1
|
Mukheja Y, Sarkar A, Arora R, Pal K, Ahuja A, Vashishth A, Kuhad A, Chopra K, Jain M. Unravelling the progress and potential of drug-eluting stents and drug-coated balloons in cardiological insurgencies. Life Sci 2024; 352:122908. [PMID: 39004270 DOI: 10.1016/j.lfs.2024.122908] [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: 02/24/2024] [Revised: 07/01/2024] [Accepted: 07/08/2024] [Indexed: 07/16/2024]
Abstract
AIM Coronary artery disease (CAD) is the leading cause of mortality. Though percutaneous transluminal angioplasty followed by stenting is still the default treatment of choice for revascularization of obstructive CAD, the high rate of restenosis compromises the outcomes of endovascular procedures. To overcome restenosis, drug-eluting stents (DES) and drug-coated balloons (DCB) are designed that release antiproliferative drugs like sirolimus, paclitaxel, everolimus, etc., over time to inhibit cell growth and proliferation. Our review aims to summarize the challenges and progress of DES/DCBs in clinical settings. MATERIAL AND METHODS The comprehensive review, search and selection encompasses in relevant articles through Google Scholar, Springer online, Cochrane library and PubMed that includes research articles, reviews, letters and communications, various viewpoints, meta-analyses, randomized trials and quasi-randomized trials. Several preclinical and clinical data have been included from National Institutes of Health and clinicaltrials.gov websites. KEY FINDINGS Challenges like delayed endothelialization, stent thrombosis (ST), and inflammation was prominent in first-generation DES. Second-generation DES with improved designs and drug coatings enhanced biocompatibility with fewer complications. Gradual absorption of bioresorbable DES over time mitigated long-term issues associated with permanent implants. Polymer-free DES addressed the inflammation concerns but still, they leave behind metallic stents in the vasculature. As an alternative therapeutic strategy, DCB were developed to minimize inflammation in the vessel. Although both DES and DCBs have shown considerable progress, challenges persist. SIGNIFICANCE This review illustrates the advancements in the designs, preparation technologies, biodegradable materials, and drugs used as well as challenges associated with DES and DCBs in clinical settings.
Collapse
Affiliation(s)
- Yashdeep Mukheja
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
| | - Ankan Sarkar
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
| | - Rubal Arora
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
| | - Kashish Pal
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
| | - Akanksha Ahuja
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
| | - Anushka Vashishth
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
| | - Anurag Kuhad
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
| | - Kanwaljit Chopra
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India
| | - Manish Jain
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, India.
| |
Collapse
|
2
|
Kretzer B, Herényi L, Csík G, Supala E, Orosz Á, Tordai H, Kiss B, Kellermayer M. TMPyP binding evokes a complex, tunable nanomechanical response in DNA. Nucleic Acids Res 2024; 52:8399-8418. [PMID: 38943349 PMCID: PMC11317170 DOI: 10.1093/nar/gkae560] [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: 10/17/2023] [Revised: 06/06/2024] [Accepted: 06/17/2024] [Indexed: 07/01/2024] Open
Abstract
TMPyP is a porphyrin capable of DNA binding and used in photodynamic therapy and G-quadruplex stabilization. Despite its broad applications, TMPyP's effect on DNA nanomechanics is unknown. Here we investigated, by manipulating λ-phage DNA with optical tweezers combined with microfluidics in equilibrium and perturbation kinetic experiments, how TMPyP influences DNA nanomechanics across wide ranges of TMPyP concentration (5-5120 nM), mechanical force (0-100 pN), NaCl concentration (0.01-1 M) and pulling rate (0.2-20 μm/s). Complex responses were recorded, for the analysis of which we introduced a simple mathematical model. TMPyP binding, which is a highly dynamic process, leads to dsDNA lengthening and softening. dsDNA stability increased at low (<10 nM) TMPyP concentrations, then decreased progressively upon increasing TMPyP concentration. Overstretch cooperativity decreased, due most likely to mechanical roadblocks of ssDNA-bound TMPyP. TMPyP binding increased ssDNA's contour length. The addition of NaCl at high (1 M) concentration competed with the TMPyP-evoked nanomechanical changes. Because the largest amplitude of the changes is induced by the pharmacologically relevant TMPyP concentration range, this porphyrin derivative may be used to tune DNA's structure and properties, hence control the wide array of biomolecular DNA-dependent processes including replication, transcription, condensation and repair.
Collapse
Affiliation(s)
- Balázs Kretzer
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
- HUNREN-SE Biophysical Virology Group, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Levente Herényi
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Gabriella Csík
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Eszter Supala
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Ádám Orosz
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Hedvig Tordai
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Bálint Kiss
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
- HUNREN-SE Biophysical Virology Group, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Miklós Kellermayer
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
- HUNREN-SE Biophysical Virology Group, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| |
Collapse
|
3
|
Ananyan GV, Karapetyan NH, Dalyan YB. The structural features of poly(dG-dC).poly(dG-dC) at complexation with some porphyrins. J Biomol Struct Dyn 2022; 40:10313-10318. [PMID: 34197714 DOI: 10.1080/07391102.2021.1942216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The binding peculiarities of the water-soluble meso-tetra-(4N-hydroxyethylpyridyl) porphyrin (H2TOEtPyP4) and its Cu- and Co-derivatives (CuTOEtPyP4 and CoTOEtPyP4) with synthetic double-stranded alternating polynucleotide poly(dG-dC).poly(dG-dC) were investigated by UV/Vis absorption and circular dichroism (CD) methods. It was shown that the porphyrins with planar structure such as H2TOEtPyP4 and CuTOEtPyP4 interact with poly(dG-dC).poly(dG-dC) via intercalation at low relative concentrations (r = [porphyrin]/[polynucleotide]), while at high r - via intercalation and external binding modes. In the case of no planar porphyrin CoTOEtPyP4 complexation occurs only by external binding mode. The binding constant Kb and the exclusion parameter n calculated for H2TOEtPyP4, CuTOEtPyP4 and CoTOEtPyP4 porphyrins with poly(dG-dC).poly(dG-dC) complexes was 1.50 x107, M-1 (n = 1.76); 9.29 x107, M-1 (n = 1.18); and 0.28 x107, M-1 (n = 2.65) correspondingly. The values of binding parameters for each porphyrin-poly(dG-dC).poly(dG-dC) complexes demonstrated good agreement with the proposed binding models. Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Gayane V Ananyan
- Department of Molecular Physics, Yerevan State University, Yerevan, Armenia
| | - Nelli H Karapetyan
- Department of Molecular Physics, Yerevan State University, Yerevan, Armenia
| | - Yeva B Dalyan
- Department of Molecular Physics, Yerevan State University, Yerevan, Armenia
| |
Collapse
|
4
|
Jabak AA, Bryden N, Westerlund F, Lincoln P, McCauley MJ, Rouzina I, Williams MC, Paramanathan T. Left versus right: Exploring the effects of chiral threading intercalators using optical tweezers. Biophys J 2022; 121:3745-3752. [PMID: 35470110 PMCID: PMC9617076 DOI: 10.1016/j.bpj.2022.04.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/27/2022] [Accepted: 04/20/2022] [Indexed: 11/02/2022] Open
Abstract
Small-molecule DNA-binding drugs have shown promising results in clinical use against many types of cancer. Understanding the molecular mechanisms of DNA binding for such small molecules can be critical in advancing future drug designs. We have been exploring the interactions of ruthenium-based small molecules and their DNA-binding properties that are highly relevant in the development of novel metal-based drugs. Previously we have studied the effects of the right-handed binuclear ruthenium threading intercalator ΔΔ-[μ-bidppz(phen)4Ru2]4+, or ΔΔ-P for short, which showed extremely slow kinetics and high-affinity binding to DNA. Here we investigate the left-handed enantiomer ΛΛ-[μ-bidppz(phen)4Ru2]4+, or ΛΛ-P for short, to study the effects of chirality on DNA threading intercalation. We employ single-molecule optical trapping experiments to understand the molecular mechanisms and nanoscale structural changes that occur during DNA binding and unbinding as well as the association and dissociation rates. Despite the similar threading intercalation binding mode of the two enantiomers, our data show that the left-handed ΛΛ-P complex requires increased lengthening of the DNA to thread, and it extends the DNA more than double the length at equilibrium compared with the right-handed ΔΔ-P. We also observed that the left-handed ΛΛ-P complex unthreads three times faster than ΔΔ-P. These results, along with a weaker binding affinity estimated for ΛΛ-P, suggest a preference in DNA binding to the chiral enantiomer having the same right-handed chirality as the DNA molecule, regardless of their common intercalating moiety. This comparison provides a better understanding of how chirality affects binding to DNA and may contribute to the development of enhanced potential cancer treatment drug designs.
