1
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Allen-Taylor D, Boro G, Cabato P, Mai C, Nguyen K, Rijal G. Staphylococcus epidermidis biofilm in inflammatory breast cancer and its treatment strategies. Biofilm 2024; 8:100220. [PMID: 39318870 PMCID: PMC11420492 DOI: 10.1016/j.bioflm.2024.100220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Revised: 09/11/2024] [Accepted: 09/12/2024] [Indexed: 09/26/2024] Open
Abstract
Bacterial biofilms represent a significant challenge in both clinical and industrial settings because of their robust nature and resistance to antimicrobials. Biofilms are formed by microorganisms that produce an exopolysaccharide matrix, protecting function and supporting for nutrients. Among the various bacterial species capable of forming biofilms, Staphylococcus epidermidis, a commensal organism found on human skin and mucous membranes, has emerged as a prominent opportunistic pathogen, when introduced into the body via medical devices, such as catheters, prosthetic joints, and heart valves. The formation of biofilms by S. epidermidis on these surfaces facilitates colonization and provides protection against host immune responses and antibiotic therapies, leading to persistent and difficult-to-treat infections. The possible involvement of biofilms for breast oncogenesis has recently created the curiosity. This paper therefore delves into S. epidermidis biofilm involvement in breast cancer. S. epidermidis biofilms can create a sustained inflammatory environment through their metabolites and can break DNA in breast tissue, promoting cellular proliferation, angiogenesis, and genetic instability. Preventing biofilm formation primarily involves preventing bacterial proliferation using prophylactic measures and sterilization of medical devices and equipment. In cancer treatment, common modalities include chemotherapy, surgery, immunotherapy, alkylating agents, and various anticancer drugs. Understanding the relationship between anticancer drugs and bacterial biofilms is crucial, especially for those undergoing cancer treatment who may be at increased risk of bacterial infections, for improving patient outcomes. By elucidating these interactions, strategies to prevent or disrupt biofilm formation, thereby reducing the incidence of infections associated with medical devices and implants, can be identified.
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Affiliation(s)
- D. Allen-Taylor
- Department of Medical Laboratory Sciences, Public Health, and Nutrition Science, College of Health Sciences, Tarleton State University, a Member of Texas A & M University System, Fort Worth, Texas, 76036, USA
| | - G. Boro
- Department of Medical Laboratory Sciences, Public Health, and Nutrition Science, College of Health Sciences, Tarleton State University, a Member of Texas A & M University System, Fort Worth, Texas, 76036, USA
| | - P.M. Cabato
- Department of Medical Laboratory Sciences, Public Health, and Nutrition Science, College of Health Sciences, Tarleton State University, a Member of Texas A & M University System, Fort Worth, Texas, 76036, USA
| | - C. Mai
- Department of Medical Laboratory Sciences, Public Health, and Nutrition Science, College of Health Sciences, Tarleton State University, a Member of Texas A & M University System, Fort Worth, Texas, 76036, USA
| | - K. Nguyen
- Department of Medical Laboratory Sciences, Public Health, and Nutrition Science, College of Health Sciences, Tarleton State University, a Member of Texas A & M University System, Fort Worth, Texas, 76036, USA
| | - G. Rijal
- Department of Medical Laboratory Sciences, Public Health, and Nutrition Science, College of Health Sciences, Tarleton State University, a Member of Texas A & M University System, Fort Worth, Texas, 76036, USA
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2
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Gómez S, Lafiosca P, Egidi F, Giovannini T, Cappelli C. UV-Resonance Raman Spectra of Systems in Complex Environments: A Multiscale Modeling Applied to Doxorubicin Intercalated into DNA. J Chem Inf Model 2023; 63:1208-1217. [PMID: 36745496 PMCID: PMC9976284 DOI: 10.1021/acs.jcim.2c01495] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
UV-Resonance Raman (RR) spectroscopy is a valuable tool to study the binding of drugs to biomolecular receptors. The extraction of information at the molecular level from experimental RR spectra is made much easier and more complete thanks to the use of computational approaches, specifically tuned to deal with the complexity of the supramolecular system. In this paper, we propose a protocol to simulate RR spectra of complex systems at different levels of sophistication, by exploiting a quantum mechanics/molecular mechanics (QM/MM) approach. The approach is challenged to investigate RR spectra of a widely used chemotherapy drug, doxorubicin (DOX) intercalated into a DNA double strand. The computed results show good agreement with experimental data, thus confirming the reliability of the computational protocol.
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Affiliation(s)
- Sara Gómez
- Scuola
Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy,E-mail:
| | - Piero Lafiosca
- Scuola
Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Franco Egidi
- Software
for Chemistry and Materials BV, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Tommaso Giovannini
- Scuola
Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Chiara Cappelli
- Scuola
Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy,E-mail:
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3
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Lafiosca P, Gómez S, Giovannini T, Cappelli C. Absorption Properties of Large Complex Molecular Systems: The DFTB/Fluctuating Charge Approach. J Chem Theory Comput 2022; 18:1765-1779. [PMID: 35184553 PMCID: PMC8908768 DOI: 10.1021/acs.jctc.1c01066] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
We report on the
first formulation of a novel polarizable QM/MM
approach, where the density functional tight binding (DFTB) is coupled
to the fluctuating charge (FQ) force field. The resulting method (DFTB/FQ)
is then extended to the linear response within the TD-DFTB framework
and challenged to study absorption spectra of large condensed-phase
systems.
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Affiliation(s)
- Piero Lafiosca
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Sara Gómez
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Tommaso Giovannini
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Chiara Cappelli
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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4
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Sinha R, Chatterjee A, Purkayastha P. Graphene Quantum Dot Assisted Translocation of Daunomycin through an Ordered Lipid Membrane: A Study by Fluorescence Lifetime Imaging Microscopy and Resonance Energy Transfer. J Phys Chem B 2022; 126:1232-1241. [PMID: 35129981 DOI: 10.1021/acs.jpcb.1c09376] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Daunomycin (DN) is a well-known chemotherapy drug frequently used in treating acute myeloid and lymphoblastic leukemia. It needs to be delivered to the therapeutic target by a delivering agent that beats the blood-brain barrier. DN is known to be specifically located at the membrane surface and scantly to the bilayer. Penetration of DN into the membrane bilayer depends on the molecular packing of the lipid. It does not travel promptly to the interior of the cells and needs a carrier to serve the purpose. Here, we have demonstrated, by fluorescence lifetime imaging spectroscopy (FLIM) and resonance energy transfer (RET) phenomenon, that ultrasmall graphene quantum dots (GQDs) can be internalized into the aqueous pool of giant unilamellar vesicles (GUVs) made from dipalmitoylphosphatidylcholine (DPPC) lipids, which, in turn, help in fast translocation of DN through the membrane without any delivery vehicle.
