| Literature DB >> 32197506 |
Eleni Tsanaktsidou1, Christina Karavasili2, Constantinos K Zacharis1, Dimitrios G Fatouros2, Catherine K Markopoulou1.
Abstract
One of the most challenging goals in modern pharmaceutical research is to develop models that can predict drugs' behavior, particularly permeability in human tissues. Since the permeability is closely related to the molecular properties, numerous characteristics are necessary in order to develop a reliable predictive tool. The present study attempts to decode the permeability by correlating the apparent permeability coefficient (Papp) of 33 steroids with their properties (physicochemical and structural). The Papp of the molecules was determined by in vitro experiments and the results were plotted as Y variable on a Partial Least Squares (PLS) model, while 37 pharmacokinetic and structural properties were used as X descriptors. The developed model was subjected to internal validation and it tends to be robust with good predictive potential (R2Y = 0.902, RMSEE = 0.00265379, Q2Y = 0.722, RMSEP = 0.0077). Based on the results specific properties (logS, logP, logD, PSA and VDss) were proved to be more important than others in terms of drugs Papp. The models can be utilized to predict the permeability of a new candidate drug avoiding needless animal experiments, as well as time and material consuming experiments.Entities:
Keywords: Partial Least Squares regression; in vitro permeability; predictive model; steroids
Mesh:
Substances:
Year: 2020 PMID: 32197506 PMCID: PMC7144563 DOI: 10.3390/molecules25061387
Source DB: PubMed Journal: Molecules ISSN: 1420-3049 Impact factor: 4.411
X Descriptors of Dataset.
| Open Melting Point Dataset | EPA DSSTox | Data Warrior | ACD/Labs | Marvin | PubChem | pkCSM |
|---|---|---|---|---|---|---|
| Melting Point | 1_cLogP | 2_logP | 3_logP | Topological PSA | MW | |
| 1_cLogS | logD, pH 7.4 | 2_logS | 4_LogP | |||
| Hydrogen Bond Acceptors | Refractivity index | pKa (Strongest Acidic) | 3_logS | |||
| Hydrogen Bond Donors | Molar Refractivity | pKa (Strongest Basic) | Double bonds | |||
| Aromatic Rings | PSA | HLB | Rotatable Bonds | |||
| Carboxyl group | Polarizability | No of Rings | Surface Area | |||
| Carbonyl group | Molar Volume | Caco2 Permeability | ||||
| Hydroxyl group | Intestinal absorption | |||||
| Total Surface Area | log Kp | |||||
| Relative PSA | VDss | |||||
| PSA | log BB | |||||
| Shape Index | logPS | |||||
| Molecular Complexity | Total Clearance | |||||
| Molecular Flexibility | ||||||
| Drug-likeness | ||||||
Figure 1Observed versus estimated values of model P with apparent permeability values as (Y) variable, RMSEE = 0.00265379.
Statistical Parameters in Partial Least Squares (PLS) regression models.
| Models | R2Y 1 | Q2 (cum) 2 | Number of Components | Excluded Observations |
|---|---|---|---|---|
| Papp | 0.902 | 0.722 | 3 | 3 |
| P2h | 0.802 | 0.567 | 3 | 1 |
| P4h | 0.847 | 0.656 | 3 | 2 |
| P6h | 0.846 | 0.659 | 3 | 2 |
| P8h | 0.872 | 0.605 | 3 | 3 |
1 ( represents the means of the true Papp values in the predictor set). 2 .
Figure 2Internal validation test with 20 permutations, for model P. Intercepts: R2 = (0.0, 0.405) marked black, Q2 = (0.0, −0.32) marked red.
Figure 3Variables’ Importance in the Projection (VIP) plot for the apparent permeability P values of model P, at 95% confidence level.
Figure 4A scatter w × c[1] versus w × c[2] plot for P model.
Models’ VIP values.
