Molecular mechanism and binding free energy of doxorubicin intercalation in DNA

Jawad, Bahaa; Poudel, Lokendra; Podgornik, Rudolf; Steinmetz, Nicole F.; Ching, Wai -Yim

doi:10.1039/c8cp06776g

Title: Molecular mechanism and binding free energy of doxorubicin intercalation in DNA

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 ΔG_ele, ΔG_vDW, ΔG_polar, ΔG_non-polar, TΔS_total, ΔG_deform, ΔG_con, and ΔG_ion. 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 (ΔG_deform), the energy cost from translational and rotational entropic contributions (TΔS_tran+rot), the total electrostatic interactions (ΔG_polar-PB/GB + ΔG_ele) of incorporation, the intramolecular electrostatic interactions (ΔG_ele) and electrostatic polar solvation interactions (ΔG_polar-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 (ΔG_vDW), the non-polar solvation interaction (ΔG_non-polar), the vibrational entropic contribution (TΔS_vib), and the standard concentration dependent free energies of DOX (ΔG_con) and the ionic solution (ΔG_ion). Specifically, the van dermore »« less

Authors:

Jawad, Bahaa ^[1]; Poudel, Lokendra ^[2]; Podgornik, Rudolf ^[3]; Steinmetz, Nicole F. ^[4];

^[2]

Univ. of Missouri-Kansas City, Kansas City, MO (United States); Univ. of Technology, Baghdad (Iraq)
Univ. of Missouri-Kansas City, Kansas City, MO (United States)
Univ. of Chinese Academy of Sciences, Beijing (China); Chinese Academy of Sciences, Beijing (China)
Univ. of California-San Diego, La Jolla, CA (United States)

Publication Date:: 2019-01-18

Research Org.:: Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Univ. of California, San Diego, CA (United States)

Sponsoring Org.:: USDOE Office of Science (SC)

OSTI Identifier:: 1543801

Grant/Contract Number:: AC03-76SF00098

Resource Type:: Journal Article: Accepted Manuscript

Journal Name:: Physical Chemistry Chemical Physics. PCCP

Additional Journal Information:: Journal Volume: 21; Journal Issue: 7; Journal ID: ISSN 1463-9076

Publisher:: Royal Society of Chemistry

Country of Publication:: United States

Language:: English

Subject:: 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; Chemistry; Physics

Citation Formats


                    Jawad, Bahaa, Poudel, Lokendra, Podgornik, Rudolf, Steinmetz, Nicole F., and Ching, Wai -Yim. Molecular mechanism and binding free energy of doxorubicin intercalation in DNA.  United States: N. p., 2019. 
        Web.  doi:10.1039/c8cp06776g.

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                    Jawad, Bahaa, Poudel, Lokendra, Podgornik, Rudolf, Steinmetz, Nicole F., & Ching, Wai -Yim. Molecular mechanism and binding free energy of doxorubicin intercalation in DNA.  United States.  https://doi.org/10.1039/c8cp06776g

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                    Jawad, Bahaa, Poudel, Lokendra, Podgornik, Rudolf, Steinmetz, Nicole F., and Ching, Wai -Yim. 2019.  
        "Molecular mechanism and binding free energy of doxorubicin intercalation in DNA".  United States.  https://doi.org/10.1039/c8cp06776g.  https://www.osti.gov/servlets/purl/1543801.

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@article{osti_1543801,

  title        = {Molecular mechanism and binding free energy of doxorubicin intercalation in DNA},

  author       = {Jawad, Bahaa and Poudel, Lokendra and Podgornik, Rudolf and Steinmetz, Nicole F. and Ching, Wai -Yim},

  abstractNote = {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. Here, 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.},

  doi          = {10.1039/c8cp06776g},

  url          = {https://www.osti.gov/biblio/1543801},
  journal      = {Physical Chemistry Chemical Physics. PCCP},