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Affiliation(s)
- Riya Sinha
- Department of Chemical Sciences and Centre for Advanced Functional Materials (CAFM), Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, WB, India
| | - Arunavo Chatterjee
- Department of Chemical Sciences and Centre for Advanced Functional Materials (CAFM), Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, WB, India
| | - Pradipta Purkayastha
- Department of Chemical Sciences and Centre for Advanced Functional Materials (CAFM), Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, WB, India
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5
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Veclani D, Tolazzi M, Cerón-Carrasco JP, Melchior A. Intercalation Ability of Novel Monofunctional Platinum Anticancer Drugs: A Key Step in Their Biological Action. J Chem Inf Model 2021; 61:4391-4399. [PMID: 34156233 PMCID: PMC8479807 DOI: 10.1021/acs.jcim.1c00430] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Phenanthriplatin
(PtPPH) is a monovalent platinum(II)-based complex
with a large cytotoxicity against cancer cells. Although the aqua-activated
drug has been assumed to be the precursor for DNA damage, it is still
under debate whether the way in which that metallodrug attacks to
DNA is dominated by a direct binding to a guanine base or rather by
an intercalated intermediate product. Aiming to capture the mechanism
of action of PtPPH, the present contribution used theoretical tools
to systematically assess the sequence of all possible mechanisms on
drug activation and reactivity, for example, hydrolysis, intercalation,
and covalent damage to DNA. Ab initio quantum mechanical
(QM) methods, hybrid QM/QM′ schemes, and independent gradient
model approaches are implemented in an unbiased protocol. The performed
simulations show that the cascade of reactions is articulated in three
well-defined stages: (i) an early and fast intercalation of the complex
between the DNA bases, (ii) a subsequent hydrolysis reaction that
leads to the aqua-activated form, and (iii) a final formation of the
covalent bond between PtPPH and DNA at a guanine site. The permanent
damage to DNA is consequently driven by that latter bond to DNA but
with a simultaneous π–π intercalation of the phenanthridine
into nucleobases. The impact of the DNA sequence and the lateral backbone
was also discussed to provide a more complete picture of the forces
that anchor the drug into the double helix.
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Affiliation(s)
- Daniele Veclani
- Dipartimento Politecnico di Ingegneria e Architettura (DPIA), Laboratori di Chimica, Università di Udine, via delle Scienze 99, 33100 Udine, Italy
| | - Marilena Tolazzi
- Dipartimento Politecnico di Ingegneria e Architettura (DPIA), Laboratori di Chimica, Università di Udine, via delle Scienze 99, 33100 Udine, Italy
| | - José P Cerón-Carrasco
- Reconocimiento y Encapsulación Molecular, Universidad Católica San Antonio de Murcia (UCAM). Campus de los Jerónimos, 30107 Murcia, Spain
| | - Andrea Melchior
- Dipartimento Politecnico di Ingegneria e Architettura (DPIA), Laboratori di Chimica, Università di Udine, via delle Scienze 99, 33100 Udine, Italy
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6
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Visone V, Szabó I, Perugino G, Hudecz F, Bánóczi Z, Valenti A. Topoisomerases inhibition and DNA binding mode of daunomycin-oligoarginine conjugate. J Enzyme Inhib Med Chem 2021; 35:1363-1371. [PMID: 32552137 PMCID: PMC7717705 DOI: 10.1080/14756366.2020.1780226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Cancer is a major health issue adsorbing the attention of a biomedical research. To fight this disease, new drugs are developed, specifically tailored to target biological pathways or peculiar components of the tumour cells. Particularly interesting is the use of intercalating agents as drugs capable to bind DNA and inhibit enzymes involved in DNA metabolism. Anthracyclines are the most commonly used anticancer drugs. In particular, daunomycin is used to cancer treatment by exploiting its ability to intercalate DNA and inhibit the activity of DNA topoisomerases implicated in the replication processes. Unfortunately, clinical application of anthracyclines is limited by their side effects. The conjugation with specific carriers could affect the selectivity and reduce side effect by improving stability and/or cellular uptake properties. We here report the biochemical characterisation of a daunomycin oligopeptide conjugate containing six residues of arginine, by the analysis of its fluorescence properties, DNA interaction and topoisomerases inhibitory effects.
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Affiliation(s)
- Valeria Visone
- Institute of Biosciences and BioResources, National Research Council of Italy, Naples, Italy
| | - Ildikó Szabó
- MTA-ELTE Research Group of Peptide Chemistry, Budapest, Hungary
| | - Giuseppe Perugino
- Institute of Biosciences and BioResources, National Research Council of Italy, Naples, Italy
| | - Ferenc Hudecz
- Department of Organic Chemistry, Eötvös Loránd University (ELTE), Budapest, Hungary
| | - Zoltán Bánóczi
- Department of Organic Chemistry, Eötvös Loránd University (ELTE), Budapest, Hungary
| | - Anna Valenti
- Institute of Biosciences and BioResources, National Research Council of Italy, Naples, Italy
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7
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Khan MI, Gulzar S, Majid A, Noor I. A computational study of intercalation of streptozotocin (STZ) into DNA base pairs. J Mol Model 2021; 27:78. [PMID: 33558970 DOI: 10.1007/s00894-020-04620-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 11/26/2020] [Indexed: 11/28/2022]
Abstract
Deoxyribonucleic acid (DNA) drug intercalation is a well-known phenomenon for the treatment of cancer. Streptozotocin (STZ) is a drug agent containing toxic properties that make it good in the pancreatic cancer. The main objective of this study is the intercalation of the anticancer drug into the stacked base pair of DNA sequence with ATGC using a density functional theory (DFT) code named as ADF-Molecule. ADF code implements DFT using the Slater-type orbitals (STO) for computational analysis of atomic and molecular structures. All the calculations were carried out with the GGA and hybrid exchange correlation functional with TZ2P basis sets. It was captivatingly studied that during the intercalation process, the bonds between the DNA base pairs broken. Moreover, during the process of intercalation, the free radicals are considered responsible for disturbance in the base configurations. It was determined that the disturbances that occurred in the base pairs lead to discontinuity in the replication of that particular sequence in the DNA strand.
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Affiliation(s)
| | - Salma Gulzar
- Department of Physics, University of Gujrat, Gujrat, Pakistan
| | - Abdul Majid
- Department of Physics, University of Gujrat, Gujrat, Pakistan
| | - Irum Noor
- Quaid e Azam Medical College, Bahawalpur, Pakistan
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8
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Petersson GA, Frisch MJ, Dobek F, Zulueta B. Three-Body Dispersion Corrections to the Spherical Atom Model: The PFD-3B Density Functional. J Phys Chem A 2020; 124:10296-10311. [DOI: 10.1021/acs.jpca.0c05940] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- George A. Petersson
- Institute for Computational Molecular Science, Temple University, 1925 N. 12th Street, Philadelphia, Pennsylvania 19122, United States
| | - Michael J. Frisch
- Gaussian, Inc., 340 Quinnipiac Street Building 40, Wallingford, Connecticut 06492, United States
| | - Frank Dobek
- Hall-Atwater Laboratories of Chemistry, Wesleyan University, Middletown, Connecticut 06459, United States
| | - Barbaro Zulueta
- Institute for Computational Molecular Science, Temple University, 1925 N. 12th Street, Philadelphia, Pennsylvania 19122, United States
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9
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Bhat AA, Younes SN, Raza SS, Zarif L, Nisar S, Ahmed I, Mir R, Kumar S, Sharawat SK, Hashem S, Elfaki I, Kulinski M, Kuttikrishnan S, Prabhu KS, Khan AQ, Yadav SK, El-Rifai W, Zargar MA, Zayed H, Haris M, Uddin S. Role of non-coding RNA networks in leukemia progression, metastasis and drug resistance. Mol Cancer 2020; 19:57. [PMID: 32164715 PMCID: PMC7069174 DOI: 10.1186/s12943-020-01175-9] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 03/02/2020] [Indexed: 12/12/2022] Open
Abstract
Early-stage detection of leukemia is a critical determinant for successful treatment of the disease and can increase the survival rate of leukemia patients. The factors limiting the current screening approaches to leukemia include low sensitivity and specificity, high costs, and a low participation rate. An approach based on novel and innovative biomarkers with high accuracy from peripheral blood offers a comfortable and appealing alternative to patients, potentially leading to a higher participation rate. Recently, non-coding RNAs due to their involvement in vital oncogenic processes such as differentiation, proliferation, migration, angiogenesis and apoptosis have attracted much attention as potential diagnostic and prognostic biomarkers in leukemia. Emerging lines of evidence have shown that the mutational spectrum and dysregulated expression of non-coding RNA genes are closely associated with the development and progression of various cancers, including leukemia. In this review, we highlight the expression and functional roles of different types of non-coding RNAs in leukemia and discuss their potential clinical applications as diagnostic or prognostic biomarkers and therapeutic targets.
