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Yadav M, Vaishkiar I, Sharma A, Shukla A, Mohan A, Girdhar M, Kumar A, Malik T, Mohan A. Oestrogen receptor positive breast cancer and its embedded mechanism: breast cancer resistance to conventional drugs and related therapies, a review. Open Biol 2024; 14:230272. [PMID: 38889771 DOI: 10.1098/rsob.230272] [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: 08/10/2023] [Accepted: 03/14/2024] [Indexed: 06/20/2024] Open
Abstract
Traditional medication and alternative therapies have long been used to treat breast cancer. One of the main problems with current treatments is that there is an increase in drug resistance in the cancer cells owing to genetic differences such as mutational changes, epigenetic changes and miRNA (microRNA) alterations such as miR-1246, miR-298, miR-27b and miR-33a, along with epigenetic modifications, such as Histone3 acetylation and CCCTC-Binding Factor (CTCF) hypermethylation for drug resistance in breast cancer cell lines. Certain forms of conventional drug resistance have been linked to genetic changes in genes such as ABCB1, AKT, S100A8/A9, TAGLN2 and NPM. This review aims to explore the current approaches to counter breast cancer, the action mechanism, along with novel therapeutic methods endowing potential drug resistance. The investigation of novel therapeutic approaches sheds light on the phenomenon of drug resistance including genetic variations that impact distinct forms of oestrogen receptor (ER) cancer, genetic changes, epigenetics-reported resistance and their identification in patients. Long-term effective therapy for breast cancer includes selective oestrogen receptor modulators, selective oestrogen receptor degraders and genetic variations, such as mutations in nuclear genes, epigenetic modifications and miRNA alterations in target proteins. Novel research addressing combinational therapies including maytansine, photodynamic therapy, guajadiol, talazoparib, COX2 inhibitors and miRNA 1246 inhibitors have been developed to improve patient survival rates.
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Affiliation(s)
- Manu Yadav
- Division of Genetics, ICAR- Indian Agricultural Research Institute , Pusa, New Delhi, India
| | - Ishita Vaishkiar
- Amity Institute of Biotechnology (AIB) University, Amity University Noida , Noida, India
| | - Ananya Sharma
- Department: Botany and Microbiology, Hemwati Nandan Bahuguna Garhwal University , Srinagar, India
| | - Akanksha Shukla
- School of Bioengineering and Biosciences, Lovely Professional University , Phagwara, Punjab, India
| | - Aradhana Mohan
- Department of Biomedical Engineering, University of Michigan , Ann Arbor, MI, USA
| | - Madhuri Girdhar
- Division of Research and Development, Lovely Professional University , Phagwara, Punjab, India
| | - Anil Kumar
- Gene Regulation Laboratory, National Institute of Immunology , New Delhi, India
| | - Tabarak Malik
- Department of Biomedical Sciences, Institute of Health, Jimma University , Jimma, Oromia 378, Ethiopia
| | - Anand Mohan
- School of Bioengineering and Biosciences, Lovely Professional University , Phagwara, Punjab, India
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Rahman MO, Ahmed SS. Anti-angiogenic potential of bioactive phytochemicals from Helicteres isora targeting VEGFR-2 to fight cancer through molecular docking and molecular dynamics simulation. J Biomol Struct Dyn 2023; 41:7447-7462. [PMID: 36099201 DOI: 10.1080/07391102.2022.2122568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 09/02/2022] [Indexed: 10/14/2022]
Abstract
Cancer is one of the leading causes of death due to its very high rate of morbidity and mortality, and there is a constant demand of effective drugs for cancer therapy. Vascular endothelial growth factor receptor-2 (VEGFR-2) plays a significant role as central modulator of angiogenesis and is targeted frequently for developing anti-angiogenic agents to fight cancer. Helicteres isora L. (Malvaceae) is reported to possess diverse medicinal properties including anti-cancer potentials. In the current investigation, 38 bioactive phytochemicals of H. isora were screened virtually to evaluate their anti-angiogenic potentials targeting VEGFR-2. The study unveiled three potential candidates such as, Diosgenin (-9.8 Kcal//mol), Trifolin (-8.4 Kcal/mol) and Yohimbine (-8.1 Kcal/mol) that showed favorable pharmacokinetic, pharmacodynamic and toxicity properties with no significant side effects. Molecular dynamics simulation employing 100 ns revealed noteworthy structural stability and compactness for all the top three candidates. The MM/GBSA binding free energy estimation corroborated the docking interactions where Yohimbine (-30.47 Kcal/mol) scored better than Diosgenin (-27.54 Kcal/mol) and Trifolin (-29.58 Kcal/mol). Target class prediction revealed enzymes in most of the cases and some FDA approved drugs were found as structurally similar analogs for Trifolin and Yohimbine. These findings could lead to the development of novel and effective anti-angiogenic agents.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- M Oliur Rahman