Collapse
Affiliation(s)
- Adam A Jabak
- Department of Physics, Photonics and Optical Engineering, Bridgewater State University, Bridgewater, Massachusetts
| | - Nicholas Bryden
- Department of Physics, Photonics and Optical Engineering, Bridgewater State University, Bridgewater, Massachusetts
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Per Lincoln
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Micah J McCauley
- Department of Physics, Northeastern University, Boston, Massachusetts
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio
| | - Mark C Williams
- Department of Physics, Northeastern University, Boston, Massachusetts.
| | - Thayaparan Paramanathan
- Department of Physics, Photonics and Optical Engineering, Bridgewater State University, Bridgewater, Massachusetts.
| |
Collapse
|
5
|
Zeng YX, Liu JS, Wang YJ, Tang S, Wang DY, Deng SM, Jia AQ. Actinomycin D: a novel Pseudomonas aeruginosa quorum sensing inhibitor from the endophyte Streptomyces cyaneochromogenes RC1. World J Microbiol Biotechnol 2022; 38:170. [PMID: 35904625 DOI: 10.1007/s11274-022-03360-y] [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: 04/05/2022] [Accepted: 07/15/2022] [Indexed: 10/16/2022]
Abstract
The infections caused by Pseudomonas aeruginosa are difficult to treat due to its multidrug resistance. A promising strategy for controlling P. aeruginosa infection is targeting the quorum sensing (QS) system. Actinomycin D isolated from the metabolite of endophyte Streptomyces cyaneochromogenes RC1 exhibited good anti-QS activity against P. aeruginosa PAO1. Actinomycin D (50, 100, and 200 μg/mL) significantly inhibited the motility as well as reduced the production of multiple virulence factors including pyocyanin, protease, rhamnolipid, and siderophores. The images of confocal laser scanning microscopy and scanning electron microscopy revealed that the treatment of actinomycin D resulted in a looser and flatter biofilm structure. Real-time quantitative PCR analysis showed that the expression of QS-related genes lasI, rhlI, rhlR, pqsR, pslA, and pilA were downregulated dramatically. The production of QS signaling molecules N-(3-oxododecanoyl)-L-homoserine lactone and N-butanoyl-L-homoserine lactone were also decreased by actinomycin D. These findings suggest that actinomycin D, a potent in vitro anti-virulence agent, is a promising candidate to treat P. aeruginosa infection by interfering with the QS systems.
Collapse
Affiliation(s)
- Yue-Xiang Zeng
- School of Pharmaceutical Sciences, Hainan University, Haikou, 570228, China.,State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China
| | - Jun-Sheng Liu
- School of Pharmaceutical Sciences, Hainan University, Haikou, 570228, China.,State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China
| | - Ying-Jie Wang
- School of Pharmaceutical Sciences, Hainan University, Haikou, 570228, China
| | - Shi Tang
- School of Pharmaceutical Sciences, Hainan University, Haikou, 570228, China.,State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China
| | - Da-Yong Wang
- School of Pharmaceutical Sciences, Hainan University, Haikou, 570228, China
| | - Shi-Ming Deng
- School of Pharmaceutical Sciences, Hainan University, Haikou, 570228, China
| | - Ai-Qun Jia
- School of Pharmaceutical Sciences, Hainan University, Haikou, 570228, China. .,State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China. .,One Health Institute, Hainan University, Haikou, 570228, China.
| |
Collapse
|
6
|
Nicolas J, Pivato CA, Chiarito M, Beerkens F, Cao D, Mehran R. Evolution of drug-eluting coronary stents: a back-and-forth journey from the bench-to-bedside. Cardiovasc Res 2022; 119:631-646. [PMID: 35788828 DOI: 10.1093/cvr/cvac105] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 05/06/2022] [Accepted: 05/11/2022] [Indexed: 11/13/2022] Open
Abstract
Coronary stents have revolutionized the treatment of coronary artery disease. Compared with balloon angioplasty, bare-metal stents effectively prevented abrupt vessel closure but were limited by in-stent restenosis due to smooth muscle cell proliferation and neointimal hyperplasia. The first-generation drug-eluting stent (DES), with its antiproliferative drug coating, offered substantial advantages over bare-metal stents as it mitigated the risk of in-stent restenosis. Nonetheless, they had several design limitations that increased the risk of late stent thrombosis. Significant advances in stent design, including thinner struts, enhanced polymers' formulation, and more potent antiproliferative agents, have led to the introduction of new-generation DES with a superior safety profile. Cardiologists have over 20 different DES types to choose from, each with its unique features and characteristics. This review highlights the evolution of stent design and summarizes the clinical data on the different stent types. We conclude by discussing the clinical implications of stent design in high-risk subsets of patients.
Collapse
Affiliation(s)
- Johny Nicolas
- The Zena and Michael A. Wiener Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carlo Andrea Pivato
- The Zena and Michael A. Wiener Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Biomedical Sciences, Humanitas University, Pieve Emanuele-Milan, Italy.,IRCCS Humanitas Research Hospital, via Manzoni 56, 20089 Rozzano, Milan, Italy
| | - Mauro Chiarito
- The Zena and Michael A. Wiener Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Biomedical Sciences, Humanitas University, Pieve Emanuele-Milan, Italy.,IRCCS Humanitas Research Hospital, via Manzoni 56, 20089 Rozzano, Milan, Italy
| | - Frans Beerkens
- The Zena and Michael A. Wiener Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Davide Cao
- The Zena and Michael A. Wiener Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Cardiovascular Department, Humanitas Gavazzeni, Bergamo, Italy
| | - Roxana Mehran
- The Zena and Michael A. Wiener Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| |
Collapse
|
7
|
Kale KB, Shinde MASA, Patil RH, Ottoor DP. Exploring the interaction of Valsartan and Valsartan-Zn(ll) complex with DNA by spectroscopic and in silico methods. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 264:120329. [PMID: 34481251 DOI: 10.1016/j.saa.2021.120329] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 08/19/2021] [Accepted: 08/24/2021] [Indexed: 05/08/2023]
Abstract
Belonging to the Sartan family, antihypertensive drug - Valsartan (Val) had been found to possess antioxidant properties. Also, the zinc complex of Valsartan (VZn) has been recently recognized as inducing agents of the reductive stress effects thus possessing anticancer activity. Hence, in this work an attempt has been made to understand the interaction of Val and VZn with DNA using spectroscopic and in silico methods as DNA has been identified as the target for many anticancer drugs. VZn has been prepared in 2:1 M ratio and characterised by absorbance, FTIR, HRMS, NMR and Job's continuous variation method. VZn has been tested against human lungs cancer cell line which exhibited good anticancer activity (IC50 = 89 µg/mL). Interaction of Val and VZn with ct-DNA under physiological conditions has been studied by spectroscopic techniques such as fluorescence, absorbance, FTIR, circular dichroism (CD) and in silico methods. Fluorescence quenching, DNA melting and viscometric studies confirmed that both ligand and complex bind to the grooves of the ct-DNA. The experimental results have revealed that VZn strongly bind with DNA compared to Val. Docking study suggested that, Val binds at major groove while VZn binds to both minor and major grooves of B-DNA.
Collapse
Affiliation(s)
- Kishor B Kale
- Department of Chemistry, Savitribai Phule Pune University, Ganeshkhind Road, Pune 411007, India; Department of Chemistry, Nowrosjee Wadia College, Pune 411001, India
| | | | - Rajendra H Patil
- Department of Biotechnology, Savitribai Phule Pune University, Pune 411007, India
| | - Divya P Ottoor
- Department of Chemistry, Savitribai Phule Pune University, Ganeshkhind Road, Pune 411007, India.
| |
Collapse
|
8
|
Mobility of Nucleostemin in Live Cells Is Specifically Related to Transcription Inhibition by Actinomycin D and GTP-Binding Motif. Int J Mol Sci 2021; 22:ijms22158293. [PMID: 34361059 PMCID: PMC8347349 DOI: 10.3390/ijms22158293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 07/24/2021] [Accepted: 07/29/2021] [Indexed: 12/04/2022] Open
Abstract
In vertebrates, nucleostemin (NS) is an important marker of proliferation in several types of stem and cancer cells, and it can also interact with the tumor-suppressing transcription factor p53. In the present study, the intra-nuclear diffusional dynamics of native NS tagged with GFP and two GFP-tagged NS mutants with deleted guanosine triphosphate (GTP)-binding domains were analyzed by fluorescence correlation spectroscopy. Free and slow binding diffusion coefficients were evaluated, either under normal culture conditions or under treatment with specific cellular proliferation inhibitors actinomycin D (ActD), 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB), or trichostatin A (TSA). When treated with ActD, the fractional ratio of the slow diffusion was significantly decreased in the nucleoplasm. The decrease was proportional to ActD treatment duration. In contrast, DRB or TSA treatment did not affect NS diffusion. Interestingly, it was also found that the rate of diffusion of two NS mutants increased significantly even under normal conditions. These results suggest that the mobility of NS in the nucleoplasm is related to the initiation of DNA or RNA replication, and that the GTP-binding motif is also related to the large change of mobility.
Collapse
|
9
|
Sharma V, Gupta M, Kumar P, Sharma A. A Comprehensive Review on Fused Heterocyclic as DNA Intercalators: Promising Anticancer Agents. Curr Pharm Des 2021; 27:15-42. [PMID: 33213325 DOI: 10.2174/1381612826666201118113311] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/02/2020] [Indexed: 12/09/2022]
Abstract
Since the discovery of DNA intercalating agents (by Lerman, 1961), a growing number of organic, inorganic, and metallic compounds have been developed to treat life-threatening microbial infections and cancers. Fused-heterocycles are amongst the most important group of compounds that have the ability to interact with DNA. DNA intercalators possess a planar aromatic ring structure that inserts itself between the base pairs of nucleic acids. Once inserted, the aromatic structure makes van der Waals interactions and hydrogen-bonding interactions with the base pairs. The DNA intercalator may also contain an ionizable group that can form ionic interactions with the negatively charged phosphate backbone. After the intercalation, other cellular processes could take place, leading ultimately to cell death. The heterocyclic nucleus present in the DNA intercalators can be considered as a pharmacophore that plays an instrumental role in dictating the affinity and selectivity exhibited by these compounds. In this work, we have carried out a revision of small organic molecules that bind to the DNA molecule via intercalation and cleaving and exert their antitumor activity. A general overview of the most recent results in this area, paying particular attention to compounds that are currently under clinical trials, is provided. Advancement in spectroscopic techniques studying DNA interaction can be examined in-depth, yielding important information on structure-activity relationships. In this comprehensive review, we have focused on the introduction to fused heterocyclic agents with DNA interacting features, from medicinal point of view. The structure-activity relationships points, cytotoxicity data, and binding data and future perspectives of medicinal compounds have been discussed in detail.
