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Liu J, Xue Y, Bai K, Yan F, Long X, Guo H, Yan H, Huang G, Zhou J, Tang Y. Experimental and computational study on anti-gastric cancer activity and mechanism of evodiamine derivatives. Front Pharmacol 2024; 15:1380304. [PMID: 38783957 PMCID: PMC11113551 DOI: 10.3389/fphar.2024.1380304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 04/15/2024] [Indexed: 05/25/2024] Open
Abstract
Introduction: Human topoisomerase 1 (TOP1) is an important target of various anticancer compounds. The design and discovery of inhibitors targeting TOP1 are of great significance for the development of anticancer drugs. Evodiamine and thieno [2,3-d] pyridine hybrids show potential antitumor activity. Herein, the anti-gastric cancer activities of these hybrids were investigated. Methods: The inhibitory effects of different concentrations of ten evodiamine derivatives on the gastric cancer cell line SGC-7901 were assessed using a methyl thiazolyl tetrazolium assay. Compounds EVO-1 and EVO-6 strongly inhibited gastric cancer cell proliferation, with inhibition rates of 81.17% ± 5.08% and 80.92% ± 2.75%, respectively. To discover the relationship between the structure and activity of these two derivatives, density functional theory was used to investigate their optimized geometries, natural population charges, frontier molecular orbitals, and molecular electrostatic potentials. To clarify their anti-gastric cancer mechanisms, molecular docking, molecular dynamics simulations, and binding free energy calculations were performed against TOP1. Results: The results demonstrated that these compounds could intercalate into the cleaved DNA-binding site to form a TOP1-DNA-ligand ternary complex, and the ligand remained secure at the cleaved DNA-binding site to form a stable ternary complex. As the binding free energy of compound EVO-1 with TOP1 (-38.33 kcal·mol-1) was lower than that of compound EVO-6 (-33.25 kcal·mol-1), compound EVO-1 could be a more potent anti-gastric cancer agent than compound EVO-6. Discussion: Thus, compound EVO-1 could be a promising anti-gastric cancer drug candidate. This study may facilitate the design and development of novel TOP1 inhibitors.
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Affiliation(s)
- Jingli Liu
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, China
| | - Yingying Xue
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, China
| | - Kaidi Bai
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, China
| | - Fei Yan
- Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, China
| | - Xu Long
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, China
| | - Hui Guo
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, China
| | - Hao Yan
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, China
| | - Guozheng Huang
- College of Chemistry and Chemical Engineering, Anhui University of Technology, Ma’anshan, Anhui, China
| | - Jing Zhou
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, China
| | - Yuping Tang
- Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, Shaanxi University of Chinese Medicine, Xianyang, Shaanxi, China
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2
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Di Martino J, Arcieri M, Madeddu F, Pieroni M, Carotenuto G, Bottoni P, Botta L, Castrignanò T, Gabellone S, Saladino R. Molecular Dynamics Investigations of Human DNA-Topoisomerase I Interacting with Novel Dewar Valence Photo-Adducts: Insights into Inhibitory Activity. Int J Mol Sci 2023; 25:234. [PMID: 38203410 PMCID: PMC10778928 DOI: 10.3390/ijms25010234] [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: 10/30/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
Chronic exposure to ultraviolet (UV) radiation is known to induce the formation of DNA photo-adducts, including cyclobutane pyrimidine dimers (CPDs) and Dewar valence derivatives (DVs). While CPDs usually occur at higher frequency than DVs, recent studies have shown that the latter display superior selectivity and significant stability in interaction with the human DNA/topoisomerase 1 complex (TOP1). With the aim to deeply investigate the mechanism of interaction of DVs with TOP1, we report here four all-atom molecular dynamic simulations spanning one microsecond. These simulations are focused on the stability and conformational changes of two DNA/TOP1-DV complexes in solution, the data being compared with the biomimetic thymine dimer counterparts. Results from root-mean-square deviation (RMSD) and root-mean-square fluctuation (RMSF) analyses unequivocally confirmed increased stability of the DNA/TOP1-DV complexes throughout the simulation duration. Detailed interaction analyses, uncovering the presence of salt bridges, hydrogen bonds, water-mediated interactions, and hydrophobic interactions, as well as pinpointing the non-covalent interactions within the complexes, enabled the identification of specific TOP1 residues involved in the interactions over time and suggested a potential TOP1 inhibition mechanism in action.
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Affiliation(s)
- Jessica Di Martino
- Department of Ecological and Biological Sciences, Tuscia University, Largo dell’Università snc, 01100 Viterbo, Italy; (J.D.M.); (R.S.)
| | - Manuel Arcieri
- Department of Health Technology, Technical University of Denmark, 2800 Kongens Lyngby, Denmark;
| | - Francesco Madeddu
- Department of Computer Science, “Sapienza” University of Rome, P.le Aldo Moro, 5, 00185 Rome, Italy (M.P.); (P.B.)
| | - Michele Pieroni
- Department of Computer Science, “Sapienza” University of Rome, P.le Aldo Moro, 5, 00185 Rome, Italy (M.P.); (P.B.)
| | - Giovanni Carotenuto
- Department of Ecological and Biological Sciences, Tuscia University, Largo dell’Università snc, 01100 Viterbo, Italy; (J.D.M.); (R.S.)
| | - Paolo Bottoni
- Department of Computer Science, “Sapienza” University of Rome, P.le Aldo Moro, 5, 00185 Rome, Italy (M.P.); (P.B.)
| | - Lorenzo Botta
- Department of Ecological and Biological Sciences, Tuscia University, Largo dell’Università snc, 01100 Viterbo, Italy; (J.D.M.); (R.S.)
| | - Tiziana Castrignanò
- Department of Ecological and Biological Sciences, Tuscia University, Largo dell’Università snc, 01100 Viterbo, Italy; (J.D.M.); (R.S.)
| | - Sofia Gabellone
- Department of Ecological and Biological Sciences, Tuscia University, Largo dell’Università snc, 01100 Viterbo, Italy; (J.D.M.); (R.S.)
