WO1999021015A2

WO1999021015A2 - Affinity ligands, their production and use

Info

Publication number: WO1999021015A2
Application number: PCT/GB1998/003148
Authority: WO
Inventors: Beining Chen; Antony Peter Francis Turner; Richard Day; Giacomo Bestetti
Original assignee: Cranfield University
Priority date: 1997-10-21
Filing date: 1998-10-21
Publication date: 1999-04-29
Also published as: AU9549798A; WO1999021015A3

Abstract

Oligopeptide affinity ligands can be produced by generating a combinatorial library of short peptides (preferably from a limited set of amino acids) and then carrying out a double screening using first a component related to the target but to be distinguished from it (e.g. haemoglobin) and then the target (e.g. glycosylated haemoglobin). 'Virtual' combinatorial synthesis can be carried out by computer modelling. Ligands for targetting NbA1c include Boc-GAIIVL, Boc-VFMPLG and FPADP. The ligands can be used to produce biosensors and sensor systems, e.g. based on the binding of a ligand to its target causing changes in optical properties (e.g. refractive index, e.g. measured by surface plasmon resonance) or changes in electrochemical properties (e.g. when the ligand is bound to the surface of an electrode).

Description

AFFINITY LIGANDS, THEIR PRODUCTION AND USE TECHNICAL FIELD

The present invention relates to affinity ligands, their production and use. One aspect relates to a screening technique for use in the production of affinity ligands. Further aspects relate to biosensor devices employing such ligands.

The ligands are in general peptides. One preferred class is ligands for haemoglobin species, e.g. ligands that selectively bind a minor component such as a glycosylated haemoglobin, in preference to haemoglobin itself.

Diabetes mellitus is a chronic disorder characterised by insulin deficiency, hyperglycaemia, and high risk for development of complications affecting the eyes, kidneys, peripheral nerves, heart and blood vessels. The development and progression of the chronic complications of diabetes are closely related to the degree of glycemic control, as measured by the level of inappropriate glycosylation.

Glycosylated haemoglobin (GHB) refers to a series of minor haemoglobin components that are stable adducts formed by haemoglobin with various sugars. The reaction between glucose and haemoglobin is an example of a non- enzymatic condensation of glucose with the free amino groups on the globin component of haemoglobin. The process is slow, continuous and irreversible. Measurement of GHB provides an index of the mean concentration of blood glucose during the preceding two to three months.

HbA_lc is the most abundant of the glycosylated haemoglobin products. Its measurement is of particular interest because HbA_lc initiates and participates in the multiple organ damage that occurs in patients suffering from diabetes. HbA_lc is well documented as an important marker of long-term complications in diabetes diagnosis (Trivelli LA, Ranney HM, Lai HT, N. Enαl . J. Med. , 1971, 284, 353-357) . The latest techniques available for monitoring levels of HbA_lc include immunoaffinity-based diagnostic kits. The highly selective properties of antibodies make them highly suitable ligands for this purpose. However antibodies are expensive to produce and have a limited shelf life. The development of a small, inexpensive and ^"rapid affinity sensor system that uses more robust synthetic ligands is most desirable. DISCLOSURE OF INVENTION

The present invention provides, in one aspect, a method for providing an affinity ligand which selectively binds to a component (A) in the presence of a component (B) having substantial homology with (A) , said method comprising:

(a) generating a combinatorial library of peptides, each different peptide being bound to a respective separate or separable support member; (b) screening the library with component (B) and separating out any peptides binding (B) to leave a residual library; and

(c) screening the residual library with component (A) and separating out any peptides binding (A) , said peptide (s) constituting one or more said affinity ligands .

The screening steps (b) and (c) represent a further aspect of the invention.

"Substantial homology" may, for example, be greater than 90% homology in the case of components or component parts that are biopolymers such as proteins or nucleic acids .