- Department of Botany, Faculty of Biological Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Sheikh Sunzid Ahmed
- Department of Botany, Faculty of Biological Sciences, University of Dhaka, Dhaka, Bangladesh
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3
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Zhang H, Xiao X, Wei W, Huang C, Wang M, Wang L, He Y, Sun J, Jiang Y, Jiang G, Zhang X. CircLIFR synergizes with MSH2 to attenuate chemoresistance via MutSα/ATM-p73 axis in bladder cancer. Mol Cancer 2021; 20:70. [PMID: 33874956 PMCID: PMC8054397 DOI: 10.1186/s12943-021-01360-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 04/06/2021] [Indexed: 12/12/2022] Open
Abstract
Background Cisplatin (CDDP) has become a standard-of-care treatment for muscle-invasive bladder cancer (MIBC), while chemoresistance remains a major challenge. Accumulating evidence indicates that circular RNAs (circRNAs) are discrete functional entities. However, the regulatory functions as well as complexities of circRNAs in modulating CDDP-based chemotherapy in bladder cancer are yet to be well revealed. Methods Through analyzing the expression profile of circRNAs in bladder cancer tissues, RNA FISH, circRNA pull-down assay, mass spectrometry analysis and RIP, circLIFR was identified and its interaction with MSH2 was confirmed. The effects of circLIFR and MSH2 on CDDP-based chemotherapy were explored by flow cytometry and rescue experiments. Co-IP and Western blot were used to investigate the molecular mechanisms underlying the functions of circLIFR and MSH2. Biological implications of circLIFR and MSH2 in bladder cancer were implemented in tumor xenograft models and PDX models. Results CircLIFR was downregulated in bladder cancer and expression was positively correlated with favorable prognosis. Moreover, circLIFR synergizing with MSH2, which was a mediator of CDDP sensitivity in bladder cancer cells, positively modulated sensitivity to CDDP in vitro and in vivo. Mechanistically, circLIFR augmented the interaction between MutSα and ATM, ultimately contributing to stabilize p73, which triggered to apoptosis. Importantly, MIBC with high expression of circLIFR and MSH2 was more sensitive to CDDP-based chemotherapy in tumor xenograft models and PDX models. Conclusions CircLIFR could interact with MSH2 to positively modulate CDDP-sensitivity through MutSα/ATM-p73 axis in bladder cancer. CircLIFR and MSH2 might be act as promising therapeutic targets for CDDP-resistant bladder cancer. Supplementary Information The online version contains supplementary material available at 10.1186/s12943-021-01360-4.
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Affiliation(s)
- Hui Zhang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Xingyuan Xiao
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Wenjie Wei
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Chao Huang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Miao Wang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Liang Wang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Yuanqiao He
- Department of Laboratory Animal Science, Nanchang University, Nanchang, 330006, China
| | - Jiayin Sun
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Yangkai Jiang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Guosong Jiang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Xiaoping Zhang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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Ramu AK, Ali D, Alarifi S, Syed Abuthakir MH, Ahmed Abdul BA. Reserpine inhibits DNA repair, cell proliferation, invasion and induces apoptosis in oral carcinogenesis via modulation of TGF-β signaling. Life Sci 2020; 264:118730. [PMID: 33160994 DOI: 10.1016/j.lfs.2020.118730] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/04/2020] [Accepted: 11/04/2020] [Indexed: 01/06/2023]
Abstract
Reserpine is a natural indole alkaloid isolated from Rauwolfia serpentina and has potent antioxidant, antimicrobial, and anti-mutagenic properties. Accordingly, this study aimed to investigate the effect of reserpine on DNA repair, cell proliferation, invasion and apoptosis in 7,12-dimethylbenz[a]anthracene(DMBA)-induced hamster buccal pouch (HBP) carcinogenesis. Transforming growth factor-β (TGF-β) was found to induce Smad2, 3 and 4 phosphorylation triggering Smad3/Snail mediated DNA repair proteins and Smad2/4 nuclear translocation. In contrast, reserpine inhibits TGF-β dependent Smad2/3/4 phosphorylation, thereby blockage Smad3/Snail activation and Smad2/4 nuclear translocation. Interruption of these oncogenic signaling pathways leads to downregulating ERCC1, XPF, Ku70, DNA-PKcs, PCNA, cyclin D1, HIF-1α, IL-6, Mcl-1 and stimulates Bax, cytochrome C, Apaf-1, caspase-9, caspase-3 and PARP protein expressions. This study provides therapeutic potential of reserpine in inhibiting DNA repair, cell proliferation, and invasion while simultaneously inducing apoptosis via modulation TGF-β signals.
