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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
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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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2
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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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3
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Nagy PR, Kállay M. Optimization of the linear-scaling local natural orbital CCSD(T) method: Redundancy-free triples correction using Laplace transform. J Chem Phys 2017; 146:214106. [PMID: 28576082 PMCID: PMC5453808 DOI: 10.1063/1.4984322] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 05/05/2017] [Indexed: 01/30/2023] Open
Abstract
An improved algorithm is presented for the evaluation of the (T) correction as a part of our local natural orbital (LNO) coupled-cluster singles and doubles with perturbative triples [LNO-CCSD(T)] scheme [Z. Rolik et al., J. Chem. Phys. 139, 094105 (2013)]. The new algorithm is an order of magnitude faster than our previous one and removes the bottleneck related to the calculation of the (T) contribution. First, a numerical Laplace transformed expression for the (T) fragment energy is introduced, which requires on average 3 to 4 times fewer floating point operations with negligible compromise in accuracy eliminating the redundancy among the evaluated triples amplitudes. Second, an additional speedup factor of 3 is achieved by the optimization of our canonical (T) algorithm, which is also executed in the local case. These developments can also be integrated into canonical as well as alternative fragmentation-based local CCSD(T) approaches with minor modifications. As it is demonstrated by our benchmark calculations, the evaluation of the new Laplace transformed (T) correction can always be performed if the preceding CCSD iterations are feasible, and the new scheme enables the computation of LNO-CCSD(T) correlation energies with at least triple-zeta quality basis sets for realistic three-dimensional molecules with more than 600 atoms and 12 000 basis functions in a matter of days on a single processor.
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Affiliation(s)
- Péter R Nagy
- MTA-BME Lendület Quantum Chemistry Research Group, Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
| | - Mihály Kállay
- MTA-BME Lendület Quantum Chemistry Research Group, Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest, Hungary
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4
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Konieczny JK, Sokalski WA. Universal short-range ab initio atom–atom potentials for interaction energy contributions with an optimal repulsion functional form. J Mol Model 2015; 21:197. [DOI: 10.1007/s00894-015-2729-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 06/08/2015] [Indexed: 11/28/2022]
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5
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Giedroyć-Piasecka W, Dyguda-Kazimierowicz E, Beker W, Mor M, Lodola A, Sokalski WA. Physical Nature of Fatty Acid Amide Hydrolase Interactions with Its Inhibitors: Testing a Simple Nonempirical Scoring Model. J Phys Chem B 2014; 118:14727-36. [PMID: 25420234 DOI: 10.1021/jp5059287] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Fatty acid amide hydrolase (FAAH) is an enzyme responsible for the deactivating hydrolysis of fatty acid ethanolamide neuromodulators. FAAH inhibitors have gained considerable interest due to their possible application in the treatment of anxiety, inflammation, and pain. In the context of inhibitor design, the availability of reliable computational tools for predicting binding affinity is still a challenging task, and it is now well understood that empirical scoring functions have several limitations that in principle could be overcome by quantum mechanics. Herein, systematic ab initio analyses of FAAH interactions with a series of inhibitors belonging to the class of the N-alkylcarbamic acid aryl esters have been performed. In contrast to our earlier studies of other classes of enzyme-inhibitor complexes, reasonable correlation with experimental results required us to consider correlation effects along with electrostatic term. Therefore, the simplest comprehensive nonempirical model allowing for qualitative predictions of binding affinities for FAAH ligands consists of electrostatic multipole and second-order dispersion terms. Such a model has been validated against the relative stabilities of the benchmark S66 set of biomolecular complexes. As it does not involve parameters fitted to experimentally derived data, this model offers a unique opportunity for generally applicable inhibitor design and virtual screening.