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Affiliation(s)
- Ajaz A Bhat
- Translational Medicine, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Salma N Younes
- Department of Biomedical Science, College of Health Sciences, Qatar University, Doha, Qatar.,Translational Research Institute, Academic Health System, Hamad Medical Corporation, P.O. Box 3050, Doha, Qatar
| | - Syed Shadab Raza
- Laboratory for Stem Cell & Restorative Neurology, Era's Lucknow Medical College and Hospital, Lucknow, Uttar Pradesh, India
| | - Lubna Zarif
- Department of Biomedical Science, College of Health Sciences, Qatar University, Doha, Qatar.,Translational Research Institute, Academic Health System, Hamad Medical Corporation, P.O. Box 3050, Doha, Qatar
| | - Sabah Nisar
- Translational Medicine, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Ikhlak Ahmed
- Translational Medicine, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Rashid Mir
- Department of Medical Lab Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Saudi Arabia
| | - Sachin Kumar
- Department of Medical Oncology, Dr. B. R. Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Surender K Sharawat
- Department of Medical Oncology, Dr. B. R. Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Sheema Hashem
- Translational Medicine, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Imadeldin Elfaki
- Department of Biochemistry, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
| | - Michal Kulinski
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, P.O. Box 3050, Doha, Qatar
| | - Shilpa Kuttikrishnan
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, P.O. Box 3050, Doha, Qatar
| | - Kirti S Prabhu
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, P.O. Box 3050, Doha, Qatar
| | - Abdul Q Khan
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, P.O. Box 3050, Doha, Qatar
| | - Santosh K Yadav
- Translational Medicine, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Wael El-Rifai
- Department of Surgery, University of Miami, Miami, Florida, USA
| | - Mohammad A Zargar
- Department of Biotechnology, Central University of Kashmir, Ganderbal, Jammu and Kashmir, India
| | - Hatem Zayed
- Department of Biomedical Science, College of Health Sciences, Qatar University, Doha, Qatar
| | - Mohammad Haris
- Translational Medicine, Sidra Medicine, P.O. Box 26999, Doha, Qatar. .,Laboratory Animal Research Center, Qatar University, Doha, Qatar.
| | - Shahab Uddin
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, P.O. Box 3050, Doha, Qatar.
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10
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Khan S, Ahmad R, Naseem I. Elucidating the interaction of aminophylline with calf thymus DNA using multispectroscopic and molecular docking approach. J Biomol Struct Dyn 2020; 39:970-976. [PMID: 31994973 DOI: 10.1080/07391102.2020.1722240] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Aminophylline (Am) is a methylxanthine compound clinically applied for chronic lung diseases like asthma, bronchitis or emphysema. Chemically, it comprises theophylline and ethylenediamine in a ratio 2:1. For the widening of the therapeutic window of any class of drug or for the designing of the newer therapeutic compound, an insight into the binding mechanics of available drugs with DNA is quite imperative. In view of that, here in this study we have investigated binding mechanics of aminophylline molecule with calf thymus DNA (Ct-DNA) using various spectroscopic techniques as well as molecular docking approach. Spectral analysis employing UV-visible and fluorescence approach confirmed the formation of aminophylline-Ct-DNA complex. The binding constant was calculated as 3.5 × 104 M-1 with 0.90 as the value of binding site suggestive of minor groove binding mode of aminophylline. The groove binding mode was further confirmed through spectrofluorimetric experiments like competitive displacement assay employing ethidium bromide, hoechst and rhodamine 6 G dyes as well as iodide quenching studies. The circular dichroic spectral evaluation and molecular docking study finally validated the minor groove binding mode of aminophylline with binding energy calculated as -4.5 Kcal/mol.
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Affiliation(s)
- Saniyya Khan
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Rizwan Ahmad
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Imrana Naseem
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
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11
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Harding DP, Kingsley LJ, Spraggon G, Wheeler SE. Importance of model size in quantum mechanical studies of DNA intercalation. J Comput Chem 2020; 41:1175-1184. [PMID: 32011009 DOI: 10.1002/jcc.26164] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/18/2019] [Accepted: 01/19/2020] [Indexed: 01/11/2023]
Abstract
The convergence of DFT-computed interaction energies with increasing binding site model size was assessed. The data show that while accurate intercalator interaction energies can be derived from binding site models featuring only the flanking nucleotides for uncharged intercalators that bind parallel to the DNA base pairs, errors remain significant even when including distant nucleotides for intercalators that are charged, exhibit groove-binding tails that engage in noncovalent interactions with distant nucleotides, or that bind perpendicular to the DNA base pairs. Consequently, binding site models that include at least three adjacent nucleotides are required to consistently predict converged binding energies. The computationally inexpensive HF-3c method is shown to provide reliable interaction energies and can be routinely applied to such large models.
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Affiliation(s)
- Drew P Harding
- Center for Computational Quantum Chemistry, Department of Chemistry, University of Georgia, Athens, Georgia.,Department of Chemistry, Texas A&M University, College Station, Texas
| | - Laura J Kingsley
- Genomics Institute of the Novartis Research Foundation, San Diego, California
| | - Glen Spraggon
- Genomics Institute of the Novartis Research Foundation, San Diego, California
| | - Steven E Wheeler
- Center for Computational Quantum Chemistry, Department of Chemistry, University of Georgia, Athens, Georgia
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12
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Waugh TM, Masters J, Aliev AE, Marson CM. Monocyclic Quinone Structure-Activity Patterns: Synthesis of Catalytic Inhibitors of Topoisomerase II with Potent Antiproliferative Activity. ChemMedChem 2019; 15:114-124. [PMID: 31778038 DOI: 10.1002/cmdc.201900548] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/28/2019] [Indexed: 12/12/2022]
Abstract
The monocyclic 1,4-benzoquinone, HU-331, the direct oxidation product of cannabidiol, inhibits the catalytic activity of topoisomerase II but without inducing DNA strand breaks or generating free radicals, and unlike many fused-ring quinones exhibits minimal cardiotoxicity. Thus, monocyclic quinones have potential as anticancer agents, and investigation of the structural origins of their biological activity is warranted. New syntheses of cannabidiol and (±)-HU-331 are here reported. Integrated synthetic protocols afforded a wide range of polysubstituted resorcinol derivatives; many of the corresponding novel 2-hydroxy-1,4-benzoquinone derivatives are potent inhibitors of the catalytic activity of topoisomerase II, some more so than HU-331, whose monoterpene unit replaced by a 3-cycloalkyl unit conferred increased antiproliferative properties in cell lines with IC50 values extending below 1 mM, and greater stability in solution than HU-331. The principal pharmacophore of quinones related to HU-331 was identified. Selected monocyclic quinones show potential for the development of new anticancer agents.
