Evolution of the Computational Pharmaceutics Approaches in the Modeling and Prediction of Drug Payload in Lipid and Polymeric Nanocarriers
Abstract
:1. Introduction
2. Solubility Parameters and Flory-Huggins Theory
2.1. Classical Approach
2.1.1. Analytical Procedure
2.1.2. Software
2.2. Computational (Modern) Approach
3. MD Simulations and Docking
3.1. Screening
3.1.1. Carriers-Oriented Screening
3.1.2. Drugs-Oriented Screening
3.2. Visualizing Interactions
4. Artificial Intelligence and Machine Learning
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
(%)DL | drug loading (percentage) |
(%)EE | entrapment efficiency (percentage) |
AI | artificial intelligence |
AlCIPc | Aluminium-chloride-phathalocyanine |
Amber FF | assisted model building with energy refinement force field |
ANN | artificial neural network |
API | active pharmaceutical ingredient |
CCM | continuous chirality measure |
CD | cyclodextrin |
CED | cohesive energy density |
CGen FF | CHARMM general force field |
CHARMM FF | chemistry at Harvard macromolecular mechanics force field |
DDS | drug delivery system |
DFT | density function theory |
EC | ethylcellulose |
Emix | mixing energy |
FF | force field |
FFT | fast fourier transform algorithm |
FH | Flory-Huggins theory |
GCM | group contribution method |
GP | Gaussian process |
HB | hydrogen bond |
HPMC | hydroxypropylmethyl cellulose |
HSPiP | Hansen solubility parameter in practice |
KNN | k-nearest neighbor |
LDHN | lipid-dendrimer hybrid nanoparticles |
LGA | Lamarckian genetic algorithm |
LPHN | lipid-polymer hybrid nanoparticles |
MD | molecular dynamics |
ML | machine learning |
MLR | multiple linear regression |
MMFF | Merck molecular force field |
MOE | molecular operating environment |
MS | materials studio |
Mwt | molecular weight |
NanoMIPs | molecularly imprinted polymeric nanopartices |
NIPAAm | N-isopropylacrylamide |
OBMD | oligobutylmorpholinediol |
ONIOM | our N-layered integrated molecular orbital+molecular mechanics |
OPLS FF | optimized potentials for liquid simulations force field |
PAA | Polyallylamine |
PAMAM | polyamidoamine |
PAS | Polyaminostyrene |
PCFF | polymer consistent force filed |
PCL | polycaprolactone |
PDLA | poly-D-lactic acid |
PEA | Polyethyleneamine |
PEG | polyethylene glycol |
PEO | polyethylene oxide |
PGA | polyglycolic acid |
PLGA | polylactic-co-glycolic acid |
PLL | poly-L-lysine |
PLLA | poly-L-lactic acid |
PM | polymeric micelles |
PN | polymeric nanoparticles |
PS-PAA | polystyrene-polyacrylic acid |
PVA1 | polyvinyl alcohol |
PVA2 | polyvinyl amine |
QM/MM | quantum mechanics/molecular mechanics |
QSPR | quantitative structure-property relationship |
R/R2 | correlation/determination coefficients |
SF | scoring function |
SLN | solid lipid nanoparticles |
SP/δ | solubility parameter |
SPF | spherical polar fourier algorithm |
SPR | surface plasmon resonance |
SVR | support vector regression |
TPSA | topological polar surface area |
UFF | universal force field |
XH | Flory-Huggins interaction parameter |
xLog P | partition coefficient |
Δδ | difference in solubility parameters (drug and carrier) |
ΔG | binding energy |
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Intended Formulation | Carrier/Carriers | Applications | Drug/Drugs | Technique | Predictive Dry-Lab Values | Validating Wet-Lab Values | Correlation | Reference | ||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
