Wo 2008/127291 A2
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(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (43) International Publication Date PCT (10) International Publication Number 23 October 2008 (23.10.2008) WO 2008/127291 A2 (51) International Patent Classification: Jeffrey, J. [US/US]; 106 Glenview Drive, Los Alamos, GOlN 33/53 (2006.01) GOlN 33/68 (2006.01) NM 87544 (US). HARRIS, Michael, N. [US/US]; 295 GOlN 21/76 (2006.01) GOlN 23/223 (2006.01) Kilby Avenue, Los Alamos, NM 87544 (US). BURRELL, Anthony, K. [NZ/US]; 2431 Canyon Glen, Los Alamos, (21) International Application Number: NM 87544 (US). PCT/US2007/021888 (74) Agents: COTTRELL, Bruce, H. et al.; Los Alamos (22) International Filing Date: 10 October 2007 (10.10.2007) National Laboratory, LGTP, MS A187, Los Alamos, NM 87545 (US). (25) Filing Language: English (81) Designated States (unless otherwise indicated, for every (26) Publication Language: English kind of national protection available): AE, AG, AL, AM, AT,AU, AZ, BA, BB, BG, BH, BR, BW, BY,BZ, CA, CH, (30) Priority Data: CN, CO, CR, CU, CZ, DE, DK, DM, DO, DZ, EC, EE, EG, 60/850,594 10 October 2006 (10.10.2006) US ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, KR, KZ, LA, LC, LK, (71) Applicants (for all designated States except US): LOS LR, LS, LT, LU, LY,MA, MD, ME, MG, MK, MN, MW, ALAMOS NATIONAL SECURITY,LLC [US/US]; Los MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PG, PH, PL, Alamos National Laboratory, Lc/ip, Ms A187, Los Alamos, PT, RO, RS, RU, SC, SD, SE, SG, SK, SL, SM, SV, SY, NM 87545 (US). CALDERA PHARMACEUTICALS, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, INC. [US/US]; 3491 Trinity Drive, Suite B, Los Alamos, ZM, ZW NM 87544 (US). (84) Designated States (unless otherwise indicated, for every (72) Inventors; and kind of regional protection available): ARIPO (BW, GH, (75) Inventors/Applicants (for US only): BIRNBAUM, Eva, GM, KE, LS, MW, MZ, NA, SD, SL, SZ, TZ, UG, ZM, R. [US/US]; 1930 Camino Mora, Los Alamos, NM 87544 ZW), Eurasian (AM, AZ, BY, KG, KZ, MD, RU, TJ, TM), (US). KOPPISCH, Andrew, T. [US/US]; 30a Verde European (AT,BE, BG, CH, CY, CZ, DE, DK, EE, ES, FI, Ridge Drive, Los Alamos, NM 87544 (US). BALDWIN, FR, GB, GR, HU, IE, IS, IT, LT,LU, LV,MC, MT, NL, PL, Sharon, M. [US/US]; 82b Calle Sinsonte, Santa Fe, NM PT, RO, SE, SI, SK, TR), OAPI (BF, BJ, CF, CG, CI, CM, 87507 (US). WARNER,Benjamin, P. [US/US] ; 903 Tewa GA, GN, GQ, GW, ML, MR, NE, SN, TD, TG). Loop, Los Alamos, NM 87544 (US). MCCLESKEY, Mark, T. [US/US]; 1930 Camino Mora, Los Alamos, Published: NM 87544 (US). BERGER, Jennifer, A. [US/US]; 103 — without international search report and to be republished Azure Drive, Los Alamos, NM 87544 (US). STEWART, upon receipt of that report (54) Title: ADVANCED DRUG DEVELOPMENT AND MANUFACTURING (57) Abstract: X-ray fluorescence (XRF) spectrometry has been used for detecting binding events and measuring binding selectiv- ities between chemicals and receptors. XRF may also be used for estimating the therapeutic index of a chemical, for estimating the binding selectivity of a chemical versus chemical analogs, for measuring post-translational modifications of proteins, and for drug manufacturing. ADVANCED DRUG DEVELOPMENT AND MANUFACTURING RELATED APPLICATIONS This application is a continuation-in-part of U. S. Patent Application serial number 09/859,701 , now U. S. Patent Application 200300271 29 entitled "Method for Detecting Binding Events Using Micro-X-ray Fluorescence Spectrometry," which was published on February 6, 2003, and a continuation-in-part of U. S. Patent Application serial number 10/206,524, now U. S. Patent Application 2004001 7884 entitled "Flow Method and Apparatus for Screening Chemicals Using Micro-X-Ray Fluorescence," which was published on January 29, 2004, and a continuation-in-part of U. S. Patent Application Serial Number 10/621 ,825 filed July 16, 2003, all hereby incorporated by reference herein. This application also claims the benefit of U.S. Provisonal Application Serial Number 60/850,594 filed October 10, 2006 hereby incorporated by reference herein. STATEMENT REGARDING FEDERAL RIGHTS This invention was made with government support under Contract No. DE- AC52-06NA25396 awarded by the U.S. Department of Energy. The government has certain rights in the invention. FIELD OF THE INVENTION The present invention relates generally to detecting binding events and more particularly to estimating binding selectivities for chemicals, analogs, and drugs being tested with receptors and then manufacturing those having a high binding selectivity to the receptors. BACKGROUND OF THE INVENTION The desire to hasten the identification of potentially important drugs, catalysts, chemical and biological sensors, medical diagnostics, and other materials is a constant challenge that has prompted the use of combinatorial synthetic and screening strategies for synthesizing these