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Affiliation(s)
- Thomas M Waugh
- Department of Chemistry, University College London Christopher Ingold Laboratories, 20 Gordon Street, London, WC1H OAJ, UK
| | - John Masters
- Prostate Cancer Research Centre Research Department of Urology Charles Bell House, University College London, 67-75 Riding House Street, London, W1 W 7EJ, UK
| | - Abil E Aliev
- Department of Chemistry, University College London Christopher Ingold Laboratories, 20 Gordon Street, London, WC1H OAJ, UK
| | - Charles M Marson
- Department of Chemistry, University College London Christopher Ingold Laboratories, 20 Gordon Street, London, WC1H OAJ, UK
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13
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Liu C, Guo L, Zhang B, Lu L. Graphene quantum dots mediated electron transfer in DNA base pairs. RSC Adv 2019; 9:31636-31644. [PMID: 35527930 PMCID: PMC9072722 DOI: 10.1039/c9ra05481b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 09/26/2019] [Indexed: 11/23/2022] Open
Abstract
Graphene quantum dots (GQDs) were connected to [Ru(bpy)3]2+ to sense DNA-mediated charge transfer. Interaction between abasic site double stranded DNA (Abasic-DNA) and [Ru(bpy)3-GQD]2+ was investigated by absorption spectroscopy, gel electrophoresis, circular dichroism, and melting temperature measurements. The results indicate that [Ru(bpy)3-GQD]2+ could be intercalated into double stranded DNA. Using [Ru(bpy)3-GQD]2+ as a signal molecule, the charge transfer performance of DNA-intercalated [Ru(bpy)3-GQD]2+ was determined using electrochemical and electrochemiluminescence measurements. Various DNA types were immobilized on Au electrodes via Au-S bonds. Electrochemiluminescence and electrochemical measurements indicate that [Ru(bpy)3-GQD]2+ could enhance DNA-mediated charge transfer when intercalated into an abasic site of double stranded DNA. And comparing with [Ru(bpy)3]2+, it can be concluded that GQDs intercalate into the DNA duplex by acting as a base analog, thus enhancing DNA charge transfer. These findings suggest that the DNA-GQD structure could aid the development of molecular devices and electric drivers, and broaden the application of DNA charge transfer.
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Affiliation(s)
- Chang Liu
- Key Laboratory of Beijing on Regional Air Pollution Control, Beijing University of Technology Beijing 100124 China
| | - Linqing Guo
- Key Laboratory of Beijing on Regional Air Pollution Control, Beijing University of Technology Beijing 100124 China
| | - Biao Zhang
- Key Laboratory of Beijing on Regional Air Pollution Control, Beijing University of Technology Beijing 100124 China
| | - Liping Lu
- Key Laboratory of Beijing on Regional Air Pollution Control, Beijing University of Technology Beijing 100124 China
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14
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Avagliano D, Sánchez-Murcia PA, González L. DNA-binding mechanism of spiropyran photoswitches: the role of electrostatics. Phys Chem Chem Phys 2019; 21:8614-8618. [PMID: 30801589 PMCID: PMC6484825 DOI: 10.1039/c8cp07508e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The binding mechanism of the protonated open form of three spiropyran derivatives into a 12-mer (poly-dAT)2 has been unveiled by means of computational methods.
The binding mechanism of the protonated open form of three spiropyran derivatives into a 12-mer (poly-dAT)2 has been unveiled by means of computational methods. It is found that the electrostatic term in the probe:DNA binding energy, modulates the binding mode, providing new guidelines for the design of spiropyran photoswitches with specific binding modes to DNA.
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Affiliation(s)
- Davide Avagliano
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Strasse 17, 1090, Vienna, Austria.
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15
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Jawad B, Poudel L, Podgornik R, Steinmetz NF, Ching WY. Molecular mechanism and binding free energy of doxorubicin intercalation in DNA. Phys Chem Chem Phys 2019; 21:3877-3893. [PMID: 30702122 DOI: 10.1039/c8cp06776g] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The intercalation process of binding doxorubicin (DOX) in DNA is studied by extensive MD simulations. Many molecular factors that control the binding affinity of DOX to DNA to form a stable complex are inspected and quantified by employing continuum solvation models for estimating the binding free energy. The modified MM-PB(GB)SA methodology provides a complete energetic profile of ΔGele, ΔGvDW, ΔGpolar, ΔGnon-polar, TΔStotal, ΔGdeform, ΔGcon, and ΔGion. To identify the sequence specificity of DOX, two different DNA sequences, d(CGATCG) or DNA1 and d(CGTACG) or DNA2, with one molecule (1 : 1 complex) or two molecule (2 : 1 complex) configurations of DOX were selected in this study. Our results show that the DNA deformation energy (ΔGdeform), the energy cost from translational and rotational entropic contributions (TΔStran+rot), the total electrostatic interactions (ΔGpolar-PB/GB + ΔGele) of incorporation, the intramolecular electrostatic interactions (ΔGele) and electrostatic polar solvation interactions (ΔGpolar-PB/GB) are all unfavorable to the binding of DOX to DNA. However, they are overcome by at least five favorable interactions: the van der Waals interactions (ΔGvDW), the non-polar solvation interaction (ΔGnon-polar), the vibrational entropic contribution (TΔSvib), and the standard concentration dependent free energies of DOX (ΔGcon) and the ionic solution (ΔGion). Specifically, the van der Waals interaction appears to be the major driving force to form a stable DOX-DNA complex. We also predict that DOX has stronger binding to DNA1 than DNA2. The DNA deformation penalty and entropy cost in the 2 : 1 complex are less than those in the 1 : 1 complex, thus they indicate that the 2 : 1 complex is more stable than the 1 : 1 complex. We have calculated the total binding free energy (BFE) (ΔGt-sim) using both MM-PBSA and MM-GBSA methods, which suggests a more stable DOX-DNA complex at lower ionic concentration. The calculated BFE from the modified MM-GBSA method for DOX-DNA1 and DOX-DNA2 in the 1 : 1 complex is -9.1 and -5.1 kcal mol-1 respectively. The same quantities from the modified MM-PBSA method are -12.74 and -8.35 kcal mol-1 respectively. The value of the total BFE ΔGt-sim in the 1 : 1 complex is in reasonable agreement with the experimental value of -7.7 ± 0.3 kcal mol-1.
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Affiliation(s)
- Bahaa Jawad
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, Missouri 64110, USA.