Collapse
Affiliation(s)
- Vikas Sharma
- IIMT College of Pharmacy, Knowledge Park III, Greater Noida, Uttar Pradesh-201308, India
| | - Mohit Gupta
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Robertson Life Sciences Building, 2730 South Moody Avenue, Portland, OR 97201, United States
| | - Pradeep Kumar
- Department of Pharmacy and Pharmacology, School of Therapeutic Sciences, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Atul Sharma
- School of Chemistry, Monash University, Clayton, Victoria, 3800, Australia
| |
Collapse
|
10
|
Peng Y, Wang Y, Wang X. Exploring the Thermodynamics of 7-Amino Actinomycin D-Induced Single-Stranded DNA Hairpin by Spectroscopic Techniques and Computational Simulations. J Phys Chem B 2020; 124:10007-10013. [PMID: 33136398 DOI: 10.1021/acs.jpcb.0c05593] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
NMR studies have indicated that the anti-tumor therapeutic agent actinomycin D (ACTD) can induce seemingly single-stranded DNA (ssDNA) oligomer 5'-CCGTT3GTGG-3' to form a hairpin structure with tandem GT mismatches at the stem region next to a loop of three stacked thymine bases. In an effort to uncover the preference of binding sequence and to elucidate the thermodynamics properties of the binding, a combination of spectroscopic techniques and computational simulation studies was performed with d(CCGTTnGTGG) and d(CCGAAnGAGG) (denoted as GTTn and GAAn, respectively; n = 3, 5, and 7) sequences. In the presence of 7-amino actinomycin D (7AACTD), all the six oligomers formed stable hairpin structures. The GTT5-7AACTD/GAA5-7AACTD hairpin structure was more stable than the corresponding GTTn-7AACTD and GAAn-7AACTD (n = 3, 7). No significant ΔG difference was observed between GTTn-7AACTD and GAAn-7AACTD complexes with the same loop length. In agreement with the 7AACTD-induced hairpin stability results, the binding affinity of GTTn and GAAn with 7AACTD increased from n = 3 to n = 5 and then decreased when n is 7. Moreover, GTTn and GAAn with the same loop length showed comparable binding affinities to 7AACTD. Furthermore, molecular dynamics simulations found that van der Waals interactions between GTTn/GAAn and 7AACTD were the primary attractive forces for 7AACTD binding, and the electrostatic interactions between the carbonyl groups of 7AACTD and bases in the hairpin were the major unfavorable forces. These findings furthered our understanding that 7AACTD is sensitive to the loop size and sequence as well as tandem GT/GA mismatches of their deoxyribonucleic acid (DNA) targets. A deep understanding of the thermodynamics and the molecular recognition mechanism of 7AACTD with ssDNAs would further the development of ACTD-like antitumor agents.
Collapse
Affiliation(s)
- Yinghua Peng
- Key Laboratory of Special Animal Molecular Biology of Jilin Province, Specialty Research Institute of Chinese Academy of Agricultural Sciences, Changchun, Jilin 130022, China
| | - Yibo Wang
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Xiaohui Wang
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China.,Department of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei 230026, China
| |
Collapse
|
11
|
Discrimination between G/C Binding Sites by Olivomycin A Is Determined by Kinetics of the Drug-DNA Interaction. Int J Mol Sci 2020; 21:ijms21155299. [PMID: 32722584 PMCID: PMC7432603 DOI: 10.3390/ijms21155299] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/20/2020] [Accepted: 07/23/2020] [Indexed: 12/25/2022] Open
Abstract
Olivomycin A (OA) exerts its cytotoxic potency due to binding to the minor groove of the G/C-rich DNA and interfering with replication and transcription. Screening of the complete set of tetranucleotide G/C sites by electrophoretic mobility gel shift assay (EMSA) revealed that the sites containing central GC or GG dinucleotides were able to bind OA, whereas the sites with the central CG dinucleotide were not. However, studies of equilibrium OA binding in solution by fluorescence, circular dichroism and isothermal titration calorimetry failed to confirm the sequence preference of OA, indicating instead a similar type of complex and comparable affinity of OA to all G/C binding sites. This discrepancy was resolved by kinetics analysis of the drug–DNA interaction: the dissociation rate significantly differed between SGCS, SGGS and SCGS sites (S stands for G or C), thereby explaining the disintegration of the complexes during EMSA. The functional relevance of the revealed differential kinetics of OA–DNA interaction was demonstrated in an in vitro transcription assay. These findings emphasize the crucial role of kinetics in the mechanism of OA action and provide an important approach to the screening of new drug candidates.
Collapse
|
12
|
Maurya N, Parray ZA, Maurya JK, Islam A, Patel R. Ionic Liquid Green Assembly-Mediated Migration of Piperine from Calf-Thymus DNA: A New Possibility of the Tunable Drug Delivery System. ACS OMEGA 2019; 4:21005-21017. [PMID: 31867492 PMCID: PMC6921251 DOI: 10.1021/acsomega.9b02246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 10/18/2019] [Indexed: 06/07/2023]
Abstract
Biocompatible surface-active ionic liquid (SAIL) was used first to study the deintercalation process of a well-known natural compound piperine (PIP) as an anticancer drug, obtained from PIP-calf thymus DNA (ctDNA) complex under controlled experimental conditions. In this study, we have been exploring the interaction of PIP in SAIL (1-butyl-3-methylimidazolium octyl sulfate ionic liquid ([C4mim][C8OSO3])), ctDNA, and deintercalation of PIP from the PIP-ctDNA complex through SAIL micelle using various spectroscopic techniques. Absorption, emission, and lifetime decay measurements provide strong evidence of the relocation of PIP molecules from ctDNA to SAIL micelle. Fluorescence quenching and steady-state fluorescence anisotropy were employed to examine the exact location of PIP in different media. Moreover, the surface tension technique was also employed to confirm the release of PIP molecules from the PIP-ctDNA complex in the presence of SAIL. Circular dichroism analysis suggested that SAIL micelle does not perturb the ctDNA structure, which supported the fact that SAIL micelle can be used as a safe vehicle for PIP. Overall, the study highlighted a novel strategy for deintercalation of drug using SAIL because the release of the drug can be controlled over a period by varying the concentration and composition of the SAIL.
Collapse
Affiliation(s)
- Neha Maurya
- Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research
in Basic Sciences and Protein Research Laboratory, Centre for Interdisciplinary
Research in Basic Sciences, Jamia Millia
Islamia, New Delhi 110025, India
| | - Zahoor Ahmad Parray
- Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research
in Basic Sciences and Protein Research Laboratory, Centre for Interdisciplinary
Research in Basic Sciences, Jamia Millia
Islamia, New Delhi 110025, India
| | - Jitendra Kumar Maurya
- Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research
in Basic Sciences and Protein Research Laboratory, Centre for Interdisciplinary
Research in Basic Sciences, Jamia Millia
Islamia, New Delhi 110025, India
| | - Asimul Islam
- Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research
in Basic Sciences and Protein Research Laboratory, Centre for Interdisciplinary
Research in Basic Sciences, Jamia Millia
Islamia, New Delhi 110025, India
| | - Rajan Patel
- Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research
in Basic Sciences and Protein Research Laboratory, Centre for Interdisciplinary
Research in Basic Sciences, Jamia Millia
Islamia, New Delhi 110025, India
| |
Collapse
|
13
|
Mukherjee A, Ghosh S, Pal M, Singh B. Deciphering the effective sequestration of DNA bounded bioactive small molecule Safranin-O by non-ionic surfactant TX-114 and diminution its cytotoxicity. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
14
|
Reddy K, Jenquin JR, Cleary JD, Berglund JA. Mitigating RNA Toxicity in Myotonic Dystrophy using Small Molecules. Int J Mol Sci 2019; 20:E4017. [PMID: 31426500 PMCID: PMC6720693 DOI: 10.3390/ijms20164017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/13/2019] [Accepted: 08/16/2019] [Indexed: 12/26/2022] Open
Abstract
This review, one in a series on myotonic dystrophy (DM), is focused on the development and potential use of small molecules as therapeutics for DM. The complex mechanisms and pathogenesis of DM are covered in the associated reviews. Here, we examine the various small molecule approaches taken to target the DNA, RNA, and proteins that contribute to disease onset and progression in myotonic dystrophy type 1 (DM1) and 2 (DM2).
Collapse
Affiliation(s)
- Kaalak Reddy
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA.
| | - Jana R Jenquin
- Center for NeuroGenetics and Biochemistry & Molecular Biology, University of Florida, Gainesville, FL 32608, USA
| | - John D Cleary
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - J Andrew Berglund
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA.
- Center for NeuroGenetics and Biochemistry & Molecular Biology, University of Florida, Gainesville, FL 32608, USA.
| |
Collapse
|
15
|
Lin S, Zhang C, Liu F, Ma J, Jia F, Han Z, Xie W, Li X. Actinomycin V Inhibits Migration and Invasion via Suppressing Snail/Slug-Mediated Epithelial-Mesenchymal Transition Progression in Human Breast Cancer MDA-MB-231 Cells In Vitro. Mar Drugs 2019; 17:E305. [PMID: 31137656 PMCID: PMC6562598 DOI: 10.3390/md17050305] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/22/2019] [Accepted: 05/22/2019] [Indexed: 02/06/2023] Open
Abstract
Actinomycin V, an analog of actinomycin D produced by the marine-derived actinomycete Streptomyces sp., possessing a 4-ketoproline instead of a 4-proline in actinomycin D. In this study, the involvement of snail/slug-mediated epithelial-mesenchymal transition (EMT) in the anti-migration and -invasion actions of actinomycin V was investigated in human breast cancer MDA-MB-231 cells in vitro. Cell proliferation effect was evaluated by 3-(4,5-Dimethylthiazol)-2,5-diphenyltetrazolium bromide (MTT) assay. Wound-healing and Transwell assay were performed to investigate the anti-migration and -invasion effects of actinomycin V. Western blotting was used to detect the expression levels of E-cadherin, N-cadherin, vimentin, snail, slug, zinc finger E-box binding homeobox 1 (ZEB1), and twist proteins and the mRNA levels were detected by rt-PCR. Actinomycin V showed stronger cytotoxic activity than that of actinomycin D. Actinomycin V up-regulated both of the protein and mRNA expression levels of E-cadherin and down-regulated that of N-cadherin and vimentin in the same cells. In this connection, actinomycin V decreased the snail and slug protein expression, and consequently inhibited cells EMT procession. Our results suggest that actinomycin V inhibits EMT-mediated migration and invasion via decreasing snail and slug expression, which exhibits therapeutic potential for the treatment of breast cancer and further toxicity investigation in vivo is needed.
