Vd - Revision history

Kirilas: Added Vd description and link to poster

2022-10-20T08:40:36Z

Added Vd description and link to poster

← Older revision		Revision as of 08:40, 20 October 2022
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	* %PPB values represent the overall fraction of drug bound in human plasma, i.e. accounts for interactions with different proteins: albumin, alpha<sub>1</sub>-acid glycoprotein, lipoproteins, SHBG, transcortin etc. ''In vitro'' measurements of the extent of plasma protein binding usually involve equilibrium dialysis, ultrafiltration or ultracentrifugation methods.		* %PPB values represent the overall fraction of drug bound in human plasma, i.e. accounts for interactions with different proteins: albumin, alpha<sub>1</sub>-acid glycoprotein, lipoproteins, SHBG, transcortin etc. ''In vitro'' measurements of the extent of plasma protein binding usually involve equilibrium dialysis, ultrafiltration or ultracentrifugation methods.
	%PPB = (1 – ''f<sub>u</sub>'') * 100% where ''f<sub>u</sub>'' is fraction of free (unbound) drug in plasma ranging from 0 to 1.		%PPB = (1 – ''f<sub>u</sub>'') * 100% where ''f<sub>u</sub>'' is fraction of free (unbound) drug in plasma ranging from 0 to 1.
	* ~~Supplementary~~ Distribution\Vd module calculates apparent Volume of Distribution of drugs in human body expressed in liters per kg body weight (L/kg).		* Distribution\Vd module calculates apparent Volume of Distribution of drugs in human body expressed in liters per kg body weight (L/kg).

	===Experimental data===		===Experimental data===
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	Both %PPB and log ''K<sub>a</sub><sup>HSA</sup>'' are '''Trainable''' meaning that their Applicability Domains may be easily extended by addition of ‘in-house’ experimental data to the module Self-training Library. Notably, the baseline statistical model does not need to be rebuilt from scratch to account for data entered by the user. The model is retrained automatically as new compounds are added to the Library. Model trainability would be particularly useful for predicting serum albumin affinity constants as literature data sets are very sparse, thus the ability to take advantage of large ‘in-house’ libraries gives the potential for a significant improvement of both accuracy and reliability of calculations.		Both %PPB and log ''K<sub>a</sub><sup>HSA</sup>'' are '''Trainable''' meaning that their Applicability Domains may be easily extended by addition of ‘in-house’ experimental data to the module Self-training Library. Notably, the baseline statistical model does not need to be rebuilt from scratch to account for data entered by the user. The model is retrained automatically as new compounds are added to the Library. Model trainability would be particularly useful for predicting serum albumin affinity constants as literature data sets are very sparse, thus the ability to take advantage of large ‘in-house’ libraries gives the potential for a significant improvement of both accuracy and reliability of calculations.

			Volume of Distribution uses a mechanistic model based on physiological Øie-Tozer equation that relates Vd to the fraction unbound in plasma (calculated using %PPB model described above) and fraction unbound in tissues (calculated by a non-linear ionization-specific model in terms of LogP and pKa). For more technical details about %PPB and Vd models please refer to [http://perceptahelp.acdlabs.com/docs/Distribution.pdf].
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Kirilas: Fixed broken links