The components A and B or derivatives thereof (to which A and B may be converted for screening) preferably have optical properties such that in the screening steps (b) and (c) , peptides binding A or B or derivatives thereof are optically, e.g. visually, detectable. Thus they may be intensely coloured (e.g. haemoglobins) so as to be detectable in normal light conditions, or they may be fluorescent. Detection may be carried out by eye or automatically (e.g. colorimetrically) . Of course such visual detectability can also be employed in assays using the affinity ligands to detect a component (A), e.g. incorporating a ligand in a colorimetric sensor. Typically, the step (a) of generating a combinatorial library of peptides employs solid phase peptide synthesis to produce a multiplicity of support members each having molecules of a respective single peptide bound to it. The combinatorial library may be based on a set of natural or unnatural amino acids, e.g. a set comprising Ala, Gly, Leu, lie, Met, Phe, Pro and Val, and preferably Glu, and optionally Asp and/or Trp. Further possibilities include Arg and/or Lys and/or Thr. Generally, in step (c) one or more peptides bound both to (A) and to a support member are isolated. At least one such peptide is then sequenced; and it may then be synthesised.

We have also used computer modelling to develop candidate ligands by the following route: a) a model of the target component (A) is provided in a computer modelling environment; b) the model is examined to determine a suitable ligand binding region (e.g. a region of A which differs from a component B of substantial homology) ; c) successive ligand fragments are selected that are calculated to interact with successive portions of the ligand binding region, leading to a theoretical ligand structure; d) a ligand having the theoretical structure is synthesised and tested, e.g. by the screening procedure described above.

Ligands for HbA_lc were designed in this way. The target component was based on an HbA₀ X-ray crystallography structure from Brookhaven Protein

Databank, refined by energy minimisation, and modified by the addition of a glucose side chain to each valine nitrogen terminating the β-chains. The modified structure underwent 1000 minimisation simulation steps to correct the conformation, bond angles and bond lengths. The LUDI de novo design program was then employed. A first fragment was thereby selected for interacting with the glycosylated valine terminal of the first β- chain. Successive fragments interacting with successive areas of interest were then found. Our programme was not capable of generating peptides, so the resulting non- peptide compound was "converted" into a peptide by empirical deduction.

Ligands derived this way included: FGAPW FPADP In a further aspect the invention provides a peptide which selectively binds to a minor haemoglobin component, e.g. glycosylated haemoglobin in preference to binding to haemoglobin itself.

Preferred peptide ligands are 3-15 residues long. They may include protecting groups, e.g. Boc. We have found that ligands with protecting groups at the N- terminals can show higher affinity. The protecting groups appear to play an important role in binding. In further aspects the invention provides peptide ligands, and the use of the ligands in assays, typically as components of biosensors.

Preferred ligands for HbA_lc include :- a) Sequences discovered by combinatorial chemistry for selective ligands to HbA_lc obtained by Edman Microsequencing :

AFMPLG VFMPLG

AVPEMI LLMMEI GAIIVL PPAAIM

AVPFAE PPVFFF

VPPGAI

b) Sequences discovered by computer aided rational design, and tested using the BIAcore 2000 Biosensor (A) real-time affinity sensor based on surface plasmon resonance) : FGAPW and FPADPA.

c) Sequences discovered by computer aided rational design, and tested by computer simulation:

FPADP AAGWAI

CAGWAI AAGWAID

AYAIG CYAI

Any of the above may be N-protected, e.g. with Boc.

The ligands Boc-GAIIVL, Boc-VFMPLG and FPADP gave outstanding performance in terms of affinity.

Synthetic affinity ligands of the invention may be used in conjunction with amperometric, potentiometric, conductimetric, impedimetric, optical, magnetic or gravimetric transducers to produce a wide range of diagnostic devices, e.g. for HbA_lc monitoring in diabetes patients. Affinity ligands are more stable, have a longer shelf life, and are more cost effective to manufacture than the antibodies used in the latest immunoassay diagnostic test kits.

The use of combinatorial libraries is an effective technique for rapid ligand discovery. Combinatorial libraries may be defined as ensembles of compounds resulting from the systematic and repetitive covalent connection of a set of different "building blocks" of varying structures to each other to yield a large array of diverse molecular entities. Theoretically, the number of possible individual compounds N=b^x, where "b" represents the number of building blocks for each step and "x", the number of synthetic steps.