Collapse
Affiliation(s)
- Shiqi Lin
- School of Ocean, Shandong University, Weihai 264209, China.
| | - Caiyun Zhang
- School of Ocean, Shandong University, Weihai 264209, China.
| | - Fangyuan Liu
- School of Ocean, Shandong University, Weihai 264209, China.
| | - Jiahui Ma
- School of Ocean, Shandong University, Weihai 264209, China.
| | - Fujuan Jia
- School of Ocean, Shandong University, Weihai 264209, China.
| | - Zhuo Han
- School of Ocean, Shandong University, Weihai 264209, China.
| | - Weidong Xie
- School of Ocean, Shandong University, Weihai 264209, China.
| | - Xia Li
- School of Ocean, Shandong University, Weihai 264209, China.
- School of Pharmaceutical Sciences, Shandong University, Jinan 250012, China.
- The Key Laboratory of Chemistry for Natural Product of Guizhou Province, Chinese Academy of Science, Guiyang 550002, China.
| |
Collapse
|
16
|
Mora AK, Basu A, Kalel R, Nath S. Polymer-assisted drug sequestration from plasma protein by a surfactant with curtailed denaturing capacity. Phys Chem Chem Phys 2019; 21:7127-7136. [PMID: 30887975 DOI: 10.1039/c8cp03576h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The capability of a surfactant to sequester a drug bound to plasma protein was investigated using steady-state and time-resolved spectroscopic techniques. Surfactants are known to denature protein, and hence are not suitable for the sequestration of a drug from protein. Herein, we show that the denaturing capacity of a surfactant is curtailed completely and its drug sequestration power is enhanced in the presence of biocompatible Pluronic micelles due to the formation of unique supramolecular assemblies. Further, our detailed studies indicate that the concentration of surfactant required for the sequestration of a drug is less than its critical micellar concentration (CMC). The extent of sequestration of drug by polymer-surfactant supramolecular assemblies can be tuned finely by controlling the concentration of surfactant. Detailed analysis showed that up to ∼85% sequestration of a drug from plasma protein could be achieved using a sub-CMC concentration of surfactant. Our results clearly show that controlled sequestration of a drug from plasma protein can be achieved with a reduction in the protein denaturing properties of surfactants.
Collapse
Affiliation(s)
- Aruna K Mora
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India.
| | | | | | | |
Collapse
|
17
|
Jia F, Wang S, Man Y, Kumar P, Liu B. Recent Developments in the Interactions of Classic Intercalated Ruthenium Compounds: [Ru(bpy)₂dppz] 2+ and [Ru(phen)₂dppz] 2+ with a DNA Molecule. Molecules 2019; 24:molecules24040769. [PMID: 30791625 PMCID: PMC6412511 DOI: 10.3390/molecules24040769] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/12/2019] [Accepted: 02/12/2019] [Indexed: 12/19/2022] Open
Abstract
[Ru(bpy)2dppz]2+ and [Ru(phen)2dppz]2+ as the light switches of the deoxyribose nucleic acid (DNA) molecule have attracted much attention and have become a powerful tool for exploring the structure of the DNA helix. Their interactions have been intensively studied because of the excellent photophysical and photochemical properties of ruthenium compounds. In this perspective, this review describes the recent developments in the interactions of these two classic intercalated compounds with a DNA helix. The mechanism of the molecular light switch effect and the selectivity of these two compounds to different forms of a DNA helix has been discussed. In addition, the specific binding modes between them have been discussed in detail, for a better understanding the mechanism of the light switch and the luminescence difference. Finally, recent studies of single molecule force spectroscopy have also been included so as to precisely interpret the kinetics, equilibrium constants, and the energy landscape during the process of the dynamic assembly of ligands into a single DNA helix.
Collapse
Affiliation(s)
- Fuchao Jia
- Laboratory of Functional Molecules and Materials, School of Physics and Optoelectronic Engineering, Shandong University of Technology, Zibo 255000, China.
| | - Shuo Wang
- Laboratory of Functional Molecules and Materials, School of Physics and Optoelectronic Engineering, Shandong University of Technology, Zibo 255000, China.
| | - Yan Man
- Beijing Research Center for Agricultural Standards and Testing, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
| | - Parveen Kumar
- Laboratory of Functional Molecules and Materials, School of Physics and Optoelectronic Engineering, Shandong University of Technology, Zibo 255000, China.
| | - Bo Liu
- Laboratory of Functional Molecules and Materials, School of Physics and Optoelectronic Engineering, Shandong University of Technology, Zibo 255000, China.
| |
Collapse
|
18
|
Das I, Halder M. Interaction of Fluoroquinolones in Their Different Prototropic States with DNA: Diversity in the Nature of Binding and the Role of External Chemical Stimulus on Drug Displacement. ChemistrySelect 2019. [DOI: 10.1002/slct.201803336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Ishita Das
- Department of Chemistry; Indian Institute of Technology Kharagpur; Kharagpur- 721302 INDIA
| | - Mintu Halder
- Department of Chemistry; Indian Institute of Technology Kharagpur; Kharagpur- 721302 INDIA
| |
Collapse
|
19
|
Paul BK, Ghosh N, Mukherjee S. Association and sequestered dissociation of an anticancer drug from liposome membrane: Role of hydrophobic hydration. Colloids Surf B Biointerfaces 2018; 170:36-44. [PMID: 29864652 DOI: 10.1016/j.colsurfb.2018.05.064] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 05/23/2018] [Accepted: 05/29/2018] [Indexed: 01/31/2023]
Abstract
Herein, the interaction of a potent anticancer drug (Sanguinarine, SG) with dimyristoyl-l-α-phosphatidylglycerol (DMPG) liposome membrane has been investigated at physiological pH. The spectroscopic fluorescence decay results demonstrate a modification of the photophysics of SG within DMPG-encapsulated state leading to preferential stabilization of the iminium ion over the alkanolamine form. This suggests a key role of electrostatic force underlying the interaction. The complex dependence of the thermodynamic parameters on temperature yields a unique finding of a positive heat capacity change (ΔCp) indicating the signature of hydrophobic hydration. The study also demonstrates the application of β-cyclodextrin (βCD) as a prospective host system resulting in release of the DMPG-bound drug. A calorimetric exploration of the DMPG-βCD interaction reveals an intrinsically complex thermodynamics of the process leading to ΔCp > 0 and thus marking the instrumental role of hydrophobic hydration which follows that the DMPG-βCD interaction is accompanied with burial of polar molecular surfaces. A systematic investigation of the diffusion of the drug within various microheterogeneous environments by Fluorescence Correlation Spectroscopy (FCS) categorically reinforces our arguments.
Collapse
Affiliation(s)
- Bijan K Paul
- Department of Chemistry, Mahadevananda Mahavidyalaya, Barrackpore, Kolkata 700120, West Bengal, India
| | - Narayani Ghosh
- Department of General Science and Humanities, Modern Institute of Engineering and Technology, Bandel, Kolkata 712123, West Bengal, India
| | - Saptarshi Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462066, Madhya Pradesh, India.
| |
Collapse
|
20
|
Kreft D, Wang Y, Rattay M, Toensing K, Anselmetti D. Binding mechanism of anti-cancer chemotherapeutic drug mitoxantrone to DNA characterized by magnetic tweezers. J Nanobiotechnology 2018; 16:56. [PMID: 30005668 PMCID: PMC6043947 DOI: 10.1186/s12951-018-0381-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 06/26/2018] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Chemotherapeutic agents (anti-cancer drugs) are small cytostatic or cytotoxic molecules that often bind to double-stranded DNA (dsDNA) resulting in modifications of their structural and nanomechanical properties and thus interfering with the cell proliferation process. METHODS We investigated the anthraquinone compound mitoxantrone that is used for treating certain cancer types like leukemia and lymphoma with magnetic tweezers as a single molecule nanosensor. In order to study the association of mitoxantrone with dsDNA, we conducted force-extension and mechanical overwinding experiments with a sensitivity of 10-14 N. RESULTS Using this method, we were able to estimate an equilibrium constant of association Ka ≈ 1 × 105 M-1 as well as a binding site size of n ≈ 2.5 base pairs for mitoxantrone. An unwinding angle of mitoxantrone-intercalation of ϑ ≈ 16° was determined. CONCLUSION Moreover, we observed a complex concentration-dependent bimodal binding behavior, where mitoxantrone associates to dsDNA as an intercalator and groove binder simultaneously at low concentrations and as a mere intercalator at high concentrations.
