US 20080220441A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2008/0220441 A1 Birnbaum et al. (43) Pub. Date: Sep. 11, 2008 (54) ADVANCED DRUG DEVELOPMENT AND Related U.S. Application Data MANUFACTURING (63) Continuation-in-part of application No. 09/859,701, filed on May 16, 2001, Continuation-in-part of appli (76) Inventors: Eva R. Birnbaum, Los Alamos, cation No. 10/206,524, filed on Jul. 25, 2002, now NM (US); Andrew T. Koppisch, abandoned, Continuation-in-part of application No. Flagstaff, AZ (US); Sharon M. 10/621,825, filed on Jul. 16, 2003, now Pat. No. 6,858, Baldwin, Santa Fe, NM (US); 148. Benjamin P. Warner, Los Alamos, (60) Provisional application No. 60/850,594, filed on Oct. NM (US); T. Mark McCleskey, 10, 2006. Los Alamos, NM (US); Jeffrey Joseph Stewart, Los Alamos, NM Publication Classification (US); Jennifer A. Berger, Los (51) Int. C. Alamos, NM (US); Michael N. GOIN 33/53 (2006.01) Harris, Los Alamos, NM (US); GOIN 2L/76 (2006.01) Anthony K. Burrell, Los Alamos, GOIN 33/68 (2006.01) NM (US) GOIN 23/223 (2006.01) (52) U.S. Cl. ............ 435/7.1; 436/501; 436/172:436/86; Correspondence Address: 378/45 LOSALAMOS NATIONAL SECURITY, LLC (57) ABSTRACT LOS ALAMOS NATIONAL LABORATORY, PPO. BOX 1663, LC/IP, MS A187 X-ray fluorescence (XRF) spectrometry has been used for LOSALAMOS, NM 87545 (US) detecting binding events and measuring binding selectivities between chemicals and receptors. XRF may also be used for estimating the therapeutic index of a chemical, for estimating (21) Appl. No.: 11/974,156 the binding selectivity of a chemical versus chemical analogs, for measuring post-translational modifications of proteins, (22) Filed: Oct. 10, 2007 and for drug manufacturing. US 2008/0220441 A1 Sep. 11, 2008 ADVANCED DRUG DEVELOPMENT AND 0006. The chemical properties and in particular, the bind MANUFACTURING ing properties of a protein depend almost entirely on the exposed Surfaceamino acid residues of the polypeptide chain. RELATED APPLICATIONS These residues can form weak noncovalent bonds with other 0001. This application is a continuation-in-part of U.S. molecules. An effective binding between the protein, one patent application Ser. No. 09/859,701, now U.S. Patent example of a group of materials herein referred to as “recep Application 20030027129 entitled “Method for Detecting tors', and the material that binds to the receptor, referred to Binding Events. Using Micro-X-ray Fluorescence Spectrom herein as “chemical, generally requires that many weak etry,” which was published on Feb. 6, 2003, and a continua bonds form between the protein receptor and the chemical. tion-in-part of U.S. patent application Ser. No. 10/206,524, Chemicals include organic molecules, inorganic molecules, salts, metal ions, and the like. The bonds between the protein now U.S. Patent Application 2004.0017884 entitled “Flow and the chemical form at the “binding site' of the protein. The Method and Apparatus for Screening Chemicals. Using binding site is usually a cavity in the protein that is formed by Micro-X-Ray Fluorescence,” which was published on Jan. a specific arrangement of amino acids that often belong to 29, 2004, and a continuation-in-part of U.S. patent applica widely separated regions of the polypeptide chain and repre tion Ser. No. 10/621,825 filed Jul. 16, 2003, all hereby incor sent only a minor fraction of the total number of amino acids porated by reference herein. This application also claims the present in the chain. Chemicals should fit precisely into the benefit of U.S. Provisional Application Ser. No. 60/850,594 binding site for effective binding to occur. The shape of these filed Oct. 10, 2006, hereby incorporated by reference herein. binding sites can differ greatly among different proteins, and STATEMENT REGARDING FEDERAL RIGHTS even among different conformations of the same protein. Even slightly different conformations of the same protein 0002 This invention was made with government support may differ greatly in their binding abilities. For further dis under Contract No. DE-AC52-06NA25396 awarded by the cussion of the structure and function of proteins, see: Bruce U.S. Department of Energy. The government has certain Alberts et al., “Molecular Biology of the Cell', 2' edition, rights in the invention. Garland Publishing, Inc., New York, 1989; and H. Lodish et al., “Molecular Cell Biology', 4' edition, W. H. Freeman and FIELD OF THE INVENTION Company, 2000. 