GSJ:Received May 29, 2005: http://wbabin.net/saba/saba43.htm

Drug resistant is a fundamental, perhaps the fundamental problem in medicine. One embodiment of the present invention is the restoration of drug susceptibility to drug-resistant targets. Figure 1 depicts drug resistant wherein the drug no longer can bind to a mutated target.

Targets often are receptors, and enzymes such as polymerases, proteases, kinases, cell wall synthases, etc...

One embodiment of the invention disclosed herein is a means of discovering molecules able to modify drug resistant targets such that their drug susceptibility is resorted. Figure 2 exemplifies the process.

An important aspect of the process in this figure is the formation of a complex comprising a drug (herein conjugated to a support), a resistant target (for example HIV protease), and an encoded modulator (herein a recombinant phage). Note that such complex formation occurs if a phage is able to bind the resistant target such that its binding to the support-affixed drug is restored. Usually resorted binding to the drug results from allosteric modification of the resistant target. To increase likelihood of complex formation, the phage library could be preselected using native and/or mutant support-affixed target.

Figure 3 depicts a similar process, utilized to find molecules which induce an unmutated drug target to efficiently bind a ligand which it would not normally bind or binds poorly. Preferably this nonbinding or poorly binding ligand is very similar in structure to a drug that does very efficiently bind the unmutated target.

Figure 4 is yet another example of utilizing the invention in drug discovery.

Herein is depicted a process for isolating peptides which inhibit a native unmutated target's binding to a support-affixed ligand. If the naturally occurring target protein (purple hexagon) is an enzyme, the support affixed ligand (yellow square) could be a modified substrate resistant to the action of the enzyme but still able to bind the target. Notice that the phage library used has been preselected to bind target, and that only those phage able to bind and modify the target such that it no longer binds the support-affixed ligand pass through the column. In Figure 4, target is modified allosterically, however other means by which the phage could interfere with the native target's binding of ligand are possible, such as direct competition with at the target's ligand-binding site.

In addition to drug discovery, an interesting in vitro utility of the process similar to that in Figure 4 would be to select for phage-displayed peptides which allosterically or otherwise gently release an affinity purification antibody from its isolated ligand. To grasp this idea, let us return to Figure 4 and assume the purple hexagon is a single chain antibody. The process would yield phage which bound this antibody and released it from the support-affixed ligand.

Now as shown in Figure 5, let us take the same single chain antibody and conjugate it to a support.

As depicted here, this support-affixed antibody has bound to and purified the ligand. The next step is to utilize the modulatory peptide previously discovered to gently release the bound ligand. Of course other highly specific target-binding proteins could replace the antibody.

Modifications of the above inventions are numerous, some of which are:

First, the encoded library can be of any sort, including cis-display and cell-based display libraries. Indeed the library need not be encoded at all, for example it could be a peptide library or synthetic small organic molecule library, and the complex-associated members thereof identified by sequencing or mass spectrometry.

Second, the 'ligand' may be a relatively large molecule such as a high molecular weight protein, and the processes could be utilized to disrupt or induce protein-protein association. Also the ligand need not be support-affixed, for example it could be precipitated with antibody subsequent to complex formation.

This invention is considered exceptionally valuable and a US patent application is anticipated to be filed. However, in the mean time it is hoped that others with laboratory facilities will investigate its full potential.

The following provisional claims are an attempt to encompass important aspects of this invention.

Addendum 5/30/05

As mentioned above, the ligand need not be support-affixed, and the potential use of antibodies in such cases was mentioned.

Figure 6 examples the use of a soluble ligand, in conjunction with a support-affixed antibody.

The depictions used in this figure are similar to those utilized in Figures 1 and 2. Important this process is that the support-affixed antibody only recognizes the the wild-type-like structured target bound to the drug.
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Addendum 5/31/05

Due to binding of phage to sites on the target which do not function to modulate its binding, it may be necessary to individually analyze prescreened and isolated phage.
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Addendum 6/3/05

When preselecting for target-binding phage, it would likely be advantageous to include the drug it binds so as to mask phage from binding at the drug-binding site of the target.