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Affiliation(s)
- Arun Kumar Ramu
- Department of Biochemistry and Biotechnology, Centre for Research and Development, PRIST Deemed University, Vallam, Thanjavur, Tamil Nadu, India.
| | - Daoud Ali
- Department of Zoology, College of Science King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Saud Alarifi
- Department of Zoology, College of Science King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | | | - Bakrudeen Ali Ahmed Abdul
- Department of Biochemistry and Biotechnology, Centre for Research and Development, PRIST Deemed University, Vallam, Thanjavur, Tamil Nadu, India.
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Ponnusamy L, Mahalingaiah PKS, Chang YW, Singh KP. Reversal of epigenetic aberrations associated with the acquisition of doxorubicin resistance restores drug sensitivity in breast cancer cells. Eur J Pharm Sci 2018; 123:56-69. [DOI: 10.1016/j.ejps.2018.07.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 06/04/2018] [Accepted: 07/12/2018] [Indexed: 12/20/2022]
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6
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Godwin RC, Gmeiner WH, Salsbury FR. All-atom molecular dynamics comparison of disease-associated zinc fingers. J Biomol Struct Dyn 2018; 36:2581-2594. [PMID: 28814200 PMCID: PMC5882596 DOI: 10.1080/07391102.2017.1363662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 07/24/2017] [Indexed: 10/19/2022]
Abstract
An important regulatory domain of NF-[Formula: see text]B Essential Modulator (NEMO) is a ubiquitin-binding zinc finger, with a tetrahedral CYS3HIS1 zinc-coordinating binding site. Two variations of NEMO's zinc finger are implicated in various disease states including ectodermal dysplasia and adult-onset glaucoma. To discern structural and dynamical differences between these disease states, we present results of 48-[Formula: see text]s of molecular dynamics simulations for three zinc finger systems each in two states, with and without zinc-bound and correspondingly appropriate cysteine thiol/thiolate configurations. The wild-type protein, often studied for its role in cancer, maintains the most rigid and conformationally stable zinc-bound configuration compared with the diseased counterparts. The glaucoma-related protein has persistent loss of secondary structure except within the dominant conformation. Conformational overlap between wild-type and glaucoma isoforms indicate a competitive binding mechanism may be substantial in the malfunctioning configuration, while the alpha-helical disruption of the ectodermal dysplasia suggests a loss of binding selectivity is responsible for aberrant function.
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Affiliation(s)
- Ryan C. Godwin
- Department of Physics, Wake Forest University, Winston-Salem, NC, USA
| | - William H. Gmeiner
- Department of Cancer Biology, WFU School of Medicine, Winston-Salem, NC, USA
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Kumar AP, Lukman S. Allosteric binding sites in Rab11 for potential drug candidates. PLoS One 2018; 13:e0198632. [PMID: 29874286 PMCID: PMC5991966 DOI: 10.1371/journal.pone.0198632] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 05/22/2018] [Indexed: 12/19/2022] Open
Abstract
Rab11 is an important protein subfamily in the RabGTPase family. These proteins physiologically function as key regulators of intracellular membrane trafficking processes. Pathologically, Rab11 proteins are implicated in many diseases including cancers, neurodegenerative diseases and type 2 diabetes. Although they are medically important, no previous study has found Rab11 allosteric binding sites where potential drug candidates can bind to. In this study, by employing multiple clustering approaches integrating principal component analysis, independent component analysis and locally linear embedding, we performed structural analyses of Rab11 and identified eight representative structures. Using these representatives to perform binding site mapping and virtual screening, we identified two novel binding sites in Rab11 and small molecules that can preferentially bind to different conformations of these sites with high affinities. After identifying the binding sites and the residue interaction networks in the representatives, we computationally showed that these binding sites may allosterically regulate Rab11, as these sites communicate with switch 2 region that binds to GTP/GDP. These two allosteric binding sites in Rab11 are also similar to two allosteric pockets in Ras that we discovered previously.
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Affiliation(s)
- Ammu Prasanna Kumar
- Department of Chemistry, College of Arts and Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Suryani Lukman
- Department of Chemistry, College of Arts and Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
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8
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Melvin RL, Xiao J, Godwin RC, Berenhaut KS, Salsbury FR. Visualizing correlated motion with HDBSCAN clustering. Protein Sci 2018; 27:62-75. [PMID: 28799290 PMCID: PMC5734272 DOI: 10.1002/pro.3268] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 07/31/2017] [Accepted: 08/02/2017] [Indexed: 12/22/2022]
Abstract
Correlated motion analysis provides a method for understanding communication between and dynamic similarities of biopolymer residues and domains. The typical equal-time correlation matrices-frequently visualized with pseudo-colorings or heat maps-quickly convey large regions of highly correlated motion but hide more subtle similarities of motion. Here we propose a complementary method for visualizing correlations within proteins (or general biopolymers) that quickly conveys intuition about which residues have a similar dynamic behavior. For grouping residues, we use the recently developed non-parametric clustering algorithm HDBSCAN. Although the method we propose here can be used to group residues using correlation as a similarity matrix-the most straightforward and intuitive method-it can also be used to more generally determine groups of residues which have similar dynamic properties. We term these latter groups "Dynamic Domains", as they are based not on spatial closeness but rather closeness in the column space of a correlation matrix. We provide examples of this method across three human proteins of varying size and function-the Nf-Kappa-Beta essential modulator, the clotting promoter Thrombin and the mismatch repair protein (dimer) complex MutS-alpha. Although the examples presented here are from all-atom molecular dynamics simulations, this visualization technique can also be used on correlations matrices built from any ensembles of conformations from experiment or computation.