2022-10-14T12:07:25Z

Fixed broken links

← Older revision		Revision as of 12:07, 14 October 2022
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	===Experimental data===		===Experimental data===
	Experimental data that were utilized to build predictive models were collected from drug prescription information, reference pharmacokinetic tabulations and many original articles. The main sources of Vd data were well-known pharmacokinetic books: "Therapeutic Drugs" (ed. by C. dollery), and Goodman & Gilman's "The Pharmacological Basis of Therapeutics", while albumin affinity constants were collected mainly from original articles by Valko K. et al. ''J Pharm Sci.'' '''2003''';92(11):2236-48. [~~http~~://~~www3~~.~~interscience~~.~~wiley~~.~~com/journal/104556357~~/~~abstract~~], and Kratochwil N.A. et al. ''Biochem Pharmacol.'' '''2002''';64(9):1355-74. [~~http~~://~~www~~.~~sciencedirect~~.~~com~~/~~science?_ob=ArticleURL&_udi=B6T4P-461XRMC-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=290e081e0775f2be854e4e503160ba2a~~]		Experimental data that were utilized to build predictive models were collected from drug prescription information, reference pharmacokinetic tabulations and many original articles. The main sources of Vd data were well-known pharmacokinetic books: "Therapeutic Drugs" (ed. by C. dollery), and Goodman & Gilman's "The Pharmacological Basis of Therapeutics", while albumin affinity constants were collected mainly from original articles by Valko K. et al. ''J Pharm Sci.'' '''2003''';92(11):2236-48. [https://pubmed.ncbi.nlm.nih.gov/14603509], and Kratochwil N.A. et al. ''Biochem Pharmacol.'' '''2002''';64(9):1355-74. [https://pubmed.ncbi.nlm.nih.gov/12392818]
	The compiled data sets contain %PPB data for almost 1500 compounds, about 340 albumin affinity constants and almost 800 Vd values.		The compiled data sets contain %PPB data for almost 1500 compounds, about 340 albumin affinity constants and almost 800 Vd values.

Kirilas at 09:59, 15 June 2017

2017-06-15T09:59:28Z

← Older revision		Revision as of 09:59, 15 June 2017
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	<div class="mw-collapsible ~~mw-collapsed~~">		<div class="mw-collapsible">

	==Technical information==		==Technical information==

Kirilas at 10:14, 25 May 2016

2016-05-25T10:14:35Z

← Older revision		Revision as of 10:14, 25 May 2016
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	==Overview==		===Overview===
	~~<br />~~

	This module ~~contains a predictive algorithm that generates a quantitative estimate~~ of the ~~apparent Volume~~ of ~~Distribution (Vd) of a compound~~. ~~Physicochemical parameters, charge state, lipophilicity and hydrogen bonding capacity are automatically computed and used as inputs to the~~ predictive model of the ~~volume~~ of ~~distribution.~~<br />		This module provides mechanistic predictions of the apprent volume of distribution at steady-state in humans. The predictive model is based on Oie-Tozer pharmacokinetic equation that accounts for the extent of drug binding in both plasma and tissues. Calculations therefore use octanol/water logP (the major determinant of tissue binding) and unbound fraction in plasma (''f''<sub>u, plasma</sub>) as customizable input parameters.

	===~~Features~~===		===Module Interface===
	* Calculates the extent of tissue binding of candidate compounds expressed as Vd values and displays a comment regarding the effect of physicochemical properties (LogP and ionization) on drug distribution in the body.
	* Experimentally measured volume of distribution is displayed for up to 5 similar structures from the training set along with the corresponding literature references.
	~~<br />~~

	~~== Interface ==~~		[[Image:Distribution_Vd.png\|center]]
	<br />
			<ol>
			<li> logP and fraction unbound in plasma (''f''<sub>u, plasma</sub>) are calculated automatically. Alter these values to simulate the limiting effect of the compound's lipophilicity and/or plasma protein binding on its tissue disposition. [[Image:Distribution_Vd_Simulation.png\|right]]

			:a. Click the "Undo" button to restore the automatically calculated property value (''f''<sub>u, plasma</sub> in the current example) for a compound and recalculate Vd using default parameter values

	~~[[Image~~:~~Distribution_Vd~~.~~png\|center]]~~		:b. Click to recalculate Vd using the currently specified parameter values
	~~<br />~~

	# Calculated apparent volume of distribution of a compound:<br>[[File:Distribution_vd_scale.png\|300px]]		</li>
	~~# A general estimate of likely volume of distribution for compounds of this type, based on chemical structure and physicochemical properties~~		<li> Calculated apparent volume of distribution of a compound:<br>[[File:Distribution_vd_scale.png\|300px]]</li>
	# Up to 5 similar structures in the training set with experimental ~~quantitative~~ values ~~of apparent volume of distribution~~ and ~~literature~~ references		<li> Up to 5 most similar structures from the training set with experimental Vd values and references</li>
	<br />		</ol>

Kirilas: /* Model development (technical details) */

2013-02-14T10:50:05Z

Model development (technical details)