- Preclinic and Osteoncology Unit, Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy
| | - Raffaele Saladino
- Department of Ecological and Biological Sciences, Tuscia University, Largo dell’Università snc, 01100 Viterbo, Italy; (J.D.M.); (R.S.)
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3
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Pieroni M, Madeddu F, Di Martino J, Arcieri M, Parisi V, Bottoni P, Castrignanò T. MD-Ligand-Receptor: A High-Performance Computing Tool for Characterizing Ligand-Receptor Binding Interactions in Molecular Dynamics Trajectories. Int J Mol Sci 2023; 24:11671. [PMID: 37511429 PMCID: PMC10380688 DOI: 10.3390/ijms241411671] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/15/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Molecular dynamics simulation is a widely employed computational technique for studying the dynamic behavior of molecular systems over time. By simulating macromolecular biological systems consisting of a drug, a receptor and a solvated environment with thousands of water molecules, MD allows for realistic ligand-receptor binding interactions (lrbi) to be studied. In this study, we present MD-ligand-receptor (MDLR), a state-of-the-art software designed to explore the intricate interactions between ligands and receptors over time using molecular dynamics trajectories. Unlike traditional static analysis tools, MDLR goes beyond simply taking a snapshot of ligand-receptor binding interactions (lrbi), uncovering long-lasting molecular interactions and predicting the time-dependent inhibitory activity of specific drugs. With MDLR, researchers can gain insights into the dynamic behavior of complex ligand-receptor systems. Our pipeline is optimized for high-performance computing, capable of efficiently processing vast molecular dynamics trajectories on multicore Linux servers or even multinode HPC clusters. In the latter case, MDLR allows the user to analyze large trajectories in a very short time. To facilitate the exploration and visualization of lrbi, we provide an intuitive Python notebook (Jupyter), which allows users to examine and interpret the results through various graphical representations.
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Affiliation(s)
- Michele Pieroni
- Department of Computer Science, "Sapienza" University of Rome, V. le Regina Elena 295, 00161 Rome, Italy
| | - Francesco Madeddu
- Department of Computer Science, "Sapienza" University of Rome, V. le Regina Elena 295, 00161 Rome, Italy
| | - Jessica Di Martino
- Department of Ecological and Biological Sciences, Tuscia University, Viale dell'Università s.n.c., 01100 Viterbo, Italy
| | - Manuel Arcieri
- Department of Health Technology, Technical University of Denmark, Anker Engelunds Vej 101, 2800 Kongens Lyngby, Denmark
| | - Valerio Parisi
- Department of Physics, "Sapienza" University of Rome, P. le Aldo Moro, 5, 00185 Rome, Italy
| | - Paolo Bottoni
- Department of Computer Science, "Sapienza" University of Rome, V. le Regina Elena 295, 00161 Rome, Italy
| | - Tiziana Castrignanò
- Department of Ecological and Biological Sciences, Tuscia University, Viale dell'Università s.n.c., 01100 Viterbo, Italy
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4
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Madeddu F, Di Martino J, Pieroni M, Del Buono D, Bottoni P, Botta L, Castrignanò T, Saladino R. Molecular Docking and Dynamics Simulation Revealed the Potential Inhibitory Activity of New Drugs against Human Topoisomerase I Receptor. Int J Mol Sci 2022; 23:ijms232314652. [PMID: 36498979 PMCID: PMC9737192 DOI: 10.3390/ijms232314652] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/13/2022] [Accepted: 11/15/2022] [Indexed: 11/25/2022] Open
Abstract
Human Topoisomerase I (hTop1p) is a ubiquitous enzyme that relaxes supercoiled DNA through a conserved mechanism involving transient breakage, rotation, and binding. Htop1p is the molecular target of the chemotherapeutic drug camptothecin (CPT). It causes the hTop1p-DNA complex to slow down the binding process and clash with the replicative machinery during the S phase of the cell cycle, forcing cells to activate the apoptotic response. This gives hTop1p a central role in cancer therapy. Recently, two artesunic acid derivatives (compounds c6 and c7) have been proposed as promising inhibitors of hTop1p with possible antitumor activity. We used several computational approaches to obtain in silico confirmations of the experimental data and to form a comprehensive dynamic description of the ligand-receptor system. We performed molecular docking analyses to verify the ability of the two new derivatives to access the enzyme-DNA interface, and a classical molecular dynamics simulation was performed to assess the capacity of the two compounds to maintain a stable binding pose over time. Finally, we calculated the noncovalent interactions between the two new derivatives and the hTop1p receptor in order to propose a possible inhibitory mechanism like that adopted by CPT.