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Affiliation(s)
- Ryan L. Melvin
- Department of PhysicsWake Forest UniversityWinston SalemNorth Carolina
- Department of Mathematics and StatisticsWake Forest UniversityWinston‐SalemNorth Carolina27109
| | - Jiajie Xiao
- Department of PhysicsWake Forest UniversityWinston SalemNorth Carolina
- Department of Computer ScienceWake Forest UniversityWinston‐SalemNorth Carolina27109
| | - Ryan C. Godwin
- Department of PhysicsWake Forest UniversityWinston SalemNorth Carolina
| | - Kenneth S. Berenhaut
- Department of Mathematics and StatisticsWake Forest UniversityWinston‐SalemNorth Carolina27109
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Xiao J, Salsbury FR. Molecular dynamics simulations of aptamer-binding reveal generalized allostery in thrombin. J Biomol Struct Dyn 2017; 35:3354-3369. [PMID: 27794633 PMCID: PMC6876308 DOI: 10.1080/07391102.2016.1254682] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 10/21/2016] [Indexed: 01/11/2023]
Abstract
Thrombin is an attractive target for antithrombotic therapy due to its central role in thrombosis and hemostasis as well as its role in inducing tumor growth, metastasis, and tumor invasion. The thrombin-binding DNA aptamer (TBA), is under investigation for anticoagulant drugs. Although aptamer binding experiments have been revealed various effects on thrombin's enzymatic activities, the detailed picture of the thrombin's allostery from TBA binding is still unclear. To investigate thrombin's response to the aptamer-binding at the molecular level, we compare the mechanical properties and free energy landscapes of the free and aptamer-bound thrombin using microsecond-scale all-atom GPU-based molecular dynamics simulations. Our calculations on residue fluctuations and coupling illustrate the allosteric effects of aptamer-binding at the atomic level, highlighting the exosite II, 60s, γ and the sodium loops, and the alpha helix region in the light chains involved in the allosteric changes. This level of details clarifies the mechanisms of previous experimentally demonstrated phenomena, and provides a prediction of the reduced autolysis rate after aptamer-binding. The shifts in thrombin's ensemble of conformations and free energy surfaces after aptamer-binding demonstrate that the presence of bound-aptamer restricts the conformational freedom of thrombin suggesting that conformational selection, i.e. generalized allostery, is the dominant mechanism of thrombin-aptamer binding. The profound perturbation on thrombin's mechanical and thermodynamic properties due to the aptamer-binding, which was revealed comprehensively as a generalized allostery in this work, may be exploited in further drug discovery and development.
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Affiliation(s)
- Jiajie Xiao
- Department of Physics, Wake Forest University, Winston-Salem, NC, USA
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Xiao J, Melvin RL, Salsbury FR. Mechanistic insights into thrombin's switch between "slow" and "fast" forms. Phys Chem Chem Phys 2017; 19:24522-24533. [PMID: 28849814 PMCID: PMC5719506 DOI: 10.1039/c7cp03671j] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Thrombin is a multifunctional enzyme that plays an important role in blood coagulation, cell growth, and metastasis. Depending upon the binding of sodium ions, thrombin presents significantly different enzymatic activities. In the environment with sodium ions, thrombin is highly active in cleaving the coagulated substrates and this is referred to as the "fast" form; in the environment without sodium ions, thrombin turns catalytically less active and is in the "slow" form. Although many experimental studies over the last two decades have attempted to reveal the structural and kinetic differences between these two forms, it remains vague and disputed how the functional switch between the "fast" and "slow" forms is mediated by Na+ cations. In this work, we employ microsecond-scale all-atom molecular dynamics simulations to investigate the differences in the structural ensembles in sodium-bound/unbound and potassium-bound/unbound thrombin. Our calculations indicate that the regulatory regions, including the 60s, γ loops, and exosite I and II, are primarily affected by both the bound and unbound cations. Conformational free energy surfaces, estimated from principal component analysis, further reveal the existence of multiple conformational states. The binding of a cation introduces changes in the distribution of these states. Through comparisons with potassium-binding, the binding of sodium ions appears to shift the population toward conformational states that might be catalytically favorable. Our study of thrombin in the presence of sodium/potassium ions suggests Na+-mediated generalized allostery is the mechanism of thrombin's functional switch between the "fast" and "slow" forms.