Collapse
Affiliation(s)
- Dennis Kreft
- Experimental Biophysics and Applied Nanoscience, Physics Department, Bielefeld Institute for Nanoscience (BINAS), Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany
| | - Ying Wang
- Experimental Biophysics and Applied Nanoscience, Physics Department, Bielefeld Institute for Nanoscience (BINAS), Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany
| | - Michael Rattay
- Baxter Oncology GmbH, Kantstrasse 2, 33790 Halle Westphalia, Germany
| | - Katja Toensing
- Experimental Biophysics and Applied Nanoscience, Physics Department, Bielefeld Institute for Nanoscience (BINAS), Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany
| | - Dario Anselmetti
- Experimental Biophysics and Applied Nanoscience, Physics Department, Bielefeld Institute for Nanoscience (BINAS), Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany
| |
Collapse
|
21
|
López-Morató M, Brook JD, Wojciechowska M. Small Molecules Which Improve Pathogenesis of Myotonic Dystrophy Type 1. Front Neurol 2018; 9:349. [PMID: 29867749 PMCID: PMC5968088 DOI: 10.3389/fneur.2018.00349] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 04/30/2018] [Indexed: 12/30/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is the most common muscular dystrophy in adults for which there is currently no treatment. The pathogenesis of this autosomal dominant disorder is associated with the expansion of CTG repeats in the 3'-UTR of the DMPK gene. DMPK transcripts with expanded CUG repeats (CUGexpDMPK) are retained in the nucleus forming multiple discrete foci, and their presence triggers a cascade of toxic events. Thus far, most research emphasis has been on interactions of CUGexpDMPK with the muscleblind-like (MBNL) family of splicing factors. These proteins are sequestered by the expanded CUG repeats of DMPK RNA leading to their functional depletion. As a consequence, abnormalities in many pathways of RNA metabolism, including alternative splicing, are detected in DM1. To date, in vitro and in vivo efforts to develop therapeutic strategies for DM1 have mostly been focused on targeting CUGexpDMPK via reducing their expression and/or preventing interactions with MBNL1. Antisense oligonucleotides targeted to the CUG repeats in the DMPK transcripts are of particular interest due to their potential capacity to discriminate between mutant and normal transcripts. However, a growing number of reports describe alternative strategies using small molecule chemicals acting independently of a direct interaction with CUGexpDMPK. In this review, we summarize current knowledge about these chemicals and we describe the beneficial effects they caused in different DM1 experimental models. We also present potential mechanisms of action of these compounds and pathways they affect which could be considered for future therapeutic interventions in DM1.
Collapse
Affiliation(s)
- Marta López-Morató
- Queen’s Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - John David Brook
- Queen’s Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Marzena Wojciechowska
- Queen’s Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- Polish Academy of Sciences, Department of Molecular Genetics, Institute of Bioorganic Chemistry, Poznan, Poland
| |
Collapse
|
22
|
Clark AG, Naufer MN, Westerlund F, Lincoln P, Rouzina I, Paramanathan T, Williams MC. Reshaping the Energy Landscape Transforms the Mechanism and Binding Kinetics of DNA Threading Intercalation. Biochemistry 2018; 57:614-619. [PMID: 29243480 DOI: 10.1021/acs.biochem.7b01036] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecules that bind DNA via threading intercalation show high binding affinity as well as slow dissociation kinetics, properties ideal for the development of anticancer drugs. To this end, it is critical to identify the specific molecular characteristics of threading intercalators that result in optimal DNA interactions. Using single-molecule techniques, we quantify the binding of a small metal-organic ruthenium threading intercalator (Δ,Δ-B) and compare its binding characteristics to a similar molecule with significantly larger threading moieties (Δ,Δ-P). The binding affinities of the two molecules are the same, while comparison of the binding kinetics reveals significantly faster kinetics for Δ,Δ-B. However, the kinetics is still much slower than that observed for conventional intercalators. Comparison of the two threading intercalators shows that the binding affinity is modulated independently by the intercalating section and the binding kinetics is modulated by the threading moiety. In order to thread DNA, Δ,Δ-P requires a "lock mechanism", in which a large length increase of the DNA duplex is required for both association and dissociation. In contrast, measurements of the force-dependent binding kinetics show that Δ,Δ-B requires a large DNA length increase for association but no length increase for dissociation from DNA. This contrasts strongly with conventional intercalators, for which almost no DNA length change is required for association but a large DNA length change must occur for dissociation. This result illustrates the fundamentally different mechanism of threading intercalation compared with conventional intercalation and will pave the way for the rational design of therapeutic drugs based on DNA threading intercalation.
Collapse
Affiliation(s)
- Andrew G Clark
- Department of Physics, Northeastern University , Boston, Massachusetts 02115, United States
| | - M Nabuan Naufer
- Department of Physics, Northeastern University , Boston, Massachusetts 02115, United States
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology , SE-412 96 Gothenburg, Sweden
| | - Per Lincoln
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology , SE-412 96 Gothenburg, Sweden
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, The Ohio State University , Columbus, Ohio 43210, United States
| | - Thayaparan Paramanathan
- Department of Physics, Bridgewater State University , Bridgewater, Massachusetts 02325, United States
| | - Mark C Williams
- Department of Physics, Northeastern University , Boston, Massachusetts 02115, United States
| |
Collapse
|
23
|
Varrica MG, Zagni C, Mineo PG, Floresta G, Monciino G, Pistarà V, Abbadessa A, Nicosia A, Castilho RM, Amata E, Rescifina A. DNA intercalators based on (1,10-phenanthrolin-2-yl)isoxazolidin-5-yl core with better growth inhibition and selectivity than cisplatin upon head and neck squamous cells carcinoma. Eur J Med Chem 2018; 143:583-590. [DOI: 10.1016/j.ejmech.2017.11.067] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 11/22/2017] [Accepted: 11/24/2017] [Indexed: 02/04/2023]
|
24
|
Das S, Chatterjee S, Pramanik S, Devi PS, Kumar GS. A new insight into the interaction of ZnO with calf thymus DNA through surface defects. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2018; 178:339-347. [DOI: 10.1016/j.jphotobiol.2017.10.039] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Revised: 10/17/2017] [Accepted: 10/30/2017] [Indexed: 01/14/2023]
|
25
|
Bhutia ZT, Prasannakumar G, Das A, Biswas M, Chatterjee A, Banerjee M. A Facile, Catalyst-Free Mechano-Synthesis of Quinoxalines and their In-Vitro Antibacterial Activity Study. ChemistrySelect 2017. [DOI: 10.1002/slct.201601672] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Zigmee T. Bhutia
- Department of Chemistry, BITS; Pilani-K. K. Birla; Goa Campus; Goa - 403726 India
| | | | - Avijit Das
- Department of Biological Sciences, BITS; Pilani-K. K. Birla; Goa Campus; Goa - 403 726 India
| | - Malabika Biswas
- Department of Biological Sciences, BITS; Pilani-K. K. Birla; Goa Campus; Goa - 403 726 India
| | - Amrita Chatterjee
- Department of Chemistry, BITS; Pilani-K. K. Birla; Goa Campus; Goa - 403726 India
| | - Mainak Banerjee
- Department of Chemistry, BITS; Pilani-K. K. Birla; Goa Campus; Goa - 403726 India
| |
Collapse
|
26
|
Bonsaii M, Gholivand K, Khosravi M, Abdi K. Negative hyperconjugation effect on the reactivity of phosphoramide mustard derivatives as a DNA alkylating agent: theoretical and experimental insights. NEW J CHEM 2017. [DOI: 10.1039/c7nj01402c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work we suggest new factors affecting the reactivity of compounds similar to cyclophosphamide; as their reactivity mainly relies on the frontier molecular orbitals, the factors causing changes in the frontier molecular orbitals, alter the reactivity of these compounds too.
Collapse
Affiliation(s)
- Mahyar Bonsaii
- Department of Chemistry
- Islamic Azad University
- North Tehran Branch
- Tehran
- Iran
| | | | - Morteza Khosravi
- Department of Chemistry
- Islamic Azad University
- North Tehran Branch
- Tehran
- Iran
| | - Khosrou Abdi
- Department of Medicinal Chemistry and Radiopharmacy
- Tehran University of Medical Sciences
- Tehran
- Iran
| |
Collapse
|
27
|
Kalel R, Mora AK, Patro BS, Palit DK, Nath S. Synergistic enhancement in the drug sequestration power and reduction in the cytotoxicity of surfactants. Phys Chem Chem Phys 2017; 19:25446-25455. [DOI: 10.1039/c7cp05042a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Surfactants in supramolecular assemblies show a significant increase in their drug sequestration power with a remarkably reduced cytotoxicity.