  issn         = {1463-9076},

  number       = 7,

  volume       = 21,

  place        = {United States},

  year         = {2019},

  month        = {1}

}

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Studies on self-aggregation of anthracycline drugs by restrained molecular dynamics approach using nuclear magnetic resonance spectroscopy supported by absorption, fluorescence, diffusion ordered spectroscopy and mass spectrometry
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Agrawal, Prashansa; Barthwal, Sudhir Kumar; Barthwal, Ritu
European Journal of Medicinal Chemistry, Vol. 44, Issue 4
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Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking
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Hou, Tingjun; Wang, Junmei; Li, Youyong
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Panneerselvam, Suresh; Yesudhas, Dhanusha; Durai, Prasannavenkatesh
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Acta Biochimica Polonica, Vol. 47, Issue 1
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Intercalators. 1. Nature of Stacking Interactions between Intercalators (Ethidium, Daunomycin, Ellipticine, and 4‘,6‘-Diaminide-2-phenylindole) and DNA Base Pairs. Ab Initio Quantum Chemical, Density Functional Theory, and Empirical Potential Study [ J. Am. Chem. Soc. 2002 , 124 , 3366−3367].
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Works referencing / citing this record:

Ultrasensitive photoelectrochemical microRNA biosensor based on doxorubicin sensitized graphitic carbon nitride assisted by a target-activated enzyme-free DNA walker
journal, January 2019

Wang, Yanlin; Xia, Lingying; Wei, Chongyao
Chemical Communications, Vol. 55, Issue 87
https://doi.org/10.1039/c9cc06556c

Deciphering the Molecular Basis of Melatonin Protective Effects on Breast Cells Treated with Doxorubicin: TWIST1 a Transcription Factor Involved in EMT and Metastasis, a Novel Target of Melatonin
journal, July 2019

Menéndez-Menéndez, Javier; Hermida-Prado, Francisco; Granda-Díaz, Rocío
Cancers, Vol. 11, Issue 7
https://doi.org/10.3390/cancers11071011

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Title: Molecular mechanism and binding free energy of doxorubicin intercalation in DNA

Abstract

Citation Formats

Kinetics of the daunomycin-DNA interaction journal, January 1985

Intercalation of Daunomycin into Stacked DNA Base Pairs. DFT Study of an Anticancer Drug journal, August 2008

MMPBSA.py : An Efficient Program for End-State Free Energy Calculations journal, August 2012

Free energy calculation on base specificity of drug - DNA interactions: Application to daunomycin and acridine intercalation into DNA journal, March 1990

Kinetic studies of anthracycline-DNA interaction by fluorescence stopped flow confirm a complex association mechanism journal, January 1989

Intercalation of antitumor drug doxorubicin and its analogue by DNA duplex: Structural features and biological implications journal, May 2014

Rigorous Free Energy Calculations in Structure-Based Drug Design journal, July 2010

pH-controlled doxorubicin anticancer loading and release from carbon nanotube noncovalently modified by chitosan: MD simulations journal, November 2016

Interactions between an anthracycline antibiotic and DNA: molecular structure of daunomycin complexed to d(CpGpTpApCpG) at 1.2-.ANG. resolution journal, February 1987

Unravelling Hot Spots: a comprehensive computational mutagenesis study journal, July 2006

Analysis of cooperativity and ion effects in the interaction of quinacrine with DNA journal, December 1979

A review of methods for the calculation of solution free energies and the modelling of systems in solution journal, January 2015

Molecular Mechanism of MBX2319 Inhibition of Escherichia coli AcrB Multidrug Efflux Pump and Comparison with Other Inhibitors journal, August 2014

Studies on interaction of anthracycline antibiotics and deoxyribonucleic acid: equilibrium binding studies on the interaction of daunomycin with deoxyribonucleic acid journal, August 1982

Accurate Estimation of the Standard Binding Free Energy of Netropsin with DNA journal, January 2018

Energetics of drug–DNA interactions journal, January 1997

Restrained molecular dynamics studies on complex of adriamycin with DNA hexamer sequence d-CGATCG journal, July 2005