materials and screening them for desirable properties. Combinatorial synthesis involves assembling a "library", i.e. a very large number of chemically related compounds and mixtures, usually in the form of an array on a substrate surface. High throughput screening of an array involves identifying which members of the array, if any, have the desirable property or properties. The array form facilitates the identification of a particular material on the substrate. Combinatorial arrays and high-throughput screening techniques have been used to solve a variety of problems related to the development of biological materials such as proteins and DNA because the screening techniques can be used to rapidly assay many biological materials. The binding properties of a protein largely depend on the exposed surface amino acid residues of its polypeptide chain (see, for example, Bruce Alberts et al., "Molecular Biology of the Cell", 2nd edition, Garland Publishing, Inc., New York, 1989; and H . Lodish et al., "Molecular Cell Biology", 4th edition, W. H. Freeman and Company, 2000). These amino acid residues can form weak noncovalent bonds with ions and molecules. Effective binding generally requires the formation of many weak bonds at a "binding site," which is usually a cavity in the protein formed by a specific arrangement of amino acids. There should be a precise fit with the binding site for effective binding to occur. The chemical properties and in particular, the binding properties of a protein depend almost entirely on the exposed surface amino acid residues of the polypeptide chain. These residues can form weak noncovalent bonds with other molecules. An effective binding between the protein, one example of a group of materials herein referred to as "receptors", and the material that binds to the receptor, referred to herein as "chemical", generally requires that many weak bonds form between the protein receptor and the chemical. Chemicals include organic molecules, inorganic molecules, salts, metal ions, and the like. The bonds between the protein and the chemical form at the "binding site" of the protein. The binding site is usually a cavity in the protein that is formed by a specific arrangement of amino acids that often belong to widely separated regions of the polypeptide chain and represent only a minor fraction of the total number of amino acids present in the chain. Chemicals should fit precisely into the binding site for effective binding to occur. The shape of these binding sites can differ greatly among different proteins, and even among different conformations of the same protein. Even slightly different conformations of the same protein may differ greatly in their binding abilities. For further discussion of the structure and function of proteins, see: Bruce Alberts et al., "Molecular Biology of the Cell", 2nd edition, Garland Publishing, Inc., New York, 1989; and H . Lodish et al., "Molecular Cell Biology", 4th edition, W . H . Freeman and Company, 2000. After a receptor array is prepared, it is screened to determine which members have the desirable property or properties. U. S. Patent 5,143,854 to M. C. Pirrung et al. entitled "Large Scale Photolithographic Solid Phase Synthesis of Polypeptides and Receptor Binding Screening Thereof, which issued September 1, 1992, hereby incorporated by reference, describes one such screening method. A polypeptide array is exposed to a ligand (an example of a chemical) to determine which members of the array bind to the ligand. The ligands described are radioactive, or are "tagged", i.e. attached via one or more chemical bonds to a chemical portion that fluoresces when exposed to non-ionizing, ultraviolet radiation. Thus, the attached portion, i.e. the tag, makes the chemical visible by interrogation with ultraviolet radiation. Tagged molecules have also been used to aid in sequencing immobilized polypeptides as described, for example, in U. S. Patent 5,902,723 to W . J. Dower et al. entitled "Analysis of Surface Immobilized Polymers Utilizing Microfluorescence Detection," which issued May 11, 1999. Immobilized polypeptides are exposed to molecules labeled with fluorescent tags. The tagged molecules bind to the terminal monomer of a polypeptide, which is then cleaved and its identity determined. The process is repeated to determine the complete sequence of the polypeptide. It is generally assumed that the attachment of a fluorescent tag to a chemical only serves to make visible the otherwise invisible chemical, and does not alter its binding properties. Since it is well known that even small changes to the structure of a molecule could affect its function, this assumption that a tagged chemical, i.e. a "surrogate", has the same binding affinity as the untagged chemical may not be a valid one. Small structural changes that accompany even a conformational change of a receptor have been known to affect the binding affinity of the receptor.