Collapse
Affiliation(s)
- Rahul Kalel
- Radiation & Photochemistry Division
- Bhabha Atomic Research Centre
- Mumbai-400085
- India
| | - Aruna K. Mora
- Radiation & Photochemistry Division
- Bhabha Atomic Research Centre
- Mumbai-400085
- India
- Homi Bhabha National Institute
| | - Birija S. Patro
- Homi Bhabha National Institute
- Training School Complex
- Anushaktinagar
- Mumbai 400094
- India
| | - Dipak K. Palit
- Radiation & Photochemistry Division
- Bhabha Atomic Research Centre
- Mumbai-400085
- India
- Homi Bhabha National Institute
| | - Sukhendu Nath
- Radiation & Photochemistry Division
- Bhabha Atomic Research Centre
- Mumbai-400085
- India
- Homi Bhabha National Institute
| |
Collapse
|
28
|
Carnerero JM, Jimenez‐Ruiz A, Castillo PM, Prado‐Gotor R. Covalent and Non‐Covalent DNA–Gold‐Nanoparticle Interactions: New Avenues of Research. Chemphyschem 2016; 18:17-33. [DOI: 10.1002/cphc.201601077] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Jose M. Carnerero
- Physical Chemistry. Faculty of Chemistry University of Seville C/Profesor Garcia Gonzalez, s/n 41012 Seville Spain
| | - Aila Jimenez‐Ruiz
- Physical Chemistry. Faculty of Chemistry University of Seville C/Profesor Garcia Gonzalez, s/n 41012 Seville Spain
| | - Paula M. Castillo
- Physical Chemistry. Faculty of Chemistry University of Seville C/Profesor Garcia Gonzalez, s/n 41012 Seville Spain
| | - Rafael Prado‐Gotor
- Physical Chemistry. Faculty of Chemistry University of Seville C/Profesor Garcia Gonzalez, s/n 41012 Seville Spain
| |
Collapse
|
29
|
Imidazolyl-Naphthalenediimide-Based Threading Intercalators of DNA. Chembiochem 2016; 17:2162-2171. [DOI: 10.1002/cbic.201600478] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Indexed: 12/22/2022]
|
30
|
Das A, Adhikari C, Chakraborty A. Lipoplex-Mediated Deintercalation of Doxorubicin from Calf Thymus DNA-Doxorubicin Complex. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:8889-8899. [PMID: 27465781 DOI: 10.1021/acs.langmuir.6b01860] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In this paper, we report the lipoplex-mediated deintercalation of anticancer drug doxorubicin (DOX) from the DOX-DNA complex under controlled experimental conditions. We used three zwitterionic liposomes, namely, 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), and 2-oleoyl-1-palmitoyl-sn-glycero-3-phosphocholine (POPC), which are widely different in their phase transition temperatures to form a lipoplex with calf thymus DNA in the presence of Ca(2+) ions. The study revealed that DPPC being in sol-gel phase was more effective in releasing the drug from the DOX-DNA complex compared with liposomes that remain in liquid crystalline phase (DMPC and POPC). The higher extent of drug release in the case of DPPC liposomes was attributed to the stronger lipoplex formation with DNA as compared with that of other liposomes. Owing to the relatively smaller head group area, the DPPC liposomes in their sol-gel phase can absorb a larger number of Ca(2+) ions and hence offer a strong electrostatic interaction with DNA. This interaction was confirmed by time-resolved anisotropy and circular dichroism spectroscopy. Apart from the electrostatic interaction, the possible hydrophobic interaction between the liposomes and DNA was also taken into account for the observed deintercalation. The successful uptake of drug molecules by liposomes from the drug-DNA complex in the post-release period was also confirmed using confocal laser scanning microscopy (CLSM).
Collapse
Affiliation(s)
- Anupam Das
- Discipline of Chemistry, Indian Institute of Technology Indore , Indore 453552, Madhya Pradesh, India
| | - Chandan Adhikari
- Discipline of Chemistry, Indian Institute of Technology Indore , Indore 453552, Madhya Pradesh, India
| | - Anjan Chakraborty
- Discipline of Chemistry, Indian Institute of Technology Indore , Indore 453552, Madhya Pradesh, India
| |
Collapse
|
31
|
Chaires JB. A small molecule--DNA binding landscape. Biopolymers 2016; 103:473-9. [PMID: 25913470 DOI: 10.1002/bip.22660] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 04/16/2015] [Indexed: 02/03/2023]
Abstract
This brief account traces the development of a "competition dialysis" method used to characterize the structural and sequence selectivity of DNA binding compounds. The method was inspired by a simple "differential dialysis" method pioneered by Don Crothers to explore base-selective intercalator binding. Results from compiled competition dialysis studies provide a small-molecule DNA binding landscape that shows a rich diversity of interactions and molecular recognition.
Collapse
Affiliation(s)
- Jonathan B Chaires
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202
| |
Collapse
|
32
|
Mora AK, Singh PK, Nath S. Controlled Sequestration of DNA Intercalated Drug by Polymer–Surfactant Supramolecular Assemblies. J Phys Chem B 2016; 120:4143-51. [DOI: 10.1021/acs.jpcb.5b12689] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Aruna K. Mora
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India
| | - Prabhat K. Singh
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India
| | - Sukhendu Nath
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India
| |
Collapse
|
33
|
Almaqwashi AA, Paramanathan T, Rouzina I, Williams MC. Mechanisms of small molecule-DNA interactions probed by single-molecule force spectroscopy. Nucleic Acids Res 2016; 44:3971-88. [PMID: 27085806 PMCID: PMC4872107 DOI: 10.1093/nar/gkw237] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 03/24/2016] [Indexed: 12/31/2022] Open
Abstract
There is a wide range of applications for non-covalent DNA binding ligands, and optimization of such interactions requires detailed understanding of the binding mechanisms. One important class of these ligands is that of intercalators, which bind DNA by inserting aromatic moieties between adjacent DNA base pairs. Characterizing the dynamic and equilibrium aspects of DNA-intercalator complex assembly may allow optimization of DNA binding for specific functions. Single-molecule force spectroscopy studies have recently revealed new details about the molecular mechanisms governing DNA intercalation. These studies can provide the binding kinetics and affinity as well as determining the magnitude of the double helix structural deformations during the dynamic assembly of DNA–ligand complexes. These results may in turn guide the rational design of intercalators synthesized for DNA-targeted drugs, optical probes, or integrated biological self-assembly processes. Herein, we survey the progress in experimental methods as well as the corresponding analysis framework for understanding single molecule DNA binding mechanisms. We discuss briefly minor and major groove binding ligands, and then focus on intercalators, which have been probed extensively with these methods. Conventional mono-intercalators and bis-intercalators are discussed, followed by unconventional DNA intercalation. We then consider the prospects for using these methods in optimizing conventional and unconventional DNA-intercalating small molecules.
Collapse
Affiliation(s)
- Ali A Almaqwashi
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | | | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
| | - Mark C Williams
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| |
Collapse
|
34
|
Interaction of an anti-cancer photosensitizer with a genomic DNA: From base pair specificity and thermodynamic landscape to tuning the rate of detergent-sequestered dissociation. J Colloid Interface Sci 2016; 470:211-220. [PMID: 26945117 DOI: 10.1016/j.jcis.2016.02.059] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 02/26/2016] [Accepted: 02/26/2016] [Indexed: 11/23/2022]
Abstract
A detailed characterization of the binding interaction of a potent cancer cell photosensitizer, norharmane (NHM) with a genomic DNA (herring sperm; hsDNA) is undertaken with particular emphasis on deciphering the strength, mode, dynamics, energetics and kinetics of binding. A major focus of the study underlies a successful exploration of the concept of detergent-sequestered dissociation of drug from the drug-DNA complex. Biophysical techniques such as absorption, steady-state and time-resolved fluorescence spectroscopy, circular dichroism, DNA helix melting, stopped-flow fluorescence kinetics and calorimetry have been used. A primarily intercalative mode of binding of NHM with DNA is shown. However, the overall interaction is governed by more than one type of binding forces. We demonstrate that the essential prerequisite of a slower dissociation rate of drug from DNA helix is achieved by tenable choice surfactants. Our results also highlight an effective tunability of the rate of dissociation of the DNA-intercalated drug via detergent-sequestration. A detailed isothermal titration calorimetric study unveils the key role of hydrophobic force underlying NHM-hsDNA association. This is further substantiated by the enthalpy-entropy compensation behavior. The major entropic contribution in detergent-induced dissociation of NHM from NHM-hsDNA complex is also demonstrated. Our results present not only a comprehensive structural and thermodynamic profile, base pair specificity, association kinetics for binding of NHM with DNA but also explore the thermodynamic and kinetic aspects of dissociation of bound drug. Characterization and tuning of the essential prerequisites for a drug to be efficient in anti-cancer functionality bear direct and widespread significance in contemporary global research.
Collapse
|
35
|
Das A, Adhikari C, Nayak D, Chakraborty A. First Evidence of the Liposome-Mediated Deintercalation of Anticancer Drug Doxorubicin from the Drug-DNA Complex: A Spectroscopic Approach. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:159-70. [PMID: 26605667 DOI: 10.1021/acs.langmuir.5b03702] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Biocompatible liposomes were used for the first time to study the deintercalation process of a prominent anticancer drug, doxorubicin (DOX), from doxorubicin-intercalated DNA (DOX-DNA complex) under controlled experimental conditions. The study revealed that anionic liposomes (DMPG liposomes) appeared to be the most effective to bring in the highest percentage of drug release while cationic liposomes (DOTAP liposomes) scored the lowest percentage of release. The drug release was primarily attributed to the electrostatic interaction between liposomes and drug molecules. Apart from this interaction, changes in the hydrophobicity of the medium upon addition of liposomes to the DNA-drug solution accompanied by lipoplex formation between DNA and liposomes were also attributed to the observed deintercalation. The CD and the time-resolved rotational relaxation studies confirmed that lipoplex formation took place between liposomes and DNA owing to electrostatic interaction. The confocal study revealed that in the postrelease period, DOX binds with liposomes. The reason behind the binding is electrostatic interaction as well as the unique bilayer structure of liposomes which helps it to act as a "hydrophobic sink" for DOX. The study overall highlighted a novel strategy for deintercalation of drug using biocompatible liposomes, as the release of the drug can be controlled over a period of time by varying the concentration and composition of the liposomes.
Collapse
Affiliation(s)
- Anupam Das
- Discipline of Chemistry, Indian Institute of Technology Indore , Indore, Madhya Pradesh, India
| | - Chandan Adhikari
- Discipline of Chemistry, Indian Institute of Technology Indore , Indore, Madhya Pradesh, India
| | - Debasis Nayak
- Bioseciences and Biomedical Engineering, Indian Institute of Technology Indore , Indore, Madhya Pradesh, India
| | - Anjan Chakraborty
- Discipline of Chemistry, Indian Institute of Technology Indore , Indore, Madhya Pradesh, India
| |
Collapse
|
36
|
Bernal WFP, Silva EF, Rocha MS. Unraveling the physical chemistry and the mixed binding modes of complex DNA ligands by single molecule stretching experiments. RSC Adv 2016. [DOI: 10.1039/c6ra22980h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
In this work we present a complete methodology to unravel the physical chemistry and the mixed binding modes of complex DNA ligands.