| Models’ VIP Values | |||||||
|---|---|---|---|---|---|---|---|
| P2h | P4h | P6h | P8h | ||||
| Var ID (Primary) | M2.VIP[3] | Var ID (Primary) | M3.VIP[3] | Var ID (Primary) | M3.VIP[3] | Var ID (Primary) | M3.VIP[3] |
| Total Clearance | 1.62825 |
| 1.41597 |
| 1.48033 |
| 1.47640 |
|
| 1.45142 |
| 1.31645 |
| 1.19879 | No. of triple bonds | 1.27167 |
|
| 1.27798 |
| 1.21737 |
| 1.19154 | Chlorine | 1.22264 |
| cMelting Point | 1.25731 | cMelting Point | 1.18929 |
| 1.18122 |
| 1.18501 |
|
| 1.21565 |
| 1.15522 |
| 1.17849 |
| 1.17937 |
|
| 1.21432 |
| 1.15097 |
| 1.17612 |
| 1.17567 |
|
| 1.19812 |
| 1.15097 | Drug-likeness | 1.16409 | Drug-likeness | 1.17289 |
|
| 1.17929 |
| 1.14560 | cMelting Point | 1.14712 | Fluoride | 1.16495 |
|
| 1.15973 |
| 1.14311 | Chlorine | 1.13175 |
| 1.16166 |
| No of triple bonds | 1.14692 | Chlorine | 1.14308 | Fluoride | 1.12684 |
| 1.15902 |
|
| 1.12114 | carboxylate group | 1.13474 |
| 1.12456 | cMelting Point | 1.13450 |
| carboxylate group | 1.11557 | No of triple bonds | 1.12947 |
| 1.11544 |
| 1.11508 |
|
| 1.09348 | Fluoride | 1.12462 |
| 1.11174 |
| 1.10855 |
| H-Donors | 1.09223 |
| 1.12262 |
| 1.10117 |
| 1.10584 |
| Chlorine | 1.08855 |
| 1.12234 | No of triple bonds | 1.09925 |
| 1.08631 |
|
| 1.07715 |
| 1.10689 |
| 1.09019 |
| 1.08316 |
|
| 1.05540 | exper_Melting Point | 1.07645 |
| 1.08878 | hydroxyl group | 1.07759 |
| Rotatable Bonds | 1.05147 |
| 1.06777 |
| 1.08517 |
| 1.06769 |
|
| 1.04603 | H-Donors | 1.05761 |
| 1.08068 | H-Donors | 1.06767 |
| exper_Melting Point | 1.03503 |
| 1.05533 | hydroxyl group | 1.06590 |
| 1.06241 |
| hydroxyl group | 1.03056 |
| 1.05320 | H-Donors | 1.06502 |
| 1.0599 |
|
| 1.00956 | hydroxyl group | 1.04762 |
| 1.04701 | exper_Melting Point | 1.05272 |
|
| 0.97296 |
| 1.04431 | exper_Melting Point | 1.03706 |
| 1.04095 |
| Caco2 Permeability | 0.96943 |
| 1.04168 | carboxylate group | 1.03300 |
| 1.02086 |
|
| 0.96517 |
| 1.03678 | Surface Area | 1.02096 |
| 0.99368 |
|
| 0.95059 | Druglikeness | 1.01070 |
| 0.99572 | Relative PSA | 0.98728 |
|
| 0.93301 | Rotatable Bonds | 0.98079 | Relative PSA | 0.98111 | carboxylate group | 0.97549 |
| H-Acceptors | 0.88952 | Caco2 Permeability | 0.96573 | Caco2 Permeability | 0.96947 | Rotatable Bonds | 0.95868 |
1 red indicates positive contribution, 2 green indicates size related descriptors, 3 blue indicates negative contribution.
Figure 5Contribution score plot of (a) 4-chlorotestosterone, (b) prednisolone and (c) prednisone, versus the remaining observations.
Structures of studied compounds.
| Steroids Structures | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Compound | Double Bonds | C2 | C3 | C4 | C5 | C7 | C9 | C10 | C11 | C13 | C16 | C17 | |