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16
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Muhammad BT, Ullah A, Muhammad MT, Arshad T. DNA physical interaction mediated b-lymphoma treatment offered by tetra benzimidazole-substituted zinc (ii) phthalocyanine derivative. J Mol Recognit 2018; 31:e2733. [PMID: 29952029 DOI: 10.1002/jmr.2733] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 04/13/2018] [Accepted: 05/07/2018] [Indexed: 11/08/2022]
Abstract
Role of heterocyclic compounds with nitrogen substitution in therapeutic frontiers is well established. The efforts made in this study are directed to dissect the biological significance of benzimidazole-substituted zinc phthalocyanine derivative. Its capacity to act as an anticancer agent against the 2 B-lymphoma cell lines (low-grade and high-grade malignancy) was found out by recording florescence using Alamar blue dye. Further cytotoxic effect at the DNA level was analyzed by performing agarose gel electrophoresis. Molecular docking studies made mechanistic details crystal clear by showing potential dual binding modes employed for interaction with DNA that include minor groove binding and intercalation between bases. This advocates this derivative as potential anticancer agent and deserves further rounds of mechanistic study for its final journey to serve as a marketed drug.
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Affiliation(s)
- Bushra Taj Muhammad
- Dr Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Azeem Ullah
- Fujian Institute of Research on the Structure of Matter, Fujian, China
| | | | - Tanzila Arshad
- Department of Applied Chemistry and Chemical technology, University of Karachi, Karachi, Pakistan
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17
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Gabra MM, Salmena L. microRNAs and Acute Myeloid Leukemia Chemoresistance: A Mechanistic Overview. Front Oncol 2017; 7:255. [PMID: 29164055 PMCID: PMC5674931 DOI: 10.3389/fonc.2017.00255] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 10/11/2017] [Indexed: 12/15/2022] Open
Abstract
Up until the early 2000s, a functional role for microRNAs (miRNAs) was yet to be elucidated. With the advent of increasingly high-throughput and precise RNA-sequencing techniques within the last two decades, it has become well established that miRNAs can regulate almost all cellular processes through their ability to post-transcriptionally regulate a majority of protein-coding genes and countless other non-coding genes. In cancer, miRNAs have been demonstrated to play critical roles by modifying or controlling all major hallmarks including cell division, self-renewal, invasion, and DNA damage among others. Before the introduction of anthracyclines and cytarabine in the 1960s, acute myeloid leukemia (AML) was considered a fatal disease. In decades since, prognosis has improved substantially; however, long-term survival with AML remains poor. Resistance to chemotherapy, whether it is present at diagnosis or induced during treatment is a major therapeutic challenge in the treatment of this disease. Certain mechanisms such as DNA damage response and drug targeting, cell cycling, cell death, and drug trafficking pathways have been shown to be further dysregulated in treatment resistant cancers. miRNAs playing key roles in the emergence of these drug resistance phenotypes have recently emerged and replacement or inhibition of these miRNAs may be a viable treatment option. Herein, we describe the roles miRNAs can play in drug resistant AML and we describe miRNA-transcript interactions found within other cancer states which may be present within drug resistant AML. We describe the mechanisms of action of these miRNAs and how they can contribute to a poor overall survival and outcome as well. With the precision of miRNA mimic- or antagomir-based therapies, miRNAs provide an avenue for exquisite targeting in the therapy of drug resistant cancers.
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Affiliation(s)
- Martino Marco Gabra
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Leonardo Salmena
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
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18
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Shen Z, Mulholland KA, Zheng Y, Wu C. Binding of anticancer drug daunomycin to a TGGGGT G-quadruplex DNA probed by all-atom molecular dynamics simulations: additional pure groove binding mode and implications on designing more selective G-quadruplex ligands. J Mol Model 2017; 23:256. [PMID: 28785893 DOI: 10.1007/s00894-017-3417-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 07/12/2017] [Indexed: 12/12/2022]
Abstract
DNA G-quadruplex structures are emerging cancer-specific targets for chemotherapeutics. Ligands that bind to and stabilize DNA G-quadruplexes have the potential to be anti-cancer drugs. Lack of binding selectivity to DNA G-quadruplex over DNA duplex remains a major challenge when attempting to develop G-quadruplex ligands into successful anti-cancer drugs. Thorough understanding of the binding nature of existing non-selective ligands that bind to both DNA quadruplex and DNA duplex will help to address this challenge. Daunomycin and doxorubicin, two commonly used anticancer drugs, are examples of non-selective DNA ligands. In this study, we extended our early all-atom binding simulation studies between doxorubicin and a DNA duplex (d(CGATCG)2) to probe the binding between daunomycin and a parallel DNA quadruplex (d(TGGGGT)4) and DNA duplex. In addition to the end stacking mode, which mimics the mode in the crystal structure, a pure groove binding mode was observed in our free binding simulations. The dynamic and energetic properties of these two binding modes are thoroughly examined, and a detailed comparison is made between DNA quadruplex binding modes and DNA duplex binding modes. Implications on the design of more selective DNA quadruplex ligands are also discussed. Graphical abstract Top stacking and groov binding modes from the MD simulations.
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Affiliation(s)
- Zhanhang Shen
- School of Physics, Shandong University, Jinan, 250100, China
| | - Kelly A Mulholland
- College of Science and Mathematics, Rowan University, Glassboro, NJ, 08028, USA
| | - Yujun Zheng
- School of Physics, Shandong University, Jinan, 250100, China.
| | - Chun Wu
- College of Science and Mathematics, Rowan University, Glassboro, NJ, 08028, USA.
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19
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Prija F, Prasad R. DrrC protein of Streptomyces peucetius removes daunorubicin from intercalated dnrI promoter. Microbiol Res 2017. [PMID: 28647120 DOI: 10.1016/j.micres.2017.05.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
DrrC is a DNA-binding protein of Streptomyces peucetius that provides self-resistance against daunorubicin, the antibiotic produced by the organism. DrrC was expressed in E.coli and purified by using N-terminal MBP-tag which retained DNA-binding property in spite of the tag. Mobility shift assay confirmed the interaction of 313bp DNA that has the dnrI promoter, daunorubicin and MBP-DrrC in the presence of ATP. Biotinylated and immobilized 313bp DNA was intercalated with daunorubicin to observe the release of the drug when MBP-DrrC is allowed to act on the DNA. The release of daunorubicin was recorded by absorption and fluorescence spectroscopy. The experiments proved that daunorubicin was released from DNA in the presence of MBP-DrrC. Fluorescence emission of daunorubicin had a maximum peak at 591nm. However, emission spectrum of released daunorubicin showed hypochromism with a maximum peak at 584nm that is possibly because it is in complex with MBP-DrrC. We propose that DrrC naturally binds at intercalated sites to eject daunorubicin; in the process both drug and protein are dislodged from DNA. Like UvrA, DrrC possibly scans the DNA for intercalated daunorubicin. When it encounters daunorubicin, DrrC dislodges it, thereby allowing DNA replication and transcription to go on unhindered. Thus a novel self resistance mechanism by DNA repair is mediated by DrrC.
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Affiliation(s)
- Francis Prija
- Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai 625021, Tamil Nadu, India.
| | - Ranjan Prasad
- Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai 625021, Tamil Nadu, India.
