HSP Application note #35
Caco-2 Permeability and Solubility Parameter (HSP)2010.4.25
HSPiP Team Senior Developer, Dr. Hiroshi Yamamoto
I got the paper about Caco-2 cell monolayer apparent Permeability.
QSAR study of pharmacological permeabilities
They build QSAR model with CODESSA Pro as descriptors generator.
And almost all important descriptors are calculated by AM1 (Semi-empirical molecular orbital method).
I know almost all these QSAR analysis are based on this technology.
But it is very strange to me.
Why permeability can be explained by HOMO or LUMO?
So, I dare to explain permeability with HSP.
Hansen Solubility Parameters (HSP)Hansen Solubility Parameters(HSP) were developed by Charles M. Hansen as a way of predicting if one material will dissolve in another and form a solution. They are based on the idea that "like dissolves like" where one molecule is defined as being 'like' another if it bonds to itself in a similar way. What can perhaps be surprising is that one can assign HSP to so many different things. Gases like carbon dioxide, solids like carbon-60, sugar, and biological materials like human skin, depot fat, DNA, and even some proteins all have HSP. The list can be continued with drugs, polymers, plasticizers, and in fact any organic material and even many inorganic materials like salts. The only requirement for an experimental confirmation is that the material must behave differently in a sufficient number of test solvents upon contact. Pirika JAVA Demo Applet calculate HSP. HSPLight is available here. |
CAS | Name | ||||||
57-50-1 | Sucrose | 67-56-1 | Methyl alcohol | 599-79-1 | Sulfasalazine | ||
129618-40-2 | Nevirapine | 52-53-9 | Verapamil | 103-90-2 | Acetaminophen | ||
3930-20-9 | Sotalol | 60142-96-3 | Gabapentin | 62571-86-2 | Captopril | ||
50-28-2 | Estradiol | 6452-71-7 | Oxprenolol | 51-34-3 | Scopolamine | ||
58-22-0 | Testosterone | 13655-52-2 | Alprenolol | 75847-73-3 | Enalapril | ||
50-24-8 | Prednisolone | 37350-58-6 | Metoprolol | 738-70-5 | Trimethoprim | ||
50-23-7 | Hydrocortisone | 23031-25-6 | Terbutaline | 60-80-0 | Antipyrine | ||
57-83-0 | Progesterone | 30516-87-1 | Zidovudine | 50-53-3 | Chlorpromazine | ||
50-22-6 | Corticosterone | 37517-30-9 | Acebutolol | 56-75-7 | Chloramphenicol | ||
39562-70-4 | Nitrendipine | 34841-39-9 | Bupropion | 15722-48-2 | Olsalazine | ||
72509-76-3 | Felodipine | 15687-27-1 | Ibuprofen | 70458-96-7 | Norfloxacine | ||
83-43-2 | Methylprednisolone | 22204-53-1 | Naproxen | 23214-92-8 | Doxorubicin | ||
50-02-2 | Dexamethasone | 6673-35-4 | Practolol | 81-81-2 | Warfarin | ||
33419-42-0 | Etoposide | 29122-68-7 | Atenolol | 126-07-8 | Griseofulvin | ||
466-06-8 | Proscillaridin | 637-07-0 | Clofibrate | 22071-15-4 | Ketoprofen | ||
114-07-8 | Erythromycin | 525-66-6 | Propranolol | 28797-61-7 | Pirenzepine | ||
59865-13-3 | Cyclosporine | 57-66-9 | Probenecid | 36322-90-4 | Piroxicam | ||
73384-59-5 | Ceftriaxone | 42200-33-9 | Nadolol | 15307-86-5 | Diclofenac | ||
54-31-9 | Furosemide | 42399-41-7 | Diltiazem | 57-41-0 | Phenytoin | ||
66357-35-5 | Ranitidine | 54910-89-3 | Fluoxetine | 79660-72-3 | Fleroxacin | ||
127779-20-8 | Saquinavir | 137-58-6 | Lidocaine | 58-93-5 | Hydrochlorothiazide | ||
59277-89-3 | Acyclovir | 51-43-4 | Epinephrine | 74103-06-3 | Ketorolac | ||
126222-34-2 | Remikiren | 77-10-1 | Phencyclidine | 91-64-5 | Coumarin | ||
59-05-2 | Methotrexate | 88495-63-0 | Artesunate | 5786-21-0 | Clozapine | ||
51481-61-9 | Cimetidine | 36894-69-6 | Labetalol | 4205-90-7 | Clonidine | ||