@@ Line 41: / Line 41: @@
 ===Model development (technical details)===
-Both %PPB and log ''K<sub>a</sub><sup>HSA</sup>'' predictive models are '''Trainable''' meaning that their Applicability Domains may be easily extended by addition of ‘in-house’ experimental data to the module Self-training Library. Notably, the baseline statistical model does not need to be rebuilt from scratch to account for data entered by the user. The model is retrained automatically as new compounds are added to the Library. Model trainability would be particularly useful for predicting serum albumin affinity constants as literature data sets are very sparse, thus the ability to take advantage of large ‘in-house’ libraries gives the potential for a significant improvement of both accuracy and reliability of calculations.
+The predictive models of %PPB and log ''K<sub>a</sub><sup>HSA</sup>'' were derived using GALAS (Global, Adjusted Locally According to Similarity) modeling methodology (please refer to [http://www.ncbi.nlm.nih.gov/pubmed/20373217] for more details).
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Kristina: /* Interface */

2012-05-29T13:16:42Z

Interface

← Older revision		Revision as of 13:16, 29 May 2012
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	<br />		<br />

	# Calculated apparent volume of distribution of a compound:<br>[[File:~~distribution_vd_scale~~.png\|300px]]		# Calculated apparent volume of distribution of a compound:<br>[[File:Distribution_vd_scale.png\|300px]]
	# A general estimate of likely volume of distribution for compounds of this type, based on chemical structure and physicochemical properties		# A general estimate of likely volume of distribution for compounds of this type, based on chemical structure and physicochemical properties
	# Up to 5 similar structures in the training set with experimental quantitative values of apparent volume of distribution and literature references		# Up to 5 similar structures in the training set with experimental quantitative values of apparent volume of distribution and literature references

Kristina: /* Features */

2012-05-17T13:52:53Z

Features

← Older revision		Revision as of 13:52, 17 May 2012
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	* Calculates the extent of tissue binding of candidate compounds expressed as Vd values and displays a comment regarding the effect of physicochemical properties (LogP and ionization) on drug distribution in the body.		* Calculates the extent of tissue binding of candidate compounds expressed as Vd values and displays a comment regarding the effect of physicochemical properties (LogP and ionization) on drug distribution in the body.
	* Experimentally measured volume of distribution is displayed for up to 5 similar structures from the training set along with the corresponding literature references.		* Experimentally measured volume of distribution is displayed for up to 5 similar structures from the training set along with the corresponding literature references.
	* A clear and straightforward interface ensures quick and easy addition of user-defined data to the Self-training Library.
	<br />		<br />

Kristina: /* Overview */

2012-05-17T13:51:04Z

Overview

← Older revision		Revision as of 13:51, 17 May 2012
Line 2:		Line 2:
	<br />		<br />

	This module contains a predictive algorithm that generates a quantitative estimate of the apparent ~~volume~~ of ~~distribution~~ of a compound. Physicochemical parameters, charge state, lipophilicity and hydrogen bonding capacity are automatically computed and used as inputs to the predictive model of the volume of distribution.<br />		This module contains a predictive algorithm that generates a quantitative estimate of the apparent Volume of Distribution (Vd) of a compound. Physicochemical parameters, charge state, lipophilicity and hydrogen bonding capacity are automatically computed and used as inputs to the predictive model of the volume of distribution.<br />

	===Features===		===Features===
			* Calculates the extent of tissue binding of candidate compounds expressed as Vd values and displays a comment regarding the effect of physicochemical properties (LogP and ionization) on drug distribution in the body.
	~~===Key product capabilities===~~		* Experimentally measured volume of distribution is displayed for up to 5 similar structures from the training set along with the corresponding literature references.
	Distribution module enables the researcher to get a quick estimation of the percentage of a compound bound in human plasma (corresponding to interactions with all major carrier proteins) prior to experimental determination by equilibrium dialysis or ultracentrifugation. Ranking and selecting lead compounds according to the influence of plasma protein binding on their pharmacokinetic behavior and free drug concentrations. The predictive algorithms for calculation of human serum albumin affinity constants and volume of distribution of drug candidates are also available. The major feature of Protein Binding module is its Trainability. ‘In-house’ measured values can be added to the model Self-training Library for an instant expansion of model Applicability Domain and improvement in accuracy and reliability of predictions.

