(12) Patent Application Publication (10) Pub. No.: US 2015/0309021 A1 Birnbaum Et Al
Total Page：16
File Type：pdf, Size：1020Kb
US 20150309021A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2015/0309021 A1 Birnbaum et al. (43) Pub. Date: Oct. 29, 2015 (54) ADVANCED DRUG DEVELOPMENT AND tion No. 10/621,825, filed on Jul. 16, 2003, now Pat. MANUFACTURING No. 6,858,148, which is a continuation-in-part of application No. 10/206,524, filed on Jul. 25, 2002, now (71) Applicant: XRpro Sciences, Inc., Cambridge, MA abandoned, which is a continuation-in-part of applica (US) tion No. 09/859,701, filed on May 16, 2001, now Pat. No. 7,858,385. (72) Inventors: Eva R. Birnbaum, Los Alamos, NM (US); Andrew T. Koppisch, Flagstaff, (60) Provisional application No. 60/850,594, filed on Oct. AZ (US); Sharon M. Baldwin, Santa Fe, 10, 2006. NM (US); Benjamin P. Warner, Los Alamos, NM (US); T. Mark Publication Classification McCleskey, Los Alamos, NM (US); Jennifer A. Berger, Los Alamos, NM (51) Int. C. (US); Jeffrey J. Stewart, Cary, NC GOIN33/566 (2006.01) (US); Michael N. Harris, Los Alamos, (52) U.S. C. NM (US); Anthony K. Burrell, CPC .......... G0IN33/566 (2013.01); G0IN 2500/04 Naperville, IL (US) (2013.01) (57) ABSTRACT (21) Appl. No.: 14/693,094 X-ray fluorescence (XRF) spectrometry has been used for Filed: Apr. 22, 2015 detecting binding events and measuring binding selectivities (22) between chemicals and receptors. XRF may also be used for estimating the therapeutic index of a chemical. Forestimating Related U.S. Application Data the binding selectivities of a chemical versus chemical ana (60) Division of application No. 1 1/974,156, filed on Oct. logs, for measuring post translational modification of pro 10, 2007, which is a continuation-in-part of applica teins, and for drug manufacturing. US 2015/0309021 A1 Oct. 29, 2015 ADVANCED DRUG DEVELOPMENT AND These residues can form weak noncovalent bonds with other MANUFACTURING molecules. An effective binding between the protein, one example of a group of materials herein referred to as “recep RELATED APPLICATIONS tors', and the material that binds to the receptor, referred to 0001. This application is a Continuation of U.S. patent herein as “chemical, generally requires that many weak application Ser. No. 1 1/974,156, filed Oct. 10, 2007, which is bonds form between the protein receptor and the chemical. a continuation-in-part of U. S. patent application Ser. No. Chemicals include organic molecules, inorganic molecules, 09/859,701, filed May 16, 2001, now U.S. Pat. No. 7,858,385 salts, metal ions, and the like. The bonds between the protein issued Dec. 28, 2010, and a continuation-in-part of U.S. and the chemical form at the “binding site' of the protein. The patent application Ser. No. 10/206,524, filed Jul. 25, 2002, binding site is usually a cavity in the protein that is formed by and a continuation-in-part of U.S. patent application Ser. No. a specific arrangement of amino acids that often belong to 10/621,825 filed Jul 16, 2003, now U.S. Pat. No. 6,858,148 widely separated regions of the polypeptide chain and repre issued Feb. 22, 2005, all hereby incorporated by reference sent only a minor fraction of the total number of amino acids herein. This application also claims the benefit of U.S. Pro present in the chain. Chemicals should fit precisely into the visional Application Ser. No. 60/850,594 filed Oct. 10, 2006, binding site for effective binding to occur. The shape of these hereby incorporated by reference herein. binding sites can differ greatly among different proteins, and even among different conformations of the same protein. STATEMENT REGARDING FEDERAL RIGHTS Even slightly different conformations of the same protein may differ greatly in their binding abilities. For further dis 0002 This invention was made with government support cussion of the structure and function of proteins, see: Bruce under Contract No. DE-AC52-06NA25396 awarded by the Alberts et al., “Molecular Biology of the Cell", 2" edition, U.S. Department of Energy. The government has certain Garland Publishing, Inc., New York, 1989; and H. Lodish et rights in the invention. al., “Molecular Cell Biology', 4' edition, W. H. Freeman and Company, 2000. FIELD OF THE INVENTION 0007. After a receptor array is prepared, it is screened to 0003. The present invention relates generally to detecting determine which members have the desirable property or binding events and more particularly to estimating binding properties. U.S. Pat. No. 5,143,854 to M. C. Pirrung et al. selectivities for chemicals, analogs, and drugs being tested entitled “Large Scale Photolithographic Solid Phase Synthe with receptors and then manufacturing those having a high sis of Polypeptides and Receptor Binding Screening binding selectivity to the receptors. 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, chemicals 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 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 0006. The chemical properties and in particular, the bind Surrogates are suspect, the binding properties of receptors and ing properties of a protein depend almost entirely on the chemicals should be evaluated using the untagged chemical exposed Surfaceamino acid residues of the polypeptide chain. or receptor and not with a tagged Surrogate. US 2015/0309021 A1 Oct. 29, 2015 0009 Pharmaceutical chemicals are the active ingredients Using Red and Green Fluorescent Proteins.” Analytical Bio in drugs, and it is believed that their therapeutic properties are chemistry, vol. 306, pp. 50-54, (2002); G. Y. J. Chen et al., linked to their ability to bind to one or more binding sites. The “Developing a Strategy for Activity-Based Detection of shapes of these binding sites may differ greatly among dif Enzymes in a Protein Microarray.” ChemBioChem, pp. 336 ferent proteins, and even among different conformations of 339, (2003); K. Martin et al., “Quantitative analysis of protein the same protein. Even slightly different conformations of the phosphorylation status and protein kinase activity on same protein may differ greatly in their binding abilities. For microarrays using a novel fluorescent phosphorylation sensor these reasons, it is extremely difficult to predict which chemi dye.” Proteomics, Vol. 3, pp. 1244-1255, (2003); J. Burbaum cals will bind effectively to proteins. and G. M. Tobal, “Proteomics in drug discovery. Current 0010 Development and manufacturing for a new pharma Opinion in Chemical Biology, Vol.