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Affiliation(s)
- Francesco Madeddu
- Department of Computer Science, “Sapienza” University of Rome, Piazzale Aldo Moro, 5, 00185 Rome, Italy
| | - Jessica Di Martino
- Department of Ecological and Biological Sciences, Tuscia University, Largo dell’Università snc, 01100 Viterbo, Italy
| | - Michele Pieroni
- Department of Computer Science, “Sapienza” University of Rome, Piazzale Aldo Moro, 5, 00185 Rome, Italy
| | - Davide Del Buono
- Department of Ecological and Biological Sciences, Tuscia University, Largo dell’Università snc, 01100 Viterbo, Italy
| | - Paolo Bottoni
- Department of Computer Science, “Sapienza” University of Rome, Piazzale Aldo Moro, 5, 00185 Rome, Italy
| | - Lorenzo Botta
- Department of Ecological and Biological Sciences, Tuscia University, Largo dell’Università snc, 01100 Viterbo, Italy
| | - Tiziana Castrignanò
- Department of Ecological and Biological Sciences, Tuscia University, Largo dell’Università snc, 01100 Viterbo, Italy
- Correspondence:
| | - Raffaele Saladino
- Department of Ecological and Biological Sciences, Tuscia University, Largo dell’Università snc, 01100 Viterbo, Italy
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5
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Singh P, Choudhury S, Sharma VK, Mitra S, Mukhopadhyay R, Das R, Pal SK. Modulation of Solvation and Molecular Recognition of a Lipid Bilayer under Dynamical Phase Transition. Chemphyschem 2018; 19:2709-2716. [PMID: 30030893 DOI: 10.1002/cphc.201800522] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Indexed: 11/09/2022]
Abstract
It is well accepted in contemporary biology that an ∼30 Å thick lipid bilayer film around living cells is a matter of life and death as the film typically delimits the environments that serve as a crucial margin. The dynamic organization of lipid molecules both across the lipid bilayer and in the lateral dimension are known to be crucial for cellular transport and molecular recognition by important biological macromolecules. Here, we study dilute (20 mM) Dioctadecyldimethylammonium bromide (DODAB) vesicles at different temperatures in aqueous dispersion with well-defined phases namely liquid crystalline, gel and subgel. The spectroscopic studies on two fluorescent probes 8-anilino-1-naphthalene sulfonic acid ammonium salt (ANS) and Coumarin 500 (C500), former in the head group region of the lipid-water interface and later located deeper in the lipid bilayer follow dynamics (solvation and fluidity) of their local environments in the vesicles. Binding of an anti-tuberculosis drug rifampicin has also been studied employing Förster resonance energy transfer (FRET) technique. The molecular insight concerning the effect of dynamical organization of the lipid molecules on the local dynamics of aqueous environments in different phases leading to molecular recognition becomes evident in our study.
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Affiliation(s)
- Priya Singh
- Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, SaltLake, Kolkata, 700 106, India
| | - Susobhan Choudhury
- Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, SaltLake, Kolkata, 700 106, India
| | - V K Sharma
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - S Mitra
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - R Mukhopadhyay
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Ranjan Das
- Department of Chemistry, West Bengal State University, Barasat, Kolkata, 700126
| | - Samir Kumar Pal
- Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, SaltLake, Kolkata, 700 106, India
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6
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Affiliation(s)
- Giovanni Capranico
- Department
of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro
8/2, 40126 Bologna, Italy
| | - Jessica Marinello
- Department
of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro
8/2, 40126 Bologna, Italy
| | - Giovanni Chillemi
- SCAI
SuperComputing Applications and Innovation Department, Cineca, Via dei Tizii 6, 00185 Rome, Italy
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7
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Huang NL, Lin JH. Recovery of the poisoned topoisomerase II for DNA religation: coordinated motion of the cleavage core revealed with the microsecond atomistic simulation. Nucleic Acids Res 2015; 43:6772-86. [PMID: 26150421 PMCID: PMC4538842 DOI: 10.1093/nar/gkv672] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 06/19/2015] [Indexed: 01/24/2023] Open
Abstract
Type II topoisomerases resolve topological problems of DNA double helices by passing one duplex through the reversible double-stranded break they generated on another duplex. Despite the wealth of information in the cleaving operation, molecular understanding of the enzymatic DNA ligation remains elusive. Topoisomerase poisons are widely used in anti-cancer and anti-bacterial therapy and have been employed to entrap the intermediates of topoisomerase IIβ with religatable DNA substrate. We removed drug molecules from the structure and conducted molecular dynamics simulations to investigate the enzyme-mediated DNA religation. The drug-unbound intermediate displayed transitions toward the resealing-compliant configuration: closing distance between the cleaved DNA termini, B-to-A transformation of the double helix, and restoration of the metal-binding motif. By mapping the contact configurations and the correlated motions between enzyme and DNA, we identified the indispensable role of the linker preceding winged helix domain (WHD) in coordinating the movements of TOPRIM, the nucleotide-binding motifs, and the bound DNA substrate during gate closure. We observed a nearly vectorial transition in the recovery of the enzyme and identified the previously uncharacterized roles of Asn508 and Arg677 in DNA rejoining. Our findings delineate the dynamic mechanism of the DNA religation conducted by type II topoisomerases.
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Affiliation(s)
- Nan-Lan Huang
- Research Center for Applied Sciences, Academia Sinica, Nangang, Taipei 11529, Taiwan
| | - Jung-Hsin Lin
- Research Center for Applied Sciences, Academia Sinica, Nangang, Taipei 11529, Taiwan Institute of Biomedical Sciences, Academia Sinica, Nangang, Taipei 11529, Taiwan School of Pharmacy, National Taiwan University, Taipei 10050, Taiwan
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8
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Arnò B, D’Annessa I, Tesauro C, Zuccaro L, Ottaviani A, Knudsen B, Fiorani P, Desideri A. Replacement of the human topoisomerase linker domain with the plasmodial counterpart renders the enzyme camptothecin resistant. PLoS One 2013; 8:e68404. [PMID: 23844196 PMCID: PMC3699648 DOI: 10.1371/journal.pone.0068404] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 05/29/2013] [Indexed: 12/17/2022] Open
Abstract
A human/plasmodial hybrid enzyme, generated by swapping the human topoisomerase IB linker domain with the corresponding domain of the Plasmodium falciparum enzyme, has been produced and characterized. The hybrid enzyme displays a relaxation activity comparable to the human enzyme, but it is characterized by a much faster religation rate. The hybrid enzyme is also camptothecin resistant. A 3D structure of the hybrid enzyme has been built and its structural-dynamical properties have been analyzed by molecular dynamics simulation. The analysis indicates that the swapped plasmodial linker samples a conformational space much larger than the corresponding domain in the human enzyme. The large linker conformational variability is then linked to important functional properties such as an increased religation rate and a low drug reactivity, demonstrating that the linker domain has a crucial role in the modulation of the topoisomerase IB activity.
