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Input CL to enter in PK-Sim from in vitro experiments #177
I some questions about the input metabolic CL to enter in PK-Sim:
Considering a first order process the three options available are:
1- Intrinsic clearance – (L/min).
I thank you in advance for your help
very good question! There are actually a number of inquiries to improve IVIVE workflow in PK-Sim (#101), and I think this question fits very well.
Just for your reference: you will also find the processes explained in the help menu in Chapter 15 (scroll down about 2/3 of the chapter).
Number 1 will be your best option:
From this, PKSim calculates a specific clearance. Then, PK-Sim does some scaling:
To obtain a value for plasma CL, you best generate a simple simulation with an IV dose only and once you have displayed the results, you can obtain the plasma CL value from the PK-Analysis which is calculated once you click the "Show PK-Analysis" button below your plot:
Hope this helps!
Hi Angèle and Stephan,
My understanding is a bit different in regards to following:
Actually, something like above fits better if you are selecting "In Vitro Metabolic Rate in Presence of Liver Microsomes - First Order" process, where you can directly plug in in vitro CL results in uL/min/mg protein format. However, for "Intrinsic Clearance - First Order", liver volume is pre-populated as 2.36 L. So, my understanding is that your input for "Intrinsic Clearance" should be scaled to whole liver. So, if you have in vitro clearance from microsomes assay and have first order clearance in let's say μL/min/mg protein format, you have to scale it to ul/min per whole human liver volume. Standard scaling factors are 39-53 mg microsomal protein/gm liver (MPPGL) and human liver 25.7 gm liver/kg body weight.
Sorry, I did not read original question thoroughly earlier. It seems like you have hepatocytes data and not microsomal enzyme assay. It also seems like you have already scaled from uL/min/million cell to mL/min/kg. I believe instead of scaling to per kg, you can just scale to average human liver weight, and then add it in Intrinsic clearance - first order process.
So, CL in uL/min/million cells * hepatocytes per gram liver (HPGL) * liver weight (gm) in average human
HPGL = 139e+6
I thank you very much for your input! I am extremely grateful for your answers that may be very complicated reading all together, but actually very helpful.
I think my issue is that I have information relative to several items of the metabolism module of PK-Sim but not to a single scaling workflow:
• But unfortunately I cannot enter this value in a microsomal system (as suggested by @krinaj and @msevestre , and commented by @StephanSchaller ) as it was not measured in microsomes. A practical solution would be the one from Stephan, ie. scaling considering how much mg proteins we have in a million hepatocytes (what you mention when writing “volume/cell and mg mic.protein/cell” right?), but to my opinion it is a manipulation that may introduce errors (ie. it is a workaround instead of a straight forward scaling, Tobias is also touching this point). I did this exercise for the sake of understanding (screenshots and explanations below) but it was not conclusive.
• The Total Hepatic Clearance option would be very handy (liver plasma CL or in vitro t1/2 that I actually have) but as I will later have to predict DDI involving CYP 3A4 metabolism, I have to define which proportion of the CL is driven by CYP 3A4.
taking the scaling factors from Krina, and simply converting uL into L. I then should enter 0.0825 l/min in the “intrinsic clearance – first order” process type, in the “intrinsic clearance” calculation parameters. That way I do not double scale or unscale what PK-Sim does, do I?
Lastly, I tried the workaround of “converting” my microsomal CL into a hepatocyte CL to see what the PK-Sim output would be.
and it results in a plasma CL of 1.32 mL/min/kg (red curve below). Of course I assume no other CL pathways (hepatic or extra hepatic).
Then in a new record I use the workaround:
and it results in a plasma CL of 0.34 mL/min/kg, still considering no other Cl pathways (green curve below). By the way, if I scale manually this CLint = 1.3205 uL/min/mg protein, using Liver blood flow and well stirred model, assuming Blood/plasma 1 as in PK-Sim and fraction unbound assay = 0.97 (calculated by PK-Sim), I get 0.23 mL/min/kg plasma CL, different from the built-in scaling.
so I understand that the workaround is not so easy and we would need to adjust other scaling factors, as I should get the same plasma CL.
Do we have a common understanding?
yes I think in principle we can agree on that. Your example shows very nicely that it might not be a good idea to scale from hepatoicyte in vitro data to microsomes.
Just one addidion regarding the scaling: I am not sure vere the liver weight value from krinaj comes from. For consistency reasons I would use the one from PK-sim: Liver volume is here 2.376 l. PK-sim assumes a general organ density of 1 so that would be 2.376 kg. As you assay uses only hepatocytes we should use only the fraction celullar for scaling. 2.3760.667 = 1.584 which is actually almost krinaj value (1561), but just for consistency I would take this one as PK-sim uses this value to normalise your intrinsic CL input to the specific clearance (Clint/(VlivF_cell).
Of course this wourkflow uses significant assumption like:
I am not sure if we can hold these and I am afraid these are the persistant trouble makers for IVIVE like e.g. here #125
Best regards, Tobias