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Jado JC, Dow M, Carolino K, Klie A, Fonseca GJ, Ideker T, Carter H, Winzeler EA. In vitro evolution and whole genome analysis to study chemotherapy drug resistance in haploid human cells. Sci Rep 2024; 14:13989. [PMID: 38886371 PMCID: PMC11183241 DOI: 10.1038/s41598-024-63943-7] [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: 02/23/2024] [Accepted: 06/03/2024] [Indexed: 06/20/2024] Open
Abstract
In vitro evolution and whole genome analysis has proven to be a powerful method for studying the mechanism of action of small molecules in many haploid microbes but has generally not been applied to human cell lines in part because their diploid state complicates the identification of variants that confer drug resistance. To determine if haploid human cells could be used in MOA studies, we evolved resistance to five different anticancer drugs (doxorubicin, gemcitabine, etoposide, topotecan, and paclitaxel) using a near-haploid cell line (HAP1) and then analyzed the genomes of the drug resistant clones, developing a bioinformatic pipeline that involved filtering for high frequency alleles predicted to change protein sequence, or alleles which appeared in the same gene for multiple independent selections with the same compound. Applying the filter to sequences from 28 drug resistant clones identified a set of 21 genes which was strongly enriched for known resistance genes or known drug targets (TOP1, TOP2A, DCK, WDR33, SLCO3A1). In addition, some lines carried structural variants that encompassed additional known resistance genes (ABCB1, WWOX and RRM1). Gene expression knockdown and knockout experiments of 10 validation targets showed a high degree of specificity and accuracy in our calls and demonstrates that the same drug resistance mechanisms found in diverse clinical samples can be evolved, discovered and studied in an isogenic background.
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Affiliation(s)
- Juan Carlos Jado
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California, San Diego, Gilman Dr., La Jolla, CA, 92093, USA
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, USA
| | - Michelle Dow
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, 92093, USA
- Health Science, Department of Biomedical Informatics, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Krypton Carolino
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Adam Klie
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Gregory J Fonseca
- Department of Medicine, Meakins-Christie Laboratories, McGill University Health Centre, 1001 Decaire Blvd, Montreal, QC, H4A 3J1, Canada
| | - Trey Ideker
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, USA.
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Hannah Carter
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, USA.
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Elizabeth A Winzeler
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California, San Diego, Gilman Dr., La Jolla, CA, 92093, USA.
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, USA.
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Germe TRM, Bush NG, Baskerville VM, Saman D, Benesch JLP, Maxwell A. Rapid, DNA-induced interface swapping by DNA gyrase. eLife 2024; 12:RP86722. [PMID: 38856655 PMCID: PMC11164529 DOI: 10.7554/elife.86722] [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] [Indexed: 06/11/2024] Open
Abstract
DNA gyrase, a ubiquitous bacterial enzyme, is a type IIA topoisomerase formed by heterotetramerisation of 2 GyrA subunits and 2 GyrB subunits, to form the active complex. DNA gyrase can loop DNA around the C-terminal domains (CTDs) of GyrA and pass one DNA duplex through a transient double-strand break (DSB) established in another duplex. This results in the conversion from a positive (+1) to a negative (-1) supercoil, thereby introducing negative supercoiling into the bacterial genome by steps of 2, an activity essential for DNA replication and transcription. The strong protein interface in the GyrA dimer must be broken to allow passage of the transported DNA segment and it is generally assumed that the interface is usually stable and only opens when DNA is transported, to prevent the introduction of deleterious DSBs in the genome. In this paper, we show that DNA gyrase can exchange its DNA-cleaving interfaces between two active heterotetramers. This so-called interface 'swapping' (IS) can occur within a few minutes in solution. We also show that bending of DNA by gyrase is essential for cleavage but not for DNA binding per se and favors IS. Interface swapping is also favored by DNA wrapping and an excess of GyrB. We suggest that proximity, promoted by GyrB oligomerization and binding and wrapping along a length of DNA, between two heterotetramers favors rapid interface swapping. This swapping does not require ATP, occurs in the presence of fluoroquinolones, and raises the possibility of non-homologous recombination solely through gyrase activity. The ability of gyrase to undergo interface swapping explains how gyrase heterodimers, containing a single active-site tyrosine, can carry out double-strand passage reactions and therefore suggests an alternative explanation to the recently proposed 'swivelling' mechanism for DNA gyrase (Gubaev et al., 2016).
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Affiliation(s)
- Thomas RM Germe
- Department Biochemistry & Metabolism, John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Natassja G Bush
- Department Biochemistry & Metabolism, John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Victoria M Baskerville
- Department Biochemistry & Metabolism, John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Dominik Saman
- Department of Chemistry, Biochemistry Building, University of OxfordOxfordUnited Kingdom
| | - Justin LP Benesch
- Department of Chemistry, Biochemistry Building, University of OxfordOxfordUnited Kingdom
| | - Anthony Maxwell
- Department Biochemistry & Metabolism, John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
- Department of Molecular Microbiology, John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
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3
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Herlah B, Pavlin M, Perdih A. Molecular choreography: Unveiling the dynamic landscape of type IIA DNA topoisomerases before T-segment passage through all-atom simulations. Int J Biol Macromol 2024; 269:131991. [PMID: 38714283 DOI: 10.1016/j.ijbiomac.2024.131991] [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: 01/09/2024] [Revised: 04/09/2024] [Accepted: 04/28/2024] [Indexed: 05/09/2024]
Abstract
Type IIA DNA topoisomerases are molecular nanomachines responsible for controlling topological states of DNA molecules. Here, we explore the dynamic landscape of yeast topoisomerase IIA during key stages of its catalytic cycle, focusing in particular on the events preceding the passage of the T-segment. To this end, we generated six configurations of fully catalytic yeast topo IIA, strategically inserted a T-segment into the N-gate in relevant configurations, and performed all-atom simulations. The essential motion of topo IIA protein dimer was characterized by rotational gyrating-like movement together with sliding motion within the DNA-gate. Both appear to be inherent properties of the enzyme and an inbuilt feature that allows passage of the T-segment through the cleaved G-segment. Coupled dynamics of the N-gate and DNA-gate residues may be particularly important for controlled and smooth passage of the T-segment and consequently the prevention of DNA double-strand breaks. QTK loop residue Lys367, which interacts with ATP and ADP molecules, is involved in regulating the size and stability of the N-gate. The unveiled features of the simulated configurations provide insights into the catalytic cycle of type IIA topoisomerases and elucidate the molecular choreography governing their ability to modulate the topological states of DNA topology.
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Affiliation(s)
- Barbara Herlah
- Theory Department, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia; University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Matic Pavlin
- Department of Catalysis and Chemical Reaction Engineering, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Andrej Perdih
- Theory Department, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia; University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000 Ljubljana, Slovenia.
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4
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Adly ME, Gedawy EM, El-Malah AA, Khalil OM. Design, synthesis and in vitro anticancer activity of some new lomefloxacin derivatives. Sci Rep 2024; 14:6175. [PMID: 38485748 PMCID: PMC10940605 DOI: 10.1038/s41598-024-56313-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 03/05/2024] [Indexed: 03/18/2024] Open
Abstract
Our main goal was to design and synthesize novel lomefloxacin derivatives that inhibit the topoisomerase II enzyme, leading to potent anticancer activity. Lomefloxacin derivatives substituted at position 3 and 7 were synthesized and screened for cytotoxic activity utilizing 60 different human cancer cell lines. Furthermore, compounds 3a,b,c,e that revealed potent broad-spectrum anticancer activity (with mean percent GI more than 47%) were further evaluated using five dose concentrations and calculating the GI50. Compound 3e was then evaluated for cell cycle analysis and demonstrated cell cycle arrest at the G2-M phase. Moreover, the mechanism of action was determined by determining the topoisomerase inhibitory activity and the molecular modeling study. Compounds 3a,b,c,e showed broad spectrum anticancer activity. Lomefloxacin derivative 5f showed selective cytotoxic activity against melanoma SK-MEL-5 cell line. Compound 3e demonstrated comparable topoisomerase II inhibition to doxorubicin with IC50 of 0.98 µM.
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Affiliation(s)
- Mina E Adly
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Cairo University, 33 Kasr El-Aini Street, Cairo, 11562, Egypt.
| | - Ehab M Gedawy
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Cairo University, 33 Kasr El-Aini Street, Cairo, 11562, Egypt
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Badr University in Cairo, Cairo, 11829, Egypt
| | - Afaf A El-Malah
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Cairo University, 33 Kasr El-Aini Street, Cairo, 11562, Egypt
| | - Omneya M Khalil
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Cairo University, 33 Kasr El-Aini Street, Cairo, 11562, Egypt
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Chang CWM, Wang SC, Wang CH, Pang AH, Yang CH, Chang YK, Wu WJ, Tsai MD. A unified view on enzyme catalysis by cryo-EM study of a DNA topoisomerase. Commun Chem 2024; 7:45. [PMID: 38418525 PMCID: PMC10901890 DOI: 10.1038/s42004-024-01129-y] [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: 12/18/2023] [Accepted: 02/14/2024] [Indexed: 03/01/2024] Open
Abstract
The theories for substrate recognition in enzyme catalysis have evolved from lock-key to induced fit, then conformational selection, and conformational selection followed by induced fit. However, the prevalence and consensus of these theories require further examination. Here we use cryogenic electron microscopy and African swine fever virus type 2 topoisomerase (AsfvTop2) to demonstrate substrate binding theories in a joint and ordered manner: catalytic selection by the enzyme, conformational selection by the substrates, then induced fit. The apo-AsfvTop2 pre-exists in six conformers that comply with the two-gate mechanism directing DNA passage and release in the Top2 catalytic cycle. The structures of AsfvTop2-DNA-inhibitor complexes show that substantial induced-fit changes occur locally from the closed apo-conformer that however is too far-fetched for the open apo-conformer. Furthermore, the ATPase domain of AsfvTop2 in the MgAMP-PNP-bound crystal structures coexist in reduced and oxidized forms involving a disulfide bond, which can regulate the AsfvTop2 function.
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Affiliation(s)
- Chiung-Wen Mary Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
- Institute of Biochemistry and Molecular Biology, China Medical University, Taichung, Taiwan
| | - Shun-Chang Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Chun-Hsiung Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Allan H Pang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Cheng-Han Yang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Yao-Kai Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Wen-Jin Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Ming-Daw Tsai
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan.
- Institute of Biochemical Sciences, National Taiwan University, Taipei, 106, Taiwan.
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Cybulski M, Sidoryk K, Zaremba-Czogalla M, Trzaskowski B, Kubiszewski M, Tobiasz J, Jaromin A, Michalak O. The Conjugates of Indolo[2,3- b]quinoline as Anti-Pancreatic Cancer Agents: Design, Synthesis, Molecular Docking and Biological Evaluations. Int J Mol Sci 2024; 25:2573. [PMID: 38473820 DOI: 10.3390/ijms25052573] [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: 01/29/2024] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
New amide conjugates of hydroxycinnamic acids (HCAs) and the known antineoplastic 5,11-dimethyl-5H-indolo[2,3-b]quinoline (DiMIQ), an analog of the natural alkaloid neocryptolepine, were synthesized and tested in vitro for anticancer activity. The compound 9-[((2-hydroxy)cinnamoyl)amino]-5,11-dimethyl-5H-indolo[2,3-b]quinoline (2), which contains the ortho-coumaric acid fragment, demonstrated dose-dependent effectiveness against both normal BxPC-3 and metastatic AsPC-1 pancreatic cancer cells. The IC50 values for AsPC-1 and BxPC-3 were 336.5 nM and 347.5 nM, respectively, with a selectivity index of approximately 5 for both pancreatic cancer cells compared to normal dermal fibroblasts. Conjugate 2 did not exhibit any hemolytic activity against human erythrocytes at the tested concentration. Computational studies were performed to predict the pharmacokinetic profile and potential mechanism of action of the synthesized conjugates. These studies focused on the ADME properties of the conjugates and their interactions with DNA, as well as DNA-topoisomerase alpha and beta complexes. All of the conjugates studied showed approximately one order of magnitude stronger binding to DNA compared to the reference DiMIQ, and approximately two orders of magnitude stronger binding to the topoisomerase II-DNA complex compared to DiMIQ. Conjugate 2 was predicted to have the strongest binding to the enzyme-DNA complex, with a Ki value of 2.8 nM.