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Affiliation(s)
- Barbara Arnò
- Department of Biology and Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB), University of Rome Tor Vergata, Rome, Italy
| | - Ilda D’Annessa
- Department of Biology and Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB), University of Rome Tor Vergata, Rome, Italy
| | - Cinzia Tesauro
- Department of Biology and Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB), University of Rome Tor Vergata, Rome, Italy
| | - Laura Zuccaro
- Department of Biology and Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB), University of Rome Tor Vergata, Rome, Italy
| | - Alessio Ottaviani
- Department of Biology and Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB), University of Rome Tor Vergata, Rome, Italy
| | - Birgitta Knudsen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Paola Fiorani
- Institute of Translational Pharmacology, National Research Council, CNR, Rome, Italy
| | - Alessandro Desideri
- Department of Biology and Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB), University of Rome Tor Vergata, Rome, Italy
- * E-mail:
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9
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Fiorani P, Tesauro C, Mancini G, Chillemi G, D'Annessa I, Graziani G, Tentori L, Muzi A, Desideri A. Evidence of the crucial role of the linker domain on the catalytic activity of human topoisomerase I by experimental and simulative characterization of the Lys681Ala mutant. Nucleic Acids Res 2009; 37:6849-58. [PMID: 19767617 PMCID: PMC2777420 DOI: 10.1093/nar/gkp669] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The functional and structural-dynamical properties of the Lys681Ala mutation in the human topoisomerase IB linker domain have been investigated by catalytic assays and molecular dynamics simulation. The mutant is characterized by a comparable cleavage and a strongly reduced religation rate when compared to the wild type protein. The mutant also displays perturbed linker dynamics, as shown by analysis of the principal components of the motion, and a reduced electrostatic interaction with DNA. Inspection of the inter atomic distances in proximity of the active site shows that in the mutant the distance between the amino group of Lys532 side chain and the 5′ OH of the scissile phosphate is longer than the wild type enzyme, providing an atomic explanation for the reduced religation rate of the mutant. Taken together these results indicate the existence of a long range communication between the linker domain and the active site region and points out the crucial role of the linker in the modulation of the catalytic activity.
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Affiliation(s)
- Paola Fiorani
- Department of Biology, University of Rome Tor Vergata, CNR National Research Council, INFM National Institute for the Physics of Matter, Rome 00133, Italy
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10
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Sanna N, Chillemi G, Gontrani L, Grandi A, Mancini G, Castelli S, Zagotto G, Zazza C, Barone V, Desideri A. UV-vis spectra of the anticancer camptothecin family drugs in aqueous solution: specific spectroscopic signatures unraveled by a combined computational and experimental study. J Phys Chem B 2009; 113:5369-75. [PMID: 19334673 DOI: 10.1021/jp809801y] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ultraviolet-visible absorption spectrum of camptothecin (CPT) has been been recorded in aqueous solution at pH 5.3, where the equilibrium among the different CPT forms is shifted toward the lactonic one. Time-dependent density functional theory (TD-DFT) computations lead to a remarkable reproduction of the experimental spectrum only upon addition of explicit water molecules in interaction with specific moieties of the camptothecin molecule. Molecular dynamics (MD) simulations enforcing boundary periodic conditions for CPT embedded with 865 water molecules, with a force field derived from DFT computations, show that the experimental spectrum is due to the contributions of CPT molecules with different solvation patterns. A similar solvent effect is observed for several CPT derivatives, including the clinically relevant SN-38 and topotecan drugs. The quantitative agreement between TD-DFT/MD computations and experimental data allow us to identify specific spectroscopic signatures diagnostic of the drug environment and to develop procedures that can be used to monitor the drug-DNA/protein interaction.
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Affiliation(s)
- Nico Sanna
- CASPUR, Consortium for Supercomputing in Research, Via dei Tizii 6, 00185 Roma, Italy.
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11
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Aquaporins are multifunctional water and solute transporters highly divergent in living organisms. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1788:1213-28. [DOI: 10.1016/j.bbamem.2009.03.009] [Citation(s) in RCA: 310] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2008] [Revised: 03/09/2009] [Accepted: 03/11/2009] [Indexed: 01/09/2023]
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12
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Szklarczyk O, Staroń K, Cieplak M. Native state dynamics and mechanical properties of human topoisomerase I within a structure-based coarse-grained model. Proteins 2009; 77:420-31. [DOI: 10.1002/prot.22450] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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13
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Chillemi G, Bruselles A, Fiorani P, Bueno S, Desideri A. The open state of human topoisomerase I as probed by molecular dynamics simulation. Nucleic Acids Res 2007; 35:3032-8. [PMID: 17439970 PMCID: PMC1888835 DOI: 10.1093/nar/gkm199] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The open state of human topoisomerase I has been probed by molecular dynamics simulation, starting from the coordinates of the closed structure of the protein complexed with DNA, after elimination of the 22-bp DNA duplex oligonucleotide. A repulsion force between the two lips of the protein has been introduced for a short time to induce destabilization of the local minimum, after which an unperturbed simulation has been carried out for 10 ns. The simulation shows that the protein undergoes a large conformational change due to rearrangements in the orientation of the protein domains, which however move as a coherent unit, fully maintaining their secondary and tertiary structures. Despite movements between the domains as large as 80-90 A, the catalytic pentad remains preassembled, the largest deviation of the active site backbone atoms from the starting crystallographic structure being only 1.7 A. Electrostatic calculation of the open protein structure shows that the protein displays a vast positive region with the active site residues located nearly at its center, in a conformation perfectly suited to interact with the negatively charged supercoiled DNA substrate.