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Affiliation(s)
| | | | - Wiktor Beker
- Department of Chemistry, Wrocław University of Technology , Wrocław, Poland
| | - Marco Mor
- Pharmacy Department, Università di Parma , Parma, Italy
| | | | - W Andrzej Sokalski
- Department of Chemistry, Wrocław University of Technology , Wrocław, Poland
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6
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Fresch B, Remacle F. Atomistic account of structural and dynamical changes induced by small binders in the double helix of a short DNA. Phys Chem Chem Phys 2014; 16:14070-82. [PMID: 24902052 DOI: 10.1039/c4cp01561d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nucleic acids are flexible molecules and their dynamical properties play a key role in molecular recognition events. Small binders interacting with DNA fragments induce both structural and dynamical changes in the double helix. We study the dynamics of a DNA dodecamer and of its complexes with Hoechst 33258, which is a minor groove binder, and with the ethidium cation, which is an intercalator, by molecular dynamics simulation. The thermodynamics of DNA-drug interaction is evaluated in connection with the structure and the dynamics of the resulting complexes. We identify and characterize the relevant changes in the configurational distribution of the DNA helix and relate them to the corresponding entropic contributions to the binding free energy. The binder Hoechst locks the breathing motion of the minor groove inducing a reduction of the configurational entropy of the helix, which amounts to 20 kcal mol(-1). In contrast, intercalations with the ethidium cation enhance the flexibility of the double helix. We show that the balance between the energy required to deform the helix for the intercalation and the gain in configurational entropy is the origin of cooperativity in the binding of a second ethidium and of anti-cooperativity in the binding of a third one. The results of our study provide an understanding of the relation between structure, dynamics and energetics in the interaction between DNA fragments and small binders, highlighting the role of dynamical changes and consequent variation of the configurational entropy of the DNA double helix for both types of binders.
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Affiliation(s)
- Barbara Fresch
- Department of Chemistry, B6c, University of Liege, B4000 Liege, Belgium.
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7
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Zawada A, Góra RW, Mikołajczyk MM, Bartkowiak W. On the Calculations of Interaction Energies and Induced Electric Properties within the Polarizable Continuum Model. J Phys Chem A 2012; 116:4409-16. [DOI: 10.1021/jp3016613] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Agnieszka Zawada
- Theoretical Chemistry Group,
Institute of Physical and Theoretical Chemistry, Chemistry Department, Wrocław University of Technology, Wybrzeże
Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Robert W. Góra
- Theoretical Chemistry Group,
Institute of Physical and Theoretical Chemistry, Chemistry Department, Wrocław University of Technology, Wybrzeże
Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Mikołaj M. Mikołajczyk
- Theoretical Chemistry Group,
Institute of Physical and Theoretical Chemistry, Chemistry Department, Wrocław University of Technology, Wybrzeże
Wyspiańskiego 27, 50-370 Wrocław, Poland
- Department of Physical Chemistry,
Faculty of Pharmacy, Wrocław Medical University, pl. Nankiera 1, 50-140 Wrocław, Poland
| | - Wojciech Bartkowiak
- Theoretical Chemistry Group,
Institute of Physical and Theoretical Chemistry, Chemistry Department, Wrocław University of Technology, Wybrzeże
Wyspiańskiego 27, 50-370 Wrocław, Poland
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8
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Rutledge LR, Wetmore SD. A computational proposal for the experimentally observed discriminatory behavior of hypoxanthine, a weak universal nucleobase. Phys Chem Chem Phys 2012; 14:2743-53. [PMID: 22270716 DOI: 10.1039/c2cp23600a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A computational model composed of six nucleobases was used to investigate why hypoxanthine does not yield duplexes of equal stability when paired opposite each of the natural DNA nucleobases. The magnitudes of all nearest-neighbor interactions in a DNA helix were calculated, including hydrogen-bonding, intra- and interstrand stacking interactions, as well as 1-3 intrastrand stacking interactions. Although the stacking interactions in DNA relevant arrangements are significant and account for at least one third of the total stabilization energy in our nucleobase complexes, the trends in the magnitude of the stacking interactions cannot explain the relative experimental melting temperatures previously reported in the literature. Furthermore, although the total hydrogen-bonding interactions explain why hypoxanthine preferentially pairs with cytosine, the experimental trend for the remaining nucleobases (A, T, G) is not explained. In fact, the calculated pairing preference of hypoxanthine matches that determined experimentally only when the sum of all types of nearest-neighbor interactions is considered. This finding highlights a strong correlation between the relative magnitude of the total nucleobase-nucleobase interactions and measured melting temperatures for DNA strands containing hypoxanthine despite the potential role of other factors (including hydration, temperature, sugar-phosphate backbone). By considering a large range of sequence combinations, we reveal that the binding preference of hypoxanthine is strongly dependent on the nucleobase sequence, which may explain the varied ability of hypoxanthine to universally bind to the natural bases. As a result, we propose that future work should closely examine the interplay between the dominant nucleobase-nucleobase interactions and the overall strand stability to fully understand how sequence context affects the universal binding properties of modified bases and to aid the design of new molecules with ambiguous pairing properties.
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Affiliation(s)
- Lesley R Rutledge
- Department of Chemistry & Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
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