0003. The present invention relates generally to detecting 0007. After a receptor array is prepared, it is screened to binding events and more particularly to estimating binding determine which members have the desirable property or selectivities for chemicals, analogs, and drugs being tested properties. U.S. Pat. No. 5,143,854 to M. C. Pirrung et al. with receptors and then manufacturing those having a high entitled “Large Scale Photolithographic Solid Phase Synthe binding selectivity to the receptors. sis of Polypeptides and Receptor Binding Screening Thereof, which issued Sep. 1, 1992, hereby incorporated by reference, describes one Such screening method. A polypep BACKGROUND OF THE INVENTION tide array is exposed to a ligand (an example of a chemical) to 0004. The desire to hasten the identification of potentially determine which members of the array bind to the ligand. The important drugs, catalysts, chemical and biological sensors, ligands described are radioactive, or are "tagged', i.e. medical diagnostics, and other materials is a constant chal attached via one or more chemical bonds to a chemical por lenge that has prompted the use of combinatorial synthetic tion that fluoresces when exposed to non-ionizing, ultraviolet and Screening strategies for synthesizing these materials and radiation. Thus, the attached portion, i.e. the tag, makes the screening them for desirable properties. Combinatorial Syn chemical visible by interrogation with ultraviolet radiation. thesis involves assembling a “library’, i.e. a very large num Tagged molecules have also been used to aid in sequencing ber of chemically related compounds and mixtures, usually in immobilized polypeptides as described, for example, in U.S. the form of an array on a Substrate Surface. High throughput Pat. No. 5,902,723 to W. J. Dower et al. entitled “Analysis of screening of an array involves identifying which members of Surface Immobilized Polymers Utilizing Microfluorescence the array, if any, have the desirable property or properties. The Detection.” which issued May 11, 1999. Immobilized array form facilitates the identification of a particular material polypeptides are exposed to molecules labeled with fluores on the Substrate. Combinatorial arrays and high-throughput cent tags. The tagged molecules bind to the terminal mono screening techniques have been used to solve a variety of mer of a polypeptide, which is then cleaved and its identity problems related to the development of biological materials determined. The process is repeated to determine the com Such as proteins and DNA because the screening techniques plete sequence of the polypeptide. can be used to rapidly assay many biological materials. 0008. It is generally assumed that the attachment of a 0005. The binding properties of a protein largely depend fluorescent tag to a chemical only serves to make visible the on the exposed Surface amino acid residues of its polypeptide otherwise invisible chemical, and does not alter its binding chain (see, for example, Bruce Alberts et al., “Molecular properties. Since it is well known that even Small changes to Biology of the Cell", 2" edition, Garland Publishing, Inc., the structure of a molecule could affect its function, this New York, 1989; and H. Lodish et al., “Molecular Cell Biol assumption that a tagged chemical, i.e. a 'surrogate', has the ogy”, 4" edition, W. H. Freeman and Company, 2000). These same binding affinity as the untagged chemical may not be a amino acid residues can form weak noncovalent bonds with valid one. Small structural changes that accompany even a ions and molecules. Effective binding generally requires the conformational change of a receptor have been known to formation of many weak bonds at a “binding site, which is affect the binding affinity of the receptor. The tagged surro usually a cavity in the protein formed by a specific arrange gates are structurally different from their untagged counter ment of amino acids. There should be a precise fit with the parts, and these structural differences could affect their bind binding site for effective binding to occur. ing affinities. Since binding affinities derived using tagged US 2008/0220441 A1 Sep. 11, 2008 Surrogates are suspect, the binding properties of receptors and which are referred to herein as “analogs of the lead com chemicals should be evaluated using the untagged chemical pound, are synthesized and tested in order to determine which or receptor and not with a tagged Surrogate. of these chemicals, if any, exhibits an even higher binding 0009 Pharmaceutical chemicals are the active ingredients affinity. in drugs, and it is believed that their therapeutic properties are 0013 The preparation and high-throughput screening of linked to their ability to bind to one or more binding sites. The biological arrays is exemplified by the following papers: H. shapes of these binding sites may differ greatly among dif Zhu and M. Snyder, “Protein Chip Technology (Review). ferent proteins, and even among different conformations of Current Opinion in Chemical Biology, Vol. 7, pp. 55-63, the same protein. Even slightly different conformations of the (2003); G. MacBeath and S. L. Schreiber, “Printing Proteins same protein may differ greatly in their binding abilities. For As Microarrays For High-Throughput Function Determina these reasons, it is extremely difficult to predict which chemi tion.” Science, vol. 289, pp. 1760-1763, (2000); E.T.