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Affiliation(s)
- Marcin Cybulski
- Pharmacy, Cosmetic Chemistry and Biotechnology Research Group, Łukasiewicz Research Network-Industrial Chemistry Institute, 01-793 Warsaw, Poland
| | - Katarzyna Sidoryk
- Pharmacy, Cosmetic Chemistry and Biotechnology Research Group, Łukasiewicz Research Network-Industrial Chemistry Institute, 01-793 Warsaw, Poland
| | - Magdalena Zaremba-Czogalla
- Department of Lipids and Liposomes, Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland
| | - Bartosz Trzaskowski
- Chemical and Biological Systems Simulation Lab, Center of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Marek Kubiszewski
- Pharmaceutical Analysis Laboratory, Łukasiewicz Research Network-Industrial Chemistry Institute, 01-793 Warsaw, Poland
| | - Joanna Tobiasz
- Pharmacy, Cosmetic Chemistry and Biotechnology Research Group, Łukasiewicz Research Network-Industrial Chemistry Institute, 01-793 Warsaw, Poland
| | - Anna Jaromin
- Department of Lipids and Liposomes, Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland
| | - Olga Michalak
- Pharmacy, Cosmetic Chemistry and Biotechnology Research Group, Łukasiewicz Research Network-Industrial Chemistry Institute, 01-793 Warsaw, Poland
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Tegegn G, Melaku Y, Aliye M, Abebe A, Abdissa N, Meresa A, Degu S, Hunsen M, Hussein AA, Endale M. In vitro antimicrobial and antioxidant activities, essential oil composition, and in silico molecular modeling analysis of secondary metabolites from roots of Verbascum sinaiticum. Z NATURFORSCH C 2024; 79:25-39. [PMID: 38414256 DOI: 10.1515/znc-2023-0157] [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: 11/29/2023] [Accepted: 02/11/2024] [Indexed: 02/29/2024]
Abstract
Verbascum sinaiticum is locally used to treat wound, stomachache, viral infection, cancer, sunstroke fever, abdominal colic, diarrhea, hemorrhage, anthrax, and hepatitis. The objective of this study was to identify the compounds and to evaluate the antimicrobial and antioxidant activity of the extracts and isolated compounds from V. sinaiticum. The 1H-NMR, 13C-NMR, and DEPT-135 were used to elucidate the structures of isolated compounds. Essential oils were extracted by hydrodistillation method and their chemical analyses were performed by GC-MS. The broth microdilution method was used to evaluate the antimicrobial activity. The radical scavenging activity of the extracts and isolated compounds were evaluated using DPPH method. Silica gel column chromatographic separation of root extracts afforded seven known compounds: 3'-(4''-methoxy phenyl)-3'-oxo-propionyl hexadecanoate (1), harpagoside (2), pulverulentoside I (3), scrophuloside B4 (4), scropolioside A (5), scropolioside-D2 (6), and harpagide 6-O-β-glucoside (7), which are all reported from this species for the first time. The EO extracts from leaves and roots were the most susceptible to Streptococcus agalactiae, with a 2 mg/mL MIC. The EO from roots was effective against Candida albicans and Trichophyton mentagrophytes, with a MIC of 8 mg/mL. The MeOH and CH2Cl2/CH3OH (1:1) root extracts showed the maximum activity against S. epidermidis with MIC values of 0.25 mg/mL. The strongest antibacterial effects were demonstrated against Staphylococcus epidermidis, which exhibited a 0.0625 mg/mL MIC for compound 1. The strongest radical scavenging activity was exhibited by the methanol extract (IC50 = 3.4 μg/mL), and compounds 4, 6, 5, 3, 7, and 2 with IC50 values of 3.2, 3.38, 3.6, 3.8, 4.2, and 4.7 μg/mL, respectively, in comparison with ascorbic acid (IC50 = 1.3 μg/mL). The results of the molecular docking analysis of compounds revealed minimal binding energies range from -38.5 to -43.1 kJ/mol, -33.1 to -42.7 kJ/mol, -34.7 to -39.3.7 kJ/mol, -25.5 to -37.6 kJ/mol against human myeloperoxidase (PDB ID: 1DNU), murA enzyme (PDB ID: 1UAE), human topoisomerase IIβ (PDB ID: 4fm9), S. epidermidis FtsZ (PDB number: 4M8I) proteins, respectively. The docking results and the in vitro antibacterial activity are in good agreement. These findings show that the isolated compounds 2-7 can act as potential antioxidants and strong antibacterials against Staphylococcus aureus and S. epidermidis. As a result, V. sinaiticum root extracts have the potential to be effective in treating diseases caused by bacteria and free radicals, as long as further investigation has been suggested for the ultimate decision of this plant's potential candidate.
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Affiliation(s)
- Getachew Tegegn
- Department of Applied Chemistry, 125545 School of Applied Natural Science, Adama Science and Technology University , P.O. Box 1888, Adama, Ethiopia
| | - Yadessa Melaku
- Department of Applied Chemistry, 125545 School of Applied Natural Science, Adama Science and Technology University , P.O. Box 1888, Adama, Ethiopia
| | - Muhdin Aliye
- Department of Applied Chemistry, 125545 School of Applied Natural Science, Adama Science and Technology University , P.O. Box 1888, Adama, Ethiopia
| | - Abiy Abebe
- Traditional and Modern Drug Research and Development Directorate, 70605 Armauer Hansen Research Institute , P.O. Box 1242, Addis Ababa, Ethiopia
| | - Negera Abdissa
- Traditional and Modern Drug Research and Development Directorate, 70605 Armauer Hansen Research Institute , P.O. Box 1242, Addis Ababa, Ethiopia
| | - Asfaw Meresa
- Traditional and Modern Drug Research and Development Directorate, 70605 Armauer Hansen Research Institute , P.O. Box 1242, Addis Ababa, Ethiopia
| | - Sileshi Degu
- Traditional and Modern Drug Research and Development Directorate, 70605 Armauer Hansen Research Institute , P.O. Box 1242, Addis Ababa, Ethiopia
| | - Mo Hunsen
- Department of Chemistry, 3475 Kenyon College , Gambier, OH 43022, USA
| | - Ahmed A Hussein
- Department of Chemistry, 70683 Cape Peninsula University of Technology , Bellville Campus, Bellville 7535, Western Cape, South Africa
| | - Milkyas Endale
- Traditional and Modern Drug Research and Development Directorate, 70605 Armauer Hansen Research Institute , P.O. Box 1242, Addis Ababa, Ethiopia
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Soliman TN, Keifenheim D, Parker PJ, Clarke DJ. Cell cycle responses to Topoisomerase II inhibition: Molecular mechanisms and clinical implications. J Cell Biol 2023; 222:e202209125. [PMID: 37955972 PMCID: PMC10641588 DOI: 10.1083/jcb.202209125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
DNA Topoisomerase IIA (Topo IIA) is an enzyme that alters the topological state of DNA and is essential for the separation of replicated sister chromatids and the integrity of cell division. Topo IIA dysfunction activates cell cycle checkpoints, resulting in arrest in either the G2-phase or metaphase of mitosis, ultimately triggering the abscission checkpoint if non-disjunction persists. These events, which directly or indirectly monitor the activity of Topo IIA, have become of major interest as many cancers have deficiencies in Topoisomerase checkpoints, leading to genome instability. Recent studies into how cells sense Topo IIA dysfunction and respond by regulating cell cycle progression demonstrate that the Topo IIA G2 checkpoint is distinct from the G2-DNA damage checkpoint. Likewise, in mitosis, the metaphase Topo IIA checkpoint is separate from the spindle assembly checkpoint. Here, we integrate mechanistic knowledge of Topo IIA checkpoints with the current understanding of how cells regulate progression through the cell cycle to accomplish faithful genome transmission and discuss the opportunities this offers for therapy.
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Affiliation(s)
- Tanya N. Soliman
- Barts Cancer Institute, Queen Mary University London, London, UK
| | - Daniel Keifenheim
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | | | - Duncan J. Clarke
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
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Zhao Y, Kuang W, An Q, Li J, Wang Y, Deng Z. Cryo-EM structures of African swine fever virus topoisomerase. mBio 2023; 14:e0122823. [PMID: 37610250 PMCID: PMC10653817 DOI: 10.1128/mbio.01228-23] [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: 05/15/2023] [Accepted: 07/10/2023] [Indexed: 08/24/2023] Open
Abstract
IMPORTANCE African swine fever virus (ASFV) is a highly contagious virus that causes lethal hemorrhagic diseases known as African swine fever (ASF) with a case fatality rate of 100%. There is an urgent need to develop anti-ASFV drugs. We determine the first high-resolution structures of viral topoisomerase ASFV P1192R in both the closed and open C-gate forms. P1192R shows a similar overall architecture with eukaryotic and prokaryotic type II topoisomerases, which have been successful targets of many antimicrobials and anticancer drugs, with the most similarity to yeast topo II. P1192R also exhibits differences in the details of active site configuration, which are important to enzyme activity. These two structures offer useful structural information for antiviral drug design and provide structural evidence to support that eukaryotic type IIA topoisomerase likely originated from horizontal gene transfer from the virus.
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Affiliation(s)
- Yan Zhao
- Wuhan Institute of Virology, Center for Antiviral Research, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wenhua Kuang
- Wuhan Institute of Virology, Center for Antiviral Research, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Qiyin An
- Wuhan Institute of Virology, Center for Antiviral Research, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jinyue Li
- Wuhan Institute of Virology, Center for Antiviral Research, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Yong Wang
- Wuhan Institute of Virology, Center for Antiviral Research, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zengqin Deng
- Wuhan Institute of Virology, Center for Antiviral Research, Chinese Academy of Sciences, Wuhan, Hubei, China
- Hubei Jiangxia Laboratory, Wuhan, Hubei, China
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Grzelczyk J, Pérez-Sánchez H, Carmena-Bargueño M, Oracz J, Budryn G. Effects of In Vitro Digestion of Polyphenols from Coffee on Binding Parameters to Human Topoisomerase II α. Molecules 2023; 28:5996. [PMID: 37630250 PMCID: PMC10457778 DOI: 10.3390/molecules28165996] [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: 07/17/2023] [Revised: 08/01/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Type II topoisomerase (TOPII) is an enzyme that influences the topology of DNA. DNA breaks generated by TOPII may result in mutagenic or cytotoxic changes in cancer cells. In this study, we characterized interactions of TOPIIα with coffee extracts and individual chlorogenic acids (CHAs) from the extracts by performing isothermal titration calorimetry (ITC) and molecular docking (MD) simulations. The study showed that the highest affinity to TOPIIα was found in green coffee (ΔG = -38.23 kJ/mol) and monochlorogenic acids fraction of coffee extracts (ΔG = -35.80 kJ/mol), resulting from the high content of polyphenols, such as CHAs, which can bind to the enzyme in the active site. Coffee extracts and their fractions maintained a high affinity for TOPIIα after simulated digestion in the presence of probiotic bacteria. It can be concluded that coffee may be a potential TOPIIα inhibitor considered as a functional food for cancer prevention.
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Affiliation(s)
- Joanna Grzelczyk
- Institute of Food Technology and Analysis, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, 90-537 Lodz, Poland;
| | - Horacio Pérez-Sánchez
- Structural Bioinformatics and High-Performance Computing Research Group (BIO-HPC), Computer Engineering Department, UCAM Universidad Católica de Murcia, Guadalupe, 30107 Murcia, Spain; (H.P.-S.); (M.C.-B.)
| | - Miguel Carmena-Bargueño
- Structural Bioinformatics and High-Performance Computing Research Group (BIO-HPC), Computer Engineering Department, UCAM Universidad Católica de Murcia, Guadalupe, 30107 Murcia, Spain; (H.P.-S.); (M.C.-B.)
| | - Joanna Oracz
- Institute of Food Technology and Analysis, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, 90-537 Lodz, Poland;
| | - Grażyna Budryn
- Institute of Food Technology and Analysis, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, 90-537 Lodz, Poland;
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Pavlin M, Herlah B, Valjavec K, Perdih A. Unveiling the interdomain dynamics of type II DNA topoisomerase through all-atom simulations: Implications for understanding its catalytic cycle. Comput Struct Biotechnol J 2023; 21:3746-3759. [PMID: 37602233 PMCID: PMC10436251 DOI: 10.1016/j.csbj.2023.07.019] [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: 04/23/2023] [Revised: 07/01/2023] [Accepted: 07/19/2023] [Indexed: 08/22/2023] Open
Abstract
Type IIA DNA topoisomerases are complex molecular nanomachines that manage topological states of the DNA molecule in the cell and play a crucial role in cellular processes such as cell division and transcription. They are also established targets of cancer chemotherapy. Starting from the available crystal structure of a fully catalytic topoisomerase IIA homodimer from Saccharomyces cerevisiae, we constructed three states of this molecular motor primarily changing the configurations of the DNA segment bound in the DNA gate and performed μs-long all-atom molecular simulations. A comprehensive analysis revealed a sliding motion within the DNA gate and a teamwork between the N-gate and DNA gate that may be associated with the necessary molecular events that allow passage of the T-segment of DNA. The observed movement of the ATPase dimer relative to the DNA domain was reflected in different interaction patterns between the K-loops of the transducer domain and the B-A-B form of the bound DNA. Based on the obtained results, we mapped simulated configurations to the structures in the proposed catalytic cycle through which type IIA topoisomerases exert their function and discussed the possible transition events. The results extend our understanding of the mechanism of action of type IIA topoisomerases and provide an atomistic interpretation of some of the observed features of these molecular motors.