A Computational Model for Anthracycline Binding to DNA: Tuning Groove-Binding Intercalators for Specific Sequences journal, March 2004

Sequence-selective DNA recognition by synthetic ligands journal, January 1991

Energetics of intercalation specificity. I. Backbone unwinding journal, May 1979

Predicted mode of intercalation of doxorubicin with dinucleotide dimers journal, July 1980

Early stage intercalation of doxorubicin to DNA fragments observed in molecular dynamics binding simulations journal, September 2012

Free Energy Simulations journal, December 1986

Assessing the Performance of MM/PBSA and MM/GBSA Methods. 3. The Impact of Force Fields and Ligand Charge Models journal, July 2013

Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches journal, January 2018

Doxorubicin as a Molecular Nanotheranostic Agent: Effect of Doxorubicin Encapsulation in Micelles or Nanoemulsions on the Ultrasound-Mediated Intracellular Delivery and Nuclear Trafficking journal, September 2010

The intercalation of DNA double helices with doxorubicin and nagalomycin journal, July 2007

Nanopore Single-Molecule Analysis of DNA–Doxorubicin Interactions journal, December 2014

Conformational diversity of anthracycline anticancer antibiotics: A density functional theory calculation journal, July 2010

Electronic Structure and Partial Charge Distribution of Doxorubicin in Different Molecular Environments journal, February 2015

The statistical-thermodynamic basis for computation of binding affinities: a critical review journal, March 1997

Free Energy Calculations by the Molecular Mechanics Poisson−Boltzmann Surface Area Method journal, January 2012

Molecular structure of an anticancer drug-DNA complex: daunomycin plus d(CpGpTpApCpG). journal, December 1980

Combined virtual screening, MMPBSA, molecular docking and dynamics studies against deadly anthrax: An in silico effort to inhibit Bacillus anthracis nucleoside hydrolase journal, May 2017

Association of anthracyclines and synthetic hexanucleotides. Structural factors influencing sequence specificity journal, November 1989

Energetics of DNA Intercalation Reactions † journal, July 2000

Doxorubicin pathways: pharmacodynamics and adverse effects journal, January 2011

Structure of a B-DNA dodecamer journal, July 1981

Assessing the performance of MM/PBSA and MM/GBSA methods. 5. Improved docking performance using high solute dielectric constant MM/GBSA and MM/PBSA rescoring journal, January 2014

Free energy calculations of protein–ligand interactions journal, August 2011

Parsing the Free Energy of Anthracycline Antibiotic Binding to DNA † journal, January 1996

β-Arm flexibility of HU from Staphylococcus aureus dictates the DNA-binding and recognition mechanism journal, November 2014

Hydration Changes for DNA Intercalation Reactions journal, January 2001

Assessing the performance of the MM/PBSA and MM/GBSA methods. 6. Capability to predict protein–protein binding free energies and re-rank binding poses generated by protein–protein docking journal, January 2016

Hydropathic analysis of the free energy differences in anthracycline antibiotic binding to DNA journal, August 2003

Anthracyclines: Molecular Advances and Pharmacologic Developments in Antitumor Activity and Cardiotoxicity journal, May 2004

Understanding the co-loading and releasing of doxorubicin and paclitaxel using chitosan functionalized single-walled carbon nanotubes by molecular dynamics simulations journal, January 2018

Efficiency of ab-initio total energy calculations for metals and semiconductors using a plane-wave basis set journal, July 1996

DNA-drug interactions journal, November 1991

3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures journal, September 2003

Thermodynamics of the daunomycin-DNA interaction: Ionic strength dependence of the enthalpy and entropy journal, February 1985

New Insights into the Mechanism of the DNA/Doxorubicin Interaction journal, January 2014

Calculating protein-ligand binding affinities with MMPBSA: Method and error analysis: Calculating Protein-Ligand Binding Affinities journal, August 2016

Theoretical studies of drug-dinucleotide interactions. Empirical energy function calculations on the interaction of ethidium, 9-aminoacridine, and proflavin cations with the base-paired dinucleotides GpC and CpG journal, February 1979