	~~===Features===~~
	* Protein binding module calculates %PPB – the cumulative percentage of the analyzed compound bound to human plasma proteins (such as albumin, alpha<sub>1</sub>-acid glycoprotein and others) and log ''K<sub>a</sub><sup>HSA</sup>'' – human serum albumin affinity constants. with Reliability Index (RI) values of the corresponding predictions.
	* RI values represent a quantitative evaluation of prediction confidence. High RI shows that the calculated value is likely to be accurate, while low RI indicates that no similar compounds with consistent data are present in the training set.
	* Main plasma proteins that mostly contribute to binding of different compound classes in human plasma are enumerated in the textual comments next to the prediction results.
	* Supplementary Vd module calculates the extent of tissue binding of candidate compounds expressed as ~~Volume of Distribution (~~Vd) values and displays a comment regarding the effect of physicochemical properties (LogP and ionization) on drug distribution in the body.
	* Experimentally measured ~~extent of plasma protein binding, human serum albumin affinity constants, and~~ volume of distribution ~~are~~ displayed for up to 5 similar structures from the training set along with the corresponding literature references.
	* Predictions of Distribution properties are also available in batch mode, allowing the user to calculate the relevant parameters for multiple molecules automatically. Large compounds libraries containing thousands of molecules are processed in a reasonable amount of time. (Do we have some metric for this statement about 'reasonable amount of time'? - PDW)
	* A clear and straightforward interface ensures quick and easy addition of user-defined data to the Self-training Library.		* A clear and straightforward interface ensures quick and easy addition of user-defined data to the Self-training Library.

	<br />		<br />

Kristina: Created page with "==Overview==
This module contains a predictive algorithm that generates a quantitative estimate of the apparent volume of distribution of a compound. Physicochemical p..."

2012-05-17T13:32:48Z

Created page with "==Overview== This module contains a predictive algorithm that generates a quantitative estimate of the apparent volume of distribution of a compound. Physicochemical p..."

New page

==Overview==
 

This module contains a predictive algorithm that generates a quantitative estimate of the apparent volume of distribution of a compound. Physicochemical parameters, charge state, lipophilicity and hydrogen bonding capacity are automatically computed and used as inputs to the predictive model of the volume of distribution. 

===Features===

===Key product capabilities===
Distribution module enables the researcher to get a quick estimation of the percentage of a compound bound in human plasma (corresponding to interactions with all major carrier proteins) prior to experimental determination by equilibrium dialysis or ultracentrifugation. Ranking and selecting lead compounds according to the influence of plasma protein binding on their pharmacokinetic behavior and free drug concentrations. The predictive algorithms for calculation of human serum albumin affinity constants and volume of distribution of drug candidates are also available. The major feature of Protein Binding module is its Trainability. ‘In-house’ measured values can be added to the model Self-training Library for an instant expansion of model Applicability Domain and improvement in accuracy and reliability of predictions.

===Features===
* Protein binding module calculates %PPB – the cumulative percentage of the analyzed compound bound to human plasma proteins (such as albumin, alpha1-acid glycoprotein and others) and log ''KaHSA'' – human serum albumin affinity constants. with Reliability Index (RI) values of the corresponding predictions.
* RI values represent a quantitative evaluation of prediction confidence. High RI shows that the calculated value is likely to be accurate, while low RI indicates that no similar compounds with consistent data are present in the training set.
* Main plasma proteins that mostly contribute to binding of different compound classes in human plasma are enumerated in the textual comments next to the prediction results.
* Supplementary Vd module calculates the extent of tissue binding of candidate compounds expressed as Volume of Distribution (Vd) values and displays a comment regarding the effect of physicochemical properties (LogP and ionization) on drug distribution in the body.
* Experimentally measured extent of plasma protein binding, human serum albumin affinity constants, and volume of distribution are displayed for up to 5 similar structures from the training set along with the corresponding literature references.
* Predictions of Distribution properties are also available in batch mode, allowing the user to calculate the relevant parameters for multiple molecules automatically. Large compounds libraries containing thousands of molecules are processed in a reasonable amount of time. (Do we have some metric for this statement about 'reasonable amount of time'? - PDW)
* A clear and straightforward interface ensures quick and easy addition of user-defined data to the Self-training Library.

