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WO 2017/087915 Al 26 May 20 17 (26.05.2017) W P O P C T

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WO 2017/087915 Al 26 May 20 17 (26.05.2017) W P O P C T (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2017/087915 Al 26 May 20 17 (26.05.2017) W P O P C T (51) International Patent Classification: (72) Inventors: HELLINGA, Homme, W.; 5212 Pine Cone G01N 33/53 (2006.01) C12M 1/34 (2006.01) Lane, Durham, NC 27705 (US). ALLERT, Malin, J.; G01N 33/533 (2006.01) G06F 19/16 (201 1.01) 7718 San Gabriel Street, Raleigh, NC 27613 (US). G01N 33/566 (2006.01) (74) Agents: BEATTIE, Ingrid, A. et al; Mintz Levin Cohn (21) International Application Number: Ferris Glovsky and Popeo, P.C., One Financial Center, Bo PCT/US20 16/062961 ston, MA 021 11 (US). (22) International Filing Date: (81) Designated States (unless otherwise indicated, for every 1 November 2016 (19.1 1.2016) kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, (25) Language: English Filing BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, (26) Publication Language: English DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, (30) Priority Data: KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, 62/257,796 20 November 2015 (20. 11.2015) US MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, 62/257,856 20 November 2015 (20. 11.2015) US OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, (71) Applicant: DUKE UNIVERSITY [US/US]; Office of Li SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, censing and Ventures, 2812 Erwin Rd., Suite 306, Box TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, 90083, Durham, NC 27705 (US). ZW. (84) Designated States (unless otherwise indicated, for every kind of regional protection available): ARIPO (BW, GH, GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, [Continued on nextpage] (54) Title: LACTATE BIOSENSORS AND USES THEREOF (57) Abstract: The preseni subject matter provides lactate biosensors as well as compositions, devices, and methods comprising such biosensors. PCS PCS Residues Residues w o 2017/087915 Ai II II II I III IIII II lll l lllll II I III II I II TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, Published: TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, — with international search report (Art. 21(3)) DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, ΓΓ, LT, LU, LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, — before the expiration of the time limit for amending the SI, SK, SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, claims and to be republished in the event of receipt of GN, GQ, GW, KM, ML, MR, NE, SN, TD, TG). amendments (Rule 48.2(h)) — with sequence listing part of description (Rule 5.2(a)) This application claims benefit of priority to U.S. Provisional Application No. 62/257,856, filed November 20, 2015 and U.S. Provisional Application No. 62/257,796, filed November 20, 2015, the entire contents of each of which are incorporated herein by reference. INCORPORATION-BY-REFERENCE OF SEQUENCE LISTING The contents of the text file named "35327-523001WO_Sequence_Listing.txt", which was created on November 19, 20 6 and is 356 KB in size, is hereby incorporated by reference in its entirety. FIELD OF THE INVENTION The present invention relates to compositions and methods for detecting and determining the concentration of lactate. BACKGROUND Current lactate sensors tend to be either electrochemical or optical biosensors using the enzyme lactate dehydrogenase, lactate oxidase, alpha-hydroxy acid oxidase, lactate monooxygenase, lactate peroxidase. Despite the number of developed lactate biosensors, there is still a need to improve stability, sensibility and applicability of such devices. Most of these sensors suffer from long response time, short stability, and poor reproducibility. SUMMARY OF THE INVENTION Aspects of the present subject matter provide improved biosensors that rapidly, reliably, and accurately detect and quantify lactate with significant advantages over previous systems. The present disclosure provides a biosensor for lactate, comprising a reporter group that is attached to a lactate-binding protein. The lactate-binding protein includes a domain or region(s) that binds the lactate. The domain or region involved in ligand binding is comprised of a plurality of residues, e.g., non-contiguous amino acids of the ligand-binding protein, which are contact points or sites of contact between the ligand and its cognate ligand- binding protein. The binding of a lactate to the lactate-binding domain of the lactate-binding protein causes a change in signaling by the reporter group. In various implementations, the biosensor may produce a signal when a lactate is bound to the lactate binding domain that is not