PN LPHN | PLGA PLGA-Nigella sativa oil | Antioxidants, anti-inflamatory and anticancer | Indomethacin Curcumin Resveratrol α-tocopherol Hydrocortisone Retinol Izohidrafural Nitrofurantoin 5-fluorouracil | GCM based SP + FH interaction parameter | Δδ PN 0.51 0.37 2.68 1.84 4.04 1.77 0.76 12.14 15.17 | Δδ LPHN 1.52 1.38 3.69 2.85 5.05 2.78 1.77 13.15 16.18 | XH PN 0.023 0.02 0.69 0.6 1.77 0.37 0.056 8.75 6.73 | XH LPHN 0.014 0.04 1.29 0.12 2.75 0.069 0.035 10.17 7.65 | %EE * PN 35 25 20 25 28 79 42 16 5 | %EE * LPHN 65 55 43 62 22 95 80 4 2 | Exponential R2 0.61 0.86 For PN and LPHN respectively | [17] |
PM | PEG-PLA copolymer | Antifungals and anticancer | Diphenylpyrazole Pyrene Clotrimazole Plerixafor BLZ945 Combretastatin Niraparib Methoxytetralone Tranilast Plinabulin Curcumin Irinotecan Griseofulvin Cabazitaxel Heptylhydroxybenzoate Olaparib Paclitaxel Docetaxel Podophyllotoxin | GCM based SP + FH interaction parameter | Δδ 5.34 1.39 3.13 1.54 5 2.17 4.93 1.67 2 5.84 1.91 1.78 1.31 1.33 0.46 6.09 4.46 3.48 5 | XH 9.32 5.93 11.82 7.24 9.72 2.12 4.31 1.27 2.68 2.92 1.11 3.44 0.82 3.51 0.88 2.76 4.74 2.81 0.61 | %DL 7.85 3.85 5.15 4.55 1.8 5.35 88.65 14.95 4.15 0.55 80.1 60.6 14.35 78.95 78.35 94.7 87.75 76.5 89.05 | Prediction results did not align with the real experimental results. | [18] | |||
PM | Poly-ethyloxazoline shell and butenyloxazoline, butyloxazoline, pentyloxazoline, or nonyloxazoline core | Anticancer | Curcumin | GCM based SP + FH interaction parameter | Δδ (core) 0.68 2.17 2.83 4.46 0.21 | XH (core) 0.05 0.48 0.82 2.03 | %EE and %DL Upto 82.7% and 11.8% respectively for butenyloxazoline | - | [19] | |||
SLN | Geleol Compritol ATO 888 Stearic acid Perciol Cetyl palmitate | Antibiotics, antivirals and corticosteroid | Minocycline- HCl Didanosine Efavirenz Clarithromycin Mometasone- furoate | Software-based Hansen SP (Yamamoto’s Molecular Breaking method in HSPiP software) | Δδ Geleol-mometasone 2.4 Geleol-minocyclin 8.65 Geleol-efavirenz 1.4 Geleol-didanosine 4.9 Compritol-didanosine 8 Stearic acid-clarithromycin 1.35 | Quantity of lipid (gm) to solubilize 10 mg drug * 12 0.67 1.8 No solubility detected 3 3 | No obvious prediction pattern was noticed. Bulky clarithromycin encountered some difficulties in Hansen calculations resulting in confusing predictions. | [20] |
Intended Formulation | Carrier/Carriers | Drug/Drugs | Technique | Predictive Dry-Lab Values | Validating Wet-Lab Values | Correlation | Reference | |
---|---|---|---|---|---|---|---|---|
PM | PEO-b-PCL | Fenofibrate Nimodipine | MD simulation-based SP (COMPASS FF in MS software). GCM based SP and FH interaction parameter. | Δδ and XH in MD 1.43–3.49 (0.05–0.33) 3–5.06 (0.23–0.68) respectively | Δδ and XH in GCM 2.3 (0.539) 1.4 (0.25) respectively | Drug solubility in PCL core 120 mmol/mol 20 mmol/mol respectively | - | [29] |
PM | PLA-PEG | Doxorubicin Cabazitaxel Beta-lapachone DrinabantSARRA | MD simulation-based Heldibrand SP and FH interaction parameter (COMPASS II FF in MS software) | XH * 0.63 0.04 0.1 0.01 0.75 Near 0 | %DL 1 5 2.2 7 2.7 10 | Exponential correlation (no associated R2) | [30] | |