An extended conformational analysis of doxorubicin journal, August 1980

Molecular dynamics simulation studies for DNA sequence recognition by reactive metabolites of anticancer compounds: DNA SEQUENCE RECOGNITION FOR REACTIVE METABOLITES journal, January 2014

Experimental and Simulation Identification of Xanthohumol as an Inhibitor and Substrate of ABCB1 journal, April 2018

Structural comparison of anticancer drug-DNA complexes: adriamycin and daunomycin journal, March 1990

Harmonic analysis of large systems. I. Methodology journal, December 1995

Coupling of local folding to site-specific binding of proteins to DNA journal, February 1994

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities journal, February 2015

Bio3d: an R package for the comparative analysis of protein structures journal, August 2006

Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set journal, October 1996

Polyelectrolyte effects on site-binding equilibria with application to the intercalation of drugs into DNA journal, December 1984

Energetic and structural aspects of ethidium cation intercalation into DNA minihelices journal, November 1979

Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf journal, January 2003

The Study of the Interaction between Doxorubicin and Single-Stranded DNA journal, August 2016

On the Molecular Mechanism of Drug Intercalation into DNA: A Simulation Study of the Intercalation Pathway, Free Energy, and DNA Structural Changes journal, July 2008

31 P NMR study of daunorubicin-d(CGTACG) complex in solution Evidence of the intercalation sites journal, August 1988

A Computational Approach to Enzyme Design: Predicting ω-Aminotransferase Catalytic Activity Using Docking and MM-GBSA Scoring journal, July 2014

Intercalators. 1. Nature of Stacking Interactions between Intercalators (Ethidium, Daunomycin, Ellipticine, and 4‘,6-Diaminide-2-phenylindole) and DNA Base Pairs. Ab Initio Quantum Chemical, Density Functional Theory, and Empirical Potential Study journal, April 2002

Structural elucidation of 4′-epiadriamycin by nuclear magnetic resonance spectroscopy and comparison with adriamycin and daunomycin using quantum mechanical and restrained molecular dynamics approach journal, June 2008

A theoretical investigation on the sequence selective binding of adriamycin to double-stranded polynucleotides journal, January 1986

Targeting Ceramide Metabolism--a Strategy for Overcoming Drug Resistance journal, March 2001

Multistep Drug Intercalation: Molecular Dynamics and Free Energy Studies of the Binding of Daunomycin to DNA journal, May 2012

Doxorubicin, DNA torsion, and chromatin dynamics journal, January 2014

Studies on self-aggregation of anthracycline drugs by restrained molecular dynamics approach using nuclear magnetic resonance spectroscopy supported by absorption, fluorescence, diffusion ordered spectroscopy and mass spectrometry journal, April 2009

Kinetics of the daunomycin-DNA interaction
journal, January 1985

Intercalation of Daunomycin into Stacked DNA Base Pairs. DFT Study of an Anticancer Drug
journal, August 2008

MMPBSA.py : An Efficient Program for End-State Free Energy Calculations
journal, August 2012

Free energy calculation on base specificity of drug - DNA interactions: Application to daunomycin and acridine intercalation into DNA
journal, March 1990

Kinetic studies of anthracycline-DNA interaction by fluorescence stopped flow confirm a complex association mechanism
journal, January 1989

Intercalation of antitumor drug doxorubicin and its analogue by DNA duplex: Structural features and biological implications
journal, May 2014

Rigorous Free Energy Calculations in Structure-Based Drug Design
journal, July 2010

pH-controlled doxorubicin anticancer loading and release from carbon nanotube noncovalently modified by chitosan: MD simulations
journal, November 2016

Interactions between an anthracycline antibiotic and DNA: molecular structure of daunomycin complexed to d(CpGpTpApCpG) at 1.2-.ANG. resolution
journal, February 1987

Unravelling Hot Spots: a comprehensive computational mutagenesis study
journal, July 2006