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Affiliation(s)
- Giovanni Chillemi
- CASPUR Inter-University Consortium for the Application of Super-Computing for Universities and Research, Via dei Tizii 6, Rome 00185, Italy and INFM National Institute for the Physics of Matter, interdisciplinary Centre of Bioinformatics and Biostatistics and Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, Rome 00133, Italy
| | - Alessandro Bruselles
- CASPUR Inter-University Consortium for the Application of Super-Computing for Universities and Research, Via dei Tizii 6, Rome 00185, Italy and INFM National Institute for the Physics of Matter, interdisciplinary Centre of Bioinformatics and Biostatistics and Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, Rome 00133, Italy
| | - Paola Fiorani
- CASPUR Inter-University Consortium for the Application of Super-Computing for Universities and Research, Via dei Tizii 6, Rome 00185, Italy and INFM National Institute for the Physics of Matter, interdisciplinary Centre of Bioinformatics and Biostatistics and Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, Rome 00133, Italy
| | - Susana Bueno
- CASPUR Inter-University Consortium for the Application of Super-Computing for Universities and Research, Via dei Tizii 6, Rome 00185, Italy and INFM National Institute for the Physics of Matter, interdisciplinary Centre of Bioinformatics and Biostatistics and Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, Rome 00133, Italy
| | - Alessandro Desideri
- CASPUR Inter-University Consortium for the Application of Super-Computing for Universities and Research, Via dei Tizii 6, Rome 00185, Italy and INFM National Institute for the Physics of Matter, interdisciplinary Centre of Bioinformatics and Biostatistics and Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, Rome 00133, Italy
- *To whom correspondence should be addressed. +39 0672594376+39 062022798
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14
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Punchihewa C, Dai J, Carver M, Yang D. Human topoisomerase I C-terminal domain fragment containing the active site tyrosine is a molten globule: implication for the formation of competent productive complex. J Struct Biol 2007; 159:111-21. [PMID: 17434318 PMCID: PMC1993844 DOI: 10.1016/j.jsb.2007.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2006] [Revised: 02/27/2007] [Accepted: 03/02/2007] [Indexed: 11/26/2022]
Abstract
Human topoisomerase I (topo I) is an essential cellular enzyme that relaxes DNA supercoiling. The 6.3 kDa C-terminal domain of topo I contains the active site tyrosine (Tyr723) but lacks enzymatic activity by itself. Activity can be fully reconstituted when the C-terminal domain is associated with the 56 kDa core domain. Even though several crystal structures of topo I/DNA complexes are available, crystal structures of the free topo I protein or its individual domain fragments have been difficult to obtain. In this report we analyze the human topo I C-terminal domain structure using a variety of biophysical methods. Our results indicate that this fragment protein (topo6.3) appears to be in a molten globule state. It appears to have a native-like tertiary fold that contains a large population of alpha-helix secondary structure and extensive surface hydrophobic regions. Topo6.3 is known to be readily activated with the association of the topo I core domain, and the molten globule state of topo6.3 is likely to be an energy-favorable conformation for the free topo I C-terminal domain protein. The structural fluctuation and plasticity may represent an efficient mechanism in the topo I functional pathway, where the flexibility aids in the complementary association with the core domain and in the formation of a fully productive topo I complex.
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Affiliation(s)
| | - Jixun Dai
- College of Pharmacy, The University of Arizona, 1703 E. Mabel St, Tucson, AZ 85721
| | - Megan Carver
- College of Pharmacy, The University of Arizona, 1703 E. Mabel St, Tucson, AZ 85721
| | - Danzhou Yang
- College of Pharmacy, The University of Arizona, 1703 E. Mabel St, Tucson, AZ 85721
- Arizona Cancer Center, 1515 N. Campbell Avenue, Tucson, AZ 85724
- To whom correspondence should be addressed. Telephone: (520) 626-5969, Fax: (520) 626-6988,
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15
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Fiorani P, Chillemi G, Losasso C, Castelli S, Desideri A. The different cleavage DNA sequence specificity explains the camptothecin resistance of the human topoisomerase I Glu418Lys mutant. Nucleic Acids Res 2006; 34:5093-100. [PMID: 16990249 PMCID: PMC1636438 DOI: 10.1093/nar/gkl670] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Yeast cells expressing the Glu418Lys human topoisomerase I mutant display a camptothecin resistance that slowly decreases as a function of time. Molecular characterization of the single steps of the catalytic cycle of the purified mutant indicates that it has a relaxation activity identical to the wild-type protein but a different DNA sequence specificity for the cleavage sites when compared to the wild-type enzyme, as assayed on several substrates. In particular the mutant has a low specificity for CPT sensitive cleavable sites. In fact, the mutant has, at variance of the wild-type enzyme, a reduced preference for cleavage sites having a thymine base in position −1 of the scissile strand. This preference, together with the strict requirement for a thymine base in position −1 for an efficient camptothecin binding, explains the temporary camptothecin resistance of the yeast cell expressing the mutant and points out the importance of the DNA sequence in the binding of the camptothecin drug.
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Affiliation(s)
- Paola Fiorani
- CNR National Research Council, University of Rome Tor VergataVia Della Ricerca Scientifica, Rome 00133, Italy
- INFM National Institute for the Physics of Matter, University of Rome Tor VergataVia Della Ricerca Scientifica, Rome 00133, Italy
- Department of Biology, University of Rome Tor VergataVia Della Ricerca Scientifica, Rome 00133, Italy
| | - Giovanni Chillemi
- CASPUR Interuniversities Consortium for Supercomputing Applications, Via dei Tizii 6bRome 00185, Italy
| | - Carmen Losasso
- Department of Biology, University of PaduaVia U. Bassi 58/B, Padua 35131, Italy
| | - Silvia Castelli
- CNR National Research Council, University of Rome Tor VergataVia Della Ricerca Scientifica, Rome 00133, Italy
- INFM National Institute for the Physics of Matter, University of Rome Tor VergataVia Della Ricerca Scientifica, Rome 00133, Italy
- Department of Biology, University of Rome Tor VergataVia Della Ricerca Scientifica, Rome 00133, Italy
| | - Alessandro Desideri
- CNR National Research Council, University of Rome Tor VergataVia Della Ricerca Scientifica, Rome 00133, Italy
- INFM National Institute for the Physics of Matter, University of Rome Tor VergataVia Della Ricerca Scientifica, Rome 00133, Italy
- Department of Biology, University of Rome Tor VergataVia Della Ricerca Scientifica, Rome 00133, Italy
- To whom correspondence should be addressed. Tel: +39 0672594376; Fax: +39 0672594326;
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16
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Sari L, Andricioaei I. Rotation of DNA around intact strand in human topoisomerase I implies distinct mechanisms for positive and negative supercoil relaxation. Nucleic Acids Res 2005; 33:6621-34. [PMID: 16314322 PMCID: PMC1298917 DOI: 10.1093/nar/gki935] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Topoisomerases are enzymes of quintessence to the upkeep of superhelical DNA, and are vital for replication, transcription and recombination. An atomic-resolution model for human topoisomerase I in covalent complex with DNA is simulated using molecular dynamics with external potentials that mimic torque and bias the DNA duplex downstream of a single-strand cut to rotate around the intact strand, according to the prevailing enzymatic mechanism. The simulations reveal the first dynamical picture of how topoisomerase accommodates large-scale motion of DNA as it changes its supercoiling state, and indicate that relaxation of positive and negative supercoils are fundamentally different. To relax positive supercoils, two separate domains (the 'lips') of the protein open up by about 10-14 A, whereas to relax negative supercoils, a continuous loop connecting the upper and lower parts (and which was a hinge for opening the lips) stretches about 12 A while the lips remain unseparated. Normal mode analysis is additionally used to characterize the functional flexibility of the protein. Remarkably, the same combination of low-frequency eigenvectors exhibit the dominant contribution for both rotation mechanisms through a see-saw motion. The simulated mechanisms suggest mutations to control the relaxation of either type of supercoiling selectively and advance a hypothesis for the debated role of the N-terminal domain in supercoil relaxation.