Combinatorial libraries have been widely used in drug industries to discover and optimise lead compounds. They have been successfully applied to the preparation of benzodiazepines, β-lactams, and other drugs (Bunin BA, Plunkett MJ, and Ellman JA, Proc. Natl. Acad. Sci. USA, 1994, 1, 4708-12) . To the best of our knowledge, we are the first group applying combinatorial library techniques to generate useful affinity ligands to be used in sensor systems outside the fields of drug design and genetic screening.

Some embodiments of the invention will now be described with reference to the accompanying drawings. BRIEF DESCRIPTION OF DRAWINGS

Fig. 1 shows a scheme of combinatorial synthesis of hexapeptide libraries;

Fig 2a,, b and c are sensorgrams illustrating the performance of biosensors embodying the invention which use optical effects (changes in refractive index) ; and Fig 3a, b and c are cyclic voltammograms relevant to the development of an electrochemical biosensor embodying the invention.

MODES FOR CARRYING OUT THE INVENTION Combinatorial synthesis was performed as shown in

Fig. 1. In a first example, a library was constructed from eight amino acids: Ala, Gly, lie, Leu, Met, Phe, Pro, and Val. Boc-protected amino acids, Boc-protected amino acids attached onto Merrifield Resin and the coupling reagent, ByBOP, were purchased from Novabiochem (Beeston, Nottingham, England) and used without further purification. Solvents such as dichloromethane (DCM) , trifluoroacetic acid (TFA) and triethylamine were purchased from Aldrich Chemical Co. (Gillingham, Dorset, England) .

General Procedure for the synthesis of a hexapeptide library

The library was synthesised using Merrifield resin as a solid support by the one-bead one compound technique (K.S. Lam et al. , Chem. Rev.. 97, 411-448, 1997).

Step 1 (Deprotection) (Kappeler et al . , Helv. Chim. Acta, 1960, ____, 1453) : Boc-protected amino acids attached onto Merrifield resin (662 mg in total) were mixed in a 50 ml flask attached to a CaCl₂ drying tube. An aliquot (20 ml) of 50% TFA/DCM was added. The mixture was filtered after 20 mins and washed with DCM.

Step 2 (Neutralisation) : The resin after deprotection was transferred into another flask and 20 ml of 5% triethylamine/DCM was added to it and stirred for about 10 mins. The resin was filtered off, washed with DCM and dried under vacuum before the coupling.

Step 3 (Coupling) : The above dried resin was evenly split into 8 portions and placed in different flasks. The resin was suspended in 5 ml of DCM and to each flask was added a calculated amount of corresponding Boc- protected amino acid, 22mg of PyBOP and 0.02 ml of triethylamine. The mixtures were stirred at room temperature for three hours. After a Kaiser test for each mixture was negative, indicating the absence of the free amino groups (Kaiser, E., Anal. Biochem. , 34 , 595, 1970) , the resins were filtered off and combined. The reaction cycle was repeated from the deprotection step.

The hexapeptide library was synthesised by repeating the three-step cycle another four times. The library was screened with the peptides tethered onto the resin beads. The final library was treated with 50% of TFA in DCM to remove the Boc-protecting group. The Screening of a Combinatorial Library

The prepared library was screened against both human haemoglobin itself (to exclude cross binding) and HbA_lc. Pure Human haemoglobin was purchased from Sigma-Aldrich Chemical Co. (Gillingham, Dorset, England) and HbA_lc was purchased from Exocell, Inc., in Philadelphia. The mixture of hexapeptides attached onto the bead was contacted with human haemoglobin at a concentration of 1 mg/ml in pH 7.4 phosphate buffer at 25°C. After filtration and washing, the beads were then examined under a microscope. The beads stained with the natural red colour of haemoglobin were removed using a tubular needle. The remaining beads were contacted with HbA_lc under the same conditions, and the red-stained beads, bearing the desired ligands, were picked up using the tubular needle.

For determining the structures of the peptides on the beads, it was found best to remove the haemoglobin prior to sequencing. This reduced the background noise. Thus the picked-up beads were washed with 3»5M sodium thiocyanate and polypropylene glycol in combination with a high salt (KC1) solution. The washed beads were then characterised by the Edman microsequencing technique.