PN | PLLA PDLA PGA PEG Cellulose Chitosan | Cyclosporine A | MD simulation (PCFF or COMPASS FF in MS software) and docking-based (mixing energy in Blends module) SP and FH interaction parameter | XH 103.6 169.2 219 206.9 17.7 43.7 | ΔG −801.98 −749.86 −828.69 −723.35 −935.26 −957.61 | Cited work | - | [31] |
Intended Formulation | Carrier/Carriers | Drug/Drugs | Technique | Predictive Dry-Lab Values | Validating Wet-Lab Values | Correlation and Correlation Coefficient | Reference | |
---|---|---|---|---|---|---|---|---|
PN PM | Chitosan Na alginate PLL NIPAAm-co-PEGPLGA | Curcumin | All-Atom MD simulation and docking (AutoDock Vina software) | ΔG (kcal/mol) −4.3 −3.3 −3.2 −2.9 −2.3 | - | - | [32] | |
PN | Chitin Chitosan | Curcumin | MD simulation (MMFF in Schrodinger Macromodel software for pure components OPLS FF in Desmond software for carrier-drug complex) and docking (rigid docking in glide software) | ΔG (kcal/mol) −2.61 −3.31 | HB count 3 6 | %EE Up to 97.6% Up to 98.4% | - | [33] |
PN | PLL PEA PAS PAA PEG-bis-amine PVA2 Chitosan Gelatin | Amphotericin B | Energy minimization of all built 2D structures (MMFF94 in ChemBioUltra software) and docking (AutoDock Vina software) | ΔG (kcal/mol) −3.1 −2.6 −3.4 −2.2 −1.7 −1.8 −3.3 −6.2 | %EE and %DL in gelatin PN 78% and 2.42% respectively | - | [34] | |
PN | HPMC Eudragit EC PVA1 PVP Pluronics | Fluticasone | All-Atom MD simulation in Amber14 software package and docking (LGA) in AutoDock Vina software) | ΔG (kcal/mol) −35.22 for HPMC−25.17 for Eudragit | %EE >90% for both polymers | - | [35] | |
NanoMIPs | Poly itaconic acidPoly methacrylic acid Polyacrylamide | E-coli endotoxin | Energy minimization and docking screening (Tripos FF and LEAPFROG algorithm in SYBYL 7.0 software) | ΔG (kcal/mol) −52.24−41.43−39.87 | Affinity by SPR 99.566.435.6 | - | [36] | |
PM | PEG-Tyrosine derived polyarylates-PEG | Curcumin Paclitaxel Vitamin D3 | All-Atom MD simulation (MMFF in MOE software) and docking (LGA in AutoDock 4 software) | ΔG (kcal/mol) −7.19 −4.36 −10.3 | %DL * 29% 12% 36% | Linear R2 0.93 | [37] | |
PN | Chitin | Rifampicin Ethionamide Methacycline | MD simulation (CHARMM FF in discovery studio 4.0 software) and docking (AutoDock Vina software) and interaction visualization (PYMOL software) | ΔG (kcal/mol) −8.1 −7.3 −5.1 | %DL 8.9% 5.6% 3.5% | Exponential/logarithmic R2 0.85 | [38] | |
PN | Chitin | Curcumin Docetaxel 5-fluorouracil | MD simulation (CHARMM FF in discovery studio 4.0 software) and docking (AutoDock Vina software) and interaction visualization (PYMOL software) | ΔG (kcal/mol) −6.9 −6.5 −5.4 | %DL 3 2 1 | Exponential/logarithmic R2 0.93 | [39] | |
PN | PLGA | Nine thiazoline derivatives | Hybrid QM/MM (ONIOM2 method in Gaussian 03 software using DFT and UFF) | ΔG (kcal/mol) D1: −8.1582 D2: −8.5694 D3: −9.0987 D4: −8.7034 D5 −8.0216 D6: −8.4022 D7: −9.4753 D8: −8.5970 D9: −8.2077 | - | - | [40] | |
PM | PLA-PEG | Doxorubicin Cabazitaxel Beta-lapachone Drinabant SAR RA | MD simulation (Monte-Carlo method in MS software) and docking (metropolis Monte-Carlo surface docking in adsorption locator of MS software) | ΔG (kcal/mol) −29 −47 −40 From −109 to −115 −57 −100 | %DL 1 5 2.2 10 2.7 7 | Linear R2 0.82 | [30] | |