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Affiliation(s)
- Matic Pavlin
- Department of Catalysis and Chemical Reaction Engineering, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Barbara Herlah
- Theory Department, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Katja Valjavec
- Theory Department, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Andrej Perdih
- Theory Department, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000 Ljubljana, Slovenia
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12
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Jian JY, Osheroff N. Telling Your Right Hand from Your Left: The Effects of DNA Supercoil Handedness on the Actions of Type II Topoisomerases. Int J Mol Sci 2023; 24:11199. [PMID: 37446377 PMCID: PMC10342825 DOI: 10.3390/ijms241311199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/05/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023] Open
Abstract
Type II topoisomerases are essential enzymes that modulate the topological state of DNA supercoiling in all living organisms. These enzymes alter DNA topology by performing double-stranded passage reactions on over- or underwound DNA substrates. This strand passage reaction generates a transient covalent enzyme-cleaved DNA structure known as the cleavage complex. Al-though the cleavage complex is a requisite catalytic intermediate, it is also intrinsically dangerous to genomic stability in biological systems. The potential threat of type II topoisomerase function can also vary based on the nature of the supercoiled DNA substrate. During essential processes such as DNA replication and transcription, cleavage complex formation can be inherently more dangerous on overwound versus underwound DNA substrates. As such, it is important to understand the profound effects that DNA topology can have on the cellular functions of type II topoisomerases. This review will provide a broad assessment of how human and bacterial type II topoisomerases recognize and act on their substrates of various topological states.
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Affiliation(s)
- Jeffrey Y. Jian
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA;
| | - Neil Osheroff
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA;
- Department of Medicine (Hematology/Oncology), Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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13
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Bartas M, Slychko K, Červeň J, Pečinka P, Arndt-Jovin DJ, Jovin TM. Extensive Bioinformatics Analyses Reveal a Phylogenetically Conserved Winged Helix (WH) Domain (Zτ) of Topoisomerase IIα, Elucidating Its Very High Affinity for Left-Handed Z-DNA and Suggesting Novel Putative Functions. Int J Mol Sci 2023; 24:10740. [PMID: 37445918 DOI: 10.3390/ijms241310740] [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: 04/19/2023] [Revised: 06/13/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023] Open
Abstract
The dynamic processes operating on genomic DNA, such as gene expression and cellular division, lead inexorably to topological challenges in the form of entanglements, catenanes, knots, "bubbles", R-loops, and other outcomes of supercoiling and helical disruption. The resolution of toxic topological stress is the function attributed to DNA topoisomerases. A prominent example is the negative supercoiling (nsc) trailing processive enzymes such as DNA and RNA polymerases. The multiple equilibrium states that nscDNA can adopt by redistribution of helical twist and writhe include the left-handed double-helical conformation known as Z-DNA. Thirty years ago, one of our labs isolated a protein from Drosophila cells and embryos with a 100-fold greater affinity for Z-DNA than for B-DNA, and identified it as topoisomerase II (gene Top2, orthologous to the human UniProt proteins TOP2A and TOP2B). GTP increased the affinity and selectivity for Z-DNA even further and also led to inhibition of the isomerase enzymatic activity. An allosteric mechanism was proposed, in which topoII acts as a Z-DNA-binding protein (ZBP) to stabilize given states of topological (sub)domains and associated multiprotein complexes. We have now explored this possibility by comprehensive bioinformatic analyses of the available protein sequences of topoII representing organisms covering the whole tree of life. Multiple alignment of these sequences revealed an extremely high level of evolutionary conservation, including a winged-helix protein segment, here denoted as Zτ, constituting the putative structural homolog of Zα, the canonical Z-DNA/Z-RNA binding domain previously identified in the interferon-inducible RNA Adenosine-to-Inosine-editing deaminase, ADAR1p150. In contrast to Zα, which is separate from the protein segment responsible for catalysis, Zτ encompasses the active site tyrosine of topoII; a GTP-binding site and a GxxG sequence motif are in close proximity. Quantitative Zτ-Zα similarity comparisons and molecular docking with interaction scoring further supported the "B-Z-topoII hypothesis" and has led to an expanded mechanism for topoII function incorporating the recognition of Z-DNA segments ("Z-flipons") as an inherent and essential element. We further propose that the two Zτ domains of the topoII homodimer exhibit a single-turnover "conformase" activity on given G(ate) B-DNA segments ("Z-flipins"), inducing their transition to the left-handed Z-conformation. Inasmuch as the topoII-Z-DNA complexes are isomerase inactive, we infer that they fulfill important structural roles in key processes such as mitosis. Topoisomerases are preeminent targets of anti-cancer drug discovery, and we anticipate that detailed elucidation of their structural-functional interactions with Z-DNA and GTP will facilitate the design of novel, more potent and selective anti-cancer chemotherapeutic agents.
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Affiliation(s)
- Martin Bartas
- Department of Biology and Ecology, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Kristyna Slychko
- Department of Biology and Ecology, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Jiří Červeň
- Department of Biology and Ecology, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Petr Pečinka
- Department of Biology and Ecology, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Donna J Arndt-Jovin
- Emeritus Laboratory of Cellular Dynamics, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Thomas M Jovin
- Emeritus Laboratory of Cellular Dynamics, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
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14
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Le TT, Wu M, Lee JH, Bhatt N, Inman JT, Berger JM, Wang MD. Etoposide promotes DNA loop trapping and barrier formation by topoisomerase II. Nat Chem Biol 2023; 19:641-650. [PMID: 36717711 PMCID: PMC10154222 DOI: 10.1038/s41589-022-01235-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 11/22/2022] [Indexed: 01/31/2023]
Abstract
Etoposide is a broadly employed chemotherapeutic and eukaryotic topoisomerase II poison that stabilizes cleaved DNA intermediates to promote DNA breakage and cytotoxicity. How etoposide perturbs topoisomerase dynamics is not known. Here we investigated the action of etoposide on yeast topoisomerase II, human topoisomerase IIα and human topoisomerase IIβ using several sensitive single-molecule detection methods. Unexpectedly, we found that etoposide induces topoisomerase to trap DNA loops, compacting DNA and restructuring DNA topology. Loop trapping occurs after ATP hydrolysis but before strand ejection from the enzyme. Although etoposide decreases the innate stability of topoisomerase dimers, it increases the ability of the enzyme to act as a stable roadblock. Interestingly, the three topoisomerases show similar etoposide-mediated resistance to dimer separation and sliding along DNA but different abilities to compact DNA and chirally relax DNA supercoils. These data provide unique mechanistic insights into the functional consequences of etoposide on topoisomerase II dynamics.
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Affiliation(s)
- Tung T Le
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY, USA
- Department of Physics and LASSP, Cornell University, Ithaca, NY, USA
| | - Meiling Wu
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY, USA
- Department of Physics and LASSP, Cornell University, Ithaca, NY, USA
| | - Joyce H Lee
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Neti Bhatt
- Department of Physics and LASSP, Cornell University, Ithaca, NY, USA
| | - James T Inman
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY, USA
- Department of Physics and LASSP, Cornell University, Ithaca, NY, USA
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michelle D Wang
- Howard Hughes Medical Institute, Cornell University, Ithaca, NY, USA.
- Department of Physics and LASSP, Cornell University, Ithaca, NY, USA.
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15
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Kumari B, Sakode C, Lakshminarayanan R, Purohit P, Bhattacharjee A, Roy PK. A mechanistic analysis of spontaneous cancer remission phenomenon: identification of genomic basis and effector biomolecules for therapeutic applicability. 3 Biotech 2023; 13:113. [PMID: 36890970 PMCID: PMC9986194 DOI: 10.1007/s13205-023-03515-0] [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: 08/29/2022] [Accepted: 02/09/2023] [Indexed: 03/07/2023] Open
Abstract
Based on the well-documented studies, numerous tumors episodically regress permanently without treatment. Knowing the host tissue-initiated causative factors would offer considerable translational applicability, as a permanent regression process may be therapeutically replicated on patients. For this, we developed a systems biological formulation of the regression process with experimental verification and identified the relevant candidate biomolecules for therapeutic utility. We devised a cellular kinetics-based quantitative model of tumor extinction in terms of the temporal behavior of three main tumor-lysis entities: DNA blockade factor, cytotoxic T-lymphocyte and interleukin-2. As a case study, we analyzed the time-wise biopsy and microarrays of spontaneously regressing melanoma and fibrosarcoma tumors in mammalian/human hosts. We analyzed the differentially expressed genes (DEGs), signaling pathways, and bioinformatics framework of regression. Additionally, prospective biomolecules that could cause complete tumor regression were investigated. The tumor regression process follows a first-order cellular dynamics with a small negative bias, as verified by experimental fibrosarcoma regression; the bias is necessary to eliminate the residual tumor. We identified 176 upregulated and 116 downregulated DEGs, and enrichment analysis showed that the most significant were downregulated cell-division genes: TOP2A-KIF20A-KIF23-CDK1-CCNB1. Moreover, Topoisomerase-IIA inhibition might actuate spontaneous regression, with collateral confirmation provided from survival and genomic analysis of melanoma patients. Candidate molecules such as Dexrazoxane/Mitoxantrone, with interleukin-2 and antitumor lymphocytes, may potentially replicate permanent tumor regression process of melanoma. To conclude, episodic permanent tumor regression is a unique biological reversal process of malignant progression, and signaling pathway understanding, with candidate biomolecules, may plausibly therapeutically replicate the regression process on tumors clinically. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03515-0.
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Affiliation(s)
- Bindu Kumari
- School of Bio-Medical Engineering, Indian Institute of Technology (B.H.U.), Varanasi, 221005 India
| | - Chandrashekhar Sakode
- Department of Applied Sciences, Indian Institute of Information Technology, Nagpur, 44005 India
| | | | - Pratik Purohit
- School of Bio-Medical Engineering, Indian Institute of Technology (B.H.U.), Varanasi, 221005 India
| | - Anindita Bhattacharjee
- School of Bio-Medical Engineering, Indian Institute of Technology (B.H.U.), Varanasi, 221005 India
| | - Prasun K. Roy
- School of Bio-Medical Engineering, Indian Institute of Technology (B.H.U.), Varanasi, 221005 India
- Department of Life Sciences, Shiv Nadar University (S.N.U.), Delhi NCR, Dadri, UP 201314 India
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16
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Vidmar V, Vayssières M, Lamour V. What's on the Other Side of the Gate: A Structural Perspective on DNA Gate Opening of Type IA and IIA DNA Topoisomerases. Int J Mol Sci 2023; 24:ijms24043986. [PMID: 36835394 PMCID: PMC9960139 DOI: 10.3390/ijms24043986] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/09/2023] [Accepted: 02/12/2023] [Indexed: 02/18/2023] Open
Abstract
DNA topoisomerases have an essential role in resolving topological problems that arise due to the double-helical structure of DNA. They can recognise DNA topology and catalyse diverse topological reactions by cutting and re-joining DNA ends. Type IA and IIA topoisomerases, which work by strand passage mechanisms, share catalytic domains for DNA binding and cleavage. Structural information has accumulated over the past decades, shedding light on the mechanisms of DNA cleavage and re-ligation. However, the structural rearrangements required for DNA-gate opening and strand transfer remain elusive, in particular for the type IA topoisomerases. In this review, we compare the structural similarities between the type IIA and type IA topoisomerases. The conformational changes that lead to the opening of the DNA-gate and strand passage, as well as allosteric regulation, are discussed, with a focus on the remaining questions about the mechanism of type IA topoisomerases.
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Affiliation(s)
- Vita Vidmar
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS UMR 7104, Inserm U 1258, 67400 Illkirch, France
| | - Marlène Vayssières
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS UMR 7104, Inserm U 1258, 67400 Illkirch, France
| | - Valérie Lamour
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS UMR 7104, Inserm U 1258, 67400 Illkirch, France
- Hôpitaux Universitaires de Strasbourg, 67098 Strasbourg, France
- Correspondence:
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17
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Elfadadny A, Ragab RF, Hamada R, Al Jaouni SK, Fu J, Mousa SA, El-Far AH. Natural bioactive compounds-doxorubicin combinations targeting topoisomerase II-alpha: Anticancer efficacy and safety. Toxicol Appl Pharmacol 2023; 461:116405. [PMID: 36716865 DOI: 10.1016/j.taap.2023.116405] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 01/07/2023] [Accepted: 01/22/2023] [Indexed: 01/29/2023]
Abstract
Cancer is one of the leading causes of death worldwide, so pursuing effective and safe therapeutics for cancer is a key research objective nowadays. Doxorubicin (DOX) is one of the commonly prescribed chemotherapeutic agents that has been used to treat cancer with its antimitotic properties via inhibition of topoisomerase II (TOP2) activity. However, many problems hinder the broad use of DOX in clinical practice, including cardiotoxicity and drug resistance. Research in drug discovery has confirmed that natural bioactive compounds (NBACs) display a wide range of biological activities correlating to anticancer outcomes. The combination of NBACs has been seen to be an ideal candidate that might increase the effectiveness of DOX therapy and decreases its unfavorable adverse consequences. The current review discusses the chemo-modulatory mechanism and the protective effects of combined DOX with NBACs with a binding affinity (pKi) toward TOP2A more than pKi of DOX. This review will also discuss and emphasize the molecular mechanisms to provide a pathway for further studies to reveal other signaling pathways. Taken together, understanding the fundamental mechanisms and implications of combined therapy may provide a practical approach to battling cancer diseases.