| 17a-hydroxyprogesterone | COMP 1 | 4 = 5 | CH3 | CH3 | COCH3, OH | ||||||||
| 4-chlorotestosterone | COMP 2 | 4 = 5 | =O | Cl | CH3 | CH3 | OCOCH3 | ||||||
| Androstanolone | COMP 3 | CH3 | CH3 | OH | |||||||||
| Betamethasone dipropionate | COMP 4 | 1 = 2, | =O | F | CH3 | OH | CH3 | CH3 | COCH2 OCOC2H5, OCOC2H5 | ||||
| Betamethasone valerate | COMP 5 | 1 = 2, | =O | F | CH3 | OH | CH3 | CH3 | COCH2OH, OCOC4H9 | ||||
| Budesonide | COMP 6 | 1 = 2, | =O | CH3 | OH | a | a, COCCH2OH | ||||||
| Cortisone acetate | COMP 7 | 4 = 5 | =O | CH3 | =O | CH3 | COCH2OCOCH3, OH | ||||||
| Dehydro-isoandrosterone | COMP 8 | 5 = 6 | OH | CH3 | CH3 | =O | |||||||
| Deoxycorticosterone acetate | COMP 9 | 4 = 5 | =O | CH3 | CH3 | COCH2OCOCH3 | |||||||
| Dexamethasone | COMP 10 | 1 = 2, | =O | F | CH3 | OH | CH3 | CH3 | CCOCH2OH, OH | ||||
| D-norgestrel | COMP 11 | 4 = 5 | =O | CH2CH3 | C≡CH, OH | ||||||||
| Estriol | COMP 12 | 1 = 2, | OH | OH | OH | ||||||||
| Estrone | COMP 13 | 2 = 3, | OH | CH3 | =O | ||||||||
| Ethinylestradiol | COMP 14 | 1 = 2, | OH | CH3 | C≡CH, OH | ||||||||
| Ethisterone | COMP 15 | 4 = 5 | =O | CH3 | CH3 | C≡CH, OH | |||||||
| Fludrocortisone acetate | COMP 16 | 4 = 5 | =O | F | CH3 | OH | CH3 | COCH 2OCOCH3, OH | |||||
| Formebolone | COMP 17 | 1 = 2, | CHO | =O | CH3 | OH | CH3 | CH3, OH | |||||
| Hydrocortisone | COMP 18 | 4 = 5 | =O | CH3 | OH | CH3 | COCH2OH, OH | ||||||
| Hydrocortisone acetate | COMP 19 | 4 = 5 | =O | CH3 | OH | CH3 | COCH2OCOCH3, OH | ||||||
| Medroxyprogesterone acetate | COMP 20 | 4 = 5 | =O | CH3 | CH3 | CH3 | OCOCH3, COCH3 | ||||||
| Methandriol | COMP 21 | 5 = 6 | OH | CH3, OH | |||||||||
| Methyl testosterone | COMP 22 | 4 = 5 | =O | CH3 | CH3 | CH3, OH | |||||||
| Norethisterone | COMP 23 | 4 = 5 | =O | CH3 | C≡CH, OH | ||||||||
| Prednisolone | COMP 24 | 1 = 2, | =O | CH3 | OH | CH3 | COCH2OH, OH | ||||||
| Prednisolone | COMP 25 | 1 = 2, | =O | CH3 | OH | CH3 | COCH2OCOCH2CH2OCOH, OH | ||||||
| Prednisolone acetate | COMP 26 | 1 = 2, | =O | CH3 | OH | CH3 | COCH2OCOCH3, OH | ||||||
| Prednisone | COMP 27 | 1 = 2, | =O | CH3 | =O | CH3 | COCH2OH, OH | ||||||
| Progesterone | COMP 28 | 4 = 5 | =O | CH3 | CH3 | COCH3 | |||||||
| Spironolactone | COMP 29 | 4 = 5 | =O | SCOCH3 | CH3 | CH3 | b | ||||||
| Testosterone | COMP 30 | 4 = 5 | =O | CH3 | CH3 | OH | |||||||
| Testosterone acetate | COMP 31 | 4 = 5 | =O | CH3 | CH3 | OCOCH3 | |||||||
| Testosterone propionate | COMP 32 | 4 = 5 | =O | CH3 | CH3 | OCOC2H5 | |||||||
| trans-Androsterone | COMP 33 | OH | CH3 | CH3 | =O | ||||||||
Chromatographic Conditions.
| Compound | Detector | Flow (mL/min) | Retention Factor ( | λ (nm) | Quantification Ion 2 (m/z) |