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Affiliation(s)
- Jiajie Xiao
- Department of Physics, Wake Forest University, Winston Salem, NC, USA.
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Yu P, Song L, Qin J, Wang J. Capturing the photo-signaling state of a photoreceptor in a steady-state fashion by binding a transition metal complex. Protein Sci 2017; 26:2249-2256. [PMID: 28856755 DOI: 10.1002/pro.3284] [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: 06/26/2017] [Accepted: 08/26/2017] [Indexed: 11/08/2022]
Abstract
Binding a small molecule to proteins causes conformational changes, but often to a limited extent. Here, we demonstrate that the interaction of a CO-releasing molecule (CORM3) with a photoreceptor photoactive yellow protein (PYP) drives large structural changes in the latter. The interaction of CORM3 and a mutant of PYP, Met100Ala, not only trigger the isomerization of its chromophore, p-coumaric acid, from its anionic trans configuration to a protonated cis configuration, but also increases the content of β-sheet at the cost of α-helix and random coil in the secondary structure of the protein. The CORM3 derived Met100Ala is found to highly resemble the signaling state, which is one of the key photo-intermediates of this photoactive protein, in both protein local conformation and chromophore configuration. The organometallic reagents hold promise as protein engineering tools. This work highlights a novel approach to structurally accessing short lived intermediates of proteins in a steady-state fashion.
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Affiliation(s)
- Pengyun Yu
- Beijing National Laboratory for Molecular Sciences; Molecular Reaction Dynamics Laboratory; CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Lei Song
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine; National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, People's Republic of China
| | - Jun Qin
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine; National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, People's Republic of China
| | - Jianping Wang
- Beijing National Laboratory for Molecular Sciences; Molecular Reaction Dynamics Laboratory; CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
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Melvin RL, Thompson WG, Godwin RC, Gmeiner WH, Salsbury FR. MutS α's Multi-Domain Allosteric Response to Three DNA Damage Types Revealed by Machine Learning. FRONTIERS IN PHYSICS 2017; 5:10. [PMID: 31938712 PMCID: PMC6959842 DOI: 10.3389/fphy.2017.00010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
MutSα is a key component in the mismatch repair (MMR) pathway. This protein is responsible for initiating the signaling pathways for DNA repair or cell death. Herein we investigate this heterodimer's post-recognition, post-binding response to three types of DNA damage involving cytotoxic, anti-cancer agents-carboplatin, cisplatin, and FdU. Through a combination of supervised and unsupervised machine learning techniques along with more traditional structural and kinetic analysis applied to all-atom molecular dynamics (MD) calculations, we predict that MutSα has a distinct response to each of the three damage types. Via a binary classification tree (a supervised machine learning technique), we identify key hydrogen bond motifs unique to each type of damage and suggest residues for experimental mutation studies. Through a combination of a recently developed clustering (unsupervised learning) algorithm, RMSF calculations, PCA, and correlated motions we predict that each type of damage causes MutSα to explore a specific region of conformation space. Detailed analysis suggests a short range effect for carboplatin-primarily altering the structures and kinetics of residues within 10 angstroms of the damaged DNA-and distinct longer-range effects for cisplatin and FdU. In our simulations, we also observe that a key phenylalanine residue-known to stack with a mismatched or unmatched bases in MMR-stacks with the base complementary to the damaged base in 88.61% of MD frames containing carboplatinated DNA. Similarly, this Phe71 stacks with the base complementary to damage in 91.73% of frames with cisplatinated DNA. This residue, however, stacks with the damaged base itself in 62.18% of trajectory frames with FdU-substituted DNA and has no stacking interaction at all in 30.72% of these frames. Each drug investigated here induces a unique perturbation in the MutSα complex, indicating the possibility of a distinct signaling event and specific repair or death pathway (or set of pathways) for a given type of damage.