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Affiliation(s)
- Ahmed Elfadadny
- Department of Animal Internal Medicine, Faculty of Veterinary Medicine, Damanhour University, Damanhour 22511, Egypt; Cooperative Division of Veterinary Sciences, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan.
| | - Rokaia F Ragab
- Cooperative Division of Veterinary Sciences, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan; Department of Biochemistry, Faculty of Veterinary Medicine, Damanhour University, Damanhour 22511, Egypt.
| | - Rania Hamada
- Department of Pathology, Faculty of Veterinary Medicine, Damanhour University, Damanhour 22511, Egypt.
| | - Soad K Al Jaouni
- Department of Hematology/Pediatric Oncology, Yousef Abdulatif Jameel Scientific Chair of Prophetic Medicine Application, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
| | - Junjiang Fu
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, China.
| | - Shaker A Mousa
- Pharmaceutical Research Institute, Albany College of Pharmacy and Health Sciences, Rensselaer, NY 12144, USA.
| | - Ali H El-Far
- Department of Biochemistry, Faculty of Veterinary Medicine, Damanhour University, Damanhour 22511, Egypt.
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18
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Soni JP, Nikitha Reddy G, Rahman Z, Sharma A, Spandana A, Phanindranath R, Dandekar MP, Nagesh N, Shankaraiah N. Synthesis and cytotoxicity evaluation of DNA-interactive β-carboline indolyl-3-glyoxamide derivatives: Topo-II inhibition and in silico modelling studies. Bioorg Chem 2023; 131:106313. [PMID: 36516521 DOI: 10.1016/j.bioorg.2022.106313] [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: 10/19/2022] [Revised: 11/18/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022]
Abstract
In a quest for effective cancer targeted drug therapy, a series of new β-carboline tethered indole-3-glyoxylamide derivatives, conjoining salient pharmacophoric properties with prominent cytotoxicity, were synthesized. The in vitro cytotoxic ability of the compounds was established, and many of the compounds exhibited remarkable cytotoxicity (IC50 < 10 μM) on human cancer cell lines like HCT116, A549, SK-MEL-28, and MCF7. Precisely, compound 12x expressed the best cytotoxic potential against melanoma cancer cell line (SK-MEL-28) with an IC50 value of 4.37 μM. In addition, cytotoxicity evaluation against normal kidney cell line (NRK52E) entrenched the cytospecificity and selectivity index of 12x. The traditional apoptosis assays advised morphological and nuclear alterations such as apoptotic body formation, condensed/horseshoe-shaped/fragmented nuclei, and generation of ROS. The flow cytometric analysis revealed significant early and slight late-stage induction of apoptosis. The target-based physiochemical assays indicated the ability of compound 12x to bind with DNA and inhibition of Topoisomerase II. Moreover, molecular modeling studies affirm the excellent DNA intercalation potential and stabilized interactions of 12x with DNA base pairs. In silico prediction of physicochemical parameters revealed the promising drug-like properties of the synthesized derivatives.
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Affiliation(s)
- Jay Prakash Soni
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500 037, India
| | - G Nikitha Reddy
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500 037, India
| | - Ziaur Rahman
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500 037, India
| | - Anamika Sharma
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500 037, India
| | - Akella Spandana
- CSIR-Centre for Cellular and Molecular Biology, Medical Biotechnology Complex, ANNEXE II, Uppal Road, Hyderabad 500007, India
| | - Regur Phanindranath
- CSIR-Centre for Cellular and Molecular Biology, Medical Biotechnology Complex, ANNEXE II, Uppal Road, Hyderabad 500007, India
| | - Manoj P Dandekar
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500 037, India.
| | - Narayana Nagesh
- CSIR-Centre for Cellular and Molecular Biology, Medical Biotechnology Complex, ANNEXE II, Uppal Road, Hyderabad 500007, India.
| | - Nagula Shankaraiah
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500 037, India.
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19
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Okoro CO, Fatoki TH. A Mini Review of Novel Topoisomerase II Inhibitors as Future Anticancer Agents. Int J Mol Sci 2023; 24:ijms24032532. [PMID: 36768852 PMCID: PMC9916523 DOI: 10.3390/ijms24032532] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/15/2023] [Accepted: 01/16/2023] [Indexed: 01/31/2023] Open
Abstract
Several reviews of inhibitors of topoisomerase II have been published, covering research before 2018. Therefore, this review is focused primarily on more recent publications with relevant points from the earlier literature. Topoisomerase II is an established target for anticancer drugs, which are further subdivided into poisons and catalytic inhibitors. While most of the topoisomerase II-based drugs in clinical use are mostly topoisomerase II poisons, their mechanism of action has posed severe concern due to DNA damaging potential, including the development of multi-drug resistance. As a result, we are beginning to see a gradual paradigm shift towards non-DNA damaging agents, such as the lesser studied topoisomerase II catalytic inhibitors. In addition, this review describes some novel selective catalytic topoisomerase II inhibitors. The ultimate goal is to bring researchers up to speed by curating and delineating new scaffolds as the leads for the optimization and development of new potent, safe, and selective agents for the treatment of cancer.
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20
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Swedan HK, Kassab AE, Gedawy EM, Elmeligie SE. Design, synthesis, and biological evaluation of novel ciprofloxacin derivatives as potential anticancer agents targeting topoisomerase II enzyme. J Enzyme Inhib Med Chem 2023; 38:118-137. [PMID: 36305290 PMCID: PMC9635472 DOI: 10.1080/14756366.2022.2136172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
A series of novel ciprofloxacin (CP) derivatives substituted at the N-4 position with biologically active moieties were designed and synthesised. 14 compounds were 1.02- to 8.66-fold more potent than doxorubicin against T-24 cancer cells. Ten compounds were 1.2- to 7.1-fold more potent than doxorubicin against PC-3 cancer cells. The most potent compounds 6, 7a, 7b, 8a, 9a, and 10c showed significant Topo II inhibitory activity (83-90% at 100 μM concentration). Compounds 6, 8a, and 10c were 1.01- to 2.32-fold more potent than doxorubicin. Compounds 6 and 8a induced apoptosis in T-24 (16.8- and 20.1-fold, respectively compared to control). This evidence was supported by an increase in the level of apoptotic caspase-3 (5.23- and 7.6-fold, sequentially). Both compounds arrested the cell cycle in the S phase in T-24 cancer cells while in PC-3 cancer cells the two compounds arrested the cell cycle in the G1 phase. Molecular docking simulations of compounds 6 and 8a into the Topo II active site rationalised their remarkable Topo II inhibitory activity.
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Affiliation(s)
- Hadeer K. Swedan
- Central Administration of Research and Health Development, Ministry of Health, and Population (MoHP), Cairo, Egypt
| | - Asmaa E. Kassab
- Faculty of Pharmacy, Department of Pharmaceutical Organic Chemistry, Cairo University, Cairo, Egypt
| | - Ehab M. Gedawy
- Faculty of Pharmacy, Department of Pharmaceutical Organic Chemistry, Cairo University, Cairo, Egypt
- Faculty of Pharmacy and Pharmaceutical Industries, Department of Pharmaceutical Chemistry, Badr University in Cairo (BUC), Badr City, Egypt
| | - Salwa E. Elmeligie
- Faculty of Pharmacy, Department of Pharmaceutical Organic Chemistry, Cairo University, Cairo, Egypt
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21
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Tavakoli N, Ghalandari B, Badalkhani-Khamseh F, Ding X, Divsalar A. Molecular Dynamics Simulation Study on the Effect of Oxali-Palladium as a Catalytic Inhibitor of Human Topoisomerase IIα. IRANIAN JOURNAL OF SCIENCE AND TECHNOLOGY, TRANSACTIONS A: SCIENCE 2022. [DOI: 10.1007/s40995-022-01384-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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22
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Dual Targeting Topoisomerase/G-Quadruplex Agents in Cancer Therapy-An Overview. Biomedicines 2022; 10:biomedicines10112932. [PMID: 36428499 PMCID: PMC9687504 DOI: 10.3390/biomedicines10112932] [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: 10/24/2022] [Revised: 11/11/2022] [Accepted: 11/12/2022] [Indexed: 11/17/2022] Open
Abstract
Topoisomerase (Topo) inhibitors have long been known as clinically effective drugs, while G-quadruplex (G4)-targeting compounds are emerging as a promising new strategy to target tumor cells and could support personalized treatment approaches in the near future. G-quadruplex (G4) is a secondary four-stranded DNA helical structure constituted of guanine-rich nucleic acids, and its stabilization impairs telomere replication, triggering the activation of several protein factors at telomere levels, including Topos. Thus, the pharmacological intervention through the simultaneous G4 stabilization and Topos inhibition offers a new opportunity to achieve greater antiproliferative activity and circumvent cellular insensitivity and resistance. In this line, dual ligands targeting both Topos and G4 emerge as innovative, efficient agents in cancer therapy. Although the research in this field is still limited, to date, some chemotypes have been identified, showing this dual activity and an interesting pharmacological profile. This paper reviews the available literature on dual Topo inhibitors/G4 stabilizing agents, with particular attention to the structure-activity relationship studies correlating the dual activity with the cytotoxic activity.
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23
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Kondaka K, Gabriel I. Targeting DNA Topoisomerase II in Antifungal Chemotherapy. Molecules 2022; 27:molecules27227768. [PMID: 36431868 PMCID: PMC9698242 DOI: 10.3390/molecules27227768] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
Topoisomerase inhibitors have been in use clinically for the treatment of several diseases for decades. Although those enzymes are significant molecular targets in antibacterial and anticancer chemotherapy very little is known about the possibilities to target fungal topoisomerase II (topo II). Raising concern for the fungal infections, lack of effective drugs and a phenomenon of multidrug resistance underlie a strong need to expand the range of therapeutic options. In this review paper, we discussed the usefulness of fungal topo II as a molecular target for new drug discovery. On the basis of previously published data, we described structural and biochemical differences between fungal and human enzymes as well as a molecular basis of differential sensitivity to known anticancer drugs targeting the latter. This review focuses especially on highlighting the differences that may underlie the selectivity of action of new inhibitors. Distinct sites within fungal topo II in comparison with human counterparts are observed and should be further studied to understand the significance of those sites and their possible usage in design of new drugs.
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Affiliation(s)
| | - Iwona Gabriel
- Correspondence: ; Tel.: +48-58-348-6078; Fax: +48-58-347-1144
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Uusküla-Reimand L, Wilson MD. Untangling the roles of TOP2A and TOP2B in transcription and cancer. SCIENCE ADVANCES 2022; 8:eadd4920. [PMID: 36322662 PMCID: PMC9629710 DOI: 10.1126/sciadv.add4920] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/12/2022] [Indexed: 06/09/2023]
Abstract
Type II topoisomerases (TOP2) are conserved regulators of chromatin topology that catalyze reversible DNA double-strand breaks (DSBs) and are essential for maintaining genomic integrity in diverse dynamic processes such as transcription, replication, and cell division. While controlled TOP2-mediated DSBs are an elegant solution to topological constraints of DNA, DSBs also contribute to the emergence of chromosomal translocations and mutations that drive cancer. The central importance of TOP2 enzymes as frontline chemotherapeutic targets is well known; however, their precise biological functions and impact in cancer development are still poorly understood. In this review, we provide an updated overview of TOP2A and TOP2B in the regulation of chromatin topology and transcription, and discuss the recent discoveries linking TOP2 activities with cancer pathogenesis.
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Affiliation(s)
- Liis Uusküla-Reimand
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Michael D. Wilson
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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Zhao H, Chen C, Song H, Qin R, Wang X, He Q, Li F, Zhao H, Li Y. DNA Topoisomerase II-α Regulated by miR-22-5p Promotes Hepatocellular Carcinoma Invasion and Migration through the Hippo Pathway. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:4277254. [PMID: 36299605 PMCID: PMC9592219 DOI: 10.1155/2022/4277254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/27/2022] [Indexed: 10/10/2023]
Abstract
DNA topoisomerases (TOPs) are dysregulated in various types of cancer. However, how TOP II-alpha (TOP2A) contributes to hepatocellular carcinoma (HCC) progression remains elusive. Cohort analysis revealed that the increased expression of TOP2A was associated with poor clinical outcomes and TOP2A was significantly upregulated in HCC tissues and cell lines. In vitro, TOP2A expression level is related to cell invasion and migration, which may be due to the alteration of epithelial-mesenchymal transition by the TOP2A. Moreover, we used verteporfin (a Hippo inhibitor) to test how the Hippo pathway promotes the effect of TOP2A on the HCC phenotype and found that TOP2A induces tumor progression through the Hippo pathway. Finally, miR-22-5p inhibited tumor progression by sponging TOP2A.