Collapse
Affiliation(s)
- W. F. P. Bernal
- Laboratório de Física Biológica
- Departamento de Física
- Universidade Federal de Viçosa
- Viçosa
- Brazil
| | - E. F. Silva
- Laboratório de Física Biológica
- Departamento de Física
- Universidade Federal de Viçosa
- Viçosa
- Brazil
| | - M. S. Rocha
- Laboratório de Física Biológica
- Departamento de Física
- Universidade Federal de Viçosa
- Viçosa
- Brazil
| |
Collapse
|
37
|
Bonsaii M, Gholivand K, Abdi K, Valmoozi AAE, Khosravi M. A combined experimental and computational study on the interaction of nitrogen mustards with DNA. MEDCHEMCOMM 2016. [DOI: 10.1039/c6md00264a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In the present work, we suggest that the role of water in the reaction of nitrogen mustards with DNA is more than what was thought before. Nitrogen mustards become activated when they are hydrated by water.
Collapse
Affiliation(s)
- Mahyar Bonsaii
- Department of Chemistry
- Islamic Azad University
- Tehran
- Iran
| | | | - Khosrou Abdi
- Department of Medicinal Chemistry and Radiopharmacy
- Tehran University of Medical Sciences
- Tehran
- Iran
| | | | | |
Collapse
|
38
|
Actinomycin D Specifically Reduces Expanded CUG Repeat RNA in Myotonic Dystrophy Models. Cell Rep 2015; 13:2386-2394. [PMID: 26686629 DOI: 10.1016/j.celrep.2015.11.028] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 09/10/2015] [Accepted: 11/06/2015] [Indexed: 01/16/2023] Open
Abstract
Myotonic dystrophy type 1 (DM1) is an inherited disease characterized by the inability to relax contracted muscles. Affected individuals carry large CTG expansions that are toxic when transcribed. One possible treatment approach is to reduce or eliminate transcription of CTG repeats. Actinomycin D (ActD) is a potent transcription inhibitor and FDA-approved chemotherapeutic that binds GC-rich DNA with high affinity. Here, we report that ActD decreased CUG transcript levels in a dose-dependent manner in DM1 cell and mouse models at significantly lower concentrations (nanomolar) compared to its use as a general transcription inhibitor or chemotherapeutic. ActD also significantly reversed DM1-associated splicing defects in a DM1 mouse model, and did so within the currently approved human treatment range. RNA-seq analyses showed that low concentrations of ActD did not globally inhibit transcription in a DM1 mouse model. These results indicate that transcription inhibition of CTG expansions is a promising treatment approach for DM1.
Collapse
|
39
|
Furusawa H, Nakayama H, Funasaki M, Okahata Y. Kinetic characterization of small DNA-binding molecules interacting with a DNA strand on a quartz crystal microbalance. Anal Biochem 2015; 492:34-42. [PMID: 26408811 DOI: 10.1016/j.ab.2015.09.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 08/25/2015] [Accepted: 09/15/2015] [Indexed: 11/18/2022]
Abstract
Quantitative studies of the binding of various DNA-binding antibiotics with dsDNA are useful for drug design, not only for effective antibiotics, but also for antitumor drugs. We studied the binding kinetics, association and dissociation rate constants, and association constants (kon, koff, and Ka, respectively) of intercalators and groove binders, including various antibiotics, to double-stranded DNA (dA30·dT30 and dG30·dC30) immobilized on a highly sensitive 27 MHz quartz-crystal microbalance (QCM) in aqueous solution. Although a simple ethidium bromide intercalator bound to both dA30·dT30 and dG30·dC30, antibiotics that are side-binding intercalators, such as daunomycin, aclacinomycin A, and actinomycin D, with sugar or peptide moieties on the intercalator parts selectively bound to dG30·dC30 with high Ka and small koff values. Nogalamycin, a dumbbell-shaped penetrating intercalator, showed low kon and koff values owing to slow duplex unwinding during the penetration process. Groove binders (Hoechst 33258, distamycin A, and mithramycin) had high Ka values owing to the high kon values. Kinetic parameters depended largely on molecular shapes and DNA-binding molecule binding modes.
Collapse
Affiliation(s)
- Hiroyuki Furusawa
- Innovative Flex Course for Frontier Organic Material Systems (iFront), Graduate School of Science and Engineering, Yamagata University, 4-3-16 Jonan, Yonezawa, Yamagata, Japan; Department of Biomolecular Engineering, Tokyo Institute of Technology, 4259, Nagatsuda, Midori-ku, Yokohama, Japan.
| | - Hajime Nakayama
- Department of Biomolecular Engineering, Tokyo Institute of Technology, 4259, Nagatsuda, Midori-ku, Yokohama, Japan
| | - Mariko Funasaki
- Department of Biomolecular Engineering, Tokyo Institute of Technology, 4259, Nagatsuda, Midori-ku, Yokohama, Japan
| | - Yoshio Okahata
- Department of Biomolecular Engineering, Tokyo Institute of Technology, 4259, Nagatsuda, Midori-ku, Yokohama, Japan
| |
Collapse
|
40
|
Bahira M, McCauley MJ, Almaqwashi AA, Lincoln P, Westerlund F, Rouzina I, Williams MC. A ruthenium dimer complex with a flexible linker slowly threads between DNA bases in two distinct steps. Nucleic Acids Res 2015; 43:8856-67. [PMID: 26365236 PMCID: PMC4605314 DOI: 10.1093/nar/gkv864] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 08/15/2015] [Indexed: 01/06/2023] Open
Abstract
Several multi-component DNA intercalating small molecules have been designed around ruthenium-based intercalating monomers to optimize DNA binding properties for therapeutic use. Here we probe the DNA binding ligand [μ-C4(cpdppz)2(phen)4Ru2]4+, which consists of two Ru(phen)2dppz2+ moieties joined by a flexible linker. To quantify ligand binding, double-stranded DNA is stretched with optical tweezers and exposed to ligand under constant applied force. In contrast to other bis-intercalators, we find that ligand association is described by a two-step process, which consists of fast bimolecular intercalation of the first dppz moiety followed by ∼10-fold slower intercalation of the second dppz moiety. The second step is rate-limited by the requirement for a DNA-ligand conformational change that allows the flexible linker to pass through the DNA duplex. Based on our measured force-dependent binding rates and ligand-induced DNA elongation measurements, we are able to map out the energy landscape and structural dynamics for both ligand binding steps. In addition, we find that at zero force the overall binding process involves fast association (∼10 s), slow dissociation (∼300 s), and very high affinity (Kd ∼10 nM). The methodology developed in this work will be useful for studying the mechanism of DNA binding by other multi-step intercalating ligands and proteins.
Collapse
Affiliation(s)
- Meriem Bahira
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Micah J McCauley
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Ali A Almaqwashi
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Per Lincoln
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Ioulia Rouzina
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Mark C Williams
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| |
Collapse
|
41
|
Ganguly A, Ghosh S, Guchhait N. Spectroscopic and viscometric elucidation of the interaction between a potential chloride channel blocker and calf-thymus DNA: the effect of medium ionic strength on the binding mode. Phys Chem Chem Phys 2015; 17:483-92. [PMID: 25407825 DOI: 10.1039/c4cp04175e] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The present study demonstrates a detailed characterization of the binding interaction of a potential chloride channel blocker 9-methyl anthroate (9-MA) with calf-thymus DNA. The modulated photophysical properties of the emissive molecule within the microheterogeneous bio-assembly have been spectroscopically exploited to monitor the drug-DNA binding interaction. Experimental results based on fluorescence and absorption spectroscopy aided with DNA-melting, viscometric and circular dichroism studies unambiguously establish the binding mode between the drug and DNA to be principally intercalative. Concomitantly, a discernible dependence of the mode of binding between the concerned moieties on the ionic strength of the medium is noteworthy. A dip-and-rise characteristic of the rotational relaxation profile of the drug within the DNA environment has been argued to be originating from a substantial difference in the lifetime as well as amplitude of the free and DNA bound drug molecule. In view of the prospective biological applications of the drug, the issue of facile dissociation of the intercalated drug from the DNA helix via a simple detergent-sequestration technique has also been unveiled. The utility of the present work resides in exploring the potential applicability of the fluorescence properties of 9-MA for studying its interactions with other relevant biological or biomimicking targets.
Collapse
Affiliation(s)
- Aniruddha Ganguly
- Department of Chemistry, University of Calcutta, 92 A. P. C. Road, Calcutta-700009, India.
| | | | | |
Collapse
|
42
|
Weeks KM. Review toward all RNA structures, concisely. Biopolymers 2015; 103:438-48. [PMID: 25546503 PMCID: PMC4446244 DOI: 10.1002/bip.22601] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 12/10/2014] [Accepted: 12/11/2014] [Indexed: 01/05/2023]
Abstract
Profound insights regarding nucleic acid structure and function can be gleaned from very simple, direct, and chemistry-based strategies. Our approach strives to incorporate the elegant physical insights that Don Crothers instilled in those who trained in his laboratory. Don emphasized the advantages of focusing on direct and concise experiments even when the final objective was to understand something complex-potentially including the large-scale architectures of the genomes of RNA viruses and the transcriptomes of cells. Here, the author reviews the intellectual path, and a few detours, that led to the development of the SHAPE-MaP and RING-MaP technologies for interrogating RNA structure and function at large scales. The author also argues that greater attention to creating direct, less inferential experiments will convert "omics" investigations into lasting and definitive contributions to our understanding of biological function.
