Application of molecular dynamics simulation in self-assembled cancer nanomedicine

Xu, Xueli; Liu, Ao; Liu, Shuangqing; Ma, Yanling; Zhang, Xinyu; Zhang, Meng; Zhao, Jinhua; Sun, Shuo; Sun, Xiao

doi:10.1186/s40824-023-00386-7

Biomaterials Research

Table 2 Application of MD simulation in nanomedicine

From: Application of molecular dynamics simulation in self-assembled cancer nanomedicine

Material composition	Composition shape	Simulation software	Force field	Treatment	Tumor types	Ref
Doxorubicin, Chitosan	chain	GROMACS	AMBER (GAFF)	Chemotherapy	---	[66]
Estrogen-related receptor α	Spiral	AMBER	ff14SB	Chemotherapy	---	[67]
Triazine-morpholino derivatives	Chain	AMBER	AMBER7FF9	Chemotherapy	Breast cancer	[68]
Genistein, AR endogenous agonist DHT	Spiral chain	GROMACS	OPLS-AA	Chemotherapy	Prostate cancer	[69]
Fullerenes, gamma-cyclodextrin; inclusion complexes	Ring	Material Studio	CVFF(Consistent Valence-Force Field)	PDT	---	[70]
Levonorgestrel	Spiral chain	GROMACS	AMBER03	Chemotherapy	Breast cancer	[71]
Mammalian target of rapamycin	Chain	GROMACS	AMBER7FF99	Chemotherapy	Lung cancer	[72]
DOX, PAX	Nanotube	GROMACS	OPLS-AA	Chemotherapy	Lung cancer, breast cancer	[73]
Anodic aluminum oxide, tantalum nitride-coated Si	Nanodot array	GROMACS	---	Chemotherapy	---	[74]
Catalase-like RuO₂@BSA@IR-808-Br2(RBIR) nanozyme	Nanotube	GROMACS	---	PTT PDT	Breast cancer	[75]
HCPT/Ce6 NRs	Nanorod	GROMACS	GROMOS53A6	PDT	Breast cancer	[76]
Epidermal growth factor receptor	Chain	AMBER	GAFF(Generation Amber-Force Field)	Chemotherapy	Lung cancer	[77]
styrylquinolines	Chain	NAMD	CHARMM27	Chemotherapy	---	[78]
Hsp90 C-terminal domain inhibitors	Chain	NAMD	CHARMM22	Chemotherapy	---	[79]
SN38, trolox, succinic acid linker	Nanoparticles	GROMACS	OPLS-AA	Chemotherapy	Colorectal cancer	[80]
TH peptides	Cyclic peptide	GROMACS	AMBER, OPLS-AA	Chemotherapy	Brain tumor	[81]
Pure drug nanoa-ssemblies	Nanoparticles	GROMACS	---	PTT, PDT	---	[11]
Daunorubicin, Etoposide	Nanotube	Gromacs5	CHARMM27	Chemotherapy	---	[82]
DOX, Aluminum Hydroxide	Nanosheet	LAMMPS	CHARMM27	Chemotherapy	Melanoma	[83]
Cu (II)-Schiff base complexes	Nanoparticles	AutoDock4	---	Chemotherapy	Human erythroleukemia cancer	[84]
Aptamer -receptor	Nanoparticles	GROMACS	CHARMM	Chemotherapy	Breast cancer	[9]
Adriamycin, chitosan, graphene	Nanosheet	GROMACS 5.0.7	---	Chemotherapy	---	[85]
P2Y1R receptor - indoline-4 carbonitrile HIC	Spiral chain	GROOMACS 4.6	GROMOS	Chemotherapy	Prostate cancer	[86]
HDAC inhibitors	Nanoparticles	NAMD	CHARMM	Chemotherapy	Prostate cancer	[87]
DOX, carbon nanotubes	Nanotube	AMBER	CHARMM36	Chemotherapy	---	[88]
DOX, black phosphorus	Nanosheet	GROMACS	CHARMM	Chemotherapy	---	[89]
Selective estrogen receptor downregulators（SERDs）	Reticular	AMBERTOOLS	---	Chemotherapy	Breast cancer	[90]
FPTT	---	GROMACS	OPLS	Chemotherapy	Breast cancer	[91]
RET kinase	Crystal, structure	AMBER18	AMBER	Chemotherapy	Thyroid cancer	[92]
MTORC1, arginine analogues	---	AMBER16	GAFF/ff144SB	Chemotherapy	Lung cancer	[93]
Au NP, Panobinostat	Nanoparticles	AMBER19	---	Chemotherapy	---	[94]
SERDs	---	AMBERTPPLS14	AMBER	Chemotherapy	Breast cancer	[95]

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ISSN: 2055-7124

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