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Affiliation(s)
- Haichao Zhao
- Shanxi Bethune Hospital, Shanxi Medical University, Taiyuan 030032, China
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 300032, China
| | - Changzhou Chen
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 300032, China
| | - Huangqin Song
- Shanxi Bethune Hospital, Shanxi Medical University, Taiyuan 030032, China
| | - Rongyi Qin
- Shanxi Bethune Hospital, Shanxi Medical University, Taiyuan 030032, China
| | - Xiaoxiao Wang
- Shanxi Bethune Hospital, Shanxi Medical University, Taiyuan 030032, China
| | - Qizu He
- Shanxi Bethune Hospital, Shanxi Medical University, Taiyuan 030032, China
| | - Feng Li
- Shanxi Bethune Hospital, Shanxi Medical University, Taiyuan 030032, China
| | - Haoliang Zhao
- Shanxi Bethune Hospital, Shanxi Medical University, Taiyuan 030032, China
| | - Yanjun Li
- Shanxi Bethune Hospital, Shanxi Medical University, Taiyuan 030032, China
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Dong J, Zhu X, Yu W, Hu X, Zhang Y, Yang K, You Z, Liu Z, Qiao X, Song Y. Pyrazolo [3,4-d]pyrimidine-based dual HDAC/Topo II inhibitors: Design, synthesis, and biological evaluation as potential antitumor agents. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Gaikwad M, Konkimalla VB, Salunke-Gawali S. Metal complexes as topoisomerase inhibitors. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2022.121089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Elton TS, Hernandez VA, Carvajal-Moreno J, Wang X, Ipinmoroti D, Yalowich JC. Intronic Polyadenylation in Acquired Cancer Drug Resistance Circumvented by Utilizing CRISPR/Cas9 with Homology-Directed Repair: The Tale of Human DNA Topoisomerase IIα. Cancers (Basel) 2022; 14:cancers14133148. [PMID: 35804920 PMCID: PMC9265003 DOI: 10.3390/cancers14133148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 12/02/2022] Open
Abstract
Simple Summary DNA topoisomerase IIα (170 kDa, TOP2α/170) resolves nucleic acid topological entanglements by generating transient double-strand DNA breaks. TOP2α inhibitors/poisons stabilize TOP2α-DNA covalent complexes resulting in persistent DNA damage and are frequently utilized to treat a variety of cancers. Acquired resistance to these chemotherapeutic agents is often associated with decreased TOP2α/170 expression levels. Studies have demonstrated that a reduction in TOP2α/170 results from a type of alternative polyadenylation designated intronic polyadenylation (IPA). As a consequence of IPA, variant TOP2α mRNA transcripts have been characterized that have resulted in the translation of C-terminal truncated TOP2α isoforms with altered biological activities. In this paper, an example is discussed where circumvention of acquired TOP2α-mediated drug resistance was achieved by utilizing CRISPR/Cas9 specific gene editing of an exon/intron boundary through homology directed repair (HDR) to reduce TOP2α IPA. These results illustrate the therapeutic potential of CRISPR/Cas9/HDR to impact drug resistance associated with aberrant IPA. Abstract Intronic polyadenylation (IPA) plays a critical role in malignant transformation, development, progression, and cancer chemoresistance by contributing to transcriptome/proteome alterations. DNA topoisomerase IIα (170 kDa, TOP2α/170) is an established clinical target for anticancer agents whose efficacy is compromised by drug resistance often associated with a reduction of nuclear TOP2α/170 levels. In leukemia cell lines with acquired resistance to TOP2α-targeted drugs and reduced TOP2α/170 expression, variant TOP2α mRNA transcripts have been reported due to IPA that resulted in the translation of C-terminal truncated isoforms with altered nuclear-cytoplasmic distribution or heterodimerization with wild-type TOP2α/170. This review provides an overview of the various mechanisms regulating pre-mRNA processing and alternative polyadenylation, as well as the utilization of CRISPR/Cas9 specific gene editing through homology directed repair (HDR) to decrease IPA when splice sites are intrinsically weak or potentially mutated. The specific case of TOP2α exon 19/intron 19 splice site editing is discussed in etoposide-resistant human leukemia K562 cells as a tractable strategy to circumvent acquired TOP2α-mediated drug resistance. This example supports the importance of aberrant IPA in acquired drug resistance to TOP2α-targeted drugs. In addition, these results demonstrate the therapeutic potential of CRISPR/Cas9/HDR to impact drug resistance associated with aberrant splicing/polyadenylation.
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Structural and Biochemical Basis of Etoposide-Resistant Mutations in Topoisomerase IIα. Symmetry (Basel) 2022. [DOI: 10.3390/sym14071309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Etoposide is a widely used anticancer drug that targets type II topoisomerases, including topoisomerase IIα (TOP2A). TOP2A is a nuclear enzyme involved in regulating DNA topology through a double-strand passage mechanism. TOP2A is a homodimeric enzyme with two symmetrical active sites formed by residues from either half of the dimer. Both active sites cleave DNA, forming an enzyme-bound, double-stranded DNA break. Etoposide acts by binding in the active site between the ends of cleaved DNA, preventing the enzyme from ligating the DNA. In the present study, biochemical and structural data are used to examine the mechanism of etoposide resistance found with specific point mutations in TOP2A. Mutations near the active site (D463A, G534R, R487K), along with some outside of the active site (ΔA429 and P716L), are examined. We hypothesize that changes in the coordination of DNA cleavage results from mutations that impact symmetrical relationships in the active site and surrounding regions. In some cases, we report the first data on purified versions of these enzymes. Based upon our results, both local and long-distance factors can impact etoposide action and may indicate interdependent relationships in structure and function.
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Ling EM, Baslé A, Cowell IG, van den Berg B, Blower TR, Austin CA. A comprehensive structural analysis of the ATPase domain of human DNA topoisomerase II beta bound to AMPPNP, ADP, and the bisdioxopiperazine, ICRF193. Structure 2022; 30:1129-1145.e3. [PMID: 35660158 PMCID: PMC9592559 DOI: 10.1016/j.str.2022.05.009] [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: 01/21/2022] [Revised: 03/25/2022] [Accepted: 05/10/2022] [Indexed: 11/16/2022]
Abstract
Human topoisomerase II beta (TOP2B) modulates DNA topology using energy from ATP hydrolysis. To investigate the conformational changes that occur during ATP hydrolysis, we determined the X-ray crystallographic structures of the human TOP2B ATPase domain bound to AMPPNP or ADP at 1.9 Å and 2.6 Å resolution, respectively. The GHKL domains of both structures are similar, whereas the QTK loop within the transducer domain can move for product release. As TOP2B is the clinical target of bisdioxopiperazines, we also determined the structure of a TOP2B:ADP:ICRF193 complex to 2.3 Å resolution and identified key drug-binding residues. Biochemical characterization revealed the N-terminal strap reduces the rate of ATP hydrolysis. Mutagenesis demonstrated residue E103 as essential for ATP hydrolysis in TOP2B. Our data provide fundamental insights into the tertiary structure of the human TOP2B ATPase domain and a potential regulatory mechanism for ATP hydrolysis. Three structures of the TOP2B ATPase domain bound to AMPPNP, ADP, or ICRF193 The QTK loop in the ADP complex is further from the active site An SO4 ion is in place of the ATP hydrolysis product, Pi Biochemical data show the N-terminal strap reduces the ATPase hydrolysis activity
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Affiliation(s)
- Elise M Ling
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Arnaud Baslé
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Ian G Cowell
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Bert van den Berg
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Tim R Blower
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK.
| | - Caroline A Austin
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
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Yuan M, Shong K, Li X, Ashraf S, Shi M, Kim W, Nielsen J, Turkez H, Shoaie S, Uhlen M, Zhang C, Mardinoglu A. A Gene Co-Expression Network-Based Drug Repositioning Approach Identifies Candidates for Treatment of Hepatocellular Carcinoma. Cancers (Basel) 2022; 14:cancers14061573. [PMID: 35326724 PMCID: PMC8946504 DOI: 10.3390/cancers14061573] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 12/21/2022] Open
Abstract
Simple Summary Hepatocellular carcinoma (HCC) is the most common malignancy of liver cancer. However, treatment of HCC is still severely limited due to limitation of drug therapy. We aimed to screen more possible target genes and candidate drugs for HCC, exploring the possibility of drug treatments from systems biological perspective. We identified ten candidate target genes, which are hub genes in HCC co-expression networks, which also possess significant prognostic value in two independent HCC cohorts. The rationality of these target genes was well demonstrated through variety analyses of patient expression profiles. We then screened candidate drugs for target genes and finally identified withaferin-a and mitoxantrone as the candidate drug for HCC treatment. The drug effectiveness was validated in in vitro model and computational analysis, providing more evidence for our drug repositioning method and results. Abstract Hepatocellular carcinoma (HCC) is a malignant liver cancer that continues to increase deaths worldwide owing to limited therapies and treatments. Computational drug repurposing is a promising strategy to discover potential indications of existing drugs. In this study, we present a systematic drug repositioning method based on comprehensive integration of molecular signatures in liver cancer tissue and cell lines. First, we identify robust prognostic genes and two gene co-expression modules enriched in unfavorable prognostic genes based on two independent HCC cohorts, which showed great consistency in functional and network topology. Then, we screen 10 genes as potential target genes for HCC on the bias of network topology analysis in these two modules. Further, we perform a drug repositioning method by integrating the shRNA and drug perturbation of liver cancer cell lines and identifying potential drugs for every target gene. Finally, we evaluate the effects of the candidate drugs through an in vitro model and observe that two identified drugs inhibited the protein levels of their corresponding target genes and cell migration, also showing great binding affinity in protein docking analysis. Our study demonstrates the usefulness and efficiency of network-based drug repositioning approach to discover potential drugs for cancer treatment and precision medicine approach.
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Affiliation(s)
- Meng Yuan
- Science for Life Laboratory, KTH—Royal Institute of Technology, SE-17165 Stockholm, Sweden; (M.Y.); (K.S.); (X.L.); (M.S.); (W.K.); (S.S.); (M.U.)
| | - Koeun Shong
- Science for Life Laboratory, KTH—Royal Institute of Technology, SE-17165 Stockholm, Sweden; (M.Y.); (K.S.); (X.L.); (M.S.); (W.K.); (S.S.); (M.U.)
| | - Xiangyu Li
- Science for Life Laboratory, KTH—Royal Institute of Technology, SE-17165 Stockholm, Sweden; (M.Y.); (K.S.); (X.L.); (M.S.); (W.K.); (S.S.); (M.U.)
- Bash Biotech Inc., 600 West Broadway, Suite 700, San Diego, CA 92101, USA
| | - Sajda Ashraf
- Heka Lab, Camlik Mah. Hearty, Sk. No:4 Heka Human Plaza Umraniye, Istanbul 34774, Turkey;
| | - Mengnan Shi
- Science for Life Laboratory, KTH—Royal Institute of Technology, SE-17165 Stockholm, Sweden; (M.Y.); (K.S.); (X.L.); (M.S.); (W.K.); (S.S.); (M.U.)
| | - Woonghee Kim
- Science for Life Laboratory, KTH—Royal Institute of Technology, SE-17165 Stockholm, Sweden; (M.Y.); (K.S.); (X.L.); (M.S.); (W.K.); (S.S.); (M.U.)
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden;
- BioInnovation Institute, DK-2200 Copenhagen, Denmark
| | - Hasan Turkez
- Department of Medical Biology, Faculty of Medicine, Atatürk University, Erzurum 25240, Turkey;
| | - Saeed Shoaie
- Science for Life Laboratory, KTH—Royal Institute of Technology, SE-17165 Stockholm, Sweden; (M.Y.); (K.S.); (X.L.); (M.S.); (W.K.); (S.S.); (M.U.)
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London SE1 9RT, UK
| | - Mathias Uhlen
- Science for Life Laboratory, KTH—Royal Institute of Technology, SE-17165 Stockholm, Sweden; (M.Y.); (K.S.); (X.L.); (M.S.); (W.K.); (S.S.); (M.U.)
| | - Cheng Zhang
- Science for Life Laboratory, KTH—Royal Institute of Technology, SE-17165 Stockholm, Sweden; (M.Y.); (K.S.); (X.L.); (M.S.); (W.K.); (S.S.); (M.U.)
- Key Laboratory of Advanced Drug Preparation Technologies, School of Pharmaceutical Sciences, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
- Correspondence: (C.Z.); (A.M.)
| | - Adil Mardinoglu
- Science for Life Laboratory, KTH—Royal Institute of Technology, SE-17165 Stockholm, Sweden; (M.Y.); (K.S.); (X.L.); (M.S.); (W.K.); (S.S.); (M.U.)