Analysis of cooperativity and ion effects in the interaction of quinacrine with DNA
journal, December 1979

A review of methods for the calculation of solution free energies and the modelling of systems in solution
journal, January 2015

Molecular Mechanism of MBX2319 Inhibition of Escherichia coli AcrB Multidrug Efflux Pump and Comparison with Other Inhibitors
journal, August 2014

Studies on interaction of anthracycline antibiotics and deoxyribonucleic acid: equilibrium binding studies on the interaction of daunomycin with deoxyribonucleic acid
journal, August 1982

Accurate Estimation of the Standard Binding Free Energy of Netropsin with DNA
journal, January 2018

Energetics of drug–DNA interactions
journal, January 1997

Restrained molecular dynamics studies on complex of adriamycin with DNA hexamer sequence d-CGATCG
journal, July 2005

A Computational Model for Anthracycline Binding to DNA: Tuning Groove-Binding Intercalators for Specific Sequences
journal, March 2004

Sequence-selective DNA recognition by synthetic ligands
journal, January 1991

Energetics of intercalation specificity. I. Backbone unwinding
journal, May 1979

Predicted mode of intercalation of doxorubicin with dinucleotide dimers
journal, July 1980

Early stage intercalation of doxorubicin to DNA fragments observed in molecular dynamics binding simulations
journal, September 2012

Free Energy Simulations
journal, December 1986

Assessing the Performance of MM/PBSA and MM/GBSA Methods. 3. The Impact of Force Fields and Ligand Charge Models
journal, July 2013

Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches
journal, January 2018

Doxorubicin as a Molecular Nanotheranostic Agent: Effect of Doxorubicin Encapsulation in Micelles or Nanoemulsions on the Ultrasound-Mediated Intracellular Delivery and Nuclear Trafficking
journal, September 2010

The intercalation of DNA double helices with doxorubicin and nagalomycin
journal, July 2007

Nanopore Single-Molecule Analysis of DNA–Doxorubicin Interactions
journal, December 2014

Conformational diversity of anthracycline anticancer antibiotics: A density functional theory calculation
journal, July 2010

Electronic Structure and Partial Charge Distribution of Doxorubicin in Different Molecular Environments
journal, February 2015

The statistical-thermodynamic basis for computation of binding affinities: a critical review
journal, March 1997

Free Energy Calculations by the Molecular Mechanics Poisson−Boltzmann Surface Area Method
journal, January 2012

Molecular structure of an anticancer drug-DNA complex: daunomycin plus d(CpGpTpApCpG).
journal, December 1980

Combined virtual screening, MMPBSA, molecular docking and dynamics studies against deadly anthrax: An in silico effort to inhibit Bacillus anthracis nucleoside hydrolase
journal, May 2017

Association of anthracyclines and synthetic hexanucleotides. Structural factors influencing sequence specificity
journal, November 1989

Energetics of DNA Intercalation Reactions ^†
journal, July 2000

Doxorubicin pathways: pharmacodynamics and adverse effects
journal, January 2011

Structure of a B-DNA dodecamer
journal, July 1981

Assessing the performance of MM/PBSA and MM/GBSA methods. 5. Improved docking performance using high solute dielectric constant MM/GBSA and MM/PBSA rescoring
journal, January 2014

Free energy calculations of protein–ligand interactions
journal, August 2011

Parsing the Free Energy of Anthracycline Antibiotic Binding to DNA ^†
journal, January 1996

β-Arm flexibility of HU from Staphylococcus aureus dictates the DNA-binding and recognition mechanism
journal, November 2014

Hydration Changes for DNA Intercalation Reactions
journal, January 2001

Assessing the performance of the MM/PBSA and MM/GBSA methods. 6. Capability to predict protein–protein binding free energies and re-rank binding poses generated by protein–protein docking
journal, January 2016

Hydropathic analysis of the free energy differences in anthracycline antibiotic binding to DNA
journal, August 2003

Anthracyclines: Molecular Advances and Pharmacologic Developments in Antitumor Activity and Cardiotoxicity
journal, May 2004