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Affiliation(s)
- Ryan L. Melvin
- Salsbury Group, Department of Physics, Wake Forest University, Winston-Salem, NC, USA
| | - William G. Thompson
- Salsbury Group, Department of Physics, Wake Forest University, Winston-Salem, NC, USA
| | - Ryan C. Godwin
- Salsbury Group, Department of Physics, Wake Forest University, Winston-Salem, NC, USA
| | - William H. Gmeiner
- Gmeiner Laboratory, Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Freddie R. Salsbury
- Salsbury Group, Department of Physics, Wake Forest University, Winston-Salem, NC, USA
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Melvin RL, Godwin RC, Xiao J, Thompson WG, Berenhaut KS, Salsbury FR. Uncovering Large-Scale Conformational Change in Molecular Dynamics without Prior Knowledge. J Chem Theory Comput 2016; 12:6130-6146. [PMID: 27802394 PMCID: PMC5719493 DOI: 10.1021/acs.jctc.6b00757] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
As the length of molecular dynamics (MD) trajectories grows with increasing computational power, so does the importance of clustering methods for partitioning trajectories into conformational bins. Of the methods available, the vast majority require users to either have some a priori knowledge about the system to be clustered or to tune clustering parameters through trial and error. Here we present non-parametric uses of two modern clustering techniques suitable for first-pass investigation of an MD trajectory. Being non-parametric, these methods require neither prior knowledge nor parameter tuning. The first method, HDBSCAN, is fast-relative to other popular clustering methods-and is able to group unstructured or intrinsically disordered systems (such as intrinsically disordered proteins, or IDPs) into bins that represent global conformational shifts. HDBSCAN is also useful for determining the overall stability of a system-as it tends to group stable systems into one or two bins-and identifying transition events between metastable states. The second method, iMWK-Means, with explicit rescaling followed by K-Means, while slower than HDBSCAN, performs well with stable, structured systems such as folded proteins and is able to identify higher resolution details such as changes in relative position of secondary structural elements. Used in conjunction, these clustering methods allow a user to discern quickly and without prior knowledge the stability of a simulated system and identify both local and global conformational changes.
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Affiliation(s)
- Ryan L. Melvin
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina 27109, United States
| | - Ryan C. Godwin
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina 27109, United States
| | - Jiajie Xiao
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina 27109, United States
| | - William G. Thompson
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina 27109, United States
| | - Kenneth S. Berenhaut
- Department of Mathematics & Statistics, Wake Forest University, Winston-Salem, North Carolina 27109, United States
| | - Freddie R. Salsbury
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina 27109, United States
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Abdelfatah SAA, Efferth T. Cytotoxicity of the indole alkaloid reserpine from Rauwolfia serpentina against drug-resistant tumor cells. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2015; 22:308-318. [PMID: 25765838 DOI: 10.1016/j.phymed.2015.01.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 12/07/2014] [Accepted: 01/12/2015] [Indexed: 06/04/2023]
Abstract
BACKGROUND The antihypertensive reserpine is an indole alkaloid from Rauwolfia serpentina and exerts also profound activity against cancer cells in vitro and in vivo. The present investigation was undertaken to investigate possible modes of action to explain its activity toward drug-resistant tumor cells. MATERIAL AND METHODS Sensitive and drug-resistant tumor cell lines overexpressing P-glycoprotein (ABCB1/MDR1), breast cancer resistance protein (ABCG2/BCRP), mutation-activated epidermal growth factor receptor (EGFR), wild-type and p53-knockout cells as well as the NCI panel of cell lines from different tumor origin were analyzed. Reserpine's cytotoxicity was investigated by resazurin and sulforhodamine assays, flow cytometry, and COMPARE and hierarchical cluster analyses of transcriptome-wide microarray-based RNA expressions. RESULTS P-glycoprotein- or BCRP overexpressing tumor cells did not reveal cross-resistance to reserpine. EGFR-overexpressing cells were collateral sensitive and p53- Knockout cells cross-resistant to this drug compared to their wild-type parental cell lines. Reserpine increased the uptake of doxorubicin in P-glycoprotein-overexpressing cells, indicating that reserpine inhibited the efflux function of P-glycoprotein. Using molecular docking, we found that reserpine bound with even higher binding energy to P-glycoprotein and EGFR than the control drugs verapamil (P-glycoprotein inhibitor) and erlotinib (EGFR inhibitor). COMPARE and cluster analyses of microarray data showed that the mRNA expression of a panel of genes predicted the sensitivity or resistance of the NCI tumor cell line panel with statistical significance. The genes belonged to diverse pathways and biological functions, e.g. cell survival and apoptosis, EGFR activation, regulation of angiogenesis, cell mobility, cell adhesion, immunological functions, mTOR signaling, and Wnt signaling. CONCLUSION The lack of cross-resistance to most resistance mechanisms and the collateral sensitivity in EGFR-transfectants compared to wild-type cells speak for a promising role of reserpine in cancer chemotherapy. Reserpine deserves further consideration for cancer therapy in the clinical setting.
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Affiliation(s)
- Sara A A Abdelfatah
- Department of Pharmaceutical Biology, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University of Mainz, Staudinger Weg 5, 55128 Mainz, Germany
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University of Mainz, Staudinger Weg 5, 55128 Mainz, Germany.