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Affiliation(s)
| | - Ioan Andricioaei
- To whom correspondence should be addressed. Tel: +1 734 763 8013; Fax: +1 734 615 6553;
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17
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Sanna N, Chillemi G, Grandi A, Castelli S, Desideri A, Barone V. New Hints on the pH-Driven Tautomeric Equilibria of the Topotecan Anticancer Drug in Aqueous Solutions from an Integrated Spectroscopic and Quantum-Mechanical Approach. J Am Chem Soc 2005; 127:15429-36. [PMID: 16262406 DOI: 10.1021/ja052637u] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The equilibria between the different forms of the topotecan anticancer drug have been studied at moderately acidic and physiological pH by an integrated computational tool rooted in the density functional theory and its time-dependent extension together with the polarizable continuum model. The results allow an unbiased selection between the different possible tautomeric forms and provide invaluable complements to experimental data. The ultraviolet-visible topotecan spectrum, recorded at moderately acidic pH, is accurately reproduced only by TD-DFT computations including solvent effects. Comparison of the experimental and calculated bands of the UV-vis spectrum at physiological pH indicates the presence of an equilibrium among different forms that is tuned by the microenvironment embedding the drug. The quantitative agreement between TD-DFT/PCM computations and experiments allows the identification of unequivocal spectroscopic signatures for different forms of topotecan.
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Affiliation(s)
- Nico Sanna
- CASPUR, Consortium for Supercomputing in Research, Via dei Tizii 6/b, 00185 Rome, Italy
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18
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Djuranovic D, Hartmann B. Molecular dynamics studies on free and bound targets of the bovine papillomavirus type I e2 protein: the protein binding effect on DNA and the recognition mechanism. Biophys J 2005; 89:2542-51. [PMID: 16055534 PMCID: PMC1366753 DOI: 10.1529/biophysj.104.057109] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2004] [Accepted: 06/08/2005] [Indexed: 12/24/2022] Open
Abstract
Molecular dynamics simulations of a total duration of 30 ns in explicit solvent were carried out on the BPV-1-E2 protein complexed to a high-affinity DNA target containing the two hydrogen-bonded ACCG.CGGT half-sites separated by the noncontacted ACGT sequence. The analysis of the trajectories focuses on the DNA structure and on the dynamics. The data are compared to those issued from recent simulations made on three free targets that recognize E2 with different affinities. E2 does not drastically perturb the mechanic properties of the free DNA: the structural relationships between the BI/BII backbone substates and some helical parameters are preserved in the complex despite a severe slowing down of the phosphate group motions. The structures of both free and bound half-sites are very close to each other although the conformational space explored by these regions is narrowed when they are contacted by the protein. The enhanced plasticity found in the best free target spacers, mainly manifested through the backbone motions, allows a clear overlap between several free and bound global DNA features such as the base displacement. Furthermore, this flexibility is preserved in the complex. Our results support the hypothesis that E2 takes advantage of free predistorted structures that may minimize the DNA deformation cost. In addition, we observe that E2 is far from totally stiffening the DNA, suggesting that the entropic penalty inherent in the complex formation could be limited.
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Affiliation(s)
- D Djuranovic
- Laboratoire de Biochimie Théorique, CNRS UPR 9080, Institut de Biologie Physico-chimique, Paris, France.
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19
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Kettmann V, Kost'álová D, Höltje HD. Human topoisomerase I poisoning: docking protoberberines into a structure-based binding site model. J Comput Aided Mol Des 2005; 18:785-96. [PMID: 16075310 DOI: 10.1007/s10822-004-7878-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2004] [Accepted: 12/14/2004] [Indexed: 10/25/2022]
Abstract
Using the X-ray crystal structure of the human topoisomerase I (top1) - DNA cleavable complex and the Sybyl software package, we have developed a general model for the ternary cleavable complex formed with four protoberberine alkaloids differing in the substitution on the terminal phenyl rings and covering a broad range of the top1-poisoning activities. This model has the drug intercalated with its planar chromophore between the -1 and +1 base pairs flanking the cleavage site, with the nonplanar portion pointing into the minor groove. The ternary complexes were geometry-optimized and relative interaction energies, computed by using the Tripos force field, were found to rank in correct order the biological potency of the compounds; in addition, the model is also consistent with the top1-poisoning inactivity of berberine, a major prototype of the protoberberine alkaloids. The model might serve as a rational basis for elaboration of the most active compound as a lead structure, in order to develop more potent top1 poisons as next generation anti-cancer drugs.