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London SE1 9RT, UK
- Correspondence: (C.Z.); (A.M.)
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Chu L, Zhang Z, Mukhina M, Zickler D, Kleckner N. Sister chromatids separate during anaphase in a three-stage program as directed by interaxis bridges. Proc Natl Acad Sci U S A 2022; 119:e2123363119. [PMID: 35235450 PMCID: PMC8915976 DOI: 10.1073/pnas.2123363119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 01/21/2022] [Indexed: 11/18/2022] Open
Abstract
During mitosis, from late prophase onward, sister chromatids are connected along their entire lengths by axis-linking chromatin/structure bridges. During prometaphase/metaphase, these bridges ensure that sister chromatids retain a parallel, paranemic relationship, without helical coiling, as they undergo compaction. Bridges must then be removed during anaphase. Motivated by these findings, the present study has further investigated the process of anaphase sister separation. Morphological and functional analyses of mammalian mitoses reveal a three-stage pathway in which interaxis bridges play a prominent role. First, sister chromatid axes globally separate in parallel along their lengths, with concomitant bridge elongation, due to intersister chromatin pushing forces. Sister chromatids then peel apart progressively from a centromere to telomere region(s), step-by-step. During this stage, poleward spindle forces dramatically elongate centromere-proximal bridges, which are then removed by a topoisomerase IIα–dependent step. Finally, in telomere regions, widely separated chromatids remain invisibly linked, presumably by catenation, with final separation during anaphase B. During this stage increased separation of poles and/or chromatin compaction appear to be the driving force(s). Cohesin cleavage licenses these events, likely by allowing bridges to respond to imposed forces. We propose that bridges are not simply removed during anaphase but, in addition, play an active role in ensuring smooth and synchronous microtubule-mediated sister separation. Bridges would thereby be the topological gatekeepers of sister chromatid relationships throughout all stages of mitosis.
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Affiliation(s)
- Lingluo Chu
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - Zheng Zhang
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
- Chinese Academy of Sciences Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, People’s Republic of China
| | - Maria Mukhina
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - Denise Zickler
- Institute for Integrative Biology of the Cell (I2BC), CNRS, University Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Nancy Kleckner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
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Fekadu M, Zeleke D, Abdi B, Guttula A, Eswaramoorthy R, Melaku Y. Synthesis, in silico molecular docking analysis, pharmacokinetic properties and evaluation of antibacterial and antioxidant activities of fluoroquinolines. BMC Chem 2022; 16:1. [PMID: 35027086 PMCID: PMC8759279 DOI: 10.1186/s13065-022-00795-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 12/30/2021] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Quinolines have demonstrated various biological activities such as antimalarial, antibacterial and anticancer. Hence, compounds with such scaffold have been used as lead in drug development. This project is, therefore, aimed to synthesis and evaluates some biological activities of quinoline analogs. METHODS 2-Chloro-7-fluoroquinoline-3-carbaldehydes were synthesized by the application of Vilsmeier-Haack reaction. The chlorine in the fluoroquinoline-3-carbaldehyde was replaced with various nucleophiles. The aldehyde functional group was also converted to carboxylic acid and imine groups using oxidizing agent and various amines, respectively. The structures of the compounds synthesized were characterized by spectroscopic methods. Disc diffusion and DPPH assays were used to evaluate the antibacterial and antioxidant activities, respectively. The in silico molecular docking analysis of the synthesized compounds were done using AutoDock Vina against E. coli DNA Gyrase B and human topoisomerase IIα. The drug likeness properties were assessed using SwissADME and PreADMET. RESULTS Nine novel quinoline derivatives were synthesized in good yields. The in vitro antibacterial activity of the synthesized compounds was beyond 9.3 mm inhibition zone (IZ). Compounds 4, 5, 6, 7, 8, 10, 15, and 16 exhibited activity against E. coli, P. aeruginosa, S. aureus and S. pyogenes with IZ ranging from 7.3 ± 0.67 to 15.3 ± 0.33 mm at 200 μg/mL. Compound 9 displayed IZ against three of the bacterial strains except S. aureus. The IC50 for the radical scavenging activity of the synthesized compounds were from 5.31 to 16.71 μg/mL. The binding affinities of the synthesized compounds were from - 6.1 to - 7.2 kcal/mol against E. coli DNA gyrase B and - 6.8 to - 7.4 kcal/mol against human topoisomerase IIα. All of the synthesized compounds obeyed Lipinski's rule of five without violation. CONCLUSION Compounds 4, 5, 6, 7, 8, 10, 15, and 16 displayed activity against Gram positive and Gram negative bacterial strains indicating that these compounds might be used as broad spectrum bactericidal activity. Compound 8 (13.6 ± 0.22 mm) showed better IZ against P. aeruginosa compared with ciprofloxacin (10.0 ± 0.45 mm) demonstrating the potential of this compound as antibacterial agent against this strain. Compounds 5, 6, 7, 8, 9 and 10 showed comparable binding affinities in their in silico molecular docking analysis against E. coli DNA gyrase B. All of the synthesized compounds also obeyed Lipinski's rule of five without violation which suggests these compounds as antibacterial agents for further study. Compounds 7 and 8 were proved to be a very potent radical scavenger with IC50 values of 5.31 and 5.41 μg/mL, respectively. Compound 5, 6, 8, 10 and 16 had comparable binding affinity against human topoisomerase IIα suggesting these compounds as a possible candidate for anticancer drugs.
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Affiliation(s)
- Mona Fekadu
- Departments of Applied Chemistry, Adama Science and Technology University, P.O.Box 1888, Adama, Ethiopia
| | - Digafie Zeleke
- Departments of Applied Chemistry, Adama Science and Technology University, P.O.Box 1888, Adama, Ethiopia
| | - Bayan Abdi
- Departments of Applied Chemistry, Adama Science and Technology University, P.O.Box 1888, Adama, Ethiopia
| | - Anuradha Guttula
- Departments of Applied Chemistry, Adama Science and Technology University, P.O.Box 1888, Adama, Ethiopia
| | - Rajalakshmanan Eswaramoorthy
- Departments of Applied Chemistry, Adama Science and Technology University, P.O.Box 1888, Adama, Ethiopia
- Department of Biomaterials, Saveetha Dental College and Hospitals, Saveetha Institute of Meidcal and Technical Sciences (SIMATS), Saveetha University, Chennai, 600 077, India
| | - Yadessa Melaku
- Departments of Applied Chemistry, Adama Science and Technology University, P.O.Box 1888, Adama, Ethiopia.
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Discovery of a 2,4-diphenyl-5,6-dihydrobenzo(h)quinolin-8-amine derivative as a novel DNA intercalating topoisomerase IIα poison. Eur J Med Chem 2021; 226:113860. [PMID: 34597897 DOI: 10.1016/j.ejmech.2021.113860] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/04/2021] [Accepted: 09/17/2021] [Indexed: 12/22/2022]
Abstract
Several anticancer agents have been developed and innovative approaches have been made toward cancer type-specific medicines for cancer treatment. As a continuous effort to develop potential chemotherapeutic agents, a novel series of 2,4-diphenyl-5,6-dihydrobenzo(h)quinolin-8-amines containing amino groups, hydroxyphenyl and fluorine functionalities were designed and synthesized. The compounds were evaluated for topo IIα inhibitory and cytotoxicity against HCT15, and HeLa human cancer cell lines. Among synthesized thirty compounds, the majority exhibited strong topo IIα inhibition and anti-proliferation against HCT15 colorectal adenocarcinoma cell line. The structure-activity relationship study revealed that compounds with -CF3 and -OCF3 substituents at 4- position and 3' or 4'-hydroxyphenyl at 2-position attached to the central pyridine ring displayed potent topo IIα and anti-proliferative activity in colorectal and cervix cancer cell line. In vitro studies provided the evidence that compounds 16, 19, 22, and 28 possess excellent topo IIα inhibition and antiproliferative activity. For a better understanding, topo IIα cleavage complex, EtBr displacement, KI quenching assays and molecular docking of compound 19 was performed and the results revealed the mode of action as a DNA intercalative topo IIα poison inhibitor. The results obtained from this study provide insight into the DNA binding mechanism of 2,4-diphenyl-5,6-dihydrobenzo(h)quinolin-8-amines and alteration in topo IIα inhibitory and antiproliferative activity with modifications in the rigid structure.
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Weyesa A, Eswaramoorthy R, Melaku Y, Mulugeta E. Antibacterial, Docking, DFT and ADMET Properties Evaluation of Chalcone-Sulfonamide Derivatives Prepared Using ZnO Nanoparticle Catalysis. Adv Appl Bioinform Chem 2021; 14:133-144. [PMID: 34924761 PMCID: PMC8674577 DOI: 10.2147/aabc.s336450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/18/2021] [Indexed: 12/23/2022] Open
Abstract
INTRODUCTION In the present work, two novel compounds were synthesized using zinc oxide nanoparticles through green synthesis protocol. The zinc oxide nanoparticles catalyzed reactions were afforded good to excellent yields of the target compounds 76.3-98.6%. METHODOLOGY The synthesized compounds were characterized by UV-Vis, IR and NMR. The antibacterial activity of the synthesized compounds was screened against two Gram-positive bacteria (Bacillus cereus and Staphylococcus aureus) and two Gram-negative bacteria (Escherichia coli and Salmonella typhimurium). RESULTS AND DISCUSSION The synthesized compounds displayed potent activity against the bacterial strains. Among them, compound 8 showed strong activity against Bacillus cereus relative to the standard drug. On the other hand, compound 9 exhibited strong activity against Escherichia coli. The molecular docking study of the synthesized compounds was conducted to investigate their binding pattern with DNA gyrase and E. coli dihydropteroate synthase and all of them were found to have minimum binding energy ranging from -6.0 to -7.3 kcal/mol, and the best result achieved with compound 8 and 9. CONCLUSION The findings of the in vitro antibacterial and molecular docking analysis demonstrated that the synthesized compounds have potential of antibacterial activity and can be further optimized to serve as a lead compound.
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Affiliation(s)
- Abdanne Weyesa
- Department of Applied Chemistry, School of Applied Natural Science, Adama Science and Technology University, Adama, Ethiopia
| | - Rajalakshmanan Eswaramoorthy
- Department of Applied Chemistry, School of Applied Natural Science, Adama Science and Technology University, Adama, Ethiopia
- Department of Biomaterials, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
| | - Yadessa Melaku
- Department of Applied Chemistry, School of Applied Natural Science, Adama Science and Technology University, Adama, Ethiopia
| | - Endale Mulugeta
- Department of Applied Chemistry, School of Applied Natural Science, Adama Science and Technology University, Adama, Ethiopia
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Znati M, Horchani M, Latapie L, Ben Jannet H, Bouajila J. New 1,2,3-triazole linked flavonoid conjugates: Microwave-assisted synthesis, cytotoxic activity and molecular docking studies. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Cebrián J, Martínez V, Hernández P, Krimer DB, Fernández-Nestosa MJ, Schvartzman JB. Two-Dimensional Gel Electrophoresis to Study the Activity of Type IIA Topoisomerases on Plasmid Replication Intermediates. BIOLOGY 2021; 10:biology10111195. [PMID: 34827187 PMCID: PMC8615216 DOI: 10.3390/biology10111195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/11/2021] [Accepted: 11/13/2021] [Indexed: 11/28/2022]
Abstract
Simple Summary During replication, DNA molecules undergo topological changes that affect supercoiling, catenation and knotting. To better understand this process and the role of topoisomerases, the enzymes that control DNA topology in in vivo, two-dimensional agarose gel electrophoresis were used to investigate the efficiency of three type II DNA topoisomerases, the prokaryotic DNA gyrase, topoisomerase IV and the human topoisomerase 2α, on partially replicated bacterial plasmids containing replication forks stalled at specific sites. The results obtained revealed that despite the fact these DNA topoisomerases may have evolved to accomplish specific tasks, they share abilities. To our knowledge, this is the first time two-dimensional agarose gel electrophoresis have been used to examine the ability of these topoisomerases to relax supercoiling in the un-replicated region and unlink pre-catenanes in the replicated one of partially replicated molecules in vitro. The methodology described here can be used to study the role of different topoisomerases in partially replicated molecules. Abstract DNA topoisomerases are the enzymes that regulate DNA topology in all living cells. Since the discovery and purification of ω (omega), when the first were topoisomerase identified, the function of many topoisomerases has been examined. However, their ability to relax supercoiling and unlink the pre-catenanes of partially replicated molecules has received little attention. Here, we used two-dimensional agarose gel electrophoresis to test the function of three type II DNA topoisomerases in vitro: the prokaryotic DNA gyrase, topoisomerase IV and the human topoisomerase 2α. We examined the proficiency of these topoisomerases on a partially replicated bacterial plasmid: pBR-TerE@AatII, with an unidirectional replicating fork, stalled when approximately half of the plasmid had been replicated in vivo. DNA was isolated from two strains of Escherichia coli: DH5αF’ and parE10. These experiments allowed us to assess, for the first time, the efficiency of the topoisomerases examined to resolve supercoiling and pre-catenanes in partially replicated molecules and fully replicated catenanes formed in vivo. The results obtained revealed the preferential functions and also some redundancy in the abilities of these DNA topoisomerases in vitro.
