Predicting Nano-Bio Interactions by Integrating Nanoparticle Libraries and Quantitative Nanostructure Activity Relationship Modeling.

The discovery of biocompatible or bioactive nanoparticles for medicinal applications is an expensive and time-consuming process that may be significantly facilitated by incorporating more rational approaches combining both experimental and computational methods. However, it is currently hindered by two limitations: (1) the lack of high-quality comprehensive data for computational modeling and (2) the lack of an effective modeling method for the complex nanomaterial structures. In this study, we tackled both issues by first synthesizing a large library of nanoparticles and obtained comprehensive data on their characterizations and bioactivities. Meanwhile, we virtually simulated each individual nanoparticle in this library by calculating their nanostructural characteristics and built models that correlate their nanostructure diversity to the corresponding biological activities. The resulting models were then used to predict and design nanoparticles with desired bioactivities. The experimental testing results of the designed nanoparticles were consistent with the model predictions. These findings demonstrate that rational design approaches combining high-quality nanoparticle libraries, big experimental data sets, and intelligent computational models can significantly reduce the efforts and costs of nanomaterial discovery.

[1]  Andrew Worth,et al.  Applying quantitative structure-activity relationship approaches to nanotoxicology: current status and future potential. , 2013, Toxicology.

[2]  A. Nel,et al.  Classification NanoSAR development for cytotoxicity of metal oxide nanoparticles. , 2011, Small.

[3]  Kavitha Pathakoti,et al.  Using experimental data of Escherichia coli to develop a QSAR model for predicting the photo-induced cytotoxicity of metal oxide nanoparticles. , 2014, Journal of photochemistry and photobiology. B, Biology.

[4]  Paul R. Gerber,et al.  MAB, a generally applicable molecular force field for structure modelling in medicinal chemistry , 1995, J. Comput. Aided Mol. Des..

[5]  A. Tropsha,et al.  Quantitative nanostructure-activity relationship modeling. , 2010, ACS nano.

[6]  Bing Yan,et al.  Enhancing cell recognition by scrutinizing cell surfaces with a nanoparticle array. , 2011, Journal of the American Chemical Society.

[7]  Yi Zhang,et al.  Tuning cell autophagy by diversifying carbon nanotube surface chemistry. , 2014, ACS nano.

[8]  Shuang Zhang,et al.  A further development of the QNAR model to predict the cellular uptake of nanoparticles by pancreatic cancer cells. , 2017, Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association.

[9]  Jerzy Leszczynski,et al.  Towards understanding mechanisms governing cytotoxicity of metal oxides nanoparticles: Hints from nano-QSAR studies , 2015, Nanotoxicology.

[10]  Aravind Subramanian,et al.  Perturbational profiling of nanomaterial biologic activity , 2008, Proceedings of the National Academy of Sciences.

[11]  T. Puzyn,et al.  Toward the development of "nano-QSARs": advances and challenges. , 2009, Small.

[12]  Xiaofeng Wang,et al.  An efficient local Chan-Vese model for image segmentation , 2010, Pattern Recognit..

[13]  A. Tropsha,et al.  Computer-aided design of carbon nanotubes with the desired bioactivity and safety profiles , 2016, Nanotoxicology.

[14]  R. Weissleder,et al.  Modeling biological activities of nanoparticles. , 2012, Nano letters.

[15]  Hongyu Zhou,et al.  Functionalized carbon nanotubes specifically bind to alpha-chymotrypsin's catalytic site and regulate its enzymatic function. , 2009, Nano letters.

[16]  Alexander Tropsha,et al.  Novel Variable Selection Quantitative Structure-Property Relationship Approach Based on the k-Nearest-Neighbor Principle , 2000, J. Chem. Inf. Comput. Sci..

[17]  Steffen Foss Hansen,et al.  Categorization framework to aid hazard identification of nanomaterials , 2007 .

[18]  Jerzy Leszczynski,et al.  Using nano-QSAR to predict the cytotoxicity of metal oxide nanoparticles. , 2011, Nature nanotechnology.

[19]  Hao Zhu,et al.  Experimental modulation and computational model of nano-hydrophobicity. , 2015, Biomaterials.

[20]  I. Vattulainen,et al.  Cationic Au Nanoparticle Binding with Plasma Membrane-like Lipid Bilayers: Potential Mechanism for Spontaneous Permeation to Cells Revealed by Atomistic Simulations , 2014 .

