/27/2022] Open
Abstract
Simple Summary The PARP family consists of 17 proteins, and some of them are responsible for cancer cells’ viability. Much attention is therefore given to the search for chemical compounds with the ability to suppress distinct PARP family members (for example, PARP-5a and 5b). Here, we present the results of a family-wide bioinformatic analysis of an important functional region in the PARP structure and describe factors that can guide the design of highly selective compounds. Abstract The PARP family consists of 17 members with diverse functions, including those related to cancer cells’ viability. Several PARP inhibitors are of great interest as innovative anticancer drugs, but they have low selectivity towards distinct PARP family members and exert serious adverse effects. We describe a family-wide study of the nicotinamide (NA) binding site, an important functional region in the PARP structure, using comparative bioinformatic analysis and molecular modeling. Mutations in the NA site and D-loop mobility around the NA site were identified as factors that can guide the design of selective PARP inhibitors. Our findings are of particular importance for the development of novel tankyrase (PARPs 5a and 5b) inhibitors for cancer therapy.
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18
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Okunlola FO, Soremekun OS, Olotu FA, Soliman MES. Investigating the Mechanistic Inhibitory Discrepancies of Novel Halogen and Alkyl Di-Substituted Oxadiazole-Based Dibenzo-Azepine-Dione Derivatives on Poly (ADP-Ribose) Polymerase-1. Chem Biodivers 2020; 18:e2000802. [PMID: 33289285 DOI: 10.1002/cbdv.202000802] [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: 09/26/2020] [Accepted: 12/01/2020] [Indexed: 11/07/2022]
Abstract
Numerous studies have established the involvement of Poly (ADP-ribose) Polymerase-1 (PARP-1) in cancer presenting it as an important therapeutic target over recent years. Although homology among the PARP protein family makes selective targeting difficult, two compounds [d11 (0.939 μM) and d21 (0.047 μM)] with disparate inhibitory potencies against PARP-1 were recently identified. In this study, free energy calculations and molecular simulations were used to decipher underlying mechanisms of differential PARP-1 inhibition exhibited by the two compounds. The thermodynamics calculation revealed that compound d21 had a relatively higher ΔGbind than d11. High involvement of van der Waal and electrostatic effects potentiated the affinity of d21 at PARP-1 active site. More so, incorporated methyl moiety in d11 accounted for steric hindrance which, in turn, prevented complementary interactions of key site residues such as TYR889, MET890, TYR896, TYR907. Conformational studies also revealed that d21 is more stabilized for interactions in the active site compared to d11. We believe that findings from this study would provide an important avenue for the development of selective PARP-1 inhibitors.
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Affiliation(s)
- Felix O Okunlola
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Opeyemi S Soremekun
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Fisayo A Olotu
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
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19
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Yüksek V, Çetin S, Usta A. The effect of vitamin E and selenium combination in repairing fluoride-induced DNA damage to NRK-52E cells. Mol Biol Rep 2020; 47:7761-7770. [PMID: 33025505 DOI: 10.1007/s11033-020-05852-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 09/19/2020] [Indexed: 01/11/2023]
Abstract
Prolonged and excessive fluoride exposure can lead to fluorosis. The kidney is one of the organs that are injured mostly due to fluoride-induced damage. Fluoride can induce DNA damage at cytotoxic concentrations. This study aims to determine the extent of NaF-induced DNA damage and to investigate the effect of vitamin E and selenium combination (ES) in preventing and repairing this damage. For this purpose, we administered different combinations of NaF and ES to NRK-52E cells and determined the effective concentrations of ES and the NaF IC50 values associated with different incubation times (3, 12, and 24 h) by using the MTT assay. The determined quantities of NaF IC50 in association with time and the NaF IC50 + ES combination were administered to the cells. The extent of DNA damage was determined with the comet assay and the expression levels of the Ku70/80 and PARP-1 genes were determined with the RT-qPCR method. DNA damage significantly increased in all experimental groups compared to the control group (p < 0.05). It was found out that the NaF and ES combination statistically reduced the DNA damage compared to the damage observed in the NaF-treated groups (p < 0.05). Treatment of the ES combination significantly increased the expressions of Ku70 and Ku80 genes involved in DNA repair (p < 0.05). We concluded that vitamin E and selenium can potentially be effective in the repair of fluoride-induced DNA damage based on the results of this in vitro study. Our results may shed light on the prevention of DNA damage associated with fluorosis.
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Affiliation(s)
- Veysel Yüksek
- Department of Medical Laboratory, Özalp Vocational High SchoolVan Yuzuncu Yil University, Van, Turkey.
| | - Sedat Çetin
- Department of Biochemistry, Faculty of Veterinary Medicine, Van Yuzuncu Yil University, Van, Turkey
| | - Ayşe Usta
- Department of Chemistry, Faculty of Science, Van Yuzuncu Yil University, Van, Turkey
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20
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Gushchina IV, Polenova AM, Suplatov DA, Švedas VK, Nilov DK. vsFilt: A Tool to Improve Virtual Screening by Structural Filtration of Docking Poses. J Chem Inf Model 2020; 60:3692-3696. [DOI: 10.1021/acs.jcim.0c00303] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Irina V. Gushchina
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Lenin hills 1, bldg. 40, 119991 Moscow, Russia
| | - Aleksandra M. Polenova
- Lomonosov Moscow State University, Faculty of Medicine, Lomonosov Ave. 27, bldg. 1, 119991 Moscow, Russia
| | - Dmitry A. Suplatov
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Lenin hills 1, bldg. 40, 119991 Moscow, Russia
| | - Vytas K. Švedas
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Lenin hills 1, bldg. 40, 119991 Moscow, Russia
| | - Dmitry K. Nilov
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Lenin hills 1, bldg. 40, 119991 Moscow, Russia
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