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20
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Czapla-Masztafiak J, Nogueira JJ, Lipiec E, Kwiatek WM, Wood BR, Deacon GB, Kayser Y, Fernandes DLA, Pavliuk MV, Szlachetko J, González L, Sá J. Direct Determination of Metal Complexes' Interaction with DNA by Atomic Telemetry and Multiscale Molecular Dynamics. J Phys Chem Lett 2017; 8:805-811. [PMID: 28151686 DOI: 10.1021/acs.jpclett.7b00070] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The lack of molecular mechanistic understanding of the interaction between metal complexes and biomolecules hampers their potential medical use. Herein we present a robust procedure combining resonant X-ray emission spectroscopy and multiscale molecular dynamics simulations, which allows for straightforward elucidation of the precise interaction mechanism at the atomic level. The report unveils an unforeseen hydrolysis process and DNA binding of [Pt{N(p-HC6F4)CH2}2py2] (Pt103), which showed potential cytotoxic activity in the past. Pt103 preferentially coordinates to adjacent adenine sites, instead of guanine sites as in cisplatin, because of its hydrogen bond ability. Comparison with previous research on cisplatin suggests that selective binding to guanine or adenine may be achieved by controlling the acidity of the compound.
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Affiliation(s)
- Joanna Czapla-Masztafiak
- Institute of Nuclear Physics, Polish Academy of Sciences , PL-31342 Krakow, Poland
- Paul Scherrer Institute (PSI) , 5232 Villigen, Switzerland
| | - Juan J Nogueira
- University of Vienna , Faculty of Chemistry, Institute of Theoretical Chemistry, Währinger Str. 17, A-1090 Vienna, Austria
| | - Ewelina Lipiec
- Institute of Nuclear Physics, Polish Academy of Sciences , PL-31342 Krakow, Poland
- ETH Zurich , Vladimir-Prelog-Weg 1-5/10, 8093 Zurich, Switzerland
| | - Wojciech M Kwiatek
- Institute of Nuclear Physics, Polish Academy of Sciences , PL-31342 Krakow, Poland
| | - Bayden R Wood
- Centre for Biospectroscopy, School of Chemistry, Monash University , 3800 Victoria, Australia
| | - Glen B Deacon
- School of Chemistry, Faculty of Science, Monash University , 3800 Victoria, Australia
| | - Yves Kayser
- Paul Scherrer Institute (PSI) , 5232 Villigen, Switzerland
| | - Daniel L A Fernandes
- Department of Chemistry-Ånsgtröm Laboratory, Uppsala University , 751 20 Uppsala, Sweden
| | - Mariia V Pavliuk
- Department of Chemistry-Ånsgtröm Laboratory, Uppsala University , 751 20 Uppsala, Sweden
| | - Jakub Szlachetko
- Paul Scherrer Institute (PSI) , 5232 Villigen, Switzerland
- Institute of Physics, Jan Kochanowski University in Kielce , Świętokrzyska 15 St., 25-406 Kielce, Poland
| | - Leticia González
- University of Vienna , Faculty of Chemistry, Institute of Theoretical Chemistry, Währinger Str. 17, A-1090 Vienna, Austria
| | - Jacinto Sá
- Department of Chemistry-Ånsgtröm Laboratory, Uppsala University , 751 20 Uppsala, Sweden
- Institute of Physical Chemistry, Polish Academy of Sciences , ul. Kasprzaka 44/52, 01-224 Warsaw, Poland
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21
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Galliot A, Gil A, Calhorda MJ. Effects of oxygenation on the intercalation of 1,10-phenanthroline-5,6/4,7-dione between DNA base pairs: a computational study. Phys Chem Chem Phys 2017. [PMID: 28621352 DOI: 10.1039/c7cp00532f] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The effects of oxygen in positions 4,7 and 5,6 of phenanthroline have been studied computationally when this ligand intercalates between DNA base pairs. Our results indicate that solvation energy could be the driving force of the process and thus, it can be also related with the cytotoxicity of the drug.
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Affiliation(s)
- Aurellia Galliot
- Centro de Química e Bioquímica
- DQB
- Faculdade de Ciências
- Universidade de Lisboa
- Campo Grande 1749-016 Lisboa
| | - Adrià Gil
- Centro de Química e Bioquímica
- DQB
- Faculdade de Ciências
- Universidade de Lisboa
- Campo Grande 1749-016 Lisboa
| | - Maria José Calhorda
- Centro de Química e Bioquímica
- DQB
- Faculdade de Ciências
- Universidade de Lisboa
- Campo Grande 1749-016 Lisboa
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22
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Haining RL, Jones TM, Hernandez A. Saturation Binding of Nicotine to Synthetic Neuromelanin Demonstrated by Fluorescence Spectroscopy. Neurochem Res 2016; 41:3356-3363. [PMID: 27662849 DOI: 10.1007/s11064-016-2068-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Revised: 09/11/2016] [Accepted: 09/15/2016] [Indexed: 12/12/2022]
Abstract
Neuromelanin (NM) has long been considered as an aging pigment, perhaps an unavoidable and undesirable byproduct of dopaminergic neural transmission. However, NM is carefully packaged into double membrane-bound structures within cells of the substantia nigra and other neural tissues, suggesting a beneficial function to maintaining these stores. It is well established that NM is able to concentrate toxic xenobiotics within pigmented cells due to its unique chemical environment. In doing so, such agents may confer susceptibility to Parkinson's disease (PD) as illustrated by model PD-inducing neurotoxins such as methyl-phenyl-pyridinium ion. It is possible that high-affinity binding interactions toward NM may contribute to the adverse effects of PD-inducing toxins, as well as neuroprotective agents. Here we aim to develop a generalized assay capable of elucidating the binding constants of chemical agents to synthetic and natural neuromelanins. Toward this end, a model neuromelanin synthesized from dopamine and cysteine was prepared according to published procedure. Using a UV/Visible spectroscopic assay, we show that dopamine, 6-hydroxy dopamine, and nicotine bind to the synthetic neuromelanin, while caffeine did not. More importantly, nicotine was further found to induce a fluorescence signal in the presence of NM which was used to establish a binding constant estimated at 0.65 mM. Dopamine appears to enhance this signal, also in a saturable manner, with an estimated Kd of 0.05 mM in our isolated chemical system. In summary, the micro-scale fluorescence assay described herein will allow us to overcome many of the problems inherent in the study of chemical interaction with NM through traditional spectroscopic means. Using a single standardized signal, it should now be possible to rank a number of PD-related toxins based on NM-binding affinity and shed further light on this important problem.
