Positional
Scanning Libraries:
Briefly we will describe the
following features of Mixture Sciences' Positional Scanning Libraries;
overview, synthesis,
deconvolution, and screening.
For a comprehensive review on "Mixture-Based Synthetic Combinatorial
Libraries" please read Houghten,
R.A., et al. J. Med. Chem. 42:3743 1999.
When searching for viable drug candidates two key factors have to be addressed; speed and economics. The goal is to find the best candidates with the least amount of time and money. There have been many advances in the past decade to meet these goals. One such method is the use of mixture based libraries and specifically Positional Scanning Libraries. Positional Scanning Libraries have given researches the ability to effectively search upwards of a trillion compounds in less than a week. This is unparalleled by any other technique.
A Positional Scanning Library is a collection of compounds with the same core structure that are organized in a manner that uses mixtures to exponentially reduce the number of samples that need to be tested.
For example the above Positional Scanning Library has the core structure of the triangle. It also has three positions of diversity R1, R2, and R3. The R1 position could contain one of the following letters B, P or S; the R2 position could contain A, E or I; and finally the R3 position could contain a N, R or T. That means that there is a possibility of 3 x 3 x 3 = 27 different compounds. Traditionally you would need to make all 27 compounds and test each one separately, however using the positional scanning method it is only necessary to make 3 + 3 + 3 = 9 samples.
The Mixture Sciences Method is able to reduce the number of samples needed by using mixtures. The mixtures are represented by an X in the above example. For example sample #1 in the Mixture Sciences Method is BXX. The X is actually a chemical mixture of A, E and I and the X is chemical mixture of N, R and T. This means that Mixture Sciences vial #1 contains an equal amount of all the compounds in vials #1 through #9 of the Traditional Method. Similarly Mixture Sciences vial #2 contains an equal amount of all the compounds in vials #10 through #18 of the Traditional Method. Finally vial #3 contains an equal amount of all the compounds in vials #21 through #27. In the same fashion we scan through the rest of the positions R2 and R3 to create the Positional Scanning Library.
By testing vials #1 through #3 you will be able to tell which letter is best in position R1, namely B, P or S. Similarly you can test vials #4 through #6 to determine if A, E or I is best in position R2. Finally you can test vials #7 through #9 to determine which letter is best in the R3 position, namely N, R, or T. You can then combine the information to predict which compound is the best, which is then synthesized and tested to confirm the activity.
The idea of a Positional
Scanning Library is to make and test every possible variation of a single
compound template that is economically viable. Our scientists begin by
searching for acceptable compound templates. A candidate compound template
must meet the following criteria: the structure is known or suspected
to be of biological importance, the structure can be produced under simple
and inexpensive synthetic conditions, and the structure contains numerous
possible diversity elements.
The above compound
template (Bicyclic Guanidine) is an ideal candidate because it meets all
the specified criteria; it contains a guanidine group which is an important
feature in receptor binding, it can be produced under simple and inexpensive
conditions and finally it contains three positions of diversity (the red
groups) which makes the total number of individual compounds possible
75 x 75 x 60 = 337,500.
After the template is selected and the synthesis conditions are optimized to include the largest number of diversity elements, the Positional Scanning Library is synthesized.
The
deconvolution procedures are an essential element in the identification
of active compounds from mixture-based combinatorial libraries. As mentioned
previously the design of Positional
Scanning Libraries
exponentially reduces the number of samples that need to be tested in
order to find active compounds. To illustrate this point we will examine
the template described in the overview.
For example let us say that we tested all 27 compounds
from the traditional method and found only one active compound #4 BEN.
When testing our Positional Scanning Library we only need to test 9 samples
to come to this same conclusion. We begin by testing the first three samples
as illustrated below.
We note that BEN
is only present in sample #1 so sample #1 is the
only one of the first three that will be active. From testing the first
three samples we now know that B
is the best choice for R1. Next we test vials #4 through #6 as illustrated
below.
We note that BEN
is only present in sample #5
so sample #5 is the only one of these three samples that will be active.
From
testing the second three samples we now know that E
is the best choice for R2. Next we test vials #7 through #9 as illustrated
below.
We
note that BEN
is only present in sample #7
so sample #7 is the only one of these three samples that will be active.
From
testing the last three samples we now know that N
is the best choice for R3. We now know that BEN
is the active compound and we only made and tested
9 samples instead of 27. A time and financial savings of over 66%. However
our Positional
Scanning Libraries are typically much larger
than 27 possible compounds. For example the Bicyclic Guanidine Positional
Scanning Library mentioned in the
synthesis section contains
75 x 75 x 60 = 337,500 total compounds, but when using the positional
scanning method you only need to make and test 210 samples, a savings
of over 99%. For information on some of the Positional
Scanning Libraries available
through Mixture Sciences, Inc. please see, peptide,
peptidomimetics, or small
molecule.
The screening of mixture is not a new concept. In vivo and in vitro biochemical interactions, such as receptor-ligand interactions, routinely occur in a vast milieu of other compounds (e.g., proteins, salts, cofactors, amino acids). Many of the existing approved therapeutics are directly identified from natural product mixtures or are derived from these compounds. Compared to natural product extracts or bacterial broths, Positional Scanning Libraries have a number of clear inherent advantages: (1) the concentration of individual compounds within the libraries is approximately equal: (2) the structures of the compounds making up the libraries are known; and (3) no synthetic hurdles have to be overcome once an active individual compound has been identified.1
In addition Positional Scanning Libraries have the advantage of greatly decreasing the economics and time constrains of screening a vast number of compounds. Screening of millions of compounds can be accomplished even in assays that are not formatted for conventional high-throughput.