PN | Gelatin | Acyclovir Amphotericin B Cryptolepine Doxorubicin 5-fluorouracil Isoniazid Resveratrol Curcumin Paclitaxel Indomethacin | MD simulation (CGenFF in GROMACS software) and docking (AScore scoring function in ArgusLab software) | ΔG (kcal/mol) −3.94 144.4 −3.81 58.29 −4.19 −4.16 −3.74 −2.59 173.5 −1.99 | DL (mg drug/100 mg gelatin) 8.74 1.16 2 2.1 25.07 22 1.96 3.5 0.52 1.91 | Exponential R2 0.95 | [44] | |
SLN PN | Tripalmitin PLGA | Twenty-one literature gathered drug | All-Atom MD simulation (CGenFF in GROMACS software) and docking (ArgusLab and AutoDock Vina) | ΔG (kcal/mol) | DL Curcumin loading = 0.75 and 0.97 mg in 100 mg tripalmitin and PLGA respectively | Exponential R2 = 0.87 and 0.9 in SLN and PN respectively. % bias in loading = 12 and 2.03 in SLN and PN respectively | [45] | |
SLN | Tripalmitin | Ten literature gathered drugs | All-Atom MD simulation (CGenFF in GROMACS software) and docking (triangle matcher placement and ASE SF in MOE software) | ΔG (kcal/mol) | DL Curcumin loading = 0.81 mg in 100 mg tripalmitin | Exponential R2 0.86 % bias in loading = 7.71 | [46] | |
PN | PLGA | Twenty-one literature gathered drugs | MD simulation (UFF in Gaussview5 software) and docking (LGA in AutoDock Vina software) | ΔG (kcal/mol) | DL | Linear R2 0.36 R 0.6 | [47] |
Intended Formulation | Carrier/Carriers | Drug/Drugs | Technique | Predictive Dry-Lab Values (kcl/mol) | Validating Wet-Lab Values | Drug(s)-Carrier(S) Binding Interactions | Reference |
---|---|---|---|---|---|---|---|
PN | PLGA OBMD | Dexamethasone | MD (AMBER FF in Ascalaph designer software) and docking(AutoDock Vina) and interaction visualization (AutoDock visualizer tool) | ΔG −2.8 to −4.3 −3.8 to −5.1 | %DL Up to 2 Up to 50 | 2 HB 3 HB | [50] |
SLN LPHN LDHN | Compritol Compritol-Eudragit Compritol-PAMAM G4 | Vancomycin | MD simulation (UFF in MS software) and docking (adsorption tool in MS software) and interaction visualization (Biovia discovery studio visualizer) | - | %DL 3.6 1.1 5.1 | Hydrophobic interactions Nearly no interactions Multiple HB | [51] |
PM | PEG-Tyrosine derived polyarylates-PEG | Curcumin Paclitaxel Vitamin D3 | All-Atom MD simulation (MMFF in MOE software) and docking (LGA in AutoDock 4 software) and interaction visualization (AutoDock visualizer tool) | ΔG −7.19 −4.36 −10.3 | %DL 29% 12% 36% | 2 HB, 4 π-π interactions 1 HB, 2 π-π interactions 1 HB, 0 π-π interactions | [37] |
Intended Formulation | Carrier/Carriers | Drug/Drugs | Technique | Predictive Dry-Lab Values | Validating Wet-Lab Values | Reference |
---|---|---|---|---|---|---|
Dendrimers | PAMAM G5 | Morphine Tramadol | MD simulation (CHARMM FF in NAMD software) and docking (LGA in AutoDock 4 software) | ΔG −0.97 to −11.79 −1.04 to −20.48 | DL (moles drug/1mole dendrimer) 114 86 | [52] |
PM | PEG-Tyrosine derived polyarylates-PEG | Camptothecin | All-Atom MD simulation (MMFF in MOE software) and docking (LGA in AutoDock 4 software) and interaction visualization (AutoDock visualizer tool) | ΔG −9.27 | %DL Up to 3% | [37] |
Polybee nanoarchitecture Lipobee nanoarchitecture | PEG cetyl ether stabilized by either PS-PAA or lecithin | Melittin (bee venom peptide) | MD simulation (Tripos FF in SYBYL-X 2.0 software) and docking (induced fit, triangle matcher placement and London dG SF in MOE 2013 software) | 1st ΔG +ve values −ve values 2nd ΔG −6.17 to −9.8−4.88 to −6.7 | MTT assay (IC50) 40 and 80 nM 70 and 100 nM | [53] |