116644-53-2 | Mibefradil | 57-13-6 | Urea | 439-14-5 | Diazepam | ||
26839-75-8 | Timolol | 58-15-1 | Aminopyrine | 58-94-6 | Chlorothiazide | ||
13523-86-9 | Pindolol | 87-08-1 | Penicillin V | 298-46-4 | Carbamazepine | ||
71125-38-7 | Meloxicam | 5051-62-7 | Guanabenz | 81-07-2 | Saccharin | ||
56-54-2 | Quinidine | 26787-78-0 | Amoxicillin | ||||
53-86-1 | Indomethacin | 54-11-5 | Nicotine | ||||
58-08-2 | Caffeine | 28395-03-1 | Bumetanide | ||||
19216-56-9 | Prazosin | 50-78-2 | Acetylsalicylic acid | ||||
58-55-9 | Theophyline | 51-61-6 | Dopamine | ||||
22916-47-8 | Miconazole | 69-72-7 | Salicylic acid | ||||
25614-03-3 | Bromocriptine | 50-49-7 | Imipramine | ||||
63590-64-7 | Terazosine | 148-82-3 | Melphalan | ||||
43200-80-2 | Zopiclone | 50-47-5 | Desipramine | ||||
65277-42-1 | Ketoconazole | 15676-16-1 | Sulpiride | ||||
78755-81-4 | Flumazenil | 66-22-8 | Uracil |
At first, I compiled CAS number for these compounds, and get the Smiles notations.
Smiles(Simplified Molecular Input Line Entry Syntax) SMILES is a string obtained by printing the symbol nodes encountered in a depth-first tree traversal of a chemical graph. Pirika JAVA Demo Applet getting Smiles. Draw2Smiles is available here. |
Once I got the Smiles, HSPiP automatically break molecule into functional groups.
Y-MB Properties EstimationY-MB break Smiles into correspponding Functional Groups and Estimate various Properties. These estimation schemes are come from Pirika technologies. Pirika JAVA Demo Applet calculate Properties. PirikaLight is available here. |
I analyzed logPapp(Coca-2) with Multiple Regression.
I can estimate logPapp(Coca-2) from only functional groups. (If this group contribution method did not converged, HOMO LUMO or other descriptions may be needed.)
And Molecular Volume, logP, logS did not have good correlation with logPapp(Caco-2).
I run the SOM analysis.
SOM: Self Organization Map Neural Network
|
-4.0> blue area > -5.0. Average of blue area [19.1, 7.1, 7.3]
-6.0> orange area >-7.0. Average of Orange Area [19.5, 12.8, 13.8]
No. 10, Ranitidine [17.8, 7.8, 7.8] |
No. 22, Cimetidine [17.8, 12.1, 6.1] |
These two are in blue area, even though -5.0 > logPapp(Caco-2)
Maybe this come from (-NH)2C=N group.
This group should increase dP or dH.
So, I need define new functional group. If someone have HPLC data of these two compounds, please give me. I will determine HSP.
No. 37 [17.8, 8.9, 14.9] |
No. 67 [20.9, 17.7, 14.1] |
No. 70 [20.1, 14.4, 12.5] |
No. 73 [19.5, 10.5, 14.2] |
These four are very near to Orange area, even though -5.0 < logPapp(Caco-2)
I can say that these compounds are so complicated and estimated HSP is very bad.
Other case, if I have new molecule, I calculate SOM and find the winner, I can predict the range of logPapp(Caco-2).
It is not Quantitative but Qualitative. But sometime you can get much simple model and you can understand phenomena more easily.
Other topic of Bio Medical
GC data of class 1, class 2 solvents in Q3C:
HSP and Tamiflu: Solubility parameter of Tamiflu or other H1N1 antiviral compounds
HSP for Rabbit: How to design eau de Cologne for rabbit. what LD50(skin, rabbit) means.
HSP and logP: logP, logKow, it is just HSP volume.
HSP and Carcinogenicity: SOM(self organization map) analysis of Poly-chlorinated compounds
HSP and Endocrine Disruptor: categorize by SOM.
HSP and AntimicroBial. Sulfa Drugs and other kind of Drugs.
Gall stone solubilizer: How to dissolve Cholesterol base Gall Stone.
Caco-2 cell monolayer apparent Permeability:SOM analysis