|---|---|---|---|---|---|
| COMP 1 | DAD 1 | 0.3 | 1.11 | 240 | - |
| COMP 2 | MS 3 | 0.5 | 4.67 | - | 365 [(M+CH3CN)+H]+ |
| COMP 3 | MS | 0.5 | 4.06 | - | 332 [(M+CH3CN)+H]+ |
| COMP 4 | DAD | 0.3 | 2.18 | 240 | - |
| COMP 5 | DAD | 0.5 | 1.45 | 240 | - |
| COMP 6 | DAD | 0.5 | 1.93 | 240 | - |
| COMP 7 | DAD | 0.4 | 3.05 | 240 | - |
| COMP 8 | DAD | 0.4 | 2.55 | 230 | - |
| COMP 9 | DAD | 0.4 | 2.43 | 240 | - |
| COMP 10 | DAD | 0.4 | 2.46 | 240 | - |
| COMP 11 | DAD | 0.4 | 3.34 | 240 | - |
| COMP 12 | DAD | 0.5 | 1.49 | 205 | - |
| COMP 13 | DAD | 0.5 | 3.98 | 205 | - |
| COMP 14 | DAD | 0.4 | 0.92 | 240 | - |
| COMP 15 | DAD | 0.3 | 2.56 | 205 | - |
| COMP 16 | DAD | 0.4 | 3.12 | 240 | - |
| COMP 17 | DAD | 0.4 | 2.58 | 220 | - |
| COMP 18 | DAD | 0.3 | 0.83 | 240 | - |
| COMP 19 | DAD | 0.5 | 0.96 | 240 | - |
| COMP 20 | DAD | 0.5 | 0.74 | 240 | - |
| COMP 21 | MS | 0.5 | 4.76 | - | 287 [(M-H2O)+H]+ |
| COMP 22 | DAD | 0.5 | 0.87 | 240 | - |
| COMP 23 | DAD | 0.4 | 2.48 | 240 | - |
| COMP 24 | DAD | 0.4 | 2.18 | 240 | - |
| COMP 25 | DAD | 0.4 | 3.11 | 244 | - |
| COMP 26 | DAD | 0.4 | 2.43 | 240 | - |
| COMP 27 | DAD | 0.4 | 2.45 | 240 | - |
| COMP 28 | DAD | 0.5 | 0.87 | 240 | - |
| COMP 29 | DAD | 0.5 | 4.04 | 238 | - |
| COMP 30 | DAD | 0.5 | 0.67 | 240 | - |
| COMP 31 | DAD | 0.5 | 1.12 | 240 | - |
| COMP 32 | DAD | 0.5 | 1.66 | 240 | - |
| COMP 33 | MS | 0.5 | 4.50 | - | 373 [(M+2CH3CN)+H]+ |
1 DAD: diode array detector, 2 performed at single ion monitoring (SIM) mode, 3 MS: mass spectrometry.
Analytical figures of merit of HPLC-UV and LC-MS methods.
| Compound | R 2 | Intercept | Slope | LOD 1 (μg/mL) | LOQ 2 (μg/mL) |
|---|---|---|---|---|---|
| COMP 1 | 0.9997 | 1123 | 43133 | 0.01 | 0.04 |
| COMP 2 | 0.9947 | −5470 | 38034 | 0.27 | 0.90 |
| COMP 3 | 0.9997 | 1252 | 16203 | 0.05 | 0.18 |
| COMP 4 | 0.9997 | −9501 | 28376 | 0.11 | 0.38 |
| COMP 5 | 0.9998 | −4479 | 20526 | 0.05 | 0.18 |
| COMP 6 | 0.9998 | 552 | 16428 | 0.04 | 0.12 |
| COMP 7 | 0.9996 | −3723 | 28562 | 0.03 | 0.12 |
| COMP 8 | 0.9997 | −993 | 4454 | 0.32 | 1.07 |
| COMP 9 | 0.9993 | −4166 | 26523 | 0.02 | 0.06 |
| COMP 10 | 0.9990 | −11577 | 13079 | 0.18 | 0.60 |
| COMP 11 | 0.9998 | −12551 | 43421 | 0.01 | 0.03 |
| COMP 12 | 1.0000 | −1090 | 51548 | 0.07 | 0.24 |
| COMP 13 | 0.9996 | −3671 | 51988 | 0.06 | 0.19 |
| COMP 14 | 0.9990 | 26763 | 79974 | 0.01 | 0.04 |
| COMP 15 | 1.0000 | 706 | 30294 | 0.01 | 0.03 |
| COMP 16 | 0.9999 | 7399 | 25115 | 0.04 | 0.14 |
| COMP 17 | 0.9992 | 12588 | 45247 | 0.05 | 0.18 |
| COMP 18 | 0.9997 | −6597 | 62213 | 0.01 | 0.03 |
| COMP 19 | 0.9985 | 26809 | 19890 | 0.03 | 0.10 |
| COMP 20 | 1.0000 | 802 | 37460 | 0.01 | 0.05 |
| COMP 21 | 0.9996 | 436 | 10500 | 0.05 | 0.16 |
| COMP 22 | 0.9999 | 798 | 25856 | 0.02 | 0.05 |
| COMP 23 | 0.9999 | −162 | 38688 | 0.01 | 0.04 |
| COMP 24 | 0.9999 | 1568 | 38840 | 0.03 | 0.10 |
| COMP 25 | 1.0000 | −353 | 13103 | 0.04 | 0.12 |
| COMP 26 | 0.9997 | −2111 | 22329 | 0.04 | 0.13 |
| COMP 27 | 0.9997 | −256 | 26564 | 0.04 | 0.14 |
| COMP 28 | 0.9997 | 916 | 32027 | 0.01 | 0.04 |
| COMP 29 | 1.0000 | −1564 | 26756 | 0.02 | 0.06 |
| COMP 30 | 1.0000 | 3599 | 113379 | 0.01 | 0.03 |
| COMP 31 | 1.0000 | 6794 | 25375 | 0.01 | 0.04 |
| COMP 32 | 1.0000 | 11227 | 54069 | 0.01 | 0.02 |
| COMP 33 | 0.9971 | −303 | 5860 | 0.03 | 0.10 |
1 LOD: based on S/N = 3 criteria, 2 LOQ: based on S/N = 10 criteria.