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Affiliation(s)
- Jorge Cebrián
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), 28040 Madrid, Spain; (J.C.); (P.H.); (D.B.K.); (J.B.S.)
- Department of Pharmacology and Toxicology, School of Medicine, Universidad Complutense de Madrid, Instituto de Investigación Sanitaria Gregorio Marañón, CIBERCV, 28040 Madrid, Spain
| | - Victor Martínez
- Bioinformatics Laboratory, Polytechnic School, National University of Asunción, San Lorenzo P.O. Box 2111, Paraguay;
| | - Pablo Hernández
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), 28040 Madrid, Spain; (J.C.); (P.H.); (D.B.K.); (J.B.S.)
| | - Dora B. Krimer
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), 28040 Madrid, Spain; (J.C.); (P.H.); (D.B.K.); (J.B.S.)
| | - María-José Fernández-Nestosa
- Bioinformatics Laboratory, Polytechnic School, National University of Asunción, San Lorenzo P.O. Box 2111, Paraguay;
- Correspondence:
| | - Jorge B. Schvartzman
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), 28040 Madrid, Spain; (J.C.); (P.H.); (D.B.K.); (J.B.S.)
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Ude Z, Flothkötter N, Sheehan G, Brennan M, Kavanagh K, Marmion CJ. Multi-targeted metallo-ciprofloxacin derivatives rationally designed and developed to overcome antimicrobial resistance. Int J Antimicrob Agents 2021; 58:106449. [PMID: 34644603 DOI: 10.1016/j.ijantimicag.2021.106449] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 09/28/2021] [Accepted: 10/02/2021] [Indexed: 10/20/2022]
Abstract
Antimicrobial resistance is a major global threat to human health due to the rise, spread and persistence of multi-drug-resistant bacteria or 'superbugs'. There is an urgent need to develop novel chemotherapeutics to overcome this overarching challenge. The authors derivatized a clinically used fluoroquinolone antibiotic ciprofloxacin (Cip), and complexed it to a copper phenanthrene framework. This resulted in the development of two novel metallo-antibiotics of general formula [Cu(N,N)(CipHA)]NO3 where N,N represents a phenanthrene ligand and CipHA represents a hydroxamic acid of Cip derivative. Comprehensive studies, including a detailed proteomic study in which Staphylococcus aureus cells were exposed to the complexes, were undertaken to gain an insight into their mode of action. These new complexes possess potent antibacterial activity against S. aureus and methicillin-resistant S. aureus. In addition, they were found to be well tolerated in vivo in Galleria mellonella larvae, which has both functional and structural similarities to the innate immune system of mammals. These findings suggest that proteins involved in virulence, pathogenesis, and the synthesis of nucleotides and DNA repair mechanisms are most affected. In addition, both complexes affected similar cell pathways when compared with clinically used Cip, including cationic antimicrobial peptide resistance. The Cu-DPPZ-CipHA (DPPZ = dipyrido[3,2-a:2',3'-c]phenazine) analogue also induces cell leakage, which leads to an altered proteome indicative of reduced virulence and increased stress.
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Affiliation(s)
- Ziga Ude
- Centre for Synthesis and Chemical Biology, Department of Chemistry, RCSI, University of Medicine and Health Sciences, Dublin, Ireland
| | - Nils Flothkötter
- Centre for Synthesis and Chemical Biology, Department of Chemistry, RCSI, University of Medicine and Health Sciences, Dublin, Ireland
| | - Gerard Sheehan
- SSPC Pharma Research Centre, Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Marian Brennan
- School of Pharmacy and Biomolecular Sciences, RCSI, University of Medicine and Health Sciences, Dublin, Ireland
| | - Kevin Kavanagh
- SSPC Pharma Research Centre, Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland.
| | - Celine J Marmion
- Centre for Synthesis and Chemical Biology, Department of Chemistry, RCSI, University of Medicine and Health Sciences, Dublin, Ireland.
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Bioinformatics Analysis Confirms the Target Protein Underlying Mitotic Catastrophe of 4T1 Cells under Combinatorial Treatment of PGV-1 and Galangin. Sci Pharm 2021. [DOI: 10.3390/scipharm89030038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Pentagamavunon-1 (PGV-1), a potential chemopreventive agent with a strong cytotoxic effect, modulates prometaphase arrest. Improvement to get higher effectiveness of PGV-1 is a new challenge. A previous study reported that the natural compound, galangin, has antiproliferative activity against cancer cells with a lower cytotoxicity effect. This study aims to develop a combinatorial treatment of PGV-1 and galangin as an anticancer agent with higher effectiveness than a single agent. In this study, 4T1, a TNBC model cell, was treated with a combination of PGV-1 and galangin. As a result, PGV-1 and galangin showed a cytotoxic effect with IC50 values of 8 and 120 µM, respectively. Combining those chemicals has a synergistic impact, as shown by the combination index (CI) value of 1. Staining with the May Grunwald-Giemsa reagent indicated mitotic catastrophe evidence, characterized by micronuclear and multinucleated morphology. Moreover, the senescence percentage was higher than the single treatment. Furthermore, bioinformatics investigations showed that PGV-1 and galangin target CDK1, PLK1, and AURKB, overexpression proteins in TNBC that are essential in regulating cell cycle arrest. In conclusion, the combination of PGV-1 and galangin exhibit a synergistic effect and potential to be a chemotherapeutic drug by the mechanism of mitotic catastrophe and senescence induction.
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Radaeva M, Ton AT, Hsing M, Ban F, Cherkasov A. Drugging the 'undruggable'. Therapeutic targeting of protein-DNA interactions with the use of computer-aided drug discovery methods. Drug Discov Today 2021; 26:2660-2679. [PMID: 34332092 DOI: 10.1016/j.drudis.2021.07.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/22/2021] [Accepted: 07/17/2021] [Indexed: 02/09/2023]
Abstract
Transcription factors (TFs) act as major oncodrivers in many cancers and are frequently regarded as high-value therapeutic targets. The functionality of TFs relies on direct protein-DNA interactions, which are notoriously difficult to target with small molecules. However, this prior view of the 'undruggability' of protein-DNA interfaces has shifted substantially in recent years, in part because of significant advances in computer-aided drug discovery (CADD). In this review, we highlight recent examples of successful CADD campaigns resulting in drug candidates that directly interfere with protein-DNA interactions of several key cancer TFs, including androgen receptor (AR), ETS-related gene (ERG), MYC, thymocyte selection-associated high mobility group box protein (TOX), topoisomerase II (TOP2), and signal transducer and activator of transcription 3 (STAT3). Importantly, these findings open novel and compelling avenues for therapeutic targeting of over 1600 human TFs implicated in many conditions including and beyond cancer.
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Affiliation(s)
- Mariia Radaeva
- Vancouver Prostate Centre and the Department of Urologic Sciences, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada
| | - Anh-Tien Ton
- Vancouver Prostate Centre and the Department of Urologic Sciences, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada
| | - Michael Hsing
- Vancouver Prostate Centre and the Department of Urologic Sciences, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada
| | - Fuqiang Ban
- Vancouver Prostate Centre and the Department of Urologic Sciences, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada
| | - Artem Cherkasov
- Vancouver Prostate Centre and the Department of Urologic Sciences, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada.
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Gupta P, Kumar RV, Kwon CH, Chen ZS. Synthesis and anticancer evaluation of sulfur containing 9-anilinoacridines. Recent Pat Anticancer Drug Discov 2021; 17:102-119. [PMID: 34323200 DOI: 10.2174/1574892816666210728122910] [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: 02/24/2021] [Revised: 03/18/2021] [Accepted: 04/17/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND DNA topoisomerases are a class of enzymes that play a critical role in fundamental biological processes of replication, transcription, recombination, repair and chromatin remodeling. Amsacrine (m-AMSA), the best-known compound of 9-anilinoacridines series was one of the first DNA-intercalating agents to be considered as a Topoisomerase II inhibitor. OBJECTIVE A series of sulfur containing 9-anilinoacridines related to amsacrine were synthesized and evaluated for their anticancer activity. METHODS Cell viability was assessed by the MTT assay. The topoisomerase II inhibitory assay was performed using the Human topoisomerase II Assay kit and flow cytometry was used to evaluate the effects on cell cycle of K562 cells. Molecular docking was performed using Schrödinger Maestro program. RESULTS Compound 36 was found to be the most cytotoxic of the sulfide series against SW620, K562, and MCF-7. The limited SAR suggested the importance of the methansulfonamidoacetamide side chain functionality, the lipophilicity and relative metabolic stability of 36 in contributing to the cytotoxicity. Topoisomerase II α inhibitory activity appeared to be involved in the cytotoxicity of 36 through inhibition of decatenation of kinetoplast DNA (kDNA) in a concentration dependent manner. Cell cycle analysis further showed the Topo II inhibition through accumulation of K562 cells in G2/M phase of cell cycle. Docking of 36 into the Topo II α-DNA complex suggested that it may be an allosteric inhibitor of Topo II α. CONCLUSION Compound 36 exhibits anticancer activity by inhibiting topoisomerase II and it could further be evaluated in in vivo models.
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Affiliation(s)
- Pranav Gupta
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, New York 11439, United States
| | - Radhika V Kumar
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, New York 11439, United States
| | - Chul-Hoon Kwon
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, New York 11439, United States
| | - Zhe-Sheng Chen
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, New York 11439, United States
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Basic residues at the C-gate of DNA gyrase are involved in DNA supercoiling. J Biol Chem 2021; 297:101000. [PMID: 34303706 PMCID: PMC8368997 DOI: 10.1016/j.jbc.2021.101000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 07/14/2021] [Accepted: 07/21/2021] [Indexed: 11/23/2022] Open
Abstract
DNA gyrase is a type II topoisomerase that is responsible for maintaining the topological state of bacterial and some archaeal genomes. It uses an ATP-dependent two-gate strand-passage mechanism that is shared among all type II topoisomerases. During this process, DNA gyrase creates a transient break in the DNA, the G-segment, to form a cleavage complex. This allows a second DNA duplex, known as the T-segment, to pass through the broken G-segment. After the broken strand is religated, the T-segment is able to exit out of the enzyme through a gate called the C-gate. Although many steps of the type II topoisomerase mechanism have been studied extensively, many questions remain about how the T-segment ultimately exits out of the C-gate. A recent cryo-EM structure of Streptococcus pneumoniae GyrA shows a putative T-segment in close proximity to the C-gate, suggesting that residues in this region may be important for coordinating DNA exit from the enzyme. Here, we show through site-directed mutagenesis and biochemical characterization that three conserved basic residues in the C-gate of DNA gyrase are important for DNA supercoiling activity, but not for ATPase or cleavage activity. Together with the structural information previously published, our data suggest a model in which these residues cluster to form a positively charged region that facilitates T-segment passage into the cavity formed between the DNA gate and C-gate.
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Relating SMCHD1 structure to its function in epigenetic silencing. Biochem Soc Trans 2021; 48:1751-1763. [PMID: 32779700 PMCID: PMC7458401 DOI: 10.1042/bst20200242] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/12/2020] [Accepted: 07/13/2020] [Indexed: 02/07/2023]
Abstract
The structural maintenance of chromosomes hinge domain containing protein 1 (SMCHD1) is a large multidomain protein involved in epigenetic gene silencing. Variations in the SMCHD1 gene are associated with two debilitating human disorders, facioscapulohumeral muscular dystrophy (FSHD) and Bosma arhinia microphthalmia syndrome (BAMS). Failure of SMCHD1 to silence the D4Z4 macro-repeat array causes FSHD, yet the consequences on gene silencing of SMCHD1 variations associated with BAMS are currently unknown. Despite the interest due to these roles, our understanding of the SMCHD1 protein is in its infancy. Most knowledge of SMCHD1 function is based on its similarity to the structural maintenance of chromosomes (SMC) proteins, such as cohesin and condensin. SMC proteins and SMCHD1 share similar domain organisation and affect chromatin conformation. However, there are important differences between the domain architectures of SMC proteins and SMCHD1, which distinguish SMCHD1 as a non-canonical member of the family. In the last year, the crystal structures of the two key domains crucial to SMCHD1 function, the ATPase and hinge domains, have emerged. These structures reveal new insights into how SMCHD1 may bind and regulate chromatin structure, and address how amino acid variations in SMCHD1 may contribute to BAMS and FSHD. Here, we contrast SMCHD1 with canonical SMC proteins, and relate the ATPase and hinge domain structures to their roles in SMCHD1-mediated epigenetic silencing and disease.