In a second example of the combinatorial synthesis technique, a set of 13 protected amino acids was used: Boc-Ala-OH Boc-Arg(Tos) -OH Boc-Glu-(OBzl)-OH Boc-Gly-OH Boc-Ile-OH Boc-Leu-OH Boc-Lys (2-Cl-Z)-OH Boc-Met-OH

Boc-Phe-OH Boc-Pro-OH Boc-Thr (Bzl)-OH Boc-Trp-OH Boc-Val-OH

Microsequencing of some of the resulting beads led to four hexapeptide structures: AFMPLG VFMPLG AVPGMI

LLMMEI The affinity of one of the sequenced hexapeptide ligands was evaluated by computer-modelling using the LUDI program (H.J. Bohm Computer-Aided Mol . Mod., 8_., 243- 256 1994) . The peptide was docked into the defined binding region of HbA_lc. The peptide-HbA_lc assembly underwent further energy minimisation simulation to find the best conformation for interaction. The Ludi score programme was used to estimate a dissociation constant of approximately lμM. An SPR biosensor instrument, Biacore 2000, was used to test the binding of some ligands to HbA_lc and HbA₀. For example, the peptide FGAPW was thus found to bind strongly to HbA_lc while no binding was observed with HbA₀. An optical sensor using the discovered ligands can therefore be constructed to detect HbA_lc. CONSTRUCTION AND USE OF AN OPTICAL (SPR) SENSOR

A surface plasmon resonance (SPR) sensor was constructed using the synthetic ligands as recognition elements. The transducer used was a commercially available SPR instrument (Biacore 2000) which measures the refractive index changes on a surface due to the binding. Preparation includes the following four steps when a carboxylated methyldextran surface is used: (a) Activation of the surface: A CM5 sensor chip precoated with carboxylated methyldextran on a gold surface was used. The chip was configurated with PBST buffer at pH 7.4 containing EDTA, CM-dextran and Tween20 at a flow rate of 5μ0/min. The surface was activated with a mixture of EDC/NHS at the above rate for 7 mins.

(b) Coupling of ligands: The ligands were coupled at different pHs depending on properties of ligands at the above flow rate over 7 mins .

(c) Blocking: The unoccupied sites were blocked with ethanolamine at the same flow rate over 7 mins. (d) The above-prepared surface was used to measure the binding of the ligands to HbA_lc and HbA₀. The binding was measured in PBS buffer at pH7.4 at a flow rate of lOμf/min for 1 min. The resulting sensorgrams are shown in Figure 2 (a-c) .

In the case of the ligand Boc-GAIIVL, the six-carbon chain with an amine group at the end enables the coupling of the ligand to the carboxyl group on the surface. The binding of HbA_lc is as high as 557 RU (resonance unit) while the highest value for HbA₀ was 44.1 RU (Fig 2a). The ligand gives more than 10 fold stronger binding to HbA_lc than A₀. In the case of Boc-VFMPLG, the same chemistry was applied to immobilise the ligand. The sensorgram in Fig 2b shows the ligand is 100% specific to HbA_lc .

The sensor surface can be modified with different chemistry. Ligands can be put onto a surface in different format depending on their properties. They can also be immobilised via thiol coupling or biotin- streptoavidin linkage. An example using such binding is shown in Figure 2(c).

CONSTRUCTION AND USE OF AN ELECTROCHEMICAL SENSOR

Electrochemical detection of haemoglobin was carried out using a screenprinted carbon working electrode with a a screenprinted carbon counter electrode and a calomel reference. Cetyl pyridinium chloride (CPC, 0.01% w/v) was used as a promoter in acetate buffer (50nM, pH 5.0). Figs 3(a-c) show cyclic voltammograms . Fig 3a relates to the acetate buffer alone (in the absence of chloride) . Fig 3b shows the effect of added CPC. Fig 3c shows the effect of added CPC and haemoglobin. Haemoglobin elicits a strong reducing current around -175 mV.