Understanding the co-loading and releasing of doxorubicin and paclitaxel using chitosan functionalized single-walled carbon nanotubes by molecular dynamics simulations
journal, January 2018

Efficiency of ab-initio total energy calculations for metals and semiconductors using a plane-wave basis set
journal, July 1996

DNA-drug interactions
journal, November 1991

3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
journal, September 2003

Thermodynamics of the daunomycin-DNA interaction: Ionic strength dependence of the enthalpy and entropy
journal, February 1985

New Insights into the Mechanism of the DNA/Doxorubicin Interaction
journal, January 2014

Calculating protein-ligand binding affinities with MMPBSA: Method and error analysis: Calculating Protein-Ligand Binding Affinities
journal, August 2016

Theoretical studies of drug-dinucleotide interactions. Empirical energy function calculations on the interaction of ethidium, 9-aminoacridine, and proflavin cations with the base-paired dinucleotides GpC and CpG
journal, February 1979

An extended conformational analysis of doxorubicin
journal, August 1980

Molecular dynamics simulation studies for DNA sequence recognition by reactive metabolites of anticancer compounds: DNA SEQUENCE RECOGNITION FOR REACTIVE METABOLITES
journal, January 2014

Experimental and Simulation Identification of Xanthohumol as an Inhibitor and Substrate of ABCB1
journal, April 2018

Structural comparison of anticancer drug-DNA complexes: adriamycin and daunomycin
journal, March 1990

Harmonic analysis of large systems. I. Methodology
journal, December 1995

Coupling of local folding to site-specific binding of proteins to DNA
journal, February 1994

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities
journal, February 2015

Bio3d: an R package for the comparative analysis of protein structures
journal, August 2006

Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set
journal, October 1996

Polyelectrolyte effects on site-binding equilibria with application to the intercalation of drugs into DNA
journal, December 1984

Energetic and structural aspects of ethidium cation intercalation into DNA minihelices
journal, November 1979

Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf
journal, January 2003

The Study of the Interaction between Doxorubicin and Single-Stranded DNA
journal, August 2016

On the Molecular Mechanism of Drug Intercalation into DNA: A Simulation Study of the Intercalation Pathway, Free Energy, and DNA Structural Changes
journal, July 2008

³¹ P NMR study of daunorubicin-d(CGTACG) complex in solution Evidence of the intercalation sites
journal, August 1988

A Computational Approach to Enzyme Design: Predicting ω-Aminotransferase Catalytic Activity Using Docking and MM-GBSA Scoring
journal, July 2014

Intercalators. 1. Nature of Stacking Interactions between Intercalators (Ethidium, Daunomycin, Ellipticine, and 4‘,6-Diaminide-2-phenylindole) and DNA Base Pairs. Ab Initio Quantum Chemical, Density Functional Theory, and Empirical Potential Study
journal, April 2002

Structural elucidation of 4′-epiadriamycin by nuclear magnetic resonance spectroscopy and comparison with adriamycin and daunomycin using quantum mechanical and restrained molecular dynamics approach
journal, June 2008

A theoretical investigation on the sequence selective binding of adriamycin to double-stranded polynucleotides
journal, January 1986

Targeting Ceramide Metabolism--a Strategy for Overcoming Drug Resistance
journal, March 2001

Multistep Drug Intercalation: Molecular Dynamics and Free Energy Studies of the Binding of Daunomycin to DNA
journal, May 2012

Doxorubicin, DNA torsion, and chromatin dynamics
journal, January 2014

Studies on self-aggregation of anthracycline drugs by restrained molecular dynamics approach using nuclear magnetic resonance spectroscopy supported by absorption, fluorescence, diffusion ordered spectroscopy and mass spectrometry
journal, April 2009

Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking
journal, October 2010

Adriamycin and daunorubicin bind in a cooperative manner to deoxyribonucleic acid
journal, August 1983

Dissection of the free energy of anthracycline antibiotic binding to DNA: electrostatic contributions
journal, June 1993