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Affiliation(s)
- Viktor Kettmann
- Department of Pharmaceutical Analysis and Nuclear Pharmacy, Faculty of Pharmacy, Comenius University, Bratislava, Slovakia.
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20
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Milev S, Bosshard HR, Jelesarov I. Enthalpic and Entropic Effects of Salt and Polyol Osmolytes on Site-Specific Protein−DNA Association: The Integrase Tn916−DNA Complex. Biochemistry 2004; 44:285-93. [PMID: 15628870 DOI: 10.1021/bi048907n] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The effect of low molecular-weight compounds on the equilibrium constant K(A) can be used to explore the energetics and molecular mechanism of protein-DNA interactions. Here we use the complex composed of the integrase Tn916 DNA-binding domain and its target DNA duplex to investigate the effects of salt and the nonionic osmolytes glycerol and sorbitol on sequence-specific protein-DNA association. Increasing Na(+) concentration from 0.12 to 0.32 M weakens the binding affinity by a factor of 20. The decrease of affinity is dominated by a large loss of binding enthalpy but only a small loss of binding entropy. This contrasts the concept that the salt-induced weakening of protein-DNA binding is mainly entropic. The large enthalpy loss is discussed in the light of recent views about the nature of the general salt effect. Addition of up to 2.5 M sorbitol and up to 3.3 M glycerol causes a slight increase of the binding affinity. However, both osmolytes lead to a large enthalpy gain and a similarly large entropy loss. This intriguing enthalpy-entropy compensation can be explained in part by an enthalpic chelate effect: The osmolyte tightens the structure of the protein-DNA complex whereby the formation of enthalpically favorable noncovalent interactions is promoted at the entropic cost of a more rigid complex. The results were obtained by isothermal titration calorimetry. They are supported by kinetic experiments showing that the rate of formation of the complex is reduced by salt, but the rate of complex dissociation is not. Glycerol and sorbitol reduce both rates in line with an only small effect on complex stability. This work clarifies the thermodynamic and kinetic response of a novel protein-DNA complex to increased salt and the presence of two common, nonionic osmolytes.
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Affiliation(s)
- Stoyan Milev
- Biochemisches Institut der Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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21
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Wadkins RM, Bearss D, Manikumar G, Wani MC, Wall ME, Von Hoff DD. Hydrophilic camptothecin analogs that form extremely stable cleavable complexes with DNA and topoisomerase I. Cancer Res 2004; 64:6679-83. [PMID: 15374984 DOI: 10.1158/0008-5472.can-04-1885] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Camptothecin (CPT) analogs that form more stable ternary complexes with DNA and topoisomerase I (termed cleavable complexes) show greater activity in their ability to inhibit tumor cell line growth in preclinical studies. Based on our earlier work, we hypothesized that analogs bearing hydrogen bonding moieties at the 7- through 10-position of CPT would result in more stable cleavable complexes. Consequently, we synthesized analogs with 7-mono-, 7-di-, and 7-trihydroxymethylaminomethyl groups. These analogs showed increasing cleavable complex stability as the number of hydroxyl groups was increased. The 7-trihydroxymethylaminomethyl analog of 10,11-methylenedioxycamptothecin (THMAM-MD) showed remarkable ternary complex stability with a half-life of 116 minutes. This is an order of magnitude more stable than any previously examined analog. Our in vitro analysis demonstrated that these analogs were all potent topoisomerase I poisons and could inhibit tumor cell growth in culture. We studied the effects of THMAM-MD in vivo in severe combined immunodeficient mice bearing HT-29 colon cancer and MiaPaCa-2 pancreatic cancer tumors. The THMAM-MD analog showed excellent, persisting activity in inhibiting tumor growth with both lines. Taken together, our results suggest that CPTs with hydrophilic, hydrogen-bonding groups at the 7-position hold the promise of excellent clinical activity.
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Affiliation(s)
- Randy M Wadkins
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, USA.
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22
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Chillemi G, Redinbo M, Bruselles A, Desideri A. Role of the linker domain and the 203-214 N-terminal residues in the human topoisomerase I DNA complex dynamics. Biophys J 2004; 87:4087-97. [PMID: 15347588 PMCID: PMC1304917 DOI: 10.1529/biophysj.104.044925] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The influence of the N-terminal residues 203-214 and the linker domain on motions in the human topoisomerase I-DNA complex has been investigated by comparing the molecular dynamics simulations of the system with (topo70) or without (topo58/6.3) these regions. Topo58/6.3 is found to fluctuate more than topo70, indicating that the presence of the N-terminal residues and the linker domain dampen the core and C-terminal fluctuations. The simulations also show that residues 203-207 and the linker domain participate in a network of correlated movements with key regions of the enzyme, involved in the human topoisomerase I catalytic cycle, providing a structural-dynamical explanation for the better DNA relaxation activity of topo70 when compared to topo58/6.3. The data have been examined in relation to a wealth of biochemical, site-directed mutagenesis and crystallographic data on human topoisomerase I. The simulations finally show the occurrence of a network of direct and water mediated hydrogen bonds in the proximity of the active site, and the presence of a water molecule in the appropriate position to accept a proton from the catalytic Tyr-723 residue, suggesting that water molecules have an important role in the stabilization and function of this enzyme.
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Affiliation(s)
- G Chillemi
- CASPUR, Consortium for Supercomputing in Research, Via dei Tizii 6b, Rome, Italy
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23
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Fiorani P, Bruselles A, Falconi M, Chillemi G, Desideri A, Benedetti P. Single mutation in the linker domain confers protein flexibility and camptothecin resistance to human topoisomerase I. J Biol Chem 2003; 278:43268-75. [PMID: 12904303 DOI: 10.1074/jbc.m303899200] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA topoisomerase I relaxes supercoiled DNA by the formation of a covalent intermediate in which the active-site tyrosine is transiently bound to the cleaved DNA strand. The antineoplastic agent camptothecin specifically targets DNA topoisomerase I, and several mutations have been isolated that render the enzyme camptothecin-resistant. The catalytic and structural dynamical properties of a human DNA topoisomerase I mutant in which Ala-653 in the linker domain was mutated into Pro have been investigated. The mutant is resistant to camptothecin and in the absence of the drug displays a cleavage-religation equilibrium strongly shifted toward religation. The shift is mainly because of an increase in the religation rate relative to the wild type enzyme, indicating that the unperturbed linker is involved in slowing religation. Molecular dynamics simulation indicates that the Ala to Pro mutation increases the linker flexibility allowing it to sample a wider conformational space. The increase in religation rate of the mutant, explained by means of the enhanced linker flexibility, provides an explanation for the mutant camptothecin resistance.