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Vanden Broeck A, Lotz C, Drillien R, Haas L, Bedez C, Lamour V. Structural basis for allosteric regulation of Human Topoisomerase IIα. Nat Commun 2021; 12:2962. [PMID: 34016969 PMCID: PMC8137924 DOI: 10.1038/s41467-021-23136-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 04/15/2021] [Indexed: 12/01/2022] Open
Abstract
The human type IIA topoisomerases (Top2) are essential enzymes that regulate DNA topology and chromosome organization. The Topo IIα isoform is a prime target for antineoplastic compounds used in cancer therapy that form ternary cleavage complexes with the DNA. Despite extensive studies, structural information on this large dimeric assembly is limited to the catalytic domains, hindering the exploration of allosteric mechanism governing the enzyme activities and the contribution of its non-conserved C-terminal domain (CTD). Herein we present cryo-EM structures of the entire human Topo IIα nucleoprotein complex in different conformations solved at subnanometer resolutions (3.6-7.4 Å). Our data unveils the molecular determinants that fine tune the allosteric connections between the ATPase domain and the DNA binding/cleavage domain. Strikingly, the reconstruction of the DNA-binding/cleavage domain uncovers a linker leading to the CTD, which plays a critical role in modulating the enzyme's activities and opens perspective for the analysis of post-translational modifications.
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Affiliation(s)
- Arnaud Vanden Broeck
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Department of Integrated Structural Biology, IGBMC, Illkirch, France
| | - Christophe Lotz
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Department of Integrated Structural Biology, IGBMC, Illkirch, France
| | - Robert Drillien
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Department of Integrated Structural Biology, IGBMC, Illkirch, France
| | - Léa Haas
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Department of Integrated Structural Biology, IGBMC, Illkirch, France
| | - Claire Bedez
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Department of Integrated Structural Biology, IGBMC, Illkirch, France
| | - Valérie Lamour
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.
- Department of Integrated Structural Biology, IGBMC, Illkirch, France.
- Hôpitaux Universitaires de Strasbourg, Strasbourg, France.
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Abstract
1,2-Naphthoquinone, a secondary metabolite of naphthalene, is an environmental pollutant found in diesel exhaust particles that displays cytotoxic and genotoxic properties. Because many quinones have been shown to act as topoisomerase II poisons, the effects of this compound on DNA cleavage mediated by human topoisomerase IIα and IIβ were examined. The compound increased the levels of double-stranded DNA breaks generated by both enzyme isoforms and did so better than a series of naphthoquinone derivatives. Furthermore, 1,2-naphthoquinone was a more efficacious poison against topoisomerase IIα than IIβ. Topoisomerase II poisons can be classified as interfacial (which interact noncovalently at the enzyme-DNA interface and increase DNA cleavage by blocking ligation) or covalent (which adduct the protein and increase DNA cleavage by closing the N-terminal gate of the enzyme). Therefore, experiments were performed to determine the mechanistic basis for the actions of 1,2-naphthoquinone. In contrast to results with etoposide (an interfacial poison), the activity of 1,2-naphthoquinone against topoisomerase IIα was abrogated in the presence of sulfhydryl and reducing agents. Moreover, the compound inhibited cleavage activity when incubated with the enzyme prior to the addition of DNA and induced virtually no cleavage with the catalytic core of the enzyme. It also induced stable covalent topoisomerase IIα-DNA cleavage complexes and was a partial inhibitor of DNA ligation. Findings were also consistent with 1,2-naphthoquinone acting as a covalent poison of topoisomerase IIβ; however, mechanistic studies with this isoform were less conclusive. Whereas the activity of 1,2-naphthoquinone was blocked in the presence of a sulfhydryl reagent, it was much less sensitive to the presence of a reducing agent. Furthermore, the reduced form of 1,2-naphthoquinone, 1,2-dihydroxynaphthalene, displayed high activity against the β isoform. Taken together, results suggest that 1,2-naphthoquinone increases topoisomerase II-mediated double-stranded DNA scission (at least in part) by acting as a covalent poison of the human type II enzymes.
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Affiliation(s)
- Jessica A. Collins
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Neil Osheroff
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
- Department of Medicine (Hematology/Oncology), Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
- VA Tennessee Valley Healthcare System, Nashville, Tennessee 37212, United States
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McKie SJ, Neuman KC, Maxwell A. DNA topoisomerases: Advances in understanding of cellular roles and multi-protein complexes via structure-function analysis. Bioessays 2021; 43:e2000286. [PMID: 33480441 PMCID: PMC7614492 DOI: 10.1002/bies.202000286] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/06/2020] [Accepted: 12/17/2020] [Indexed: 12/15/2022]
Abstract
DNA topoisomerases, capable of manipulating DNA topology, are ubiquitous and indispensable for cellular survival due to the numerous roles they play during DNA metabolism. As we review here, current structural approaches have revealed unprecedented insights into the complex DNA-topoisomerase interaction and strand passage mechanism, helping to advance our understanding of their activities in vivo. This has been complemented by single-molecule techniques, which have facilitated the detailed dissection of the various topoisomerase reactions. Recent work has also revealed the importance of topoisomerase interactions with accessory proteins and other DNA-associated proteins, supporting the idea that they often function as part of multi-enzyme assemblies in vivo. In addition, novel topoisomerases have been identified and explored, such as topo VIII and Mini-A. These new findings are advancing our understanding of DNA-related processes and the vital functions topos fulfil, demonstrating their indispensability in virtually every aspect of DNA metabolism.
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Affiliation(s)
- Shannon J. McKie
- Department Biological Chemistry, John Innes Centre, Norwich, UK
- Laboratory of Single Molecule Biophysics, NHLBI, Bethesda, Maryland, USA
| | - Keir C. Neuman
- Laboratory of Single Molecule Biophysics, NHLBI, Bethesda, Maryland, USA
| | - Anthony Maxwell
- Department Biological Chemistry, John Innes Centre, Norwich, UK
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Yasuda K, Kato Y, Ikeda S, Kawano S. Regulation of catalytic activity and nucleolar localization of rat DNA topoisomerase IIα through its C-terminal domain. Genes Genet Syst 2021; 95:291-302. [PMID: 33551432 DOI: 10.1266/ggs.20-00038] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Type II DNA topoisomerase (topo II) catalyzes double-stranded DNA cleavage and re-ligation, thus solving problems in DNA topology. Vertebrates have two isozymes (α and β). Recently, the C-terminal regulatory domain (CRD), which regulates catalytic activity and subnuclear localization by associating with RNA, was identified within the C-terminal domain (CTD) of rat topo IIβ. In contrast, it is unclear whether a β CRD-like domain is present in the CTD of topo IIα. In this study, we aimed to identify an RNA-mediated regulatory domain in the rat topo IIα CTD. First, we exchanged the CTDs of rat topo IIα (amino acids 1,192-1,528) and β (1,201-1,614) and examined the two chimeras' in vitro catalytic activities. Interestingly, the relaxation activities of topo IIα WT enzyme and both of the CTD-swapped mutants were inhibited in the presence of isolated cellular RNA, suggesting that the α CTD is involved in the RNA-mediated regulation of catalytic activity in topo IIα. The results of on-bead assays using a CTD-deleted mutant of rat topo IIα indicated that the RNA-mediated inhibition of the relaxation activity was caused by an interaction between the α CTD and RNA. Further, to identify the domain within the CTD that is associated with subnuclear localization of rat topo IIα, we transiently expressed EGFP-tagged CTD deletion mutants in human cells. The data indicated that the 1,192-1,289 region of rat topo IIα was required for targeting the enzyme to nucleoli. Finally, a relaxation assay using 1-1,289 and Δ1,192-1,289 truncated mutants indicated that the 1,192-1,289 region is involved in RNA-mediated inhibition. These results indicated that the CTD of rat topo IIα, containing the 1,192-1,289 region, is involved in the regulation of catalytic activity by associating with RNA, as well as in the localization to nucleoli in interphase cells.
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Affiliation(s)
- Kazushi Yasuda
- Department of Biochemistry, Faculty of Science, Okayama University of Science
| | - Yuri Kato
- Department of Biochemistry, Faculty of Science, Okayama University of Science
| | - Shogo Ikeda
- Department of Biochemistry, Faculty of Science, Okayama University of Science
| | - Shinji Kawano
- Department of Biochemistry, Faculty of Science, Okayama University of Science
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Towards Conformation-Sensitive Inhibition of Gyrase: Implications of Mechanistic Insight for the Identification and Improvement of Inhibitors. Molecules 2021; 26:molecules26051234. [PMID: 33669078 PMCID: PMC7956263 DOI: 10.3390/molecules26051234] [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: 02/04/2021] [Revised: 02/19/2021] [Accepted: 02/20/2021] [Indexed: 12/17/2022] Open
Abstract
Gyrase is a bacterial type IIA topoisomerase that catalyzes negative supercoiling of DNA. The enzyme is essential in bacteria and is a validated drug target in the treatment of bacterial infections. Inhibition of gyrase activity is achieved by competitive inhibitors that interfere with ATP- or DNA-binding, or by gyrase poisons that stabilize cleavage complexes of gyrase covalently bound to the DNA, leading to double-strand breaks and cell death. Many of the current inhibitors suffer from severe side effects, while others rapidly lose their antibiotic activity due to resistance mutations, generating an unmet medical need for novel, improved gyrase inhibitors. DNA supercoiling by gyrase is associated with a series of nucleotide- and DNA-induced conformational changes, yet the full potential of interfering with these conformational changes as a strategy to identify novel, improved gyrase inhibitors has not been explored so far. This review highlights recent insights into the mechanism of DNA supercoiling by gyrase and illustrates the implications for the identification and development of conformation-sensitive and allosteric inhibitors.
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Matias-Barrios VM, Radaeva M, Song Y, Alperstein Z, Lee AR, Schmitt V, Lee J, Ban F, Xie N, Qi J, Lallous N, Gleave ME, Cherkasov A, Dong X. Discovery of New Catalytic Topoisomerase II Inhibitors for Anticancer Therapeutics. Front Oncol 2021; 10:633142. [PMID: 33598437 PMCID: PMC7883873 DOI: 10.3389/fonc.2020.633142] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 12/15/2020] [Indexed: 01/23/2023] Open
Abstract
Poison inhibitors of DNA topoisomerase II (TOP2) are clinically used drugs that cause cancer cell death by inducing DNA damage, which mechanism of action is also associated with serious side effects such as secondary malignancy and cardiotoxicity. In contrast, TOP2 catalytic inhibitors induce limited DNA damage, have low cytotoxicity, and are effective in suppressing cancer cell proliferation. They have been sought after to be prospective anticancer therapies. Herein the discovery of new TOP2 catalytic inhibitors is described. A new druggable pocket of TOP2 protein at its DNA binding domain was used as a docking site to virtually screen ~6 million molecules from the ZINC15 library. The lead compound, T60, was characterized to be a catalytic TOP2 inhibitor that binds TOP2 protein and disrupts TOP2 from interacting with DNA, resulting in no DNA cleavage. It has low cytotoxicity, but strongly inhibits cancer cell proliferation and xenograft growth. T60 also inhibits androgen receptor activity and prostate cancer cell growth. These results indicate that T60 is a promising candidate compound that can be further developed into new anticancer drugs.
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Affiliation(s)
- Victor M Matias-Barrios
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Mariia Radaeva
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Yi Song
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada.,Department of Geriatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zaccary Alperstein
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Ahn R Lee
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Veronika Schmitt
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Joseph Lee
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Fuqiang Ban
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Ning Xie
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Jianfei Qi
- Department of Biochemistry and Molecular Biology, University of Maryland, Baltimore, Baltimore, MD, United States
| | - Nada Lallous
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Martin E Gleave
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Artem Cherkasov
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Xuesen Dong
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
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50
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Bicyclic Basic Merbarone Analogues as Antiproliferative Agents. Molecules 2021; 26:molecules26030557. [PMID: 33494519 PMCID: PMC7866144 DOI: 10.3390/molecules26030557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 11/17/2022] Open
Abstract
Pyrimido-pyrimidine derivatives have been developed as rigid merbarone analogues. In a previous study, these compounds showed potent antiproliferative activity and efficiently inhibited topoisomerase IIα. To further extend the structure-activity relationships on pyrimido-pyrimidines, a novel series of analogues was synthesized by a two-step procedure. Analogues 3-6 bear small alky groups at positions 1 and 3 of the pyrimido-pyrimidine scaffold whereas at position 6a (4-chloro)phenyl substituent was inserted. The basic side chains introduced at position 7 were selected on the basis of the previously developed structure-activity relationships. The antiproliferative activity of the novel compounds proved to be affected by both the nature of the basic side chain and the substituents on the pyrimido-pyrimidine moiety. Derivatives 5d and 5e were identified as the most promising molecules still showing reduced antiproliferative activity in comparison with the previously prepared pyrimido-pyrimidine analogues. In topoisomerase IIα-5d docking complex, the ligand would poorly interact with the enzyme and assume a different orientation in comparison with 1d bioactive conformation.
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