Table 1.
Examples of software used to build and simulate different types of dendrimers; * NA: the software was not disclosed; § Free use; ƚ Commercial use.
| Dendrimer Type | Software for Dendrimer Construct | Software Used for Simulations | Force Field | Aim of the Study |
|---|---|---|---|---|
| Conformational analysis | ||||
| PAMAM G2 to G6 [87] | Insight II | Insight II ƚ CHARMM ƚ | CVFF CHARMM | Structural features at different pH and generations |
| PAMAM G5 [88] | NA* | MPsim | DREIDING | Effect of pH to study the water dynamics on dendrimers |
| PAMAM G50% and 90% acetylated [89] | Insight II | AMBER8 ƚ | GAFF | Effect of acetylation on structural features |
| Glycosylated PAMAM G3.5 [90] | XPLOR | Desmond § | OPLS_2005 | Effect of glycosylation on structural features |
| Triazine G3 and G5 with DOTA terminals [91] | AMBER 11 | AMBER 11 ƚ | GAFF and parm99 | Location of DOTA groups complexed with Gd ions |
| PEgylated PAMAM G3 to G5 [92] | NA * | GROMACS § | MARTINI | Effect of PEGylation on the structure and interparticle interaction |
| Pegylated triazine dendrimers linked with paclitaxel [72] | Material Studio 5 | AMBER 11 ƚ | parm99 | Effect of PEGylation on availability of linkers |
| Carboxylic modified PAMAM G5 with gold, fluorescein isothiocyanate (FI) and folic acid (FA) [93] | Insight II | Insight II ƚ | CVFF | Conformation and location of FI and FA |
| PAMAM G5 with amine, carboxyl and acetamide groups linked to fluorescein and folic acid [80] | Insight II | Insight II ƚ | CVFF | Location of folic acid and its availability |
| PAMAM G5 with methotrexate [29] | CHARMM | CHARMM ƚ | CHARMM | Location of MTX when directly linked or with a spacer |
| Poly(l-lysine) and Poly(amide) G4 dendrimers [94] | Starmaker (Silico) | NAMD § | OPLS-AA | Comparison of dendrimer architectures in solution |
| Dendrimer-small molecule interactions | ||||
| PAMAM G5 with different terminal 81] | Insight II | Insight II ƚ | CVFF | Influence of terminal groups on the complexation |
| PAMAM G4 + polyphenols [55] | ChemOffice Ultra 6.0 | HyperChem Pro 7.0 ƚ | MM+ | Free binding energies |
| PAMAM G3 + nicotinic acid, nicotinate and 3-pyridiniumcarboxylate [95] | HyperChem | NAMD § | CHARMM27 | Free energy of binding and the effect of pH variation on binding |
| Peptide dendrimers + hydroxypyrene trisulfonate butyrate ester [38] | CORINA | GROMACS § | GROMOS-96 43a1 | Conformation and docking site location |
| PAMAM G5-Folic acid + Morphine and Tramadol [96] | ICM | NAMD § | CHARMM 27; ParamChem | Different pHs; Binding mechanism elucidadtion; Location of folic acid |
| PAMAM G5 + salicylic acid, L-alanine, phenylbutazone, primidone [97] | DBT/AMBER | AMBER9 ƚ | GAFF | Effect of pH on interaction and relation with drug release |
| Poly(l-lysine) G4 dendrimer + doxorubicin [83] | ChemBioOffice | Desmond § | OPLS-AA | Complex formation |
| Dendrimer-nucleic acid interaction | ||||
| Triazine G2dendrimers + siRNA or DNA [98] | AMBER 10 | AMBER 10 ƚ | Parm99 | Binding mechanism and energy contributions |
| PAMAM ssDNA [49] | AMBER 7 | AMBER 7 ƚ | AMBER 95 (DNA) DREIDING (dendrimer) | Binding interaction and energy contributions |
| PAMAM G3 DNA [75] | NA * | NAMD § | CHARMM 27 | Complexation mechanism |
| PAMAM G0 and G1 + siRNA [43] | Material Studio 5 | AMBER9 ƚ | Ff99 FF for RNA GAFF for dendrimers | Effects of pH on the complexation |
| PAMAM G7 + siRNA [99] | Material Studio 5 | AMBER10 ƚ | GAFF (non-standard residues); parm99 | Complex interaction |
| Dendrimer-protein interaction | ||||
| Glycosylated PAMAM G3.5 + MD-2 protein [52] | XPLOR | Desmond § | OPLS_2005 | Docking and interaction between active and non-active forms |
| PAMAM G4 Albumin [47] | NA * | NA * | DREIDING | Contact points between dendrimer-albumin at physiological pH |
| PAMAM G0 with guanidinium terminal groups α-chymotrypsinogen A [73] | NA * | NAMD § | CHARMM 27 | Site of interaction with the protein and effect of salt types |
| Dendrimer-lipid bilayer interaction | ||||
| Acetylated and non-acetylated PAMAM G5 and G7 + DMPC [53] | Insight II | GROMACS § | MARTINI and adapted MARTINI | Effect of size, charge and concentration on dendrimer-membrane interaction |
| PAMAM G3 and G5 with different acetylation levels + DPPC [60] | Insight II | GROMACS § | MARTINI | Effect of size, charge and lipid phase on dendrimer-membrane interaction |
| PAMAM G3 with amine, acetyl and carboxyl terminals + DMPC [74] | CHARMM | CHARMM ƚ | CHARMM27 (lipid) and CHARMM 22 (dendrimer) | Effect of terminal groups and lipid phase |