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Affiliation(s)
- Paola Fiorani
- Department of Biology, University of Padua, Via U. Bassi 58/B, Padua 35131, Italy
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24
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Chillemi G, Fiorani P, Benedetti P, Desideri A. Protein concerted motions in the DNA-human topoisomerase I complex. Nucleic Acids Res 2003; 31:1525-35. [PMID: 12595561 PMCID: PMC149835 DOI: 10.1093/nar/gkg242] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The collective motions of the core and C-terminal domains of human topoisomerase I (topo I) have been analysed by molecular dynamics simulation of the protein in covalent complex with a 22 bp DNA duplex. The analysis evidenced a great number of correlated movements of core subdomain I and II residues, and a central role for helix 5 in the protein-DNA communication, in particular with the scissile strand downstream of the cleavage site. The flow of information between these core subdomains and DNA suggests that subdomains I and II play an essential role in the DNA relaxation process. In core subdomain III the majority of DNA contacting residues do not communicate with protein regions far from DNA, suggesting that they have a structural role. However, selected core subdomain III residues, involved in the orientation of the active site region, show correlated movements with residues distant from DNA, indicating that the information concerning the catalytic event is also transmitted. The flexibility of two loops formed by residues 519-520 and 580-584 seems indispensable to the dynamic participation of core subdomain III to the DNA cleavage and religation steps. The motion of specific residues has also been found to explain the effect of single point mutations that make topo I resistant to the anticancer drug camptothecin.
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Affiliation(s)
- Giovanni Chillemi
- CASPUR, c/o University of Rome La Sapienza, P. le Aldo Moro 5, 00185 Rome, Italy
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25
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Bailly C. Homocamptothecins: potent topoisomerase I inhibitors and promising anticancer drugs. Crit Rev Oncol Hematol 2003; 45:91-108. [PMID: 12482574 DOI: 10.1016/s1040-8428(02)00090-2] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Homocamptothecins (hCPTs) represent a new generation of antitumor agents targeting DNA topoisomerase I. The expanded seven-membered lactone E-ring that characterizes hCPTs enhances the plasma stability of the drug and reinforces the inhibition of topoisomerase I compared with conventional six-membered CPTs. hCPTs are more efficient than the CPTs at promoting cleavage at T/G sites and induce additional cleavage at C/G sites. Compound BN80765 and its difluoro analogue diflomotecan (DN80915) are potent cytotoxic agents and efficiently induce apoptosis in tumor cells. They display strong antiproliferative activities against specific tumor types. Diflomotecan is remarkably efficient at inhibiting the growth of human colon cancer cells in vivo and, administered orally, it also shows superior activities against human prostate cancers compared with the benchmark products topotecan (TPT) and irinotecan (IRT). Diflomotecan has entered phase I clinical testing and antitumor activity has been observed in patients. This 9,10-difluoro-hCPTs derivative is one of the most promising new members of the 'tecan' family. This review summarizes the recent discoveries in the topoisomerase I field and presents the different camptothecin (CPT) analogues currently evaluated as anticancer agents. The specific properties of hCPTs are highlighted.
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Affiliation(s)
- Christian Bailly
- INSERM UR524, Institut de Recherches sur le Cancer, Place de Verdun, F-59045 Lille, France.
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26
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Castrignanò T, Chillemi G, Varani G, Desideri A. Molecular dynamics simulation of the RNA complex of a double-stranded RNA-binding domain reveals dynamic features of the intermolecular interface and its hydration. Biophys J 2002; 83:3542-52. [PMID: 12496121 PMCID: PMC1302429 DOI: 10.1016/s0006-3495(02)75354-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The interaction between double-stranded RNA (dsRNA) and the third double-stranded domain (dsRBD) from Drosophila Staufen protein represents a paradigm to understand how the dsRBD protein family, one of the most common RNA-binding protein units, binds dsRNA. The nuclear magnetic resonance (NMR) structure of this complex and the x-ray structure of another family member revealed the stereochemical basis for recognition, but also raised new questions. Although the crystallographic studies revealed a highly ordered interface containing numerous water-mediated contacts, NMR suggested extensive residual motion at the interface. To address how interfacial motion contributes to molecular recognition in the dsRBD-dsRNA system, we conducted a 2-ns molecular dynamics simulation of the complex derived from Staufen protein and of the separate protein and RNA components. The results support the observation that a high degree of conformational flexibility is retained upon complex formation and that this involves interfacial residues that are critical for dsRBD-dsRNA binding. The structural origin of this residual flexibility is revealed by the analysis of the trajectory of motion. Individual basic side chains switch continuously from one RNA polar group to another with a residence time seldom exceeding 100 ps, while retaining favorable interaction with RNA throughout much of the simulation. Short-lived water molecules mediate some of these interactions for a large fraction of the trajectory studied here. This result indicates that water molecules are not statically associated with the interface, but continuously exchange with the bulk solvent on a 1-10-ps time scale. This work provides new insight into dsRBD-dsRNA recognition and builds upon a growing body of evidence, suggesting that short-lived dynamic interactions play important roles in protein-nucleic acid interactions.
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Affiliation(s)
- Tiziana Castrignanò
- Consorzio interuniversitario per le Applicazioni di Supercalculo per Università e Ricerca, University of Rome La Sapienza, 00185 Rome, Italy
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