Collapse
Affiliation(s)
- Kevin M. Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290,
| |
Collapse
|
43
|
Hartlieb KJ, Witus LS, Ferris DP, Basuray AN, Algaradah MM, Sarjeant AA, Stern CL, Nassar MS, Botros YY, Stoddart JF. Anticancer activity expressed by a library of 2,9-diazaperopyrenium dications. ACS NANO 2015; 9:1461-1470. [PMID: 25555133 PMCID: PMC4344210 DOI: 10.1021/nn505895j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 01/02/2015] [Indexed: 06/04/2023]
Abstract
Polyaromatic compounds are well-known to intercalate DNA. Numerous anticancer chemotherapeutics have been developed upon the basis of this recognition motif. The compounds have been designed such that they interfere with the role of the topoisomerases, which control the topology of DNA during the cell-division cycle. Although many promising chemotherapeutics have been developed upon the basis of polyaromatic DNA intercalating systems, these candidates did not proceed past clinical trials on account of their dose-limiting toxicity. Herein, we discuss an alternative, water-soluble class of polyaromatic compounds, the 2,9-diazaperopyrenium dications, and report in vitro cell studies for a library of these dications. These investigations reveal that a number of 2,9-diazaperopyrenium dications show similar activities as doxorubicin toward a variety of cancer cell lines. Additionally, we report the solid-state structures of these dications, and we relate their tendency to aggregate in solution to their toxicity profiles. The addition of bulky substituents to these polyaromatic dications decreases their tendency to aggregate in solution. The derivative substituted with 2,6-diisopropylphenyl groups proved to be the most cytotoxic against the majority of the cell lines tested. In the solid state, the 2,6-diisopropylphenyl-functionalized derivative does not undergo π···π stacking, while in aqueous solution, dynamic light scattering reveals that this derivative forms very small (50-100 nm) aggregates, in contrast with the larger ones formed by dications with less bulky substituents. Alteration of the aromaticitiy in the terminal heterocycles of selected dications reveals a drastic change in the toxicity of these polyaromatic species toward specific cell lines.
Collapse
Affiliation(s)
- Karel J. Hartlieb
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Leah S. Witus
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Daniel P. Ferris
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Ashish N. Basuray
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Mohammed M. Algaradah
- Joint Center of Excellence in Integrated Nano-Systems (JCIN), King Abdul-Aziz City for Science and Technology (KACST), P.O. Box 6068, Riyadh 11442, Kingdom of Saudia Arabia
| | - Amy A. Sarjeant
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Charlotte L. Stern
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Majed S. Nassar
- Joint Center of Excellence in Integrated Nano-Systems (JCIN), King Abdul-Aziz City for Science and Technology (KACST), P.O. Box 6068, Riyadh 11442, Kingdom of Saudia Arabia
| | - Youssry Y. Botros
- University Research Office, Intel Corporation, Building RNB-6-61, 2200 Mission College Boulevard, Santa Clara, California 95054, United States
| | - J. Fraser Stoddart
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| |
Collapse
|
44
|
Rocha MS. Extracting physical chemistry from mechanics: a new approach to investigate DNA interactions with drugs and proteins in single molecule experiments. Integr Biol (Camb) 2015; 7:967-86. [DOI: 10.1039/c5ib00127g] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
In this review we focus on the idea of establishing connections between the mechanical properties of DNA–ligand complexes and the physical chemistry of DNA–ligand interactions.
Collapse
Affiliation(s)
- M. S. Rocha
- Laboratório de Física Biológica
- Departamento de Física
- Universidade Federal de Viçosa
- Viçosa
- Brazil
| |
Collapse
|
45
|
Kundu P, Ghosh S, Chattopadhyay N. Exploration of the binding interaction of a potential nervous system stimulant with calf-thymus DNA and dissociation of the drug–DNA complex by detergent sequestration. Phys Chem Chem Phys 2015; 17:17699-709. [DOI: 10.1039/c5cp02101d] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The binding interaction of a potential nervous system stimulant with calf-thymus DNA has been divulged and dissociation of the drug–DNA complex has been achieved by the detergent sequestration method.
Collapse
Affiliation(s)
- Pronab Kundu
- Department of Chemistry
- Jadavpur University
- Kolkata – 700 032
- India
| | - Saptarshi Ghosh
- Department of Chemistry
- Jadavpur University
- Kolkata – 700 032
- India
| | | |
Collapse
|
46
|
Waring MJ. Don Crothers and biomolecular science in the DDR. Biopolymers 2014; 103:418-23. [PMID: 25196281 DOI: 10.1002/bip.22559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 08/27/2014] [Indexed: 11/07/2022]
|
47
|
Pradhan AB, Haque L, Roy S, Das S. Binding of phenazinium dye safranin T to polyriboadenylic acid: spectroscopic and thermodynamic study. PLoS One 2014; 9:e87992. [PMID: 24498422 PMCID: PMC3912202 DOI: 10.1371/journal.pone.0087992] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 01/02/2014] [Indexed: 11/18/2022] Open
Abstract
Here, we report results from experiments designed to explore the association of the phenazinium dye safranin T (ST, 3,7-diamino-2,8-dimethyl-5-phenylphenazinium chloride) with single and double stranded form of polyriboadenylic acid (hereafter poly-A) using several spectroscopic techniques. We demonstrate that the dye binds to single stranded polyriboadenylic acid (hereafter ss poly-A) with high affinity while it does not interact at all with the double stranded (ds) form of the polynucleotide. Fluorescence and absorption spectral studies reveal the molecular aspects of binding of ST to single stranded form of the polynucleotide. This observation is also supported by the circular dichroism study. Thermodynamic data obtained from temperature dependence of binding constant reveals that association is driven by negative enthalpy change and opposed by negative entropy change. Ferrocyanide quenching studies have shown intercalative binding of ST to ss poly-A. Experiments on viscosity measurements confirm the binding mode of the dye to be intercalative. The effect of [Na⁺] ion concentration on the binding process suggests the role of electrostatic forces in the complexation. Present studies reveal the utility of the dye in probing nucleic acid structure.
Collapse
Affiliation(s)
| | - Lucy Haque
- Department of Chemistry, Jadavpur University, Jadavpur, Kolkata, India
| | - Snigdha Roy
- Department of Chemistry, Jadavpur University, Jadavpur, Kolkata, India
| | - Suman Das
- Department of Chemistry, Jadavpur University, Jadavpur, Kolkata, India
| |
Collapse
|
48
|
Patra A, Hazra S, Suresh Kumar G, Mitra RK. Entropy Contribution toward Micelle-Driven Deintercalation of Drug–DNA Complex. J Phys Chem B 2014; 118:901-8. [DOI: 10.1021/jp4091816] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Animesh Patra
- Unit for Nano Science & Technology Department of Chemical Biological and Macromolecular Sciences S.N. Bose National Centre for Basic Sciences Block JD, Sector III, Salt Lake, Kolkata 700098, INDIA
| | - Soumitra Hazra
- Biophysical
Chemistry Laboratory Chemistry Division CSIR- Indian Institute of Chemical Biology 4, Raja S.C. Mullick Road, Kolkata 700032, INDIA
| | - Gopinatha Suresh Kumar
- Biophysical
Chemistry Laboratory Chemistry Division CSIR- Indian Institute of Chemical Biology 4, Raja S.C. Mullick Road, Kolkata 700032, INDIA
| | - Rajib Kumar Mitra
- Unit for Nano Science & Technology Department of Chemical Biological and Macromolecular Sciences S.N. Bose National Centre for Basic Sciences Block JD, Sector III, Salt Lake, Kolkata 700098, INDIA
| |
Collapse
|
49
|
Rescifina A, Zagni C, Varrica MG, Pistarà V, Corsaro A. Recent advances in small organic molecules as DNA intercalating agents: synthesis, activity, and modeling. Eur J Med Chem 2014; 74:95-115. [PMID: 24448420 DOI: 10.1016/j.ejmech.2013.11.029] [Citation(s) in RCA: 178] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 11/26/2013] [Accepted: 11/28/2013] [Indexed: 11/28/2022]
Abstract
The interaction of small molecules with DNA plays an essential role in many biological processes. As DNA is often the target for majority of anticancer and antibiotic drugs, study about the interaction of drug and DNA has a key role in pharmacology. Moreover, understanding the interactions of small molecules with DNA is of prime significance in the rational design of more powerful and selective anticancer agents. Two of the most important and promising targets in cancer chemotherapy include DNA alkylating agents and DNA intercalators. For these last the DNA recognition is a critical step in their anti-tumor action and the intercalation is not only one kind of the interactions in DNA recognition but also a pivotal step of several clinically used anti-tumor drugs such as anthracyclines, acridines and anthraquinones. To push clinical cancer therapy, the discovery of new DNA intercalators has been considered a practical approach and a number of intercalators have been recently reported. The intercalative binding properties of such molecules can also be harnessed as diagnostic probes for DNA structure in addition to DNA-directed therapeutics. Moreover, the problem of intercalation site formation in the undistorted B-DNA of different length and sequence is matter of tremendous importance in molecular modeling studies and, nowadays, three models of DNA intercalation targets have been proposed that account for the binding features of intercalators. Finally, despite DNA being an important target for several drugs, most of the docking programs are validated only for proteins and their ligands. Therefore, a default protocol to identify DNA binding modes which uses a modified canonical DNA as receptor is needed.
Collapse
Affiliation(s)
- Antonio Rescifina
- Dipartimento di Scienze del Farmaco, Università di Catania, Viale Andrea Doria 6, 95125 Catania, Italy.
| | - Chiara Zagni
- Dipartimento di Scienze del Farmaco, Università di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Maria Giulia Varrica
- Dipartimento di Scienze del Farmaco, Università di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Venerando Pistarà
- Dipartimento di Scienze del Farmaco, Università di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Antonino Corsaro
- Dipartimento di Scienze del Farmaco, Università di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| |
Collapse
|
50
|
dsDNA, ssDNA, G-quadruplex DNA, and nucleosomal DNA electrochemical screening using canthin-6-one alkaloid-modified electrodes. Electrochim Acta 2014. [DOI: 10.1016/j.electacta.2013.11.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|