[21]  Alexander Tropsha,et al.  Chembench: a cheminformatics workbench , 2010, Bioinform..

[22]  A. Kyrychenko,et al.  Atomistic Simulations of Coating of Silver Nanoparticles with Poly(vinylpyrrolidone) Oligomers: Effect of Oligomer Chain Length , 2015 .

[23]  Alexander Tropsha,et al.  Quantitative structure-activity relationship modeling of rat acute toxicity by oral exposure. , 2009, Chemical research in toxicology.

[24]  J. Dearden,et al.  QSAR modeling: where have you been? Where are you going to? , 2014, Journal of medicinal chemistry.

[25]  W. Liu,et al.  Impact of silver nanoparticles on human cells: Effect of particle size , 2010, Nanotoxicology.

[26]  Guibin Jiang,et al.  Steering carbon nanotubes to scavenger receptor recognition by nanotube surface chemistry modification partially alleviates NFκB activation and reduces its immunotoxicity. , 2011, ACS nano.

[27]  Marnik Vanclooster,et al.  Modeling of ground-penetrating Radar for accurate characterization of subsurface electric properties , 2004, IEEE Transactions on Geoscience and Remote Sensing.

[28]  Michael C. Böhm,et al.  Interface of Grafted and Ungrafted Silica Nanoparticles with a Polystyrene Matrix: Atomistic Molecular Dynamics Simulations , 2011 .

[29]  Marlene T. Kim,et al.  Predicting chemical ocular toxicity using a combinatorial QSAR approach. , 2012, Chemical research in toxicology.

[30]  Richard A. L. Jones Nanotechnology, energy and markets. , 2009, Nature nanotechnology.

[31]  Ruili Huang,et al.  Mechanism Profiling of Hepatotoxicity Caused by Oxidative Stress Using Antioxidant Response Element Reporter Gene Assay Models and Big Data , 2015, Environmental health perspectives.

[32]  Marlene T. Kim,et al.  Critical Evaluation of Human Oral Bioavailability for Pharmaceutical Drugs by Using Various Cheminformatics Approaches , 2013, Pharmaceutical Research.

[33]  A. Alexander-Katz,et al.  Pathway for insertion of amphiphilic nanoparticles into defect-free lipid bilayers from atomistic molecular dynamics simulations. , 2015, Soft matter.

[34]  Lei Yang,et al.  Enhancement of cell recognition in vitro by dual-ligand cancer targeting gold nanoparticles. , 2011, Biomaterials.

[35]  M. Roco Nanotechnology: convergence with modern biology and medicine. , 2003, Current opinion in biotechnology.

[36]  Harald F. Krug Nanosafety Research — Are We on the Right Track? , 2015 .

[37]  J L Sussman,et al.  Protein Data Bank (PDB): database of three-dimensional structural information of biological macromolecules. , 1998, Acta crystallographica. Section D, Biological crystallography.

[38]  Jerzy Leszczynski,et al.  QSAR as a random event: modeling of nanoparticles uptake in PaCa2 cancer cells. , 2013, Chemosphere.

[39]  Andrew Emili,et al.  Protein corona fingerprinting predicts the cellular interaction of gold and silver nanoparticles. , 2014, ACS nano.

[40]  Bin Zhao,et al.  Modulation of Carbon Nanotubes' Perturbation to the Metabolic Activity of CYP3A4 in the Liver , 2016 .

[41]  Ran Chen,et al.  Quantification of nanoparticle pesticide adsorption: computational approaches based on experimental data , 2016, Nanotoxicology.

[42]  Alexander Tropsha,et al.  Exploring quantitative nanostructure-activity relationships (QNAR) modeling as a tool for predicting biological effects of manufactured nanoparticles. , 2011, Combinatorial chemistry & high throughput screening.

[43]  Marlene T. Kim,et al.  Developing Enhanced Blood–Brain Barrier Permeability Models: Integrating External Bio-Assay Data in QSAR Modeling , 2015, Pharmaceutical Research.

[44]  T. Xia,et al.  Understanding biophysicochemical interactions at the nano-bio interface. , 2009, Nature materials.

[45]  Hongyu Zhou,et al.  A nano-combinatorial library strategy for the discovery of nanotubes with reduced protein-binding, cytotoxicity, and immune response. , 2008, Nano letters.