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Affiliation(s)
- Robert L Haining
- School of Science and Technology, Georgia Gwinnett College, 1000 University Center Ln, Lawrenceville, GA, 30043, USA.
| | - Travis M Jones
- School of Science and Technology, Georgia Gwinnett College, 1000 University Center Ln, Lawrenceville, GA, 30043, USA
| | - Aubrey Hernandez
- School of Science and Technology, Georgia Gwinnett College, 1000 University Center Ln, Lawrenceville, GA, 30043, USA
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23
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Fu Z, Cui Y, Cui F, Zhang G. Modeling techniques and fluorescence imaging investigation of the interactions of an anthraquinone derivative with HSA and ctDNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2016; 153:572-579. [PMID: 26436845 DOI: 10.1016/j.saa.2015.09.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 08/31/2015] [Accepted: 09/20/2015] [Indexed: 06/05/2023]
Abstract
A new anthraquinone derivative (AORha) was synthesized. Its interactions with human serum albumin (HSA) and calf thymus DNA (ctDNA) were investigated by fluorescence spectroscopy, UV-visible absorption spectroscopy and molecular modeling. Cell viability assay and cell imaging experiment were performed using cervical cancer cells (HepG2 cells). The fluorescence results revealed that the quenching mechanism was static quenching. At different temperatures (290, 300, 310 K), the binding constants (K) and the number of binding sites (n) were determined, respectively. The positive ΔH and ΔS values showed that the binding of AORha with HSA was hydrophobic force, which was identical with the molecular docking result. Studying the fluorescence spectra, UV spectra and molecular modeling also verified that the binding mode of AORha and ctDNA might be intercalative. When HepG2 cells were treated with AORha, the fluorescence became brighter and turned green, which could be used for bioimaging.
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Affiliation(s)
- Zheng Fu
- College of Chemistry and Chemical Engineering, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Normal University, Xinxiang 453007, China; Department of Electrical Engineering, Henan Mechanical and Electrical Engineering College, Xinxiang 453000, China
| | - Yanrui Cui
- College of Chemistry and Chemical Engineering, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Normal University, Xinxiang 453007, China
| | - Fengling Cui
- College of Chemistry and Chemical Engineering, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Normal University, Xinxiang 453007, China.
| | - Guisheng Zhang
- College of Chemistry and Chemical Engineering, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Normal University, Xinxiang 453007, China
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24
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Kocak A, Yilmaz H, Faiz O, Andac O. Experimental and theoretical studies on Cu(II) complex of N,N′-disalicylidene-2,3-diaminopyridine ligand reveal indirect evidence for DNA intercalation. Polyhedron 2016. [DOI: 10.1016/j.poly.2015.11.037] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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25
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A pyrene dihydrodioxin with pyridinium “arms”: A photochemically active DNA cleaving agent with unusual duplex stabilizing and electron trapping properties. J Photochem Photobiol A Chem 2015. [DOI: 10.1016/j.jphotochem.2015.03.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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26
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Yang L, Fu Z, Niu X, Zhang G, Cui F, Zhou C. Probing the interaction of anthraquinone with DNA by spectroscopy, molecular modeling and cancer cell imaging technique. Chem Biol Interact 2015; 233:65-70. [DOI: 10.1016/j.cbi.2015.03.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 03/16/2015] [Accepted: 03/23/2015] [Indexed: 11/30/2022]
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27
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Airoldi M, Barone G, Gennaro G, Giuliani AM, Giustini M. Interaction of doxorubicin with polynucleotides. A spectroscopic study. Biochemistry 2014; 53:2197-207. [PMID: 24641674 DOI: 10.1021/bi401687v] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The interaction of doxorubicin (DX) with model polynucleotides poly(dG-dC)·poly(dG-dC) (polyGC), poly(dA-dT)·poly(dA-dT) (polyAT), and calf thymus DNA has been studied by several spectroscopic techniques in phosphate buffer aqueous solutions. UV-vis, circular dichroism, and fluorescence spectroscopic data confirm that intercalation is the prevailing mode of interaction, and also reveal that the interaction with AT-rich regions leads to the transfer of excitation energy to DX not previously documented in the literature. Moreover, the DX affinity for AT sites has been found to be on the same order of magnitude as that reported for GC sites.
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Affiliation(s)
- Marta Airoldi
- Dipartimento STEBICEF, Università di Palermo, Viale delle Scienze , Parco D'Orleans, Pad. 17, 90128 Palermo, Italy
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28
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DNA-binding of nickel(II), copper(II) and zinc(II) complexes: Structure–affinity relationships. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2013.02.023] [Citation(s) in RCA: 203] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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29
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Ebrahimi A, Karimi P, Akher FB, Behazin R, Mostafavi N. Investigation of the π–π stacking interactions without direct electrostatic effects of substituents: the aromatic∥aromatic and aromatic∥anti-aromatic complexes. Mol Phys 2013. [DOI: 10.1080/00268976.2013.830784] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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30
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Barone G, Fonseca Guerra C, Bickelhaupt FM. B-DNA Structure and Stability as Function of Nucleic Acid Composition: Dispersion-Corrected DFT Study of Dinucleoside Monophosphate Single and Double Strands. ChemistryOpen 2013; 2:186-93. [PMID: 24551565 PMCID: PMC3892189 DOI: 10.1002/open.201300019] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Indexed: 11/16/2022] Open
Abstract
We have computationally investigated the structure and stability of all 16 combinations of two out of the four natural DNA bases A, T, G and C in a di-2′-deoxyribonucleoside-monophosphate model DNA strand as well as in 10 double-strand model complexes thereof, using dispersion-corrected density functional theory (DFT-D). Optimized geometries with B-DNA conformation were obtained through the inclusion of implicit water solvent and, in the DNA models, of sodium counterions, to neutralize the negative charge of the phosphate groups. The results obtained allowed us to compare the relative stability of isomeric single and double strands. Moreover, the energy of the Watson–Crick pairing of complementary single strands to form double-helical structures was calculated. The latter furnished the following increasing stability trend of the double-helix formation energy: d(TpA)2 <d(CpA)2 <d(ApT)2 <d(ApA)2 <d(GpT)2 <d(GpA)2 <d(ApG)2 <d(CpG)2 <d(GpG)2 <d(GpC)2, where the energy differences between the last four dimers, d(ApG)2, d(CpG)2, d(GpG)2 and d(GpC)2, is within 4.0 kcal mol−1, and the energy between the most and the least stable isomers is 13.4 kcal mol−1. This trend shows that the formation energy essentially increases with the number of hydrogen bonds per base pair, that is two between A and T and three between G and C. Superimposed on this main trend are more subtle effects that depend on the order in which bases occur within a strand from the 5’- to the 3’-end.