A carbon electrode as used in these experiments can be adapted as a sensor embodying the present invention by depositing a ligand on its surface. It may be retained by a selective polymer membrane.

Claims

1. A method for providing an affinity ligand which selectively binds to a component (A) in the presence of a component (B) having substantial homology with (A) , said method comprising:

2. A method according to claim 1 wherein components A and B or derivatives thereof have optical properties such that in the screening steps (b) and (c) , peptides binding A or B or derivatives thereof are optically detectable and are optically detected.

3. A method according to claim 2 wherein components A and B are haemoglobins.

4. A method according to any preceding claim wherein said step (a) of generating a combinatorial library of peptides employs solid phase peptide synthesis to produce a multiplicity of support members each having molecules of a respective single peptide bound to it.

5. A method according to any preceding claim wherein said peptides are of 3-15 amino acid residues.

6. A method according to any preceding claim wherein in step (c) one or more peptides bound both to (A) and to a support member are isolated from other peptides, optionally still bound to a support member;

(d) at least one said peptide is sequenced; and (e) at least one said sequenced peptide is synthesised.

7. A peptide which selectively binds to a minor haemoglobin component in preference to binding to haemoglobin itself.

8. A peptide which selectively binds to glycosylated haemoglobin in preference to binding to haemoglobin itself .

9. A peptide selected from

VFMPLG

AVPEMI

LLMMEI GAIIVL

PPAAIM

AVPFAE

PPVFFF

VPPGAI FGAPW

FPADPA

FPADP

AAGWAI

CAGWAI AAGWAID

AYAIG

GYAI

10. An affinity sensor system employing a peptide according to claim 7, 8 or 9 or as produced by the method of claim 6 or a derivative thereof as an affinity ligand.

11. An affinity assay for a component A employing as an affinity ligand a peptide produced by the method of claim 6 or a derivative thereof.

12. An affinity sensor system according to claim 10 or an assay according to claim 11 wherein binding of the affinity ligand to a target species produces a change in absorbance, and absorbance is monitored to determine the binding of the target species.

13. A system or assay according to claim 12 wherein absorbance is monitored colorimetrically .

14. An affinity sensor system according to claim 10 or an assay according to claim 11 wherein binding of the affinity ligand to a target species produces a change in refractive index, and refractive index is monitored to determine the binding of the target species.

15. A system or assay according to claim 14 which employs surface plasmon resonance.

16. An affinity sensor system according to claim 10 or an assay according to claim 11 wherein binding of the affinity ligand to a target species produces a change in electrochemical properties of an electrode, and said electrode is monitored to determine the binding of the target species.

17. A system or assay according to claim 16 wherein the ligand is bound to the surface of the electrode.

18. A system or assay according to claim 16 or claim 17 wherein the electrode is a carbon electrode.

19. A system or assay according to any of claims 16 to 18 wherein the electrode is monitored voltammetrically .

20. A biosensor for a component A employing as an affinity ligand a peptide produced by the method of claim 6 or a derivative thereof.

21. A screening method for use in finding an affinity ligand which selectively binds to a component (A) in the presence of a component (B) having substantial homology with (A), said method comprising:

(a) screening a ligand or plurality of ligands with component (B) and discarding any ligands binding (B) ; (b) if the or any of the ligands remains, screening with component (A) and detecting any ligand binding (A) , said ligand (s) constituting one or more said affinity ligands .

22. A method according to claim 21 wherein components A and B or derivatives thereof have optical properties such that in the screening steps (a) and (b) , ligands binding A or B or derivatives thereof are optically detectable and are optically detected.

23. A method according to claim 22 wherein components A and B are haemoglobins.

24. A method for providing an affinity ligand for a target component A wherein: a) a model of the target component (A) is provided in a computer modelling environment; b) the model is examined to determine a suitable ligand binding region (e.g. a region of A which differs from a component B of substantial homology) ; c) successive ligand fragments are selected that are calculated to interact with successive portions of the ligand binding region, leading to a theoretical ligand structure; d) a ligand having the theoretical structure is synthesised and tested.

25. A method according to claim 24 wherein said testing of the ligand employs a method of screening according to claim 21, 22 or 23.