produced (and/or tha is different from a signal that is produced) when the lactate is absent from the lactate binding domain. These biosensors have widespread utility including in clinical, food and beverage, industrial, and environmental settings. A reporter group that transduces a detectable signal may be attached to the lactate- binding proteins (biosensors) described herein. As used herein, "transduce" means the conversion of ligand occupancy in the binding site of a ligand-binding protein to a detectable signal. Occupancy refers to the state of ligand being bound or not bound to a cognate ligand- binding protein. In embodiments, detectable signal comprises a fluorescent, electrochemical, nuclear magnetic resonance (NMR), or electron paramagnetic resonance (EPR) signal. The reporter group is attached to the lactate-binding protein so that a signal transduced by the reporter group when the lactate-binding protein is bound to lactate differs from a signal transduced by the reporter group when the lactate-binding protein is not bound to lactate. The proteins may be engineered to include a single cysteine to which the detectable label, e.g., a fluorophore is covalently attached. The biosensors are reagentless in that their monitoring mechanism requires neither additional substrates for a signal to develop, nor measurement of substrate consumption or product generation rates to determine lactate concentrations. The lactate-binding proteins (as well as biosensors comprising the ligand-binding proteins) provided herein lack enzymatic activity and are not enzymes. As used herein, an "enzyme" is a protein that catalyzes a specific biochemical reaction. The lactate is not chemically altered (i.e., no chemical bond or atom of the lactate is added or removed) by the lactate-binding protein. Thus, when lactate dissociates from a lactate-binding protein described herein, the lactate contains the same chemical structure it had before it became bound to the lactate-binding protein. In some embodiments, the biosensor proteins include a second fluorophore, thereby permitting ratiometric sensing/detection of an analyte using establishing non-geometrically modulated Forster resonance energy transfer (ngmFRET). Among the advantages of these fluorophore-containing protein constructs is their high durability. The constructs retain their ability to b nd lactate, change shape and thus detect the analyte, lactate, (a) even when immobilized (directly or indirectly) onto a solid surface such as a bead, plate, or sheet; (b) even after desiccation (and subsequent reconstitution in a physiological buffer solution); (c) even when subjected to ambient conditions, e.g., conditions that can be encountered in storage and/or transportation; and (d) even when aged/stored for extended periods of time, e.g., weeks, months, or even years. Thus, the biosensors do not require refrigeration or a cold chain for distribution, permitting a wider range of applicability such as in-the-field use and reducing the cost of the sensor product. For clinical applications, microliter volumes (e.g., less than 0.1, 0.5, I , 2, 3, 4, 5, 6, 7, 8, 9, or 10, or less than 0 µΐ) of a bodily fluid such as blood may be used. Moreover compared to conventional enzyme-based or antibody based assay systems, the results are achieved virtually instantaneously, e.g., 0.1-5 minutes, e.g., 0.1-1 minutes, or within 30-60 seconds. A further advantage is that the sensors consistently and reliably bind to and detect the analyte (lactate) in complex fluids such as whole blood, plasma, serum, saliva, urine, and environmental fluids. Thus in a clinical setting, whole blood need not be processed, thereby reducing time and cost of the diagnostic procedure. Alternatively or in addition, the biosensors provided herein may be used to monitor lactate levels continuously. In a non- limiting example, one or more biosensors is immobilized at the tip of a thin optical fiber to construct a lactate-responsive optode. Such an optode can be introduced into the body (e.g., subcutaneously). The sensor may be in continuous contact with the sample, and excitation and emission light are passed to and from the immobilized sensor, respectively. Fluctuations in the lactate sample alter the dynamic equilibrium between the open and closed states of the lactate-binding protein, which is transduced into fluctuations of the fluorescent emission signal, by virtue of the sensing mechanism of the conjugated fiuorophore. The emitted light intensities may be read by a reader connected to the optode. n non-clinical situations, e.g., food and beverage composition (e.g, meat, canned food, dairy, nondairy, a fermented food, a fruit, a vegetable, a tuber, astarch, a grain, pasta, yogurt, soup, ice cream, a broth, a puree,
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