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Affiliation(s)
- Giampaolo Barone
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università di Palermo Viale delle Scienze, Edificio 17, 90128, Palermo (Italy) E-mail:
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, VU University De Boelelaan 1083, 1081 HV Amsterdam (The Netherlands) E-mail:
| | - F Matthias Bickelhaupt
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, VU University De Boelelaan 1083, 1081 HV Amsterdam (The Netherlands) E-mail: ; Institute for Molecules and Materials, Radboud University Nijmegen Heyendaalseweg 135, 6525 AJ Nijmegen (The Netherlands)
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31
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Metal complex–DNA binding: Insights from molecular dynamics and DFT/MM calculations. J Inorg Biochem 2013; 124:63-9. [DOI: 10.1016/j.jinorgbio.2013.03.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2012] [Revised: 03/19/2013] [Accepted: 03/20/2013] [Indexed: 11/19/2022]
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Doughty B, Rao Y, Kazer SW, Kwok SJJ, Turro NJ, Eisenthal KB. Binding of the Anti-Cancer Drug Daunomycin to DNA Probed by Second Harmonic Generation. J Phys Chem B 2013; 117:15285-9. [DOI: 10.1021/jp311634a] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Benjamin Doughty
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York
10027, United States
| | - Yi Rao
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York
10027, United States
| | - Samuel W. Kazer
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York
10027, United States
| | - Sheldon J. J. Kwok
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York
10027, United States
| | - Nicholas J. Turro
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York
10027, United States
| | - Kenneth B. Eisenthal
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York
10027, United States
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Terenzi A, Ducani C, Male L, Barone G, Hannon MJ. DNA interaction of CuII, NiII and ZnII functionalized salphen complexes: studies by linear dichroism, gel electrophoresis and PCR. Dalton Trans 2013; 42:11220-6. [DOI: 10.1039/c3dt51090e] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Lei H, Wang X, Wu C. Early stage intercalation of doxorubicin to DNA fragments observed in molecular dynamics binding simulations. J Mol Graph Model 2012; 38:279-89. [PMID: 23079648 DOI: 10.1016/j.jmgm.2012.05.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2012] [Revised: 05/06/2012] [Accepted: 05/15/2012] [Indexed: 11/19/2022]
Abstract
The intercalation mode between doxorubicin (an anticancer drug) and two 6-base-pair DNA model fragments (d(CGATCG)₂ and d(CGTACG)₂) has been well studied by X-ray crystallography and NMR experimental methods. Yet, the detailed intercalation pathway at molecular level remains elusive. In this study, we conducted molecular dynamics binding simulations of these two systems using AMBER DNA (parmbsc0) and drug (GAFF) force fields starting from the unbound state. We observed outside binding (minor groove binding or end-binding) in all six independent binding simulations (three for each DNA fragment), followed by the complete intercalation of a drug molecule in two simulations (one for each DNA fragment). First, our data directly supported that the minor groove binding is the dominant pre-intercalation step. Second, we observed that the opening and flipping of a local base pair (A3-T10 for d(CGATCG)₂ and C1-G12 for d(CGTACG)₂) in the two intercalation trajectories. This locally cooperative flipping-intercalation mechanism was different from the previously proposed rise-insertion mechanism by which the distance between two neighboring intact base pairs increases to create a space for the drug insertion. Third, our simulations provided the first set of data to support the applicability of the AMBER DNA and drug force fields in drug-DNA atomistic binding simulations. Implications on the kinetics pathway and drug action are also discussed.
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Affiliation(s)
- Hongxing Lei
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China.
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Beckford SJ, Dixon DW. Molecular Dynamics of Anthraquinone DNA Intercalators with Polyethylene Glycol Side Chains. J Biomol Struct Dyn 2012; 29:1065-80. [DOI: 10.1080/073911012010525031] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Langner KM, Janowski T, Góra RW, Dziekoński P, Sokalski WA, Pulay P. The Ethidium–UA/AU Intercalation Site: Effect of Model Fragmentation and Backbone Charge State. J Chem Theory Comput 2011; 7:2600-9. [DOI: 10.1021/ct200121f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Karol M. Langner
- Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Tomasz Janowski
- Department of Chemistry and Biochemistry, Fulbright College of Arts and Sciences, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Robert W. Góra
- Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Paweł Dziekoński
- Wrocław Center for Networking and Supercomputing, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - W. Andrzej Sokalski
- Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Peter Pulay
- Department of Chemistry and Biochemistry, Fulbright College of Arts and Sciences, University of Arkansas, Fayetteville, Arkansas 72701, United States
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Mahalakshmi A, Shenbagarathai R. Homology modeling of Cry10Aa toxin from B. thuringiensis israelensis and B. thuringiensis subsp. LDC-9. J Biomol Struct Dyn 2011; 28:363-78. [PMID: 20919752 DOI: 10.1080/07391102.2010.10507366] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
A three dimensional model was developed for Cry10Aa protein sequence of B. thuringiensis LDC-9 and B. thuringiensis israelensis that has not been solved empirically by X-ray crystallography or NMR. Homology modeling was employed for the structure prediction using Cry2Aa as template protein, a high-resolution X-ray crystallography structure. The model predicted for the B. thuringiensis LDC-9 Cry10Aa protein reveals a partial N-terminal domain only due to its partial sequence of 104 amino acids. B. thuringiensis israelensis Cry10Aa model contains three domains such as domain I, a bundle of eight alpha helices with the central relatively hydrophobic helix surrounded by amphipathic helices while domain II and III contain mostly beta-sheets. Significant structural differences within domain II in this model among all Cry protein structures indicates that it is involved in recognition and binding to cell surfaces. Comparison of B. thuringiensis israelensis predicted structure with available experimentally determined Cry structures reveals identical folds. The distribution of electrostatic potential on the surface of the molecules in the model is non-uniform and identifies one side of the alpha-helical domain as negatively charged indicating orientation of toxic molecules toward the cell membrane during the initial binding with a cell surface receptor. The collective knowledge of Cry toxin structures will lead to a more critical understanding of the structural basis for receptor binding and pore formation, as well as allowing the scope of diversity to be better appreciated. This model will serve as a starting point for the design of mutagenesis experiments aimed to improve the toxicity and to provide a new tool for the elucidation of the mechanism of action of these mosquitocidal proteins.
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Affiliation(s)
- A Mahalakshmi
- PG and Research Department of Zoology and Biotechnology, Lady Doak College, Madurai-625 002, TamilNadu, India.
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Bhargavi K, Chaitanya PK, Ramasree D, Vasavi M, Murthy DK, Uma V. Homology Modeling and Docking Studies of Human Bcl-2L10 Protein. J Biomol Struct Dyn 2010; 28:379-91. [DOI: 10.1080/07391102.2010.10507367] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Aman MJ, Karauzum H, Bowden MG, Nguyen TL. Structural model of the pre-pore ring-like structure of Panton-Valentine leukocidin: providing dimensionality to biophysical and mutational data. J Biomol Struct Dyn 2010; 28:1-12. [PMID: 20476791 DOI: 10.1080/073911010010524952] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Panton-Valentine leukocidin (PVL) is a bipartite toxin that plays an important role in the pathogenesis of methicillin-resistant Staphylococcus aureus. Recent clinical data suggest a correlation between PVL and severe cases of S. aureus pneumonia. A clear understanding of the structure and function of PVL is critical to the development of novel, effective treatments. Here, we report an all-atom model of the macromolecular structure of Panton-Valentine leukocidin in its octameric, pre-pore conformation that confirms and extends our understanding of the toxin's mechanism of action.
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Affiliation(s)
- M Javad Aman
- Integrated BioTherapeutics, Inc., Germantown, MD 20876, USA.
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Dalyan Y, Vardanyan I, Chavushyan A, Balayan G. Peculiarities of Interaction of Porphyrins with tRNA at Low Ionic Strength. J Biomol Struct Dyn 2010; 28:123-31. [DOI: 10.1080/07391102.2010.10507348] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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41
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Conformational diversity of anthracycline anticancer antibiotics: A density functional theory calculation. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2010.04.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Borkar A, Ghosh I, Bhattacharyya D. Structure and Dynamics of Double Helical DNA in Torsion Angle Hyperspace: A Molecular Mechanics Approach. J Biomol Struct Dyn 2010; 27:695-712. [DOI: 10.1080/07391102.2010.10508582] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Ruiz R, García B, Ruisi G, Silvestri A, Barone G. Computational study of the interaction of proflavine with d(ATATATATAT)2 and d(GCGCGCGCGC)2. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2009.08.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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