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Godwin RC, Melvin R, Salsbury FR. Molecular Dynamics Simulations and Computer-Aided Drug Discovery. METHODS IN PHARMACOLOGY AND TOXICOLOGY 2015. [DOI: 10.1007/7653_2015_41] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Negureanu L, Salsbury FR. Destabilization of the MutSα's protein-protein interface due to binding to the DNA adduct induced by anticancer agent carboplatin via molecular dynamics simulations. J Mol Model 2013; 19:4969-89. [PMID: 24061854 DOI: 10.1007/s00894-013-1998-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 09/05/2013] [Indexed: 12/22/2022]
Abstract
DNA mismatch repair (MMR) proteins maintain genetic integrity in all organisms by recognizing and repairing DNA errors. Such alteration of hereditary information can lead to various diseases, including cancer. Besides their role in DNA repair, MMR proteins detect and initiate cellular responses to certain type of DNA damage. Its response to the damaged DNA has made the human MMR pathway a useful target for anticancer agents such as carboplatin. This study indicates that strong, specific interactions at the interface of MutSα in response to the mismatched DNA recognition are replaced by weak, non-specific interactions in response to the damaged DNA recognition. Data suggest a severe impairment of the dimerization of MutSα in response to the damaged DNA recognition. While the core of MutSα is preserved in response to the damaged DNA recognition, the loss of contact surface and the rearrangement of contacts at the protein interface suggest a different packing in response to the damaged DNA recognition. Coupled in response to the mismatched DNA recognition, interaction energies, hydrogen bonds, salt bridges, and solvent accessible surface areas at the interface of MutSα and within the subunits are uncoupled or asynchronously coupled in response to the damaged DNA recognition. These pieces of evidence suggest that the loss of a synchronous mode of response in the MutSα's surveillance for DNA errors would possibly be one of the mechanism(s) of signaling the MMR-dependent programed cell death much wanted in anticancer therapies. The analysis was drawn from dynamics simulations.
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Negureanu L, Salsbury FR. Non-specificity and synergy at the binding site of the carboplatin-induced DNA adduct via molecular dynamics simulations of the MutSα-DNA recognition complex. J Biomol Struct Dyn 2013; 32:969-92. [PMID: 23799640 DOI: 10.1080/07391102.2013.799437] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
MutSα is the most abundant mismatch-binding factor of human DNA mismatch repair (MMR) proteins. MMR maintains genetic stability by recognizing and repairing DNA defects. Failure to accomplish their function may lead to cancer. In addition, MutSα recognizes at least some types of DNA damage making it a target for anticancer agents. Here, complementing scarce experimental data, we report unique hydrogen-bonding motifs associated with the recognition of the carboplatin induced DNA damage by MutSα. These data predict that carboplatin and cisplatin induced damaging DNA adducts are recognized by MutSα in a similar manner. Our simulations also indicate that loss of base pairing at the damage site results in (1) non-specific binding and (2) changes in the atomic flexibility at the lesion site and beyond. To further quantify alterations at MutSα-DNA interface in response to damage recognition, non-bonding interactions and salt bridges were investigated. These data indicate (1) possible different packing and (2) disruption of the salt bridges at the MutSα-DNA interface in the damaged complex. These findings (1) underscore the general observation of disruptions at the MutSα-DNA interface and (2) highlight the nature of the anticancer effect of the carboplatin agent. The analysis was carried out from atomistic simulations.
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Shams I, Malik A, Manov I, Joel A, Band M, Avivi A. Transcription pattern of p53-targeted DNA repair genes in the hypoxia-tolerant subterranean mole rat Spalax. J Mol Biol 2013; 425:1111-8. [PMID: 23318952 DOI: 10.1016/j.jmb.2013.01.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 12/31/2012] [Accepted: 01/08/2013] [Indexed: 10/27/2022]
Abstract
The tumor suppressor gene p53 induces growth arrest and/or apoptosis in response to DNA damage/hypoxia. Inactivation of p53 confers a selective advantage to tumor cells under a hypoxic microenvironment during tumor progression. The subterranean blind mole rat, Spalax, spends its life underground at low-oxygen tensions, hence developing a wide range of respiratory/molecular adaptations to hypoxic stress, including critical changes in p53 structure and signaling pathway. The highly conserved p53 Arg(R)-172 is substituted by lysine (K) in Spalax, identical with a tumor-associated mutation. Functionality assays revealed that Spalax p53 is unable to activate apoptotic target genes but is still capable of activating cell cycle arrest genes. Furthermore, we have shown that the transcription patterns of representative p53-induced genes (Apaf1 and Mdm2) in Spalax are influenced by hypoxia. Cell cycle arrest allows the cells to repair DNA damage via different DNA repair genes. We tested the transcription pattern of three p53-related DNA repair genes (p53R2, Mlh1, and Msh2) under normoxia and short-acute hypoxia in Spalax, C57BL/6 wild-type mice, and two strains of mutant C57BL/6 mice, each carrying a different mutation at the R172 position. Our results show that while wild-type/mutant mice exhibit strong hypoxia-induced reductions of repair gene transcript levels, no such inhibition is found in Spalax under hypoxia. Moreover, unlike mouse p53R2, Spalax p53R2 transcript levels are strongly elevated under hypoxia. These results suggest that critical repair functions, which are known to be inhibited under hypoxia in mice, remain active in Spalax, as part of its unique hypoxia tolerance mechanisms.