 

== Interface ==
 

[[Image:Distribution_Vd.png|center]]
 

# Calculated apparent volume of distribution of a compound: [[File:distribution_vd_scale.png|300px]]
# A general estimate of likely volume of distribution for compounds of this type, based on chemical structure and physicochemical properties
# Up to 5 similar structures in the training set with experimental quantitative values of apparent volume of distribution and literature references
 

<div class="mw-collapsible mw-collapsed">

==Technical information==
 

<div class="mw-collapsible-content">
===Calculated quantitative parameters===
Parameters calculated by Distribution\Protein Binding module include percentage plasma protein binding values (%PPB) and log ''KaHSA'' constants.
These properties are related, but characterize provide slightly different information about the considered process.
* log ''KaHSA'' represents the drug’s affinity constant to human serum albumin – the major carrier protein in plasma. Experimental data come from direct chromatographic determination of binding strength to that particular protein.
log ''KaHSA'' = log ([LA]/([L][A])) where [LA] is concentration of ligand bound to albumin, [L] – that of free ligand, and [A] – concentration of free albumin which is estimated at ~0.6 mM in human plasma.
* %PPB values represent the overall fraction of drug bound in human plasma, i.e. accounts for interactions with different proteins: albumin, alpha1-acid glycoprotein, lipoproteins, SHBG, transcortin etc. ''In vitro'' measurements of the extent of plasma protein binding usually involve equilibrium dialysis, ultrafiltration or ultracentrifugation methods.
%PPB = (1 – ''fu'') * 100% where ''fu'' is fraction of free (unbound) drug in plasma ranging from 0 to 1.
* Supplementary Distribution\Vd module calculates apparent Volume of Distribution of drugs in human body expressed in liters per kg body weight (L/kg).

===Experimental data===
Experimental data that were utilized to build predictive models were collected from drug prescription information, reference pharmacokinetic tabulations and many original articles. The main sources of Vd data were well-known pharmacokinetic books: "Therapeutic Drugs" (ed. by C. dollery), and Goodman & Gilman's "The Pharmacological Basis of Therapeutics", while albumin affinity constants were collected mainly from original articles by Valko K. et al. ''J Pharm Sci.'' '''2003''';92(11):2236-48. [http://www3.interscience.wiley.com/journal/104556357/abstract], and Kratochwil N.A. et al. ''Biochem Pharmacol.'' '''2002''';64(9):1355-74. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T4P-461XRMC-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=290e081e0775f2be854e4e503160ba2a]
The compiled data sets contain %PPB data for almost 1500 compounds, about 340 albumin affinity constants and almost 800 Vd values.

===Model development (technical details)===
The models for predicting %PPB and log ''KaHSA'' constants were developed with Algorithm Builder using a novel methodology consisting of two parts:
* Global baseline statistical model employing binomial PLS with multiple bootstrapping using a predefined set of fragmental descriptors.
* Local correction to baseline prediction based on analysis of experimental data for similar compounds.
The underlying methodology enables obtaining an intrinsic evaluation of prediction confidence by the means of Reliability Index (RI) values calculated for each prediction. RI ranging from 0 to 1 serves as an indication whether a submitted compound falls within the Model Applicability Domain. Two criteria influence the calculation od Reliability Index of a prediction:
* Similarity of the analyzed molecule to compounds in the Self-training Library (prediction is unreliable if no similar compounds have been found in the Library).
* Consistency of experimental data for similar compounds – reliability of calculated values is lower is data for similar compounds are discrepant.

Both %PPB and log ''KaHSA'' predictive models are '''Trainable''' meaning that their Applicability Domains may be easily extended by addition of ‘in-house’ experimental data to the module Self-training Library. Notably, the baseline statistical model does not need to be rebuilt from scratch to account for data entered by the user. The model is retrained automatically as new compounds are added to the Library. Model trainability would be particularly useful for predicting serum albumin affinity constants as literature data sets are very sparse, thus the ability to take advantage of large ‘in-house’ libraries gives the potential for a significant improvement of both accuracy and reliability of calculations.
</div>
</div>