PN | Chitin Chitosan | Insulin | MD (MMFF in Schrodinger Macromodel software for pure components and Optimized Potentials for Liquid Simulations (OPLS) FF in Desmond software for drug-carrier complex) and docking (SPF) and (FFT) algorithms in Hex software | ΔG −438.46 −420.69 | %EE 80–83.97 86.4–89.13 | [33] |
Intended Formulation | Carrier/Carriers | Drug/Drugs | Technique | Predictive Dry-Lab Values | Validating Wet-Lab Values | Correlation | Reference |
---|---|---|---|---|---|---|---|
SLN PN | Tripalmitin PLGA | Twenty one literature gathered drug | Molecular descriptors calculation (Bioclipse software) and ANN model (jmp software) | Inputs Mwt, xLogP, TPSA and fragment complexity Output ΔG | % bias Up to 15% (3.66–14.9%) | R2 of the model: 0.999 0.999 | [45] |
SLN | Tripalmitin | Ten literature gathered drugs | Molecular descriptors calculation (Bioclipse software) and Gaussian process model (jmp software) | Inputs Mwt, xLogP, TPSA and fragment complexity Output ΔG | % bias 3.35% | Correlation between actual and predicted outputs: All the points were in close proximity to the 450 line | [46] |
PN | PLGA | Twenty one literature gathered drugs | Molecular descriptors and M5P QSPR model | Inputs logP, SiRMS-lip, SiRMS-EO and CCM Output DL | - | R2 between actual and predicted outputs >0.9 | [47] |
PN | PLGA 50:50 | Twenty two literature gathered drug | Molecular descriptors (DRAGON, MOE and VolSurf+ programs) and MLR model (STATISTICA software) | Initial No. of descriptors 1504 201 128 Selected descriptors (inputs) Mor29u, GATS5m, C-019, T(N…O) and MATS2m E_Strain, Reactive, SMR_VSA4, MINDO_HF and SMR_VSA7 LgS10, WO6, DD4 and DRACAC Output Log DL | R2 of the model 0.889 0.826 0.818 for DRAGON, MOE anf VolSurf+ respectively | [67] | |
Liposomes | Different phospholipids | Sixty literature gathered drug | Molecular descriptors (MOE software) and kNN or SVR model (ChemBench software) | Inputs Hybrid of 185 1D-2D molecular descriptors, and eleven experimental conditions Output D/L mole ratio | - | R2 between actual and predicted outputs 0.758 0.789 R20 between actual and predicted outputs 0.732 0.734 R20 between actual and predicted outputs (without outliers) 0.919 0.883 | [68] |
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Abd-algaleel, S.A.; Abdel-Bar, H.M.; Metwally, A.A.; Hathout, R.M. Evolution of the Computational Pharmaceutics Approaches in the Modeling and Prediction of Drug Payload in Lipid and Polymeric Nanocarriers. Pharmaceuticals 2021, 14, 645. https://doi.org/10.3390/ph14070645
Abd-algaleel SA, Abdel-Bar HM, Metwally AA, Hathout RM. Evolution of the Computational Pharmaceutics Approaches in the Modeling and Prediction of Drug Payload in Lipid and Polymeric Nanocarriers. Pharmaceuticals. 2021; 14(7):645. https://doi.org/10.3390/ph14070645
Chicago/Turabian StyleAbd-algaleel, Shaymaa A., Hend M. Abdel-Bar, Abdelkader A. Metwally, and Rania M. Hathout. 2021. "Evolution of the Computational Pharmaceutics Approaches in the Modeling and Prediction of Drug Payload in Lipid and Polymeric Nanocarriers" Pharmaceuticals 14, no. 7: 645. https://doi.org/10.3390/ph14070645
APA StyleAbd-algaleel, S. A., Abdel-Bar, H. M., Metwally, A. A., & Hathout, R. M. (2021). Evolution of the Computational Pharmaceutics Approaches in the Modeling and Prediction of Drug Payload in Lipid and Polymeric Nanocarriers. Pharmaceuticals, 14(7), 645. https://doi.org/10.3390/ph14070645