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Affiliation(s)
- Imad Shams
- Institute of Evolution, University of Haifa, Haifa 31905, Israel.
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AbdelHafez EMN, Diamanduros A, Negureanu L, Luy Y, Bean JH, Zielke K, Crowe B, Vasilyeva A, Clodfelter JE, Aly OM, Abuo-Rahma GEDAA, Scarpinato KD, Salsbury FR, King SB. Computational and synthetic studies towards improving rescinnamine as an inducer of MSH2-dependent apoptosis in cancer treatment. MOLECULAR CANCER BIOLOGY 2013; 1:44. [PMID: 25485184 PMCID: PMC4254817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
We, and others, have previously shown that mismatch repair proteins, in addition to their repair function, contribute to cell death initiation. In response to some drugs, this cell death activity is independent of the repair function of the proteins. Rescinnamine, a derivative of the indole alkaloid reserpine, a drug used to treat hypertension several decades ago, was shown to target the cell death-initiating activity of mismatch repair proteins. When used in animals, the hypotensive action of this drug prevents applying appropriate concentrations for statistically significant tumor reduction. Using a combination of computational modeling, chemical synthesis and cell assays, we determine how rescinnamine can be structurally modified and what effect these modifications have on cell survival. These results inform further computational modeling to suggest new synthetic lead molecules to move toward further biological testing.
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Affiliation(s)
| | | | | | - Yan Luy
- Department of Physics, Wake Forest University, Winston-Salem, NC
| | - J. Hayley Bean
- Department of Biology, Georgia Southern University, Statesboro, GA
| | - Katherine Zielke
- Department of Biology, Georgia Southern University, Statesboro, GA
| | - Brittany Crowe
- Department of Biology, Georgia Southern University, Statesboro, GA
| | - Aksana Vasilyeva
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC; now: St. Jude Hospital, Memphis, TN
| | - Jill E. Clodfelter
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Omar M. Aly
- Department of Medicinal Chemistry, Faculty of Pharmacy, Minia University, Minia , Egypt
| | | | | | | | - S. Bruce King
- Department of Chemistry, Wake Forest University, Winston-Salem, NC
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Salsbury FR. Molecular dynamics simulations of protein dynamics and their relevance to drug discovery. Curr Opin Pharmacol 2011; 10:738-44. [PMID: 20971684 DOI: 10.1016/j.coph.2010.09.016] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2010] [Revised: 09/29/2010] [Accepted: 09/30/2010] [Indexed: 11/18/2022]
Abstract
Molecular dynamics simulations have become increasingly useful in studying biological systems of biomedical interest, and not just in the study of model or toy systems. In this article, the methods and principles of all-atom molecular dynamics will be elucidated with several examples provided of their utility to investigators interested on drug discovery.
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Affiliation(s)
- Freddie R Salsbury
- Department of Physics, Wake Forest University, 1834 Wake Forest Road, Winston-Salem, NC 27106, USA.
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Vasilyeva A, Clodfelter JE, Gorczynski MJ, Gerardi AR, King SB, Salsbury F, Scarpinato KD. Parameters of Reserpine Analogs That Induce MSH2/MSH6-Dependent Cytotoxic Response. J Nucleic Acids 2010; 2010. [PMID: 20936178 PMCID: PMC2946608 DOI: 10.4061/2010/162018] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2010] [Revised: 06/02/2010] [Accepted: 06/18/2010] [Indexed: 11/20/2022] Open
Abstract
Mismatch repair proteins modulate the cytotoxicity of several chemotherapeutic agents. We have recently proposed a "death conformation" of the MutS homologous proteins that is distinguishable from their "repair conformation." This conformation can be induced by a small molecule, reserpine, leading to DNA-independent cell death. We investigated the parameters for a small reserpine-like molecule that are required to interact with MSH2/MSH6 to induce MSH2/MSH6-dependent cytotoxic response. A multidisciplinary approach involving structural modeling, chemical synthesis, and cell biology analyzed reserpine analogs and modifications. We demonstrate that the parameters controlling the induction of MSH2/MSH6-dependent cytotoxicity for reserpine-analogous molecules reside in the specific requirements for methoxy groups, the size of the molecule, and the orientation of molecules within the protein-binding pocket. Reserpine analog rescinnamine showed improved MSH2-dependent cytotoxicity. These results have important implications for the identification of compounds that require functional MMR proteins to exhibit their full cytotoxicity, which will avoid resistance in MMR-deficient cells.
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Affiliation(s)
- Aksana Vasilyeva
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
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